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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:
Publisher: Berlin/Heidelberg: Springer-Verlag
ID: ISSN: 0040-5752
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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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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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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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5Base Sequence
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7Biochemistry
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10Biomedical and Life Sciences
11Biotechnology
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13Classical genetics, quantitative genetics, hybrids
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15Crop yields
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17Fundamental and applied biological sciences. Psychology
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19Genes, Plant
20Genetic aspects
21Genetic Linkage
22Genetic research
23Genetics of eukaryotes. Biological and molecular evolution
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28Lotus japonicus
29Medicago truncatula
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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