The Experts below are selected from a list of 672 Experts worldwide ranked by ideXlab platform

Juanjose Arranz - One of the best experts on this subject based on the ideXlab platform.

  • High-resolution analysis of selection sweeps identified between fine-Wool Merino and Coarse-Wool Churra sheep breeds
    Genetics Selection Evolution, 2017
    Co-Authors: Beatriz Gutiérrez-gil, Pamela Wiener, P K Chitneedi, Cristina Esteban-blanco, Aroa Suarez-vega, Juanjose Arranz
    Abstract:

    AbstractBackgroundWith the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine Wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for Wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a Coarse-Wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequencing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identified as putative selection signals.ResultsBased on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identified by four selection sweep mapping analyses (that detect genetic differentiation, reduced heterozygosity and patterns of haplotype diversity) to define 18 convergence candidate regions (CCR), five associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identified 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defined CCR. Annotation of 1291 variants that were significantly associated with breed identity between Churra and Merino samples identified 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes. Among these, four synonymous and four missense variants (NPR2_His847Arg, NCAPG_Ser585Phe, LCORL_Asp1214Glu and LCORL_Ile1441Leu) were included.ConclusionsHere, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be viewed as candidates involved in the phenotypic differences for Wool, growth and meat production/quality traits between the breeds analyzed. The four missense variants located in the NPR2, NCAPG and LCORL genes may be related to selection sweep regions previously identified and various QTL reported in sheep in relation to growth traits and carcass composition.

  • high resolution analysis of selection sweeps identified between fine Wool merino and Coarse Wool churra sheep breeds
    Genetics Selection Evolution, 2017
    Co-Authors: B Gutierrezgil, Cristina Estebanblanco, Pamela Wiener, P K Chitneedi, Aroa Suarezvega, Juanjose Arranz
    Abstract:

    With the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine Wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for Wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a Coarse-Wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequencing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identified as putative selection signals. Based on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identified by four selection sweep mapping analyses (that detect genetic differentiation, reduced heterozygosity and patterns of haplotype diversity) to define 18 convergence candidate regions (CCR), five associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identified 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defined CCR. Annotation of 1291 variants that were significantly associated with breed identity between Churra and Merino samples identified 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes. Among these, four synonymous and four missense variants (NPR2_His847Arg, NCAPG_Ser585Phe, LCORL_Asp1214Glu and LCORL_Ile1441Leu) were included. Here, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be viewed as candidates involved in the phenotypic differences for Wool, growth and meat production/quality traits between the breeds analyzed. The four missense variants located in the NPR2, NCAPG and LCORL genes may be related to selection sweep regions previously identified and various QTL reported in sheep in relation to growth traits and carcass composition.

Gottfried Brem - One of the best experts on this subject based on the ideXlab platform.

  • Population structure and genetic diversity of 25 Russian sheep breeds based on whole-genome genotyping
    Genetics Selection Evolution, 2018
    Co-Authors: T E Deniskova, Marina I. Selionova, Alexei A. Traspov, A V Dotsev, Henry Reyer, Maurizio Barbato, Klaus Wimmers, Ivica Medugorac, Elisabeth Kunz, Gottfried Brem
    Abstract:

    BackgroundRussia has a diverse variety of native and locally developed sheep breeds with Coarse, fine, and semi-fine Wool, which inhabit different climate zones and landscapes that range from hot deserts to harsh northern areas. To date, no genome-wide information has been used to investigate the history and genetic characteristics of the extant local Russian sheep populations. To infer the population structure and genome-wide diversity of Russian sheep, 25 local breeds were genotyped with the OvineSNP50 BeadChip. Furthermore, to evaluate admixture contributions from foreign breeds in Russian sheep, a set of 58 worldwide breeds from publicly available genotypes was added to our data.ResultsWe recorded similar observed heterozygosity (0.354–0.395) and allelic richness (1.890–1.955) levels across the analyzed breeds and they are comparable with those observed in the worldwide breeds. Recent effective population sizes estimated from linkage disequilibrium five generations ago ranged from 65 to 543. Multi-dimensional scaling, admixture, and neighbor-net analyses consistently identified a two-step subdivision of the Russian local sheep breeds. A first split clustered the Russian sheep populations according to their Wool type (fine Wool, semi-fine Wool and Coarse Wool). The Dagestan Mountain and Baikal fine-fleeced breeds differ from the other Merino-derived local breeds. The semi-fine Wool cluster combined a breed of Romanian origin, Tsigai, with its derivative Altai Mountain, the two Romney-introgressed breeds Kuibyshev and North Caucasian, and the Lincoln-introgressed Russian longhaired breed. The Coarse-Wool group comprised the Nordic short-tailed Romanov, the long-fat-tailed outlier Kuchugur and two clusters of fat-tailed sheep: the Caucasian Mountain breeds and the Buubei, Karakul, Edilbai, Kalmyk and Tuva breeds. The Russian fat-tailed breeds shared co-ancestry with sheep from China and Southwestern Asia (Iran).ConclusionsIn this study, we derived the genetic characteristics of the major Russian local sheep breeds, which are moderately diverse and have a strong population structure. Pooling our data with a worldwide genotyping set gave deeper insight into the history and origin of the Russian sheep populations.

