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全基因组关联研究揭示了藜麦的选择模式，这与育种历史较短的作物典型模式相似。

Genome-wide association study in quinoa reveals selection pattern typical for crops with a short breeding history.

机构信息

Plant Breeding Institute, Christian-Albrechts-University of Kiel, Kiel, Germany.

King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences & Engineering Division (BESE), Thuwal, Saudi Arabia.

出版信息

Elife. 2022 Jul 8;11:e66873. doi: 10.7554/eLife.66873.

DOI:10.7554/eLife.66873
PMID:35801689
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9388097/
Abstract

Quinoa germplasm preserves useful and substantial genetic variation, yet it remains untapped due to a lack of implementation of modern breeding tools. We have integrated field and sequence data to characterize a large diversity panel of quinoa. Whole-genome sequencing of 310 accessions revealed 2.9 million polymorphic high confidence single nucleotide polymorphism (SNP) loci. Highland and Lowland quinoa were clustered into two main groups, with divergence of 0.36 and linkage disequilibrium (LD) decay of 6.5 and 49.8 kb, respectively. A genome-wide association study using multi-year phenotyping trials uncovered 600 SNPs stably associated with 17 traits. Two candidate genes are associated with thousand seed weight, and a resistance gene analog is associated with downy mildew resistance. We also identified pleiotropically acting loci for four agronomic traits important for adaptation. This work demonstrates the use of re-sequencing data of an orphan crop, which is partially domesticated to rapidly identify marker-trait association and provides the underpinning elements for genomics-enabled quinoa breeding.

摘要

藜麦种质资源保留了有用且大量的遗传变异，但由于缺乏现代育种工具的应用，这些资源尚未得到开发。我们整合了田间数据和序列数据，对大量藜麦多样性进行了分析。对 310 个品系进行全基因组测序，共发现 290 万个多态性高置信单核苷酸多态性（SNP）位点。高地和低地藜麦聚集成两个主要群体，其分化度为 0.36，连锁不平衡（LD）衰减分别为 6.5 和 49.8 kb。利用多年表型试验进行的全基因组关联研究发现，有 600 个 SNP 与 17 个性状稳定相关。两个候选基因与千粒重有关，一个抗病基因类似物与霜霉病抗性有关。我们还发现了四个与适应有关的重要农艺性状的多效作用位点。这项工作展示了对部分驯化的孤儿作物进行重测序数据的利用，这可以快速识别标记-性状关联，并为基于基因组学的藜麦育种提供基础要素。

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