Genome wide association study (GWAS) identified novel SNPs associated to efficient biological nitrogen fixation in chickpea (Cicer arietinum L.)

Chandana B S¹Rohit Kumar Mahto¹Rajesh Kumar Singh¹Ramachandra V²K K Singh³Sunita Kushwah⁴Gera Rupa Lavanya⁵Himabindu Kudapa⁶Vinod Kumar Valluri⁶Anilkumar Vemula⁶Raju Ratan Yadav⁷Lal Bahadur Yadav⁸H D Upadhyaya⁶Aladdin Hamwieh^9*Rajendra Kumar^10*

• ¹Genetics, Indian Agricultural Research Institute (ICAR), New Delhi, India
• ²Genetics and Plant Breeding, University of Agricultural Sciences Bangalore, Bengaluru, India
• ³Regional Station, PUSA, BIHAR, ICAR - Indian Agricultural Research Institute, New Delhi, India
• ⁴KVK, Vaishali, Dr Rajendra Prasad Central Agricultural University, Samastipur, India
• ⁵Genetics and Plant Breeding, Sam Higginbottom University of Agriculture Technology and Sciences, Allahabad, India
• ⁶International Crops Research Institute for the Semi-Arid Tropics, Patancheru, India
• ⁷Molecular Biology and Genetic Engineering, Govind Ballabh Pant University of Agriculture & Technology, Pantnagar, India
• ⁸Plant Pathology, Govind Ballabh Pant University of Agriculture & Technology, Pantnagar, India
• ⁹International Center for Agricultural Research in the Dry Areas Egypt, Cairo, Egypt
• ¹⁰Genetics, ICAR - Indian Agricultural Research Institute, New Delhi, India

Chickpea (Cicer arietinum L.) is second most important food legume crop, having capability to convert atmospheric nitrogen (N2) into ammonia (NH3) in symbiotic association with Mesorhizobium ciceri through a process of biological nitrogen fixation (BNF). The BNF stands promising avenue for effectively diminishing the reliance on exogenous nitrogen application enhancing soil sustainability and productivity in pulse crops. Notably there are limited studies on molecular basis of root nodulation in chickpea. In order to identify new sources of highly nodulating genotypes and gain deep insights into genomic regions governing BNF, diverse chickpea global germplasm collection (284) was evaluated for nodulation and yield traits in four different environments in augmented randomized block design. The genotypes exhibited significant trait variation, encompassing all traits under study. Correlation analysis revealed significant positive correlation of nodulation traits on yield within the chickpea population. The genotypes ICC 7390, ICC 15, ICC 8348and ICC 2474 were identified as high nodulating across the locations. Genome wide association study (GWAS) identified noteworthy and stable marker trait associations (MTA) linked to the traits of interest. For the traits, number of nodules (NON) and nodule fresh weight (NFW), 65 and 109 significant MTAs were identified, respectively. In addition, two SNPs Ca1pos289.52482.1 and 6_33340878 identified in our earlier studies were validated by independent population studies, which are decisive in evaluating the accuracy and reliability of the projections. Subsequent analysis unveiled that a substantial proportion of these MTAs were situated within intergenic regions, with the potential to modulate genes associated with the focal traits. The candidate genes identified could be converted to Kompetitive allele specific PCR (KASP) markers and exploited in marker assisted breeding, accentuating their impact on future chickpea breeding efforts.