Genes, Vol. 13, Pages 794: Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice

Genes, Vol. 13, Pages 794: Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice
Genes doi: 10.3390/genes13050794
Authors:
Chaewon Lee
Kyeong-Seong Cheon
Yunji Shin
Hyoja Oh
Young-Min Jeong
Hoon Jang
Yong-Chan Park
Kyung-Yun Kim
Hang-Chul Cho
Yong-Jae Won
Jeongho Baek
Young-Soon Cha
Song-Lim Kim
Kyung-Hwan Kim
Hyeonso Ji

The development of efficient, robust, and high-throughput SNP genotyping platforms is pivotal for crop genetics and breeding. Recently, SNP genotyping platforms based on target capture sequencing, which is very flexible in terms of the number of SNP markers, have been developed for maize, cassava, and fava bean. We aimed to develop a target capture sequencing SNP genotyping platform for rice. A target capture sequencing panel containing 2565 SNPs, including 1225 SNPs informative for japonica and 1339 SNPs informative for indica, was developed. This platform was used in diversity analysis of 50 rice varieties. Of the 2565 SNP markers, 2341 (91.3%) produced useful polymorphic genotype data, enabling the production of a phylogenetic tree of the 50 varieties. The mean number of markers polymorphic between any two varieties was 854. The platform was used for QTL mapping of preharvest sprouting (PHS) resistance in an F8 recombinant inbred line population derived from the cross Odae × Joun. A genetic map comprising 475 markers was constructed, and two QTLs for PHS resistance were ...

Source: Genes - April 28, 2022 Category: Genetics & Stem Cells Authors: Chaewon Lee Kyeong-Seong Cheon Yunji Shin Hyoja Oh Young-Min Jeong Hoon Jang Yong-Chan Park Kyung-Yun Kim Hang-Chul Cho Yong-Jae Won Jeongho Baek Young-Soon Cha Song-Lim Kim Kyung-Hwan Kim Hyeonso Ji Tags: Article Source Type: research