Genomic Diversity Analysis and Association Mapping of Cotton Germplasm for Cotton Leaf Curl Disease (CLCuD) Resistance Using SSR Markers in Two Hotspots of Punjab, Pakistan

The cotton crop is the major contributor to Pakistan's economy. In the recent past, cotton crops faced many issues including leaf curl virus disease which resulted in decreased cotton production in Pakistan. The present research work was designed to discover tolerance/resistance sources through extensive experimentation using conventional and biotechnological tools. For this purpose, 71 genotypes from all over Pakistan and some lines from India and Turkey were sown at two hotspots, i.e., Faisalabad and Vehari in the month of June to find superior genotypes that can tolerate/resist this threatening disease. The sick plot method of screening was adopted for screening the genotypes against CLCuD. The variety FH-118 was used as a spreader line in this experiment. For genomic analysis of cotton germplasm for cotton leaf curl disease (CLCuD) resistance using SSR markers in two hotspot regions of Punjab, 25 SSR primers were utilized to estimate the genetic variation among cotton genotypes and 12 were identified as highly polymorphic. Primers BNL-1551, JESPER-247, NAU-1103, NAU-1230, NAU-1233, NAU-1369, NAU-2152, NAU-2317, NAU-2336, NAU-2355, NAU-2503, NAU-2691 provided PIC values of 0.51, 0.57, 0.52, 0.64, 0.62, 0.55, 0.50, 0.63, 0.57, 0.56, 0.64 and 0.55 respectively. The maximum genetic similarity coefficient value was found to be 6.85 between FH-479 and NS-161 which showed that these genotypes might have common ancestors or same morphological traits while lowest coefficient value was found 2.449 between genotypes FH-315 and Tarzan-5 which indicated that they have different parental origin or distinct morphological characteristics. Based on similarity of genotypes dendrogram clustered all genotypes into 37 clusters. Most diverse genotype identified was FH-315 which can be used as a parent in future breeding programs. Association mapping studies revealed that five markers NAU3254-1600, dPL0526-260, NAU5163-200, CIR094-700, and cgr6356-150 are associated with CLCuD resistance at CRS, Faisalabad. While At CRS, Vehari the marker NAU3385-500 is different while 4 others are common at both locations. The study demonstrates that DNA-based molecular markers like SSR associated with CLCuD resistance could be used for screening resistant/tolerant cotton lines.