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Barani S, Nejati-Javaremi A, Moradi MH, Moradi-Sharbabak M, Gholizadeh M, Esfandyari H. Genome-wide study of linkage disequilibrium, population structure, and inbreeding in Iranian indigenous sheep breeds. PLoS One 2023; 18:e0286463. [PMID: 37267244 DOI: 10.1371/journal.pone.0286463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 05/16/2023] [Indexed: 06/04/2023] Open
Abstract
Knowledge of linkage disequilibrium (LD), genetic structure and genetic diversity are some key parameters to study the breeding history of indigenous small ruminants. In this study, the OvineSNP50 Bead Chip array was used to estimate and compare LD, genetic diversity, effective population size (Ne) and genomic inbreeding in 186 individuals, from three Iranian indigenous sheep breeds consisting of Baluchi (n = 96), Lori-Bakhtiari (n = 47) and Zel (n = 47). The results of principal component analysis (PCA) revealed that all animals were allocated to the groups that they sampled and the admixture analysis revealed that the structure within the populations is best explained when separated into three groups (K = 3). The average r2 values estimated between adjacent single nucleotide polymorphisms (SNPs) at distances up to 10Kb, were 0.388±0.324, 0.353±0.311, and 0.333±0.309 for Baluchi, Lori-Bakhtiari and Zel, respectively. Estimation of genetic diversity and effective population size (Ne) showed that the Zel breed had the highest heterozygosity and Ne, whereas the lowest value was found in Baluchi breed. Estimation of genomic inbreeding using FROH (based on the long stretches of consecutive homozygous genotypes) showed the highest inbreeding coefficient in Baluchi and the lowest in Zel breed that could be due to higher pressure of artificial selection on Baluchi breed. The results of genomic inbreeding and Ne showed an increase in sharing haplotypes in Baluchi, leading to the enlargement of LD and the consequences of linkage disequilibrium and haplotype blocks confirmed this point. Also, the persistence of the LD phase between Zel and Lori-Bakhtiari was highest indicating that these two breeds would be combined in a multi-breed training population in genomic selection studies.
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Affiliation(s)
- S Barani
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - A Nejati-Javaremi
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - M H Moradi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak University, Arak, Iran
| | - M Moradi-Sharbabak
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - M Gholizadeh
- Department of Animal Science, Sari Agricultural Sciences and Natural Resources University, Sari, Mazandaran, Iran
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The association of gene polymorphisms with milk production and mastitis resistance phenotypic traits in dairy cattle. ANNALS OF ANIMAL SCIENCE 2023. [DOI: 10.2478/aoas-2022-0091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
Abstract
The aim of this study was to evaluate the association between gene polymorphisms (SNPs) and mastitis indicators and their relationship with milk production profitability in dairy herd.A functional analysis was also performed of five genes containing the studied SNPs and those located close by. DNA was isolated from the hair bulb of 320 dairy cows kept in three herds and SNP-microarray analysis was performed. The data on 299 cows was subjected to final statistical analysis using AI-REML method with one-trait repeatability test-day animal model and pedigree information using the DMU4 package. Five from 35 SNPs significantly associated with mastitis indicators or production traits and located within a gene or no more than 500,000 nucleotides from the gene were selected for the functional and economic analysis. A questionnaire was also developed to collect associated economic data of 219 cows from three herds, such as the value of milk production and direct costs incurred over three years; this allowed the gross margin, direct profitability index and direct costs incurred to produce one liter of milk to be determined, among others. None of the five studied SNPs were related to protein content. The rs110785912(T/A), found near CXCR4, and rs136813430(T/C), located in the TLR4 gene exon, were associated with lnSCC, while rs110455063(C/G), located near IGFI, was associated with milk yield, fat and total solid contents. rs109421300(T/C), associated with fat/protein content ratio, as well as fat and total solid content, is located in the DGAT1 gene intron. rs41587003(A/C), located in the DLG2 gene intron, was associated with lactose content. The economic analysis revealed differences between the variants of the three tested SNPs. The T/C variant of the rs136813430(T/C) SNP was characterized by the highest gross margin, the highest direct profitability index and the lowest costs incurred to produce 1 liter of milk. The T/A variant of rs110785912(T/A) was related to low lnSCC and was characterized by the highest direct profitability index. In turn, the C/C variant of the rs41587003(T/C) was related to the lowest level of lactose and the highest costs of milk production. It appears that rs136813430(T/C) may be the most promising of the tested SNPs for increasing the profitability of milk production. To our knowledge, it is the first effort to assess directly a correlation between the DNA polymorphism and economic output of a dairy enterprise.
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Jasielczuk I, Gurgul A, Szmatoła T, Semik-Gurgul E, Pawlina-Tyszko K, Stefaniuk-Szmukier M, Polak G, Tomczyk-Wrona I, Bugno-Poniewierska M. Linkage disequilibrium, haplotype blocks and historical effective population size in Arabian horses and selected Polish native horse breeds. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.104095] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Tarsani E, Kranis A, Maniatis G, Avendano S, Hager-Theodorides AL, Kominakis A. Discovery and characterization of functional modules associated with body weight in broilers. Sci Rep 2019; 9:9125. [PMID: 31235723 PMCID: PMC6591351 DOI: 10.1038/s41598-019-45520-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 06/04/2019] [Indexed: 12/31/2022] Open
Abstract
Aim of the present study was to investigate whether body weight (BW) in broilers is associated with functional modular genes. To this end, first a GWAS for BW was conducted using 6,598 broilers and the high density SNP array. The next step was to search for positional candidate genes and QTLs within strong LD genomic regions around the significant SNPs. Using all positional candidate genes, a network was then constructed and community structure analysis was performed. Finally, functional enrichment analysis was applied to infer the functional relevance of modular genes. A total number of 645 positional candidate genes were identified in strong LD genomic regions around 11 genome-wide significant markers. 428 of the positional candidate genes were located within growth related QTLs. Community structure analysis detected 5 modules while functional enrichment analysis showed that 52 modular genes participated in developmental processes such as skeletal system development. An additional number of 14 modular genes (GABRG1, NGF, APOBEC2, STAT5B, STAT3, SMAD4, MED1, CACNB1, SLAIN2, LEMD2, ZC3H18, TMEM132D, FRYL and SGCB) were also identified as related to body weight. Taken together, current results suggested a total number of 66 genes as most plausible functional candidates for the trait examined.
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Affiliation(s)
- Eirini Tarsani
- Department of Animal Science and Aquaculture, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece.
| | - Andreas Kranis
- Aviagen Ltd., Newbridge, Midlothian, EH28 8SZ, UK.,The Roslin Institute, University of Edinburgh, EH25 9RG, Midlothian, United Kingdom
| | | | | | - Ariadne L Hager-Theodorides
- Department of Animal Science and Aquaculture, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
| | - Antonios Kominakis
- Department of Animal Science and Aquaculture, Agricultural University of Athens, Iera Odos 75, 11855, Athens, Greece
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Jemaa SB, Thamri N, Mnara S, Rebours E, Rocha D, Boussaha M. Linkage disequilibrium and past effective population size in native Tunisian cattle. Genet Mol Biol 2019; 42:52-61. [PMID: 30776288 PMCID: PMC6428135 DOI: 10.1590/1678-4685-gmb-2017-0342] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 05/14/2018] [Indexed: 12/30/2022] Open
Abstract
To carry out effective genome-wide association studies, information about linkage disequilibrium (LD) is essential. Here, we used medium-density SNP chips to provide estimates of LD in native Tunisian cattle. The two measures of LD that were used, mean r2 and D', decreased from 0.26 to 0.05 and from 0.73 to 0.40, respectively, when the distance between markers increased from less than 20 Kb to 200 Kb. The decay in LD over physical distance occurred at a faster rate than that reported for European and other indigenous breeds, and reached background levels at less than 500 Kb distance. This is consistent with the absence of strong selective pressure within the Tunisian population and suggests that, in order to be effective, any potential genome-wide association mapping studies will need to use chips with higher marker density. An analysis of effective population size (Ne) based on LD data showed a decline in past Ne, with a sudden drop starting about eight generations ago. This finding, combined with the high levels of recent inbreeding revealed by runs of homozygosity (ROH) analysis, indicate that this population is endangered and may be in urgent need of a conservation plan that includes a well-designed genetic management program.
