棉花是全球重要的纤维和油料作物，也是我国国计民生的重要战略物资和棉纺织工业的关键原料。新疆是中国最大的棉花生产基地，其种植面积、单产、总产、商品调出量连续29年居全国第一，形成了“中国棉花看新疆”的格局。但是，新疆棉花种植面临着水资源短缺、土壤退化等生产环境恶化的问题，同时棉花品种“多乱杂”现象突出，机采棉的质量较差，导致新疆棉花的整体质量和经济效益不高，阻碍了棉花产业的发展。研发抗逆、早熟和紧凑型棉花株型品种是新疆棉花育种的重要目标之一。棉花植株的高度、分枝、成熟时间和生长习性等性状决定着其物种特异性，也影响着棉花栽培适应性、管理模式、产量和收获效率。因此，挖掘控制果枝发育的关键基因，解析棉花果枝发育的分子调控机制，为棉花育种提供科学依据，具有重要的理论和现实意义。本研究通过重离子辐射诱变陆地棉品种新陆早62号(XLZ62)获得不同果枝类型的棉花种质，在此基础上对一个长果枝突变棉花种质和XLZ62果枝3个发育时期的组织进行转录组测序(RNA-seq)分析，探索长短果枝基因表达差异，挖掘控制果枝发育的关键基因，并解析这些基因在果枝发育中的功能，旨在为高产和机械化收获棉花品种的培育提供理论指导和基因资源。本论文的主要研究内容和结果如下：

1. 重离子辐射诱变XLZ62创制陆地棉新种质

本研究利用重离子束诱变技术对XLZ62种子进行处理，经田间连续种植多代获得了107份在分枝数目与长度、株高和叶片大小等相关的突变体棉花材料。通过调查统计XLZ62和不同突变体在株高、棉铃数目、第一果枝高度、第四果枝长度、叶片数量和果枝夹角等农艺性状，进一步筛选到7份具有较大表型变异的突变体种质，包括：III式型果枝(M41)、营养枝生长旺盛型(M55)；叶枝生长旺盛的丛生铃(M38)；叶枝旺盛的塔型(M49)、果枝长且分枝少(M71)；矮杆(M50)等。其中，M41果枝长度和数目显著增加，棉铃数增多，与XLZ62的果枝相比具有明显差异。本研究以XLZ62和M41为主要研究材料，开展果枝发育过程中的RNA-seq研究。

2. 长短果枝陆地棉果枝发育3个时期的RNA-seq分析

分别取样XLZ62和M41第四果枝的初始腋芽(S1)、腋芽伸长形成果枝第一节间时期的顶芽(S2)、第二节间时期的顶芽(S3)组织。其中，XLZ62的3个发育时期分别命名为XS1、XS2、XS3，M41的3个发育时期分别命名为MS1、MS2、MS3，每个样品三次独立重复，共18个样本进行RNA-seq分析。文库测序获得了总计937,872,376条clean reads，总序列量达到144.63 Gb。在6个组织中总共识别出45,203个表达基因，其中12,420个基因在所有组织中均有表达。XLZ62中有36,708个表达基因，14,741个在3个发育时期均有表达。M41中有36,534个表达基因，14,901个在3个发育时期均有表达。比较XLZ62和M41在三个发育时期的差异表达基因(Differentially expressed gene, DEG)，XLZ62在XS2 vs XS1中的DEGs最多，上调724个，下调1378个；共有的DEGs为39个；M41在MS3 vs MS2的DEGs最多，上调1576个，下调1437个；共有的DEGs为64个。XLZ62和M41两品种间比较显示，MS3 vs XS3的DEGs最多，上调871个，下调1810个；3个发育时期共有的DEGs为410个。GO富集分析发现，这410个DEGs主要涉及蛋白磷酸化、跨膜运输和谷胱甘肽代谢过程；KEGG分析显示主要富集在内分泌抵抗、mRNA监控和植物激素信号通路。其中，植物激素信号通路AUXs、CKs、SLs在调控棉花果枝发育中起关键作用，特别是GhSMAX1基因在M41中差异明显。因此，我们对棉花SMXL基因家族成员进行了全基因组鉴定和分子特征分析。

3. 棉花SMXL基因家族成员的全基因组鉴定、分子进化和表达特征分析

拟南芥SUPPRESSOR OF MAX2 1 (SMAX1)-like (SMXL)蛋白SMXL6, SMXL7, SMXL8和水稻D53作为SLs信号通路中重要的靶蛋白促进分枝。SMXL基因家族在棉花中还未开展系统的鉴定和功能研究。本研究首先对绿藻门、苔藓门和被子植物中已经测序的21个物种的SMXL基因家族成员开展全基因组鉴定，并探讨了这些基因在植物中的系统进化史。从陆地棉(Gossypium hirsutum)、海岛棉(G. barbadense)、亚洲棉(G. arboreum)、雷蒙德氏棉(G. raimondii)和草棉(G. herbaceum)中分别鉴定出18、18、9、9和9个共63个SMXL基因成员，分为4个进化分枝。氨基酸比对表明SMXL蛋白具有一个保守的Clp-N domains、P-loop NTPase和EAR基序。不同组织中的表达(qRT-PCR)分析表明，GhSMAX1-1在叶中高表达，GhSMAX1-2、GhSMXL6/7-1/7-2在茎中高表达。GR24处理棉花幼苗48 h后，发现GhSMXL6/7-1/7-2响应GR24上调表达。在胁迫条件4 ℃、37 ℃、0.4 mol/L NaCl以及200 g/L PEG6000处理24 h后，GhSMAX1-1/2的表达量在4 ℃和37 ℃胁迫下上调。GhSMXL6的表达量在盐胁迫后下调。在干旱条件下，除GhSMAX1-2以外的所有基因的表达量均上调。蛋白共表达网络分析发现GhSMXL6、GhSMXL7-1和GhSMXL7-2主要与促进生长发育和诱导芽分化的蛋白互作，如bZIP、MYB和AP2/ERF等转录因子。

4. GhSMXL基因家族成员的功能分析

利用烟草脆裂病毒(Tobacco rattle virus, TRV)诱导的基因沉默(Virus-induced gene silence, VIGS)实验表明GhSMAX1-1/1-2以及GhSMXL6/7-1/7-2沉默后均抑制腋芽的发育，并且这5个GhSMXL基因的沉默均导致植株矮化，其中GhSMAX1基因沉默的株高降低最明显。此外，GhSMXL6和GhSMXL7-1/2沉默后叶片还表现出黄化和萎蔫的表型。另外，沉默一个负调控因子BRC1抑制子的编码基因GhTIE1促进了顶芽和侧芽的生长。拟南芥原生质体的亚细胞定位分析显示，GhSMAX1蛋白定位在细胞核中，GhD14蛋白定位在细胞质和细胞核中。酵母双杂交(Y₂H)显示GhSMAX1和GhD14蛋白并不互作。在模式植物拟南芥(Col-0)中过表达GhSMAX1基因，发现转基因拟南芥的茎分枝数量和株高均显著高于Col-0，并且幼苗的下胚轴明显伸长。这些结果初步表明GhSMXL基因促进棉花分枝发育，GhSMAX1基因在控制株高和腋芽发育方面起着重要的作用。VIGS植株TRV:GhSMAX1和对照TRV:00植株顶芽的RNA-seq分析。发现GhSMAX1基因沉默后抑制了大量AUXs信号通路相关基因的表达，例如ARF9、LAX5和GH3.6；而促进了ETHs信号通路相关基因的表达，例如EIN3、ERF1B、ERF.C.3、ARF、ARR-B和AP2-EREBP等。

总之，本研究通过重离子束诱变获得长果枝突变体M41，并利用RNA-seq技术分析了果枝发育的调控网络。发现了一个编码SLs信号转导靶蛋白的GhSMAX1基因，并对棉花SMXL基因家族进行了生物信息学和表达特征分析。5个GhSMXL基因的沉默均抑制了棉花果枝发育和植株高度。其中，过量表达GhSMAX1基因促进拟南芥植株分枝和株高。本研究为优化棉花株型结构，提高棉花机械化收获和生产效率提供了理论基础和优质基因资源。

Cotton is a globally important fiber and oil crop, as well as a critical strategic resource for China’s national economy and people’s livelihood and a key raw material for the cotton textile industry. Xinjiang is the largest cotton production base in China, leading the country for 29 consecutive years in planting area, unit yield, total yield, and commercial output, thereby establishing the pattern of “Chinese cotton depends on Xinjiang”. However, Xinjiang’s cotton cultivation faces issues such as water resource scarcity and soil degradation, which deteriorate the production environment. Additionally, the prominence of mixed and disordered cotton varieties and the poor quality of machine-picked cotton result in low overall quality and economic efficiency of Xinjiang cotton, hindering the development of the cotton industry. Developing stress-resistant, early maturing, and compact cotton plant varieties is one of the crucial goals of Xinjiang cotton breeding. The agronomic traits such as plant height, branching, maturity time, and growth habits determine cotton species specificity and affect their adaptability to cultivation, management mode, yield, and harvesting efficiency. Therefore, exploring key genes controlling fruit branch development and analyzing the molecular regulatory mechanisms of cotton fruit branch development to provide a scientific basis for cotton breeding have substantial theoretical and practical significance. In this study, we obtained different fruit branch types of cotton germplasm by heavy ion radiation mutagenesis of the upland cotton variety Xinluzao 62 (XLZ62). Transcriptome sequencing (RNA-seq) analysis was conducted on tissues of a long fruit branch mutant cotton germplasm and XLZ62 fruit branches at three developmental stages to explore the gene expression differences between long and short fruit branches, identify key genes controlling fruit branch development, and analyze the functions of these genes in fruit branch development, aiming to provide theoretical guidance and genetic resources for the breeding of high-yield and mechanized cotton varieties. The main research contents and results of this study are as follows:

1. Creation of new upland cotton germplasm by heavy ion radiation mutagenesis of XLZ62

The heavy ion beam mutagenesis technology was utilized to treat XLZ62 cotton seeds, yielding 107 mutant lines with variations in branching number and length, plant height, and leaf size after multiple generations of continuous field planting. Comprehensive investigations and statistical analyses of agronomic traits, such as plant height, number of cotton bolls, height of the first fruit branch, length of the fourth fruit branch, number of leaves, and angles of fruit branches, were conducted on XLZ62 and its mutants. As a result, seven mutant germplasms exhibiting significant phenotypic variations were identified, including: type III fruit branch (M41), vigorous vegetative branch growth type (M55); cluster bolls with vigorous vegetative branches (M38); tower type with vigorous leaf branch growth (M49), long fruit branch with few branches (M71); dwarf type (M50). Among them, M41 had significantly increased fruit branch length and number of cotton bolls, showing obvious differences compared to XLZ62 fruit branches. This study used XLZ62 and M41 as the main research materials to conduct RNA-seq studies during the fruit branch development process.

