Genome-Wide Association Study Reveals the Genetic Architecture of Seed Vigor in Oats

Author:

Huang Ching-Ting1,Klos Kathy Esvelt2,Huang Yung-Fen1

Affiliation:

1. Department of Agronomy, National Taiwan University, Taipei, 10617, Taiwan

2. Small Grains and Potato Germplasm Research, USDA, ARS, Aberdeen, ID 83210

Abstract

Abstract Seed vigor is crucial for crop early establishment in the field and is particularly important for forage crop production. Oat (Avena sativa L.) is a nutritious food crop and also a valuable forage crop. However, little is known about the genetics of seed vigor in oats. To investigate seed vigor-related traits and their genetic architecture in oats, we developed an easy-to-implement image-based phenotyping pipeline and applied it to 650 elite oat lines from the Collaborative Oat Research Enterprise (CORE). Root number, root surface area, and shoot length were measured in two replicates. Variables such as growth rate were derived. Using a genome-wide association (GWA) approach, we identified 34 and 16 unique loci associated with root traits and shoot traits, respectively, which corresponded to 41 and 16 unique SNPs at a false discovery rate < 0.1. Nine root-associated loci were organized into four sets of homeologous regions, while nine shoot-associated loci were organized into three sets of homeologous regions. The context sequences of five trait-associated markers matched to the sequences of rice, Brachypodium and maize (E-value < 10−10), including three markers matched to known gene models with potential involvement in seed vigor. These were a glucuronosyltransferase, a mitochondrial carrier protein domain containing protein, and an iron-sulfur cluster protein. This study presents the first GWA study on oat seed vigor and data of this study can provide guidelines and foundation for further investigations.

Publisher

Oxford University Press (OUP)

Subject

Genetics(clinical),Genetics,Molecular Biology

Reference91 articles.

1. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.;Altschul;Nucleic Acids Res.,1997

2. Aravind, J., S. Mukesh Sankar, D. P. Wankhede, and V. Kaur, 2020 augmentedRCBD: analysis of augmented randomised complete block designs. R package version 0.1.2. https://aravind-j.github.io/augmentedRCBD/; https://cran.r-project.org/package=augmentedRCBD.

3. WinRHlZOTM, a root-measuring system with a unique overlap correction method.;Arsenault;HortScience,1995

4. Phenotyping pipeline reveals major seedling root growth QTL in hexaploid wheat.;Atkinson;J. Exp. Bot.,2015

5. Fitting linear mixed-effects models using lme4.;Bates,2015

同舟云学术

1.学者识别学者识别

2.学术分析学术分析

3.人才评估人才评估

"同舟云学术"是以全球学者为主线,采集、加工和组织学术论文而形成的新型学术文献查询和分析系统,可以对全球学者进行文献检索和人才价值评估。用户可以通过关注某些学科领域的顶尖人物而持续追踪该领域的学科进展和研究前沿。经过近期的数据扩容,当前同舟云学术共收录了国内外主流学术期刊6万余种,收集的期刊论文及会议论文总量共计约1.5亿篇,并以每天添加12000余篇中外论文的速度递增。我们也可以为用户提供个性化、定制化的学者数据。欢迎来电咨询!咨询电话:010-8811{复制后删除}0370

www.globalauthorid.com

TOP

Copyright © 2019-2024 北京同舟云网络信息技术有限公司
京公网安备11010802033243号  京ICP备18003416号-3