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Affiliation(s)
- Slim Ben Jemaa
- National Institute of Agronomic Research of Tunisia, Laboratoire des Productions Animales et Fourragères, Ariana, Tunisia
| | - Nejia Thamri
- Livestock and Pasture Office, Tunis Belvedere, Tunisia
| | | | - Emmanuelle Rebours
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | - Dominique Rocha
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
| | - Mekki Boussaha
- GABI, INRA, AgroParisTech, Université Paris Saclay, Jouy-en-Josas, France
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Mastrangelo S, Biscarini F, Tolone M, Auzino B, Ragatzu M, Spaterna A, Ciampolini R. Genomic characterization of the Braque Français type Pyrénées dog and relationship with other breeds. PLoS One 2018; 13:e0208548. [PMID: 30517199 PMCID: PMC6281230 DOI: 10.1371/journal.pone.0208548] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Accepted: 11/18/2018] [Indexed: 01/16/2023] Open
Abstract
The evaluation of genetic variability is a useful research tool for the correct management of selection and conservation strategies in dog breeds. In addition to pedigree genealogies, genomic data allow a deeper knowledge of the variability and genetic structure of populations. To date, many dog breeds, such as small regional breeds, still remain uncharacterized. Braque Français type Pyrénées (BRA) is a dog breed originating from a very old type of gun-dog used for pointing the location of game birds to hunters. Despite the ancient background, the knowledge about levels of genetic diversity, degree of inbreeding and population structure is scarce. This may raise concerns on the possibility that few inbred bloodlines may dominate the breed, and on its future health. The aim of this work was therefore to provide a high-resolution representation of the genome-wide diversity and population structure of BRA dogs, using the 170K genome-wide SNP array. Genome-wide polymorphisms in BRA were compared with those of other worldwide dog breeds. Between-dog relationships estimated from genomic data were very similar to pedigree relationships (Pearson correlation rg,a = 0.92). Results showed that BRA generally presents moderate levels of genetic diversity when compared with the major canine breeds. The estimated effective population size (recent Ne = 51) shows a similar declining pattern over generations as all other dog breeds, pointing at a common demographic history of modern canine breeds, clearly different from the demography of feral wolves. Multidimensional scaling (MDS), Bayesian clustering and Neighbor Joining tree were used to visualize and explore the genetic relationships among breeds, and revealed that BRA was highly differentiated and presented only low levels of admixture with other breeds. Brittany Spaniel, English Setter, Gordon Setter and Weimaraner dogs are the closest breeds to BRA. The exact reason for BRA being so divergent from other dog breeds, based on these results, is not yet clear. Further studies including additional ≪braccoid≫ breeds will be needed to refine the results presented here and to investigate the origin of the BRA breed. Nonetheless, the genome-wide characterization reported here provides a comprehensive insight into the genome diversity and population structure of the Braque Français, type Pyrénées breed.
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Affiliation(s)
- Salvatore Mastrangelo
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | | | - Marco Tolone
- Dipartimento di Scienze Agrarie, Alimentari e Forestali, Università di Palermo, Palermo, Italy
| | - Barbara Auzino
- Dipartimento di Scienze Veterinarie, Università di Pisa, V.le delle Piagge 2, 56124 Pisa, Italy
| | - Marco Ragatzu
- Club Italiano Braque Français Type Pyrénées, Capalbio, GR, Italy
| | - Andrea Spaterna
- Scuola di Scienze Mediche Veterinarie, University of Camerino, Matelica, MC, Italy
- Centro Interuniversitario di Ricerca e di Consulenza sulla Genetica e la Clinica del cane, Matelica, MC, Italy
| | - Roberta Ciampolini
- Dipartimento di Scienze Veterinarie, Università di Pisa, V.le delle Piagge 2, 56124 Pisa, Italy
- Centro Interuniversitario di Ricerca e di Consulenza sulla Genetica e la Clinica del cane, Matelica, MC, Italy
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Cozzi MC, Strillacci MG, Valiati P, Rogliano E, Bagnato A, Longeri M. Genetic variability of Akhal-Teke horses bred in Italy. PeerJ 2018; 6:e4889. [PMID: 30202639 PMCID: PMC6129384 DOI: 10.7717/peerj.4889] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 05/14/2018] [Indexed: 12/13/2022] Open
Abstract
Background The Akhal-Teke horse (AKH) is native of the modern Turkmenistan area. It was introduced in Italy from 1991 to 2000 mainly as an endurance horse. This paper characterizes the genetic variability of the whole Italian AKH horse population and evaluates their inbreeding level by analyzing microsatellite markers and mitochondrial D-Loop sequences. Methods Seventeen microsatellite marker loci were genotyped on 95 DNA samples from almost all the AKH horses bred in Italy in the last 20 years. Standard genetic variability measures (Ho, He, FIS) were compared against the same variables published on other eight AKH populations. In addition, 397 bp of mtDNA D-loop region were sequenced on a sub-group of 22 unrelated AKH out of the 95 sampled ones, and on 11 unrelated Arab horses. The haplotypes identified in the Italian population were aligned to sequences of AKH (56), Arab (five), Caspian Pony (13), Przewalskii (two) and Barb (15) horses available in GenBank. The Median Joining Network (MJN), Principal Component Analysis (PCA) and Neighbor-joining (NJ) tree were calculated on the total 126 sequences. Results Nucleic markers showed a high degree of polymorphism (Ho = 0.642; He = 0.649) and a low inbreeding level (FIS = 0.016) in Italian horses, compared to other AKH populations (ranged from −0.103 AKH from Estonia to 0.114 AKH from Czech Republic). High variability was also recorded in the D-Loop region. 11 haplotypes were identified with haplotype diversity (hd), nucleotide diversity (π) and average number of nucleotide differences (k) of 0.938, 0.021 and 6.448, respectively. When all the 126 D-Loop sequences were compared, 51 haplotypes were found, and four were here found only in the Italian AKH horses. The 51 haplotypes were conformed to eight recognized mtDNA haplogroups (A, C, F, G, L, M, P and Q) and confirmed by MJN analysis, Italian horses being assigned to five haplogroups (A, C, G, L and M). Using a PCA approach to the same data, the total haplotypes were grouped into two clusters including A+C+M+P and G+F haplogroups, while L and Q haplogroups remained ungrouped. Finally, the NJ algorithm effectively discretizes only the L haplogroup. All the above data univocally indicate good genetic variability and accurate management of the Akhal-Teke population in Italy.
