Xiuxiu Li
Hongwei Lu
Qiang Gao
Huilong Du
Hua Peng
Peng Qin
Chengzhi Liang
aState Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
bUniversity of Chinese Academy of Sciences, Beijing 100049, China
cRice Research Institute, State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
More InformationCorresponding author: E-mail address: cliang@genetics.ac.cn (Chengzhi Liang)
Publish Date:2020-10-25
Abstract
Abstract
The long history of cultivation and breeding has left a variety of footprints in the genomes of Asian cultivated rice (Oryza sativa L.). In this study, we focus on two types of genomic footprints, introgression and differentiation, in a population of more than 1200 Chinese rice accessions. We found that a Xian/indica and a temperate Geng/japonica accession respectively contained an average of 19.3-Mb and 6.8-Mb alien introgressed chromosomal segments, of which many contained functional sequence variants, quantitative trait loci, or genes controlling flowering, grain, and resistance traits. Notably, we found most introgressions, including the known heterotic loci Hd3a and TAC1, were distributed differentially between the female and male parents of three-line indica hybrid rice, indicating their potential contribution to heterosis. We also found many differentiated regions between subgroups within a subpopulation contained agronomically important loci, such as DTH7, Hd1 for heading date, and qCT7 for cold tolerance, providing new candidates for studying local adaptation or heterosis. Tracing these footprints allows us to better understand the genetic exchange or differentiation underlying agronomic traits in modern Chinese rice cultivars. These findings also provide potential targets for rice genetic research and breeding.Keywords: Rice,
Introgression,
Differentiation,
Genome-wide association study,
Adaptation,
Heterosis
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http://www.jgenetgenomics.org/article/exportPdf?id=2dd553a2-62c0-4153-8033-11c95fd8c850&language=en
