Integrated genome-wide differentiation and association analyses identify causal genes underlying breeding-selected grain quality traits in japonica rice.

Autor: Yoshida H; Institute of Fermentation Sciences, Fukushima University, Fukushima 960-1248, Japan., Okada S; Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Uzurano, Kasai, Hyogo 675-2103, Japan., Wang F; Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan; Research Center of Genetic Resources, NARO, 2-1-1 Kannondai, Tsukuba, Ibaraki 305-8602, Japan., Shiota S; Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan., Mori M; Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan., Kawamura M; Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan., Zhao X; Rice Research Institute, Shenyang Agricultural University, Shenyang, China., Wang Y; Rice Research Institute, Shenyang Agricultural University, Shenyang, China., Nishigaki N; Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, Japan., Kobayashi A; Fukui Agricultural Experiment Station, Fukui 918-8215, Japan., Miura K; Department of Bioscience and Biotechnology, Fukui Prefectural University, Fukui 910-1195, Japan., Yoshida S; Hyogo Prefectural Research Center for Agriculture, Forestry and Fisheries, Kasai, Hyogo 679-0198, Japan; Research Institute for Food and Agriculture, Ryukoku University, Ootsu, Shiga 520-2194, Japan., Ikegami M; Hyogo Prefectural Research Center for Agriculture, Forestry and Fisheries, Kasai, Hyogo 679-0198, Japan., Ito A; Food Research Centre, Aichi Centre for Industry and Science Technology, 2-1-1 Shimpukuji-cho, Nagoya, Aichi 451-0083, Japan., Huang LT; Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, China; Department of Agronomy, National Taiwan University, Taipei, Taiwan, China., Caroline Hsing YI; Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan, China; Department of Agronomy, National Taiwan University, Taipei, Taiwan, China., Yamagata Y; Plant Breeding Laboratory, Faculty of Agriculture, Kyushu University, 744, Motooka, Nishiku, Fukuoka, Japan., Morinaka Y; Department of Bioscience and Biotechnology, Fukui Prefectural University, Fukui 910-1195, Japan., Yamasaki M; Food Resources Education and Research Center, Graduate School of Agricultural Science, Kobe University, Uzurano, Kasai, Hyogo 675-2103, Japan., Kotake T; Division of Life Science, Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama, Japan., Yamamoto E; Graduate School of Agriculture, Meiji University, 1-1-1 Higashi-Mita, Tama-ku, Kawasaki, Kanagawa 214-8571, Japan., Sun J; Rice Research Institute, Shenyang Agricultural University, Shenyang, China. Electronic address: sunjian811119@syau.edu.cn., Hirano K; Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan. Electronic address: hirano773y@yahoo.co.jp., Matsuoka M; Institute of Fermentation Sciences, Fukushima University, Fukushima 960-1248, Japan. Electronic address: matsuoka@agri.fukushima-u.ac.jp.
Jazyk: angličtina
Zdroj: Molecular plant [Mol Plant] 2023 Sep 04; Vol. 16 (9), pp. 1460-1477. Date of Electronic Publication: 2023 Sep 09.
DOI: 10.1016/j.molp.2023.09.002
Abstrakt: Improving grain quality is a primary objective in contemporary rice breeding. Japanese modern rice breeding has developed two different types of rice, eating and sake-brewing rice, with different grain characteristics, indicating the selection of variant gene alleles during the breeding process. Given the critical importance of promptly and efficiently identifying genes selected in past breeding for future molecular breeding, we conducted genome scans for divergence, genome-wide association studies, and map-based cloning. Consequently, we successfully identified two genes, OsMnS and OsWOX9D, both contributing to rice grain traits. OsMnS encodes a mannan synthase that increases the white core frequency in the endosperm, a desirable trait for sake brewing but decreases the grain appearance quality. OsWOX9D encodes a grass-specific homeobox-containing transcription factor, which enhances grain width for better sake brewing. Furthermore, haplotype analysis revealed that their defective alleles were selected in East Asia, but not Europe, during modern improvement. In addition, our analyses indicate that a reduction in grain mannan content during African rice domestication may also be caused a defective OsMnS allele due to breeding selection. This study not only reveals the delicate balance between grain appearance quality and nutrition in rice but also provides a new strategy for isolating causal genes underlying complex traits, based on the concept of "breeding-assisted genomics" in plants.
(Copyright © 2023 The Author. Published by Elsevier Inc. All rights reserved.)
Databáze: MEDLINE
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