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Affiliation(s)
- Maria C Cozzi
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Maria G Strillacci
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Paolo Valiati
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Elisa Rogliano
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Alessandro Bagnato
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
| | - Maria Longeri
- Department of Veterinary Medicine, Università degli Studi di Milano, Milan, Italy
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Alvarenga AB, Rovadoscki GA, Petrini J, Coutinho LL, Morota G, Spangler ML, Pinto LFB, Carvalho GGP, Mourão GB. Linkage disequilibrium in Brazilian Santa Inês breed, Ovis aries. Sci Rep 2018; 8:8851. [PMID: 29892085 PMCID: PMC5995818 DOI: 10.1038/s41598-018-27259-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 05/25/2018] [Indexed: 11/13/2022] Open
Abstract
For genomic selection to be successful, there must be sufficient linkage disequilibrium between the markers and the causal mutations. The objectives of this study were to evaluate the extent of LD in ovine using the Santa Inês breed and to infer the minimum number of markers required to reach reasonable prediction accuracy. In total, 38,168 SNPs and 395 samples were used. The mean LD between adjacent marker pairs measured by r2 and |D′| were 0.166 and 0.617, respectively. LD values between adjacent marker pairs ranged from 0.135 to 0.194 and from 0.568 to 0.650 for r2 for |D′| across all chromosomes. The average r2 between all pairwise SNPs on each chromosome was 0.018. SNPs separated by between 0.10 to 0.20 Mb had an estimated average r2 equal to 0.1033. The identified haplotype blocks consisted of 2 to 21 markers. Moreover, estimates of average coefficients of inbreeding and effective population size were 0.04 and 96, respectively. LD estimated in this study was lower than that reported in other species and was characterized by short haplotype blocks. Our results suggest that the use of a higher density SNP panel is recommended for the implementation of genomic selection in the Santa Inês breed.
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Affiliation(s)
- Amanda Botelho Alvarenga
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil
| | - Gregori Alberto Rovadoscki
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil
| | - Juliana Petrini
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil
| | - Gota Morota
- Department of Animal Science, University of Nebraska, Lincoln, NE, USA
| | | | | | | | - Gerson Barreto Mourão
- Department of Animal Science, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, SP, Brazil.
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Bejarano D, Martínez R, Manrique C, Parra LM, Rocha JF, Gómez Y, Abuabara Y, Gallego J. Linkage disequilibrium levels and allele frequency distribution in Blanco Orejinegro and Romosinuano Creole cattle using medium density SNP chip data. Genet Mol Biol 2018; 41:426-433. [PMID: 30088613 PMCID: PMC6082240 DOI: 10.1590/1678-4685-gmb-2016-0310] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 09/20/2017] [Indexed: 11/22/2022] Open
Abstract
The linkage disequilibrium (LD) between molecular markers affects the accuracy of
genome-wide association studies and genomic selection application. High-density
genotyping platforms allow identifying the genotype of thousands of single
nucleotide polymorphisms (SNPs) distributed throughout the animal genomes, which
increases the resolution of LD evaluations. This study evaluated the
distribution of minor allele frequencies (MAF) and the level of LD in the
Colombian Creole cattle breeds Blanco Orejinegro (BON) and Romosinuano (ROMO)
using a medium density SNP panel (BovineSNP50K_v2). The LD decay in these breeds
was lower than those reported for other taurine breeds, achieving optimal LD
values (r2 ≥ 0.3) up to a distance of 70 kb in BON and 100 kb in
ROMO, which is possibly associated with the conservation status of these cattle
populations and their effective population size. The average MAF for both breeds
was 0.27 ± 0.14 with a higher SNP proportion having high MAF values (≥ 0.3). The
LD levels and distribution of allele frequencies found in this study suggest
that it is possible to have adequate coverage throughout the genome of these
breeds using the BovineSNP50K_v2, capturing the effect of most QTL related with
productive traits, and ensuring an adequate prediction capacity in genomic
analysis.
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Affiliation(s)
- Diego Bejarano
- Corporación Colombiana de Investigación Agropecuaria - Corpoica. Centro de Investigación Tibaitatá, Cundinamarca, Colombia
| | - Rodrigo Martínez
- Corporación Colombiana de Investigación Agropecuaria - Corpoica. Centro de Investigación Tibaitatá, Cundinamarca, Colombia
| | | | - Luis Miguel Parra
- Corporación Colombiana de Investigación Agropecuaria - Corpoica. Centro de Investigación Tibaitatá, Cundinamarca, Colombia
| | - Juan Felipe Rocha
- Corporación Colombiana de Investigación Agropecuaria - Corpoica. Centro de Investigación Obonuco, Nariño, Colombia
| | - Yolanda Gómez
- Corporación Colombiana de Investigación Agropecuaria - Corpoica. Centro de Investigación Tibaitatá, Cundinamarca, Colombia
| | - Yesid Abuabara
- Corporación Colombiana de Investigación Agropecuaria - Corpoica. Centro de Investigación Turipaná, Córdoba, Colombia
| | - Jaime Gallego
- Corporación Colombiana de Investigación Agropecuaria - Corpoica. Centro de Investigación El Nus, Antioquia, Colombia
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Abdullaev AA, Salakhutdinov IB, Egamberdiev SS, Khurshut EE, Rizaeva SM, Ulloa M, Abdurakhmonov IY. Genetic diversity, linkage disequilibrium, and association mapping analyses of Gossypium barbadense L. germplasm. PLoS One 2017; 12:e0188125. [PMID: 29136656 PMCID: PMC5685624 DOI: 10.1371/journal.pone.0188125] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2017] [Accepted: 11/01/2017] [Indexed: 02/05/2023] Open
Abstract
Limited polymorphism and narrow genetic base, due to genetic bottleneck through historic domestication, highlight a need for comprehensive characterization and utilization of existing genetic diversity in cotton germplasm collections. In this study, 288 worldwide Gossypium barbadense L. cotton germplasm accessions were evaluated in two diverse environments (Uzbekistan and USA). These accessions were assessed for genetic diversity, population structure, linkage disequilibrium (LD), and LD-based association mapping (AM) of fiber quality traits using 108 genome-wide simple sequence repeat (SSR) markers. Analyses revealed structured population characteristics and a high level of intra-variability (67.2%) and moderate interpopulation differentiation (32.8%). Eight percent and 4.3% of markers revealed LD in the genome of the G. barbadense at critical values of r2 ≥ 0.1 and r2 ≥ 0.2, respectively. The LD decay was on average 24.8 cM at the threshold of r2 ≥ 0.05. LD retained on average distance of 3.36 cM at the threshold of r2 ≥ 0.1. Based on the phenotypic evaluations in the two diverse environments, 100 marker loci revealed a strong association with major fiber quality traits using mixed linear model (MLM) based association mapping approach. Fourteen marker loci were found to be consistent with previously identified quantitative trait loci (QTLs), and 86 were found to be new unreported marker loci. Our results provide insights into the breeding history and genetic relationship of G. barbadense germplasm and should be helpful for the improvement of cotton cultivars using molecular breeding and omics-based technologies.
