Identification of Single Nucleotide Polymorphisms and analysis of Linkage Disequilibrium in sunflower elite inbred lines using the candidate gene approach

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Background. Association analysis is a powerful tool to identify gene loci that may contribute to phenotypic variation. This includes the estimation of nucleotide diversity, the assessment of linkage disequilibrium structure (LD) and the evaluation of selection processes. Trait mapping by allele asso...

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Autores principales: Fusari, C.M., Lia, V.V., Hopp, H.E., Heinz, R.A., Paniego, N.B.
Formato: Artículo publishedVersion
Publicado: 2008
Materias:
Helianthus
primer DNA
article
breeding
gene linkage disequilibrium
genetics
polymerase chain reaction
single nucleotide polymorphism
sunflower
Breeding
DNA Primers
Linkage Disequilibrium
Polymerase Chain Reaction
Polymorphism, Single Nucleotide
Acceso en línea:http://hdl.handle.net/20.500.12110/paper_14712229_v8_n_p_Fusari
https://repositoriouba.sisbi.uba.ar/gsdl/cgi-bin/library.cgi?a=d&c=artiaex&d=paper_14712229_v8_n_p_Fusari_oai
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spelling I28-R145-paper_14712229_v8_n_p_Fusari_oai2024-08-16 Fusari, C.M. Lia, V.V. Hopp, H.E. Heinz, R.A. Paniego, N.B. 2008 Background. Association analysis is a powerful tool to identify gene loci that may contribute to phenotypic variation. This includes the estimation of nucleotide diversity, the assessment of linkage disequilibrium structure (LD) and the evaluation of selection processes. Trait mapping by allele association requires a high-density map, which could be obtained by the addition of Single Nucleotide Polymorphisms (SNPs) and short insertion and/or deletions (indels) to SSR and AFLP genetic maps. Nucleotide diversity analysis of randomly selected candidate regions is a promising approach for the success of association analysis and fine mapping in the sunflower genome. Moreover, knowledge of the distance over which LD persists, in agronomically meaningful sunflower accessions, is important to establish the density of markers and the experimental design for association analysis. Results. A set of 28 candidate genes related to biotic and abiotic stresses were studied in 19 sunflower inbred lines. A total of 14,348 bp of sequence alignment was analyzed per individual. In average, 1 SNP was found per 69 nucleotides and 38 indels were identified in the complete data set. The mean nucleotide polymorphism was moderate ( = 0.0056), as expected for inbred materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 1.88). Model-based population structure analysis allowed detection of admixed individuals within the set of accessions examined. Two putative gene pools were identified (G1 and G2), with a large proportion of the inbred lines being assigned to one of them (G1). Consistent with the absence of population sub-structuring, LD for G1 decayed more rapidly (r 2= 0.48 at 643 bp; trend line, pooled data) than the LD trend line for the entire set of 19 individuals (r2= 0.64 for the same distance). Conclusion. Knowledge about the patterns of diversity and the genetic relationships between breeding materials could be an invaluable aid in crop improvement strategies. The relatively high frequency of SNPs within the elite inbred lines studied here, along with the predicted extent of LD over distances of 100 kbp (r2∼0.1) suggest that high resolution association mapping in sunflower could be achieved with marker densities lower than those usually reported in the literature. Fil:Fusari, C.M. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Lia, V.V. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Hopp, H.E. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Fil:Heinz, R.A. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. application/pdf http://hdl.handle.net/20.500.12110/paper_14712229_v8_n_p_Fusari info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by/2.5/ar BMC Plant Biol. 2008;8 Helianthus primer DNA article breeding gene linkage disequilibrium genetics polymerase chain reaction single nucleotide polymorphism sunflower Breeding DNA Primers Helianthus Linkage Disequilibrium Polymerase Chain Reaction Polymorphism, Single Nucleotide Identification of Single Nucleotide Polymorphisms and analysis of Linkage Disequilibrium in sunflower elite inbred lines using the candidate gene approach info:eu-repo/semantics/article info:ar-repo/semantics/artículo info:eu-repo/semantics/publishedVersion https://repositoriouba.sisbi.uba.ar/gsdl/cgi-bin/library.cgi?a=d&c=artiaex&d=paper_14712229_v8_n_p_Fusari_oai
institution Universidad de Buenos Aires
institution_str I-28
repository_str R-145
collection Repositorio Digital de la Universidad de Buenos Aires (UBA)
topic Helianthus
primer DNA
article
breeding
gene linkage disequilibrium
genetics
polymerase chain reaction
single nucleotide polymorphism
sunflower
Breeding
DNA Primers
Helianthus
Linkage Disequilibrium
Polymerase Chain Reaction
Polymorphism, Single Nucleotide
spellingShingle Helianthus
primer DNA
article
breeding
gene linkage disequilibrium
genetics
polymerase chain reaction
single nucleotide polymorphism
sunflower
Breeding
DNA Primers
Helianthus
Linkage Disequilibrium
Polymerase Chain Reaction
Polymorphism, Single Nucleotide
Fusari, C.M.
