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Effects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data

The capability of molecular markers to provide information of genetic structure is influenced by their number and the way they are chosen. This study evaluates the effects of single nucleotide polymorphism (SNP) number and selection strategy on estimates of germplasm diversity and population structu... Full description

Journal Title: Theoretical and applied genetics 2010-02-16, Vol.120 (8), p.1525-1534
Main Author: Moragues, M
Other Authors: Comadran, J , Waugh, R , Milne, I , Flavell, A. J , Russell, Joanne R
Format: Electronic Article Electronic Article
Language: English
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Publisher: Berlin/Heidelberg: Springer-Verlag
ID: ISSN: 0040-5752
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title: Effects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data
format: Article
creator:
  • Moragues, M
  • Comadran, J
  • Waugh, R
  • Milne, I
  • Flavell, A. J
  • Russell, Joanne R
subjects:
  • Agriculture
  • Algorithms
  • Barley
  • Biochemistry
  • Biological and medical sciences
  • Biological diversity
  • Biomedical and Life Sciences
  • Biotechnology
  • Classical genetics, quantitative genetics, hybrids
  • Expressed Sequence Tags
  • Fundamental and applied biological sciences. Psychology
  • general
  • Genes, Plant
  • Genetic aspects
  • Genetic Markers
  • Genetic research
  • Genetic Variation
  • Genetics of eukaryotes. Biological and molecular evolution
  • Genome, Plant
  • Genomic structural variations
  • Genotype
  • Hordeum - genetics
  • Hordeum vulgare
  • Life Sciences
  • Models, Genetic
  • Models, Statistical
  • Original Paper
  • Physiological aspects
  • Plant Biochemistry
  • Plant Breeding/Biotechnology
  • Plant genetics
  • Plant Genetics and Genomics
  • Polymorphism, Single Nucleotide
  • Pteridophyta, spermatophyta
  • Sequence Analysis, DNA
  • Single nucleotide polymorphisms
  • Species Specificity
  • Vegetals
ispartof: Theoretical and applied genetics, 2010-02-16, Vol.120 (8), p.1525-1534
description: The capability of molecular markers to provide information of genetic structure is influenced by their number and the way they are chosen. This study evaluates the effects of single nucleotide polymorphism (SNP) number and selection strategy on estimates of germplasm diversity and population structure for different types of barley germplasm, namely cultivar and landrace. One hundred and sixty-nine barley landraces from Syria and Jordan and 171 European barley cultivars were genotyped with 1536 SNPs. Different subsets of 384 and 96 SNPs were selected from the 1536 set, based on their ability to detect diversity in landraces or cultivated barley in addition to corresponding randomly chosen subsets. All SNP sets except the landrace-optimised subsets underestimated the diversity present in the landrace germplasm, and all subsets of SNP gave similar estimates for cultivar germplasm. All marker subsets gave qualitatively similar estimates of the population structure in both germplasm sets, but the 96 SNP sets showed much lower data resolution values than the larger SNP sets. From these data we deduce that pre-selecting markers for their diversity in a germplasm set is very worthwhile in terms of the quality of data obtained. Second, we suggest that a properly chosen 384 SNP subset gives a good combination of power and economy for germplasm characterization, whereas the rather modest gain from using 1536 SNPs does not justify the increased cost and 96 markers give unacceptably low performance. Lastly, we propose a specific 384 SNP subset as a standard genotyping tool for middle-eastern landrace barley.
language: eng
source:
identifier: ISSN: 0040-5752
fulltext: no_fulltext
issn:
  • 0040-5752
  • 1432-2242
url: Link