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Affiliation(s)
- Alisher A. Abdullaev
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Ilkhom B. Salakhutdinov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Sharof S. Egamberdiev
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Ernest E. Khurshut
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Sofiya M. Rizaeva
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan, Tashkent, Uzbekistan
| | - Mauricio Ulloa
- Cropping Systems Research Laboratory, United States Department of Agriculture - Agricultural Research Services, Lubbock, Texas, United States of America
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Berton MP, de Oliveira Silva RM, Peripolli E, Stafuzza NB, Martin JF, Álvarez MS, Gavinã BV, Toro MA, Banchero G, Oliveira PS, Eler JP, Baldi F, Ferraz JBS. Genomic regions and pathways associated with gastrointestinal parasites resistance in Santa Inês breed adapted to tropical climate. J Anim Sci Biotechnol 2017; 8:73. [PMID: 28878894 PMCID: PMC5584554 DOI: 10.1186/s40104-017-0190-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 06/12/2017] [Indexed: 12/26/2022] Open
Abstract
Background The aim of this study was to estimate variance components and to identify genomic regions and pathways associated with resistance to gastrointestinal parasites, particularly Haemonchus contortus, in a breed of sheep adapted to tropical climate. Phenotypes evaluations were performed to verify resistance to gastrointestinal parasites, and were divided into two categories: i) farm phenotypes, assessing body condition score (BCS), degree of anemia assessed by the famacha chart (FAM), fur score (FS) and feces consistency (FC); and ii) lab phenotypes, comprising blood analyses for hematocrit (HCT), white blood cell count (WBC), red blood cell count (RBC), hemoglobin (HGB), platelets (PLT) and transformed (log10) egg per gram of feces (EPGlog). A total of 576 animals were genotyped with the Ovine SNP12k BeadChip (Illumina, Inc.), that contains 12,785 bialleleic SNP markers. The variance components were estimated using a single trait model by single step genomic BLUP procedure. Results The overall linkage disequilibrium (LD) mean between pairs of markers measured by r2 was 0.23. The overall LD mean between markers considering windows up to 10 Mb was 0.07. The mean LD between adjacent SNPs across autosomes ranged from 0.02 to 0.10. Heritability estimates were low for EPGlog (0.11), moderate for RBC (0.18), PLT (0.17) HCT (0.20), HGB (0.16) and WBC (0.22), and high for FAM (0.35). A total of 22, 21, 23, 20, 26, 25 and 23 windows for EPGlog for FAM, WBC, RBC, PLT, HCT and HGB traits were identified, respectively. Among the associated windows, 10 were shown to be common to HCT and HGB traits on OAR1, OAR2, OAR3, OAR5, OAR8 and OAR15. Conclusion The traits indicating gastrointestinal parasites resistance presented an adequate genetic variability to respond to selection in Santa Inês breed, and it is expected a higher genetic gain for FAM trait when compared to the others. The level of LD estimated for markers separated by less than 1 Mb indicated that the Ovine SNP12k BeadChip might be a suitable tool for identifying genomic regions associated with traits related to gastrointestinal parasite resistance. Several candidate genes related to immune system development and activation, inflammatory response, regulation of lymphocytes and leukocytes proliferation were found. These genes may help in the selection of animals with higher resistance to parasites. Electronic supplementary material The online version of this article (doi:10.1186/s40104-017-0190-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Mariana Piatto Berton
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, SP CEP 14884-900 Brazil
| | - Rafael Medeiros de Oliveira Silva
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, SP CEP 14884-900 Brazil
| | - Elisa Peripolli
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, SP CEP 14884-900 Brazil
| | - Nedenia Bonvino Stafuzza
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, SP CEP 14884-900 Brazil
| | - Jesús Fernández Martin
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria INIA, Crta. de la Coruña, km 7,5 -, 28040 Madrid, Spain
| | - Maria Saura Álvarez
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria INIA, Crta. de la Coruña, km 7,5 -, 28040 Madrid, Spain
| | - Beatriz Villanueva Gavinã
- Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria INIA, Crta. de la Coruña, km 7,5 -, 28040 Madrid, Spain
| | - Miguel Angel Toro
- Departamento de Producción Agraria, School of Agricultural, Food and Byosystems Engineering, Universisdad Politécnica de Madrid, Campus Ciudad Universitaria Avda. Complutense 3 - Avda. Puerta Hierro, 28040 Madrid, Spain
| | - Georgget Banchero
- Instituto Nacional de Investigación Agropecuária (INIA), Ruta 50 Km. 12, Colonia, Uruguay
| | - Priscila Silva Oliveira
- Faculdade de Zootecnia e Engenharia de Alimentos, Nucleo de Apoio à Pesquisa em Melhoramento Animal, Biotecnologia e Transgenia, Universidade de São Paulo, Rua Duque de Caxias Norte, 225, Pirassununga, SP CEP 13635-900 Brazil
| | - Joanir Pereira Eler
- Faculdade de Zootecnia e Engenharia de Alimentos, Nucleo de Apoio à Pesquisa em Melhoramento Animal, Biotecnologia e Transgenia, Universidade de São Paulo, Rua Duque de Caxias Norte, 225, Pirassununga, SP CEP 13635-900 Brazil
| | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, Via de acesso Prof. Paulo Donato Castellane, s/no, Jaboticabal, SP CEP 14884-900 Brazil
| | - José Bento Sterman Ferraz
- Faculdade de Zootecnia e Engenharia de Alimentos, Nucleo de Apoio à Pesquisa em Melhoramento Animal, Biotecnologia e Transgenia, Universidade de São Paulo, Rua Duque de Caxias Norte, 225, Pirassununga, SP CEP 13635-900 Brazil
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Ademe MS, He S, Pan Z, Sun J, Wang Q, Qin H, Liu J, Liu H, Yang J, Xu D, Yang J, Ma Z, Zhang J, Li Z, Cai Z, Zhang X, Zhang X, Huang A, Yi X, Zhou G, Li L, Zhu H, Pang B, Wang L, Jia Y, Du X. Association mapping analysis of fiber yield and quality traits in Upland cotton (Gossypium hirsutum L.). Mol Genet Genomics 2017; 292:1267-1280. [PMID: 28748394 DOI: 10.1007/s00438-017-1346-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 06/29/2017] [Indexed: 12/15/2022]
Abstract
Fiber yield and quality are the most important traits for Upland cotton (Gossypium hirsutum L.). Identifying high yield and good fiber quality genes are the prime concern of researchers in cotton breeding. Association mapping offers an alternative and powerful method for detecting those complex agronomic traits. In this study, 198 simple sequence repeats (SSRs) were used to screen markers associated with fiber yield and quality traits with 302 elite Upland cotton accessions that were evaluated in 12 locations representing the Yellow River and Yangtze River cotton growing regions of China. Three subpopulations were found after the estimation of population structure. The pair-wise kinship values varied from 0 to 0.867. Only 1.59% of the total marker locus pairs showed significant linkage disequilibrium (LD, p < 0.001). The genome-wide LD decayed within the genetic distance of ~30 to 32 cM at r 2 = 0.1, and decreased to ~1 to 2 cM at r 2 = 0.2, indicating the potential for association mapping. Analysis based on a mixed linear model detected 57 significant (p < 0.01) marker-trait associations, including seven associations for fiber length, ten for fiber micronaire, nine for fiber strength, eight for fiber elongation, five for fiber uniformity index, five for fiber uniformity ratio, six for boll weight and seven for lint percent, for a total of 35 SSR markers, of which 11 markers were associated with more than one trait. Among marker-trait associations, 24 associations coincided with the previously reported quantitative trait loci (QTLs), the remainder were newly identified QTLs/genes. The QTLs identified in this study will potentially facilitate improvement of fiber yield and quality in the future cotton molecular breeding programs.
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Affiliation(s)
- Mulugeta Seyoum Ademe
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), P. O. Box 455000, Anyang, Henan, China
| | - Shoupu He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), P. O. Box 455000, Anyang, Henan, China
| | - Zhaoe Pan
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), P. O. Box 455000, Anyang, Henan, China
| | - Junling Sun
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), P. O. Box 455000, Anyang, Henan, China
| | - Qinglian Wang
- Henan Institute of Science and Technology, Xinxiang, China
| | - Hongde Qin
- Cash Crop Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Jinhai Liu
- Zhongmian Cotton Seed Industry Technology Co., Ltd, Zhengzhou, China
| | - Hui Liu
- Jing Hua Seed Industry Technologies Inc, Jingzhou, China
| | - Jun Yang
- Cotton Research Institute of Jiangxi Province, Jiujiang, China
| | - Dongyong Xu
- Guoxin Rural Technical Service Association, Hebei, China
| | - Jinlong Yang
- Zhongmian Cotton Seed Industry Technology Co., Ltd, Zhengzhou, China
| | - Zhiying Ma
- Key Laboratory of Crop Germplasm Resources of Hebei, Agricultural University of Hebei, Baoding, China
| | | | - Zhikun Li
- Key Laboratory of Crop Germplasm Resources of Hebei, Agricultural University of Hebei, Baoding, China
| | - Zhongmin Cai
- Zhongmian Cotton Seed Industry Technology Co., Ltd, Zhengzhou, China
| | | | - Xin Zhang
- Henan Institute of Science and Technology, Xinxiang, China
| | - Aifen Huang
- Sanyi Seed Industry of Changde in Hunan Inc, Changde, China
| | - Xianda Yi
- Cash Crop Institute, Hubei Academy of Agricultural Sciences, Wuhan, China
| | - Guanyin Zhou
- Zhongmian Cotton Seed Industry Technology Co., Ltd, Zhengzhou, China
| | - Lin Li
- Zhongli Company of Shandong, Shandong, China
| | - Haiyong Zhu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), P. O. Box 455000, Anyang, Henan, China
| | - Baoyin Pang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), P. O. Box 455000, Anyang, Henan, China
| | - Liru Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), P. O. Box 455000, Anyang, Henan, China
| | - Yinhua Jia
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), P. O. Box 455000, Anyang, Henan, China.
| | - Xiongming Du
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences (ICR, CAAS), P. O. Box 455000, Anyang, Henan, China.
