Exome-wide variation in a diverse barley panel reveals genetic associations with ten agronomic traits in Eastern landraces

June-Sik Kim; Kotaro Takahagi; Komaki Inoue; Minami Shimizu; Yukiko Uehara-Yamaguchi; Asaka Kanatani; Daisuke Saisho; Ryuei Nishii; Alexander E. Lipka; Takashi Hirayama; Kazuhiro Sato; Keiichi Mochida

doi:10.1016/j.jgg.2022.12.001

Volume 50 Issue 4

Apr. 2023

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Article Navigation > Journal of Genetics and Genomics > 2023 > 50(4): 241-252

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Exome-wide variation in a diverse barley panel reveals genetic associations with ten agronomic traits in Eastern landraces

doi: 10.1016/j.jgg.2022.12.001

a. Bioproductivity Informatics Research Team, RIKEN Center for Sustainable Resource Science, Yokohama 230-0045, Japan;
b. Institute of Plant Science and Resources, Okayama University, Kurashiki 710-0046, Japan;
c. Kihara Institute for Biological Research, Yokohama City University, Yokohama 244-0813, Japan;
d. Graduate School of Nanobioscience, Yokohama City University, Yokohama 236-0027, Japan;
e. School of Information and Data Sciences, Nagasaki University, Nagasaki 852-8521, Japan;
f. Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA;
g. Microalgae Production Control Technology Laboratory, RIKEN Baton Zone Program, RIKEN Cluster for Science, Technology and Innovation Hub, Yokohama 230-0045, Japan

Funds:

We especially thank Ms. Naomi Yamaji (Okayama University, Japan) for her excellent technical assistance. Barley seeds used in this study were supplied by the National BioResource Project (NBRP) Barley, Japan (https://nbrp.jp/en/resource/barley-en/). This work was supported by a Grant-in-Aid for Scientific Research (B) (grant no. 15KT0038 to K.M.) and a Grant-in-Aid for Scientific Research (C) (grant no. 19K11861 to K.M. and R.N.) of the Japan Society for the Promotion of Science, and by CREST (grant no. JPMJCR16O4 to K.M.) of the Japan Science and Technology Agency.

Received Date: 2022-11-15
Accepted Date: 2022-12-09
Rev Recd Date: 2022-12-08
Publish Date: 2023-04-30

Abstract

Abstract

Barley (Hordeum vulgare ssp. vulgare) is one of the first crops to be domesticated and is adapted to a wide range of environments. Worldwide barley germplasm collections possess valuable allelic variations that could further improve barley productivity. Although barley genomics has offered a global picture of allelic variation among varieties and its association with various agronomic traits, polymorphisms from East Asian varieties remain scarce. In this study, we analyze exome polymorphisms in a panel of 274 barley varieties collected worldwide, including 137 varieties from East Asian countries and Ethiopia. We reveal the underlying population structure and conduct genome-wide association studies for 10 agronomic traits. Moreover, we examin genome-wide associations for traits related to grain size such as awn length and glume length. Our results demonstrate the value of diverse barley germplasm panels containing Eastern varieties, highlighting their distinct genomic signatures relative to Western subpopulations.
- Barley,
- Exome-seq,
- Genome-wide association study (GWAS),
- Population structure,
- Allelic variation

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References(71)

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