Chloroplast and mitochondrial SSR help to distinguish allo-cytoplasmic male sterile types in cabbage (Brassica oleracea L. var. capitata)

Abstract

The profiles of single sequence repeat (SSR) in six distinct allo-cytoplasmic male sterile (CMS) types of cabbage (Brassica oleracea L. var. capitata) were generated using 32 SSR primer pairs derived from the Arabidopsis thaliana chloroplast (cp) genome and another 21 SSR primers from the B. napus mitochondrial (mt) genome sequences. In total, 11 cpSSR and 4 mtSSR primers revealed polymorphism among the six cabbage CMS types, namely NigCMS, OguCMSR1, OguCMSR2, OguCMSR3, OguCMSHY and PolCMS. Through cluster analysis, six cabbage CMS types could be unambiguously differentiated with just three sets of primers (ACP43, ACP47, mtSSR2). Analysis of the selected amplicon sequences showed high identity to that of the corresponding sequences in A. thaliana, B. rapa and B. napus. The aligned cluster analysis revealed that the polymorphism mainly included SSR number variation, single nucleotide polymorphism (SNP), and sequence insertion or deletion (InDel). Our results demonstrated that specific mitochondrial or chloroplast SSR analysis could be a feasible alternative means for cabbage CMS type identification.