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Outi Savolainen - One of the best experts on this subject based on the ideXlab platform.
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search for Nucleotide Diversity patterns of local adaptation in dehydrins and other cold related candidate genes in scots pine pinus sylvestris l
Tree Genetics & Genomes, 2009Co-Authors: Witold Wachowiak, Peter A Balk, Outi SavolainenAbstract:Nucleotide variation at several cold candidate genes including seven members of the dehydrin gene family was surveyed in haplotypes of Scots pine (Pinus sylvestris) sampled in populations showing divergence for cold tolerance in Europe. Patterns of Nucleotide Diversity, linkage disequilibrium, and frequency spectrum of alleles were compared between north and south populations to search for signs of directional selection potentially underlying adaptation to cold. Significant differentiation between populations in allelic frequency or haplotype structure was detected at dhn1, dhn3, and abaH loci. Allelic dimorphism with no evidence of haplotype clustering by geographical distribution was found at dhn9. An excess of fixed non-synonymous mutations as compared to the outgroup P. pinaster pine species was found at dhn1. Differences in Nucleotide polymorphisms were found between the members of the Kn class of dehydrin upregulated during cold acclimation (average πsil = 0.004) as compared to the SKn class (average πsil = 0.024). The multilocus Nucleotide Diversity at silent sites (θ W = 0.009) was moderate compared to other conifer species, but higher than previous estimates for Scots pine. There was an excess of rare and high frequency derived variants as revealed by significantly negative multilocus value of Tajima’s D (D = −0.72, P < 0.01) and negative mean value of Fay and Wu H statistics (H = −0.50). The level of linkage disequilibrium decayed rapidly with an average expected r 2 of 0.2 at about 200 bp. Overall, there was a positive correlation between polymorphism and divergence at ten loci when outgroup sequence was available. The discovered polymorphism will be used for further evaluation of the adaptive role of genes through association mapping studies.
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demographic history has influenced Nucleotide Diversity in european pinus sylvestris populations
Genetics, 2007Co-Authors: Tanja Pyhajarvi, Rosario M Garciagil, Timo Knurr, Merja Mikkonen, Witold Wachowiak, Outi SavolainenAbstract:To infer the role of natural selection in shaping standing genetic Diversity, it is necessary to assess the genomewide impact of demographic history on Nucleotide Diversity. In this study we analyzed sequence Diversity of 16 nuclear loci in eight Pinus sylvestris populations. Populations were divided into four geographical groups on the basis of their current location and the geographical history of the region: northern Europe, central Europe, Spain, and Turkey. There were no among-group differences in the level of silent Nucleotide Diversity, which was ∼0.005/bp in all groups. There was some evidence that linkage disequilibrium extended further in northern Europe than in central Europe: the estimates of the population recombination rate parameter, ρ, were 0.0064 and 0.0294, respectively. The summary statistics of Nucleotide Diversity in central and northern European populations were compatible with an ancient bottleneck rather than the standard neutral model.
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low Nucleotide Diversity at the pal1 locus in the widely distributed pinus sylvestris
Molecular Biology and Evolution, 2002Co-Authors: Volodymyr Dvornyk, Merja Mikkonen, Anu Sirvio, Outi SavolainenAbstract:Nucleotide polymorphism in Scots pine (Pinus sylvestris) was studied in the gene encoding phenylalanine ammonia-lyase (Pal, EC 4.3.1.5). Scots pine, like many other pine species, has a large current population size. The observed levels of inbreeding depression suggest that Scots pine may have a high mutation rate to deleterious alleles. Many Scots pine markers such as isozymes, RFLPs, and microsatellites are highly variable. These observations suggest that the levels of Nucleotide variation should be higher than those in other plant species. A 2,045-bp fragment of the pal1 locus was sequenced from five megagametophytes each from a different individual from each of four populations, from northern and southern Finland, central Russia, and northern Spain. There were 12 segregating sites in the locus. The synonymous site overall Nucleotide Diversity was only 0.0049. In order to compare pal1 with other pine genes, sequence was obtained from two alleles of 11 other loci (total length 4,606 bp). For these, the synonymous Nucleotide Diversity was 0.0056. These estimates are lower than those from other plants. This is most likely because of a low mutation rate, as estimated from between-pine species synonymous site divergence. In other respects, Scots pine has the characteristics of a species with a large effective population. There was no linkage disequilibrium even between closely linked sites. This resulted in high haplotype Diversity (14 different haplotypes among 20 sequences). This could also give rise to high per locus Diversity at the protein level. Divergence between populations in the main range was low, whereas an isolated Spanish population had slightly lower Diversity and higher divergence than the remaining populations.
Leif Andersson - One of the best experts on this subject based on the ideXlab platform.
