Unintended effects of gene edit crops may pose safety issues. Omics is a useful tool for researchers to evaluate these unexpected effects. Transcriptome and proteomics analyses were performed for two gene editors, CRISPR-Cas9 and adenine base editor (ABE) gene edit rice, as well as corresponding wild-type plants (Nipponbare). Transcriptome revealed 520 and 566 rice differentially expressed genes (DEGs) in the Cas9/Nip and ABE/Nip comparisons, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that most DEGs participated in metabolism of terpenoids and polyketones, plant-pathogen interactions, and plant signal transduction. It mainly belongs to environmental adaptation. Proteomics revealed 298 and 54 rice differentially expressed proteins (DEPs) in the Cas9/Nip and ABE/Nip comparisons, respectively. KEGG pathway enrichment analysis showed that most DEPs participated in the biosynthesis of secondary metabolite and metabolic pathways.According to integrated transcriptomes and proteomics analysis, the results showed that no newly generated genes were identified as new transcripts of these differentially expressed genes, and gene edit tools had little effect on rice transcription levels and no new proteins were generated in the gene-edited rice.

Selenium （Se） is an essential microelement for human,and Se enriched products are important sources for Se intake in human.Tea plants （Camellia sinensis） have strong selenium enrichment ability.However,there is limited research on the molecular mechanism of phosphate transporters involved in Se absorption.In this study,CsPHT1;3 gene was cloned and its characteristics and responses to Se concentrations,valence,pH,time and expression in various Se-enriched tea resources were investigated.Gene characteristic analysis of CsPHT1;3 shows that CsPHT1;3 is grouped into phosphate transporter PHT1 subfamily and localized in the plasma membrane.The Cs PHT1;3 protein contains the conserved domain GGDYPLSATIxSE,which belongs to the PHT1 protein.Expression pattern analysis of CsPHT1;3 in various tissues suggests that the expression levels of CsPHT1;3 in mature leaves and root tissues were significantly higher than those in other tissues.The induction results of different Se concentrations and valence states indicate that CsPHT1;3 was significantly induced by Se 4+ at 1 d and 7 d after treatments.The expression of CsPHT1;3 in roots was obviously induced by Se 6+ except for 3 d after treatment but largely unaffected by Se 6+ concentration.The results of different pH and Se 4+ treatments show that,at pH5,the highest expression of CsPHT1;3 in tea roots was observed at 24 h.While at pH3,the highest expression of CsPHT1;3 in tea roots was observed at 48 h.Moreover,at pH7,the highest expression of CsPHT1;3 in tea roots was observed at 72 h.The results of sodium selenate treatment on different Se-enriched tea resources indicate that the expression of CsPHT1;3 in the leaves and roots did not respond to sodium selenate treatment.However,the results of sodium selenite treatment on different Se-enriched tea resources suggest that CsPHT1;3 is significantly up-regulated in the leaves of Se-enriched tea resources.The above studies indicated that CsPHT1;3 may participate in the absorption and redistribution of selenite by roots in tea plants,which is important for the breeding of Se-enriched tea cultivars.

Nowadays, with the rapid development of biotechnology, the CRISPR/Cas technology in particular has produced many new traits and products. Therefore, rapid and high-resolution detection methods for biotechnology products are urgently needed, which is extremely important for safety regulation. Recently, in addition to being gene editing tools, CRISPR/Cas systems have also been used in detection of various targets. CRISPR/Cas systems can be successfully used to detect nucleic acids, proteins, metal ions and others in combination with a variety of technologies, with great application prospects in the future. However, there are still some challenges need to be addressed. In this review, we will list some detection methods of genetically modified (GM) crops, gene-edited crops and single-nucleotide polymorphisms (SNPs) based on CRISPR/Cas systems, hoping to bring some inspiration or ideas to readers.

