Identification of Highly Polymorphic Molecular Markers and Potential Genotypes for Harnessing Chickpea Breeding Strategies

Background: STMS markers and morphological traits were used to investigate the genetic relationship and allelic diversity in chickpea. In this study, we focused on the selection and more efficient utilization of core germplasm in breeding programs for chickpea crop improvement using STMS and quantitative / morphological traits. Methods: Seeds of elite accessions of chickpea were obtained from ICRISAT, Patancheru, Andhra Pradesh, India. 50 STMS markers and 11 quantitative traits were used for exploring the genetic variability and relationship in 35 chickpea accessions. Result: A total of 97 alleles were produced out of the 32 polymorphic STMS loci with an average of 3.03 alleles per locus ranging between 2-6 alleles per primer. The PIC value ranged from 0.029 to 0.768 with an average of 0.502. PIC value showed a highly positive correlation (r = 0.718) with number of alleles at the STMS loci. In both molecular and morphological markers / traits-based clustering, out of 35 chickpea accessions only one accession ICC-13892 was isolated at the end of clustering. The results indicated that highly polymorphic microsatellite markers NCPGR 68, NCPGR 50, NCPGR 81, NCPGR 48 and NCPGR 77 along with the accessions ICC-13892 having distant associations with ICC-13816, ICC-15697, ICC-15610, ICC-15868, ICC-15888, ICC-15996 with novel findings should be useful resources for strategies of allele mining, association genetics, mapping and cloning of gene(s) and in applied breeding to broaden the genetic base of chickpea.

Genetic diversity analysis among selected short duration chickpeacultivars and breeding lines based on STMS markers.

Genetic diversity among 30 chickpea genotypes was evaluated using simple sequence repeat (SSR) molecular markers. The studies using Sequence Tagged Microsatellite Site (STMS) markers markers revealed that among the primers used across the genotypes produced a total of 35 alleles representing 21 SSR loci with frequencies ranging from one to two (mean 1.66) alleles per locus. Polymorphic Information Content (PIC) ranged from 0.098 to 0.500 (CAM0443, CAM0446). These primers might be an effective and useful tool to determine the genetic differences among chickpea genotypes and to study the phylogenetic relationships. Polymorphic percentage was 96.42. Hierarchical neighbour-joining UPGMA cluster analysis based on simple matching similarity matrix resolved the 30 genotypes into seven clusters. Based on STMS markers highest similarity index 0.850 was observed between BGD 72 and Annigeri-1whereas BGD 9920 and ICC 92944 showed the lowest similarity index 0.214 between them. The STMS clustering pattern indicated the presence of wide genetic diversity between the genotypes. Overall, the study ascertained that SSRs provide powerful marker tools in revealing genetic diversity and relationships in chickpeas, thereby proving useful for selection of parents in breeding programs and also for DNA fingerprinting for identification of cultivars.

Molecular characterization of chickpea (Cicer arietinum L.) genotypes using sequence tagged microsatellite site (STMS) markers

Chickpea (Cicer arietinum L.) commonly also known as gram, Chana, Bengal gram and Garbanzo beans is the second most important pulse crop of the world mainly grown in arid and semi-arid regions. Assessment of genetic variability in the base population is the first step in any breeding programme for selection of genetically divergent parents and their use in the crop improvement programme. In the present investigation 20 genotypes of chickpea were characterized using a specific set of 15 numbers of Sequence tagged microsatellite site (STMS) markers. The number of alleles, allelic distribution and their frequency was estimated and found that the 36 alleles amplified with 15 STMS loci having an average of 2.4 alleles per locus. The number of alleles amplified varied from 1 to 4. The Polymorphic information content value ranged from 0 to 0.965 with an average of 0.373 indicated the considerable efficiency of markers for studying the polymorphism level. All primer showed higher polymorphism among the genotypes except two primers namely, TAA59 and GA105 which were monomorphic in nature. Genetic similarity based on UPGMA clustering the dendrogram grouped the 20 genotypes in three clusters, cluster I, II, III comprised of 2, 4, 14 genotypes, respectively. The maximum similarity was found between genotypes ICRISAT-4183 and ICRISAT- 7722 (0.972). The present study provided an insight of the inter-relationship among the genotypes and highlights the genetic distance by STMS markers. The genetic diversity revealed in this study could be exploited for selective breeding programme of chickpea improvement.