SSR marker-based study of the effects of genomic regions on Fe, Mn, Zn, and protein content in a rice diversity panel

Abstract

Rice is one of the most important basic foods, especially in developing countries. However, rice production is negatively affected by drought and decreased water availability. Over the recent decades, aerobic rice has been considered as a promising approach to reduce water input. However, the rice genotypes suitable for aerobic rice should also be evaluated for other important characteristics such as grain micronutrient content. Studying the genetic variability of grain Fe, Mn, Zn, and protein content in aerobic rice genotypes compared to other rice varieties can be useful for improving nutritive value via plant breeding programs. In this study, 50 rice genotypes, including aerobic rice, Iranian-improved, and landrace varieties were studied for Fe, Mn, Zn, and protein content in brown rice and also for their association with 77 SSR markers. There was a significant diversity among the rice genotypes: 13.91–44.91 mg/kg for Fe, 5.85–35.93 mg/kg for Mn, 11.79–34.33 mg/kg for Zn, and 4.38–16.63% for protein. According to the cluster analysis, group (I) contained five Iranian landrace rice varieties (Champaboudar, Gharib, Alikazemi, Anbarbou, and Sangetarom) well-known for their eating and cooking quality and aroma; furthermore, 10 aerobic rice genotypes had the highest level of Fe and Zn content among other groups. According to the results some aerobic rice genotypes had high grain micronutrient values such as IR 82,639-B-B-103–4, which also had 16.63% protein content in the grain. Based on the results of association analysis, out of 55 random SSRs, 11 markers, and out of 22 linked SSRs, 17 markers were found to be associated with grain protein, Fe, Zn, and Mn in the present population. Out of 28 significant markers, RM488 associated with grain Fe, RM574 with Mn, and RM248 with Mn and Zn and the associated was detected in both the years. In addition, out of 11 newly detected SSR markers, five were substantially associated with rice grain quality traits. The markers, which are showing association, can be utilized to enhance the nutritional value of rice in plant breeding programs.