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ARS Home » Pacific West Area » Aberdeen, Idaho » Small Grains and Potato Germplasm Research » Research » Publications at this Location » Publication #373587
Research Project: Improvement of Barley and Oat for Enhanced Productivity, Quality, and Stress Resistance

Location: Small Grains and Potato Germplasm Research

Title: Genome-wide association study reveals the genetic architecture of seed vigor in oats

Author
item HUANG, CHING-TING - National Taiwan University
item Esvelt Klos, Kathy
item HUANG, YUNG-FEN - National Taiwan University

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 10/2/2020
Publication Date: 12/1/2020
Citation: Huang, C., Esvelt Klos, K.L., Huang, Y. 2020. Genome-wide association study reveals the genetic architecture of seed vigor in oats. G3, Genes/Genomes/Genetics. 10(12):4489-4503. https://doi.org/10.1534/g3.120.401602.
DOI: https://doi.org/10.1534/g3.120.401602

Interpretive Summary: Seed vigor is important to early crop establishment,. However, little is known about its genetic control in oats. We developed an image-based phenotyping pipeline to assess seed vigor and performed genome-wide association study on an oat diversity panel in order to investigate the genetic architecture of seed vigor in oats. Trait-associated loci were found in genomic regions with similarity to one-another, and three trait-associated markers matched genes in rice and maize which probably involve seed vigor traits.

Technical 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. In order to investigate seed vigor-related traits and 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. Most traits were variable among lines. 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 homoeologous regions, while nine shoot-associated loci were organized into three sets of homoeologous regions, suggesting reliability of results. The context sequences of five trait-associated markers matched to 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.