2. RNA-seq analysis of upland cotton fruit branch development at three stages of long and short fruit branches

Tissues were sampled from the initial axillary bud (S1), the top bud at the first internode formation stage of the axillary bud elongating to form the fruit branch (S2), and the top bud at the second internode stage (S3) of the fourth fruit branch of XLZ62 and M41. The three developmental stages of XLZ62 were named XS1, XS2, XS3, and those of M41 were named MS1, MS2, MS3, respectively. RNA-seq analysis was performed on a total of 18 samples, with three independent replicates for each sample. Library sequencing yielded a total of 937,872,376 clean reads, with a total sequence amount of 144.63 Gb. A total of 45,203 expressed genes were identified across the six tissues, of which 12,420 genes were expressed in all tissues. In XLZ62, 36,708 genes were expressed, and 14,741 were expressed in all three developmental stages. In M41, 36,534 genes were expressed, and 14,901 were expressed in all three developmental stages. Comparing differentially expressed genes (DEGs) between XLZ62 and M41 at three developmental stages, the most DEGs in XLZ62 were in XS2 vs XS1, with 724 upregulated and 1378 downregulated genes; the shared DEGs were 39. In M41, the most DEGs were in MS3 vs MS2, with 1576 upregulated and 1437 downregulated genes; the shared DEGs were 64. Comparison between the two varieties showed the most DEGs in MS3 vs XS3, with 871 upregulated and 1810 downregulated genes; the shared DEGs in three developmental stages were 410. GO enrichment analysis revealed that these 410 DEGs mainly involved protein phosphorylation, transmembrane transport, and glutathione metabolic processes; KEGG analysis showed they were mainly enriched in endocrine resistance, mRNA surveillance, and plant hormone signal transduction pathways. Among them, AUXs, CKs, and SLs in the plant hormone signal transduction pathway played key roles in regulating cotton fruit branch development, especially the GhSMAX1 gene, which was significantly different in M41. Therefore, we conducted genome-wide identification and molecular characterization analysis of the cotton SMXL gene family members.

3. Genome-wide identification, molecular evolution, and expression characteristics analysis of cotton SMXL gene family members

Arabidopsis SUPPRESSOR OF MAX2 1 (SMAX1)-like (SMXL) proteins SMXL6, SMXL7, SMXL8, and rice D53 are important target proteins in the SLs signal pathway promoting branching. The SMXL gene family has not yet been systematically identified and functionally studied in cotton. This study first conducted genome-wide identification of SMXL gene family members in 21 sequenced species from Chlorophyta, Bryophyta, and Angiosperms, and explored the phylogenetic evolutionary history of these genes in plants. A total of 63 SMXL gene members were identified from Gossypium hirsutum (18), G. barbadense (18), G. arboreum (9), G. raimondii (9), and G. herbaceum (9), which are classified into four evolutionary clades. Amino acid alignment indicated that SMXL proteins have a conserved Clp-N domain, P-loop NTPase, and EAR motif. Expression analysis (qRT-PCR) in different tissues showed that GhSMAX1-1 was highly expressed in leaves, and GhSMAX1-2, GhSMXL6/7-1/7-2 were highly expressed in stems. After 48 h of GR24 treatment of cotton seedlings, GhSMXL6/7-1/7-2 were upregulated in response to GR24. Under stress conditions of 4 °C, 37 °C, 0.4 mol/L NaCl, and 200 g/L PEG6000 treatments for 24 h, respectively. The expression levels of GhSMAX1-1 and GhSMAX1-2 were upregulated at both 4 °C and 37 °C treatments. In contrast, GhSMXL6 was notably downregulated under 0.4 mol/L NaCl stress. Furthermore, under 37 °C conditions, all examined genes, except GhSMAX1-2, exhibited upregulation. Protein co-expression network analysis found that GhSMXL6, GhSMXL7-1, and GhSMXL7-2 mainly interacted with proteins promoting growth and inducing bud differentiation, such as transcription factors bZIP, MYB, and AP2/ERF.

4. Functional analysis of GhSMXL gene members

Tobacco rattle virus (TRV)-induced gene silencing (Virus-induced gene silence, VIGS) experiments showed that silencing GhSMAX1-1/1-2 and GhSMXL6/7-1/7-2 inhibited axillary bud development and silencing these five GhSMXL genes led to plant dwarfing, with the most significant reduction in plant height observed in GhSMAX1 gene silencing. In addition, silencing GhSMXL6 and GhSMXL7-1/2 resulted in leaf chlorosis and wilting phenotypes. Moreover, silencing GhTIE1, encoding a negative regulator BRC1 inhibitor, promoted the growth of apical and lateral buds. Overexpressing the GhSMAX1 gene in Arabidopsis (Col-0) significantly increased the number of stem branches and plant height in transgenic Arabidopsis compared to Col-0, and the hypocotyls of seedlings were significantly elongated. These results preliminarily indicated that GhSMXL genes promote cotton branching development, and the GhSMAX1 gene plays an important role in controlling plant height and axillary bud development. Subcellular localization analysis of Arabidopsis protoplasts showed that GhD14 protein was localized in the cytoplasm and nucleus, while GhSMAX1 protein was localized in the nucleus. Yeast two-hybrid (Y₂H) showed that GhSMAX1 and GhD14 proteins did not interact. RNA-seq analysis of apical buds from TRV:GhSMAX1 and control TRV:00 plants demonstrated that silencing the GhSMAX1 gene inhibited the expression of multiple genes within the AUXs signaling pathway, including ARF9, LAX5, and GH3.6. Conversely, it upregulated genes associated with the ETHs signaling pathway, such as EIN3, ERF1B, ERF. C. 3, ARF, ARR-B, and AP2-EREBP.

In conclusion, this study obtained a long fruit branch mutant M41 through heavy ion beam mutagenesis and analyzed the regulatory network of fruit branch development using RNA-seq technology. A GhSMAX1 gene encoding an SLs signal transduction target protein was discovered, and bioinformatics and expression characteristic analyses of the cotton SMXL gene family were performed. Silencing five GhSMXL genes inhibited cotton fruit branch development and plant height. Overexpression of the GhSMAX1 gene promoted plant branching and height in Arabidopsis. This study provides a theoretical foundation and high-quality genetic resources for optimizing cotton plant architecture and improving cotton mechanized harvesting and production efficiency.

[1]Najib D C S, Fei C, Dilanchiev A, et al. Modeling the impact of cotton production on economic development in benin: a technological innovation perspective[J]. Frontiers in Environmental Science, 2022, 10:926350.

[2]Wang K B, Wang Z W, Li F, et al. The draft genome of a diploid cotton Gossypium raimondii[J]. Nature Genetics, 2012, 44(10):1098.

[3]Yu J, Jung S, Cheng C H, et al. CottonGen: The community database for cotton genomics, genetics, and breeding research[J]. Plants (Basel, Switzerland), 2021, 10(12):2805.

[4]Billings G T, Jones M A, Rustgi S, et al. Outlook for implementation of genomics-based selection in public cotton breeding programs[J]. Plants (Basel, Switzerland), 2022, 11(11):1446.

[5]Wei Y, Liu Y, Ali A, et al. Rich variant phenotype of Gossypium hirsutum L. saturated mutant library provides resources for cotton functional genomics and breeding[J]. Industrial Crops and Products, 2022, 186:115232

[6]Li C, Zhang B. Genome editing in cotton using CRISPR/Cas9 system[J]. Methods in molecular biology (Clifton N.J.), 2019, 1902:95-104.

[7]Guo W F, Guo D D, Li F, et al. Efficient genome editing in cotton using the virus-mediated CRISPR/Cas9 and grafting system[J]. Plant Cell Reports, 2023, 42(11):1833-1836.

[8]张媛, 田玲枝. 棉花滴灌施肥技术研究与应用[J]. 石河子科技, 2018, 1(1):3-4.

[9]沈丽. 棉花精量播种技术现状及应用[J]. 农业技术与装备, 2022, 1(04):84-86.

[10]Gemtos T A, Alexandrou A, Pateras D. Soil tillage irrigation and fertilization effects in cotton crops[J]. Applied Engineering in Agriculture, 2002, 18(3):269-276.

[11]娄善伟, 董合忠, 田晓莉, 田立文. 新疆棉花“矮、密、早”栽培历史、现状和展望[J]. 中国农业科学, 2021, 54(04):720-732.

[12]Teichmann T, Muhr M. Shaping plant architecture[J]. Frontiers in Plant Science, 2015, 6:233.

[13]Wickett N J, Mirarab S, Nguyen N, et al. Phylotranscriptomic analysis of the origin and early diversification of land plants[J]. Proceedings of the National Academy of Sciences of the United States of America, 2014, 111(45):E4859-E4868.

[14]Coudert Y, Palubicki W, Ljung K, et al. Three ancient hormonal cues co-ordinate shoot branching in a moss[J]. Elife, 2015, 4:e06808.

[15]Wang S B, Li L Z, Li H Y, et al. Genomes of early-diverging streptophyte algae shed light on plant terrestrialization[J]. Nature Plants, 2020, 6(2):95-106.

[16]Sunchu B, Cabernard C. Principles and mechanisms of asymmetric cell division[J]. Development, 2020, 147(13):167650.

[17]Yang Y R, Hu Y L, Li P, et al. Research progress and application of plant branching[J]. Phyton-International Journal of Experimental Botany, 2023, 92(3):679-689.

[18]Tameshige T, Hirakawa Y, Torii K U, et al. Cell walls as a stage for intercellular communication regulating shoot meristem development[J]. Frontiers in Plant Science, 2015, 6:324.

[19]Shin Y, Chane A, Jung M, et al. Recent advances in understanding the roles of pectin as an active participant in plant signaling networks[J]. Plants-Basel, 2021, 10(8):1712.

[20]Richardson A C, Walton E F, Meekings J S, et al. Carbohydrate changes in kiwifruit buds during the onset and release from dormancy[J]. Scientia Horticulturae, 2010, 124(4):463-468.

[21]Cai Z Q, Xie T, Xu J. Source-sink manipulations differentially affect carbon and nitrogen dynamics fruit metabolites and yield of Sacha Inchi plants[J]. BMC Plant Biology, 2021, 21(1):160.

[22]Krouk G, Kiba T. Nitrogen and Phosphorus interactions in plants: from agronomic to physiological and molecular insights[J]. Current Opinion in Plant Biology, 2020, 57:104-109.

