Ultrahigh-Density Linkage Map for Cultivated Cucumber (Cucumis sativus L.) Using a Single-Nucleotide Polymorphism Genotyping Array (original) (raw)
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Genotyping arrays are tools for high-throughput genotyping, which is beneficial in constructing saturated genetic maps and therefore high-resolution mapping of complex traits. Since the report of the first cucumber genome draft, genetic maps have been constructed mainly based on simple-sequence repeats (SSRs) or on combinations of SSRs and sequencerelated amplified polymorphism (SRAP). In this study, we developed the first cucumber genotyping array consisting of 32,864 single-nucleotide polymorphisms (SNPs). These markers cover the cucumber genome with a median interval of~2 Kb and have expected genotype calls in parents/F 1 hybridizations as a training set. The training set was validated with Fluidigm technology and showed 96% concordance with the genotype calls in the parents/F 1 hybridizations. Application of the genotyping array was illustrated by constructing a 598.7 cM genetic map based on a '9930' × 'Gy14' recombinant inbred line (RIL) population comprised of 11,156 SNPs. Marker collinearity between the genetic map and reference genomes of the two parents was estimated at R 2 = 0.97. We also used the array-derived genetic map to investigate chromosomal rearrangements, regional recombination rate, and specific regions with segregation distortions. Finally, 82% of the linkage-map bins were polymorphic in other cucumber variants, suggesting that the array can be applied for genotyping in other lines. The genotyping array presented here, together with the genotype calls of the parents/F 1 hybridizations as a training set, should be a powerful tool in future studies with high-throughput cucumber genotyping. An ultrahigh-density linkage map constructed PLOS ONE |
An Integrated Genetic and Cytogenetic Map of the Cucumber Genome
PLOS One, 2009
The Cucurbitaceae includes important crops such as cucumber, melon, watermelon, squash and pumpkin. However, few genetic and genomic resources are available for plant improvement. Some cucurbit species such as cucumber have a narrow genetic base, which impedes construction of saturated molecular linkage maps. We report herein the development of highly polymorphic simple sequence repeat (SSR) markers originated from whole genome shotgun sequencing and the subsequent construction of a high-density genetic linkage map. This map includes 995 SSRs in seven linkage groups which spans in total 573 cM, and defines ,680 recombination breakpoints with an average of 0.58 cM between two markers. These linkage groups were then assigned to seven corresponding chromosomes using fluorescent in situ hybridization (FISH). FISH assays also revealed a chromosomal inversion between Cucumis subspecies [C. sativus var. sativus L. and var. hardwickii (R.) Alef], which resulted in marker clustering on the genetic map. A quarter of the mapped markers showed relatively high polymorphism levels among 11 inbred lines of cucumber. Among the 995 markers, 49%, 26% and 22% were conserved in melon, watermelon and pumpkin, respectively. This map will facilitate whole genome sequencing, positional cloning, and molecular breeding in cucumber, and enable the integration of knowledge of gene and trait in cucurbits.
Agronomy
Cucumbers are an important economic vegetable crop that is used for fresh or processing purposes worldwide. In this study, we used 264 accessions that consisted of world-wide wild germplasms and advanced breeding lines in order to understand the genetic diversity and the genetic correlation among the germplasm collection. A genotyping-by-sequencing (GBS) approach was applied to obtain dense genome-wide markers coverage (>12,082 SNPs) to construct a high-density haplotype map. Various population stratification methods were performed, and three subgroups were divided based on the genetic diversity, which reflected their geographic regions. According to the phylogenetic analysis, the breeding lines were separated from wild germplasms, and the two distinct groups were divided within the breeding lines. One of the groups mainly consisted of East-Asian varieties, which showed the unique homogenous genotype patterns. Using this germplasm collection, three important horticultural traits ...
2021
In several regions of the world, low productivity in this crop is attributed to several factors including poor understanding of the genomic complexity of important traits associated with fruit quality and yield. Therefore, genome wide association analysis was performed for important traits using simple sequence repeats (SSR) markers. Significant variation was recorded for all the studied traits in 78 cucumber genotypes under two environments (open field and net house) which indicated that the constituted association panel was suitable for association mapping. Genotyping was done using 60 highly polymorphic SSRs. By performing genome scanning out of 60 SSR markers, using mixed linear model (MLM) approach 4 and 6 markers explained an average of 23.93% and 17.37 % of the trait variation under net house and open field condition, respectively. Based on MLM approach two markers on 3rd chromosome (UW084942) and 4th chromosome (UW062953) found to be associated with the average fruit weight ...
