title: Pedigree-based analysis of derivation of genome segments of an elite rice reveals key regions during its breeding.
abstract: Analyses of genome variations with high-throughput assays have improved our understanding of genetic basis of crop domestication and identified the selected genome regions, but little is known about that of modern breeding, which has limited the usefulness of massive elite cultivars in further breeding. Here we deploy pedigree-based analysis of an elite rice, Huanghuazhan, to exploit key genome regions during its breeding. The cultivars in the pedigree were resequenced with 7.6× depth on average, and 2.1 million high-quality single nucleotide polymorphisms (SNPs) were obtained. Tracing the derivation of genome blocks with pedigree and information on SNPs revealed the chromosomal recombination during breeding, which showed that 26.22% of Huanghuazhan genome are strictly conserved key regions. These major effect regions were further supported by a QTL mapping of 260 recombinant inbred lines derived from the cross of Huanghuazhan and a very dissimilar cultivar, Shuanggui 36, and by the genome profile of eight cultivars and 36 elite lines derived from Huanghuazhan. Hitting these regions with the cloned genes revealed they include numbers of key genes, which were then applied to demonstrate how Huanghuazhan were bred after 30 years of effort and to dissect the deficiency of artificial selection. We concluded the regions are helpful to the further breeding based on this pedigree and performing breeding by design. Our study provides genetic dissection of modern rice breeding and sheds new light on how to perform genomewide breeding by design.
authors.affiliation: Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
authors.forename: Degui
authors.initials: D
authors.lastname: Zhou
authors.affiliation: State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and College of Life Sciences, Peking University, Beijing, China.|School of Information and Engineering, Wenzhou Medical University, Wenzhou, China.
authors.forename: Wei
authors.initials: W
authors.lastname: Chen
authors.affiliation: State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and College of Life Sciences, Peking University, Beijing, China.
authors.forename: Zechuan
authors.initials: Z
authors.lastname: Lin
authors.affiliation: State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and College of Life Sciences, Peking University, Beijing, China.|Shenzhen Institute of Crop Molecular Design, Shenzhen, China.
authors.forename: Haodong
authors.initials: H
authors.lastname: Chen
authors.affiliation: Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
authors.forename: Chongrong
authors.initials: C
authors.lastname: Wang
authors.affiliation: Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Li
authors.affiliation: State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and College of Life Sciences, Peking University, Beijing, China.|Shenzhen Institute of Crop Molecular Design, Shenzhen, China.
authors.forename: Renbo
authors.initials: R
authors.lastname: Yu
authors.affiliation: Agricultural College, Hunan Agricultural University, Changsha, China.
authors.forename: Fengyun
authors.initials: F
authors.lastname: Zhang
authors.affiliation: State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and College of Life Sciences, Peking University, Beijing, China.|Shenzhen Institute of Crop Molecular Design, Shenzhen, China.
authors.forename: Gang
authors.initials: G
authors.lastname: Zhen
authors.affiliation: Agricultural College, Hunan Agricultural University, Changsha, China.
authors.forename: Junliang
authors.initials: J
authors.lastname: Yi
authors.affiliation: Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.
authors.forename: Kanghuo
authors.initials: K
authors.lastname: Li
authors.affiliation: College of Life Sciences, South China Agricultural University, Guangzhou, China.
authors.forename: Yaoguang
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Biology, Wilkes University, Wilkes-Barre, PA, USA.
authors.forename: William
authors.initials: W
authors.lastname: Terzaghi
authors.affiliation: Shenzhen Institute of Crop Molecular Design, Shenzhen, China.|Frontier Laboratories of Systems Crop Design Co., Ltd., Beijing, China.
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Tang
authors.affiliation: State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and College of Life Sciences, Peking University, Beijing, China.|Shenzhen Institute of Crop Molecular Design, Shenzhen, China.|Frontier Laboratories of Systems Crop Design Co., Ltd., Beijing, China.
authors.forename: Hang
authors.initials: H
authors.lastname: He
authors.affiliation: Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, China.|Agricultural College, Hunan Agricultural University, Changsha, China.
authors.forename: Shaochuan
authors.initials: S
authors.lastname: Zhou
authors.affiliation: State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agricultural Sciences and College of Life Sciences, Peking University, Beijing, China.|Shenzhen Institute of Crop Molecular Design, Shenzhen, China.|Frontier Laboratories of Systems Crop Design Co., Ltd., Beijing, China.
authors.forename: Xing Wang
authors.initials: XW
authors.lastname: Deng
mesh_terms: D032461:Chromosomes, Plant / Q000235:genetics; D017124:Conserved Sequence; D051456:Gene Flow; D017343:Genes, Plant; D018745:Genome, Plant; D012275:Oryza / Q000235:genetics*; D010375:Pedigree; D000069600:Plant Breeding / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D019655:Quantitative Trait, Heritable; D017422:Sequence Analysis, DNA
keywords: artificial selection; breeding; genetic improvement; pedigree; resequencing; single nucleotide polymorphisms