title: Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.).
abstract: Single nucleotide polymorphisms (SNPs) are the most abundant DNA markers in plant genomes. In this study, based on 54,465 SNPs between the genomes of two Indica varieties, Minghui 63 (MH63) and Zhenshan 97 (ZS97) and additional 20,705 SNPs between the MH63 and Nipponbare genomes, we identified and confirmed 1,633 well-distributed SNPs by PCR and Sanger sequencing. From these, a set of 372 SNPs were further selected to analyze the patterns of genetic diversity in 300 representative rice inbred lines from 22 rice growing countries worldwide. Using this set of SNPs, we were able to uncover the well-known Indica-Japonica subspecific differentiation and geographic differentiations within Indica and Japonica. Furthermore, our SNP results revealed some common and contrasting patterns of the haplotype diversity along different rice chromosomes in the Indica and Japonica accessions, which suggest different evolutionary forces possibly acting in specific regions of the rice genome during domestication and evolution of rice. Our results demonstrated that this set of SNPs can be used as anchor SNPs for large scale genotyping in rice molecular breeding research involving Indica-Japonica and Indica-Indica crosses.
authors.affiliation: Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, 100871 Beijing, China.
authors.forename: Haodong
authors.initials: H
authors.lastname: Chen
authors.forename: Hang
authors.initials: H
authors.lastname: He
authors.forename: Yanjiao
authors.initials: Y
authors.lastname: Zou
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.forename: Renbo
authors.initials: R
authors.lastname: Yu
authors.forename: Xia
authors.initials: X
authors.lastname: Liu
authors.forename: Yang
authors.initials: Y
authors.lastname: Yang
authors.forename: Yong-Ming
authors.initials: YM
authors.lastname: Gao
authors.forename: Jian-Long
authors.initials: JL
authors.lastname: Xu
authors.forename: Liu-Min
authors.initials: LM
authors.lastname: Fan
authors.forename: Yi
authors.initials: Y
authors.lastname: Li
authors.forename: Zhi-Kang
authors.initials: ZK
authors.lastname: Li
authors.forename: Xing Wang
authors.initials: XW
authors.lastname: Deng
mesh_terms: D001483:Base Sequence; D032461:Chromosomes, Plant / Q000235:genetics*; D003433:Crosses, Genetic; D032621:DNA Shuffling / Q000379:methods*; D018744:DNA, Plant; D005787:Gene Frequency; D005819:Genetic Markers; D014644:Genetic Variation; D018745:Genome, Plant; D005838:Genotype; D012275:Oryza / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers