Combined QTL-Seq and Traditional Linkage Analysis to Identify Candidate Genes for Purple Skin of Radish Fleshy Taproots

A novel SNP within the Rsa10025320 gene is highly associated with hollowness in red-skinned radish fleshy roots

Hollowness is a physiological disorder that frequently occurs during the growth and postharvest storage phases of fleshy radish roots, significantly diminishing quality, yield, and marketability. However, the molecular mechanism for hollowness remains elusive. To identify the QTLs and potential candidate genes for hollowness tolerance in radish, F2 and BC1 populations were constructed from hollowness-tolerant radish (C16) and hollowness-sensitive radish (C17) in the present study. Genetic analysis indicated that hollowness tolerance may be governed by two independent recessive genes. By employing bulked segregant analysis sequencing (BSA-seq), two significant candidate genomic intervals were pinpointed on chromosomes R04 (960 kb, 6.48-7.44 Mb) and R05 (600 kb, 31.44-32.04 Mb), which together harbor 107 annotated genes. Transcriptomic sequencing revealed that the downregulated differentially expressed genes (DEGs) were significantly enriched in biological processes related to cell death and the response to water stress, whereas the upregulated DEGs were significantly associated with the chitin catabolic process and the cell wall macromolecule metabolic process. A total of 46 intersecting genes were identified among these DEGs within the genomic intervals of interest. One gene with high expression (Rsa10025345) and two with low expression (Rsa10025320 and Rsa10018106) were detected in the tolerant variety C16. Furthermore, a SNP within Rsa10025320 resulting in an amino acid change (A188E) was characterized through sequence variation observed in both BSA-seq and RNA-seq data and further developed as a derived cleaved amplified polymorphic sequence (dCAPS) marker. Our study reveals potential target genes for tolerance to hollowness and paves the way for marker-assisted breeding of hollowness tolerance in red-skinned radishes.

Sequence and epigenetic variations of R2R3-MYB transcription factors determine the diversity of taproot skin and flesh colors in different cultivated types of radish (Raphanus sativus L.)

KEY MESSAGE

This study found that three paralogous R2R3-MYB transcription factors exhibit functional divergence among different subspecies and cultivated types in radish. Cultivated radish taproots exhibit a wide range of color variations due to unique anthocyanin accumulation patterns in various tissues. This study investigated the universal principles of taproot color regulation that developed during domestication of different subspecies and cultivated types. The key candidate genes RsMYB1 and RsMYB2, which control anthocyanin accumulation in radish taproots, were identified using bulked segregant analysis in two genetic populations. We introduced the RsMYB1-RsF3'H-RsMYB1Met genetic model to elucidate the complex and unstable genetic regulation of taproot flesh color in Xinlimei radish. Furthermore, we analyzed the expression patterns of three R2R3-MYB transcription factors in lines with different taproot colors and investigated the relationship between RsMYB haplotypes and anthocyanin accumulation in a natural population of 56 germplasms. The results revealed that three paralogous RsMYBs underwent functional divergence during radish domestication, with RsMYB1 regulating the red flesh of Xinlimei radish, and RsMYB2 and RsMYB3 regulating the red skin of East Asian big long radish (R. sativus var. hortensis) and European small radish (R. sativus var. sativus), respectively. Moreover, RsMYB1-H1, RsMYB2-H10, and RsMYB3-H6 were identified as the primary haplotypes exerting regulatory functions on anthocyanin synthesis. These findings provide an understanding of the genetic mechanisms regulating anthocyanin synthesis in radish and offer a potential strategy for early prediction of color variations in breeding programs.

