Genetic diversity, population structure and marker trait associations for alkaloid content and licit opium yield in India-wide collection of poppy ( Papaver somniferum L.)

The importance of alkaloids of opium poppy is increasing constantly worldwide to fulfill the demand of pharmaceutical industries. India is one of the countries to produce gum opium and contain many potential genotypes to attend the recent demand of alkaloids. So, for proper utilization of the available potential genotypes, the present investigation was carried out to study the genetic diversity and genetic differentiation along with marker-trait association based on quantitative traits as well as AFLP marker in a large number of germplasm lines of opium poppy which were collected from different parts of India. Various genetic parameters and correlation among different traits were also worked out to find out the particular traits enhancing yield potential. Eight AFLP primer pairs were deployed that generated 140 polymorphic bands with fragment ranging in size from 50 to 498 bp in size. The maximum gene diversity was found in the germplasm lines of UP. Most of the variability (96%) was partitioned into within populations implying that collection strategies for conservation should focus on a few populations with many individuals across the ecological amplitude of the population. Genetic differentiation was FST = 0.0413, that implies more or less complete panmixis. The morphine was found associated with seven AFLP loci, such as E-AAG/M-CAG_76, E-AAC/M-CAG_102, E-ACT/M-CTA_181, E-ACG/M-CTC_167, E-ACG/M-CTC_176, E-ACG/M-CTC_194, and E-ACG/M-CTC_102 which showed stability by both models (GLM, MLM) of analysis while three markers (E-ACT/M-CAA_53,E-ACT/M-CAA_243,E-AGG/M-CTG_241) for codeine, four markers (E-ACT/M-CAA_193,E-AAC/M-CAG_151, E-AAC/M-CAG_91, and E-AGC/M-CTA_75) for thebaine, six for narcotine (E-ACT/M-CAA_85, E-AGG/M-CTG_75, E-AAC/M-CAG_116, E-ACT/M-CTA_122, E-ACT/M-CTA_182, and E-ACT/M-CTA_209), two markers (E-AAG/M-CAG_303, and E-AAC/M-CAG_210) for papaverine and five markers (E-ACT/M-CAA_76, E-AAG/M-CAG_122, E-AAG/M-CAG_245, E-AGG/M-CTG_84, and E-AGG/M-CTG_219) for opium yield were found associated (P