Abstract
Colored rice is rich in nutrition and also a good source of valuable genes/quantitative trait loci (QTL) for nutrition, grain quality, and pest and disease resistance traits for use in rice breeding. Genome-wide association analysis using high-density single nucleotide polymorphism (SNP) is useful in precisely detecting QTLs and genes. We carried out genome-wide association analysis in 152 colored rice accessions, using 22,112 SNPs to map QTLs for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits. Wide variations and normal frequency distributions were observed for most of the traits except anthocyanin content and BLB resistance. The structural and principal component analysis revealed two subgroups. The linkage disequilibrium (LD) analysis showed 74.3% of the marker pairs in complete LD, with an average LD distance of 1000 kb and, interestingly, 36% of the LD pairs were less than 5 Kb, indicating high recombination in the panel. In total, 57 QTLs were identified for ten traits at p < 0.0001, and the phenotypic variance explained (PVE) by these QTLs varied from 9% to 18%. Interestingly, 30 (53%) QTLs were co-located with known or functionally-related genes. Some of the important candidate genes for grain Zinc (Zn) and BLB resistance were OsHMA9, OsMAPK6, OsNRAMP7, OsMADS13, and OsZFP252, and Xa1, Xa3, xa5, xa13 and xa26, respectively. Red rice genotype, Sayllebon, which is high in both Zn and anthocyanin content, could be a valuable material for a breeding program for nutritious rice. Overall, the QTLs identified in our study can be used for QTL pyramiding as well as genomic selection. Some of the novel QTLs can be further validated by fine mapping and functional characterization. The results show that pigmented rice is a valuable resource for mineral elements and antioxidant compounds; it can also provide novel alleles for disease resistance as well as for yield component traits. Therefore, large opportunities exist to further explore and exploit more colored rice accessions for use in breeding.
Highlights
Rice, being a dominant cereal and staple food, provides energy and nutrition for a majority of theAsian population [1]
All the accessions were phenotyped for nine agronomic traits, days to heading (DH), number of panicles (NP), panicle length (PL), number of spikelets per panicle (NSP), ripening ratio (RR), grain length (GL); grain width (GW), thousand-grain weight (TGW), and anthocyanin (AC) in Korea, and for DH, TGW, Fe, and Zn at the IRRI
We characterized colored rice accessions for nutritional, agronomic, and bacterial leaf blight (BLB) resistance traits, and carried out association mapping and candidate gene analysis to facilitate the development of healthier rice varieties
Summary
Rice, being a dominant cereal and staple food, provides energy and nutrition for a majority of theAsian population [1]. White rice is consumed as a major part of the daily diet, which is low in nutritional value in comparison with brown rice or pigmented rice [2]. Because of increased health consciousness in recent years, there has been a greater awareness among the general population of the health and nutritional benefits of brown rice or pigmented rice. [17]; whereas oxidative stress causes several health problems such as stroke, psoriasis, dermatitis, and rheumatoid arthritis [19]. These health and nutritional problems have to be addressed urgently in order to achieve sustainable development goals by reducing the mortality of children and women, and improving people’s general health by providing a nutritious diet. Fe, Zn, and antioxidant compounds have been prioritized for their enrichment in staple foods through biofortification [18,20,21]
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