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Ventura RV, Miller SP, Dodds KG, Auvray B, Lee M, Bixley M, Clarke SM, McEwan JC. Assessing accuracy of imputation using different SNP panel densities in a multi-breed sheep population. Genet Sel Evol 2016; 48:71. [PMID: 27663120 PMCID: PMC5035503 DOI: 10.1186/s12711-016-0244-7] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Accepted: 08/31/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genotype imputation is a key element of the implementation of genomic selection within the New Zealand sheep industry, but many factors can influence imputation accuracy. Our objective was to provide practical directions on the implementation of imputation strategies in a multi-breed sheep population genotyped with three single nucleotide polymorphism (SNP) panels: 5K, 50K and HD (600K SNPs). RESULTS Imputation from 5K to HD was slightly better (0.6 %) than imputation from 5K to 50K. Two-step imputation from 5K to 50K and then from 50K to HD outperformed direct imputation from 5K to HD. A slight loss in imputation accuracy was observed when a large fixed reference population was used compared to a smaller within-breed reference (including all 50K genotypes on animals from different breeds excluding those in the validation set i.e. to be imputed), but only for a few animals across all imputation scenarios from 5K to 50K. However, a major gain in imputation accuracy for a large proportion of animals (purebred and crossbred), justified the use of a fixed and large reference dataset for all situations. This study also investigated the loss in imputation accuracy specifically for SNPs located at the ends of each chromosome, and showed that only chromosome 26 had an overall imputation (5K to 50K) accuracy for 100 SNPs at each end higher than 60 % (r2). Most of the chromosomes displayed reduced imputation accuracy at least at one of their ends. Prediction of imputation accuracy based on the relatedness of low-density genotypes to those of the reference dataset, before imputation (without running an imputation software) was also investigated. FIMPUTE V2.2 outperformed BEAGLE 3.3.2 across all imputation scenarios. CONCLUSIONS Imputation accuracy in sheep breeds can be improved by following a set of recommendations on SNP panels, software, strategies of imputation (one- or two-step imputation), and choice of the animals to be genotyped using both high- and low-density SNP panels. We present a method that predicts imputation accuracy for individual animals at the low-density level, before running imputation, which can be used to restrict genomic prediction only to the animals that can be imputed with sufficient accuracy.
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Affiliation(s)
- Ricardo V Ventura
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G2W1, Canada.,Beef Improvement Opportunities, Guelph, ON, N1K1E5, Canada
| | - Stephen P Miller
- Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, N1G2W1, Canada. .,Invermay Agricultural Centre, AgResearch Limited, Mosgiel, 9053, New Zealand.
| | - Ken G Dodds
- Invermay Agricultural Centre, AgResearch Limited, Mosgiel, 9053, New Zealand
| | - Benoit Auvray
- Department of Mathematics and Statistics, University of Otago, Dunedin, 9016, New Zealand
| | - Michael Lee
- Department of Mathematics and Statistics, University of Otago, Dunedin, 9016, New Zealand
| | - Matthew Bixley
- Invermay Agricultural Centre, AgResearch Limited, Mosgiel, 9053, New Zealand
| | - Shannon M Clarke
- Invermay Agricultural Centre, AgResearch Limited, Mosgiel, 9053, New Zealand
| | - John C McEwan
- Invermay Agricultural Centre, AgResearch Limited, Mosgiel, 9053, New Zealand
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14
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Macciotta NPP, Mele M, Cappio-Borlino A, Secchiari P. Issues and perspectives in dairy sheep breeding. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2005.5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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15
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Biegelmeyer P, Gulias-Gomes CC, Caetano AR, Steibel JP, Cardoso FF. Linkage disequilibrium, persistence of phase and effective population size estimates in Hereford and Braford cattle. BMC Genet 2016; 17:32. [PMID: 26832943 PMCID: PMC4736111 DOI: 10.1186/s12863-016-0339-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2015] [Accepted: 01/20/2016] [Indexed: 11/25/2022] Open
Abstract
Background The existence of moderate to high levels of linkage disequilibrium (LD) between genetic markers and quantitative trait loci (QTL) affecting traits of interest is fundamental for the success of genome-wide association (GWAS) and genomic selection (GS) studies. Knowledge about the extent and the pattern of LD in livestock populations is essential to determine the density of single nucleotide polymorphisms (SNP) required for accurate GWAS and GS. Moreover, observed LD is related to historical effective population sizes (Ne), and can provide insights into the genetic diversity history of populations. Estimates of the consistency of linkage phase across breeds (RH,B) can be used to determine if there is sufficient relationship to use pooled reference populations in multi-breed GS programs. The objective of this study was to estimate LD levels, persistence of phase and effective population size in Hereford and Braford cattle populations sampled in Brazil. Results Mean LD estimates, measured using the squared correlation of alleles at two loci (r2), obtained between adjacent SNP across all chromosomes were 0.21 ± 0.27 for Herefords (391 samples with 41,241 SNP) and 0.16 ± 0.22 for Brafords (2044 samples and 41,207 SNP). Estimated r2 was > 0.2 and 0.3, respectively, for 34 and 25 % of adjacent markers in Herefords, and 26 and 17 % in Brafords. Estimated Ne for Brafords and Herefords at the current generation was 220 and 153 individuals, respectively. The two breeds demonstrated moderate to strong persistence of phase at all distances (RH,B = 0.53 to 0.97). The largest phase correlations were found in the 0 to 50 Kb bins (RH,B = 0.92 to 0.97). Estimated LD decreased rapidly with increasing distance between SNP, however, useful linkage for GWAS and GS (r2 > 0.2) was found spanning to ~50 Kb. Conclusions Panels containing about 50,000 and 150,000 SNP markers are necessary to detect minimal levels of LD between adjacent markers that would be useful for GWAS and GS studies to Hereford and Braford breeds, respectively. Markers are expected to be linked to the same QTL alleles in distances < 50 Kb in both populations due to observed high persistence of phase levels.
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Affiliation(s)
- Patrícia Biegelmeyer
- Programa de Pós-Graduação em Zootecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão do Leão, Rio Grande do Sul, Brazil.
| | | | - Alexandre R Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Brasília, Distrito Federal, Brazil. .,Programa de Pós-Graduação em Ciências Animais, Faculdade de Agronomia e Medicina Veterinária, Universidade de Brasília, Brasília, Distrito Federal, Brazil. .,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brasília, Distrito Federal, Brazil.
| | | | - Fernando F Cardoso
- Programa de Pós-Graduação em Zootecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Capão do Leão, Rio Grande do Sul, Brazil. .,Embrapa Pecuária Sul, Bagé, Rio Grande do Sul, Brazil. .,Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), Brasília, Distrito Federal, Brazil.
