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Ultrahigh-density linkage map for cultivated cucumber (Cucumis sativus L.) using a single-nucleotide polymorphism genotyping array
Year:
2015
Source of publication :
PLoS ONE
Authors :
Eshed, Ravit
;
.
Katzir, Nurit
;
.
Ophir, Ron
;
.
Rosen, Ada
;
.
Rubinstein, Mor
;
.
Sherman, Amir
;
.
Volume :
10
Co-Authors:
Rubinstein, M., Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center Rishon, Lezion, Israel
Katzenellenbogen, M., Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center Rishon, Lezion, Israel, Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
Eshed, R., Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center Rishon, Lezion, Israel
Rozen, A., Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center Rishon, Lezion, Israel
Katzir, N., Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Newe-Yaar Center, Ramat Yishai, Israel
Colle, M., Plant Breeding, Genetics, Genomics and Biotechnology, Department of Horticulture, Michigan State University, East Lansing, MI, United States
Yang, L., Department of Horticulture, University of Wisconsin, Madison, WI, United States
Grumet, R., Plant Breeding, Genetics, Genomics and Biotechnology, Department of Horticulture, Michigan State University, East Lansing, MI, United States
Weng, Y., Department of Horticulture, University of Wisconsin, Madison, WI, United States, United States Department of Agriculture (USDA)-ARS, Vegetable Crops Research Unit, Madison, WI, United States
Sherman, A., Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center Rishon, Lezion, Israel
Ophir, R., Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center Rishon, Lezion, Israel
Facilitators :
From page:
To page:
(
Total pages:
1
)
Abstract:
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/F1 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 R2 = 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/F1 hybridizations as a training set, should be a powerful tool in future studies with high-throughput cucumber genotyping. An ultrahigh-density linkage map constructed by this genotyping array on RIL population may be invaluable for assembly improvement, and for mapping important cucumber QTLs.
Note:
Related Files :
chromosome mapping
genetic recombination
Genetics
hybridization
phenotype
Show More
Related Content
More details
DOI :
10.1371/journal.pone.0124101
Article number:
Affiliations:
Database:
Scopus
Publication Type:
article
;
.
Language:
English
Editors' remarks:
ID:
31253
Last updated date:
02/03/2022 17:27
Creation date:
17/04/2018 01:01
Scientific Publication
Ultrahigh-density linkage map for cultivated cucumber (Cucumis sativus L.) using a single-nucleotide polymorphism genotyping array
10
Rubinstein, M., Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center Rishon, Lezion, Israel
Katzenellenbogen, M., Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center Rishon, Lezion, Israel, Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, Rehovot, Israel
Eshed, R., Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center Rishon, Lezion, Israel
Rozen, A., Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center Rishon, Lezion, Israel
Katzir, N., Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Newe-Yaar Center, Ramat Yishai, Israel
Colle, M., Plant Breeding, Genetics, Genomics and Biotechnology, Department of Horticulture, Michigan State University, East Lansing, MI, United States
Yang, L., Department of Horticulture, University of Wisconsin, Madison, WI, United States
Grumet, R., Plant Breeding, Genetics, Genomics and Biotechnology, Department of Horticulture, Michigan State University, East Lansing, MI, United States
Weng, Y., Department of Horticulture, University of Wisconsin, Madison, WI, United States, United States Department of Agriculture (USDA)-ARS, Vegetable Crops Research Unit, Madison, WI, United States
Sherman, A., Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center Rishon, Lezion, Israel
Ophir, R., Department of Fruit Trees Sciences, Institute of Plant Sciences, Agricultural Research Organization, Volcani Center Rishon, Lezion, Israel
Ultrahigh-density linkage map for cultivated cucumber (Cucumis sativus L.) using a single-nucleotide polymorphism genotyping array
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/F1 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 R2 = 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/F1 hybridizations as a training set, should be a powerful tool in future studies with high-throughput cucumber genotyping. An ultrahigh-density linkage map constructed by this genotyping array on RIL population may be invaluable for assembly improvement, and for mapping important cucumber QTLs.
Scientific Publication
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