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通过结合QTL-seq和全基因组关联分析快速鉴定水稻中胚轴长度的QTL

Rapid Identification of QTL for Mesocotyl Length in Rice Through Combining QTL-seq and Genome-Wide Association Analysis.

作者信息

Wang Yamei, Liu Jindong, Meng Yun, Liu Hongyan, Liu Chang, Ye Guoyou

机构信息

Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.

CAAS-IRRI Joint Laboratory for Genomics-Assisted Germplasm Enhancement, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China.

出版信息

Front Genet. 2021 Jul 19;12:713446. doi: 10.3389/fgene.2021.713446. eCollection 2021.

DOI:10.3389/fgene.2021.713446
PMID:34349792
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8326918/
Abstract

Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in direct-seeded rice. Thus, the identification of quantitative trait loci (QTL) associated with mesocotyl length (ML) could accelerate genetic improvement of rice for direct seeding cultivation. In this study, QTL sequencing (QTL-seq) applied to 12 F populations identified 14 QTL for ML, which were distributed on chromosomes 1, 3, 4, 5, 6, 7, and 9 based on the Δ(SNP-index) or -value statistics. Besides, a genome-wide association study (GWAS) using two diverse panels identified five unique QTL on chromosomes 1, 8, 9, and 12 (2), respectively, explaining 5.3-14.6% of the phenotypic variations. Among these QTL, seven were in the regions harboring known genes or QTLs, whereas the other 10 were potentially novel. Six of the QTL were stable across two or more populations. Eight high-confidence candidate genes related to ML were identified for the stable loci based on annotation and expression analyses. Association analysis revealed that two PCR gel-based markers for the loci co-located by QTL-seq and GWAS, and for loci and respectively, were significantly associated with ML in a collection of 140 accessions and could be used as breeder-friendly markers in further breeding.

摘要

中胚轴是促使芽破土而出的关键器官，在直播水稻的幼苗出土和定植过程中起着至关重要的作用。因此，鉴定与中胚轴长度（ML）相关的数量性状位点（QTL）能够加速水稻直播栽培的遗传改良。在本研究中，对12个F群体应用QTL测序（QTL-seq）鉴定出14个控制ML的QTL，基于Δ(SNP-index)或P值统计，这些QTL分布在第1、3、4、5、6、7和9号染色体上。此外，利用两个不同的群体进行全基因组关联研究（GWAS），分别在第1、8、9和12号染色体（2个）上鉴定出5个独特的QTL，解释了5.3%-14.6%的表型变异。在这些QTL中，7个位于含有已知基因或QTL的区域，而另外10个可能是新的。其中6个QTL在两个或更多群体中是稳定的。基于注释和表达分析，为稳定位点鉴定出8个与ML相关的高置信度候选基因。关联分析表明，QTL-seq和GWAS共定位的两个位点的基于PCR凝胶的标记，分别为位点 和 的标记，在140份材料中与ML显著相关，可在进一步育种中用作对育种者友好的标记。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/f00e5ab88c4d/fgene-12-713446-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/7f1525ebb713/fgene-12-713446-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/683dd77c6a51/fgene-12-713446-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/b73693043b78/fgene-12-713446-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/eb92b765bc6e/fgene-12-713446-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/cfa772c25c1a/fgene-12-713446-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/f5c134f285d5/fgene-12-713446-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/c2aa07f6b7b3/fgene-12-713446-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/838b1309c838/fgene-12-713446-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/f00e5ab88c4d/fgene-12-713446-g009.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/7f1525ebb713/fgene-12-713446-g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/683dd77c6a51/fgene-12-713446-g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/b73693043b78/fgene-12-713446-g003.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/eb92b765bc6e/fgene-12-713446-g004.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/cfa772c25c1a/fgene-12-713446-g005.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/f5c134f285d5/fgene-12-713446-g006.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/c2aa07f6b7b3/fgene-12-713446-g007.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/838b1309c838/fgene-12-713446-g008.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/5b8c/8326918/f00e5ab88c4d/fgene-12-713446-g009.jpg

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