INVESTIGADORES
LIA Veronica Viviana
artículos
Título:
Identification of Single Nucleotide Polymorphisms and analysis of elite inbred lines using the candidate gene approach
Autor/es:
FUSARI C.; LIA V.V.; HOPP H.E.; HEINZ R.A.; PANIEGO N.
Revista:
BMC Plant Biology
Editorial:
BioMed Central
Referencias:
Año: 2008 vol. 8 p. 7 - 21
ISSN:
1471-2229
Resumen:
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.
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.
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.
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 (è = 0.0056), as expected for inbred
materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 ± 1.88). Modelbased
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 (r2 = 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).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 ± 1.88). Modelbased
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 (r2 = 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).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 ± 1.88). Modelbased
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 (r2 = 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).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
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 (è = 0.0056), as expected for inbred
materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 ± 1.88). Modelbased
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 (r2 = 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).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 ± 1.88). Modelbased
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 (r2 = 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).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 ± 1.88). Modelbased
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 (r2 = 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).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
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 (è = 0.0056), as expected for inbred
materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 ± 1.88). Modelbased
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 (r2 = 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).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 ± 1.88). Modelbased
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 (r2 = 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).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 ± 1.88). Modelbased
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 (r2 = 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).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
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 (è = 0.0056), as expected for inbred
materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 ± 1.88). Modelbased
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 (r2 = 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).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 ± 1.88). Modelbased
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 (r2 = 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).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 ± 1.88). Modelbased
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 (r2 = 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).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
è = 0.0056), as expected for inbred
materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 ± 1.88). Modelbased
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 (r2 = 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).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance).
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).2 = 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.
could be achieved with marker densities lower than those usually reported in the literature.
could be achieved with marker densities lower than those usually reported in the literature.
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.
could be achieved with marker densities lower than those usually reported in the literature.
could be achieved with marker densities lower than those usually reported in the literature.
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.
could be achieved with marker densities lower than those usually reported in the literature.
could be achieved with marker densities lower than those usually reported in the literature.
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.
could be achieved with marker densities lower than those usually reported in the literature.
could be achieved with marker densities lower than those usually reported in the literature.
2~0.1) suggest that high resolution association mapping in sunflower
could be achieved with marker densities lower than those usually reported in the literature.