Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice

Abstract

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 identified on chromosomes 4 and 11. This system is a powerful tool for rice genetics and breeding and will facilitate QTL studies and gene mapping, germplasm diversity analysis, and marker-assisted selection.

Keywords: QTL; SNP; genotyping; preharvest sprouting; rice; target capture sequencing.

Figure 1

Distribution of SNP markers included in the target capture panel across the rice reference genome. Columns represent chromosomes, and rows represent physical positions (1 Mbp intervals). The numbers of SNP markers per Mbp are shown in each row; cell colors differ according to SNP marker density, as indicated in the legend in the lower right-hand corner of the figure.

Figure 2

Polymorphism information content (PIC) values of SNP markers present on the target capture panel.

Figure 3

Population structure and phylogeny analysis of the 50 rice varieties used in this study. (a) Assignment of the rice varieties to two populations (japonica and indica) using the STRUCTURE 2.3.4 program. (b) Phylogenetic tree of the rice varieties. Their evolutionary history was inferred using the Neighbor-Joining method. The optimal tree with the sum of branch length = 5.76867357 is shown. The tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the Maximum Composite Likelihood method and are in the units of the number of base substitutions per site.

Figure 4

Construction of a genetic map using genotype data from 162 F₈ recombinant inbred lines (RILs) derived from an Odae × Joun cross obtained from the target capture panel. Chromosomes are numbered at the top. Marker names are indicated on the right-hand side of each chromosome, and the genetic distance of each marker from the first marker at the top of the chromosome is shown on the left-hand side. Genetic distances, measured in cM, were calculated using the Kosambi function.

Figure 5

Phenotypic variation in preharvest sprouting (PHS) in the rice varieties Odae and Joun and a recombinant inbred line (RIL) population derived from an Odae × Joun cross. (a) PHS phenotypes of the parental varieties and representative RILs. Scale bar: 20 mm. (b) Distribution of PHS rates across 162 RILs and their parental lines. Inverted triangles indicate the parental varieties.

Figure 6

Positions of two QTLs affecting preharvest sprouting (PHS) rate in the genetic map of 162 RILs derived from the cross Odae × Joun. The names of each marker and their genetic distances from the first marker at the top of each chromosome are shown on the left-hand side. The LOD score (red line) is shown on the right-hand side.