Wang Siyuan, Wu Hongyu, Zhao Yongyan, Wang Luyao, Guan Xueying, Zhao Ting
Zhejiang Provincial Key Laboratory of Crop Genetic Resources, Institute of Crop Science, Plant Precision Breeding Academy, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 300058, China.
Hainan Institute of Zhejiang University, Building 11, Yonyou Industrial Park, Yazhou Bay Science and Technology City, Yazhou District, Sanya, 572025, Hainan, China.
Plant Methods. 2023 Jul 21;19(1):72. doi: 10.1186/s13007-023-01048-4.
Alternative splicing (AS) of mRNA plays an important roles in transcriptome diversity, involving regulation of plant growth and stress response. Understanding the variation of AS events underlying GWAS loci in a crop population can provide insight into the molecular mechanisms of complex agronomic traits. To date, genome-wide association studies relating AS events to agronomic traits have rarely been conducted at the population level in crops.
Here, a pipeline was constructed to identify candidate AS events related to complex traits. Firstly, ovule transcriptome data were used to characterize intron retention (IR), the predominant type of AS in plants, on a genome-wide scale. This was done in a natural population consisting of 279 upland cotton lines. Secondly, splice quantitative trait locus (sQTL) analysis was carried out, which yielded a total of 2295 sQTLs involving 1607 genes. Of these, 14.25% (n = 427) were cis-regulatory loci. Integration with expression quantitative trait loci (eQTL) revealed that 53 (21.4%) cis-sGenes were regulated by both cis-sQTLs and cis-eQTLs. Finally, co-localization analysis integrated with GWAS loci in this population showed 32 cis-QTLs to be co-located with genetic regulatory loci related to fiber yield and quality traits, indicating that sQTLs are likely to participate in regulating cotton fiber yield and quality. An in-depth evaluation confirmed that differences in the IR rates of sQTL-regulated candidate genes such as GhLRRK1 and GhGC1 are associated with lint percentage (LP), which has potential in breeding applications.
This study provides a clue that AS of mRNA has an impact on crop yield, along with functional sQTLs are new genetic resources for cotton precision breeding.
mRNA的可变剪接（AS）在转录组多样性中发挥重要作用，涉及植物生长调控和胁迫响应。了解作物群体中全基因组关联研究（GWAS）位点潜在的AS事件变异，有助于深入了解复杂农艺性状的分子机制。迄今为止，在作物群体水平上，很少开展将AS事件与农艺性状相关联的全基因组关联研究。
本文构建了一个流程来鉴定与复杂性状相关的候选AS事件。首先，利用胚珠转录组数据在全基因组范围内对植物中主要的AS类型——内含子保留（IR）进行表征。这一工作在由279个陆地棉品系组成的自然群体中完成。其次，进行了剪接定量性状位点（sQTL）分析，共获得2295个涉及1607个基因的sQTL。其中，14.25%（n = 427）为顺式调控位点。与表达定量性状位点（eQTL）整合分析发现，53个（21.4%）顺式s基因受顺式sQTL和顺式eQTL共同调控。最后将该群体中的GWAS位点进行共定位分析，结果显示32个顺式QTL与纤维产量和品质性状的遗传调控位点共定位，表明sQTL可能参与调控棉花纤维产量和品质。深入评估证实，sQTL调控的候选基因如GhLRRK1和GhGC1的IR率差异与皮棉产量（LP）相关，具有育种应用潜力。
本研究表明mRNA的AS对作物产量有影响，并提供了功能性sQTL作为棉花精准育种新遗传资源的线索。