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moderate Nucleotide Diversity in the atlantic herring is associated with a low mutation rate
eLife, 2017Co-Authors: Chungang Feng, Nima Rafati, Mats E. Pettersson, Sangeet Lamichhaney, Carljohan Rubin, Leif Andersson, Michele Casini, Arild FolkvordAbstract:The Atlantic herring is one of the most abundant vertebrates on earth but its Nucleotide Diversity is moderate (π = 0.3%), only three-fold higher than in human. Here, we present a pedigree-based estimation of the mutation rate in this species. Based on whole-genome sequencing of four parents and 12 offspring, the estimated mutation rate is 2.0 × 10-9 per base per generation. We observed a high degree of parental mosaicism indicating that a large fraction of these de novo mutations occurred during early germ cell development. The estimated mutation rate - the lowest among vertebrates analyzed to date - partially explains the discrepancy between the rather low Nucleotide Diversity in herring and its huge census population size. But a species like the herring will never reach its expected Nucleotide Diversity because of fluctuations in population size over the millions of years it takes to build up high Nucleotide Diversity.
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moderate Nucleotide Diversity in the atlantic herring is associated with a low mutation rate
bioRxiv, 2017Co-Authors: Chungang Feng, Nima Rafati, Mats E. Pettersson, Sangeet Lamichhaney, Carljohan Rubin, Michele Casini, Arild Folkvord, Leif AnderssonAbstract:The Atlantic herring (Clupea harengus) is one of the most abundant vertebrates on earth but its Nucleotide Diversity is moderate (π=0.3%), only three-fold higher than in human. The expected Nucleotide Diversity for selectively neutral alleles is a function of population size and the mutation rate, and it is strongly affected by demographic history. Here, we present a pedigree-based estimation of the mutation rate in the Atlantic herring. Based on whole-genome sequencing of four parents and 12 offspring, the estimated mutation rate is 1.7 x 10-9 per base per generation. There was no significant difference in the frequency of paternal and maternal mutations (8 and 7, respectively). Furthermore, we observed a high degree of parental mosaicism indicating that a large fraction of these de novo mutations occurred during early germ cell development when we do not expect a strong gender effect. The now estimated mutation rate — the lowest among vertebrates analyzed to date — partially explains the discrepancy between the rather low Nucleotide Diversity in herring and its huge census population size (>10^11). But our analysis indicates that a species like the herring will never reach its expected Nucleotide Diversity for selectively neutral alleles primarily because of fluctuations in population size due to climate variation during the millions of years it takes to build up a high Nucleotide Diversity. In addition, background selection and selective sweeps lead to reductions in Nucleotide Diversity at linked neutral sites.
Harold Corke - One of the best experts on this subject based on the ideXlab platform.
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Nucleotide Diversity in starch synthase iia and validation of single Nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice oryza sativa l
Theoretical and Applied Genetics, 2006Co-Authors: Harold CorkeAbstract:The characteristics of starch, such as gelatinization temperature (GT), apparent amylose content (AAC), pasting temperature (PT) and other physicochemical properties, determine the quality of various products of rice, e.g., eating, cooking and processing qualities. The GT of rice flour is controlled by the alk locus, which has been co-mapped to the starch synthase IIa (SSIIa) locus. In this study, we sequenced a 2,051 bp DNA fragment spanning part of intron 6, exon 7, intron 7, exon 8 and part of 3′ untranslated region of SSIIa for 30 rice varieties with diverse geographical distribution and variation in starch physicochemical properties. A total of 24 single Nucleotide polymorphisms (SNPs) and one insertion/deletion (InDel) were identified, which could be classified into nine haplotypes. The mean pairwise Nucleotide Diversity π was 0.00292, and Watterson’s estimator θ was 0.00296 in this collection of rice germplasm. Tajima’s D test for selection showed no significant deviation from the neutral expectation (D = − 0.04612, P > 0.10). However, significant associations were found between seven of the SNPs and peak GT (T p) at P < 0.05, of which two contiguous SNPs (GC/TT) showed a very strong association with T p (P < 0.0001). With some rare exception, this GC/TT polymorphism alone can differentiate rice varieties with high or intermediate GT (possessing the GC allele) from those with low GT (possessing the TT allele). In contrast, none of these SNPs or InDel was significantly associated with amylose content. A further 509 rice varieties with known physicochemical properties (e.g., AAC and PT) and known alleles of other starch synthesizing genes were genotyped for the SSIIa GC/TT alleles. Association analysis indicated that 82% of the total variation of AAC in these samples could be explained by a (CT)n simple sequence repeat (SSR) and a G/T SNP of Waxy gene (Wx), and 62.4% of the total variation of PT could be explained by the GC/TT polymorphism. An additional association analysis was performed between these molecular markers and the thermal and retrogradation properties for a subset of 245 samples from the 509 rice varieties. The SSIIa GC/TT polymorphism explained more than 60% of the total variation in thermal properties, whereas the SSR and SNP of Wx gene explained as much as the SSIIa GC/TT of the total variation in retrogradation properties. Our study provides further support for the utilization of the GC/TT polymorphism in SSIIa. As shown in our study of 509 rice varieties, the GC/TT SNP could differentiate rice with high or intermediate GT from those with low GT in about 90% of cases. Using four primers in a single PCR reaction, the GC/TT polymorphism can be surveyed on a large scale. Thus, this SNP polymorphism can be very useful in marker-assisted selection for the improvement of GT and other physicochemical properties of rice.
