Genomic investigation of 18,421 lines reveals the genetic architecture of rice-Reference-Cited by-同舟云学术

Genomic investigation of 18,421 lines reveals the genetic architecture of rice

Published:2024-07-05 Issue:6704 Volume:385 Page:
ISSN:0036-8075
Container-title:Science
language:en
Short-container-title:Science

Author:

Wei Xin¹^ORCID,Chen Mengjiao¹^ORCID,Zhang Qi¹^ORCID,Gong Junyi²^ORCID,Liu Jie¹^ORCID,Yong Kaicheng¹^ORCID,Wang Qin¹^ORCID,Fan Jiongjiong²,Chen Suhui¹^ORCID,Hua Hua¹,Luo Zhaowei¹,Zhao Xiaoyan¹,Wang Xuan¹^ORCID,Li Wei¹,Cong Jia¹,Yu Xiting¹,Wang Zhihan¹,Huang Ruipeng¹,Chen Jiaxin¹,Zhou Xiaoyi¹^ORCID,Qiu Jie¹^ORCID,Xu Ping¹^ORCID,Murray Jeremy³^ORCID,Wang Hai⁴^ORCID,Xu Yang⁵^ORCID,Xu Chenwu⁵^ORCID,Xu Gen⁶^ORCID,Yang Jinliang⁶^ORCID,Han Bin³^ORCID,Huang Xuehui¹^ORCID

Affiliation:

1. Shanghai Key Laboratory of Plant Molecular Sciences, Development Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China.

2. State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou 310006, China.

3. CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200233, China.

4. State Key Laboratory of Plant Physiology and Biochemistry, College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.

5. Key Laboratory of Plant Functional Genomics of Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China.

6. Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.

Abstract

Understanding how numerous quantitative trait loci (QTL) shape phenotypic variation is an important question in genetics. To address this, we established a permanent population of 18,421 (18K) rice lines with reduced population structure. We generated reference-level genome assemblies of the founders and genotyped all 18K-rice lines through whole-genome sequencing. Through high-resolution mapping, 96 high-quality candidate genes contributing to variation in 16 traits were identified, including OsMADS22 and OsFTL1 verified as causal genes for panicle number and heading date, respectively. We identified epistatic QTL pairs and constructed a genetic interaction network with 19 genes serving as hubs. Overall, 170 masking epistasis pairs were characterized, serving as an important factor contributing to genetic background effects across diverse varieties. The work provides a basis to guide grain yield and quality improvements in rice.

Publisher

American Association for the Advancement of Science (AAAS)

Link

https://www.science.org/doi/pdf/10.1126/science.adm8762

Reference62 articles.

1. Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

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