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.
A genus-level pan-genome was constructed through de novo genome assemblies of 11 accessions covering most of the typical sub-species and varieties of domesticated, wild, and weedy radishes from East Asia, South Asia, Europe, and America. 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.
Cytokinins (CKs) are a group of phytohormones that are involved in plant growth, development, and disease resistance. The isopentenyl transferase (IPT) and cytokinin oxidase/dehydrogenase (CKX) ...families comprise key enzymes controlling CK biosynthesis and degradation. However, an integrated analysis of these two gene families in radish has not yet been explored. In this study, 13 RsIPT and 12 RsCKX genes were identified and characterized, most of which had four copies in Brassica napus and two copies in radish and other diploid Brassica species. Promoter analysis indicated that the genes contained at least one phytohormone or defense and stress responsiveness cis-acting element. RsIPTs and RsCKXs were expanded through segmental duplication. Moreover, strong purifying selection drove the evolution of the two gene families. The expression of the RsIPT and RsCKX genes distinctly showed diversity in different tissues and developmental stages of the root. Expression profiling showed that RsCKX1-1/1-2/1-3 was significantly upregulated in club-resistant materials during primary infection, suggesting their vital function in clubroot resistance. The interaction network of CKX proteins with similar 3D structures also reflected the important role of RsCKX genes in disease resistance. This study provides a foundation for further functional study on the IPT and CKX genes for clubroot resistance improvement in Raphanus.
Radish (
) is an important cruciferous root crop with a close relationship to Chinese cabbage (
). RT-qPCR is used extensively to evaluate the expression levels of target genes, and accurate ...measurement of target gene expression with this method is determined by the valid reference genes used for data nomalization in different experimental conditions. Screening for appropriate reference genes with stable expression based on RT-qPCR data is important for gene expression and functional analysis research in radish and its relatives. However, many researches have thought that almost no single reference gene is widely suitable for all experimental conditions, and few researchers have paid attention to the validation of reference genes in radish gene expression analysis. In the present study, 12 candidate reference genes were selected for analysis. Their expression in 28 samples, including 20 radish samples from different organs and conditions, four Chinese cabbage organs and four organs of their distant hybrid, was assessed by RT-qPCR and then five software tools-ΔCt, geNorm, NormFinder, BestKeeper and RefFinder-were used to compare their expression stability. The results showed that the most suitable reference genes were different in different organs and conditions.
, and
were optimal reference genes for gene expression analysis in all organs and conditions in radish.
, and
were the most stable reference genes in different radish organs.
and
were suitable reference genes for radish pistil development studies.
, and
had the most stable expression in radish under various stresses.
, and
were the optimal reference genes for Chinese cabbage organs, whereas
was optimal for the distant hybrid.
, and
were appropriate reference genes for all of the samples together. The optimal reference genes we identified,
, and
were verified by normalizing the expression patterns of
, and
. These results will provide important information for selecting target reference genes in different research contexts and improve the accuracy and precision of gene expression analysis for radish, Chinese cabbage and their distant hybrid.
Cucumbers (Cucumis sativus) are known for their plasticity in sex expression. DNA methylation status determines gene activity but is susceptible to environmental condition changes. Thus, DNA ...methylation-based epigenetic regulation may at least partially account for the instability of cucumber sex expression. Do temperature and photoperiod that are the two most important environmental factors have equal effect on cucumber sex expression by similar epigenetic regulation mechanism? To answer this question, we did a two-factor experiment of temperature and photoperiod and generated methylome and transcriptome data from cucumber shoot apices.
