title: Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era.
abstract: Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remains challenging, it is important to establish practical methods to manage them. A core collection, by definition, refers to a subset of the entire population that preserves the majority of genetic diversity, enhancing the efficiency of germplasm utilization.
  
  
  
  Here, we report whole-genome resequencing of the 137 rice mini core collection or Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in the Korean genebank of the Rural Development Administration (RDA). We implemented the Illumina HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8 depths using Nipponbare as a reference. Comparisons of the sequences with the reference genome yielded more than 15 million (M) single nucleotide polymorphisms (SNPs) and 1.3 M INDELs. Phylogenetic and population analyses using 2,046,529 high-quality SNPs successfully assigned rice accessions to the relevant rice subgroups, suggesting that these SNPs capture evolutionary signatures that have accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for four exemplary agronomic traits in the KRIC_CORE manifest the utility of KRICE_CORE; that is, identifying previously defined genes or novel genetic factors that potentially regulate important phenotypes.
  
  
  
  This study provides strong evidence that the size of KRICE_CORE is small but contains high genetic and functional diversity across the genome. Thus, our resequencing results will be useful for future breeding, as well as functional and evolutionary studies, in the post-genomic era.
authors.affiliation: Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 340-702, Republic of Korea.|Legume Bio-Resource Center of Green Manure (LBRCGM), Kongju National University, Yesan, 340-702, Republic of Korea.
authors.forename: Tae-Sung
authors.initials: TS
authors.lastname: Kim
authors.affiliation: Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 340-702, Republic of Korea.
authors.forename: Qiang
authors.initials: Q
authors.lastname: He
authors.affiliation: Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 340-702, Republic of Korea.|Legume Bio-Resource Center of Green Manure (LBRCGM), Kongju National University, Yesan, 340-702, Republic of Korea.
authors.forename: Kyu-Won
authors.initials: KW
authors.lastname: Kim
authors.affiliation: Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 340-702, Republic of Korea.
authors.forename: Min-Young
authors.initials: MY
authors.lastname: Yoon
authors.affiliation: Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 340-702, Republic of Korea.
authors.forename: Won-Hee
authors.initials: WH
authors.lastname: Ra
authors.affiliation: Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 340-702, Republic of Korea.
authors.forename: Feng Peng
authors.initials: FP
authors.lastname: Li
authors.affiliation: Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 340-702, Republic of Korea.
authors.forename: Wei
authors.initials: W
authors.lastname: Tong
authors.affiliation: Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 340-702, Republic of Korea.
authors.forename: Jie
authors.initials: J
authors.lastname: Yu
authors.affiliation: Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 340-702, Republic of Korea.
authors.forename: Win Htet
authors.initials: WH
authors.lastname: Oo
authors.affiliation: Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 340-702, Republic of Korea.
authors.forename: Buung
authors.initials: B
authors.lastname: Choi
authors.affiliation: Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 340-702, Republic of Korea.
authors.forename: Eun-Beom
authors.initials: EB
authors.lastname: Heo
authors.affiliation: Department of Industrial & Systems Engineering, Kongju National University, Cheonan, 330-717, Republic of Korea.
authors.forename: Byoung-Kook
authors.initials: BK
authors.lastname: Yun
authors.affiliation: Korea Atomic Energy Research Institute, Advanced Radiation Technology Institute, 29 Geumgu-gil, Jeongeup-si, Jeollabuk-do, 580-185, Korea.|University of Science and Technology, Radiation Biotechnology and Applied Radioisotope Science, 217 Gajungro Yuseong-gu, Daejeon, 305-350, Korea.
authors.forename: Soon-Jae
authors.initials: SJ
authors.lastname: Kwon
authors.affiliation: Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, Milyang, 627-706, Republic of Korea.
authors.forename: Soon-Wook
authors.initials: SW
authors.lastname: Kwon
authors.affiliation: Seedpia, 85, Maesil-ro, Kwonsun-ku, Suwon, 441-882, Republic of Korea.
authors.forename: Yoo-Hyun
authors.initials: YH
authors.lastname: Cho
authors.affiliation: Department of Industrial & Systems Engineering, Kongju National University, Cheonan, 330-717, Republic of Korea.
authors.forename: Chang-Yong
authors.initials: CY
authors.lastname: Lee
authors.affiliation: The Agricultural Genome Center, National Acedemy of Agricultural Science, Rural Development Adiministration, Wanju, 565-851, Republic of Korea.
authors.forename: Beom-Seok
authors.initials: BS
authors.lastname: Park
authors.affiliation: Department of Plant Resources, College of Industrial Sciences, Kongju National University, Yesan, 340-702, Republic of Korea. yjpark@kongju.ac.kr.|Legume Bio-Resource Center of Green Manure (LBRCGM), Kongju National University, Yesan, 340-702, Republic of Korea. yjpark@kongju.ac.kr.
authors.forename: Yong-Jin
authors.initials: YJ
authors.lastname: Park
mesh_terms: D001947:Breeding; D019143:Evolution, Molecular; D014644:Genetic Variation; D005828:Genetics, Population; D018745:Genome, Plant; D055106:Genome-Wide Association Study; D023281:Genomics / Q000379:methods*; D054643:INDEL Mutation; D012275:Oryza / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA
keywords: Core collection; GWAS; Germplasm; INDEL; Rice; SNP; Whole-genome resequencing