[23]Gaarslev N, Swinnen G, Soyk S. Meristem transitions and plant architecture-learning from domestication for crop breeding[J]. Plant Physiology, 2021, 187(3):1045-1056.

[24]Wang Y, Jiao Y. Axillary meristem initiation - a way to branch out[J]. Current Opinion in Plant Biology, 2018, 41:61-66.

[25]杜雄明, 刘国强, 傅怀勤, 等. 陆地棉不同果枝类型品种若干性状的鉴定和分析[J]. 华北农学报, 1997, (03):61-66.

[26]杜雄明. 棉花果枝类型划分的统一化[J]. 中国棉花, 1996, (04):19.

[27]Zhu Y, Wagner D. Plant Inflorescence Architecture: The Formation Activity and Fate of Axillary Meristems[J]. Cold Spring Harbor Perspectives in Biology, 2020, 12(1):a034652.

[28]Domagalska M A, Leyser O. Signal integration in the control of shoot branching[J]. Nature Reviews Molecular Cell Biology, 2011, 12(4):211-221.

[29]Moreno-Pachon N M, Mutimawurugo M C, Heynen E, et al. Role of Tulipa gesneriana TEOSINTE BRANCHED1 (TgTB1) in the control of axillary bud outgrowth in bulbs[J]. Plant Reproduction, 2018, 31(2):145-157.

[30]Greb T, Clarenz O, Schäfer E, et al. Molecular analysis of the LATERAL SUPPRESSOR gene in Arabidopsis reveals a conserved control mechanism for axillary meristem formation[J]. Genes & Development, 2003, 17(9):1175-1187.

[31]Balkunde R, Kitagawa M, Xu X, et al. SHOOT MERISTEMLESS trafficking controls axillary meristem formation meristem size and organ boundaries in Arabidopsis[J]. Plant Journal, 2017, 90(3):435-446.

[32]Tian C H, Zhang X N, He J, et al. An organ boundary-enriched gene regulatory network uncovers regulatory hierarchies underlying axillary meristem initiation[J]. Molecular Systems Biology, 2014, 10(10):755.

[33]Tanaka W, Ohmori Y, Ushijima T, et al. Axillary meristem formation in rice requires the WUSCHEL ortholog TILLERS ABSENT1[J]. Plant Cell, 2015, 27(4):1173-1184.

[34]Li X Y, Qian Q, Fu Z M, et al. Control of tillering in rice[J]. Nature, 2003, 422(6932):618-621.

[35]Zhang B, Liu X, Xu W N, et al. Novel function of a putative MOC1 ortholog associated with spikelet number per spike in common wheat[J]. Scientific Reports, 2015, 5:12211.

[36]Schmitz G, Tillmann E, Carriero F, et al. The tomato Blind gene encodes a MYB transcription factor that controls the formation of lateral meristems[J]. Proceedings of the National Academy of Sciences of the United States of America, 2002, 99(2):1064-1069.

[37]Müller D, Schmitz G, Theres K. Blind homologous R2R3 Myb genes control the pattern of lateral meristem initiation in Arabidopsis[J]. Plant Cell, 2006, 18(3):586-597.

[38]Guo D, S, Zhang J Z, Wang X L, et al. The WRKY Transcription Factor WRKY71/EXB1 Controls Shoot Branching by Transcriptionally Regulating RAX Genes in Arabidopsis[J]. Plant Cell, 2015, 27(11):3112-3127.

[39]Lu Z, Shao G N, Xiong J S, et al. MONOCULM 3 an ortholog of WUSCHEL in rice is required for tiller bud formation[J]. Journal of Genetics and Genomics, 2015, 42(2):71-78.

[40]Baker R L, Emmo S, Claire R L, et al. Developmental plasticity of shoot architecture: morphological expression and ecologically relevant onset in locally adapted populations of Mimulus Guttatus[J]. International Journal of Plant Sciences, 2014, 175(1):59–69.

[41]Tavares H, Readshaw A, Kania U, et al. Artificial selection reveals complex genetic architecture of shoot branching and its response to nitrate supply in Arabidopsis[J]. PLOS Genetics, 2023, 19(8):e1010863.

[42]Wang B, Smith S M, Li J. Genetic regulation of shoot architecture[J]. Annual review of plant biology, 2018, 69:437-468.

[43]Martín-Fontecha E S, Tarancón C, Cubas P. To grow or not to grow a power-saving program induced in dormant buds[J]. Current Opinion in Plant Biology, 2018, 41:102-109.

[44]Mason M G, Ross J J, Babst B A, et al. Sugar demand not auxin is the initial regulator of apical dominance[J]. Proceedings of the National Academy of Sciences, 2014, 111(16):6092-6097.

[45]Heuvelink E, Buiskool R P M. Influence of sink-source interaction on dry matter production in tomato[J]. Annals of Botany, 1995, 75(4):381-389.

[46]Salam B B, Barbier F, Danieli R, et al. Sucrose promotes stem branching through cytokinin[J]. Plant Physiology, 2021, 185(4):1708-1721.

[47]Salam B B, Malka S K, Zhu X B, et al. Etiolated stem branching is a result of systemic signaling associated with sucrose level[J]. Plant Physiology, 2017, 175(2):734-745.

[48]Meng L S, Bao Q X, Mu X R, et al. Glucose and sucrose signaling modules regulate the arabidopsis juvenile-to-adult phase transition[J]. Cell Reports, 2021, 36(2):109348.

[49]Wang M, Pérez-Garcia M D, Davière J M, et al. Outgrowth of the axillary bud in rose is controlled by sugar metabolism and signalling[J]. Journal of Experimental Botany, 2021, 72(8):3044-3060.

[50]Schluepmann H, Pellny T, van Dijken A, et al. Trehalose 6-phosphate is indispensable for carbohydrate utilization and growth in Arabidopsis thaliana[J]. Proceedings of the National Academy of Sciences of the United States of America, 2003, 100(11):6849-6854.

[51]Hwang G, Kim S, Cho J-Y, et al. Trehalose-6-phosphate signaling regulates thermoresponsive hypocotyl growth in Arabidopsis thaliana[J]. Embo Reports, 2019, 20(10):e47828.

[52]Zheng Z L. Carbon and nitrogen nutrient balance signaling in plants[J]. Plant signaling & behavior, 2009, 4(7):584-591.

[53]Dong N Q, Lin H X. Higher yield with less nitrogen fertilizer[J]. Nature Plants, 2020, 6(9):1078-1079.

[54]Liu K H, Liu M H, Lin Z, et al. NIN-like protein 7 transcription factor is a plant nitrate sensor[J]. Science, 2022, 377(6613):1419.

[55]de Jong M, George G, Ongaro V, et al. Auxin and strigolactone signaling are required for modulation of Arabidopsis shoot branching by nitrogen supply[J]. Plant Physiology, 2014, 166(1):95-384.

[56]Drummond R S M, Janssen B J, Luo Z W, et al. Environmental control of branching in Petunia[J]. Plant Physiology, 2015, 168(2):735.

[57]Xu J X, Zha M R, Li Y, et al. The interaction between nitrogen availability and auxin cytokinin and strigolactone in the control of shoot branching in rice (Oryza sativa L.)[J]. Plant Cell Reports, 2015, 34(9):1647-1662.

[58]Liu Y, Jafari F, Wang H. Integration of light and hormone signaling pathways in the regulation of plant shade avoidance syndrome[J]. aBIOTECH, 2021, 2(2):131-145.

[59]Tegeder M. Transporters involved in source to sink partitioning of amino acids and ureides: opportunities for crop improvement[J]. Journal of Experimental Botany, 2014, 65(7):1865-1878.

[60]Fischer W N, André B, Rentsch D, et al. Amino acid transport in plants[J]. Trends in Plant Science, 1998, 3(5):188-195.

[61]Fichtner F, Barbier F F, Feil R, et al. Trehalose 6-phosphate is involved in triggering axillary bud outgrowth in garden pea (Pisum sativum L.)[J]. Plant Journal, 2017, 92(4):611-623.

[62]Ohashi M, Ishiyama K, Kojima S, et al. Asparagine synthetase1 but not asparagine synthetase2 is responsible for the biosynthesis of asparagine following the supply of ammonium to rice roots[J]. Plant and Cell Physiology, 2015, 56(4):769-778.

[63]Ohashi M, Ishiyama K, Kojima S, et al. Lack of cytosolic glutamine synthetase1;2 activity reduces nitrogen-dependent biosynthesis of cytokinin required for axillary bud outgrowth in rice seedlings[J]. Plant and Cell Physiology, 2017, 58(4):679-690.

[64]Ohashi M, Ishiyama K, Kojima S, et al. Outgrowth of rice tillers requires availability of glutamine in the basal portions of shoots[J]. Rice, 2018, 11:31.

[65]Urriola J, Rathore K S. Overexpression of a glutamine synthetase gene affects growth and development in sorghum[J]. Transgenic Research, 2015, 24(3):397-407.

[66]Le Moigne M A, Guérin V, Furet P, et al. Asparagine and sugars are both required to sustain secondary axis elongation after bud outgrowth in Rosa hybrida[J]. Journal of Plant Physiology, 2018, 222:17-27.

[67]Yoneyama K, Xie X N, Kim H I, et al. How do nitrogen and phosphorus deficiencies affect strigolactone production and exudation?[J]. Planta, 2012, 235(6):1197-1207.

[68]Kamada-Nobusada T, Makita N, Kojima M, et al. Nitrogen-dependent regulation of de novo cytokinin biosynthesis in Rice: The role of glutamine metabolism as an additional signal[J]. Plant and Cell Physiology, 2013, 54(11):1881-1893.

[69]Krouk G. Hormones and nitrate: a two-way connection[J]. Plant Molecular Biology, 2016, 91(6):599-606.

[70]Barbier F F, Dun E A, Kerr S C, et al. An update on the signals controlling shoot branching[J]. Trends Plant Sciences, 2019, 24(3):220-236.

[71]Del Bianco M, Friml J, Strader L, et al. Auxin research: creating tools for a greener future[J]. Journal of Experimental Botany, 2023, 74(22):6889-6892.

[72]Teale W D, Paponov I A, Palme K. Auxin in action: signalling transport and the control of plant growth and development[J]. Nature Reviews Molecular Cell Biology, 2006, 7(11):847-859.

[73]Pernisová M, Vernoux T. Auxin Does the SAMba: Auxin signaling in the shoot apical meristem[J]. Cold Spring Harb Perspect Biology, 2021, 13(12):a039925.

