title: Genome-wide study of an elite rice pedigree reveals a complex history of genetic architecture for breeding improvement.
abstract: Improving breeding has been widely utilized in crop breeding and contributed to yield and quality improvement, yet few researches have been done to analyze genetic architecture underlying breeding improvement comprehensively. Here, we collected genotype and phenotype data of 99 cultivars from the complete pedigree including Huanghuazhan, an elite, high-quality, conventional indica rice that has been grown over 4.5 million hectares in southern China and from which more than 20 excellent cultivars have been derived. We identified 1,313 selective sweeps (SSWs) revealing four stage-specific selection patterns corresponding to improvement preference during 65 years, and 1113 conserved Huanghuazhan traceable blocks (cHTBs) introduced from different donors and conserved in >3 breeding generations were the core genomic regions for superior performance of Huanghuazhan. Based on 151 quantitative trait loci (QTLs) identified for 13 improved traits in the pedigree, we reproduced their improvement process in silico, highlighting improving breeding works well for traits controlled by major/major + minor effect QTLs, but was inefficient for traits controlled by QTLs with complex interactions or explaining low levels of phenotypic variation. These results indicate long-term breeding improvement is efficient to construct superior genetic architecture for elite performance, yet molecular breeding with designed genotype of QTLs can facilitate complex traits improvement.
authors.affiliation: School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, and School of Advanced Agriculture Sciences, Peking University, Beijing 100871, China.|Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program (PTN), Peking University, China.
authors.forename: Shaoxia
authors.initials: S
authors.lastname: Chen
authors.affiliation: School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, and School of Advanced Agriculture Sciences, Peking University, Beijing 100871, China.
authors.forename: Zechuan
authors.initials: Z
authors.lastname: Lin
authors.affiliation: Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
authors.forename: Degui
authors.initials: D
authors.lastname: Zhou
authors.affiliation: Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, 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 510640, China.
authors.forename: Hong
authors.initials: H
authors.lastname: Li
authors.affiliation: School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, and School of Advanced Agriculture Sciences, Peking University, Beijing 100871, China.
authors.forename: Renbo
authors.initials: R
authors.lastname: Yu
authors.affiliation: Shenzhen Institute of Molecular Crop Design, Shenzhen 518107, China.
authors.forename: Hanchao
authors.initials: H
authors.lastname: Deng
authors.affiliation: Shenzhen Institute of Molecular Crop Design, Shenzhen 518107, China.|Guangdong Key Lab of Biotechnology for Plant Development, College of Life Sciences, South China Normal University, Guangzhou 510631, China.
authors.forename: Xiaoyan
authors.initials: X
authors.lastname: Tang
authors.affiliation: Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.
authors.forename: Shaochuan
authors.initials: S
authors.lastname: Zhou
authors.affiliation: School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, and School of Advanced Agriculture Sciences, Peking University, Beijing 100871, China.|Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program (PTN), Peking University, China.
authors.forename: Xing
authors.initials: X
authors.lastname: Wang Deng
authors.affiliation: School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, and School of Advanced Agriculture Sciences, Peking University, Beijing 100871, China.|Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program (PTN), Peking University, China.
authors.forename: Hang
authors.initials: H
authors.lastname: He
mesh_terms: D002681:China; D018745:Genome, Plant / Q000235:genetics*; D055106:Genome-Wide Association Study / Q000379:methods; D005838:Genotype; D012275:Oryza / Q000235:genetics*; D010375:Pedigree; D010641:Phenotype; D000069600:Plant Breeding / Q000379:methods; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D040641:Quantitative Trait Loci / Q000235:genetics