Genetic Diversity and Population Structure Analysis in Indian Mustard Germplasm Using Phenotypic Traits and SSR Markers

Indian mustard is an economically important oilseed crop in India; therefore, exploring the genetic diversity of various germplasm collections is quite relevant for its genetic improvement. In the present study, we investigated genetic diversity and population structure among a panel of 145 Indian mustard germplasm accessions using 11 agro-morphological traits and 182 SSR markers. The result of variance analysis exhibited significant differences among the tested genotypes inferring the presence of a high degree of variability. The phenotypic coefficient of variation for seed yield (CV = 28.26%) was the highest among all the studied traits followed by biological yield (CV = 25.72%). Days to maturity ranged from 130 to 141 days (CV = 1.88%), which was the minimum variation exhibited by Indian mustard genotypes. Out of 235 SSR primer pairs evaluated, 182 (77.45%) SSRs resulted in polymorphic amplicons, while 53 (22.55%) SSRs amplified monomorphic loci. Allele number varied from 2 to 7 with 3.97 average number of alleles per SSR marker. PIC value varied from 0.03 (SJ1668I) to 0.71 (EJU4) with an average value of 0.39 per SSR marker. Gene diversity in the present study ranged from 0.03 (SJ1668I) to 0.75 (EJU4) with an average value of 0.46. Cluster analysis using morphological traits and SSR markers grouped all 145 accessions into two major clusters each, respectively. Population structure analysis grouped all the genotypes into three subpopulations with varying degrees of admixture genotypes. Analysis of molecular variance inferred that 88% of the total variation resides within the groups. The resulting estimates of genetic diversity and population structure may be useful for the effective management of Indian mustard germplasm resources and for future mustard breeding programs.