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Nucleotide Diversity in starch synthase iia and validation of single Nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice oryza sativa l
Theoretical and Applied Genetics, 2006Co-Authors: Harold Corke, Jinsong Bao, Mei SunAbstract:The characteristics of starch, such as gelatinization temperature (GT), apparent amylose content (AAC), pasting temperature (PT) and other physicochemical properties, determine the quality of various products of rice, e.g., eating, cooking and processing qualities. The GT of rice flour is controlled by the alk locus, which has been co-mapped to the starch synthase IIa (SSIIa) locus. In this study, we sequenced a 2,051 bp DNA fragment spanning part of intron 6, exon 7, intron 7, exon 8 and part of 3' untranslated region of SSIIa for 30 rice varieties with diverse geographical distribution and variation in starch physicochemical properties. A total of 24 single Nucleotide polymorphisms (SNPs) and one insertion/deletion (InDel) were identified, which could be classified into nine haplotypes. The mean pairwise Nucleotide Diversity pi was 0.00292, and Watterson's estimator theta was 0.00296 in this collection of rice germplasm. Tajima's D test for selection showed no significant deviation from the neutral expectation (D = - 0.04612, P > 0.10). However, significant associations were found between seven of the SNPs and peak GT (T (p)) at P < 0.05, of which two contiguous SNPs (GC/TT) showed a very strong association with T (p) (P < 0.0001). With some rare exception, this GC/TT polymorphism alone can differentiate rice varieties with high or intermediate GT (possessing the GC allele) from those with low GT (possessing the TT allele). In contrast, none of these SNPs or InDel was significantly associated with amylose content. A further 509 rice varieties with known physicochemical properties (e.g., AAC and PT) and known alleles of other starch synthesizing genes were genotyped for the SSIIa GC/TT alleles. Association analysis indicated that 82% of the total variation of AAC in these samples could be explained by a (CT)n simple sequence repeat (SSR) and a G/T SNP of Waxy gene (Wx), and 62.4% of the total variation of PT could be explained by the GC/TT polymorphism. An additional association analysis was performed between these molecular markers and the thermal and retrogradation properties for a subset of 245 samples from the 509 rice varieties. The SSIIa GC/TT polymorphism explained more than 60% of the total variation in thermal properties, whereas the SSR and SNP of Wx gene explained as much as the SSIIa GC/TT of the total variation in retrogradation properties. Our study provides further support for the utilization of the GC/TT polymorphism in SSIIa. As shown in our study of 509 rice varieties, the GC/TT SNP could differentiate rice with high or intermediate GT from those with low GT in about 90% of cases. Using four primers in a single PCR reaction, the GC/TT polymorphism can be surveyed on a large scale. Thus, this SNP polymorphism can be very useful in marker-assisted selection for the improvement of GT and other physicochemical properties of rice.
Witold Wachowiak - One of the best experts on this subject based on the ideXlab platform.
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search for Nucleotide Diversity patterns of local adaptation in dehydrins and other cold related candidate genes in scots pine pinus sylvestris l
Tree Genetics & Genomes, 2009Co-Authors: Witold Wachowiak, Peter A Balk, Outi SavolainenAbstract:Nucleotide variation at several cold candidate genes including seven members of the dehydrin gene family was surveyed in haplotypes of Scots pine (Pinus sylvestris) sampled in populations showing divergence for cold tolerance in Europe. Patterns of Nucleotide Diversity, linkage disequilibrium, and frequency spectrum of alleles were compared between north and south populations to search for signs of directional selection potentially underlying adaptation to cold. Significant differentiation between populations in allelic frequency or haplotype structure was detected at dhn1, dhn3, and abaH loci. Allelic dimorphism with no evidence of haplotype clustering by geographical distribution was found at dhn9. An excess of fixed non-synonymous mutations as compared to the outgroup P. pinaster pine species was found at dhn1. Differences in Nucleotide polymorphisms were found between the members of the Kn class of dehydrin upregulated during cold acclimation (average πsil = 0.004) as compared to the SKn class (average πsil = 0.024). The multilocus Nucleotide Diversity at silent sites (θ W = 0.009) was moderate compared to other conifer species, but higher than previous estimates for Scots pine. There was an excess of rare and high frequency derived variants as revealed by significantly negative multilocus value of Tajima’s D (D = −0.72, P < 0.01) and negative mean value of Fay and Wu H statistics (H = −0.50). The level of linkage disequilibrium decayed rapidly with an average expected r 2 of 0.2 at about 200 bp. Overall, there was a positive correlation between polymorphism and divergence at ten loci when outgroup sequence was available. The discovered polymorphism will be used for further evaluation of the adaptive role of genes through association mapping studies.
