DEVELOPMENT OF GENOMIC MICROSATELLITE MARKERS USING WHOLE GENOME SEQUENCES, VALIDATION AND MICRONUTRIENTS VARIATION IN COWPEA [Vigna unguiculata (L.) Walp)]
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Date
2023-04-14
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University of Agricultural Sciences, Bangalore
Abstract
The genomic microsatellite markers were developed using whole genome sequence (WGS) of two cultivars viz. cv.1 (IT97K-499-35) and cv.2 (Xiabao 2). The chromosomes were 11 in both the cultivars and ‘AT’ repeats were recorded abundantly followed by ‘TA’. Total SSRs detected in cv. Xiabao 2 using GMATA programme were 2, 70,425 with a relative abundance of 452.57 SSR per MB and in cv. IT97K-499-35 the total SSR detected were of 2,41,001 with a relative abundance of 509.02 SSR per MB. Total SSR loci with designed primer pair were 81,420 in cv. Xiabao 2 and 87,326 in cv. IT97K-499-35. For e- Mapping, total markers mapped to input sequences 66,233 in cv. Xiabao 2 and 73,348 in cv. IT97K-499-35. Total amplicons PCRed from mapped markers 1,99,298 in cv. Xiabao 2 and 1,99,842 in cv. IT97K-499-35. Twenty primer pairs were synthesized for in-vivo validation of cowpea, of which seven primer pairs were amplified across 50 different cowpea genotypes. The gene diversity ranged from 0.00-0.49, with average of 0.27. The PIC ranged from 0.18 to 0.91, with an average of 0.51. All the indigenous accessions were clustered in one cluster as per the molecular diversity analysis, whereas the exotic accessions were divided into two clusters. To assess the genetic diversity of 50 cowpea genotypes, the mean, range, and genotypic coefficient of variance were utilized. A significant genotypic difference between genotypes was discovered for each of the 17 yield and yield contributing traits. The traits with the highest estimates of GCV included copper weight (96.63%) and manganese (98.37%). The genotypic association between seed production and haulm yield per plant showed the strongest positive significant correlation (r = 0.784), followed by biomass production (r = 0.741), NDVI at 60DAS (r = 0.467), plant height (r = 0.456), and number of seeds per pod (r=0.385).