Genetic Dissection of Grain Nutritional Traits and Leaf Blight Resistance in Rice

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.

Genetic Analysis of Agronomic Traits and Grain Iron and Zinc Concentrations in a Doubled Haploid Population of Rice (Oryza sativa L.)

“…Consequently, these QTLs were detected in different environments and genetic backgrounds. The above results clearly showed the complexity of agronomic traits and grain Zn concentration 14,15,42 . Since the present study used BLUE values which excluded environmental effects and magnify genetic effects, the QTLs identified in this study may well prove more useful in rice biofortification breeding programs than the QTLs identified using single environment phenotypic values.…”

“…However, the huge genetic variability in grain mineral nutrients available in the rice germplasm can be exploited to develop biofortified high yielding rice varieties 12 . Even though genetic complexity and G x E were reported to be a hindrance for improving mineral content with high yield, much progress has been achieved in elucidating the genetic basis and G x E effect on grain micronutrient accumulation, yield and yield related traits in rice 13,14 .…”

Profiling of Nutraceuticals and Proximates in Peanut Genotypes Differing for Seed Coat Color and Seed Size

“…The relation between TPC, flavonoids and AOA was studied with grain color in 481 accessions of rice with white, red and black colored genotypes and correlation studies indicated a negative correlation between a * and antioxidant capacity (33). The grain color was also found to be associated with anthocyanin and Zn content when 156 rice accessions varying in grain color were screened and analyzed through genome-wide association studies (34). Similar findings were revealed from transcriptomics and proteomics studies in colored rice (22).…”

“…The association of skin color with various nutritional parameters is well established in various vegetables and fruits (30). In food crops, the relationship between flavonoids and antioxidant activity was studied with grain color in colored rice (33,34). However, in peanut the studies are limited to studying the relation between PKS with nutraceuticals like total polyphenol content and antioxidant capacity (31,32).…”

Analysis of QTL responsible for grain iron and zinc content in doubled haploid lines of rice (Oryza sativa) derived from an intra‐japonica cross

“…They also consistently observed qZn1.1, a QTL for zinc content, across seasons and locations. In another study involving 152 coloured rice accessions, Descalsota‐Empleo, Noraziyah, et al () identified qZn1.1. The consistent location of QTL for grain iron and zinc contents on chromosomes 1, 2, 4, 7, 10, 11 and 12 across various genetic backgrounds and environments indicates that these QTL are useful for breeding biofortified crops.…”