Tea plants (Camellia sinensis) show discrepancies in selenium accumulation and transportation, the molecular mechanisms of which are not well understood. Hence, we aimed to conduct a systematic investigation of selenium accumulation and transportation mechanisms in different tea cultivars via transcriptome analysis. The Na2SeO3 and Na2SeO4 treatments improved selenium contents in the roots and leaves of three tea cultivars. The high selenium-enrichment ability (HSe) tea cultivars accumulated higher selenium contents in the leaves than did the low selenium-enrichment ability (LSe) tea cultivars. Transcriptome analysis revealed that differentially expressed genes (DEGs) under the Na2SeO3 and Na2SeO4 treatments were enriched in flavonoid biosynthesis in leaves. DEGs under the Na2SeO3 treatment were enriched in glutathione metabolism in the HSe tea cultivar roots compared to those of the LSe tea cultivar. More transporters and transcription factors involved in improving selenium accumulation and transportation were identified in the HSe tea cultivars under the Na2SeO3 treatment than in the Na2SeO4 treatment. In the HSe tea cultivar roots, the expression of sulfate transporter 1;2 (SULTR1;2) and SULTR3;4 increased in response to Na2SeO4 exposure. In contrast, ATP-binding cassette transporter genes (ABCs), glutathione S-transferase genes (GSTs), phosphate transporter 1;3 (PHT1;3), nitrate transporter 1 (NRT1), and 34 transcription factors were upregulated in the presence of Na2SeO3. In the HSe tea cultivar leaves, ATP-binding cassette subfamily B member 11 (ABCB11) and 14 transcription factors were upregulated under the Na2SeO3 treatment. Among them, WRKY75 was explored as a potential transcription factor that regulated the accumulation of Na2SeO3 in the roots of HSe tea cultivars. This study preliminary clarified the mechanism of selenium accumulation and transportation in tea cultivars, and the findings have important theoretical significance for the breeding and cultivation of selenium-enriched tea cultivars.

Unintended effects of gene edit crops may pose safety issues. Omics is a useful tool for researchers to evaluate these unexpected effects. Transcriptome and proteomics analyses were performed for two gene editors, CRISPR-Cas9 and adenine base editor (ABE) gene edit rice, as well as corresponding wild-type plants (Nipponbare). Transcriptome revealed 520 and 566 rice differentially expressed genes (DEGs) in the Cas9/Nip and ABE/Nip comparisons, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that most DEGs participated in metabolism of terpenoids and polyketones, plant-pathogen interactions, and plant signal transduction. It mainly belongs to environmental adaptation. Proteomics revealed 298 and 54 rice differentially expressed proteins (DEPs) in the Cas9/Nip and ABE/Nip comparisons, respectively. KEGG pathway enrichment analysis showed that most DEPs participated in the biosynthesis of secondary metabolite and metabolic pathways.According to integrated transcriptomes and proteomics analysis, the results showed that no newly generated genes were identified as new transcripts of these differentially expressed genes, and gene edit tools had little effect on rice transcription levels and no new proteins were generated in the gene-edited rice.

[目的]探究在茶树不同生育时期叶面喷施不同硒肥对夏茶产量、品质及硒含量的影响,为生产富硒茶提供技术依据.[方法]田间试验在浙江嵊州进行,供试茶树品种为'中茶108'.试验采用二因素列区设计,主处理为硒肥种类(A因素),副处理为硒肥喷施时期(B因素).主处理设喷施清水对照(A0)、硒酸钠(A1)、亚硒酸钠(A2)和酵母硒(A3);副处理设夏茶顶芽萌发前(5月12日,B1)与1芽1叶期(5月20日,B2)两个喷施时期.硒肥喷施浓度均为Se50mg/L,硒肥溶液喷施量为1.8 L/m2.当茶树蓬面1芽2叶占比达30％左右时,每个小区随机选取30 cm×30 cm茶蓬,调查蓬面新梢总数、1芽2叶数量、1芽2叶长度和百芽重.同时,取1芽2叶新梢样品,测定茶多酚、儿茶素、咖啡碱、游离氨基酸、花青素以及硒含量.[结果]与A0B1处理相比,A3B1处理茶树萌展值显著降低了 0.14,但对茶树蓬面新梢总数无明显影响;A2B1处理茶树1芽2叶新梢长度和百芽重分别显著降低了 1.04 cm和1.94 g.A1B2和A3B2处理茶树蓬面新梢总数分别显著降低了17.66和22.33,但不影响其萌展值;A1B2显著降低茶树1芽2叶新梢长度和百芽重,分别降低0.88 cm和1.70 g.A1B1和A2B1处理的茶叶总硒含量分别显著提高了 1.15和1.47mg/kg,有机硒含量分别显著提高了 1.13和1.38mg/kg,但A3B1处理未显著提高茶叶硒含量.A1B2、A2B2和A3B2处理均显著提高了茶叶总硒和有机硒含量,其中总硒增加量分别为5.97、7.88和2.61mg/kg,有机硒含量分别增加了 5.17、7.51和2.48 mg/kg.另外,A1B1显著降低了茶叶咖啡碱、没食子酸和儿茶素含量;A1B2处理显著降低了茶叶游离氨基酸含量,但显著增加了茶多酚和儿茶素总量,儿茶素组成中的没食子酸、表没食子儿茶素没食子酸酯和表儿茶素没食子酸酯等酯型儿茶素显著增加.[结论]夏茶萌芽前喷施外源硒能够提高茶叶总硒和有机硒含量,改善茶叶品质,尤以硒酸钠的效果最好.

