Genetic diversity analysis among pigeonpea genotypes adapted to South American regions based on microsatellite markers

Abstract

The pigeonpea [Cajanus cajan (L) Millspaugh] is one of the most important perennial legume crops utilized in the food, fodder, soil conservation, crop-livestock integrated systems, reclaiming of degraded pastures and symbiotic nitrogen fixation. Microsatellite markers were used to estimate the genetic diversity of 77 pigeonpea genotypes selected from the germplasm collections at Embrapa Cattle-Southeast and, to evaluate their transferability to Phaseolus vulgaris and Vigna unguiculata species. The number of alleles per locus ranged from 2 to12, with an average of 5.1 alleles. The PIC values ranged from 0.11 to 0.80 (average 0.49) and the D values from 0.23 to 0.91 (average 0.58). The averages of observed and expected heterozygosity were 0.25 and 0.47, respectively, showing a deficit in heterozygosity. A model-based Bayesian approach implemented in the software STRUCTURE was used to assign genotypes into clusters. A dendrogram was constructed based on the modified Roger's genetic distances using a neighbor-joining method (NJ). A total of four clusters were assembled by STRUCTURE and a strong tendency of correspondence between the Bayesian clusters in the NJ tree was observed. The genetic distance ranged from 0.09 to 0.62 (average 0.37), showing a low genetic diversity in the pigeonpea genotypes. Transferability of pigeonpea-specific microsatellites revealed a cross-amplification and the presence of polymorphic alleles in P. vulgaris and V. unguiculata

Analysis of Genetic Diversity and Population Structure of Pigeonpea [Cajanus cajan (L.) Millsp] Accessions Using SSR Markers

“…The estimated average PIC value (0.46) recorded in the current study was similar to PIC value (0.49) reported by Sousa et al [18], lower than a mean PIC (0.57) reported by Zavinon et al [19] but relatively higher than the average PIC value of 0.37 as reported by Bohra et al [30]. Similarly, Singh et al [31] observed a PIC value of 0.515.…”

“…In the present study, the observed heterozygosity of the genotypes was low. Comparable results were obtained from a microsatellite-based study that involved 77 accessions from Brazil using 43 SSR markers [18]. The low level of observed heterozygosity is mostly likely attributable to the farmers selection pressure that might have reduced polymorphism in the populations.…”

“…This result is supporting the earlier findings by Bohra et al [30] who reported two subpopulations among 94 tested pigeonpea. By contrast, population structure of South American pigeonpea accessions by Sousa et al [18] reported four subpopulations.…”

“…Genetic improvement of crops depends on the amount of genetic variation among the breeding material. Previous studies of genetic diversity in Brazilian pigeonpea genotypes by Sousa et al [18] and Malawian germplasm by Njung'e et al [17], using SSR markers reported a higher average number of alleles of 5.1 and 5.58, respectively. An earlier study of Kenyan pigeonpea and Indian accessions by Songok et al [38] using 88 genotypes and six SSR markers reported a high average number of alleles per locus.…”

“…Among the DNA molecular markers, the simple sequence repeat (SSR) markers have been found to be the most suitable for use in pigeonpea [16]. A number of studies have been reported using SSR markers for detecting population structure and reconstructing the evolutionary history of the species [17][18][19]. The SSR markers are chosen because of high polymorphism, detection of multi-allelic variation, co-dominance, they are reproducible, they are easy to detect by polymerase chain reaction (PCR), are relatively abundant with a uniform coverage, require small amount of DNA and act as a universal genetic marker for the genetic reagent mapping [14,15,20].…”