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demographic history has influenced Nucleotide Diversity in european pinus sylvestris populations
Genetics, 2007Co-Authors: Tanja Pyhajarvi, Rosario M Garciagil, Timo Knurr, Merja Mikkonen, Witold Wachowiak, Outi SavolainenAbstract:To infer the role of natural selection in shaping standing genetic Diversity, it is necessary to assess the genomewide impact of demographic history on Nucleotide Diversity. In this study we analyzed sequence Diversity of 16 nuclear loci in eight Pinus sylvestris populations. Populations were divided into four geographical groups on the basis of their current location and the geographical history of the region: northern Europe, central Europe, Spain, and Turkey. There were no among-group differences in the level of silent Nucleotide Diversity, which was ∼0.005/bp in all groups. There was some evidence that linkage disequilibrium extended further in northern Europe than in central Europe: the estimates of the population recombination rate parameter, ρ, were 0.0064 and 0.0294, respectively. The summary statistics of Nucleotide Diversity in central and northern European populations were compatible with an ancient bottleneck rather than the standard neutral model.
Jinsong Bao - One of the best experts on this subject based on the ideXlab platform.
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Nucleotide Diversity in starch synthase iia and validation of single Nucleotide polymorphisms in relation to starch gelatinization temperature and other physicochemical properties in rice oryza sativa l
Theoretical and Applied Genetics, 2006Co-Authors: Harold Corke, Jinsong Bao, Mei SunAbstract:The characteristics of starch, such as gelatinization temperature (GT), apparent amylose content (AAC), pasting temperature (PT) and other physicochemical properties, determine the quality of various products of rice, e.g., eating, cooking and processing qualities. The GT of rice flour is controlled by the alk locus, which has been co-mapped to the starch synthase IIa (SSIIa) locus. In this study, we sequenced a 2,051 bp DNA fragment spanning part of intron 6, exon 7, intron 7, exon 8 and part of 3' untranslated region of SSIIa for 30 rice varieties with diverse geographical distribution and variation in starch physicochemical properties. A total of 24 single Nucleotide polymorphisms (SNPs) and one insertion/deletion (InDel) were identified, which could be classified into nine haplotypes. The mean pairwise Nucleotide Diversity pi was 0.00292, and Watterson's estimator theta was 0.00296 in this collection of rice germplasm. Tajima's D test for selection showed no significant deviation from the neutral expectation (D = - 0.04612, P > 0.10). However, significant associations were found between seven of the SNPs and peak GT (T (p)) at P < 0.05, of which two contiguous SNPs (GC/TT) showed a very strong association with T (p) (P < 0.0001). With some rare exception, this GC/TT polymorphism alone can differentiate rice varieties with high or intermediate GT (possessing the GC allele) from those with low GT (possessing the TT allele). In contrast, none of these SNPs or InDel was significantly associated with amylose content. A further 509 rice varieties with known physicochemical properties (e.g., AAC and PT) and known alleles of other starch synthesizing genes were genotyped for the SSIIa GC/TT alleles. Association analysis indicated that 82% of the total variation of AAC in these samples could be explained by a (CT)n simple sequence repeat (SSR) and a G/T SNP of Waxy gene (Wx), and 62.4% of the total variation of PT could be explained by the GC/TT polymorphism. An additional association analysis was performed between these molecular markers and the thermal and retrogradation properties for a subset of 245 samples from the 509 rice varieties. The SSIIa GC/TT polymorphism explained more than 60% of the total variation in thermal properties, whereas the SSR and SNP of Wx gene explained as much as the SSIIa GC/TT of the total variation in retrogradation properties. Our study provides further support for the utilization of the GC/TT polymorphism in SSIIa. As shown in our study of 509 rice varieties, the GC/TT SNP could differentiate rice with high or intermediate GT from those with low GT in about 90% of cases. Using four primers in a single PCR reaction, the GC/TT polymorphism can be surveyed on a large scale. Thus, this SNP polymorphism can be very useful in marker-assisted selection for the improvement of GT and other physicochemical properties of rice.