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titleEffects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data
creatorMoragues, M ; Comadran, J ; Waugh, R ; Milne, I ; Flavell, A. J ; Russell, Joanne R
creatorcontribMoragues, M ; Comadran, J ; Waugh, R ; Milne, I ; Flavell, A. J ; Russell, Joanne R
descriptionThe capability of molecular markers to provide information of genetic structure is influenced by their number and the way they are chosen. This study evaluates the effects of single nucleotide polymorphism (SNP) number and selection strategy on estimates of germplasm diversity and population structure for different types of barley germplasm, namely cultivar and landrace. One hundred and sixty-nine barley landraces from Syria and Jordan and 171 European barley cultivars were genotyped with 1536 SNPs. Different subsets of 384 and 96 SNPs were selected from the 1536 set, based on their ability to detect diversity in landraces or cultivated barley in addition to corresponding randomly chosen subsets. All SNP sets except the landrace-optimised subsets underestimated the diversity present in the landrace germplasm, and all subsets of SNP gave similar estimates for cultivar germplasm. All marker subsets gave qualitatively similar estimates of the population structure in both germplasm sets, but the 96 SNP sets showed much lower data resolution values than the larger SNP sets. From these data we deduce that pre-selecting markers for their diversity in a germplasm set is very worthwhile in terms of the quality of data obtained. Second, we suggest that a properly chosen 384 SNP subset gives a good combination of power and economy for germplasm characterization, whereas the rather modest gain from using 1536 SNPs does not justify the increased cost and 96 markers give unacceptably low performance. Lastly, we propose a specific 384 SNP subset as a standard genotyping tool for middle-eastern landrace barley.
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subjectAgriculture ; Algorithms ; Barley ; Biochemistry ; Biological and medical sciences ; Biological diversity ; Biomedical and Life Sciences ; Biotechnology ; Classical genetics, quantitative genetics, hybrids ; Expressed Sequence Tags ; Fundamental and applied biological sciences. Psychology ; general ; Genes, Plant ; Genetic aspects ; Genetic Markers ; Genetic research ; Genetic Variation ; Genetics of eukaryotes. Biological and molecular evolution ; Genome, Plant ; Genomic structural variations ; Genotype ; Hordeum - genetics ; Hordeum vulgare ; Life Sciences ; Models, Genetic ; Models, Statistical ; Original Paper ; Physiological aspects ; Plant Biochemistry ; Plant Breeding/Biotechnology ; Plant genetics ; Plant Genetics and Genomics ; Polymorphism, Single Nucleotide ; Pteridophyta, spermatophyta ; Sequence Analysis, DNA ; Single nucleotide polymorphisms ; Species Specificity ; Vegetals
ispartofTheoretical and applied genetics, 2010-02-16, Vol.120 (8), p.1525-1534
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descriptionThe capability of molecular markers to provide information of genetic structure is influenced by their number and the way they are chosen. This study evaluates the effects of single nucleotide polymorphism (SNP) number and selection strategy on estimates of germplasm diversity and population structure for different types of barley germplasm, namely cultivar and landrace. One hundred and sixty-nine barley landraces from Syria and Jordan and 171 European barley cultivars were genotyped with 1536 SNPs. Different subsets of 384 and 96 SNPs were selected from the 1536 set, based on their ability to detect diversity in landraces or cultivated barley in addition to corresponding randomly chosen subsets. All SNP sets except the landrace-optimised subsets underestimated the diversity present in the landrace germplasm, and all subsets of SNP gave similar estimates for cultivar germplasm. All marker subsets gave qualitatively similar estimates of the population structure in both germplasm sets, but the 96 SNP sets showed much lower data resolution values than the larger SNP sets. From these data we deduce that pre-selecting markers for their diversity in a germplasm set is very worthwhile in terms of the quality of data obtained. Second, we suggest that a properly chosen 384 SNP subset gives a good combination of power and economy for germplasm characterization, whereas the rather modest gain from using 1536 SNPs does not justify the increased cost and 96 markers give unacceptably low performance. Lastly, we propose a specific 384 SNP subset as a standard genotyping tool for middle-eastern landrace barley.
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0Agriculture
1Algorithms
2Barley
3Biochemistry
4Biological and medical sciences
5Biological diversity
6Biomedical and Life Sciences
7Biotechnology
8Classical genetics, quantitative genetics, hybrids
9Expressed Sequence Tags
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13Genetic aspects
14Genetic Markers
15Genetic research
16Genetic Variation
17Genetics of eukaryotes. Biological and molecular evolution
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19Genomic structural variations
20Genotype
21Hordeum - genetics
22Hordeum vulgare
23Life Sciences
24Models, Genetic
25Models, Statistical
26Original Paper
27Physiological aspects
28Plant Biochemistry
29Plant Breeding/Biotechnology
30Plant genetics
31Plant Genetics and Genomics
32Polymorphism, Single Nucleotide
33Pteridophyta, spermatophyta
34Sequence Analysis, DNA
35Single nucleotide polymorphisms
36Species Specificity
37Vegetals
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abstractThe capability of molecular markers to provide information of genetic structure is influenced by their number and the way they are chosen. This study evaluates the effects of single nucleotide polymorphism (SNP) number and selection strategy on estimates of germplasm diversity and population structure for different types of barley germplasm, namely cultivar and landrace. One hundred and sixty-nine barley landraces from Syria and Jordan and 171 European barley cultivars were genotyped with 1536 SNPs. Different subsets of 384 and 96 SNPs were selected from the 1536 set, based on their ability to detect diversity in landraces or cultivated barley in addition to corresponding randomly chosen subsets. All SNP sets except the landrace-optimised subsets underestimated the diversity present in the landrace germplasm, and all subsets of SNP gave similar estimates for cultivar germplasm. All marker subsets gave qualitatively similar estimates of the population structure in both germplasm sets, but the 96 SNP sets showed much lower data resolution values than the larger SNP sets. From these data we deduce that pre-selecting markers for their diversity in a germplasm set is very worthwhile in terms of the quality of data obtained. Second, we suggest that a properly chosen 384 SNP subset gives a good combination of power and economy for germplasm characterization, whereas the rather modest gain from using 1536 SNPs does not justify the increased cost and 96 markers give unacceptably low performance. Lastly, we propose a specific 384 SNP subset as a standard genotyping tool for middle-eastern landrace barley.
copBerlin/Heidelberg
pubSpringer-Verlag
pmid20157694
doi10.1007/s00122-010-1273-1