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SWEET (Sugars Will Eventually be Exported Transporter) genes play essential roles in various biological processes, including phloem loading, sugar efflux, plant development and stress response. In this study, a total of 33 RsSWEET gene members were identified in the radish genome. They could be divided into four subfamilies and are distributed on eight radish chromosomes. Cis-acting regulatory element analysis indicated that these RsSWEET genes were potentially involved in the radish growth and development and stress response process, including circadian control and light response and responses to numerous stresses, including low-temperature and drought stress. Transcriptome data analysis revealed that a number of RsSWEET genes exhibited specific expression patterns in different tissues and developmental stages of radish. Moreover, several RsSWEET genes (e.g., RsSWEET2a, RsSWEET3a, RsSWEET16b and RsSWEET17) showed differential expression profiles under various abiotic stresses, including cold, heat, salt, Cd and Pb stress. Remarkably, the RsSWEET17 was specifically expressed in the cambium of radish. RsSWEET17 was heterologously expressed in yeast strain EBY.VW4000, which suggested that it has the ability to transport sugar. Notably, RsSWEET17-overexpressing Arabidopsis plants exhibited excessive root length, greater fresh weight and higher soluble sugar content (SSC) accumulation compared with wild-type (WT) plants, indicating that RsSWEET17 might positively regulate radish taproot development by strategically manipulating sugar accumulation. Collectively, these results clarify the molecular mechanisms underlying RsSWEET-mediated sugar accumulation and root growth and development in radish. [ABSTRACT FROM AUTHOR]

Summary: High‐quality radish (Raphanus sativus) genome represents a valuable resource for agronomical trait improvements and understanding genome evolution among Brassicaceae species. However, existing radish genome assembly remains fragmentary, which greatly hampered functional genomics research and genome‐assisted breeding. Here, using a NAU‐LB radish inbred line, we generated a reference genome of 476.32 Mb with a scaffold N50 of 56.88 Mb by incorporating Illumina, PacBio and BioNano optical mapping techniques. Utilizing Hi‐C data, 448.12 Mb (94.08%) of the assembled sequences were anchored to nine radish chromosomes with 40 306 protein‐coding genes annotated. In total, 249.14 Mb (52.31%) comprised the repetitive sequences, among which long terminal repeats (LTRs, 30.31%) were the most abundant class. Beyond confirming the whole‐genome triplication (WGT) event in R. sativus lineage, we found several tandem arrayed genes were involved in stress response process, which may account for the distinctive phenotype of high disease resistance in R. sativus. By comparing against the existing Xin‐li‐mei radish genome, a total of 2 108 573 SNPs, 7740 large insertions, 7757 deletions and 84 inversions were identified. Interestingly, a 647‐bp insertion in the promoter of RsVRN1 gene can be directly bound by the DOF transcription repressor RsCDF3, resulting into its low promoter activity and late‐bolting phenotype of NAU‐LB cultivar. Importantly, introgression of this 647‐bp insertion allele, RsVRN1In‐536, into early‐bolting genotype could contribute to delayed bolting time, indicating that it is a potential genetic resource for radish late‐bolting breeding. Together, this genome resource provides valuable information to facilitate comparative genomic analysis and accelerate genome‐guided breeding and improvement in radish. [ABSTRACT FROM AUTHOR]

CLAVATA3/EMBRYO SURROUNDING REGION-related (CLE) peptides are a class of small molecules involved in plant growth and development. Although radish (Raphanus sativus) is an important root vegetable crop worldwide, the functions of CLE peptides in its taproot formation remain elusive. Here, a total of 48 RsCLE genes were identified from the radish genome. RNA in situ hybridization showed that RsCLE22a gene was highly expressed in the vascular cambium. Overexpression of RsCLE22a inhibited root growth by impairing stem cell proliferation in Arabidopsis, and radish plants with exogenous supplementation of RsCLE22 peptide (CLE22p) showed a similar phenotype. The vascular cambial activity was increased in RsCLE22a -silenced plants. Transcriptome analysis revealed that CLE22p altered the expression of several genes involved in meristem development and hormone signal transduction in radish. Immunolocalization results showed that CLE22p increased auxin accumulation in vascular cambium. Yeast one-hybrid and dual-luciferase assays showed that the WUSCHEL-RELATED HOMEOBOX 4 (RsWOX4) binds to RsCLE22a promoter and activates its transcription. The expression level of RsWOX4 was related to vascular cambial activity and was regulated by auxin. Furthermore, a RsCLE22a–RsWOX4 module is proposed to regulate taproot vascular cambium activity through an auxin signaling-related pathway in radish. These findings provide novel insights into the regulation of root growth in a horticultural crop. [ABSTRACT FROM AUTHOR]