The seasonal change in the femaleness of a cucumber core germplasm collection was investigated over five consecutive years. As a result, 71.3% of the 359 cucumber accessions significantly decreased their femaleness in early autumn when compared with spring. High temperature and long-day photoperiod treatments, which mimic early autumn conditions, are both unfavorable for female flower formation, and temperature is the predominant factor. High temperatures and long-day treatments both predominantly resulted in hypermethylation compared to demethylation, and temperature effect was decisive. The targeted cytosines shared in high-temperature and long-day photoperiod treatment showed the same change in DNA methylation level. Moreover, differentially expressed TEs (DETs) and the predicted epiregulation sites were clustered across chromosomes, and importantly, these sites were reproducible among different treatments. Essentially, the photoperiod treatment preferentially and significantly influenced flower development processes, while temperature treatment produced stronger responses from phytohormone-pathway-related genes. Cucumber AGAMOUS was likely epicontrolled exclusively by photoperiod while CAULIFLOWER A and CsACO
were likely epicontrolled by both photoperiod and temperature.
Seasonal change of sex expression is a germplasm-wide phenomenon in cucumbers. High temperature and long-day photoperiod might have the same effect on the methylome via the same mechanism of gene-TE interaction but resulted in different epicontrol sites that account for different mechanisms between temperature- and photoperiod-dependent sex expression changes.
Radish (Raphanus sativus L.) belongs to the family Brassicaceae, and is an economically important root crop grown worldwide. Flowering is necessary for plant propagation, but it is also an important ...agronomic trait influencing R. sativus fleshy taproot yield and quality in the case of an imbalance between vegetative and reproductive growth. There is currently a lack of detailed information regarding the pathways regulating the flowering genes or their evolution in R. sativus. The release of the R. sativus genome sequence provides an opportunity to identify and characterize the flowering genes using a comparative genomics approach.
We identified 254 R. sativus flowering genes based on sequence similarities and analyses of syntenic regions. The genes were unevenly distributed on the various chromosomes. Furthermore, we discovered the existence of R. sativus core function genes in the flowering regulatory network, which revealed that basic flowering pathways are relatively conserved between Arabidopsis thaliana and R. sativus. Additional comparisons with Brassica oleracea and Brassica rapa indicated that the retained flowering genes differed among species after genome triplication events. The R. sativus flowering genes were preferentially retained, especially those associated with gibberellin signaling and metabolism. Moreover, analyses of selection pressures suggested that the genes in vernalization and autonomous pathways were more variable than the genes in other R. sativus flowering pathways.
Our results revealed that the core flowering genes are conserved between R. sativus and A. thaliana to a certain extent. Moreover, the copy number variation and functional differentiation of the homologous genes in R. sativus increased the complexity of the flowering regulatory networks after genome polyploidization. Our study provides an integrated framework for the R. sativus flowering pathways and insights into the evolutionary relationships between R. sativus flowering genes and the genes from A. thaliana and close relatives.
Low temperature is a major environmental constraint that limits crop productivity. In this investigation, 256 diverse garlic germplasm were tested for their cold tolerance at the seedling stage by ...being exposed to natural low-temperature stress −10∼-15 °C for the lowest at night for eight days. Several plant development indicators, as well as the cold index (CI), were studied. The findings showed a significant range of CI among these accessions, ranging from 16.98 to 70.38. All germplasms were divided into five groups according to their CI and different grades of tolerance to low-temperature stress. Four highly tolerant and eight low temperature-tolerant germplasm were screened out. Multivariate analysis of the acquired phenomic data using principal component analysis (PCA) addressed sufficient variability, i.e., 70.5% revealed a significant influence of low-temperature stress on growth and bulb attributes. PCA and cluster analysis classified accessions into three groups representing high diversity, providing feasibility for their use in breeding programs. In many phenotypic variables, different germplasm responded differently to low-temperature stress. Furthermore, an exceptionally significantly negative correlation was observed between CI and agronomic traits (PH, LL, LW, RHL) and initiation of bulb traits (Bulb height, width, weight). This study provides a sustainable solution and useful resources for the garlic low temperature tolerant genetic enhancement.
