Comparative molecular markers\u27 based analyses of cotton (Gossypium L.) lines

This study focuses on AFLP based molecular marker analyses of the breeding lines developed from two cotton species, i.e., Upland cotton (Gossypium hirsutum), well known for its high yields and Pima cotton ( Gossypium barbadense), known for its exceptional fiber fineness. This study used an aneuploid, CS-B17 breeding line of Upland cotton produced by deleting chromosome 17 of G. hirsutum variety TM-1 and replacing it with 3-79 variety of Pima cotton for combining their diverse adaptability and superior fiber quality, respectively. This study also used 47 Recombinant Inbred Lines (RILs) that were developed by crossing CS-B17 with TM-1 and also two commercial Pima cotton varieties, DP-393 and PHY-370 WR, known to have good fiber quality. AFLP System Analysis Kit from Li-Cor including fluorescent dye IRD-700 and IRD-800 labeled primers designed for EcoRI adapters was used in this study. One hundred and twenty eight primer combinations were used and 14 AFLP primer pairs were found suitable for producing polymorphic markers when using IRDye 700 labeled primers for cotton samples. Similarly, 17 IRDye 800 labeled AFLP primer pairs were found usable for these cotton lines. Saga™ Generation 2- AFLP® Analysis Software Version 3.1 (Li-Cor) mediated confirmed gel images were used to prepare the report on comparative presence or absence of AFLP markers among 47 RILs, TM-1, 3-79, CS-B17 as well as two commercial varieties DP-393 and PHY-370 WR. Sixteen markers produced by each AFLP IRDye 700 and 800 labeled primers were used to enrich 3-79 chromosome 17 in TM-1 genetic background. Eight IRDye 700 labeled primers and five IRDye 800 labeled primers were used for producing AFLP markers to compare 47 CS-B17 RILs with fine fiber cotton varieties DP-393 and PHY-370 WR and three markers were found common among them