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16
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Makina SO, Taylor JF, van Marle-Köster E, Muchadeyi FC, Makgahlela ML, MacNeil MD, Maiwashe A. Extent of Linkage Disequilibrium and Effective Population Size in Four South African Sanga Cattle Breeds. Front Genet 2015; 6:337. [PMID: 26648975 PMCID: PMC4664654 DOI: 10.3389/fgene.2015.00337] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 11/09/2015] [Indexed: 11/13/2022] Open
Abstract
Knowledge on the extent of linkage disequilibrium (LD) in livestock populations is essential to determine the minimum distance between markers required for effective coverage when conducting genome-wide association studies (GWAS). This study evaluated the extent of LD, persistence of allelic phase and effective population size (Ne) for four Sanga cattle breeds in South Africa including the Afrikaner (n = 44), Nguni (n = 54), Drakensberger (n = 47), and Bonsmara breeds (n = 46), using Angus (n = 31) and Holstein (n = 29) as reference populations. We found that moderate LD extends up to inter-marker distances of 40–60 kb in Angus (0.21) and Holstein (0.21) and up to 100 kb in Afrikaner (0.20). This suggests that genomic selection and association studies performed within these breeds using an average inter-marker r2≥ 0.20 would require about 30,000–50,000 SNPs. However, r2≥ 0.20 extended only up to 10–20 kb in the Nguni and Drakensberger and 20–40 kb in the Bonsmara indicating that 75,000 to 150,000 SNPs would be necessary for GWAS in these breeds. Correlation between alleles at contiguous loci indicated that phase was not strongly preserved between breeds. This suggests the need for breed-specific reference populations in which a much greater density of markers should be scored to identify breed specific haplotypes which may then be imputed into multi-breed commercial populations. Analysis of effective population size based on the extent of LD, revealed Ne = 95 (Nguni), Ne = 87 (Drakensberger), Ne = 77 (Bonsmara), and Ne = 41 (Afrikaner). Results of this study form the basis for implementation of genomic selection programs in the Sanga breeds of South Africa.
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Affiliation(s)
- Sithembile O Makina
- Agricultural Research Council-Animal Production Institute Pretoria, South Africa ; Department of Animal and Wildlife Sciences, University of Pretoria Pretoria, South Africa
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri Columbia, MO, USA
| | - Este van Marle-Köster
- Department of Animal and Wildlife Sciences, University of Pretoria Pretoria, South Africa
| | - Farai C Muchadeyi
- Agricultural Research Council-Biotechnology Platform Pretoria, South Africa
| | - Mahlako L Makgahlela
- Agricultural Research Council-Animal Production Institute Pretoria, South Africa
| | - Michael D MacNeil
- Agricultural Research Council-Animal Production Institute Pretoria, South Africa ; Department of Animal, Wildlife and Grassland Sciences, University of Free State Bloemfontein, South Africa ; Delta G Miles City, MT, USA
| | - Azwihangwisi Maiwashe
- Agricultural Research Council-Animal Production Institute Pretoria, South Africa ; Department of Animal, Wildlife and Grassland Sciences, University of Free State Bloemfontein, South Africa
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17
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Al-Mamun HA, Clark SA, Kwan P, Gondro C. Genome-wide linkage disequilibrium and genetic diversity in five populations of Australian domestic sheep. Genet Sel Evol 2015; 47:90. [PMID: 26602211 PMCID: PMC4659207 DOI: 10.1186/s12711-015-0169-6] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2014] [Accepted: 11/02/2015] [Indexed: 01/23/2023] Open
Abstract
Background Knowledge of the genetic structure and overall diversity of livestock species is important to maximise the potential of genome-wide association studies and genomic prediction. Commonly used measures such as linkage disequilibrium (LD), effective population size (Ne), heterozygosity, fixation index (FST) and runs of homozygosity (ROH) are widely used and help to improve our knowledge about genetic diversity in animal populations. The development of high-density single nucleotide polymorphism (SNP) arrays and the subsequent genotyping of large numbers of animals have greatly increased the accuracy of these population-based estimates. Methods In this study, we used the Illumina OvineSNP50 BeadChip array to estimate and compare LD (measured by r2 and D′), Ne, heterozygosity, FST and ROH in five Australian sheep populations: three pure breeds, i.e., Merino (MER), Border Leicester (BL), Poll Dorset (PD) and two crossbred populations i.e. F1 crosses of Merino and Border Leicester (MxB) and MxB crossed to Poll Dorset (MxBxP). Results Compared to other livestock species, the sheep populations that were analysed in this study had low levels of LD and high levels of genetic diversity. The rate of LD decay was greater in Merino than in the other pure breeds. Over short distances (<10 kb), the levels of LD were higher in BL and PD than in MER. Similarly, BL and PD had comparatively smaller Ne than MER. Observed heterozygosity in the pure breeds ranged from 0.3 in BL to 0.38 in MER. Genetic distances between breeds were modest compared to other livestock species (highest FST = 0.063) but the genetic diversity within breeds was high. Based on ROH, two chromosomal regions showed evidence of strong recent selection. Conclusions This study shows that there is a large range of genome diversity in Australian sheep breeds, especially in Merino sheep. The observed range of diversity will influence the design of genome-wide association studies and the results that can be obtained from them. This knowledge will also be useful to design reference populations for genomic prediction of breeding values in sheep. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0169-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Samuel A Clark
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.
| | - Paul Kwan
- School of Science and Technology, University of New England, Armidale, NSW, 2351, Australia.
| | - Cedric Gondro
- School of Environmental and Rural Science, University of New England, Armidale, NSW, 2351, Australia.
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18
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Miller JM, Poissant J, Malenfant RM, Hogg JT, Coltman DW. Temporal dynamics of linkage disequilibrium in two populations of bighorn sheep. Ecol Evol 2015; 5:3401-12. [PMID: 26380673 PMCID: PMC4569035 DOI: 10.1002/ece3.1612] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Linkage disequilibrium (LD) is the nonrandom association of alleles at two markers. Patterns of LD have biological implications as well as practical ones when designing association studies or conservation programs aimed at identifying the genetic basis of fitness differences within and among populations. However, the temporal dynamics of LD in wild populations has received little empirical attention. In this study, we examined the overall extent of LD, the effect of sample size on the accuracy and precision of LD estimates, and the temporal dynamics of LD in two populations of bighorn sheep (Ovis canadensis) with different demographic histories. Using over 200 microsatellite loci, we assessed two metrics of multi-allelic LD, D', and χ ('2). We found that both populations exhibited high levels of LD, although the extent was much shorter in a native population than one that was founded via translocation, experienced a prolonged bottleneck post founding, followed by recent admixture. In addition, we observed significant variation in LD in relation to the sample size used, with small sample sizes leading to depressed estimates of the extent of LD but inflated estimates of background levels of LD. In contrast, there was not much variation in LD among yearly cross-sections within either population once sample size was accounted for. Lack of pronounced interannual variability suggests that researchers may not have to worry about interannual variation when estimating LD in a population and can instead focus on obtaining the largest sample size possible.
