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Traditional breeding methods usually involve field tests carried out by experienced breeders. However, such methods are costly and time-consuming. Recently, with the development of Next-Generation Sequencing (NGS) technology, molecular markers are being utilized for selection processes in breeding. To implement a high-throughput system using molecular markers in Chinese cabbage (Brassica rapa subsp. pekinensis) breeding, we developed single nucleotide polymorphism (SNP) marker sets for background selection and testing F1 purity using Fluidigm genotyping assays. SNPs were generated using NGS technology on 209 varieties of Chinese cabbage collected from around the world. Those with minor allele frequency ≥ 5% and polymorphism information content ≥ 0.3 were screened, and then based on the physical distribution among the 10 chromosomes, 177 SNPs were selected and synthesized for testing. To obtain marker sets with high selection efficiency, we tested 192 SNPs on 45 types of inbred lines and 29 types of F1 hybrids. Among the 192 SNPs, we selected 96 markers sets for background selection and 24 marker sets for F1 purity testing according to the following criteria; the genotype of the parents was homozygous, and the F1 follows the parents’ genotypes. These SNP sets are suitable for high-throughput systems using the 96.96 and 192.24 integrated fluidic circuit platforms of Fluidigm genotyping assays. These SNP marker sets are not only efficient for selecting of early fixed lines as background selection but are also useful for testing the purity of F1 hybrids.

The CCCH-type zinc finger proteins are characterized by their signature motif of three cysteine and one histidine residues. These proteins are RNA binding proteins that function in plant growth, developmental processes, and responses to various environmental stress conditions. In this study, a comprehensive analysis using computational methods allowed the identification of 63 functionally important CCCH genes in the Brassica rapa genome. Several analyses were carried out on the identified genes to understand their roles in this plant. Comparative phylogenetic analysis classified CCCH genes into six clusters, while motif and structural analyses revealed four unique CCCH motifs including different functional motifs and intron/exon variations unique to plants compared to those in other species. Real-time qRT-PCR analysis of 10 randomly selected genes indicated they function at the early stages rather than the later stages of cold and salt stress. This study provides a basic understanding of potential candidate CCCH genes in B. rapa, their structural variation, expression patterns, and their roles under different stress conditions.

To better understand carotenoid biosynthesis in Brassica rapa, a genome-wide investigation was performed using the EST/mRNA sequences and the draft genome of B. rapa. We have identified 46 full-length coding sequences in the B. rapa genome by comparing with the Arabidopsis thaliana genes that were involved in carotenoid biosynthesis. The identified genes were categorized to belong to 11 protein families encoding various enzymes involving the biosynthesis. A detailed domain structural analysis of the enzymes showed that these were highly conserved and overlapping. The genes were localized to all 10 chromosomes of the plant, six of which were single-copy genes; whereas others had more than one paralogue. Phylogenetic analysis of A. thaliana and B. rapa sequences revealed sequence identities ranging from 70–90%, indicating the conservation of genes among the species. Approximately 185 single nucleotide polymorphisms (SNPs) were annotated at the exonic and intronic regions of these genes, while comparing the resequenced parental lines RcBr and Kenshin against Chiifu as reference genome. Expression profiling was done for all the identified genes with the available microarray data of inbred lines, Chiifu and RcBr. Finally, a knowledge-based carotenoid biosynthesis pathway was proposed for B. rapa using details retrieved from the comparative study.

The inheritance of leaf and heading-related traits in Chinese cabbage (Brassica rapa ssp. pekinensis) are poorly understood since only a handful of studies of these traits are available till date. In this study, QTL mapping was done for seven leaf and heading related traits that includes gross weight, number of non-wrapper leaves, head weight, head length, head width, head length/head width ratio, and the number of head-forming leaves in 139 F3 families derived from a cross between two diverse Chinese cabbage lines, ‘501’ with small head and ‘601’ with large head. A total of 27 QTL spread over the nine linkage groups were identified for seven leaf and head-related traits, many of which showed major effects clustered in A2, A4, A6, and A8. The results provided a better understanding of the genetic factors controlling leaf and head-related traits in Chinese cabbage.