Genetic diversity of cucumber genotypes revealed by SSR markers and agronomic traits
Genetika, 2019
Understanding the level of genetic diversity and structure of landraces is essential for economical use of genetic resources. In the present study, we investigated the genetic diversity of 36 representative sample of cucumber genotypes based on 10 quantitative traits and 17 polymorphic simple sequence repeat (SSR) markers. Our result revealed variability in flowering behavior, growth habit and fruit characters. We found that the traits, days to opening of first female flower varied from 39.03 to 51.94, fruit length 6.09 to 30.01(cm), fruit weight 104.39 to 277.05(g) and yield per plant 699.38 to 1670.93(g). Genetic distance based on 17 SSR markers among 36 genotypes was quantified ranging from 0.03 to 0.70 indicated a wide diversity among the genotypes selected for evaluation in the present study. These primers produced 2-4 number of alleles with an average 2.76. Polymorphism information content varied from 0.005 to 0.550 with an average of 0.348. The observed heterozygosity mean was 0.098, while gene diversity or expected heterozygosity was 0.625 to 0.057. The distinct genotypes found in this study based on 406
BMC Plant Biology, 2013
Background: Cucumber is an important vegetable crop that is susceptible to many pathogens, but no disease resistance (R) genes have been cloned. The availability of whole genome sequences provides an excellent opportunity for systematic identification and characterization of the nucleotide binding and leucine-rich repeat (NB-LRR) type R gene homolog (RGH) sequences in the genome. Cucumber has a very narrow genetic base making it difficult to construct high-density genetic maps. Development of a consensus map by synthesizing information from multiple segregating populations is a method of choice to increase marker density. As such, the objectives of the present study were to identify and characterize NB-LRR type RGHs, and to develop a high-density, integrated cucumber genetic-physical map anchored with RGH loci. Results: From the Gy14 draft genome, 70 NB-containing RGHs were identified and characterized. Most RGHs were in clusters with uneven distribution across seven chromosomes. In silico analysis indicated that all 70 RGHs had EST support for gene expression. Phylogenetic analysis classified 58 RGHs into two clades: CNL and TNL. Comparative analysis revealed high-degree sequence homology and synteny in chromosomal locations of these RGH members between the cucumber and melon genomes. Fifty-four molecular markers were developed to delimit 67 of the 70 RGHs, which were integrated into a genetic map through linkage analysis. A 1,681-locus cucumber consensus map including 10 gene loci and spanning 730.0 cM in seven linkage groups was developed by integrating three component maps with a bin-mapping strategy. Physically, 308 scaffolds with 193.2 Mbp total DNA sequences were anchored onto this consensus map that covered 52.6% of the 367 Mbp cucumber genome.
Spanish Journal of Agricultural Research, 2018
The cucumber (Cucumis sativus L.) is an important crop worldwide. In the present study, the molecular genetic diversity of 131 Spanish accessions was analyzed using 23 simple sequence repeat (SSRs). Eighteen of these SSRs were polymorphic; the mean number of alleles, mean observed heterozygosity and mean polymorphic information content were 3.2, 0.065 and 0.229, respectively. Seven SSRs showed a polymorphic information content (PIC) ranging from 0.31 to 0.44, therefore they were reasonably informative. Around 60% of the alleles showed a frequency higher than 0.05, and only one allele in the SSR31399 showed a frequency lower than 0.01. In addition, three accession-specific alleles were found. A high proportion of variation among accessions was obtained. In no case all plants of any accession showed the same genotype and only 18 of 131 Spanish accessions had at least two plants with the same genotype. A cluster analysis did not show any relation with morphological types or geographica...
Linkage map of Cucumis melo including phenotypic traits and sequence-characterized genes
Genome, 2003
A new linkage map of Cucumis melo, derived from the F 2 progeny of a cross between PI 414723 and C. melo 'TopMark' is presented. The map spans a total of 1421 cM and includes 179 points consisting of random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP), inter-simple sequence repeats (ISSRs), simple sequence repeats (SSRs), and restriction fragment length polymorphism (RFLP) markers. The map also includes an aphid resistance trait (Vat) and the sex type gene, andromonoecious (a), the two of which are important in resistance breeding and the control of hybrid seed production, as well as a seed-color gene, Wt-2. Most RFLPs represent sequence-characterized cDNA probes from C. melo and Cucumis sativus. These include resistance gene homologues and genes involved in various aspects of plant development and metabolism. A sub-set of our SSR and RFLP markers were also mapped, as part of this study, on additional mapping populations that were published for this species. This provides important reference points ("anchors"), enabling us to identify several linkage groups with respect to other melon maps.
BMC Genomics, 2012
Background: Cucurbita pepo is a member of the Cucurbitaceae family, the second-most important horticultural family in terms of economic importance after Solanaceae. The "summer squash" types, including Zucchini and Scallop, rank among the highest-valued vegetables worldwide. There are few genomic tools available for this species. The first Cucurbita transcriptome, along with a large collection of Single Nucleotide Polymorphisms (SNP), was recently generated using massive sequencing. A set of 384 SNP was selected to generate an Illumina GoldenGate assay in order to construct the first SNP-based genetic map of Cucurbita and map quantitative trait loci (QTL). Results: We herein present the construction of the first SNP-based genetic map of Cucurbita pepo using a population derived from the cross of two varieties with contrasting phenotypes, representing the main cultivar groups of the species' two subspecies: Zucchini (subsp. pepo) × Scallop (subsp. ovifera). The mapping population was genotyped with 384 SNP, a set of selected EST-SNP identified in silico after massive sequencing of the transcriptomes of both parents, using the Illumina GoldenGate platform. The global success rate of the assay was higher than 85%. In total, 304 SNP were mapped, along with 11 SSR from a previous map, giving a map density of 5.56 cM/marker. This map was used to infer syntenic relationships between C. pepo and cucumber and to successfully map QTL that control plant, flowering and fruit traits that are of benefit to squash breeding. The QTL effects were validated in backcross populations.