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. | Turkish Journal of Agriculture and Forestry Research Article Turk J Agric For (2015) 39: 403-412 © TÜBİTAK doi: Cytoplasmic-nuclear variation in a diversity-fixed foundation set of Brassica juncea (L.) Czern & Coss. Javed AKHATAR, Nitin KUMAR, Chhaya ATRI, Surinder Singh BANGA* Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India Received: Accepted: Published Online: Printed: Abstract: 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. Key words: Cytoplasmic lineage, gene pool, germplasm, Indian mustard, phylogenetic tree 1. Introduction Brassica is an agriculturally important genus comprising species with a range of morphologies and food utilities. Oilseed forms include Brassica napus, Brassica juncea, Brassica