[74]Aloni R, Langhans M, Aloni E, et al. Root-synthesized cytokinin in Arabidopsis is distributed in the shoot by the transpiration stream[J]. Journal of Experimental Botany, 2005, 56(416):1535-1544.

[75]Jones B, Gunnerås S A, Petersson S V, et al. Cytokinin regulation of auxin synthesis in arabidopsis involves a homeostatic feedback loop regulated via auxin and cytokinin signal transduction[J]. Plant Cell, 2010, 22(9):2956-2969.

[76]Wu W Q, Du K, Kang X Y, et al. The diverse roles of cytokinins in regulating leaf development[J]. Horticulture Research, 2021, 8(1):118.

[77]Richards D E, King K E, Ait-ali T, et al. How gibberellin regulates plant growth and development: A molecular genetic analysis of gibberellin signaling[J]. Annual Review of Plant Physiology and Plant Molecular Biology, 2001, 52:67-88.

[78]Sun T P. Gibberellin-GID1-DELLA: A pivotal regulatory module for plant growth and development[J]. Plant Physiology, 2010, 154(2):567-570.

[79]Ni J, Zhao M L, Chen M S, et al. Comparative transcriptome analysis of axillary buds in response to the shoot branching regulators gibberellin A3 and 6-benzyladenine in Jatropha curcas[J]. Scientific Reports, 2017, 7:11417.

[80]Cao D, Chabikwa T, Barbier F, et al. Auxin-independent effects of apical dominance induce changes in phytohormones correlated with bud outgrowth[J]. Plant Physiology, 2023, 192(2):1420-1434.

[81]Aslam M M, Waseem M, Jakada B H, et al. Mechanisms of abscisic acid-mediated drought stress responses in plants[J]. International Journal of Molecular Sciences, 2022, 23(3):1084.

[82]Barbier F, Fichtner F, Beveridge C. The strigolactone pathway plays a crucial role in integrating metabolic and nutritional signals in plants[J]. Nature Plants, 2023, 9(8):1191-1200.

[83]Wasternack C, Hause B. Jasmonates: biosynthesis perception signal transduction and action in plant stress response growth and development[J]. An update to the 2007 review in Annals of Botany, Annals of Botany, 2013, 111(6):1021-1058.

[84]Chrétien L T S, David A, Daikou E, et al. Caterpillars induce jasmonates in flowers and alter plant responses to a second attacker[J]. New Phytologist, 2018, 217(3):1279-1291.

[85]Siddiqi K S, Husen A. Plant response to jasmonates: current developments and their role in changing environment[J]. Bulletin of the National Research Centre, 2019, 43:1-11.

[86]Gallavotti A. The role of auxin in shaping shoot architecture[J]. Journal of Experimental Botany, 2013, 64(9):2593-2608.

[87]Holland J J, Roberts D, Liscum E. Understanding phototropism: from Darwin to today[J]. Journal of Experimental Botany, 2009, 60(7):1969-1978.

[88]Pennazio S. The discovery of the chemical nature of the plant hormone auxin[J]. Rivista Di Biologia-Biology Forum, 2002, 95(2):289-307.

[89]Ongaro V, Leyser O. Hormonal control of shoot branching[J]. Journal of Experimental Botany, 2008, 59(1):67-74.

[90]Barbier F, Péron T, Lecerf M, et al. Sucrose is an early modulator of the key hormonal mechanisms controlling bud outgrowth in Rosa hybrida[J]. Journal of Experimental Botany, 2015, 66(9):2569-2582.

[91]Robert H S, Friml J. Auxin and other signals on the move in plants[J]. Nature Chemical Biology, 2009, 5(5):325-332.

[92]Gao L W, Lyu S W, Tang J, et al. Genome-wide analysis of auxin transport genes identifies the hormone responsive patterns associated with leafy head formation in Chinese cabbage[J]. Scientific Reports, 2017, 7:42229.

[93]Hagen G. Auxin signal transduction[J]. Essays in biochemistry, 2015, 58:1-12.

[94]Rameau C, Bertheloot J, Leduc N, et al. Multiple pathways regulate shoot branching[J]. Frontiers in Plant Science, 2015, 5:741.

[95]Waldie T, Leyser O. Cytokinin targets auxin transport to promote shoot branching[J]. Plant Physiology, 2018, 177(2):803-818.

[96]Adamowski M, Friml J. PIN-dependent auxin transport: action regulation and evolution[J]. Plant Cell, 2015, 27(1):20-32.

[97]Ning J Y, Yamauchi T, Takahashi H, et al. Asymmetric auxin distribution establishes a contrasting pattern of aerenchyma formation in the nodal roots of Zea nicaraguensis during gravistimulation[J]. Frontiers in Plant Science, 2023, 14:1133009.

[98]Miller C O, Skoog F, Okumura F S, et al. Isolation structure and synthesis of kinetin a substance promoting cell division1, 2[J]. Journal of the American Chemical Society, 1956, 78(7):1375-1380.

[99]Tanaka M, Takei K, Kojima M, et al. Auxin controls local cytokinin biosynthesis in the nodal stem in apical dominance[J]. Plant Journal, 2006, 45(6):1028-1036.

[100]Müller D, Waldie T, Miyawaki K, et al. Cytokinin is required for escape but not release from auxin mediated apical dominance[J]. Plant Journal, 2015, 82(5):874-886.

[101]Shimizu-Sato S, Tanaka M, Mori H. Auxin-cytokinin interactions in the control of shoot branching[J]. Plant Molecular Biology, 2009, 69(4):429-435.

[102]Skylar A, Hong F X, Chory J, et al. STIMPY mediates cytokinin signaling during shoot meristem establishment in Arabidopsis seedlings[J]. Development, 2010, 137(4):541-549.

[103]Wang J, Tian C H, Zhang C, et al. Cytokinin signaling activates WUSCHEL expression during axillary meristem initiation[J]. Plant Cell, 2017, 29(6):1373-1387.

[104]Braun N, de Saint Germain A, Pillot J P, et al. The Pea TCP transcription factor PsBRC1 acts downstream of strigolactones to control shoot branching[J]. Plant Physiology, 2012, 158(1):225-238.

[105]Ferguson B J, Beveridge C A. Roles for Auxin cytokinin and strigolactone in regulating shoot branching[J]. Plant Physiology, 2009, 149(4):1929-1944.

[106]Ligerot Y, de Saint Germain A, Waldie T, et al. The pea branching RMS2 gene encodes the PsAFB4/5 auxin receptor and is involved in an auxin-strigolactone regulation loop[J]. Plos Genetics, 2017, 13(12):e1007089.

[107]Spielmeyer W, Ellis M, Robertson M, et al. Isolation of gibberellin and metabolic pathway genes from barley and comparative mapping in barley wheat and rice[J]. Theoretical and Applied Genetics, 2004, 109(4):847-855.

[108]Nagai K, Mori Y, Ishikawa S, et al. Antagonistic regulation of the gibberellic acid response during stem growth in rice[J]. Nature, 2020, 584(7819):109-114.

[109]Gao S P, Chu C C. Gibberellin metabolism and signaling: Targets for improving agronomic performance of crops[J]. Plant and Cell Physiology, 2020, 61(11):1902-1911.

[110]Xie Y Y, Chen L T. Epigenetic regulation of gibberellin metabolism and signaling[J]. Plant and Cell Physiology, 2020, 61(11):1912-1918.

[111]Yamaguchi S. Gibberellin metabolism and its regulation[J]. Annual Review of Plant Biology, 2008, 59:225-251.

[112]Lange T, Kramer C, Pimenta Lange M J. The class III Gibberellin 2-Oxidases AtGA2ox9 and AtGA2ox10 contribute to cold stress tolerance and fertility[J]. Plant Physiology, 2020, 184(1):478-486.

[113]Ci J B, Wang X Y, Wang Q, et al. Genome-wide analysis of gibberellin-dioxygenases gene family and their responses to GA applications in maize[J]. Plos One, 2021, 16(5):e0250349.

[114]He Y, Liu W, Huang Z, et al. Genome-wide analysis of the rice gibberellin dioxygenases family genes[J]. Agronomy-Basel, 2022, 12(7):1627.

[115]Han F, Zhu B. Evolutionary analysis of three gibberellin oxidase genes in rice Arabidopsis and soybean[J]. Gene, 2011, 473(1):23-35.

[116]Honi U, Amin M R, Kabir S M T, et al. Genome-wide identification characterization and expression profiling of gibberellin metabolism genes in jute[J]. BMC Plant Biology, 2020, 20(1):306.

[117]Pan C, Tian K, Ban Q, et al. Genome-wide analysis of the biosynthesis and deactivation of gibberellin-dioxygenases gene family in Camellia sinensis (L.) O. Kuntze[J]. Genes, 2017, 8(9):235.

[118]He H H, Liang G P, Lu S X, et al. Genome-wide identification and expression analysis of ga2ox ga3ox and ga20ox are related to gibberellin oxidase genes in grape (Vitis vinifera L.)[J]. Genes, 2019, 10(9):680.

[119]Cheng J, Ma J J, Zheng X B, et al. Functional analysis of the gibberellin 2-oxidase gene family in peach[J]. Frontiers in Plant Science, 2021, 12:619158.

[120]Zhou W, Malabanan P B, Abrigo E. OsHox4 regulates GA signaling by interacting with DELLA-like genes and GA oxidase genes in rice[J]. Euphytica, 2014, 201(1):97-107.

[121]Ashikari M, Sasaki A, Ueguchi-Tanaka M, et al. Loss-of-function of a Rice Gibberellin Biosynthetic Gene GA20 oxidase (GA20ox-2) Led to the Rice ‘Green Revolution’[J]. Breeding Science, 2002, 52(2):143-150.

[122]Mo Y, Pearce S, Dubcovsky J. Phenotypic and transcriptomic characterization of a wheat tall mutant carrying an induced mutation in the C-terminal PFYRE motif of RHT-B1b[J]. BMC Plant Biology, 2018, 18(1):253.

[123]Hartweck L M. Gibberellin signaling[J]. Planta, 2008, 229(1):1-13.

[124]Huang L J, Luo J, Wang Y, et al. From green revolution to green balance: The nitrogen and gibberellin mediated rice tiller growth[J]. Plant signaling & behavior, 2021, 16(7):1917838.

[125]Li S, Tian Y H, Wu K, et al. Modulating plant growth-metabolism coordination for sustainable agriculture[J]. Nature, 2018, 560:595-600.

[126]Liu Y Q, Wang H R, Jiang Z M, et al. Genomic basis of geographical adaptation to soil nitrogen in rice[J]. Nature, 2021, 590(7847):600-605.

