Identification and Characterization of Co-localized Expressed Sequence Tags (ESTs) underlying Putative Candidate Genes in Rice (Oryza sativa)

Abstract

Abstract Rice (Oryza sativa L.) is a “Global Grain” cultivated widely across the world feeding millions of mankind. Rice as a grain rich in iron and zinc content is a polygenic complex trait having additive effect of multiple genes thus identification of Quantitative trait loci (QTLs) can lead to develop Fe/Zn rich rice using marker assisted breeding techniques. Several QTLs for the grain micronutrient contents have been identified and mapped on rice chromosome but their refinement and genetic dissection are yet to truly understand. Therefore, present study was conducted to identify and validate candidate gene based QTLs specific markers related to GPC and micronutrient content in rice to identify novel microsatellite markers within known QTLs controlling grain Fe and Zn content. Co-segregation analysis was performed with the F6 mapping population derived from a cross between rice cultivar Swarna x Moroberekan. The grain Fe content ranged from 9.68 to 19.98 µg/g with an average of 16.87 µg/g and grain Zn content ranged from 15.85 to 20.84 µg/g with an average of 25.76µg/g among the 73 homozygous rice mapping population. Similarly the grain protein content ranged from 5.34–7.18% with an average of 9.23%. Out of 1063 novel SSRs loci present within the 5 QTL regions, 161 Class I SSRs with 2–6 nt long repeat motifs and 12–80 nt repeat lengths were identified. On the basis of position of metal related transporter or membrane transporter genes primers were designed for 22 novels Class- I SSR and validated in the parents for their polymorphism. Among them, only 18 markers were found to be polymorphic. Out of 18 polymorphic SSRs, only five markers were significantly associated to grain iron and zinc contents. The allelic segregation analysis indicated that parent Swarna contributed about 60.6% whereas, parent Moroberekan contributed about 34.32% of total amplified alleles on an average. The identification of specific novel microsatellite markers in this study will help for marker-assisted breeding of grain micronutrient content in rice.