•The findings showed a significant range of CI among these accessions, ranging from 16.98 to 70.38. All germplasms were divided into five groups according to their CI's and different grades of tolerance to low-temperature stress.•Four highly tolerant and eight low temperature-tolerant germplasm were screened out.•Multivariate analysis of the acquired phenomic data using principal component analysis (PCA) addressed sufficient variability, i.e., 70.5% revealed a significant influence of low-temperature stress on growth and bulb attributes.•PCA and cluster analysis classified accessions into three groups representing high diversity, providing feasibility for their use in breeding programs.•In many phenotypic variables, different germplasm responded differently to low-temperature stress. Furthermore, an exceptionally significantly negative correlation was observed between CI and agronomic traits (PH, LL, LW, RHL) and initiation of bulb traits (Bulb height, width, weight).
Radish (
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 (
,
,
,
,
,
,
,
,
,
,
,
, and
) were significantly higher co-expressed in the high content genotypes than in low content genotype. Notably, correlation analysis indicated that the expression level of
, as an R2R3 transcription factor directly regulating aliphatic glucosinolate biosynthesis, was positively correlated with the GRH content. Co-expression network showed that
probably positively regulated the expression of the above genes, particularly
, 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.
Knowing the extent and structure of genetic variation in germplasm collections is essential for the conservation and utilization of biodiversity in cultivated plants. Cucumber is the fourth most ...important vegetable crop worldwide and is a model system for other Cucurbitaceae, a family that also includes melon, watermelon, pumpkin and squash. Previous isozyme studies revealed a low genetic diversity in cucumber, but detailed insights into the crop's genetic structure and diversity are largely missing. We have fingerprinted 3,342 accessions from the Chinese, Dutch and U.S. cucumber collections with 23 highly polymorphic Simple Sequence Repeat (SSR) markers evenly distributed in the genome. The data reveal three distinct populations, largely corresponding to three geographic regions. Population 1 corresponds to germplasm from China, except for the unique semi-wild landraces found in Xishuangbanna in Southwest China and East Asia; population 2 to Europe, America, and Central and West Asia; and population 3 to India and Xishuangbanna. Admixtures were also detected, reflecting hybridization and migration events between the populations. The genetic background of the Indian germplasm is heterogeneous, indicating that the Indian cucumbers maintain a large proportion of the genetic diversity and that only a small fraction was introduced to other parts of the world. Subsequently, we defined a core collection consisting of 115 accessions and capturing over 77% of the SSR alleles. Insight into the genetic structure of cucumber will help developing appropriate conservation strategies and provides a basis for population-level genome sequencing in cucumber.
China has a long history in garlic cultivation and is the biggest country of garlic production in the world. 375 accessions of garlic from 23 provinces and areas in China has been collected and ...preserved in national germplasm repository for vegetatively propagated vegetables in Beijing since 2002. However, the genetic background and diversity of garlic from China has not been well characterized. In this study, 212 of 375 accessions of garlic were evaluated based on 29 morphological traits and allicin content. Cluster, principal compound, principal ordinates, Shannon diversity index and Pearson correlation analysis were used. The results showed that the garlic clones from China had a widely diversity among all traits. Principal component analysis showed the cumulative proportion of the first eight components explained 71.35 % of total morphological variation in all accessions. Germplasm cluster analysis whether based on 29 morphological traits or bulb yield-related traits could distinguish all germplasm. All accessions were divided into two groups with bolting and non-bolting respectively, or into five subgroups with different traits based on 29 morphological traits. Principal coordinate analysis based on eight bulb related traits divided all accessions into 6 groups. Yield among the accessions ranged from 1.60 to 16.78 t/ha, and three accessions yielded above 15 t/ha. Pearson analysis suggested bulb yield was significantly positively correlated with bulb weight (r = 0.99), bulb diameter (r = 0.73), bulb height (r = 0.53), clove number (r = 0.52), leaf width (r = 0.52). Allicin content ranged from 0.81 to 3.01 %. Pseudostem diameter was found to be significantly positively correlated with allicin content but with the low correlation coefficient (r = 0.23). The result will obviously be helpful for breeder and researchers to comprehensively understand the genetic background of the collection and more easily select the target accessions, especially those with high yield and allicin content.
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, F
2
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.
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