title: Population genetic structure of Oryza sativa in East and Southeast Asia and the discovery of elite alleles for grain traits.
abstract: We investigated the nuclear simple sequence repeat (SSR) genotypes of 532 rice (Oryza sativa L.) accessions collected from East and Southeast Asia and detected abundant genetic diversity within the population. We identified 6 subpopulations and found a tendency towards directional evolution in O. sativa from low to high latitudes, with levels of linkage disequilibrium (LD) in the 6 subpopulations ranging from 10 to 30 cM. We then investigated the phenotypic data for grain length, grain width, grain thickness and 1,000-grain weight over 4 years. Using a genome-wide association analysis, we identified 17 marker-trait associations involving 14 SSR markers on 12 chromosome arms, and 8 of the 17 associations were novel. The elite alleles were mined based on the phenotypic effects of the detected quantitative trait loci (QTLs). These elite alleles could be used to improve target traits through optimal cross designs, with the expected results obtained by pyramiding or substituting the elite alleles per QTL (independent of possible epistatic effects). Together, these results provide an in-depth understanding of the genetic diversity pattern among rice-grain traits across a broad geographic scale, which has potential use in future research work, including studies related to germplasm conservation and molecular breeding by design.
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Xiaojing
authors.initials: X
authors.lastname: Dang
authors.affiliation: 1] State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China [2] College of Agronomy, Hue University of Agriculture and Forestry, Hue University,102 Phung Hung Street, Hue City, Vietnam.
authors.forename: Thu
authors.initials: T
authors.lastname: Giang Tran Thi
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Wisdom
authors.initials: W
authors.lastname: Mawuli Edzesi
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Lijun
authors.initials: L
authors.lastname: Liang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Qiangming
authors.initials: Q
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Erbao
authors.initials: E
authors.lastname: Liu
authors.affiliation: 1] State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China [2] Department of Agricultural Resource and Environment, Heilongjiang University, Harbin, 150080, China.
authors.forename: Yang
authors.initials: Y
authors.lastname: Wang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Sheng
authors.initials: S
authors.lastname: Qiang
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Linglong
authors.initials: L
authors.lastname: Liu
authors.affiliation: State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
authors.forename: Delin
authors.initials: D
authors.lastname: Hong
mesh_terms: D000483:Alleles; D001208:Asia; D017343:Genes, Plant; D012275:Oryza / Q000235:genetics*; D040641:Quantitative Trait Loci