Effect of structural variation in the promoter region of RsMYB1.1 on the skin color of radish taproot

Accumulation of anthocyanins in the taproot of radish is an agronomic trait beneficial for human health. Several genetic loci are related to a red skin or flesh color of radish, however, the functional divergence of candidate genes between non-red and red radishes has not been investigated. Here, we report that a novel genetic locus on the R2 chromosome, where RsMYB1.1 is located, is associated with the red color of the skin of radish taproot. A genome-wide association study (GWAS) of 66 non-red-skinned (nR) and 34 red-skinned (R) radish accessions identified three nonsynonymous single nucleotide polymorphisms (SNPs) in the third exon of RsMYB1.1. Although the genotypes of SNP loci differed between the nR and R radishes, no functional difference in the RsMYB1.1 proteins of nR and R radishes in their physical interaction with RsTT8 was detected by yeast-two hybrid assay or in anthocyanin accumulation in tobacco and radish leaves coexpressing RsMYB1.1 and RsTT8. By contrast, insertion- or deletion-based GWAS revealed that one large AT-rich low-complexity sequence of 1.3-2 kb was inserted in the promoter region of RsMYB1.1 in the nR radishes (RsMYB1.1nR), whereas the R radishes had no such insertion; this represents a presence/absence variation (PAV). This insertion sequence (RsIS) was radish specific and distributed among the nine chromosomes of Raphanus genomes. Despite the extremely low transcription level of RsMYB1.1nR in the nR radishes, the inactive RsMYB1.1nR promoter could be functionally restored by deletion of the RsIS. The results of a transient expression assay using radish root sections suggested that the RsIS negatively regulates the expression of RsMYB1.1nR, resulting in the downregulation of anthocyanin biosynthesis genes, including RsCHS, RsDFR, and RsANS, in the nR radishes. This work provides the first evidence of the involvement of PAV in an agronomic trait of radish.

The long noncoding RNA LINC15957 regulates anthocyanin accumulation in radish

Radish (Raphanus sativus L.) is an important root vegetable crop belonging to the Brassicaceae family. Anthocyanin rich radish varieties are popular among consumers because of their bright color and high nutritional value. However, the underlying molecular mechanism responsible for skin and flesh induce anthocyanin biosynthesis in transient overexpression, gene silencing and transcriptome sequencing were used to verify its function in radish anthocyanin accumulation, radish remains unclear. Here, we identified a long noncoding RNA LINC15957, overexpression of LINC15957 was significantly increased anthocyanin accumulation in radish leaves, and the expression levels of structural genes related to anthocyanin biosynthesis were also significantly increased. Anthocyanin accumulation and expression levels of anthocyanin biosynthesis genes were significantly reduced in silenced LINC15957 flesh when compared with control. By the transcriptome sequencing of the overexpressed LINC15957 plants and the control, 5,772 differentially expressed genes were identified. A total of 3,849 differentially expressed transcription factors were identified, of which MYB, bHLH, WD40, bZIP, ERF, WRKY and MATE were detected and differentially expressed in the overexpressed LINC15957 plants. KEGG enrichment analysis revealed the genes were significant enriched in tyrosine, L-Phenylalanine, tryptophan, phenylpropanol, and flavonoid biosynthesis. RT-qPCR analysis showed that 8 differentially expressed genes (DEGs) were differentially expressed in LINC15957-overexpressed plants. These results suggested that LINC15957 involved in regulate anthocyanin accumulation and provide abundant data to investigate the genes regulate anthocyanin biosynthesis in radish.

Combined widely targeted metabolomics and transcriptomics analysis reveals differentially accumulated metabolites and the underlying molecular bases in fleshy taproots of distinct radish genotypes

Radish is an important taproot crop with medicinal and edible uses that is cultivated worldwide. However, the differences in metabolites and the underlying molecular bases among different radish types remain largely unknown. In the present study, a combined analysis of liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) and RNA-Seq data was conducted to uncover important differentially accumulated metabolites (DAMs) among radish accessions with green, white and red taproot flesh colours. A total of 657 metabolites were identified and 138 DAMs were commonly present in red vs. green and red vs. white accessions. Red accessions were rich in phenolic compounds, while green and white accessions had more amino acids. Additionally, 41 metabolites and 98 genes encoding 37 enzymes were enriched in the shikimate and phenolic biosynthesis pathways. CHS is the rate-limiting enzyme determining flavonoid differences among accessions. A total of 119 candidate genes might contribute to red accession-specific accumulated metabolites. Specifically, one gene cluster consisting of 16 genes, including one RsMYB1, RsMYBL2, RsTT8, RsDFR, RsANS, Rs4CL3, RsSCPL10, Rs3AT1 and RsSAP2 gene, two RsTT19 and RsWRKY44 genes and three RsUGT genes, might be involved in anthocyanin accumulation in red radish fleshy taproots. More importantly, an InDel marker was developed based on an RsMYB1 promoter mutation, and the accuracy reached 95.9% when it was used to select red-fleshed radishes. This study provides comprehensive insights into the metabolite differences and underlying molecular mechanisms in fleshy taproots among different radish genotypes and will be beneficial for the genetic improvement of radish nutritional quality.

