A genome-wide association study uncovers a critical role of the RsPAP2 gene in red-skinned Raphanus sativus L.

Radish(Raphanus sativus L.)taproot contains high concentrations of flavonoids,including anthocyanins(ATCs),in redskinned genotypes.However,little information on the genetic regulation of ATC biosynthesis in radish is available.A genome-wide association study of radish red skin color was conducted using whole-genome sequencing data derived from 179 radish genotypes.The R2R3-MYB transcription factor production of anthocyanin pigment 2(PAP2)gene was found in the region associated with a leading SNP located on chromosome 2.The amino acid sequence encoded by the RsPAP2 gene was different from those of the other published RsMYB genes responsible for the red skin color of radish.The overexpression of the RsPAP2 gene resulted in ATC accumulation in Arabidopsis and radish,which was accompanied by the upregulation of several ATC-related structural genes.RsPAP2 was found to bind the RsUFGT and RsTT8 promoters,as shown by a dual-luciferase reporter system and a yeast one-hybrid assay.The promoter activities of the RsANS,RsCHI,RsPAL,and RsUFGT genes could be strongly activated by coinfiltration with RsPAP2 and RsTT8.These findings showed the effectiveness of GWAS in identifying candidate genes in radish and demonstrated that RsPAP2 could(either directly or together with its cofactor RsTT8)regulate the transcript levels of ATC-related genes to promote ATC biosynthesis,facilitating the genetic enhancement of ATC contents and other related traits in radish.

Melatonin-induced DNA demethylation of metal transporters and antioxidant genes alleviates lead stress in radish plants

Melatonin(MT)is a tryptophan-derived natural product that plays a vital role in plant response to abiotic stresses,including heavy metals(HMs).However,it remains elusive how exogenous MT mediates lead(Pb)accumulation and detoxification at the methylation and transcriptional levels in radish.In this study,decreased Pb accumulation and increased antioxidant enzyme activity were detected under MT treatment in radish.Single-base resolution maps of DNA methylation under Pb stress(Pb200)and Pb plus MT treatment(Pb_50MT)were first generated.The genome-wide methylation level was increased under Pb stress,while an overall loss of DNA methylation was observed under MT treatment.The differentially methylated region(DMR)-associated genes between Pb_50MT and Pb200 were uniquely enriched in ion binding terms,including cation binding,iron ion binding,and transition metal ion binding.Hyper-DMRs between Pb200 and Control exhibited a decreasing trend of methylation under Pb_50MT treatment.A few critical upregulated antioxidant genes(e.g.,RsAPX2,RsPOD52 and RsGST)exhibited decreased methylation levels under MT treatment,which enabled the radish plants to scavenge lead-induced reactive oxygen species(ROS)and decrease oxidative stress.Notably,several MT-induced HM transporter genes with low methylation(e.g.,RsABCF5,RsYSL7 and RsHMT)and transcription factors(e.g.,RsWRKY41 and RsMYB2)were involved in reducing Pb accumulation in radish roots.These findings could facilitate comprehensive elucidation of the molecular mechanism underlying MT-mediated Pb accumulation and detoxification in radish and other root vegetable crops.

Comparative proteomic analysis provides insight into a complex regulatory network of taproot formation in radish (Raphanus sativus L.)

The fleshy taproot of radish is an important storage organ determining its yield and quality.Taproot thickening is a complex developmental process in radish.However,the molecular mechanisms governing this process remain unclear at the proteome level.In this study,a comparative proteomic analysis was performed to analyze the proteome changes at three developmental stages of taproot thickening using iTRAQ approach.In total,1862 differentially expressed proteins(DEPs)were identified from 6342 high-confidence proteins,among which 256 up-regulated proteins displayed overlapped accumulation in S1(pre-cortex splitting stage)vs.S2(cortex splitting stage)and S1 vs.S3(expanding stage)pairs,whereas 122 up-regulated proteins displayed overlapped accumulation in S1 vs.S3 and S2 vs.S3 pairs.Gene Ontology(GO)and pathway enrichment analysis showed that these DEPs were mainly involved in several processes such as“starch and sucrose metabolism”,“plant hormone signal transduction”,and“biosynthesis of secondary metabolites”.A high concordance existed between iTRAQ and RT-qPCR at the mRNA expression levels.Furthermore,association analysis showed that 187,181,and 96 DEPs were matched with their corresponding differentially expressed genes(DEGs)in S1 vs.S2,S1 vs.S3,and S2 vs.S3 comparison,respectively.Notably,several functional proteins including cell division cycle 5-like protein(CDC5),expansin B1(EXPB1),and xyloglucan endotransglucosylase/hydrolase protein 24(XTH24)were responsible for cell division and expansion during radish taproot thickening process.These results could facilitate a better understanding of the molecular mechanism underlying taproot thickening,and provide valuable information for the identification of critical genes/proteins responsible for taproot thickening in root vegetable crops.