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Syntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean (Phaseolus vulgaris L.)

Molecular linkage maps are an important tool for gene discovery and cloning, crop improvement, further genetic studies, studies on diversity and evolutionary history, and cross-species comparisons. Linkage maps differ in both the type of marker and type of population used. In this study, gene-based... Full description

Journal Title: Theoretical and applied genetics 2010-07-06, Vol.121 (6), p.1103-1116
Main Author: McConnell, Melody
Other Authors: Mamidi, Sujan , Lee, Rian , Chikara, Shireen , Rossi, Monica , Papa, Roberto , McClean, Phillip
Format: Electronic Article Electronic Article
Language: English
Subjects:
Agricultural research
Agriculture
Arabidopsis thaliana
Arachis - genetics
Arachis hypogaea
Base Sequence
Beans
Biochemistry
Biological and medical sciences
Biomarkers
Biomedical and Life Sciences
Biotechnology
Chromosome Mapping
Classical genetics, quantitative genetics, hybrids
Cloning
Crop yields
Fabaceae - genetics
Fundamental and applied biological sciences. Psychology
general
Genes, Plant
Genetic aspects
Genetic Linkage
Genetic research
Genetics of eukaryotes. Biological and molecular evolution
Genotype
Legumes
Life Sciences
Loteae - genetics
Lotus japonicus
Medicago truncatula
Medicago truncatula - genetics
Methods, theories and miscellaneous
Mimosaceae
Original Paper
Phaseolus - genetics
Phaseolus vulgaris
Plant Biochemistry
Plant Breeding/Biotechnology
Plant Genetics and Genomics
Pteridophyta, spermatophyta
Vegetals
Zea mays
Publisher: Berlin/Heidelberg: Springer-Verlag
ID: ISSN: 0040-5752
Zum Text:
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recordid: cdi_proquest_miscellaneous_755179831
title: Syntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean (Phaseolus vulgaris L.)
format: Article
creator:
  • McConnell, Melody
  • Mamidi, Sujan
  • Lee, Rian
  • Chikara, Shireen
  • Rossi, Monica
  • Papa, Roberto
  • McClean, Phillip
subjects:
  • Agricultural research
  • Agriculture
  • Arabidopsis thaliana
  • Arachis - genetics
  • Arachis hypogaea
  • Base Sequence
  • Beans
  • Biochemistry
  • Biological and medical sciences
  • Biomarkers
  • Biomedical and Life Sciences
  • Biotechnology
  • Chromosome Mapping
  • Classical genetics, quantitative genetics, hybrids
  • Cloning
  • Crop yields
  • Fabaceae - genetics
  • Fundamental and applied biological sciences. Psychology
  • general
  • Genes, Plant
  • Genetic aspects
  • Genetic Linkage
  • Genetic research
  • Genetics of eukaryotes. Biological and molecular evolution
  • Genotype
  • Legumes
  • Life Sciences
  • Loteae - genetics
  • Lotus japonicus
  • Medicago truncatula
  • Medicago truncatula - genetics
  • Methods, theories and miscellaneous
  • Mimosaceae
  • Original Paper
  • Phaseolus - genetics
  • Phaseolus vulgaris
  • Plant Biochemistry
  • Plant Breeding/Biotechnology
  • Plant Genetics and Genomics
  • Pteridophyta, spermatophyta
  • Vegetals
  • Zea mays
ispartof: Theoretical and applied genetics, 2010-07-06, Vol.121 (6), p.1103-1116
description: Molecular linkage maps are an important tool for gene discovery and cloning, crop improvement, further genetic studies, studies on diversity and evolutionary history, and cross-species comparisons. Linkage maps differ in both the type of marker and type of population used. In this study, gene-based markers were used for mapping in a recombinant inbred (RI) population of Phaseolus vulgaris L. P. vulgaris , common dry bean, is an important food source, economic product, and model organism for the legumes. Gene-based markers were developed that corresponded to genes controlling mutant phenotypes in Arabidopsis thaliana , genes undergoing selection during domestication in maize, and genes that function in a biochemical pathway in A. thaliana . Sequence information, including introns and 3′ UTR, was generated for over 550 genes in the two genotypes of P. vulgaris . Over 1,800 single nucleotide polymorphisms and indels were found, 300 of which were screened in the RI population. The resulting LOD 2.0 map is 1,545 cM in length and consists of 275 gene-based and previously mapped core markers. An additional 153 markers that mapped at LOD
language: eng
source:
identifier: ISSN: 0040-5752
fulltext: no_fulltext
issn:
  • 0040-5752
  • 1432-2242
url: Link


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titleSyntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean (Phaseolus vulgaris L.)