[127]Tomlinson L, Yang Y, Emenecker R, et al. Using CRISPR/Cas9 genome editing in tomato to create a gibberellin-responsive dominant dwarf DELLA allele[J]. Plant Biotechnology Journal, 2019, 17(1):132-140.

[128]Cook C E, Whichard L P, Turner B, et al. Germination of witchweed (Striga lutea Lour.): isolation and properties of a potent stimulant[J]. Science(New York N.Y.), 1966, 154(3753):1189-1190.

[129]Akiyama K, & Hayashi H. Strigolactones: Chemical signals for fungal symbionts and parasitic weeds in plant roots[J]. Annals of Botany, 2006, 97(6):925-931.

[130]Delaux P M, Xie X N, Timme R E, et al. Origin of strigolactones in the green lineage[J]. New Phytologist, 2012, 195(4):857-871.

[131]Brewer P B, Koltai H, Beveridge C A. Diverse roles of strigolactones in plant development[J]. Molecular Plant, 2013, 6(1):18-28.

[132]Gomez-Roldan V, Fermas S, Brewer P B, et al. Strigolactone inhibition of shoot branching[J]. Nature, 2008, 455(7210):94-189.

[133]Agusti J, Herold S, Schwarz M, et al. Strigolactone signaling is required for auxin-dependent stimulation of secondary growth in plants[J]. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(35):14277-14277.

[134]Rasmussen A, Mason M G, De Cuyper C, et al. Strigolactones suppress adventitious rooting in Arabidopsis and Pea[J]. Plant Physiology, 2012, 158(4):1976-1987.

[135]Ueda H, Kusaba M. Strigolactone regulates leaf senescence in concert with ethylene in Arabidopsis[J]. Plant Physiology, 2015, 169(1):138-147.

[136]Jia K P, Baz L, Al-Babili S. From carotenoids to strigolactones[J]. Journal of Experimental Botany, 2018, 69(9):2189-2204.

[137]Marzec M, Muszynska A, Gruszka D. The role of strigolactones in nutrient-stress responses in plants[J]. International Journal of Molecular Sciences, 2013, 14(5):9286-9304.

[138]Yao R F, Ming Z H, Yan L, et al. DWARF14 is a non-canonical hormone receptor for strigolactone[J]. Nature, 2016, 536(7617):73-469.

[139]Jiang L, Liu X, Xiong G S, et al. DWARF 53 acts as a repressor of strigolactone signalling in rice[J]. Nature, 2013, 504(7480):401.

[140]Soundappan I, Bennett T, Morffy N, et al. SMAX1-LIKE/D53 family members enable distinct MAX2-Dependent Responses to Strigolactones and Karrikins in Arabidopsis[J]. Plant Cell, 2015, 27(11):3143-3159.

[141]Wang L, Wang B, Jiang L, et al. Strigolactone Signaling in Arabidopsis Regulates Shoot Development by Targeting D53-Like SMXL Repressor Proteins for Ubiquitination and Degradation[J]. Plant Cell, 2015, 27(11):3128-3142.

[142]Kerr S C, Patil S B, de Saint Germain A, et al. Integration of the SMXL/D53 strigolactone signalling repressors in the model of shoot branching regulation in Pisum sativum[J]. The Plant journal: for cell and molecular biology, 2021, 107(6):1756-1770.

[143]Wallner E S, López-Salmerón V, Belevich I, et al. Strigolactone and karrikin-independent SMXL proteins are central regulators of phloem formation[J]. Current biology: CB, 2017, 27(8):1241-1247.

[144]Li Q T, Martin-Fontecha E S, Khosla A, et al. The strigolactone receptor D14 targets SMAX1 for degradation in response to GR24 treatment and osmotic stress[J]. Plant Communications, 2022, 3(2):100303.

[145]Wang L, Xu Q, Yu H, et al. Strigolactone and karrikin signaling pathways elicit ubiquitination and proteolysis of SMXL2 to regulate hypocotyl elongation in Arabidopsis[J]. The Plant cell, 2020, 32(7):2251-2270.

[146]Zheng X, Yang X, Chen Z, et al. Arabidopsis SMAX1 overaccumulation suppresses rosette shoot branching and promotes leaf and petiole elongation[J]. Biochemical and biophysical research communications, 2021, 553:44-50.

[147]Swarbreck S M, Guerringue Y, Matthus E, et al. Impairment in karrikin but not strigolactone sensing enhances root skewing in Arabidopsis thaliana[J]. The Plant journal: for cell and molecular biology, 2019, 98(4):607-621.

[148]Xie Y, Liu Y, Ma M, et al. Arabidopsis FHY3 and FAR1 integrate light and strigolactone signaling to regulate branching[J]. Nature communications, 2020, 11(1):1955.

[149]Zürcher E, Müller B. Cytokinin synthesis signaling and function-advances and new insights[J]. In International Review of Cell and Molecular Biology, 2016, 2016:324:1-38.

[150]Seale M, Bennett T, Leyser O. BRC1 expression regulates bud activation potential but is not necessary or sufficient for bud growth inhibition in Arabidopsis[J]. Development, 2017, 144(9):1661-1673.

[151]Zhang J, Mazur E, Balla J, et al. Strigolactones inhibit auxin feedback on PIN-dependent auxin transport canalization[J]. Nature Communications, 2020, 11(1):3508.

[152]Pino L E, Lima J E, Vicente M H, et al. Increased branching independent of strigolactone in cytokinin oxidase 2-overexpressing tomato is mediated by reduced auxin transport[J]. Molecular horticulture, 2022, 2(1):12.

[153]Hayward A, Stirnberg P, Beveridge C, et al. Interactions between auxin and strigolactone in shoot branching Control[J]. Plant Physiology, 2009, 151(1):400-412.

[154]Zha M R, Zhao Y H, Wang Y, et al. Strigolactones and cytokinin interaction in buds in the control of rice tillering[J]. Frontiers in Plant Science, 2022, 13:837136.

[155]Hu Z Y, Yamauchi T, Yang J H, et al. Strigolactone and cytokinin act antagonistically in regulating rice mesocotyl elongation in darkness[J]. Plant and Cell Physiology, 2014, 55(1):30-41.

[156]Abelenda J A, Barrero-Gil J. ABA signaling branches out: emerging ABA-related signaling functions in Solanum tuberosum[J]. Journal of Experimental Botany, 2023, 74(21):6405-6408.

[157]Nicolas M, Torres-Pérez R, Wahl V, et al. Spatial control of potato tuberization by the TCP transcription factor BRANCHED1b[J]. Nature Plants, 2022, 8(3):281-294.

[158]Liu T, Dong L, Wang E, et al. StHAB1, a negative regulatory factor in abscisic acid signaling, plays crucial roles in potato drought toleranc e and shoot branching[J]. Journal of Experimental Botany, 2023, 74(21):6708-6721.

[159]Yuan C Q, Ahmad S, Cheng T R, et al. Red to far-red light ratio modulates hormonal and genetic control of axillary bud outgrowth in chrysanthemum (Dendranthema grandiflorum “Jinba”)[J]. International Journal of Molecular Sciences, 2018, 19(6):1590.

[160]Nguyen T Q, Emery R J N. Is ABA the earliest upstream inhibitor of apical dominance?[J]. Journal of Experimental Botany, 2017, 68(5):881-884.

[161]González-Grandío E, Pajoro A, Franco-Zorrilla J M, et al. Abscisic acid signaling is controlled by a BRANCHED1/HD-ZIP I cascade in Arabidopsis axillary buds[J]. Proceedings of the National Academy of Sciences of the United States of America, 2017, 114(2):E245-E254.

[162]Pierik R, Fankhauser C, Strader L C, et al. Architecture and plasticity: optimizing plant performance in dynamic environments[J]. Plant Physiology, 2021, 18(3):1029-1032.

[163]Yuan Y D, Khourchi S, Li S J, et al. Unlocking the multifaceted mechanisms of bud outgrowth: advances in understanding shoot branching[J]. Plants-Basel, 2023, 12(20):3628.

[164]Sun R, Okabe M, Miyazaki S, et al. Biosynthesis of gibberellin-related compounds modulates far-red light responses in the liverwort Marchantia polymorpha[J]. The Plant cell, 2023, 35(11):4111-4132.

[165]Li Y M, Jiang H Z, Gao M F, et al. Far-red-light-induced morphology changes phytohormone and transcriptome reprogramming of chinese kale (Brassica alboglabra Bailey)[J]. International Journal of Molecular Sciences, 2023, 24(6):5563.

[166]Jenkins G I. The UV-B photoreceptor UVR8: From structure to physiology[J]. Plant Cell, 2014, 26(1):21-37.

[167]Hectors K, Prinsen E, De Coen W, et al. Arabidopsis thaliana plants acclimated to low dose rates of ultraviolet B radiation show specific changes in morphology and gene expression in the absence of stress symptoms[J]. New Phytologist, 2007, 175(2):255-270.

[168]Wargent J J, Gegas V C, Jenkins G I, et al. UVR8 in Arabidopsis thaliana regulates multiple aspects of cellular differentiation during leaf development in response to ultraviolet B radiation[J]. New Phytologist, 2009, 183(2):315-326.

[169]Greenham K, McClung C R. Integrating circadian dynamics with physiological processes in plants[J]. Nature Reviews Genetics, 2015, 16(10):598-610.

[170]Yang C W, Huang S, Zeng Y, et al. Two bHLH transcription factors bHLH48 and bHLH60 associate with phytochrome interacting factor 7 to regulate hypocotyl elongation in Arabidopsis[J]. Cell Reports, 2021, 35(5):109054.

[171]Mallet J, Laufs P, Leduc N, et al. Photocontrol of axillary bud outgrowth by microRNAs: Current state-of-the-art and novel perspectives gained from the rosebush model[J]. Frontiers in Plant Science, 2022, 12:770363.

[172]Lloret A, Quesada-Traver C, Conejero A, et al. Regulatory circuits involving bud dormancy factor PpeDAM6[J]. Horticulture Research, 2021, 8(1):261.

[173]Li G, Kuijer H N J, Yang X J, et al. MADS1 maintains barley spike morphology at high ambient temperatures[J]. Nature Plants, 2021, 7(8):1093.

[174]Wang X, Li Z, Shi Y, et al. Strigolactones promote plant freezing tolerance by releasing the WRKY41-mediated inhibition of CBF/DREB1 expression[J]. The EMBO journal, 2023, 42(19):e112999.

[175]McDowell N, Pockman W T, Allen C D, et al. Mechanisms of plant survival and mortality during drought: why do some plants survive while others succumb to drought?[J]. New Phytologist, 2008, 178(4):719-739.

[176]Yan Y Y, Zhao N, Tang H M, et al. Shoot branching regulation and signaling[J]. Plant Growth Regulation, 2020, 92(2):131-140.

