结论:通过将GWAS与转录组相结合,鉴定了两个已报道的分till角基因和11个水稻分till角候选基因的新等位基因,qRT-PCR和单倍型分析。水稻分枝角是决定水稻籽粒产量的关键农艺性状。在过去的几十年中,已经定位了几个影响水稻分till角的数量性状位点(QTL)。关于水稻分till角的遗传基础知之甚少,因为水稻分耕角是一个复杂的多基因性状。在这项研究中,我们使用来自3K水稻基因组计划(3KRGP)的164个粳稻品种进行了水稻分till角的全基因组关联研究(GWAS)。我们基于三个GWAS模型(GLM,FastLMM和FarmCPU)。其中,两个确定的QTL,qTA8.3和qTA8.4,分别与PAY1和TIG1重叠,首次发现另外16个QTL。结合单倍型和表达分析,我们进一步揭示了PAY1在其编码区具有一个非同义变异,可能导致人口中不同的耕种角度,TIG1启动子的自然变异显著影响其表达,与till角表型密切相关。同样,使用qRT-PCR和单倍型分析,我们在qTA6.1和qTA8.1中鉴定了1个和7个候选基因,这些基因通常由两个GWAS模型检测到,分别。此外,通过转录组分析和qRT-PCR筛选后,我们在其余14个新QTL中鉴定出3个候选基因。总之,本研究为水稻分耕角的遗传结构和候选基因的育种提供了新的见解。
CONCLUSIONS: Novel alleles of two reported tiller angle genes and eleven candidate genes for rice tiller angle were identified by combining GWAS with transcriptomic, qRT-PCR and haplotype analysis. Rice tiller angle is a key agronomic trait determining rice grain yield. Several quantitative trait loci (QTLs) affecting rice tiller angle have been mapped in the past decades. Little is known about the genetic base of tiller angle in rice, because rice tiller angle is a complex polygenic trait. In this study, we performed genome-wide association study (GWAS) on tiller angle in rice using a population of 164 japonica varieties derived from the 3 K Rice Genomes Project (3 K RGP). We detected a total of 18 QTLs using 1135519 single-nucleotide polymorphisms (SNP) based on three GWAS models (GLM, FastLMM and FarmCPU). Among them, two identified QTLs, qTA8.3 and qTA8.4, overlapped with PAY1 and TIG1, respectively, and additional 16 QTLs were identified for the first time. Combined with haplotype and expression analyses, we further revealed that PAY1 harbors one non-synonymous variation at its coding region, likely leading to variable tiller angle in the population, and that nature variations in the promoter of TIG1 significantly affect its expression, closely correlating with tiller angle phenotypes observed. Similarly, using qRT-PCR and haplotype analysis, we identified 1 and 7 candidate genes in qTA6.1 and qTA8.1 that were commonly detected by two GWAS models, respectively. In addition, we identified 3 more candidate genes in the remaining 14 novel QTLs after filtering by transcriptome analysis and qRT-PCR. In summary, this study provides new insights into the genetic architecture of rice tiller angle and candidate genes for rice breeding.