  • MOESM4 of Population structure and genetic diversity of 25 Russian sheep breeds based on whole-genome genotyping
    2018
    Co-Authors: T E Deniskova, Marina I. Selionova, Alexei A. Traspov, A V Dotsev, Henry Reyer, Klaus Wimmers, Ivica Medugorac, Elisabeth Kunz, Mario Barbato, Gottfried Brem
    Abstract:

    Additional file 4: Figure S1 Slope changes in historical effective population size (Ne) trends. The graphs show the changes in slope trends for historical effective population size (Ne) for the period starting from approximately 18 generations ago for the Russian sheep breeds with the Coarse Wool (above), semi-fine Wool (in the middle) and fine Wool (below). For a description of the sheep breeds (see Additional file 1: Table S1, Additional file 2: Table S2)

  • MOESM3 of Population structure and genetic diversity of 25 Russian sheep breeds based on whole-genome genotyping
    2018
    Co-Authors: T E Deniskova, Marina I. Selionova, Alexei A. Traspov, A V Dotsev, Henry Reyer, Klaus Wimmers, Ivica Medugorac, Elisabeth Kunz, Mario Barbato, Gottfried Brem
    Abstract:

    Additional file 3: Table S3 Genetic differentiation of 25 Russian sheep breeds based on Weir and Cockerham’s fixation index (FST). This table provides information about FST values between the Russian breeds under study. The breeds’ groups of the same Wool type are framed in blue (for Coarse Wool breeds), red (for semi-fine Wool breeds) and green (for fine Wool breeds). For a description of the sheep breeds (see Additional file 1: Table S1, Additional file 2: Table S2)

T E Deniskova - One of the best experts on this subject based on the ideXlab platform.

  • Population structure and genetic diversity of 25 Russian sheep breeds based on whole-genome genotyping
    Genetics Selection Evolution, 2018
    Co-Authors: T E Deniskova, Marina I. Selionova, Alexei A. Traspov, A V Dotsev, Henry Reyer, Maurizio Barbato, Klaus Wimmers, Ivica Medugorac, Elisabeth Kunz, Gottfried Brem
    Abstract:

    BackgroundRussia has a diverse variety of native and locally developed sheep breeds with Coarse, fine, and semi-fine Wool, which inhabit different climate zones and landscapes that range from hot deserts to harsh northern areas. To date, no genome-wide information has been used to investigate the history and genetic characteristics of the extant local Russian sheep populations. To infer the population structure and genome-wide diversity of Russian sheep, 25 local breeds were genotyped with the OvineSNP50 BeadChip. Furthermore, to evaluate admixture contributions from foreign breeds in Russian sheep, a set of 58 worldwide breeds from publicly available genotypes was added to our data.ResultsWe recorded similar observed heterozygosity (0.354–0.395) and allelic richness (1.890–1.955) levels across the analyzed breeds and they are comparable with those observed in the worldwide breeds. Recent effective population sizes estimated from linkage disequilibrium five generations ago ranged from 65 to 543. Multi-dimensional scaling, admixture, and neighbor-net analyses consistently identified a two-step subdivision of the Russian local sheep breeds. A first split clustered the Russian sheep populations according to their Wool type (fine Wool, semi-fine Wool and Coarse Wool). The Dagestan Mountain and Baikal fine-fleeced breeds differ from the other Merino-derived local breeds. The semi-fine Wool cluster combined a breed of Romanian origin, Tsigai, with its derivative Altai Mountain, the two Romney-introgressed breeds Kuibyshev and North Caucasian, and the Lincoln-introgressed Russian longhaired breed. The Coarse-Wool group comprised the Nordic short-tailed Romanov, the long-fat-tailed outlier Kuchugur and two clusters of fat-tailed sheep: the Caucasian Mountain breeds and the Buubei, Karakul, Edilbai, Kalmyk and Tuva breeds. The Russian fat-tailed breeds shared co-ancestry with sheep from China and Southwestern Asia (Iran).ConclusionsIn this study, we derived the genetic characteristics of the major Russian local sheep breeds, which are moderately diverse and have a strong population structure. Pooling our data with a worldwide genotyping set gave deeper insight into the history and origin of the Russian sheep populations.

