Tagging high zinc content in the grain, and zinc deficiency tolerance genes in rice (Oryza sativa L.) using simple sequence repeats (SSR)

The present study was undertaken to identify and map the gene for high zinc content in the grain and QTL [quantitative trait loci] for zinc deficiency tolerance using Simple Sequence Repeat (SSR) markers. A population of 93 recombinant inbred lines (RILs) comprising extreme low and high zinc content in the grain was used. The mapping population was developed from the cross Madhukar and IR26, one with high zinc (36.8 ppm) and the other with low zinc (16.6 ppm) content respectively were used to mapping. Zinc deficiency tolerance was also observed and scored in the field based on standard evaluation system. Variation was recorded among RILs and tested for zinc deficiency symptoms. The RIL population was screened against 120 microsatellite markers and 25.8% polymorphism was produced. Low polymorphism was observed because both parents (Madhukar and IR26) were of Indica type. A linkage map was constructed comprising the 31 SSR markers using MAPMAKER. Grouping of SSR marker, map order and distance was determined. Map distance was derived using Kosambi function. Linkage analysis identified the high zinc gene to be located on chromosome 5 between marker OSR 35 and RM267. Marker RM 267 is 12.5 cM from the gene responsible for high zinc in the grain. On the other hand QTL analysis was done for zinc deficiency tolerance using the same mapping population and it was mapped on chromosome 5 between markers RM164 and RM87 showing a variation of 61.9% with a LOD [log of odds] value of 3.45. Fine mapping of the gene (high zinc content in grain and zinc deficiency tolerance) should be done using other molecular markers like AFLP [amplified fragment length polymorphism], STS [sequence tagged sites], and RAPD [random amplified polymorphism DNA]. Markers should be identified with a distance 5 cM on either side of the locus for it to have any practical utility for plant breeding as Marker Aided Selection (MAS) for enhancing zinc content in the grain and zinc deficiency tolerance in rice