creatorMcConnell, Melody ; Mamidi, Sujan ; Lee, Rian ; Chikara, Shireen ; Rossi, Monica ; Papa, Roberto ; McClean, Phillip
creatorcontribMcConnell, Melody ; Mamidi, Sujan ; Lee, Rian ; Chikara, Shireen ; Rossi, Monica ; Papa, Roberto ; McClean, Phillip
descriptionMolecular linkage maps are an important tool for gene discovery and cloning, crop improvement, further genetic studies, studies on diversity and evolutionary history, and cross-species comparisons. Linkage maps differ in both the type of marker and type of population used. In this study, gene-based markers were used for mapping in a recombinant inbred (RI) population of Phaseolus vulgaris L. P. vulgaris , common dry bean, is an important food source, economic product, and model organism for the legumes. Gene-based markers were developed that corresponded to genes controlling mutant phenotypes in Arabidopsis thaliana , genes undergoing selection during domestication in maize, and genes that function in a biochemical pathway in A. thaliana . Sequence information, including introns and 3′ UTR, was generated for over 550 genes in the two genotypes of P. vulgaris . Over 1,800 single nucleotide polymorphisms and indels were found, 300 of which were screened in the RI population. The resulting LOD 2.0 map is 1,545 cM in length and consists of 275 gene-based and previously mapped core markers. An additional 153 markers that mapped at LOD <1.0 were placed in genetic bins. By screening the parents of other mapping populations, it was determined that the markers were useful for other common Mesoamerican × Andean mapping populations. The location of the mapped genes relative to their homologs in Arabidopsis thaliana (At), Medicago truncatula (Mt), and Lotus japonicus (Lj) were determine by using a tblastx analysis with the current pseduochromosome builds for each of the species. While only short blocks of synteny were observed with At, large-scale macrosyntenic blocks were observed with Mt and Lj. By using Mt and Lj as bridging species, the syntenic relationship between the common bean and peanut was inferred.
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languageeng
publisherBerlin/Heidelberg: Springer-Verlag
subjectAgricultural research ; Agriculture ; Arabidopsis thaliana ; Arachis - genetics ; Arachis hypogaea ; Base Sequence ; Beans ; Biochemistry ; Biological and medical sciences ; Biomarkers ; Biomedical and Life Sciences ; Biotechnology ; Chromosome Mapping ; Classical genetics, quantitative genetics, hybrids ; Cloning ; Crop yields ; Fabaceae - genetics ; Fundamental and applied biological sciences. Psychology ; general ; Genes, Plant ; Genetic aspects ; Genetic Linkage ; Genetic research ; Genetics of eukaryotes. Biological and molecular evolution ; Genotype ; Legumes ; Life Sciences ; Loteae - genetics ; Lotus japonicus ; Medicago truncatula ; Medicago truncatula - genetics ; Methods, theories and miscellaneous ; Mimosaceae ; Original Paper ; Phaseolus - genetics ; Phaseolus vulgaris ; Plant Biochemistry ; Plant Breeding/Biotechnology ; Plant Genetics and Genomics ; Pteridophyta, spermatophyta ; Vegetals ; Zea mays
ispartofTheoretical and applied genetics, 2010-07-06, Vol.121 (6), p.1103-1116
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2Lee, Rian
3Chikara, Shireen
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5Papa, Roberto
6McClean, Phillip
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0Syntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean (Phaseolus vulgaris L.)