  • MOESM4 of Population structure and genetic diversity of 25 Russian sheep breeds based on whole-genome genotyping
    2018
    Co-Authors: T E Deniskova, Marina I. Selionova, Alexei A. Traspov, A V Dotsev, Henry Reyer, Klaus Wimmers, Ivica Medugorac, Elisabeth Kunz, Mario Barbato, Gottfried Brem
    Abstract:

    Additional file 4: Figure S1 Slope changes in historical effective population size (Ne) trends. The graphs show the changes in slope trends for historical effective population size (Ne) for the period starting from approximately 18 generations ago for the Russian sheep breeds with the Coarse Wool (above), semi-fine Wool (in the middle) and fine Wool (below). For a description of the sheep breeds (see Additional file 1: Table S1, Additional file 2: Table S2)

  • MOESM3 of Population structure and genetic diversity of 25 Russian sheep breeds based on whole-genome genotyping
    2018
    Co-Authors: T E Deniskova, Marina I. Selionova, Alexei A. Traspov, A V Dotsev, Henry Reyer, Klaus Wimmers, Ivica Medugorac, Elisabeth Kunz, Mario Barbato, Gottfried Brem
    Abstract:

    Additional file 3: Table S3 Genetic differentiation of 25 Russian sheep breeds based on Weir and Cockerham’s fixation index (FST). This table provides information about FST values between the Russian breeds under study. The breeds’ groups of the same Wool type are framed in blue (for Coarse Wool breeds), red (for semi-fine Wool breeds) and green (for fine Wool breeds). For a description of the sheep breeds (see Additional file 1: Table S1, Additional file 2: Table S2)

Pamela Wiener - One of the best experts on this subject based on the ideXlab platform.

  • High-resolution analysis of selection sweeps identified between fine-Wool Merino and Coarse-Wool Churra sheep breeds
    Genetics Selection Evolution, 2017
    Co-Authors: Beatriz Gutiérrez-gil, Pamela Wiener, P K Chitneedi, Cristina Esteban-blanco, Aroa Suarez-vega, Juanjose Arranz
    Abstract:

    AbstractBackgroundWith the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine Wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for Wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a Coarse-Wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequencing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identified as putative selection signals.ResultsBased on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identified by four selection sweep mapping analyses (that detect genetic differentiation, reduced heterozygosity and patterns of haplotype diversity) to define 18 convergence candidate regions (CCR), five associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identified 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defined CCR. Annotation of 1291 variants that were significantly associated with breed identity between Churra and Merino samples identified 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes. Among these, four synonymous and four missense variants (NPR2_His847Arg, NCAPG_Ser585Phe, LCORL_Asp1214Glu and LCORL_Ile1441Leu) were included.ConclusionsHere, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be viewed as candidates involved in the phenotypic differences for Wool, growth and meat production/quality traits between the breeds analyzed. The four missense variants located in the NPR2, NCAPG and LCORL genes may be related to selection sweep regions previously identified and various QTL reported in sheep in relation to growth traits and carcass composition.

  • high resolution analysis of selection sweeps identified between fine Wool merino and Coarse Wool churra sheep breeds
    Genetics Selection Evolution, 2017
    Co-Authors: B Gutierrezgil, Cristina Estebanblanco, Pamela Wiener, P K Chitneedi, Aroa Suarezvega, Juanjose Arranz
    Abstract:

    With the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine Wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for Wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a Coarse-Wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequencing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identified as putative selection signals. Based on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identified by four selection sweep mapping analyses (that detect genetic differentiation, reduced heterozygosity and patterns of haplotype diversity) to define 18 convergence candidate regions (CCR), five associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identified 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defined CCR. Annotation of 1291 variants that were significantly associated with breed identity between Churra and Merino samples identified 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes. Among these, four synonymous and four missense variants (NPR2_His847Arg, NCAPG_Ser585Phe, LCORL_Asp1214Glu and LCORL_Ile1441Leu) were included. Here, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be viewed as candidates involved in the phenotypic differences for Wool, growth and meat production/quality traits between the breeds analyzed. The four missense variants located in the NPR2, NCAPG and LCORL genes may be related to selection sweep regions previously identified and various QTL reported in sheep in relation to growth traits and carcass composition.

