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

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.

Evaluation of African Cultivated Rice Oryza glaberrima for Resistance to Bacterial Blight.

Xanthomonas oryzae pv. oryzae is the causal agent of bacterial blight in rice, one of the most devastating diseases of rice worldwide. African X. oryzae pv. oryzae strains belong to a clear genetic group distinct from those of Asia. Three new races of the pathogen were characterized among strains from West Africa. We evaluated 107 Oryza glaberrima accessions for resistance to bacterial blight under greenhouse conditions. Six-week-old seedlings were inoculated with five different African X. oryzae pv. oryzae strains originating from the West African nations of Burkina and Mali and representing different races (A1, A2, and A3). Philippine X. oryzae pv. oryzae strain PXO86 (race 2) was also used. Most (48%) of the accessions of O. glaberrima were highly susceptible to X. oryzae pv. oryzae strains from Burkina, while 20 and 36 were resistant to X. oryzae pv. oryzae strains from Mali and the Philippines, respectively. CAPS markers and dot blot assays were used for detection of resistance genes xa5 and Xa21 from a selected set of O. glaberrima accessions. Our results suggest that the O. glaberrima germplasm contains a narrow genetic base for resistance to X. oryzae pv. oryzae. Sources of resistance identified among O. glaberrima are recommended for rice breeding programs to develop bacterial blight-resistant cultivars for West Africa.