The Cucurbitaceae family hosts many economically important fruit vegetables (cucurbits) such as cucumber, melon, watermelon, pumpkin/squash, and various gourds. The cucurbits are probably best known ...for the diverse fruit sizes and shapes, but little is known about their genetic basis and molecular regulation. Here, we reviewed the literature on fruit size (FS), shape (FSI), and fruit weight (FW) QTL identified in cucumber, melon, and watermelon, from which 150 consensus QTL for these traits were inferred. Genome-wide survey of the three cucurbit genomes identified 253 homologs of eight classes of fruit or grain size/weight-related genes cloned in Arabidopsis, tomato, and rice that encode proteins containing the characteristic CNR (cell number regulator), CSR (cell size regulator), CYP78A (cytochrome P450), SUN, OVATE, TRM (TONNEAU1 Recruiting Motif), YABBY, and WOX domains. Alignment of the consensus QTL with candidate gene homologs revealed widespread structure and function conservation of fruit size/shape gene homologs in cucurbits, which was exemplified with the fruit size/shape candidate genes
CsSUN25-26-27a
and
CsTRM5
in cucumber,
CmOFP1a
in melon, and
ClSUN25-26-27a
in watermelon. In cucurbits, the
andromonoecy
(for 1-aminocyclopropane-1-carboxylate synthase) and the
carpel number
(for CLAVATA3) loci are known to have pleiotropic effects on fruit shape, which may complicate identification of fruit size/shape candidate genes in these regions. The present work illustrates the power of comparative analysis in understanding the genetic architecture of fruit size/shape variation, which may facilitate QTL mapping and cloning for fruit size-related traits in cucurbits. The limitations and perspectives of this approach are also discussed.
Summary
Domestication and improvement are two important stages in crop evolution. Melon (Cucumis melo L.) is an important vegetable crop with wide phenotypic diversity in many horticultural traits, ...especially fruit size, flesh thickness and aroma, which are likely the results of long‐term extensive selection during its evolution. However, selective signals in domestication and improvement stages for these remarkable variations remain unclear. We resequenced 297 wild, landrace and improved melon accessions and obtained 2 045 412 high‐quality SNPs. Population structure and genetic diversity analyses revealed independent and two‐step selections in two subspecies of melon: ssp. melo and ssp. agrestis during melon breeding. We detected 233 (~18.35 Mbp) and 159 (~17.71 Mbp) novel potential selective signals during the improvement stage in ssp. agrestis and spp. melo, respectively. Two alcohol acyltransferase genes (CmAATs) unique to the melon genome compared with other cucurbit crops may have undergone stronger selection in ssp. agrestis for the characteristic aroma as compared with other cucurbits. Genome‐wide association analysis identified eight fruit size and seven flesh thickness signals overlapping with selective sweeps. Compared with thin‐skinned ssp. agrestis, thick‐skinned ssp. melo has undergone a stronger selection for thicker flesh. In most melon accessions, CmCLV3 has pleiotropic effects on carpel number and fruit shape. Findings from this study provide novel insights into melon crop evolution, and new tools to advance melon breeding.
Key Message
Two genes for resistance to
Podosphaera xanthii
race 1 in melon were identified on chromosomes 10 and 12 of the
Cucumis melo
cultivar MR-1.
Cucumis melo
L. is an economically important ...crop, the production of which is threatened by the prevalence of melon powdery mildew (PM) infections. We herein utilized the MR-1 (P
1
; resistant to PM) and M4-7 (P
2
; susceptible to PM) accessions to assess the heritability of PM (race 1) resistance in these melon plants. PM resistance in MR-1 leaves was linked to a dominant gene (
CmPMRl
), whereas stem resistance was under the control of a recessive gene (
CmPMrs
), with the dominant gene having an epistatic effect on the recessive gene. The
CmPMRl
gene was mapped to a 50 Kb interval on chromosome 12, while
CmPMrs
was mapped to an 89 Kb interval on chromosome 10. The
CmPMRl
candidate gene
MELO3C002441
and the
CmPMrs
candidate gene
MELO3C012438
were identified through sequence alignment, functional annotation, and expression pattern analyzes of all genes within these respective intervals.
MELO3C002441
and
MELO3C012438
were both localized to the cellular membrane and were contained conserved NPR gene-like and MLO domains, respectively, which were linked to PM resistance. In summary, we identified patterns of PM resistance in the disease-resistant MR-1 melon cultivar and identified two putative genes linked to resistance. Our results offer new genetic resources and markers to guide future marker-assisted breeding for PM resistance in melon.
Key message
A gene controlling golden flesh trait in watermelon was discovered and fine mapped to a 39.08 Kb region on chromosome 1 through a forward genetic strategy, and Cla97C01G008760 (annotated ...as phytoene synthase protein, ClPsy1 ) was recognized as the most likely candidate gene.