Certain tea plants (Camellia sinensis) have the ability to accumulate selenium. In plants, the predominant forms of bioavailable Se are selenite (SeO32-) and selenate (SeO42-). We applied transcriptomics and proteomics to hydroponically grown plants treated with selenite or selenate for 48 h in the attempt to elucidate the selenium absorption and assimilation mechanisms in tea. A total of 1,844 differentially expressed genes (DEGs) and 691 differentially expressed proteins (DEPs) were obtained by comparing the Na2SeO3 and Na2SeO4 treatments against the control. A GO analysis showed that the genes related to amino acid and protein metabolism and redox reaction were strongly upregulated in the plants under the Na2SeO3 treatment. A KEGG pathway analysis revealed that numerous genes involved in amino acid and glutathione metabolism were upregulated, genes and proteins associated with glutathione metabolism and ubiquinone and terpenoid-quinone biosynthesis were highly expressed. Genes participating in DNA and RNA metabolism were identified and proteins related to glutathione metabolism were detected in tea plants supplemented with Na2SeO4. ABC, nitrate and sugar transporter genes were differentially expressed in response to selenite and selenate. Phosphate transporter (PHT3;1a, PHT1;3b, and PHT1;8) and aquaporin (NIP2;1) genes were upregulated in the presence of selenite. Sulfate transporter (SULTR1;1 and SULTR2;1) expression increased in response to selenate exposure. The results of the present study have clarified Se absorption and metabolism in tea plants, and play an important theoretical reference significance for the breeding and cultivation of selenium-enriched tea varieties.

茶树具有较强的富硒能力,但其吸收硒的生理特性仍不明确.以'中茶108'茶树品种为研究对象,探究pH、培养时间、硒浓度以及能量代谢、水通道蛋白、离子通道抑制剂对茶树根系摄取硒酸盐和亚硒酸盐的影响.pH试验结果表明,茶树根系对亚硒酸盐的吸收速率随着pH升高而降低,在pH 3.0时最高,在pH 4.0～7.0间保持稳定.不同处理时间试验表明,茶树根系对亚硒酸盐和硒酸盐的摄取均存在累积效应,根系总硒含量在亚硒酸盐处理下随培养时间的增加而显著递增,在硒酸盐处理下随培养时间的增加呈现先上升后降低的趋势.不同硒浓度的试验表明,茶树根系对硒酸盐和亚硒酸盐的吸收速率与硒浓度之间存在线性正相关,且对亚硒酸盐的吸收速率显著高于硒酸盐.为明确茶树根系吸收硒酸盐和亚硒酸盐的途径,在pH 5.0,硒浓度5 μmol·L-1培养条件下进行抑制剂添加试验.结果表明,能量代谢抑制剂CCCP和DNP,以及水通道蛋白抑制剂AgNO3均能显著抑制茶树根系对硒酸盐和亚硒酸盐的吸收,说明硒酸盐和亚硒酸盐进入茶树体内依赖于能量代谢参与的主动运输以及水通道蛋白运输.阴离子通道抑制剂NPPB显著抑制茶树根系对亚硒酸盐的吸收,但并不影响对硒酸盐的吸收,表明阴离子通道也是亚硒酸盐进入茶树体内的途径之一.

