QTL mapping and improvement of pre-harvest sprouting resistance using japonica weedy rice

Abstract

The stability of cultivation and production in terms of crop yield has been threatened by climate change due to global warming. Pre-harvest sprouting (PHS) is a threat to crops, especially staple foods, including rice, because of reductions in yield and quality. To address the problem of precocious germination before harvest, we performed quantitative trait loci (QTL) analysis for PHS using F8 RILs populations derived from japonica weedy rice in Korea. QTL analysis revealed that two stable QTLs, qPH7 and qPH2, associated with PHS resistance were identified on chromosomes 7 and 2, respectively, explaining approximately 38% of the phenotypic variation. The QTL effect in the tested lines significantly decreased the degree of PHS, based on the number of QTLs included. Through fine mapping for main QTL qPH7, the region for the PHS was found to be anchored within 23.575–23.785 Mbp on chromosome 7 using 13 cleaved amplified sequence (CAPS) markers. Among 15 open reading frames (ORFs) within the detected region, one ORF, Os07g0584366, exhibited upregulated expression in the resistant donor, which was approximately nine times higher than that of susceptible japonica cultivars under PHS-inducing conditions. Japonica lines with QTLs related to PHS resistance were developed to improve the characteristics of PHS and design practical PCR-based DNA markers for marker-assisted backcrosses of many other PHS-susceptible japonica cultivars.

RicePilaf: a post-GWAS/QTL dashboard to integrate pangenomic, coexpression, regulatory, epigenomic, ontology, pathway, and text-mining information to provide functional insights into rice QTLs and GWAS loci

“…Preharvest sprouting (PHS) is a condition in which seeds lose dormancy and germinate prior to harvest, thus negatively affecting grain yield and quality [ 56 ]. A recent GWAS on PHS using a panel of 277 accessions representing temperate and tropical japonica and indica populations found the loci Chr01:1523,625-1770814 and Chr04:4662701-4670717 to be significantly associated with this trait [ 12 ].…”

Genetic Enhancement of Cereals Using Genomic Resources for Nutritional Food Security

“…Helps in rapid breeding for a particular trait [95] Marker-assisted selection Pyramided genes of high grain weight, stripe rust, and leaf rust resistance [96] Rice QTL mapping Heat tolerance [97] QTL mapping Pre-harvest sprouting resistance [98] SNP genotyping array RiceSNP50 Functional genomics and molecular breeding [99] 580 K SNP array Genomic selection and GWAS [100] Genotyping-by-sequencing Pre-breeding and improvement [101] Genomic prediction Rice improvement [102] GWAS Adaptability to dry direct-seeded rice (DDSR) system [103] Rice pangenome genotyping array (RPGA) SNP genotyping Genetic improvement [104] QTL-seq using NIL-F 2 Grain length and weight [103] SNP-based QTL mapping Panicle traits [104] Table 2. Cont.…”