Vitamin A deficiency is a worldwide public nutrition problem, and β-carotene is the precursor for vitamin A synthesis. Watermelon with golden flesh (gf, which occurs due to an accumulated abundance of β-carotene) is an important germplasm resource. In this study, a genetic analysis of segregated
gf
gene populations indicated that
gf
was controlled by a single recessive gene. BSA-seq (Bulked segregation analysis) and an initial linkage analysis placed the
gf
locus in a 290-Kb region on watermelon chromosome 1. Further fine mapping in a large population including over 1000 F
2
plants narrowed this region to 39.08 Kb harboring two genes,
Cla97C01G008760
and
Cla97C01G008770
, which encode phytoene synthase (
ClPsy1
) and GATA zinc finger domain-containing protein, respectively. Gene sequence alignment and expression analysis between parental lines revealed
Cla97C01G008760
as the best possible candidate gene for the gf trait. Nonsynonymous SNP mutations in the first exon of
ClPsy1
between parental lines co-segregated with the gf trait only among individuals in the genetic population and were not related to flesh color in natural watermelon panels. Promoter sequence analysis of 26 watermelon accessions revealed two SNPs in the
cis
-acting element sequences corresponding to MYB and MYC2 transcription factors. RNA-seq data and qRT-PCR verification showed that two MYBs exhibited expression trends similar to that of
ClPsy1
in the parental lines and may regulate the
ClPsy1
expression. Further research findings indicate that the gf trait is determined not only by
ClPsy1
but also by
ClLCYB
,
ClCRTISO
and
ClNCED7
, which play important roles in watermelon β-carotene accumulation.
Cucurbits (Cucurbitaceae family) include many economically important fruit vegetable crops such as watermelon, pumpkin/squash, cucumber, and melon. Seed size (SS) is an important trait in cucurbits ...breeding, which is controlled by quantitative trait loci (QTL). Recent advances have deciphered several signaling pathways underlying seed size variation in model plants such as Arabidopsis and rice, but little is known on the genetic basis of SS variation in cucurbits. Here we conducted literature review on seed size QTL identified in watermelon, pumpkin/squash, cucumber and melon, and inferred 14, 9 and 13 consensus SS QTL based on their physical positions in respective draft genomes. Among them, four from watermelon (
,
,
, and
), two from cucumber (
and
), and one from melon (
) were major-effect, stable QTL for seed size and weight. Whole genome sequence alignment revealed that these major-effect QTL were located in syntenic regions across different genomes suggesting possible structural and functional conservation of some important genes for seed size control in cucurbit crops. Annotation of genes in the four watermelon consensus SS QTL regions identified genes that are known to play important roles in seed size control including members of the zinc finger protein and the E3 ubiquitin-protein ligase families. The present work highlights the utility of comparative analysis in understanding the genetic basis of seed size variation, which may help future mapping and cloning of seed size QTL in cucurbits.
Summary
Cucumber, Cucumis sativus L. is the only taxon with 2n = 2x = 14 chromosomes in the genus Cucumis. It consists of two cross‐compatible botanical varieties: the cultivated C. sativus ...var. sativus and the wild C. sativus var. hardwickii. There is no consensus on the evolutionary relationship between the two taxa. Whole‐genome sequencing of the cucumber genome provides a new opportunity to advance our understanding of chromosome evolution and the domestication history of cucumber. In this study, a high‐density genetic map for cultivated cucumber was developed that contained 735 marker loci in seven linkage groups spanning 707.8 cM. Integration of genetic and physical maps resulted in a chromosome‐level draft genome assembly comprising 193 Mbp, or 53% of the 367 Mbp cucumber genome. Strategically selected markers from the genetic map and draft genome assembly were employed to screen for fosmid clones for use as probes in comparative fluorescence in situ hybridization analysis of pachytene chromosomes to investigate genetic differentiation between wild and cultivated cucumbers. Significant differences in the amount and distribution of heterochromatins, as well as chromosomal rearrangements, were uncovered between the two taxa. In particular, six inversions, five paracentric and one pericentric, were revealed in chromosomes 4, 5 and 7. Comparison of the order of fosmid loci on chromosome 7 of cultivated and wild cucumbers, and the syntenic melon chromosome I suggested that the paracentric inversion in this chromosome occurred during domestication of cucumber. The results support the sub‐species status of these two cucumber taxa, and suggest that C. sativus var. hardwickii is the progenitor of cultivated cucumber.
Watermelon Citrullus lanatus (Thunb.) Matsum. & Nakai is an economically important crop with an attractive ripe fruit that has colorful flesh. Fruit ripening is a complex, genetically programmed ...process.