Low temperature stress limits the geographical distribution of tea plants (Camellia sinensis) and the yield and quality of tea. CsICE1 is a crucial regulator of tea plant’s cold signaling pathway; however, the regulatory mechanism of CsICE1 is still unclear. In this study, we found that the N-terminus of CsICE1 contains a transcriptional activation domain and a region of protein interaction. Yeast two-hybrid and bimolecular fluorescence complementation experiments confirmed that CsWRKY4 and CsOCP3 interacted with CsICE1 in the nucleus. Like CsICE1, CsWRKY4 and CsOCP3 were localized in the nucleus, and CsOCP3 was also targeted to the chloroplast. The expression of CsWRKY4 and CsOCP3 was downregulated under cold stress, unlike that of CsICE1. Under biotic stresses and salicylic acid treatment, the expression of all three genes was increased, whereas jasmonic acid treatment resulted in decreased expression of all three genes. Dual-luciferase transient assays revealed that CsICE1 promoted the expression of CsCBF1 and CsCBF3, whereas CsWRKY4 and CsOCP3 inhibited the expression of CsCBF1 and CsCBF3 and attenuated their induction by CsICE1. Taken together, these results suggest that CsWRKY4 and CsOCP3 interact with CsICE1 and regulate CsCBF1/3, thus mediating the stress response in tea plant. Furthermore, these results highlight that CsICE1 is not only a key component in the low temperature signal response pathway, but it may also serve as a point of confluence for cold and other signaling pathways.

Radish (Raphanus sativus L.) is rich in specific glucosinolates (GSLs), which benefit human health and special flavor formation. Although the basic GSLs metabolic pathway in Brassicaceae plants is clear, the regulating mechanism for specific glucosinolates content in radish fleshy taproots is not well understood. In this study, we discovered that there was a significant difference in the GSLs profiles and the content of various GSLs components. Glucoraphasatin (GRH) is the most predominant GSL in radish taproots of different genotypes as assessed by HPLC analysis. Further, we compared the taproot transcriptomes of three radish genotypes with high and low GSLs content by employing RNA-seq. Totally, we identified forty-one differentially expressed genes related to GSLs metabolism. Among them, thirteen genes (RsBCAT4, RsIPMDH1, RsMAM1a, RsMAM1b, RsCYP79F1, RsGSTF9, RsGGP1, RsSUR1, RsUGT74C1, RsST5b, RsAPK1, RsGSL-OH, and RsMYB28) were significantly higher co-expressed in the high content genotypes than in low content genotype. Notably, correlation analysis indicated that the expression level of RsMYB28, as an R2R3 transcription factor directly regulating aliphatic glucosinolate biosynthesis, was positively correlated with the GRH content. Co-expression network showed that RsMYB28 probably positively regulated the expression of the above genes, particularly RsSUR1, and consequently the synthesis of GRH. Moreover, the molecular mechanism of the accumulation of this 4-carbon (4C) GSL in radish taproots was explored. This study provides new perspectives on the GSLs accumulation mechanism and genetic improvements in radish taproots.

Excessive rainfall provides a favorable condition for field mold infection of plants, which triggers field mold (FM) stress. If FM stress occurs during the late maturation stage of soybean seed, it negatively affects seed yield and quality. To investigate the responses of soybean seed against FM stress and identify the underlying biochemical pathways involved, a greenhouse was equipped with an artificial rain producing system to allow the induction of mold growth on soybean seed. The induced quality changes and stress responses were revealed on the levels of both transcriptome and metabolome. The results showed that soybean seeds produced under FM stress conditions had an abnormal and inferior appearance, and also contained less storage reserves, such as protein and polysaccharide. Transcriptional analysis demonstrated that genes involved in amino acid metabolism, glycolysis, tricarboxylic acid, β-oxidation of fatty acids, and isoflavone biosynthesis were induced by FM stress. These results were supported by a multiple metabolic analysis which exhibited increases in the concentrations of a variety of amino acids, sugars, organic acids, and isoflavones, as well as reductions of several fatty acids. Reprogramming of these metabolic pathways mobilized and consumed stored protein, sugar and fatty acid reserves in the soybean seed in order to meet the energy and substrate demand on the defense system, but led to deterioration of seed quality. In general, FM stress induced catabolism of storage reserves and diminished the quality of soybean seed in the field. This study provides a more profound insight into seed deterioration caused by FM stress.

Post-polyploid diploidization associated with descending dysploidy and interspecific introgression drives plant genome evolution by unclear mechanisms. Raphanus is an economically and ecologically important Brassiceae genus and model system for studying post-polyploidization genome evolution and introgression. Here, we report the de novo sequence assemblies for 11 genomes covering most of the typical sub-species and varieties of domesticated, wild and weedy radishes from East Asia, South Asia, Europe, and America. Divergence among the species, sub-species, and South/East Asian types coincided with Quaternary glaciations. A genus-level pan-genome was constructed with family-based, locus-based, and graph-based methods, and whole-genome comparisons revealed genetic variations ranging from single-nucleotide polymorphisms (SNPs) to inversions and translocations of whole ancestral karyotype (AK) blocks. Extensive gene flow occurred between wild, weedy, and domesticated radishes. High frequencies of genome reshuffling, biased retention, and large-fragment translocation have shaped the genomic diversity. Most variety-specific gene-rich blocks showed large structural variations. Extensive translocation and tandem duplication of dispensable genes were revealed in two large rearrangement-rich islands. Disease resistance genes mostly resided on specific and dispensable loci. Variations causing the loss of function of enzymes modulating gibberellin deactivation were identified and could play an important role in phenotype divergence and adaptive evolution. This study provides new insights into the genomic evolution underlying post-polyploid diploidization and lays the foundation for genetic improvement of radish crops, biological control of weeds, and protection of wild species' germplasms.