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Affiliation(s)
- Joshua M Miller
- Department of Biological Sciences, University of Alberta Edmonton, Alberta, Canada
| | - Jocelyn Poissant
- Centre for Ecology and Conservation, University of Exeter Penryn Campus, UK
| | - René M Malenfant
- Department of Biological Sciences, University of Alberta Edmonton, Alberta, Canada
| | - John T Hogg
- Montana Conservation Science Institute 5200 Upper Miller Creek Road, Missoula, Montana, USA
| | - David W Coltman
- Department of Biological Sciences, University of Alberta Edmonton, Alberta, Canada
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19
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Fünfstück T, Vigilant L. The geographic distribution of genetic diversity within gorillas. Am J Primatol 2015; 77:974-985. [DOI: 10.1002/ajp.22427] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2015] [Revised: 04/23/2015] [Accepted: 04/26/2015] [Indexed: 11/06/2022]
Affiliation(s)
| | - Linda Vigilant
- Max Planck Institute for Evolutionary Anthropology; Leipzig Germany
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20
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Nietlisbach P, Camenisch G, Bucher T, Slate J, Keller LF, Postma E. A microsatellite-based linkage map for song sparrows (Melospiza melodia). Mol Ecol Resour 2015; 15:1486-96. [PMID: 25865627 DOI: 10.1111/1755-0998.12414] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 04/01/2015] [Accepted: 04/03/2015] [Indexed: 01/15/2023]
Abstract
Although linkage maps are important tools in evolutionary biology, their availability for wild populations is limited. The population of song sparrows (Melospiza melodia) on Mandarte Island, Canada, is among the more intensively studied wild animal populations. Its long-term pedigree data, together with extensive genetic sampling, have allowed the study of a range of questions in evolutionary biology and ecology. However, the availability of genetic markers has been limited. We here describe 191 new microsatellite loci, including 160 high-quality polymorphic autosomal, 7 Z-linked and 1 W-linked markers. We used these markers to construct a linkage map for song sparrows with a total sex-averaged map length of 1731 cM and covering 35 linkage groups, and hence, these markers cover most of the 38-40 chromosomes. Female and male map lengths did not differ significantly. We then bioinformatically mapped these loci to the zebra finch (Taeniopygia guttata) genome and found that linkage groups were conserved between song sparrows and zebra finches. Compared to the zebra finch, marker order within small linkage groups was well conserved, whereas the larger linkage groups showed some intrachromosomal rearrangements. Finally, we show that as expected, recombination frequency between linked loci explained the majority of variation in gametic phase disequilibrium. Yet, there was substantial overlap in gametic phase disequilibrium between pairs of linked and unlinked loci. Given that the microsatellites described here lie on 35 of the 38-40 chromosomes, these markers will be useful for studies in this species, as well as for comparative genomics studies with other species.
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Affiliation(s)
- Pirmin Nietlisbach
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Glauco Camenisch
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Thomas Bucher
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Jon Slate
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Lukas F Keller
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
| | - Erik Postma
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057, Zurich, Switzerland
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Corbin LJ, Blott SC, Swinburne JE, Vaudin M, Bishop SC, Woolliams JA. Linkage disequilibrium and historical effective population size in the Thoroughbred horse. Anim Genet 2015; 41 Suppl 2:8-15. [PMID: 21070270 DOI: 10.1111/j.1365-2052.2010.02092.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many genomic methodologies rely on the presence and extent of linkage disequilibrium (LD) between markers and genetic variants underlying traits of interest, but the extent of LD in the horse has yet to be comprehensively characterized. In this study, we evaluate the extent and decay of LD in a sample of 817 Thoroughbreds. Horses were genotyped for over 50,000 single nucleotide polymorphism (SNP) markers across the genome, with 34,848 autosomal SNPs used in the final analysis. Linkage disequilibrium, as measured by the squared correlation coefficient (r(2)), was found to be relatively high between closely linked markers (>0.6 at 5 kb) and to extend over long distances, with average r(2) maintained above non-syntenic levels for single nucleotide polymorphisms (SNPs) up to 20 Mb apart. Using formulae which relate expected LD to effective population size (N(e)), and assuming a constant actual population size, N(e) was estimated to be 100 in our population. Values of historical N(e), calculated assuming linear population growth, suggested a decrease in N(e) since the distant past, reaching a minimum twenty generations ago, followed by a subsequent increase until the present time. The qualitative trends observed in N(e) can be rationalized by current knowledge of the history of the Thoroughbred breed, and inbreeding statistics obtained from published pedigree analyses are in agreement with observed values of N(e). Given the high LD observed and the small estimated N(e), genomic methodologies such as genomic selection could feasibly be applied to this population using the existing SNP marker set.
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Affiliation(s)
- L J Corbin
- Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin Biocentre, EH25 9PS, UK.
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Qin H, Chen M, Yi X, Bie S, Zhang C, Zhang Y, Lan J, Meng Y, Yuan Y, Jiao C. Identification of associated SSR markers for yield component and fiber quality traits based on frame map and Upland cotton collections. PLoS One 2015; 10:e0118073. [PMID: 25635680 PMCID: PMC4311988 DOI: 10.1371/journal.pone.0118073] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2014] [Accepted: 01/04/2015] [Indexed: 11/19/2022] Open
Abstract
Detecting QTLs (quantitative trait loci) that enhance cotton yield and fiber quality traits and accelerate breeding has been the focus of many cotton breeders. In the present study, 359 SSR (simple sequence repeat) markers were used for the association mapping of 241 Upland cotton collections. A total of 333 markers, representing 733 polymorphic loci, were detected. The average linkage disequilibrium (LD) decay distances were 8.58 cM (r2 > 0.1) and 5.76 cM (r2 > 0.2). 241 collections were arranged into two subgroups using STRUCTURE software. Mixed linear modeling (MLM) methods (with population structure (Q) and relative kinship matrix (K)) were applied to analyze four phenotypic datasets obtained from four environments (two different locations and two years). Forty-six markers associated with the number of bolls per plant (NB), boll weight (BW), lint percentage (LP), fiber length (FL), fiber strength (FS) and fiber micornaire value (FM) were repeatedly detected in at least two environments. Of 46 associated markers, 32 were identified as new association markers, and 14 had been previously reported in the literature. Nine association markers were near QTLs (at a distance of less than 1-2 LD decay on the reference map) that had been previously described. These results provide new useful markers for marker-assisted selection in breeding programs and new insights for understanding the genetic basis of Upland cotton yields and fiber quality traits at the whole-genome level.
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Affiliation(s)
- Hongde Qin
- Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjiang River (Wuhan), Ministry of Agriculture, Wuhan, P. R. China
| | - Min Chen
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjiang River (Wuhan), Ministry of Agriculture, Wuhan, P. R. China
| | - Xianda Yi
- Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjiang River (Wuhan), Ministry of Agriculture, Wuhan, P. R. China
| | - Shu Bie
- Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjiang River (Wuhan), Ministry of Agriculture, Wuhan, P. R. China
| | - Cheng Zhang
- Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjiang River (Wuhan), Ministry of Agriculture, Wuhan, P. R. China
| | - Youchang Zhang
- Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjiang River (Wuhan), Ministry of Agriculture, Wuhan, P. R. China
| | - Jiayang Lan
- Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjiang River (Wuhan), Ministry of Agriculture, Wuhan, P. R. China
| | - Yanyan Meng
- Institute of Cash Crops, Hubei Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Cotton Biology and Breeding in the Middle Reaches of the Changjiang River (Wuhan), Ministry of Agriculture, Wuhan, P. R. China
| | - Youlu Yuan
- Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyan, China
| | - Chunhai Jiao
- Hubei Academy of Agricultural Sciences, Wuhan, China
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Cuyabano BCD, Su G, Lund MS. Genomic prediction of genetic merit using LD-based haplotypes in the Nordic Holstein population. BMC Genomics 2014; 15:1171. [PMID: 25539631 PMCID: PMC4367958 DOI: 10.1186/1471-2164-15-1171] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2013] [Accepted: 12/12/2014] [Indexed: 11/17/2022] Open
Abstract
Background A haplotype approach to genomic prediction using high density data in dairy cattle as an alternative to single-marker methods is presented. With the assumption that haplotypes are in stronger linkage disequilibrium (LD) with quantitative trait loci (QTL) than single markers, this study focuses on the use of haplotype blocks (haploblocks) as explanatory variables for genomic prediction. Haploblocks were built based on the LD between markers, which allowed variable reduction. The haploblocks were then used to predict three economically important traits (milk protein, fertility and mastitis) in the Nordic Holstein population. Results The haploblock approach improved prediction accuracy compared with the commonly used individual single nucleotide polymorphism (SNP) approach. Furthermore, using an average LD threshold to define the haploblocks (LD≥0.45 between any two markers) increased the prediction accuracies for all three traits, although the improvement was most significant for milk protein (up to 3.1 % improvement in prediction accuracy, compared with the individual SNP approach). Hotelling’s t-tests were performed, confirming the improvement in prediction accuracy for milk protein. Because the phenotypic values were in the form of de-regressed proofs, the improved accuracy for milk protein may be due to higher reliability of the data for this trait compared with the reliability of the mastitis and fertility data. Comparisons between best linear unbiased prediction (BLUP) and Bayesian mixture models also indicated that the Bayesian model produced the most accurate predictions in every scenario for the milk protein trait, and in some scenarios for fertility. Conclusions The haploblock approach to genomic prediction is a promising method for genomic selection in animal breeding. Building haploblocks based on LD reduced the number of variables without the loss of information. This method may play an important role in the future genomic prediction involving while genome sequences.