[177]Luo L, Zhang Y, Xu G. How does nitrogen shape plant architecture?[J]. Journal of Experimental Botany, 2020, 71(15):4415-4427.

[178]Hashim M M, Yusop M K, Othman R, et al. Characterization of nitrogen uptake pattern in malaysian rice MR219 at different growth stages using 15N isotope[J]. Rice Science, 2015, 22(5):250-254.

[179]Ericsson T. Growth and shoot-root ratio of seedlings in relation to nutrient availability[J]. Plant and Soil, 1995, 168-169(2004):205-214.

[180]Kiba T, Kudo T, Kojima M, et al. Hormonal control of nitrogen acquisition: roles of auxin abscisic acid and cytokinin[J]. Journal of Experimental Botany, 2011, 62(4):1399-1409.

[181]McGarry R C, Ayre B G. Geminivirus-mediated delivery of florigen promotes determinate growth in aerial organs and uncouples flowering from photoperiod in cotton[J]. Plos One, 2012, 7(8):36746-36747.

[182]Lifschitz E, Ayre B G, Eshed Y. Florigen and anti-florigen-a systemic mechanism for coordinating growth and termination in flowering plants[J]. Frontiers in Plant Science, 2014, 5:465.

[183]Karlgren A, Gyllenstrand N, Källman T, et al. Evolution of the PEBP gene family in plants: functional diversification in seed plant evolution[J]. Plant Physiology, 2011, 156(4):1967-1977.

[184]Moraes T S, Dornelas M C, Martinelli A P. FT/TFL1: Calibrating plant architecture[J]. Frontiers in Plant Science, 2019, 10:97.

[185]Jin S, Nasim Z, Susila H, et al. Evolution and functional diversification of FLOWERING LOCUS T/TERMINAL FLOWER 1 family genes in plants[J]. Seminars in Cell & Developmental Biology, 2021, 109:20-30.

[186]Susila H, Juric S, Liu L, et al. Florigen sequestration in cellular membranes modulates temperature-responsive flowering[J]. Science, 2021, 373(6559):1137-1141.

[187]Abe M, Kobayashi Y, Yamamoto S, et al. FD a bZIP protein mediating signals from the floral pathway integrator FT at the shoot apex[J]. Science, 2005, 309(5737):1052-1056.

[188]Wigge P A, Kim M C, Jaeger K E, et al. Integration of spatial and temporal information during floral induction in Arabidopsis[J]. Science, 2005, 309(5737):1056-1059.

[189]Taoka K, Ohki I, Tsuji H, et al. 14-3-3 proteins act as intracellular receptors for rice Hd3a florigen[J]. Nature, 2011, 476(7360):332-335.

[190]McGarry R C, Ayre B G. Manipulating plant architecture with members of the CETS gene family[J]. Plant Science, 2012, 188(88):71-81.

[191]Li C, Zhang Y N, Zhang K, et al. Promoting flowering lateral shoot outgrowth leaf development and flower abscission in tobacco plants overexpressing cotton FLOWERING LOCUS T (FT)-like gene GhFT1[J]. Frontiers in Plant Science, 2015, 6:454.

[192]Bradley D, Carpenter R, Copsey L, et al. Control of inflorescence architecture in Antirrhinum[J]. Nature, 1996, 379(6568):791-797.

[193]Bradley D, Ratcliffe O, Vincent C, et al. Inflorescence commitment and architecture in Arabidopsis[J]. Science, 1997, 275(5296):80-83.

[194]Pnueli L, Carmel-Goren L, Hareven D, et al. The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1[J]. Development, 1998, 125(11):1979-1989.

[195]Tian Z X, Wang X B, Lee R, et al. Artificial selection for determinate growth habit in soybean[J]. Proceedings of the National Academy of Sciences of the United States of America, 2010, 107(19):8563-8568.

[196]Eshed Y, Lippman Z B. Revolutions in agriculture chart a course for targeted breeding of old and new crops[J]. Science, 2019, 366(6466):25-25.

[197]Huang X Z, Liu H, Ma B. The current progresses in the genes and networks regulating cotton plant architecture[J]. Frontiers in Plant Science, 2022, 13:882583.

[198]Zhao H, Huang X, Yang Z, et al. Synergistic optimization of crops by combining early maturation with other agronomic traits[J]. Trends in Plant Science, 2023, 28(10):1178-1191.

[199]Chen W, Yao J B, Chu L, et al. Genetic mapping of the nulliplex-branch gene (gb_nb1) in cotton using next-generation sequencing[J]. Theoretical and Applied Genetics, 2015, 128(3):539-547.

[200]Liu D X, Teng Z H, Kong J, et al. Natural variation in a CENTRORADIALIS homolog contributed to cluster fruiting and early maturity in cotton[J]. BMC Plant Biology, 2018, 18:286.

[201]Si Z F, Liu H, Zhu J K, et al. Mutation of SELF-PRUNING homologs in cotton promotes short-branching plant architecture[J]. Journal of Experimental Botany, 2018, 69(10):2543-2553.

[202]Chen W, Yao J B, Li Y, et al. Nulliplex-branch a TERMINAL FLOWER 1 ortholog controls plant growth habit in cotton[J]. Theoretical and Applied Genetics, 2019, 132(1):97-112.

[203]Pin P A, Benlloch R, Bonnet D, et al. An antagonistic pair of FT homologs mediates the control of flowering time in sugar beet[J]. Science, 2010, 330(6009):1397-1400.

[204]McGarry R C, Prewitt S F, Culpepper S, et al. Monopodial and sympodial branching architecture in cotton is differentially regulated by the Gossypium hirsutum SINGLE FLOWER TRUSS and SELF-PRUNING orthologs[J]. New Phytologist, 2016, 212(1):244-258.

[205]Liu H, Huang X, Z, Ma B, et al. Components and Functional Diversification of Florigen Activation Complexes in Cotton[J]. Plant and Cell Physiology, 2021, 62(10):1542-1555.

[206]Sang N, Liu H, Ma B, et al. Roles of the 14-3-3 gene family in cotton flowering[J]. BMC Plant Biology, 2021, 21(1):162.

[207]Collani S, Neumann M, Yant L, et al. FT modulates genome-wide DNA-binding of the bZIP transcription factor FD[J]. Plant Physiology, 2019, 180(1): 367-380.

[208]Romera-Branchat M, Severing E, Pocard C, et al. Functional divergence of the Arabidopsis florigen-interacting bZIP transcription factors FD and FDP[J]. Cell Reports, 2020, 31(9):107717.

[209]Hanano S, Goto K. Arabidopsis TERMINAL FLOWER1 is involved in the regulation of flowering time and inflorescence development through transcriptional repression[J]. Plant Cell, 2011, 23(9):3172-3184.

[210]Aguilar-Martínez J A, Poza-Carrión C, Cubas P. Arabidopsis BRANCHED1 acts as an integrator of branching signals within axillary buds[J]. Plant Cell, 2007, 19(2):458-472,

[211]Doebley J, Stec A, Hubbard L. The evolution of apical dominance in maize[J]. Nature, 1997, 386(6624):485-488.

[212]Hubbard L, McSteen P, Doebley J, et al. Expression patterns and mutant phenotype of teosinte branched1 correlate with growth suppression in maize and teosinte[J]. Genetics, 2002, 162(4):1927-1935.

[213]Nicolas M, Cubas P. TCP factors: new kids on the signaling block[J]. Current Opinion in Plant Biology, 2016, 33:33-41.

[214]Takeda T, Suwa Y, Suzuki M, et al. The OsTB1 gene negatively regulates lateral branching in rice[J]. The Plant journal, 2003, 33(3):513-520.

[215]Kebrom T H, Burson B L, Finlayson S A. Phytochrome B represses Teosinte Branched1 expression and induces sorghum axillary bud outgrowth in response to light signals[J]. Plant physiology, 2006, 140(3):1109-1117.

[216]Dixon L E, Pasquariello M, Boden S A. TEOSINTE BRANCHED1 regulates height and stem internode length in bread wheat[J]. Journal of Experimental Botany, 2020, 71(16):4742-4750.

[217]Sun Q, Xie Y, Li H, et al. Cotton GhBRC1 regulates branching, flowering, and growth by integrating multiple hormone pathways[J]. The Crop Journal, 2021, 10(1):75-87.

[218]Yang Y, Nicolas M, Zhang J, et al. The TIE1 transcriptional repressor controls shoot branching by directly repressing BRANCHED1 in Arabidopsis[J]. PLoS genetics, 2018, 14(8):1007565.

[219]Diao Y Y, Zhan J J, Zhao Y Y, et al. GhTIE1 regulates branching through modulating the transcriptional activity of TCPs in Cotton and Arabidopsis[J]. Frontiers in Plant Science, 2019, 10:1348.

[220]Wang L, Wang B, Yu H, et al. Transcriptional regulation of strigolactone signalling in Arabidopsis[J]. Nature, 2020, 583(7815):277-281.

[221]Li G F, Tan M, Ma J J, et al. Molecular mechanism of MdWUS2 MdTCP12 interaction in mediating cytokinin signaling to control axillary bud outgrowth[J]. Journal of Experimental Botany, 2021, 72(13):4822-4838.

[222]Endrizzi J E, Turcotte E L, Kohel R J. Qualitative genetics cytology and cytogenetics[J]. cotton agronomy monograph, 1984, 1(11):1.

[223]Rafalski J A. Association genetics in crop improvement[J]. Current Opinion in Plant Biology, 2010, 13(2):174-180.

[224]Huang C, Nie X H, Shen C, et al. Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs[J]. Plant Biotechnology Journal, 2017, 15(11):1374-1386.

[225]Su J J, Li L B, Zhang C, et al. Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton[J]. Theoretical and Applied Genetics, 2018, 131(6):1299-1314.

[226]Wang C X, Ma Q, Xie X Y, et al. Identification of favorable haplotypes/alleles and candidate genes for three plant architecture-related traits via a restricted two-stage multilocus genome-wide association study in upland cotton[J]. Industrial Crops and Products, 2022, 177:114458.

[227]Grover C E, Yoo M J, Lin M, et al. Genetic analysis of the transition from wild to domesticated Cotton (Gossypium hirsutum L.)[J]. G3-Genes Genomes Genetics, 2020, 10(2):731-754.

[228]Guo D L, Li C, Dong R, et al. Molecular cloning and functional analysis of the FLOWERING LOCUS T (FT) homolog GhFT1 from Gossypium hirsutum[J]. Journal of Integrative Plant Biology, 2015, 57(6):522-533.

