Study on Analysis of Molecular Diversity and Trait Association for Zinc Deficiency Tolerance in Rice under Submerged Conditions

Abstract

Background: Rice is the most important human food crop in the world and its production is affected by various biotic and abiotic stress including low soil fertility. Zinc deficiency is one of the most important micronutrient deficiencies limiting rice yield. The vast reserve of germplasm of rice grown in different eco systems could be screened to exploit the genotypic differences bfor zinc deficiency tolerance. With the advent of molecular markers, association mapping strategy based on non-random associations between causative loci and phenotype could be employed to resolve the complex traits like zinc deficiency tolerance. With this background, the current study is focused to explore the extent of variability for zinc deficiency tolerance using zinc deficiency score and quantitative traits among 44 germplasm accessions and to identify quantitative trait loci associated with zinc deficiency tolerance using Simple Sequence Repeat (SSR) marker-based association mapping.Methods: A set of 44 accessions consisting of landraces and improved varieties were selected based on their zinc deficiency score in field (Zn=0.64 ppm) screening experiment conducted in Regional Research Station, Paiyur, Tamil Nadu. Eight accessions from each Zn Def score group along with four other genotypes namely Savulu Samba, Kotta Nel, Paiyur 1 and ADT 39 were chosen for the study. Molecular analysis was carried out among the selected accessions using a total of 40 random Simple Sequence Repeat (SSR) primers.Result: Our study revealed the existence of diversity at molecular level among the selected accessions. Clustering analysis separated the accessions in two major clusters which were in accordance with the population structure analysis which resulted with two sub-populations. Through our study we identified certain accessions namely, Karuppu Nel, Manipur Local and BAM 440 which recorded high yields along with least zinc deficiency scores implying their ability to act as donors for zinc deficiency tolerance under submerged condition. Subsequent association analysis which resulted in putative association of zinc deficiency score with critical plant traits such as plant height and number of productive tillers, revealed that association mapping could be a viable strategy for understanding genetic mechanism of zinc deficiency tolerance in rice.