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利用转座子标记探索水稻农艺性状相关等位基因变异。

Exploring transposable element-based markers to identify allelic variations underlying agronomic traits in rice.

机构信息

School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA.

School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; Graduate Program in Genetics, Bioinformatics and Computational Biology (GBCB), Virginia Tech, Blacksburg, VA 24061, USA.

出版信息

Plant Commun. 2022 May 9;3(3):100270. doi: 10.1016/j.xplc.2021.100270. Epub 2021 Dec 20.

DOI:10.1016/j.xplc.2021.100270
PMID:35576152
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9251385/
Abstract

Transposable elements (TEs) are a major force in the production of new alleles during domestication; nevertheless, their use in association studies has been limited because of their complexity. We have developed a TE genotyping pipeline (TEmarker) and applied it to whole-genome genome-wide association study (GWAS) data from 176 Oryza sativa subsp. japonica accessions to identify genetic elements associated with specific agronomic traits. TE markers recovered a large proportion (69%) of single-nucleotide polymorphism (SNP)-based GWAS peaks, and these TE peaks retained ca. 25% of the SNPs. The use of TEs in GWASs may reduce false positives associated with linkage disequilibrium (LD) among SNP markers. A genome scan revealed positive selection on TEs associated with agronomic traits. We found several cases of insertion and deletion variants that potentially resulted from the direct action of TEs, including an allele of LOC_Os11g08410 associated with plant height and panicle length traits. Together, these findings reveal the utility of TE markers for connecting genotype to phenotype and suggest a potential role for TEs in influencing phenotypic variations in rice that impact agronomic traits.

摘要

转座元件 (TEs) 是在驯化过程中产生新等位基因的主要力量；然而，由于其复杂性，它们在关联研究中的应用受到限制。我们开发了一种 TE 基因分型管道 (TEmarker)，并将其应用于来自 176 个水稻亚种粳稻的全基因组全基因组关联研究 (GWAS) 数据，以鉴定与特定农艺性状相关的遗传元件。TE 标记回收了很大一部分（69%）基于单核苷酸多态性 (SNP) 的 GWAS 峰，这些 TE 峰保留了大约 25%的 SNPs。在 GWAS 中使用 TEs 可以减少与 SNP 标记之间连锁不平衡 (LD) 相关的假阳性。基因组扫描显示 TE 与农艺性状之间存在正选择。我们发现了几种插入和缺失变异的情况，这些变异可能是 TEs 直接作用的结果，包括与株高和穗长性状相关的 LOC_Os11g08410 等位基因。总之，这些发现揭示了 TE 标记在将基因型与表型联系起来的实用性，并表明 TEs 在影响影响农艺性状的水稻表型变异方面可能发挥作用。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b82/9251385/049e4aab4982/gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b82/9251385/af77d65aeac6/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b82/9251385/d5ddb9625e3e/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b82/9251385/4a23e4f175cd/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b82/9251385/4d2ca07ff223/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b82/9251385/976f05dc5834/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b82/9251385/049e4aab4982/gr6.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b82/9251385/af77d65aeac6/gr1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b82/9251385/d5ddb9625e3e/gr2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b82/9251385/4a23e4f175cd/gr3.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b82/9251385/4d2ca07ff223/gr4.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b82/9251385/976f05dc5834/gr5.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/4b82/9251385/049e4aab4982/gr6.jpg

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