In this study, a comparative transcriptome analysis was performed to identify the regulators and pathways that are involved in the fruit ripening of pale-yellow-flesh cultivated watermelon (COS) and red-flesh cultivated watermelon (LSW177). We first identified 797 novel genes to extend the available reference gene set. Second, 3958 genes in COS and 3503 genes in LSW177 showed at least two-fold variation in expression, and a large number of these differentially expressed genes (DEGs) during fruit ripening were related to carotenoid biosynthesis, plant hormone pathways, and sugar and cell wall metabolism. Third, we noted a correlation between ripening-associated transcripts and metabolites and the key function of these metabolic pathways during fruit ripening.
The results revealed several ripening-associated actions and provide novel insights into the molecular mechanisms underlying the regulation of watermelon fruit ripening.
The sex-control system involves several mechanisms in melon. The present study identified a novel bisexual flower control gene from the hermaphroditic melon germplasm, different from the previously ...recognized one. Genetic analysis showed that a single recessive gene in the newly identified locus
controlled the bisexual flower phenotype in melons. We generated 1431 F
segregating individuals for genetic mapping of locus
, which was delimited to a 47.94 kb region. Six candidate genes were identified in the delimited interval, and candidate No. 4 encoding melon CPR5 protein was selected as the suitable one for locus
and was denoted
. CPR5 reportedly interacted with ethylene receptor ETR1 to regulate ethylene signal transduction. Moreover, the ethephon assays showed that the parental lines (unisexual line and bisexual line) had contrasting expression patterns of
. The BiFC and LCI assays also confirmed that CmCPR5 interacted with CmETR1 in 0426 but not in Y101. However, crossover tests showed that CmETR1 functioned normally in both parental lines, suggesting CPR5 malfunction in Y101. This study proposed a corollary mechanism of bisexual flower regulation during stamen primordium development in which the inhibition of stamen primordia development was prevented by the malfunctioning CmCPR5, resulting in bisexual flowers.
Powdery mildew (PM) significantly and negatively affects the yield and quality of melon (
) worldwide. Race 2F is the predominant physiological race of the pathogen
in many regions. We used ...accessions PMR 6 (P
; resistant to PM) and M1-7 (P
; susceptible to PM) to analyze the inheritance of resistance to PM (race 2F). The ratio between resistant and susceptible individuals fits a Mendelian segregation ratio of 13:3 in a total of 256 F
individuals and 1:1 in BC
P
. The resistance to PM in PMR 6 was governed by two genes: a dominant (AA) gene with an epistatic effect and a recessive gene (bb). Only individuals with
or
genotypes were susceptible to PM. Two PM resistance loci,
and
, were mapped on chromosomes 2 and 12 by bulked segregant analysis and secondary mapping by quantitative trait loci analysis with 18 markers. A new marker-assisted selection system to identify melon genotypes resistant or susceptible to PM was developed and tested in 93 melon accessions. Nucleotide diversity (π) and fixation index (Fst) for the two PM resistance loci were estimated using resequencing data of 336 melons from three groups:
subsp.
,
subsp.
, and the intermediate type. The lowest π was observed in
ssp.
, and the highest Fst value was between
ssp.
and
ssp.
. The findings provide a promising tool that can be used to accelerate breeding for durable resistance to PM.
Lycopene content and flesh color are important traits determined by a network of carotenoid metabolic pathways in watermelon. Based on our previous study of genetic inheritance and initial mapping ...using F
2
populations of LSW-177 (red flesh) × cream of Saskatchewan (pale yellow flesh), red flesh color was controlled by one recessive gene regulating red and pale yellow pigmentation, and a candidate region related to lycopene content was detected spanning a 392,077-bp region on chromosome 4. To obtain a more precise result for further study, three genetic populations and a natural panel of 81 watermelon accessions with different flesh colors were used in this research. Herein, we narrowed the preliminary mapping region to 41,233 bp with the linkage map generated from F
2
populations of LSW-177 (red flesh) × cream of Saskatchewan (pale yellow flesh) with 1,202 individuals. Two candidate genes,
Cla005011
and
Cla005012
, were found in the fine mapping region; therein
Cla005011
was a key locus annotated as a lycopene β-cyclase gene. Phylogenetic tree analysis showed that
Cla005011
was the closest relative gene in gourd. LSW-177 × PI 186490 (white flesh) and another BC
1
population derived from garden female (red flesh) × PI 186490 were generated to verify the accuracy of the red flesh candidate gene region. By analyzing the expression levels of candidate genes in different developmental stages of different color watermelon varieties,
Cla005011
for the expression differences was not the main reason for the flesh color variation between COS and LSW-177. This indicated that the
LCYB
gene might regulate fruit color changes at the protein level. A new marker-assisted selection system to identify red and yellow flesh colors in watermelon was developed with flesh color–specific CAPS markers and tested in 81 watermelon accessions.
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