[229]Prewitt S F, Ayre B G, McGarry R C. Cotton CENTRORADIALIS/TERMINAL FLOWER 1/SELF-PRUNING genes functionally diverged to differentially impact plant architecture[J]. Journal of Experimental Botany, 2018, 69(22):5403-5417.

[230]Liu J, Miao P F, Qin W Q, et al. A novel single nucleotide mutation of TFL1 alters the plant architecture of Gossypium arboreum through changing the pre-mRNA splicing[J]. Plant Cell Reports, 2024, 43(1):26.

[231]Ji G X, Liang C Z, Cai Y F, et al. A copy number variant at the HPDA-D12 locus confers compact plant architecture in cotton[J]. New Phytologist, 2021, 229(4):2091-2103.

[232]Wang P, Zhang S, Qiao J, et al. Functional analysis of the GbDWARF14 gene associated with branching development in cotton[J]. Peerj, 2019, 7:e6901.

[233]Pei X X, Wang X Y, Fu G Y, et al. Identification and functional analysis of 9-cis-epoxy carotenoid dioxygenase (NCED) homologs in G, hirsutum[J]. International Journal of Biological Macromolecules, 2021, 182:298-310.

[234]Yang Z R, Zhang C J, Yang X J, et al. (2014), PAG1 a cotton brassinosteroid catabolism gene modulates fiber elongation[J]. New Phytologist, 2014, 203(2):437-448.

[235]Wu H H, Ren Z Y, Zheng L, et al. The bHLH transcription factor GhPAS1 mediates BR signaling to regulate plant development and architecture in cotton[J]. Crop Journal, 2021, 9(5):1049-1059.

[236]Wen T W, Dai B S, Wang T, et al. Genetic variations in plant architecture traits in cotton (Gossypium hirsutum) revealed by a genome wide association study[J]. Crop Journal, 2019, 7(2):209-216.

[237]Wang G, Wang F, Xu Z, et al. Precise fine-turning of GhTFL1 by base editing tools defines ideal cotton plant architecture[J]. Genome biology, 2024, 25(1):59.

[238]Du Y, Luo S W, Yu L, et al. Strategies for identification of mutations induced by carbon-ion beam irradiation in Arabidopsis thaliana by whole genome re-sequencing[J]. Mutation Research-Fundamental and Molecular Mechanisms of Mutagenesis, 2018, 807:21-30.

[239]Xu X, Liu B, Zhang L, et al. Mutagenic effects of heavy ion irradiation on rice seeds[J]. Nuclear Instruments & Methods in Physics Research Section B-Beam Interactions with Materials and Atoms, 2012, 290:19-25.

[240]苑严伟, 白圣贺, 牛康, 等. 棉花种植机械化关键技术与装备研究进展[J]. 农业工程学报, 2023, 39(6):1-11.

[241]Mishra P K, Sharma A, Prakash A. Current research and development in cotton harvesters: A review with application to Indian cotton production systems[J]. Heliyon, 2023, 9(5):e16124.

[242]Gibson S I, Laby R J, Kim D. The sugar-insensitive1 (sis1) mutant of Arabidopsis is allelic to ctr1. Biochemical and biophysical research communications[J]. 2001, 280(1):196-203.

[243]Gao Y, Yang X, Yang X, et al. Characterization and expression pattern of the trehalose-6-phosphate synthase and trehalose-6-phosphate phosphatase gene families in Populus[J]. International journal of biological macromolecules, 2021, 187:9-23.

[244]Engle KA, Amos RA, Yang JY, et al. Multiple Arabidopsis galacturonosyltransferases synthesize polymeric homogalacturonan by oligosaccharide acceptor-dependent or de novo synthesis[J]. The Plant journal : for cell and molecular biology, 2022, 109(6):1441-1456.

[245]Kayum M A, Park J I, Nath U K, et al. Genome-wide expression profiling of aquaporin genes confer responses to abiotic and biotic stresses in Brassica rapa[J]. BMC plant biology, 2017, 17(1):23.

[246]Kwon Y J, Shin S, Chun Y J. Biological roles of cytochrome P450 1A1, 1A2, and 1B1 enzymes[J]. Archives of pharmacal research, 2021, 44(1):63-83.

[247]Schmidlin L, Poutaraud A, Claudel P, et al. A stress-inducible resveratrol O-methyltransferase involved in the biosynthesis of pterostilbene in grapevine[J]. Plant Physiology, 2008, 148(3):1630-1639.

[248]Nishio S, Hayashi T, Shirasawa K, et al. Genome-wide association study of individual sugar content in fruit of Japanese pear (Pyrus spp.)[J]. BMC Plant Biology, 2021, 21(1):378.

[249]Trujillo M. News from the PUB: plant U-box type E3 ubiquitin ligases[J]. Journal of experimental botany, 2018, 69(3):371-384.

[250]Spencer V M R, Bentall L, Harrison C J. Diverse branching forms regulated by a core auxin transport mechanism in plants[J]. Development, 2023, 150(6):201209.

[251]Schwarz I, Scheirlinck M T, Otto E, et al. Cytokinin regulates the activity of the inflorescence meristem and components of seed yield in oilseed rape[J]. Journal of experimental botany, 2020, 71(22):7146-7159.

[252]Takei K, Yamaya T, Sakakibara H. Arabidopsis CYP735A1 and CYP735A2 encode cytokinin hydroxylases that catalyze the biosynthesis of trans-Zeatin[J]. The Journal of biological chemistry, 2004, 279(40):41866-41872.

[253]Hutchison C E, Li J, Argueso C, et al. The Arabidopsis histidine phosphotransfer proteins are redundant positive regulators of cytokinin signaling[J]. Plant Cell, 2006, 18(11):3073-3087.

[254]Hutchison C E, Kieber J J. Signaling via histidine-containing phosphotransfer proteins in Arabidopsis[J]. Plant signaling behavior, 2007, 2(4):287-289.

[255]Reinecke D M, Wickramarathna A D, Ozga J A, et al. Gibberellin 3-oxidase gene expression patterns influence gibberellin biosynthesis, growth, and development in pea[J]. Plant physiology, 2013, 163(2):929-945.

[256]Liu Y, Chen S, Chen J, et al. Comprehensive analysis and expression profiles of the AP2/ERF gene family during spring bud break in tea plant (Camellia sinensis)[J]. BMC plant biology, 2023, 23(1):206.

[257]Feng K, Hou X L, Xing G M, et al. Advances in AP2/ERF super-family transcription factors in plant[J]. Critical reviews in biotechnology, 2020, 40(6):750-776.

[258]Dierck R, De Keyser E, De Riek J, et al. Change in auxin and cytokinin levels coincides with altered expression of branching genes during axillary bud outgrowth in Chrysanthemum[J]. PLoS One, 2016, 11(8):e0161732.

[259]Del Rosario Cárdenas-Aquino M, Sarria-Guzmán Y, Martínez-Antonio A. Review: Isoprenoid and aromatic cytokinins in shoot branching[J]. Plant Science, 2022, 319:111240.

[260]Kotov A A, Kotova L M, Romanov G A. Signaling network regulating plant branching: Recent advances and new challenges[J]. Plant Science, 2021, 307:110880.

[261]Dun E A, Brewer P B, Gillam E M J, et al. Strigolactones and shoot branching: what is the real hormone and how does it work?[J]. Plant and Cell Physiology, 2023, 64(9):967-983.

[262]Wu H, Li H, Chen H, et al. Identification and expression analysis of strigolactone biosynthetic and signaling genes reveal strigolactones are involved in fruit development of the woodland strawberry (Fragaria vesca)[J]. BMC plant biology, 2019, 19(1):73.

[263]Zhang L, Fang W, Chen F, S et al. The role of transcription factors in the regulation of plant shoot branching[J]. Plants (Basel), 2022, 11(15):1997.

[264]Ribone P A, Capella M, Chan R L. Functional characterization of the homeodomain leucine zipper I transcription factor AtHB13 reveals a crucial role in Arabidopsis development[J]. Journal of experimental botany, 2015, 66(19):5929-5943.

[265]Martín-Trillo M, Grandío EG, Serra F, et al. Role of tomato BRANCHED1-like genes in the control of shoot branching[J]. The Plant journal, 2011, 67(4):701-714.

[266]Schlegel J, Denay G, Wink R, et al. Control of Arabidopsis shoot stem cell homeostasis by two antagonistic CLE peptide signalling pathways[J]. Elife, 2021, 10:e70934.

[267]Yang Y, Hu Y, Li P, et al. Research progress and application of plant branching[J]. Phyton-International Journal of Experimental Botany, 2023, 92(3):679-689.

[268]Chen J, Liu L, Wang G, et al. The AGAMOUS-LIKE 16-GENERAL REGULATORY FACTOR 1 module regulates axillary bud outgrowth via catabolism of abscisic acid in cucumber[J]. Plant cell, 2024, 6:108-108.

[269]Carrera D A, George G M, Fischer-Stettler M, et al. Distinct plastid fructose bisphosphate aldolases function in photosynthetic and non-photosynthetic metabolism in Arabidopsis[J]. Journal of Experimental Botany, 2021, 72(10):3739-3755.

[270]Cai D, Liu H, Sang N, et al. Identification and characterization of CONSTANS-like (COL) gene family in upland cotton (Gossypium hirsutum L.)[J]. Plos One, 2017, 12(6):e0179038.

[271]Meng X, Li Y, Yuan Y, et al. The regulatory pathways of distinct flowering characteristics in Chinese jujube[J]. Horticulture Research, 2020, 7:123.

[272]Salava H, Thula S, Sanchez A S, et al. Genome wide identification and annotation of NGATHA transcription factor family in crop plants[J]. International Journal of Molecular Sciences, 2022, 23(13):7063.

[273]Wang Y, Wang N, Lan J, et al. Arabidopsis transcription factor TCP4 controls the identity of the apical gynoecium[J]. Plant cell, 2024, 6(1):107-107.

[274]Hu J, Sun S, Wang X. Regulation of shoot branching by strigolactones and brassinosteroids: conserved and specific functions of Arabidopsis BES1 and rice BZR1[J]. Molecular plant, 2020, 13(6):808-810.

[275]Xu E, Chai L, Zhang S, et al. Catabolism of strigolactones by a carboxylesterase[J]. Nature plants, 2021, 7(11):1495-1504.

[276]Yang Y, Abuauf H, Song S, et al. The Arabidopsis D27-LIKE1 is a cis/cis/trans-β-carotene isomerase that contributes to Strigolactone biosynthesis and negatively impacts ABA level[J]. The Plant journal, 2023, 113(5):986-1003.