Radish (Raphanus sativus L.) is an important root vegetable crop that is easily infected by various pathogens that result in decreased yield and quality. Nucleotide-binding site and leucine-rich repeat (NBS-LRR) genes play vital roles in resisting pathogen infection in plants. However, the genome-wide characterization and functional roles of NBS-LRR genes remain largely unexplored in radish. Here, a total of 187 RsNBS-LRR genes were identified at the whole-genome level in radish, among which 80 RsNBS-LRR genes were unevenly distributed on nine radish chromosomes. Interestingly, 15 clusters containing 36 RsNBS-LRR genes occurred in eight chromosomes. RNA-Seq data showed that several RsNBS-LRR genes exhibited significant differential expression profiles in different radish tissues. Moreover, a range of cis-acting regulatory elements associated with ABA, MeJA, or SA were identified in the promoter region of some RsNBS-LRR genes. RT-qPCR analysis showed that the expression of a few RsNBS-LRR genes (e.g., RsNBS021 and RsNBS163) was significantly induced under Peronospora parasitica infection and/or ABA treatment, indicating that they might play critical roles in ABA-dependent defense resistance processes. These results could enhance our understanding of the evolutionary relationship of RsNBS-LRR genes and facilitate the genetic manipulation of disease resistance in radish breeding programs. [ABSTRACT FROM AUTHOR]

In most higher plants, sucrose is the significant form of carbohydrate for long-distance transportation. Sucrose transporters/sucrose carriers (SUTs/SUCs) are involved in the loading and unloading of sucrose in phloem and play an important role in the growth and development of plants. In this study, 12 RsSUC genes were first identified from the radish genome, and their phylogenetic relationships, gene structure, and conserved motifs were further analyzed. RT-qPCR results indicated that RsSUC genes exhibited various expression patterns in different tissues and development stages of the radish. Overexpression of RsSUC1b in Arabidopsis significantly improved the uptake efficiency of exogenous sucrose, and promoted leaves and lateral root growth. In addition, the transgenic plants flowered significantly earlier than wild-type (WT) plants, and the soluble sugar contents (SSCs) including sucrose, glucose, and fructose in the mature leaves and pods were increased. It could be inferred that RsSUC1b is a plasma membrane sucrose transporter and plays a vital role in sucrose transportation and sugar accumulation during plant growth and development. These findings provided novel insights into the biological function of RsSUC genes and facilitate dissecting the molecular mechanism underlying sugar transport during radish development. [ABSTRACT FROM AUTHOR]

Radish is a typical self-incompatible crop. The rapid and accurate identification of S haplotypes can circumvent the blindness of the hybrid combination process, which is critical in radish heterosis utilization and the breeding of new varieties. In this study, based on the gene sequence which encodes the S-locus receptor kinase (SRK) of radish, and the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis, the S haplotypes were identified among 79 cultivated radish genotypes. The PCR results indicated that 79 radish genotypes could be divided into 48 Class I, 13 Class II, and 17 Class I/II S haplotypes. Sequence alignment confirmed that the Class I materials contained 19 S haplotypes, of which three haplotypes ('NAU-S53', 'NAU-S54' and 'NAU-S55') were identified for the first time in radish. After digestion using the Hinf I restriction endonuclease, the SRK domain of DNA fragments of different genotypes showed high polymorphism. Homozygous materials S haplotypes could be quickly distinguished by the differences in the digested bands. Molecular identification of the S haplotype was highly consistent with the field pollination and pollen tube germination results. These results would provide an important approach for the rapid identification of radish S haplotypes and the efficient utilization of self-incompatibility in heterosis breeding. [ABSTRACT FROM AUTHOR]

