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Genome-Wide Association Study Reveals Novel Marker-Trait Associations (MTAs) Governing the Localization of Fe and Zn in the Rice Grain.

ABSTRACT: Micronutrient malnutrition due to Fe and Zn, affects around two billion people globally particularly in the developing countries. More than 90% of the Asian population is dependent on rice-based diets, which is low in these micronutrients. In the present study, a set of 192 Indian rice germplasm accessions, grown at two locations, were evaluated for Fe and Zn in brown rice (BR) and milled rice (MR). A significant variation was observed in the rice germplasm for these micronutrients. The grain Fe concentration was in the range of 6.2–23.1 ppm in BR and 0.8–12.3 ppm in MR, while grain Zn concentration was found to be in the range of 11.0–47.0 ppm and 8.2–40.8 ppm in the BR and MR, respectively. Grain Fe exhibited maximum loss upon milling with a mean retention of 24.9% in MR, while Zn showed a greater mean retention of 74.2% in MR. A genome-wide association study (GWAS) was carried out implementing the FarmCPU model to control the population structure and kinship, and resulted in the identification of 29 marker-trait associations (MTAs) with significant associations for traits viz. FeBR (6 MTAs), FeMR (7 MTAs), ZnBR (11 MTAs), and ZnMR (5 MTAs), which could explain the phenotypic variance from 2.1 to as high as 53.3%. The MTAs governing the correlated traits showed co-localization, signifying the possibility of their simultaneous improvement. The robust MTAs identified in the study could be valuable resource for enhancing Fe and Zn concentration in the rice grain and addressing the problem of Fe and Zn malnutrition among rice consumers.

SUBMITTER: Bollinedi H

PROVIDER: S-EPMC7188789 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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Project description:BACKGROUND:High yielding rice varieties are usually low in grain iron (Fe) and zinc (Zn) content. These two micronutrients are involved in many enzymatic activities, lack of which cause many disorders in human body. Bio-fortification is a cheaper and easier way to improve the content of these nutrients in rice grain. RESULTS:A population panel was prepared representing all the phenotypic classes for grain Fe-Zn content from 485 germplasm lines. The panel was studied for genetic diversity, population structure and association mapping of grain Fe-Zn content in the milled rice. The population showed linkage disequilibrium showing deviation of Hardy-Weinberg's expectation for Fe-Zn content in rice. Population structure at K?=?3 categorized the panel population into distinct sub-populations corroborating with their grain Fe-Zn content. STRUCTURE analysis revealed a common primary ancestor for each sub-population. Novel quantitative trait loci (QTLs) namely qFe3.3 and qFe7.3 for grain Fe and qZn2.2, qZn8.3 and qZn12.3 for Zn content were detected using association mapping. Four QTLs, namely qFe3.3, qFe7.3, qFe8.1 and qFe12.2 for grain Fe content were detected to be co-localized with qZn3.1, qZn7, qZn8.3 and qZn12.3 QTLs controlling grain Zn content, respectively. Additionally, some Fe-Zn controlling QTLs were co-localized with the yield component QTLs, qTBGW, OsSPL14 and qPN. The QTLs qFe1.1, qFe3.1, qFe5.1, qFe7.1, qFe8.1, qZn6, qZn7 and gRMm9-1 for grain Fe-Zn content reported in earlier studies were validated in this study. CONCLUSION:Novel QTLs, qFe3.3 and qFe7.3 for grain Fe and qZn2.2, qZn8.3 and qZn12.3 for Zn content were detected for these two traits. Four Fe-Zn controlling QTLs and few yield component QTLs were detected to be co-localized. The QTLs, qFe1.1, qFe3.1, qFe5.1, qFe7.1, qFe8.1, qFe3.3, qFe7.3, qZn6, qZn7, qZn2.2, qZn8.3 and qZn12.3 will be useful for biofortification of the micronutrients. Simultaneous enhancement of Fe-Zn content may be possible with yield component traits in rice.

Project description:IntroductionWheat is grown and consumed worldwide, making it an important staple food crop for both its calorific and nutritional content. In places where wheat is used as a staple food, suboptimal micronutrient content levels, especially of grain iron (Fe) and zinc (Zn), can lead to malnutrition. Grain nutrient content is influenced by abiotic stresses, such as drought and heat stress. The best method for addressing micronutrient deficiencies is the biofortification of food crops. The prerequisites for marker-assisted varietal development are the identification of the genomic region responsible for high grain iron and zinc contents and an understanding of their genetics.MethodsA total of 193 diverse wheat genotypes were evaluated under drought and heat stress conditions across the years at the Indian Agricultural Research Institute (IARI), New Delhi, under timely sown irrigated (IR), restricted irrigated (RI) and late sown (LS) conditions. Grain iron content (GFeC) and grain zinc content (GZnC) were estimated from both the control and treatment groups. Genotyping of all the lines under study was carried out with the single nucleotide polymorphisms (SNPs) from Breeder's 35K Axiom Array.Result and discussionThree subgroups were observed in the association panel based on both principal component analysis (PCA) and dendrogram analysis. A large whole-genome linkage disequilibrium (LD) block size of 3.49 Mb was observed. A genome-wide association study identified 16 unique stringent marker trait associations for GFeC, GZnC, and 1000-grain weight (TGW). In silico analysis demonstrated the presence of 28 potential candidate genes in the flanking region of 16 linked SNPs, such as synaptotagmin-like mitochondrial-lipid-binding domain, HAUS augmin-like complex, di-copper center-containing domain, protein kinase, chaperonin Cpn60, zinc finger, NUDIX hydrolase, etc. Expression levels of these genes in vegetative tissues and grain were also found. Utilization of identified markers in marker-assisted breeding may lead to the rapid development of biofortified wheat genotypes to combat malnutrition.

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Genome-Wide Association Study Reveals Novel Marker-Trait Associations (MTAs) Governing the Localization of Fe and Zn in the Rice Grain.

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