[277]Zhao, L L, Fang J J, Xing J P, et al. Identification and functional analysis of two cotton orthologs of MAX2 which control shoot lateral branching[J]. Plant Molecular Biology, 2017, 35: 480-490.

[278]Peng H, Zhang H, Zhang L, et al. (2022). The GhMAX2 gene regulates plant growth and fiber development in cotton[J]. Journal of Integrative Agriculture, 2022, 21(6): 1563-1575.

[279]Wang, M J, Tu, L., Yuan, D. et al. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense[J]. Nature Genetics, 2019, 51(2):224-229.

[280]Liu X, Zhao B, Zheng HJ, et al. Gossypium barbadense genome sequence provides insight into the evolution of extra-long staple fiber and specialized metabolites[J]. Scientific reports, 2015, 5:14139.

[281]Hu Y, Chen J, Fang L, et al. Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton[J]. Nature Genetics, 2019, 51(4):739-748.

[282]Huang G, Wu Z, Percy RG, et al. Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution[J]. Nature Genetics, 2020, 52(5):516-524.

[283]Tamura K, Stecher G, Kumar S. MEGA11: molecular evolutionary genetics analysis version 11[J]. Molecular biology and evolution, 2021, 38(7):3022-3027.

[284]Larkin M A, Blackshields G, Brown N P, et al. Clustal W and Clustal X version 2.0[J]. Bioinformatics, 2007, 23(21):2947-2948.

[285]Chen C, Chen H, Zhang Y, et al. TBtools: An integrative toolkit developed for interactive analyses of big biological data[J]. Molecular plant, 2020, 13(8):1194-1202.

[286]Lescot M, Déhais P, Thijs G, et al. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences[J]. Nucleic acids research, 2002, 30(1):325-327.

[287]Jumper J, Evans R, Pritzel A, et al. Highly accurate protein structure prediction with AlphaFold[J]. Nature, 2021, 596(7873):583-589.

[288]Chao J T, Kong Y Z, Wang Q, et al. MapGene2Chrom, a tool to draw gene physical map based on Perl and SVG languages[J]. Yi Chuan, 2015, 37(1):91-97.

[289]Wang Y, Tang H, Debarry J D, et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity[J]. Nucleic acids research, 2012, 40(7):e49.

[290]Rasche H, Hiltemann S. Galactic circos: user-friendly circos plots within the galaxy platform[J]. GigaScience, 2020, 9(6):65-65.

[291]Zhang Z, Xiao J, Wu J, et al. ParaAT: a parallel tool for constructing multiple protein-coding DNA alignments[J]. Biochemical and biophysical research communications, 2012, 419(4):779-781.

[292]Yadav C B, Bonthala V S, Muthamilarasan M, et al. Genome-wide development of transposable elements-based markers in foxtail millet and construction of an integrated database[J]. DNA research, 2015, 22(1):79-90.

[293]Nakamura H, Xue Y L, Miyakawa T, et al. Molecular mechanism of strigolactone perception by DWARF14[J]. Nature communications, 2013, 4:2613.

[294]Livak K J, Schmittgen T D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method[J]. Methods, 2001, 25(4):402-408.

[295]Khosla A, Morffy N, Li Q, et al. Structure-function analysis of SMAX1 reveals domains that mediate its karrikin-induced proteolysis and interaction with the receptor KAI2[J]. Plant Cell, 2020, 32(8):2639-2659.

[296]Ikeda T, Tanaka W, Toriba T, et al. BELL1-like homeobox genes regulate inflorescence architecture and meristem maintenance in rice[J]. The Plant journal, 2019, 98(3):465-478.

[297]Li S F, Milliken O N, Pham H, et al. The Arabidopsis MYB5 transcription factor regulates mucilage synthesis, seed coat development, and trichome morphogenesis[J]. Plant Cell, 2009, 21(1):72-89.

[298]Li H, Chen J, Zhao Q, et al. Basic leucine zipper (bZIP) transcription factor genes and their responses to drought stress in ginseng, Panax ginseng C.A. Meyer[J]. BMC Genomics, 2021, 22(1):316.

[299]Waseem M, Nkurikiyimfura O, Niyitanga S, et al. GRAS transcription factors emerging regulator in plants growth, development, and multiple stresses[J]. Molecular biology reports, 2022, 49(10):9673-9685.

[300]Xie W, Ding C, Hu H, et al. Molecular events of rice AP2/ERF transcription factors[J]. International journal of molecular sciences, 2022, 23(19):12013.

[301]Sakamoto T, Kobayashi M, Itoh H, et al. Expression of a gibberellin 2-oxidase gene around the shoot apex is related to phase transition in rice[J]. Plant physiology, 2001, 125(3):1508-1516.

[302]Shi L, Olszewski NE. Gibberellin and abscisic acid regulate GAST1 expression at the level of transcription[J]. Plant molecular biology, 1998, 38(6):1053-1060.

[303]Gao L, Liu Q, Zhong M, et al. Blue light-induced phosphorylation of Arabidopsis cryptochrome 1 is essential for its photosensitivity[J]. Journal of integrative plant biology, 2022, 64(9):1724-1738.

[304]Cornet F, Pillot JP, Le Bris P, et al. Strigolactones (SLs) modulate the plastochron by regulating KLUH (KLU) transcript abundance in Arabidopsis[J]. New phytologist, 2021, 232(5):1909-1916.

[305]Wang X, Du Y, Yu D. Trehalose phosphate synthase 5-dependent trehalose metabolism modulates basal defense responses in Arabidopsis thaliana[J]. Journal of integrative plant biology, 2019, 61(4):509-527.

[306]Xiao W, Sheen J, Jang J C. The role of hexokinase in plant sugar signal transduction and growth and development[J]. Plant molecular biology, 2000, 44(4):451-461.

[307]Taylor-Teeples M, Lin L, de Lucas M, et al. An Arabidopsis gene regulatory network for secondary cell wall synthesis[J]. Nature, 2015, 517(7536):571-575.

[308]Moturu T R, Thula S, Singh R K, et al. Molecular evolution and diversification of the SMXL gene family[J]. Journal of experimental botany, 2018, 69(9):2367-2378.

[309]Li R, An J P, You C X, et al. Genome-wide analysis and identification of the SMXL gene family in apple (Malus x domestica)[J]. Tree Genet Genomes, 2018, 14(4):61-61.

[310]Zhang H, Wang L, Gao Y, et al. Genome-wide identification of SMXL gene family in soybean and expression analysis of GmSMXLs under Shade Stress[J]. Plants, 2022, 11(18):2410.

[311]Yang Z, Gao C, Zhang Y, et al. Recent progression and future perspectives in cotton genomic breeding[J]. Journal of integrative plant biology, 2022, 65(2):548-569.

[312]Xu G, Guo C, Shan H, et al. Divergence of duplicate genes in exon-intron structure[J]. Proceedings of the National Academy of Sciences of the United States of America, 2012, 109(4):1187-1192.

[313]Liang Y, Ward S, Li P, et al. SMAX1-LIKE7 signals from the nucleus to regulate shoot development in Arabidopsis via partially EAR motif-independent mechanisms[J]. The Plant cell, 2016, 28(7):1581-1601.

[314]Shabek N, Ticchiarelli F, Mao H, et al. Structural plasticity of D3-D14 ubiquitin ligase in strigolactone signalling[J]. Nature, 2018, 563(7733):652-656.

[315]Osnato M. Not too short and not too long: SMAX1 optimizes hypocotyl length at warmer temperature[J]. The Plant cell, 2022, 34(7):2580-2581.

[316]Xu P P, Hu J B, Chen H Y, et al. SMAX1 interacts with DELLA protein to inhibit seed germination under weak light conditions via gibberellin biosynthesis in Arabidopsis[J]. Cell Reports, 2023, 42(7):112740.

[317]Wang Y H, Li J Y. Molecular basis of plant architecture[J]. Annual Review of Plant Biology, 2008, 59:253-279.

[318]Wu F H, Gao Y P, Yang W J, et al. Biological functions of strigolactones and their crosstalk with other phytohormones[J]. Frontiers in Plant Science, 2022, 24:13:821563.

[319]Bennett T, Liang Y, Seale M, et al. Strigolactone regulates shoot development through a core signalling pathway[J]. Biology Open, 2016, 5(12):1806-1820.

[320]Zhou F, Lin Q, Zhu L, et al. D14-SCF (D3)-dependent degradation of D53 regulates strigolactone signalling[J]. Nature, 2013, 504(7480):406-410.

[321]Stanga J P, Smith S M, Briggs W R, et al. SUPPRESSOR OF MORE AXILLARY GROWTH2 1 controls seed germination and seedling development in Arabidopsis[J]. Plant physiology, 2013, 163(1):318-330.

[322]Villaécija-Aguilar JA, Hamon-Josse M, Carbonnel S, et al. SMAX1/SMXL2 regulate root and root hair development downstream of KAI2-mediated signalling in Arabidopsis[J]. PLoS genetics, 2019, 15(8):e1008327.

[323]Park Y J, Kim J Y, Park C M. SMAX1 potentiates phytochrome B-mediated hypocotyl thermomorphogenesis[J]. Plant Cell, 2022, 34(7):2671-2687.

[324]Ori N. Dissecting the biological functions of ARF and Aux/IAA genes[J]. The Plant cell, 2019, 31(6):1210-1211.

[325]Tan X, Calderon-Villalobos L I A, Sharon M, et al. Mechanism of auxin perception by the TIR1 ubiquitin ligase[J]. Nature, 2007, 446(7136):640-645.

[326]Swarup R, Bhosale R. Developmental Roles of AUX1/LAX auxin influx carriers in plants[J]. Frontiers in Plant Science, 2019, 10:1306.

[327]Thirugnanasambantham K, Durairaj S, Saravanan S, et al. Role of ethylene response transcription factor (ERF) and its regulation in response to stress encountered by plants[J]. Plant Molecular Biology, 2015, 33:347–357.

[328]Zhao H, Yin C C, Ma B, et al. Ethylene signaling in rice and Arabidopsis: New regulators and mechanisms[J]. Journal of integrative plant biology, 2021, 63(1):102-125.

[329]Iqbal N, Khan N A, Ferrante A, et al. Ethylene role in plant growth, development and senescence: interaction with other phytohormones[J]. Frontiers in plant science, 2017, 8:475.

[330]Kapulnik Y, Delaux P M, Resnick N, et al. Strigolactones affect lateral root formation and root-hair elongation in Arabidopsis[J]. Planta, 2011, 233:209-216.

[331]Koltai H. Strigolactones activate different hormonal pathways for regulation of root development in response to phosphate growth conditions[J]. Annals of Botany, 2013, 112:409-441.