Construction of a high-density genetic map based on specific-locus amplified fragment sequencing and identification of loci controlling anthocyanin pigmentation in Yunnan red radish

Radish (Raphanus sativus L.) belongs to the family Brassicaceae. The Yunnan red radish variety contains fairly relatively large amounts of anthocyanins, making them important raw materials for producing edible red pigment. However, the genetic mechanism underlying this pigmentation has not been fully characterized. Herein, the radish inbred line YAAS-WR1 (white root-skin and white root-flesh) was crossed with the inbred line YAAS-RR1 (red root-skin and red root-flesh) to produce F1, F2, BC1P1, and BC1P2 populations. Genetic analyses revealed that the pigmented/non-pigmented (PiN) and purple/red (PR) traits were controlled by two genetic loci. The F2 population and the specific-locus amplified fragment sequencing (SLAF-seq) technique were used to construct a high-density genetic map (1230.16 cM), which contained 4032 markers distributed in nine linkage groups, with a mean distance between markers of 0.31 cM. Additionally, two QTL (QAC1 and QAC2) considerably affecting radish pigmentation were detected. A bioinformatics analysis of the QAC1 region identified 58 predicted protein-coding genes. Of these genes, RsF3'H, which is related to anthocyanin biosynthesis, was revealed as a likely candidate gene responsible for the PR trait. The results were further verified by analyzing gene structure and expression. Regarding QAC2, RsMYB1.3 was determined to be a likely candidate gene important for the PiN trait, with a 4-bp insertion in the first exon that introduced a premature termination codon in the YAAS-WR1 sequence. Assays demonstrated that RsMYB1.3 interacted with RsTT8 and activates RsTT8 and RsUFGT expression. These findings may help clarify the complex regulatory mechanism underlying radish anthocyanin synthesis. Furthermore, this study's results may be relevant for the molecular breeding of radish to improve the anthocyanin content and appearance of the taproots.

Pan-genome of Raphanus highlights genetic variation and introgression among domesticated, wild, and weedy radishes

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.

Development of Molecular Markers for Predicting Radish (Raphanus sativus) Flesh Color Based on Polymorphisms in the RsTT8 Gene

Red radish (Raphanus sativus L.) cultivars are a rich source of health-promoting anthocyanins and are considered a potential source of natural colorants used in the cosmetic industry. However, the development of red radish cultivars via conventional breeding is very difficult, given the unusual inheritance of the anthocyanin accumulation trait in radishes. Therefore, molecular markers linked with radish color are needed to facilitate radish breeding. Here, we characterized the RsTT8 gene isolated from four radish genotypes with different skin and flesh colors. Sequence analysis of RsTT8 revealed a large number of polymorphisms, including insertion/deletions (InDels), single nucleotide polymorphisms (SNPs), and simple sequence repeats (SSRs), between the red-fleshed and white-fleshed radish cultivars. To develop molecular markers on the basis of these polymorphisms for discriminating between radish genotypes with different colored flesh tissues, we designed four primer sets specific to the RsTT8 promoter, InDel, SSR, and WD40/acidic domain (WD/AD), and tested these primers on a diverse collection of radish lines. Except for the SSR-specific primer set, all primer sets successfully discriminated between red-fleshed and white-fleshed radish lines. Thus, we developed three molecular markers that can be efficiently used for breeding red-fleshed radish cultivars.

QTL-Seq and Transcriptome Analysis Disclose Major QTL and Candidate Genes Controlling Leaf Size in Sesame (Sesamum indicum L.)

