Abstract
BackgroundNon-heading Chinese cabbage (NHCC), belonging to Brassica, is an important leaf vegetable in Asia. Although genetic analyses have been performed through conventional selection and breeding efforts, the domestication history of NHCC and the genetics underlying its morphological diversity remain unclear. Thus, the reliable molecular markers representative of the whole genome are required for molecular-assisted selection in NHCC.ResultsA total of 20,836 simple sequence repeats (SSRs) were detected in NHCC, containing repeat types from mononucleotide to nonanucleotide. The average density was 62.93 SSRs/Mb. In gene regions, 5,435 SSRs were identified in 4,569 genes. A total of 5,008 primer pairs were designed, and 74 were randomly selected for validation. Among these, 60 (81.08%) were polymorphic in 18 Cruciferae. The number of polymorphic bands ranged from two to five, with an average of 2.70 for each primer. The average values of the polymorphism information content, observed heterozygosity, Hardy-Weinberg equilibrium, and Shannon’s information index were 0.2970, 0.4136, 0.5706, and 0.5885, respectively. Four clusters were classified according to the unweighted pair-group method with arithmetic average cluster analysis of 18 genotypes. In addition, a total of 1,228,979 single nucleotide polymorphisms (SNPs) were identified in the NHCC through a comparison with the genome of Chinese cabbage, and the average SNP density in the whole genome was 4.33/Kb. The number of SNPs ranged from 341,939 to 591,586 in the 10 accessions, and the average heterozygous SNPs ratio was ~42.53%. All analyses showed these markers were high quality and reliable. Therefore, they could be used in the construction of a linkage map and for genetic diversity studies for NHCC in future.ConclusionsThis is the first systematic and comprehensive analysis and identification of SSRs in NHCC and 17 species. The development of a large number of SNP and SSR markers was successfully achieved for NHCC. These novel markers are valuable for constructing genetic linkage maps, comparative genome analysis, quantitative trait locus (QTL) mapping, genome-wide association studies, and marker-assisted selection in NHCC breeding system research.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1534-0) contains supplementary material, which is available to authorized users.
Highlights
Non-heading Chinese cabbage (NHCC), belonging to Brassica, is an important leaf vegetable in Asia
A total of 20,836 Simple sequence repeats (SSRs) with repeats were detected in the non-heading Chinese cabbage (NHCC) genome, which translated to an overall density across the genome of 62.93 SSRs/Mb
The insufficient genomic and transcriptome data in public databases have limited our understanding of the molecular mechanisms underlying the adaptation of NHCC
Summary
Non-heading Chinese cabbage (NHCC), belonging to Brassica, is an important leaf vegetable in Asia. The reliable molecular markers representative of the whole genome are required for molecular-assisted selection in NHCC. NHCC is widely used as a vegetable crop because of the strong adaptability, short growth period, good quality, unique flavor, and rich nutrition. It is widely cultivated in Southeast Asia, Japan, USA, and Europe, and is gradually becoming an important vegetable worldwide. The development of molecular markers for the detection and exploitation of DNA polymorphisms is a significant application in the field of molecular genetics. Since the advent of restriction fragment length polymorphism (RFLP) markers, a range of other markers, such as random amplified polymorphism DNA (RAPD), amplified fragment length polymorphism (AFLP), sequence tag sites (STSs), SNPs, and SSRs, have been introduced during the 20th century to fulfill various demands of breeders [8,9]
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