Cytoplasmic-nuclear variation in a diversity-fixed foundation set of Brassica juncea (L.) Czern Coss.

A core subset of genetically fixed lines was selected through stratified sampling to represent the allelic variations within Brassica juncea gene pools. It included germplasm accessions from India, China, and Australia, as well as B. juncea introgression lines carrying alien genetic variation and/or cytoplasm from wild crucifers, namely Diplotaxis cardaminoides, Diplotaxis tenuisiliqua, and Erucastrum abyssinicum. The aim of the study was to infer the influence of underlying cytoplasm on population structure and trait variation. Molecular characterization using nuclear SSR markers (158) and chloroplast SSR markers (9) revealed interesting germplasm patterns and trait variations. Diversity groups obtained using distance-based clustering were not fully compliant with structure analysis, especially for the nuclear genetic variation. Association between population structure and phenotypic variation was indicated by significant interactions between chlorotype and seed/biological yields. Thus, there may be a need to factor in the impact of background cytoplasm on population structure in association studies of crops where different cytoplasmic lineages are known.