Lia, V.V.
Hopp, H.E.
Heinz, R.A.
Paniego, N.B.
Identification of Single Nucleotide Polymorphisms and analysis of Linkage Disequilibrium in sunflower elite inbred lines using the candidate gene approach
topic_facet Helianthus
primer DNA
article
breeding
gene linkage disequilibrium
genetics
polymerase chain reaction
single nucleotide polymorphism
sunflower
Breeding
DNA Primers
Helianthus
Linkage Disequilibrium
Polymerase Chain Reaction
Polymorphism, Single Nucleotide
description Background. Association analysis is a powerful tool to identify gene loci that may contribute to phenotypic variation. This includes the estimation of nucleotide diversity, the assessment of linkage disequilibrium structure (LD) and the evaluation of selection processes. Trait mapping by allele association requires a high-density map, which could be obtained by the addition of Single Nucleotide Polymorphisms (SNPs) and short insertion and/or deletions (indels) to SSR and AFLP genetic maps. Nucleotide diversity analysis of randomly selected candidate regions is a promising approach for the success of association analysis and fine mapping in the sunflower genome. Moreover, knowledge of the distance over which LD persists, in agronomically meaningful sunflower accessions, is important to establish the density of markers and the experimental design for association analysis. Results. A set of 28 candidate genes related to biotic and abiotic stresses were studied in 19 sunflower inbred lines. A total of 14,348 bp of sequence alignment was analyzed per individual. In average, 1 SNP was found per 69 nucleotides and 38 indels were identified in the complete data set. The mean nucleotide polymorphism was moderate ( = 0.0056), as expected for inbred materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 1.88). Model-based population structure analysis allowed detection of admixed individuals within the set of accessions examined. Two putative gene pools were identified (G1 and G2), with a large proportion of the inbred lines being assigned to one of them (G1). Consistent with the absence of population sub-structuring, LD for G1 decayed more rapidly (r 2= 0.48 at 643 bp; trend line, pooled data) than the LD trend line for the entire set of 19 individuals (r2= 0.64 for the same distance). Conclusion. Knowledge about the patterns of diversity and the genetic relationships between breeding materials could be an invaluable aid in crop improvement strategies. The relatively high frequency of SNPs within the elite inbred lines studied here, along with the predicted extent of LD over distances of 100 kbp (r2∼0.1) suggest that high resolution association mapping in sunflower could be achieved with marker densities lower than those usually reported in the literature.
format Artículo
Artículo
publishedVersion
author Fusari, C.M.
Lia, V.V.
Hopp, H.E.
Heinz, R.A.
Paniego, N.B.
author_facet Fusari, C.M.
Lia, V.V.
Hopp, H.E.
Heinz, R.A.
Paniego, N.B.
author_sort Fusari, C.M.
title Identification of Single Nucleotide Polymorphisms and analysis of Linkage Disequilibrium in sunflower elite inbred lines using the candidate gene approach
title_short Identification of Single Nucleotide Polymorphisms and analysis of Linkage Disequilibrium in sunflower elite inbred lines using the candidate gene approach
title_full Identification of Single Nucleotide Polymorphisms and analysis of Linkage Disequilibrium in sunflower elite inbred lines using the candidate gene approach
title_fullStr Identification of Single Nucleotide Polymorphisms and analysis of Linkage Disequilibrium in sunflower elite inbred lines using the candidate gene approach
title_full_unstemmed Identification of Single Nucleotide Polymorphisms and analysis of Linkage Disequilibrium in sunflower elite inbred lines using the candidate gene approach
title_sort identification of single nucleotide polymorphisms and analysis of linkage disequilibrium in sunflower elite inbred lines using the candidate gene approach
publishDate 2008
url http://hdl.handle.net/20.500.12110/paper_14712229_v8_n_p_Fusari
https://repositoriouba.sisbi.uba.ar/gsdl/cgi-bin/library.cgi?a=d&c=artiaex&d=paper_14712229_v8_n_p_Fusari_oai
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