Radish (Raphanus sativus L.), an important annual or biennial root vegetable crop, is widely cultivated in the world for its high nutritive value. Isolated microspore culture (IMC) is one of the most effective methods for rapid development of homozygous lines. Due to imperfection of the IMC technology system, it is particularly important to establish an efficient IMC system in radish. In this study, the effects of different factors on radish microspore embryogenesis were investigated with 23 genotypes. Buds with the largest population of late-uninucleate-stage microspores were most suitable for embryogenesis, with a ratio of petal length to anther length (P/A) in buds of about 3/4 ~ 1. Cold pretreatment was found to be genotype specific, and the highest microspore-derived embryoid (MDE) yield occurred for treatment of the heat shock of 48 h. In addition, the supplement of 0.75 g/L activated charcoal (AC) could increase the yield of embryoids. It was found that genotypes, bud size, as well as temperature treatments had significant effects on microspore embryogenesis. Furthermore, somatic embryogenesis–related kinase (SERK) genes were profiled by reverse transcription quantitative polymerase chain reaction (RT-qPCR) analysis, which indicated that they are involved in the process of MDE formation and plantlet regeneration. The ploidy of microspore-derived plants was identified by chromosome counting and flow cytometry, and the microspore-derived plants were further proved as homozygous plants through expressed sequence tags-simple sequence repeats (EST-SSR) and genetic-SSR markers. The results would facilitate generating the large-scale double haploid (DH) from various genotypes, and promoting further highly efficient genetic improvement in radish. [ABSTRACT FROM AUTHOR]

• Totally 42 members of the Histone gene family were firstly identified in radish. • Seven RsCENH3 genes exhibited specifically high expression level in the radish bud. • RsCENH3 gene might be involved in promoting microspore development in radish. Histone, a predominant protein component of chromatin, participates in DNA packaging and transcriptional regulation. However, the available information of Histone gene family is limited in radish. In this study, a total of 42 Histone gene family members were identified from the radish genome. Sequence alignment and phylogenetic analyses classified the Histone family into three groups (H2A, H2B and H3). Motif analysis showed that the functions of some motifs shared by H3 subfamily genes were related to chromosome regulation and cell development activities, such as motif 5 containing Cks1 and PPR region. Analysis of intron/exon structure indicated that RsCENH3 (RsHistone 18) has the characteristics of variant Histone. Furthermore, several motifs, including the LTR, G-box and TC-elements, were found in the promoters of RsHistone genes, which involved in cell development or various abiotic stresses responses. Transcriptome analysis indicated that the RsHistone genes exhibited higher expression level in floral buds than in roots and leaves. Subcellular localization showed that the RsCENH3 was localized on the nucleus, and it was highly expressed in the floral bud of 3.0–4.0 mm in radish. These findings would provide valuable information for characterization and potential utilization of Histone genes, and facilitate the efficient induction of double haploid plants in radish. [ABSTRACT FROM AUTHOR]

• The identified 65 Aux/IAA genes show an uneven chromosomal distribution in radish. • Six Aux/IAA genes exhibit specifically high expression level in radish root tissues. • RsIAA33 gene might involve in promoting taproot thickening and development in radish. Auxin/indole–3–acetic acid (Aux/IAA) genes encode short lived nuclear proteins that cooperated with auxin or auxin response factor (ARF), which are involved in plant growth and developmental processes. However, it's still ambiguous how the Aux/IAA genes regulate the process governing taproot thickening in radish. Herein, 65 Aux/IAA genes were identified from the radish genome. Gene duplication analysis showed that two pairs of tandem duplication and 17 (27%) segmental duplication events were identified among Aux/IAA family genes in radish. Transcriptomic analysis revealed that most of Aux/IAA genes (52/65) exhibited differential expression pattern in different root tissues, and six root–specific genes were highly expressed in root cortex, cambium, xylem, and root tip in radish. RT–qPCR analysis showed that the expression level of RsIAA33 was the highest at cortex splitting stage (CSS), and early expanding stage (ES). Furthermore, amiRNA–mediated gene silencing of RsIAA33 indicated that it could inhibit the reproductive growth, thus promoting taproot thickening and development. These results would provide valuable information for elucidating the molecular function of Aux/IAA genes involved in taproot thickening in radish. [ABSTRACT FROM AUTHOR]