Search

Chinese kale is a characteristic vegetable crop originating from China and being suggested to be a possible ancestor of various cultivated B. oleracea vegetables. It has both white and yellow petals and is therefore a desirable plant for use in research on petal color formation. In our study, the Chinese kale landrace YCK-1 (yellow petals) was crossed with the Chinese kale inbred line Lb07M (white petals) to construct mapping populations for genetic analysis and fine mapping of the petal color gene. The results indicated that yellow petal color is controlled by a single recessive gene named ckpc, which was preliminarily located in a 2.06-Mb candidate region of chromosome C03 using whole-genome resequencing combined with bulked segregant analysis (BSA). Fine mapping with traditional molecular marker technology was used to narrow down the ckpc gene in a 69.0-kb interval flanked by the markers M916 and SNP4 at genetic distances of 0.07 cM and 0.04 cM, respectively. Gene annotation revealed 5 genes in that region, and Bo3g158650 was annotated as a carotenoid cleavage dioxygenase 4 (CCD4) gene, which is known to function in flower and flesh color formation. Sequence analysis revealed that the Bo3g158650 gene in the white-petaled parent, Lb07M, had an identical sequence to that in the ‘TO1000’ reference genome, while a 7.61-kb CACTA-like transposable element 1 (TE1) insertion was found in this gene in the yellow-petaled parent, YCK-1. These results increase the understanding of the mechanism underlying petal color formation in Brassica.

Background Caixin and Zicaitai (Brassica rapa) belong to Southern and Central China respectively. Zicaitai contains high amount of anthocyanin in leaf and stalk resulting to the purple color. Stalk is the major edible part and stalk color is an economically important trait for the two vegetables. The aim of this study is to construct a high density genetic map using the specific length amplified fragment sequencing (SLAF-seq) technique to explore genetic basis for anthocyanin pigmentation traits via quantitative trait loci (QTL) mapping. Results We constructed a high generation linkage map with a mapping panel of F2 populations derived from 150 individuals of parental lines “Xianghongtai 01” and “Yinong 50D” with purple and green stalk respectively. The map was constructed containing 4253 loci, representing 10,940 single nucleotide polymorphism (SNP) markers spanning 1030.04 centiMorgans (cM) over 10 linkage groups (LGs), with an average distance between markers of 0.27 cM. Quantitative trait loci (QTL) analysis revealed that a major locus on chromosome 7 and 4 minor QTLs explaining 2.69–61.21% of phenotypic variation (PVE) were strongly responsible for variation in stalk color trait. Bioinformatics analysis of the major locus identified 62 protein-coding genes. Among the major locus, there were no biosynthetic genes related to anthocyanin. However, there were several transcription factors like helix-loop-helix (bHLH) bHLH, MYB in the locus. Seven predicted candidate genes were selected for the transcription level analysis. Only bHLH49 transcription factor, was significantly higher expressed in both stalks and young leaves of Xianghongtai01 than Yinong50D. An insertion and deletion (InDel) marker developed from deletion/insertion in the promoter region of bHLH49 showed significant correlation with the stalk color trait in the F2 population. Conclusion Using the constructed high-qualified linkage map, this study successfully identified QTLs for stalk color trait. The identified valuable markers and candidate genes for anthocyanin accumulation in stalk will provide useful information for molecular regulation of anthocyanin biosynthesis. Overall our findings will lay a foundation for functional gene cloning, marker-assisted selection (MAS) and molecular breeding of important economic traits in B. rapa. Electronic supplementary material The online version of this article (10.1186/s12864-019-5693-2) contains supplementary material, which is available to authorized users.

Annotation of the genes in the major QTL locus. (PDF 96 kb)

Primers involved in this study. (PDF 94 kb)

QTL analysis of purple stalk. (PDF 1004 kb)

Spearman factor of each linkage group. (PDF 91 kb)

A proteomic examination of Sinorhizobium meliloti strain 1021 was undertaken using a combination of 2-D gel electrophoresis, peptide mass fingerprinting, and bioinformatics. Our goal was to identify (i) putative symbiosis- or nutrientstress-specific proteins, (ii) the biochemical pathways active under different conditions, (iii) potential new genes, and (iv) the extent of posttranslational modifications of S. meliloti proteins. In total, we identified the protein products of 810 genes (13.1% of the genome's coding capacity). The 810 genes generated 1,180 gene products, with chromosomal genes accounting for 78% of the gene products identified (18.8% of the chromosome's coding capacity). The activity of 53 metabolic pathways was inferred from bioinformatic analysis of proteins with assigned Enzyme Commission numbers. Of the remaining proteins that did not encode enzymes, ABC-type transporters composed 12.7% and regulatory proteins 3.4% of the total. Proteins with up to seven transmembrane domains were identified in membrane preparations. A total of 27 putative nodulespecific proteins and 35 nutrient-stress-specific proteins were identified and used as a basis to define genes and describe processes occurring in S. meliloti cells in nodules and under stress. Several nodule proteins from the plant host were present in the nodule bacteria preparations. We also identified seven potentially novel proteins not predicted from the DNA sequence. Post-translational modifications such as N-terminal processing could be inferred from the data. The posttranslational addition of UMP to the key regulator of nitrogen metabolism, PII, was demonstrated. This work demonstrates the utility of combining mass spectrometry with protein arraying or separation techniques to identify candidate genes involved in important biological processes and niche occupations that may be intransigent to other methods of gene expression profiling.

The fast-growing cowpea Rhizobium strain NGR234 is able to nodulate a wide range of tropical legumes as well as the non-legume Parasponia (1). Nodulation and structural nitrogenase genes are located on a large Symplasmid in this strain (2). A cryptic megaplasmid of greater than 450 Mdals also exists in NGR234.