Mildew severely reduces soybean yield and quality, and pods are the first line of defence against pathogens. Maize-soybean intercropping (MSI) reduces mildew incidence on soybean pods; however, the mechanism remains unclear. Changing light (CL) from maize shading is the most important environmental feature in MSI. We hypothesized that CL affects isoflavone accumulation in soybean pods, affecting their disease resistance. In the present study, shading treatments were applied to soybean plants during different developmental stages according to various CL environments under MSI. Chlorophyll fluorescence imaging (CFI) and classical evaluation methods confirmed that CL, especially vegetative stage shading (VS), enhanced pod resistance to mildew. Further metabolomic analyses and exogenous jasmonic acid (JA) and biosynthesis inhibitor experiments revealed the important relationship between JA and isoflavone biosynthesis, which had a synergistic effect on the enhanced resistance of CL-treated pods to mildew. VS promoted the biosynthesis and accumulation of constitutive isoflavones upstream of the isoflavone pathway, such as aglycones and glycosides, in soybean pods. When mildew infects pods, endogenous JA signalling stimulated the biosynthesis of downstream inducible malonyl isoflavone (MIF) and glyceollin to improve pod resistance.

植物类黄酮是重要的药用成分,其生物学功能与化学结构密切相关.O-甲基化修饰可提高类黄酮的稳定性、蛋白亲和力和生物利用度,从而增强其药用活性.O-甲基转移酶(O-methyltransferase)催化类黄酮合成O-甲基化衍生物,是类黄酮代谢途径中的关键修饰酶.本文综述了植物O-甲基化类黄酮的化学结构、药用功能及其药用价值提高机理;并对植物类黄酮O-甲基转移酶的生物学功能、表达调控与开发潜力等进行了总结展望,以期为植物甲基化类黄酮的进一步研究提供新的思路与途径.

Raphanus has undergone a lengthy evolutionary process and has rich diversity. However, the inter- and intraspecific phylogenetic relationships and genetic diversity of this genus are not well understood. Through SSR-sequencing and multi-analysis of 939 wild, semi-wild and cultivated accessions, we discovered that the European wild radish (EWR) population is separated from cultivated radishes and has a higher genetic diversity. Frequent intraspecific genetic exchanges occurred in the whole cultivated radish (WCR) population; there was considerable genetic differentiation within the European cultivated radish (ECR) population, which could drive radish diversity formation. Among the ECR subpopulations, European primitive cultivated radishes (EPCRs) with higher genetic diversity are most closely related to the EWR population and exhibit a gene flow with rat-tail radishes (RTRs) and black radishes (BRs)/oil radishes (ORs). Among Asian cultivated radishes (ACRs), Chinese big radishes (CBRs) with a relatively high diversity are furthest from the EWR population, and most Japanese/Korean big radishes (JKBRs) are close to CBR accessions, except for a few old Japanese landraces that are closer to the EPCR. The CBR and JKBR accessions are independent of RTR accessions; however, phylogenetic analysis indicates that the RTR is sister to the clade of CBR (including JWR), which suggests that the RTR may share the most recent common ancestry with CBRs and JWRs. In addition, Japanese wild radishes (JWRs), (namely, R. sativus forma raphanistroides) are mainly scattered between CBRs and EPCRs in PCoA analysis. Moreover, JWRs have a strong gene exchange with the JKBR, OR and RTR subpopulations. American wild radishes (AWRs) are closely related to European wild and cultivated radishes, and have a gene flow with European small radishes (ESRs), suggesting that the AWR developed from natural hybridization between the EWR and the ESR. Overall, this demonstrates that Europe was the origin center of the radish, and that Europe, South Asia and East Asia appear to have been three independent domestication centers. The EPCR, AWR and JWR, as semi-wild populations, might have played indispensable transitional roles in radish evolution. Our study provides new perspectives into the origin, evolution and genetic diversity of Raphanus and facilitates the conservation and exploitation of radish germplasm resources.