1Theoretical and applied genetics
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descriptionMolecular linkage maps are an important tool for gene discovery and cloning, crop improvement, further genetic studies, studies on diversity and evolutionary history, and cross-species comparisons. Linkage maps differ in both the type of marker and type of population used. In this study, gene-based markers were used for mapping in a recombinant inbred (RI) population of Phaseolus vulgaris L. P. vulgaris , common dry bean, is an important food source, economic product, and model organism for the legumes. Gene-based markers were developed that corresponded to genes controlling mutant phenotypes in Arabidopsis thaliana , genes undergoing selection during domestication in maize, and genes that function in a biochemical pathway in A. thaliana . Sequence information, including introns and 3′ UTR, was generated for over 550 genes in the two genotypes of P. vulgaris . Over 1,800 single nucleotide polymorphisms and indels were found, 300 of which were screened in the RI population. The resulting LOD 2.0 map is 1,545 cM in length and consists of 275 gene-based and previously mapped core markers. An additional 153 markers that mapped at LOD <1.0 were placed in genetic bins. By screening the parents of other mapping populations, it was determined that the markers were useful for other common Mesoamerican × Andean mapping populations. The location of the mapped genes relative to their homologs in Arabidopsis thaliana (At), Medicago truncatula (Mt), and Lotus japonicus (Lj) were determine by using a tblastx analysis with the current pseduochromosome builds for each of the species. While only short blocks of synteny were observed with At, large-scale macrosyntenic blocks were observed with Mt and Lj. By using Mt and Lj as bridging species, the syntenic relationship between the common bean and peanut was inferred.
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2Arabidopsis thaliana
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4Arachis hypogaea
5Base Sequence
6Beans
7Biochemistry
8Biological and medical sciences
9Biomarkers
10Biomedical and Life Sciences
11Biotechnology
12Chromosome Mapping
13Classical genetics, quantitative genetics, hybrids
14Cloning
15Crop yields
16Fabaceae - genetics
17Fundamental and applied biological sciences. Psychology
18general
19Genes, Plant
20Genetic aspects
21Genetic Linkage
22Genetic research
23Genetics of eukaryotes. Biological and molecular evolution
24Genotype
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26Life Sciences
27Loteae - genetics
28Lotus japonicus
29Medicago truncatula
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36Plant Biochemistry
37Plant Breeding/Biotechnology
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41Zea mays
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titleSyntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean (Phaseolus vulgaris L.)
authorMcConnell, Melody ; Mamidi, Sujan ; Lee, Rian ; Chikara, Shireen ; Rossi, Monica ; Papa, Roberto ; McClean, Phillip
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2Arabidopsis thaliana
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5Base Sequence
6Beans
7Biochemistry
8Biological and medical sciences
9Biomarkers
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13Classical genetics, quantitative genetics, hybrids
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15Crop yields
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39Pteridophyta, spermatophyta
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atitleSyntenic relationships among legumes revealed using a gene-based genetic linkage map of common bean (Phaseolus vulgaris L.)
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abstractMolecular linkage maps are an important tool for gene discovery and cloning, crop improvement, further genetic studies, studies on diversity and evolutionary history, and cross-species comparisons. Linkage maps differ in both the type of marker and type of population used. In this study, gene-based markers were used for mapping in a recombinant inbred (RI) population of Phaseolus vulgaris L. P. vulgaris , common dry bean, is an important food source, economic product, and model organism for the legumes. Gene-based markers were developed that corresponded to genes controlling mutant phenotypes in Arabidopsis thaliana , genes undergoing selection during domestication in maize, and genes that function in a biochemical pathway in A. thaliana . Sequence information, including introns and 3′ UTR, was generated for over 550 genes in the two genotypes of P. vulgaris . Over 1,800 single nucleotide polymorphisms and indels were found, 300 of which were screened in the RI population. The resulting LOD 2.0 map is 1,545 cM in length and consists of 275 gene-based and previously mapped core markers. An additional 153 markers that mapped at LOD <1.0 were placed in genetic bins. By screening the parents of other mapping populations, it was determined that the markers were useful for other common Mesoamerican × Andean mapping populations. The location of the mapped genes relative to their homologs in Arabidopsis thaliana (At), Medicago truncatula (Mt), and Lotus japonicus (Lj) were determine by using a tblastx analysis with the current pseduochromosome builds for each of the species. While only short blocks of synteny were observed with At, large-scale macrosyntenic blocks were observed with Mt and Lj. By using Mt and Lj as bridging species, the syntenic relationship between the common bean and peanut was inferred.
copBerlin/Heidelberg
pubSpringer-Verlag
pmid20607211
doi10.1007/s00122-010-1375-9