Association between seed yield-related traits and cDNA-AFLP markers in cumin (Cuminum cyminum) under drought and irrigation regimes

Abstract

Cumin (Cuminum cyminum L.) is an aromatic medicinal herb with beneficial essential oil being used in antibacterial activities and industry of creams, lotions, and perfumes. Use of functional markers expedites breeding cumin for drought tolerance. The objective of this study was to identify association of plant height and several seed yield- related traits with complementary DNA-amplified fragment length polymorphism (cDNA-AFLP) markers in 15 cumin (Cuminum cyminum) accessions under normal irrigation (NI) and drought stress (DS) conditions. Cumin accessions were grown in the field and subjected to NI practice and post-heading DS in two years in Kerman, Iran. The mean seed yield ranged between 448.72 and 994.18 kg/ha in NI and was from 211.05 to 452.05.06 kg/ha in DS. Reduction in plant height and seed yield-related traits ranged 27–28% in the first and 29–50% in the second year in DS compared with NI. Twelve EcoR I-Mse I primer combinations were used to amplify AFLP markers in cDNA fragments isolated from RNA samples. The identified markers were subjected to analysis of marker-trait associations (MTAs) using the generalized linear model (GLM) and mixed linear model (MLM). A number of 239 and 208 reliable transcript-derived fragments (TDFs) were amplified in cumin genotypes tested in NI and DS, respectively. Of the identified TDFs, highly significant markers were used for association analysis, only. Higher number of MTAs was identified for traits in NI compared with DS. Of the identified linked markers, 5 in NI and 3 in DS were significantly associated with more than one trait under two water status conditions. None of markers were identified as common MTAs between the two moisture conditions. Analysis of population structure demonstrated cumin accessions could be divided into 3 and 4 sub-populations. Overall, high variation was identified in cumin with respect to biological yield, seed yield and seed related traits and the identified linked markers can be incorporated into marker-assisted selection programs for the improvement of seed yield in drought condition.