The accumulation of soybean seed constituents such as anthocyanin, proanthocyanidin (PA), and sucrose is affected by various environmental stresses. Considerable information is available on the effects of different environmental stresses; however, the effect of shade at various development stages on the accumulation of the various seed constituents remains elusive. We investigated the effect of shade application on anthocyanin, PA, and sucrose contents at different seed development stages of two black soybean [Glycine max (L.) Merr.] varieties. This study comprised two separate trials: maize-soybean relay intercropping (IC) and soybean monoculture. The shade treatments in the soybean monoculture trial comprised shade applications at whole growth stage, at vegetative stage (SV), and at reproductive stage (SR) and a no-shade control. Anthocyanin, PA, and sucrose contents were analyzed from seeds obtained at development stages of full-size seed (R6), physiological maturity (R7), full maturity, 95% mature pods on the plant (R8), and natural air dry (AD). Genotype, shade, and planting season and their interactions had a strong influence on anthocyanin, PA, and sucrose accumulation in soybean seeds at the different seed development stages. Among all the shade treatments, relay IC recorded the highest anthocyanin contents in 2017 (1.88 mg g(-1)) and 2018 (1.76 mg g(-1)) in AD seeds. In addition, the application of shade increased PA, and maximum PA (27.14 mg g(-1)) was obtained in the SV treatment at R6 stage. The overall best sucrose contents (6.14 mg g(-1) in 2017 and 7.04 mg g(-1) in 2018) were obtained in soybean seeds harvested at R8 under SV treatment.

As a type of secondary metabolites produced by plants during long-term ecological adaptation, cutin and wax are widely involved in many resistance physiological processes including stress defense and resistance to pests and diseases, playing critical roles in the plant-pathogen interaction, thus becoming an important part of plant disease resistance mechanism. With the development of molecular biology, there is an increasing understanding on the cutin and wax metabolism and their mechanisms against fungal disease in plant. With prior researches mainly focused on the constitutive resistance and inducible resistance of plant cutin and wax, the present study, with a review of the research progress achieved on the plant cutin and wax biosynthesis and its disease resistance mechanism, is aimed to put forward prospects for future research. It was concluded that (1) as the main components of the cuticle, the first line of defense for plants against pathogen infection, cutin and wax play a critical role in physical resistance (physical barrier) and chemical resistance (bacteriostasis) as constitutive resistance components, (2) They can also play the role of inducible resistance components and (3) in addition to being the main component of the cuticle to exert physical resistance, the inducible cutin and wax component can also act as a signal molecule or inducer to activate downstream resistance reactions and exert its chemical resistance function. In the future, the research concerning cutin and wax can be focused on an in-depth explanation of the mechanism of cutin and wax inducible resistance, so as to further enrich the theoretical system of plant chemical ecology. In addition, cutin and wax biopesticides (plant immunity inducers) can be developed based on the inducible resistance of cutin and wax to provide new insight for the plant diseases control. [Ch, 1 fig. 71 ref.]

Taproot skin color is a crucial visual and nutritional quality trait of radish, and purple skin is most attractive to consumers. However, the genetic mechanism underlying this character is unknown. Herein, F2 segregating populations were constructed to investigate radish genomic regions with purple skin genes. Segregation analysis suggested that pigment presence was controlled by one dominant gene, Rsps. A bulk segregant approach coupled to whole-genome sequencing (QTL-seq) and classical linkage mapping narrowed the Rsps location to a 238.51-kb region containing 18 genes. A gene in this region, designated RsMYB1.1 (an Arabidopsis PAP1 homolog), was a likely candidate gene because semiquantitative RT-PCR and quantitative real-time PCR revealed RsMYB1.1 expression in only purple-skinned genotypes, sequence variation was found between white- and purple-skinned radishes, and an InDel marker in this gene correctly predicted taproot skin color. Furthermore, four RsMYB1.1 homologs (RsMYB1.1-1.4) were found in "XYB36-2" radish. RsMYB1.1 and the previously mapped and cloned RsMYB1.4 (contributing to red skin) were located on different chromosomes and in different subclades of a phylogenetic tree; thus, they are different genes. These findings provide insight into the complex anthocyanin biosynthesis regulation in radish and information for molecular breeding to improve the anthocyanin content and appearance of radish taproots.