Phylogenetic Analysis of First Generation Cotton Leaf Curl Virus (CLCuV) Resistant Cotton Varieties

Abstract

ABSTRACTCotton is a major cash crop of Pakistan. During the last few years, cotton production has been hampered by cotton leaf curl virus (CLCuV) disease. Cotton breeders successfully combated CLCuV by developing resistant varieties, however it resurfaced in 2001, all the varieties proving susceptible. This study was conducted to explore the genetic diversity among cotton varieties approved as first defense line against CLCuV using DNA markers. The four cotton varieties, CIM-448, CIM-1100, FH-900 and FH-901, were subjected to random amplified polymorphic DNA (RAPD) and simple sequence repeats (SSR) finger printing assay to reveal genetic relatedness. A total of 110 RAPD primers were surveyed out of which 16 were found polymorphic. The size of 449 amplified loci ranged from 250 to 1500 bp with an average of 4.08 loci per primer. Similarity matrix revealed 96% similarity among the varieties assayed. For SSR genetic analysis, 92 primer pairs were surveyed and only six primers were found informative. A total of 149 loci were amplified with an average of 1.61 loci per primer. Out of these, 13 loci (8.69%) were informative. The amplicons ranged from 58 to 500 bp. Like RAPD analysis, genetic distance among accessions was just 3%. The results obtained here revealed high similarity among the varieties studied, illuminating the reason why first and second generation of CLCuV resistant cotton varieties became susceptible to the new virus strain. Moreover, the correspondence between SSR and RAPD data sets suggests that either method or a combination of both is applicable to diversity studies in cotton varieties.