QTL mapping for pre-harvest sprouting resistance in japonica rice varieties utilizing genome re-sequencing

Abstract

Pre-harvest sprouting (PHS) leads to serious economic losses because of reductions in yield and quality. To analyze the quantitative trait loci (QTLs) for PHS resistance in japonica rice, PHS rates on panicles were measured in 160 recombinant inbred lines (RILs) derived from a cross between the temperate japonica varieties Odae (PHS resistant) and Unbong40 (PHS susceptible) under two different environmental conditions-field (summer) and greenhouse (winter) environments. Genome re-sequencing of the parental varieties detected 266,773 DNA polymorphisms including 248,255 single nucleotide polymorphisms and 18,518 insertions/deletions. We constructed a genetic map comprising 239 kompetitive allele-specific PCR and 49 cleaved amplified polymorphic sequence markers. In the field environment, two major QTLs, qPHS-3^FD and qPHS-11^FD, were identified on chromosomes 3 and 11, respectively, whereas three major QTLs, qPHS-3^GH, qPHS-4^GH, and qPHS-11^GH, were identified on chromosomes 3, 4, and 11, respectively, in the greenhouse environment. qPHS-11^GH and qPHS-11^FD had similar locations on chromosome 11, suggesting the existence of a gene conferring stable PHS resistance effects under different environmental conditions. The QTLs identified in this study can be used to improve the PHS resistance of japonica varieties, and they may improve our understanding of the genetic basis of PHS resistance.

Keywords: Japonica rice; Pre-harvest sprouting; Quantitative trait locus; Re-sequencing.

Fig. 1

Phenotypic variations of pre-harvest sprouting (PHS) in the parental varieties under two environmental conditions. a PHS of parental varieties. Panicles were harvested 35 days after flowering and incubated for 7 days under 25 °C and 100% humidity. Each bar indicates 3 cm. b The distribution of the PHS rates of 160 recombinant inbred lines derived from a cross between Odae and Unbong40. FD and GH denote field and greenhouse conditions, respectively. Solid inversed triangles on the histogram indicate the PHS rates of the parental varieties Odae and Unbong40

Fig. 2

Construction of a genetic map using 239 kompetitive allele-specific PCR and 49 cleaved amplified polymorphic sequence markers with genotypes of 160 recombinant inbred line plants derived from a cross between the varieties Odae and Unbong40. The chromosome number is indicated at the top of each chromosome, the name of each marker is indicated on the right side of each chromosome, and the genetic distance of each marker from the first marker at the top of each chromosome is shown on the left side. Genetic distances, measured in cM, were calculated using the Kosambi function. The quantitative trait locus interval at 95% probability is indicated by the filled black box

Fig. 3

Boxplot showing the pre-harvest sprouting rate distribution of the four groups of recombinant inbred lines derived from a cross between Odae and Unbong40 classified by genotype combination of the two markers qLTG3-1ind and KJ11_090. The first letter in the genotype combination indicates the genotype of qLTG3-1ind, and the second letter indicates that of KJ11_090. ‘A’ denotes an Odae allele, and ‘B’ denotes an Unbong40 allele