Association mapping for identification of ISSR and AFLP markers linked with resin yield in Himalayan Chir Pine (Pinus roxburghii Sarg

In Pinus roxburghii, marker-trait associations were studied for resin yield using a set of 238 DNA based markers derived from 9 ISSR and 5 AFLP primer pairs. A total of 240 genotypes of P. roxburghii from a natural population in Chakrata division (Tiunee range), Uttarakhand (India) were evaluated for resin yield. Based on stable resin production in consecutive years, 53 genotypes that were best representatives of the variation in resin yield (0.25 to 8.0 kg/tree/year) were used for genotyping and association analysis. For carrying out the association studies, two approaches were used. First, using simple linear regression, resin yield was regressed on all 238 available polymorphic markers (148 ISSR markers and 90 AFLP markers) and second, evidence for association was examined applying population structure information using STRUCTURE and STRAT to avoid any spurious associations between a candidate marker and phenotype. In regression analysis, 16 ISSR and 12 AFLP markers showed significant association with resin yield. In the second approach, 18 ISSR and 18 AFLP loci were found to be associated with resin yield in the absence of population structure out of which 2 ISSR and 3 AFLP loci were common with those associated in regression analysis. After accounting for population structure, 38 ISSR, and 3 AFLP loci revealed association out of which one ISSR and one AFLP locus was found to be common with both simple linear regression and test of association in the absence of population stratification. There was no obvious correlation between population structure and resin yield.