P K Chitneedi - One of the best experts on this subject based on the ideXlab platform.

  • High-resolution analysis of selection sweeps identified between fine-Wool Merino and Coarse-Wool Churra sheep breeds
    Genetics Selection Evolution, 2017
    Co-Authors: Beatriz Gutiérrez-gil, Pamela Wiener, P K Chitneedi, Cristina Esteban-blanco, Aroa Suarez-vega, Juanjose Arranz
    Abstract:

    AbstractBackgroundWith the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine Wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for Wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a Coarse-Wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequencing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identified as putative selection signals.ResultsBased on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identified by four selection sweep mapping analyses (that detect genetic differentiation, reduced heterozygosity and patterns of haplotype diversity) to define 18 convergence candidate regions (CCR), five associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identified 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defined CCR. Annotation of 1291 variants that were significantly associated with breed identity between Churra and Merino samples identified 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes. Among these, four synonymous and four missense variants (NPR2_His847Arg, NCAPG_Ser585Phe, LCORL_Asp1214Glu and LCORL_Ile1441Leu) were included.ConclusionsHere, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be viewed as candidates involved in the phenotypic differences for Wool, growth and meat production/quality traits between the breeds analyzed. The four missense variants located in the NPR2, NCAPG and LCORL genes may be related to selection sweep regions previously identified and various QTL reported in sheep in relation to growth traits and carcass composition.

  • high resolution analysis of selection sweeps identified between fine Wool merino and Coarse Wool churra sheep breeds
    Genetics Selection Evolution, 2017
    Co-Authors: B Gutierrezgil, Cristina Estebanblanco, Pamela Wiener, P K Chitneedi, Aroa Suarezvega, Juanjose Arranz
    Abstract:

    With the aim of identifying selection signals in three Merino sheep lines that are highly specialized for fine Wool production (Australian Industry Merino, Australian Merino and Australian Poll Merino) and considering that these lines have been subjected to selection not only for Wool traits but also for growth and carcass traits and parasite resistance, we contrasted the OvineSNP50 BeadChip (50 K-chip) pooled genotypes of these Merino lines with the genotypes of a Coarse-Wool breed, phylogenetically related breed, Spanish Churra dairy sheep. Genome re-sequencing datasets of the two breeds were analyzed to further explore the genetic variation of the regions initially identified as putative selection signals. Based on the 50 K-chip genotypes, we used the overlapping selection signals (SS) identified by four selection sweep mapping analyses (that detect genetic differentiation, reduced heterozygosity and patterns of haplotype diversity) to define 18 convergence candidate regions (CCR), five associated with positive selection in Australian Merino and the remainder indicating positive selection in Churra. Subsequent analysis of whole-genome sequences from 15 Churra and 13 Merino samples identified 142,400 genetic variants (139,745 bi-allelic SNPs and 2655 indels) within the 18 defined CCR. Annotation of 1291 variants that were significantly associated with breed identity between Churra and Merino samples identified 257 intragenic variants that caused 296 functional annotation variants, 275 of which were located across 31 coding genes. Among these, four synonymous and four missense variants (NPR2_His847Arg, NCAPG_Ser585Phe, LCORL_Asp1214Glu and LCORL_Ile1441Leu) were included. Here, we report the mapping and genetic variation of 18 selection signatures that were identified between Australian Merino and Spanish Churra sheep breeds, which were validated by an additional contrast between Spanish Merino and Churra genotypes. Analysis of whole-genome sequencing datasets allowed us to identify divergent variants that may be viewed as candidates involved in the phenotypic differences for Wool, growth and meat production/quality traits between the breeds analyzed. The four missense variants located in the NPR2, NCAPG and LCORL genes may be related to selection sweep regions previously identified and various QTL reported in sheep in relation to growth traits and carcass composition.