陆地棉GhSUVs开花关键基因功能鉴定及育种演化

doi:10.3864/j.issn.0578-1752.2026.15.002

摘要/Abstract

摘要：

【目的】早熟是我国棉花遗传改良的重要目标性状，开花期是衡量早熟性的重要指标。H3K9组蛋白赖氨酸甲基转移酶（SUV）在拟南芥、水稻等模式植物中参与植物发育与开花调控，探究陆地棉SUV家族成员开花调控作用，并解析其关键成员的优异等位变异，为选育早熟棉花新品种提供基因资源。【方法】以拟南芥SUV家族蛋白序列作为参考序列，采用HMMER、MEME、TBtools等分析工具对SUV家族成员在陆地棉中进行全基因组水平鉴定和分析。基于RNA-seq与RT-qPCR联合分析筛选该家族成员中调控开花的候选基因。通过病毒诱导基因沉默（virus induced gene silencing，VIGS）技术验证候选基因在调控陆地棉开花中的功能。基于419份陆地棉种质资源的重测序数据，并通过Sanger测序验证GhSUV1内部SNP；分析不同棉花生态区等位基因频率和遗传分化指标。【结果】通过全基因组鉴定，在水稻等9种高等植物中共鉴定到200个SUV同源蛋白，系统发育分析将其划分为SUVH类和SUVR类，整体进化较为保守。陆地棉中共鉴定到28个GhSUV基因，其扩张主要由多倍化事件驱动，且多数共线基因对Ka/Ks<1，表明其受到强烈纯化选择。结构与基序分析显示，同一类群成员具有较高一致性。启动子分析表明，GhSUV基因富集光信号和激素响应元件，提示其在棉花生长发育过程中参与多种调控路径。RNA-seq数据和RT-qPCR分析表明，GhSUV1和GhSUV13在早熟材料中相对表达量较高，同时，在叶片与部分花器官中高水平表达。利用VIGS对GhSUV1和GhSUV13进行功能鉴定。结果表明，与对照相比，抑制GhSUV1表达的植株现蕾和开花分别延迟5.6和6.0 d，抑制GhSUV13表达植株较对照延迟5.8和6.8 d。此外，抑制GhSUV1和GhSUV13表达后棉花中开花相关基因GhSOC1、GhAP1、GhFT和GhCAL的表达量显著降低，而GhSVP的表达量显著升高，表明GhSUV1和GhSUV13均参与开花调控。序列分析发现GhSUV1外显子区域存在一个与开花时间显著相关的SNP位点，其早花GG等位变异随纬度升高而增加。遗传分化指数和核苷酸多样性分析显示，GhSUV1基因组区域在早熟和晚熟品种间存在显著差异，提示其可能受到育种选择。【结论】GhSUV1和GhSUV13参与陆地棉开花调控，其中，GhSUV1的优异等位变异与早花性状密切相关并受到育种选择。

关键词: 陆地棉, 早熟, H3K9组蛋白赖氨酸甲基转移酶, 开花调控, 等位变异

Abstract:

