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.

Grain Fe and Zn Contents Linked SSR Markers Based Genetic Diversity Reveal Perspective for Marker Assisted Biofortification Breeding in Rice

“…Therefore, pooled grain Fe and Zn data of two years is more reliable than single-year data. Significant genetic variation was observed among 56 fine and coarse grain accessions for Fe and Zn contents in brown rice (Figure 1A), which is in accordance with recent reports [13,36]. The Fe and Zn contents in unpolished grains of fine/aromatic rice accessions were relatively higher than coarse grain accessions (Figure 1B).…”

“…Significant positive correlation was present between Fe and Zn contents (Figure 1C). Several other studies have also reported a positive association between these two mineral contents [10,36,45,46]. Overall, these results indicate the prevalence of wide genetic variability in studied rice accessions for grain Fe and Zn contents and possibility of their simultaneous improvement.…”

“…During recent years, SSR markers based genotyping has proven to be very useful for exploring a variety of surreptitious information in plants, ranging from domestication traits to crop improvement through marker-assisted breeding [37][38][39][40]. Although, individual reports on micronutrient density and SSR based genetic diversity in rice have been recently published [10,12,13,36,41], however, to date, a combined study of grain Fe and Zn contents and trait linked SSR markers based genetic diversity is obscure.…”

“…Overall, these results indicate the prevalence of wide genetic variability in studied rice accessions for grain Fe and Zn contents and possibility of their simultaneous improvement. However, mineral densities in polished or white rice need to be assessed before utilizing these accessions in rice biofortification breeding programs, as loss of significant quantities of both micronutrients have been reported during the polishing process [12,36,47].…”

Grain Fe and Zn contents linked SSR markers based genetic diversity in rice

“…During recent years, SSR markers based genotyping has proven to be very useful for exploring a variety of surreptitious information in plants, ranging from domestication traits to crop improvement through marker-assisted breeding [37][38][39][40]. Although, individual reports on micronutrient density and SSR based genetic diversity in rice have been recently published [10,12,13,36,41], however, to date, a combined study of grain Fe and Zn contents and trait linked SSR markers based genetic diversity is obscure. In this study, we assessed genetic diversity in the representative subset of a large collection of local and exotic rice germplasm for grain Fe and Zn contents using trait linked SSR markers.…”