Background: The HongXin radish (Raphanus sativus L.), which contains the natural red pigment (red radish pigment), is grown in the Fuling district of Chongqing City. However, the molecular mechanisms underlying anthocyanin synthesis for the formation of natural red pigment in the fleshy roots of HongXin radish are not well studied. Results: De novo transcriptome of HX-1 radish, as well as that of the advanced inbred lines HX-2 and HX-3 were characterized using next generation sequencing (NGS) technology. In total, approximately 66.22 million paired-end reads comprising 34, 927 unigenes (N50 = 1, 621 bp) were obtained. Based on sequence similarity search with known proteins, total of 30, 127 (about 86.26%) unigenes were identified. Additionally, functional annotation and classification of these unigenes indicated that most of the unigenes were predominantly enriched in the metabolic process-related terms, especially for the biosynthetic pathways of secondary metabolites. Moreover, majority of the anthocyanin biosynthesis-related genes (ABRGs) involved in the regulation of anthocyanin biosynthesis were identified by targeted search for their annotation. Subsequently, the expression of 15 putative ABRGs involved in the anthocyanin synthesis-related pathways were validated using quantitative real-time polymerase chain reaction (qRT-PCR). Of those, RsPAL2, RsCHS-B2, RsDFR1, RsDFR2, RsFLS, RsMT3 and RsUFGT73B2-like were identified significantly associated with anthocyanin biosynthesis. Especially for RsDFR1, RsDFR2 and RsFLS, of those, RsDFR1 and RsDFR2 were highest enriched in the HX-3 and WG-3, but RsFLS were down-regulated in HX-3 and WG-3. We proposed that the transcripts of RsDFR1, RsDFR2 and RsFLS might be act as key regulators in anthocyanin biosynthesis pathway. Conclusions: The assembled radish transcript sequences were analysed to identify the key ABRGs involved in the regulation of anthocyanin biosynthesis. Additionally, the expression patterns of candidate ABRGs involved in the anthocyanin biosynthetic pathway were validated by qRT-PCR. We proposed that the transcripts of RsDFR1, RsDFR2 and RsFLS might be acted as key regulators in anthocyanin biosynthesis pathway. This study will enhance our understanding of the biosynthesis and metabolism of anthocyanin in radish.

Carmine radish produced in Chongqing is famous for containing a natural red pigment (red radish pigment). However, the anthocyanin biosynthesis transcriptome and the expression of anthocyanin biosynthesis-related genes in carmine radish have not been fully investigated. Uncovering the mechanism of anthocyanin biosynthesis in the ‘Hongxin 1’ carmine radish cultivar has become a dominant research topic in this field. In this study, a local carmine radish cultivar named ‘Hongxin 1’ containing a highly natural red pigment was used to analyze transcription factors (TFs) related to anthocyanin biosynthesis during the dynamic development of fleshy roots. Based on RNA sequencing data, a total of 1,747 TFs in 64 TF families were identified according to their DNA-binding domains. Of those, approximately 71 differentially expressed transcription factors (DETFs) were commonly detected in any one stage compared with roots in the seedling stage (SS_root). Moreover, 26 transcripts of DETFs targeted by 74 miRNAs belonging to 25 miRNA families were identified, including MYB, WRKY, bHLH, ERF, GRAS, NF-YA, C2H2-Dof, and HD-ZIP. Finally, eight DETF transcripts belonging to the C2C2-Dof, bHLH and ERF families and their eight corresponding miRNAs were selected for qRT-PCR to verify their functions related to anthocyanin biosynthesis during the development of carmine radish fleshy roots. Finally, we propose a putative miRNA-target regulatory model associated with anthocyanin biosynthesis in carmine radish. Our findings suggest that sucrose synthase might act as an important regulator to modulate anthocyanin biosynthesis in carmine radish by inducing several miRNAs (miR165a-5p, miR172b, miR827a, miR166g and miR1432-5p) targeting different ERFs than candidate miRNAs in the traditional WMBW complex in biological processes.

Because of their local adaptation and economic factors that limit the adoption of commercial hybrids, farmer-saved maize landraces are still grown over a considerable area concentrated in southwest China. To evaluate the potential of using maize landraces, the germplasm characteristics of 96 landraces from southwest China were evaluated at phenotypic, cellular, and molecular levels. The existence of high phenotypic variation and elite germplasm tolerant to low-N, low-P, as well as drought stress was observed. Of the total landraces, 81.25, 7.29, 5.21, and 2.08% were found with 0, 1, 2, 3, and 4 B chromosomes. Using 42 microsatellite (simple sequence repeat) loci, 246 alleles were detected among the landraces. The number of alleles per SSR locus varied from 2 to 10, averaging 5.67 allele per locus, which revealed a high level of genetic diversity of maize landraces in southwest China. Cluster analysis showed that 96 landraces could distinctly be clustered into four groups, which tended to associate with their geographic origins. We propose that the genetic diversity center of maize landraces in southwest China might be in Sichuan. A sharp genetic deviation from Hardy-Weinberg equilibrium was observed from heterozygosity deficiency and a considerable genetic variation was revealed within, rather than among, the landraces. Based on their germplasm characteristics, the innovation and utilization of maize landraces in southwestern China for theoretical and applied research could be achieved by constructing heterosis groups, developing inbred lines with high combining ability, and maintaining the landraces with elite germplasm and B chromosomes using bulked pollen.