Leaf size is a crucial component of sesame (Sesamum indicum L.) plant architecture and further influences yield potential. Despite that it is well known that leaf size traits are quantitative traits controlled by large numbers of genes, quantitative trait loci (QTL) and candidate genes for sesame leaf size remain poorly understood. In the present study, we combined the QTL-seq approach and SSR marker mapping to identify the candidate genomic regions harboring QTL controlling leaf size traits in an RIL population derived from a cross between sesame varieties Zhongzhi No. 13 (with big leaves) and ZZM2289 (with small leaves). The QTL mapping revealed 56 QTL with phenotypic variation explained (PVE) from 1.87 to 27.50% for the length and width of leaves at the 1/3 and 1/2 positions of plant height. qLS15-1, a major and environmentally stable pleiotropic locus for both leaf length and width explaining 5.81 to 27.50% phenotypic variation, was located on LG15 within a 408-Kb physical genomic region flanked by the markers ZMM6185 and ZMM6206. In this region, a combination of transcriptome analysis with gene annotations revealed three candidate genes SIN_1004875, SIN_1004882, and SIN_1004883 associated with leaf growth and development in sesame. These findings provided insight into the genetic characteristics and variability for sesame leaf and set up the foundation for future genomic studies on sesame leaves and will serve as gene resources for improvement of sesame plant architecture.

Targeted amplicon sequencing + next-generation sequencing-based bulked segregant analysis identified genetic loci associated with preharvest sprouting tolerance in common buckwheat (Fagopyrum esculentum)

BACKGROUND

Common buckwheat (2n = 2x = 16) is an outcrossing pseudocereal whose seeds contain abundant nutrients and potential antioxidants. As these beneficial compounds are damaged by preharvest sprouting (PHS) and PHS is likely to increase with global warming, it is important to find efficient ways to develop new PHS-tolerant lines. However, genetic loci and selection markers associated with PHS in buckwheat have not been reported.

RESULTS

By next-generation sequencing (NGS) of whole-genome of parental lines, we developed a genome-wide set of 300 markers. By NGS- based bulked segregant analysis (NGS-BSA), we developed 100 markers linked to PHS tolerance. To confirm the effectiveness of marker development from NGS-BSA data, we developed 100 markers linked to the self-compatibility (SC) trait from previous NGS-BSA data. Using these markers, we developed genetic maps with AmpliSeq technology, which can quickly detect polymorphisms by amplicon-based multiplex targeted NGS, and performed quantitative trait locus (QTL) analysis for PHS tolerance in combination with NGS-BSA. QTL analysis detected two major and two minor QTLs for PHS tolerance in a segregating population developed from a cross between the PHS-tolerant 'Kyukei 29' and the self-compatible susceptible 'Kyukei SC7'. We found different major and minor QTLs in other segregating populations developed from the PHS-tolerant lines 'Kyukei 28' and 'NARO-FE-1'. Candidate markers linked to PHS developed by NGS-BSA were located near these QTL regions. We also investigated the effectiveness of markers linked to these QTLs for selection of PHS-tolerant lines among other segregating populations.

CONCLUSIONS

We efficiently developed genetic maps using a method combined with AmpliSeq technology and NGS-BSA, and detected QTLs associated with preharvest sprouting tolerance in common buckwheat. This is the first report to identify QTLs for PHS tolerance in buckwheat. Our marker development system will accelerate genetic research and breeding in common buckwheat.

Genetic Mapping of Climbing and Mimicry: Two Behavioral Traits Degraded During Silkworm Domestication

Behavioral changes caused by domestication in animals are an important issue in evolutionary biology. The silkworm, Bombyx mori, is an ideal fully domesticated insect model for studying both convergent domestication and behavior evolution. We explored the genetic basis of climbing for foraging and mimicry, two degraded behaviors during silkworm domestication, in combination of bulked segregant analysis (BSA) and selection sweep screening. One candidate gene, ASNA1, located in the 3-5 Mb on chromosome 19, harboring a specific non-synonymous mutation in domestic silkworm, might be involved in climbing ability. This mutation was under positive selection in Lepidoptera, strongly suggesting its potential function in silkworm domestication. Nine candidate domesticated genes related to mimicry were identified on chromosomes 13, 21, and 27. Most of the candidate domesticated genes were generally expressed at higher levels in the brain of the wild silkworm. This study provides valuable information for deciphering the molecular basis of behavioral changes associated with silkworm domestication.

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 red-skinned 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.