Application of DNA markers for estimating genetic diversity and warranting marker-assisted selection in chickpea

Chickpea is a premier legume crop of Pakistan, the productivity of which is hampered by multiple biotic and abiotic stresses. Blight [Ascochyta rabiei Pass.) Lab.,] and wilt [Fusarium oxysporum f. sp. ciceris (Padwick) Matuo and K. Sato] are the most devastating diseases that cause substantial yield depression in total production of chickpea. Development of cultivars conferring resistance to the diseases is a farmer friendly strategy. Knowledge about the genetics of resistance in host plant and characterization of the pathogens is vital for expediting the breeding progress for the development of resistant cultivars. The efficiency of evolution of new chickpea varieties can be enhanced by deploying DNA marker assays. \ud In the present study, stable mutants (induced) and hybrids of chickpea have been used to validate previously reported DNA markers associated with resistance genes to blight and wilt diseases. These markers have successfully differentiated between blight and wilt resistant and susceptible genotypes and can be used routinely in chickpea breeding program. In case of wilt, the marker data correlated with phenotypic study, except for race 3 of F. oxysporum f.sp. ciceris (Foc). A portion of QTLs on LG4 is involved in conferring resistance to blight in local chickpea genotypes resulting in partial resistance to blight disease. \ud The pathogenic variability, mating types and genetic diversity of Pakistani A. rabiei (AR) were compared with US-AR isolates and found that medium and highly aggressive pathotypes are prevalent in Pakistan. Unequal mating type distributions showed less frequency of sexual reproduction in AR population of Pakistan. PakistaniAR (PAR) isolates were found to be genetically diverse from US population and two clusters of PAR isolates are not strictly linked to the different geographic locations, suggesting frequent gene flow of AR among different regions of Pakistan. \ud Molecular and conventional tools were used to identify races of Foc in major chickpea growing areas of Pakistan. Study detected race 2 from Thal area whereas an ecotype of race 6 was identified from Thar and Faisalabad regions. Also, breeding for high yielding cultivars, double podded (dp) trait was studied in induced chickpea mutants using STMS marker that distinguished dp mutants from single podded (sp) parent genotypes. Allelic variation was also found in sp genotypes that may be used for genotypic fingerprinting. \ud Genetic diversity of high yielding mutants and hybrids was detected by surveying 41 SSR loci in comparison with elite genotypes that have resistance to blight and wilt diseases. UPGMA based cluster analysis differentiated exotic genotypes from local germplasm and narrow genetic diversity was estimated among hybrids as compared to induced mutants, reflecting the importance and usefulness of induced mutagenesis. The results concluded that the selection of DNA markers would facilitate integration of marker-assisted selection (MAS) procedures in breeding programs enabling the pyramiding of favorable alleles. Study on genetics of pathogen population has an immediate impact on resistance breeding; therefore it is a need to focus on pathogen?s genetic diversity and pathogenic variability to design a strategy for effective and sustainable resistance breeding