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- 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.
- Authors
Tae-Sung Kim; Qiang He; Kyu-Won Kim; Min-Young Yoon; Won-Hee Ra; Feng Peng Li; Wei Tong; Jie Yu; Win Htet Oo; Buung Choi; Eun-Beom Heo; Byoung-Kook Yun; Soon-Jae Kwon; Soon-Wook Kwon; Yoo-Hyun Cho; Chang-Yong Lee; Beom-Seok Park; Yong-Jin Park
- Abstract
Background: 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. Results: 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. Conclusion: 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.
- Subjects
NUCLEOTIDE sequencing; PLANT germplasm; RICE breeding; SINGLE nucleotide polymorphisms; PLANT gene banks
- Publication
BMC Genomics, 2016, Vol 17, p1
- ISSN
1471-2164
- Publication type
Article
- DOI
10.1186/s12864-016-2734-y