Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era

BMC Genomics

Research Article

Chang-Yong Lee¹  Byoung-Kook Yun¹  Soon-Wook Kwon²  Buung Choi³  Eun-Beom Heo³  Qiang He³  Win Htet Oo³  Won-Hee Ra³  Feng Peng Li³  Wei Tong³  Jie Yu³  Min-Young Yoon³  Tae-Sung Kim⁴  Yong-Jin Park⁴  Kyu-Won Kim⁴  Soon-Jae Kwon⁵  Yoo-Hyun Cho⁶  Beom-Seok Park⁷ 

[1] Department of Industrial & Systems Engineering, Kongju National University, 330-717, Cheonan, Republic of Korea;Department of Plant Bioscience, College of Natural Resources and Life Science, Pusan National University, 627-706, Milyang, Republic of Korea;Department of Plant Resources, College of Industrial Sciences, Kongju National University, 340-702, Yesan, Republic of Korea;Department of Plant Resources, College of Industrial Sciences, Kongju National University, 340-702, Yesan, Republic of Korea;Legume Bio-Resource Center of Green Manure (LBRCGM), Kongju National University, 340-702, Yesan, Republic of Korea;Korea Atomic Energy Research Institute, Advanced Radiation Technology Institute, 29 Geumgu-gil, 580-185, Jeongeup-si, Jeollabuk-do, Korea;University of Science and Technology, Radiation Biotechnology and Applied Radioisotope Science, 217 Gajungro Yuseong-gu, 305-350, Daejeon, Korea;Seedpia, 85, Maesil-ro, Kwonsun-ku, 441-882, Suwon, Republic of Korea;The Agricultural Genome Center, National Acedemy of Agricultural Science, Rural Development Adiministration, 565-851, Wanju, Republic of Korea;

关键词: Whole-genome resequencing;    Rice;    Core collection;    Germplasm;    SNP;    INDEL;    GWAS;   

DOI  :  10.1186/s12864-016-2734-y

 received in 2015-08-27, accepted in 2016-05-12,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundRice 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.ResultsHere, 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.ConclusionThis 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.

【 授权许可】

CC BY   
© Kim et al. 2016