【Objective】Early maturity is an important target trait in cotton genetic improvement in China, and flowering time is a key indicator of earliness. H3K9 histone lysine methyltransferases (SUVs) are involved in plant development and flowering regulation in model plants such as Arabidopsis thaliana and rice. This study aimed to investigate the role of the SUV gene family in flowering regulation in upland cotton and to identify elite allelic variations of key members. The findings provide valuable genetic resources for breeding early-maturing cotton cultivars.【Method】Protein sequences of the SUV family from Arabidopsis were used as reference sequences. HMMER, MEME, and TBtools were employed to identify and analyze SUV family members in upland cotton at the whole-genome level. Candidate genes involved in flowering regulation were screened through integrated RNA-seq and RT-qPCR analyses. Virus-induced gene silencing (VIGS) was used to validate the functions of candidate genes in flowering regulation. Resequencing data from 419 upland cotton accessions were analyzed to identify SNPs within GhSUV1, which were further validated by Sanger sequencing. Allele frequencies and genetic differentiation were examined across different cotton ecological regions.【Result】A total of 200 SUV homologous proteins were identified in nine higher plant species, including rice. Phylogenetic analysis divided them into SUVH and SUVR clades, indicating a relatively conserved evolutionary pattern. In upland cotton, 28 GhSUV genes were identified. Their expansion was mainly driven by polyploidization events. Most collinear gene pairs showed Ka/Ks<1, suggesting strong purifying selection. Gene structure and motif analyses revealed high similarity among members within the same clade. Promoter analysis showed that GhSUV genes are enriched in light-responsive and hormone-responsive cis-elements, indicating their involvement in multiple developmental regulatory pathways. RNA-seq and RT-qPCR analyses showed that GhSUV1 and GhSUV13 were expressed at higher levels in early-maturing materials. They were also highly expressed in leaves and certain floral organs. Functional validation using VIGS demonstrated that silencing GhSUV1 delayed squaring and flowering by 5.6 and 6.0 days, respectively. Silencing GhSUV13 delayed these stages by 5.8 and 6.8 days compared with the control. Moreover, suppression of GhSUV1 and GhSUV13 significantly reduced the expression of flowering-related genes GhSOC1, GhAP1, GhFT, and GhCAL, while significantly increasing GhSVP expression. These results indicate that both genes participate in flowering regulation. Sequence analysis identified a SNP in the exon region of GhSUV1 that was significantly associated with flowering time. The early-flowering GG allele increased in frequency with latitude. Genetic differentiation index and nucleotide diversity analyses revealed significant differences in the GhSUV1 genomic region between early- and late-maturing cultivars, suggesting that this locus has undergone breeding selection.【Conclusion】GhSUV1 and GhSUV13 are involved in flowering regulation in upland cotton. The elite allele of GhSUV1 is closely associated with early flowering and has been subject to breeding selection. These findings provide important genetic resources for the improvement of early-maturing cotton varieties.

Key words: Upland cotton, early maturity, H3K9 histone lysine methyltransferase, flowering regulation, allelic variation

魏佳智, 张文姣, 赵岩, 李颖, 巨吉生, 杨军宁, 冯誉誉, 马雄风, 宿俊吉, 王彩香. 陆地棉GhSUVs开花关键基因功能鉴定及育种演化[J]. 中国农业科学, 2026, 59(15): 3252-3266.

WEI JIAZHI, ZHANG WENJIAO, ZHAO YAN, LI YING, JU JISHENG, YANG JUNNING, FENG YUYU, MA XIONGFENG, SU JUNJI, WANG CAIXIANG. Functional Identification and Breeding Evolution of the Key Flowering Gene GhSUVs in Upland Cotton[J]. Scientia Agricultura Sinica, 2026, 59(15): 3252-3266.

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引物 Primer	引物序列 Primer sequence (5′-3′)	备注 Remark
GhSUV1-F	GTGCTCAACCGACTCCAGAA	克隆Clone
GhSUV1-R	TAATGGCCAGTCAGCCCTTG
GhSUV13-F	TTTAGAGCCGAACCACCACC
GhSUV13-R	CCGTACCCCTTTCGTGAACA
MQGhSUV1-F	cggaattcGTGCTCAACCGACTCCAGAA	带酶切位点引物 Primers with restriction sites
MQGhSUV1-R	ggggtaccTAATGGCCAGTCAGCCCTTG
MQGhSUV13-F	cggaattcTTTAGAGCCGAACCACCACC
MQGhSUV13-R	ggggtaccCCGTACCCCTTTCGTGAACA
qGhSUV1-F	AAGTTCGCCGTGCAGATACA	实时荧光定量PCR RT-qPCR
qGhSUV1-R	CAAAGTCGTGGTGTTAGCAG
qGhSUV13-F	GTCCTTTCCCGACTGGGTTT
qGhSUV13-R	GGTGGTGGTTCGGCTCTAAA
SNPGhSUV1-F	TGATGCCTTGCACAGAGGAG	SNP验证SNP verification
SNPGhSUV1-R	GGCCAATGGCAATGGAACAG	SNP验证SNP verification