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Affiliation(s)
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, Denmark.
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QTLs associated with dry matter intake, metabolic mid-test weight, growth and feed efficiency have little overlap across 4 beef cattle studies. BMC Genomics 2014; 15:1004. [PMID: 25410110 PMCID: PMC4253998 DOI: 10.1186/1471-2164-15-1004] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 10/31/2014] [Indexed: 11/21/2022] Open
Abstract
Background The identification of genetic markers associated with complex traits that are expensive to record such as feed intake or feed efficiency would allow these traits to be included in selection programs. To identify large-effect QTL, we performed a series of genome-wide association studies and functional analyses using 50 K and 770 K SNP genotypes scored in 5,133 animals from 4 independent beef cattle populations (Cycle VII, Angus, Hereford and Simmental × Angus) with phenotypes for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake. Results A total of 5, 6, 11 and 10 significant QTL (defined as 1-Mb genome windows with Bonferroni-corrected P-value <0.05) were identified for average daily gain, dry matter intake, metabolic mid-test body weight and residual feed intake, respectively. The identified QTL were population-specific and had little overlap across the 4 populations. The pleiotropic or closely linked QTL on BTA 7 at 23 Mb identified in the Angus population harbours a promising candidate gene ACSL6 (acyl-CoA synthetase long-chain family member 6), and was the largest effect QTL associated with dry matter intake and mid-test body weight explaining 10.39% and 14.25% of the additive genetic variance, respectively. Pleiotropic or closely linked QTL associated with average daily gain and mid-test body weight were detected on BTA 6 at 38 Mb and BTA 7 at 93 Mb confirming previous reports. No QTL for residual feed intake explained more than 2.5% of the additive genetic variance in any population. Marker-based estimates of heritability ranged from 0.21 to 0.49 for residual feed intake across the 4 populations. Conclusions This GWAS study, which is the largest performed for feed efficiency and its component traits in beef cattle to date, identified several large-effect QTL that cumulatively explained a significant percentage of additive genetic variance within each population. Differences in the QTL identified among the different populations may be due to differences in power to detect QTL, environmental variation, or differences in the genetic architecture of trait variation among breeds. These results enhance our understanding of the biology of growth, feed intake and utilisation in beef cattle.
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25
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Lee YS, Woo Lee J, Kim H. Estimating effective population size of thoroughbred horses using linkage disequilibrium and theta (4Nμ) value. Livest Sci 2014. [DOI: 10.1016/j.livsci.2014.08.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Kijas JW, Porto-Neto L, Dominik S, Reverter A, Bunch R, McCulloch R, Hayes BJ, Brauning R, McEwan J. Linkage disequilibrium over short physical distances measured in sheep using a high-density SNP chip. Anim Genet 2014; 45:754-7. [PMID: 25040320 DOI: 10.1111/age.12197] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2014] [Indexed: 01/08/2023]
Abstract
The extent of linkage disequilibrium (LD) between genetic loci has implications for both association studies and the accuracy of genomic prediction. To characterise the persistence of LD in diverse sheep breeds, two SNP genotyping platforms were used. First, existing SNP genotypes from 63 breeds obtained using the ovine SNP50 BeadChip (49,034 loci) were used to estimate LD decay in populations with contrasting levels of genetic diversity. Given the paucity of marker pairs separated by short physical distances on the SNP50 BeadChip, genotyping was subsequently performed for four breeds using the recently developed ovine HD BeadChip that assays approximately 600,000 SNPs with an average genomic spacing of 5 kb. This facilitated a highly accurate estimate of LD over short genomic distances (<30 kb) and revealed LD varies considerably between sheep breeds. Further, sheep appear to contain generally lower levels of LD than do other domestic species, likely a reflection of aspects of their past population history.
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Affiliation(s)
- James W Kijas
- CSIRO Agriculture Flagship, St Lucia, Qld 4067, Australia
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27
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The application of genome-wide SNP genotyping methods in studies on livestock genomes. J Appl Genet 2014; 55:197-208. [PMID: 24566962 DOI: 10.1007/s13353-014-0202-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/14/2014] [Accepted: 02/04/2014] [Indexed: 01/07/2023]
Abstract
Animal genomics is currently undergoing dynamic development, which is driven by the flourishing of high-throughput genome analysis methods. Recently, a large number of animals has been genotyped with the use of whole-genome genotyping assays in the course of genomic selection programmes. The results of such genotyping can also be used for studies on different aspects of livestock genome functioning and diversity. In this article, we review the recent literature concentrating on various aspects of animal genomics, including studies on linkage disequilibrium, runs of homozygosity, selection signatures, copy number variation and genetic differentiation of animal populations. Our work is aimed at providing insight into certain achievements of animal genomics and to arouse interest in basic research on the complexity and structure of the genomes of livestock.
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Yang J, Zhu W, Chen J, Zhang Q, Wu S. Genome-wide two-marker linkage disequilibrium mapping of quantitative trait loci. BMC Genet 2014; 15:20. [PMID: 24507412 PMCID: PMC4015628 DOI: 10.1186/1471-2156-15-20] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 01/31/2014] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In a natural population, the alleles of multiple tightly linked loci on the same chromosome co-segregate and are passed non-randomly from generation to generation. Capitalizing on this phenomenon, a group of mapping methods, commonly referred to as the linkage disequilibrium-based mapping (LD mapping), have been developed recently for detecting genetic associations. However, most current LD mapping methods mainly employed single-marker analysis, overlooking the rich information contained within adjacent linked loci. RESULTS We extend the single-marker LD mapping to include two linked loci and explicitly incorporate their LD information into genetic mapping models (tmLD). We establish the theoretical foundations for the tmLD mapping method and also provide a thorough examination of its statistical properties. Our simulation studies demonstrate that the tmLD mapping method significantly improves the detection power of association compared to the single-marker based and also haplotype based mapping methods. The practical usage and properties of the tmLD mapping method were further elucidated through the analysis of a large-scale dental caries GWAS data set. It shows that the tmLD mapping method can identify significant SNPs that are missed by the traditional single-marker association analysis and haplotype based mapping method. An R package for our proposed method has been developed and is freely available. CONCLUSIONS The proposed tmLD mapping method is more powerful than single marker mapping generally used in GWAS data analysis. We recommend the usage of this improved method over the traditional single marker association analysis.
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Affiliation(s)
| | | | | | | | - Song Wu
- Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY 11790, USA.
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Garcia-Gámez E, Gutiérrez-Gil B, Suarez-Vega A, de la Fuente LF, Arranz JJ. Identification of quantitative trait loci underlying milk traits in Spanish dairy sheep using linkage plus combined linkage disequilibrium and linkage analysis approaches. J Dairy Sci 2013; 96:6059-69. [PMID: 23810588 DOI: 10.3168/jds.2013-6824] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2013] [Accepted: 05/22/2013] [Indexed: 12/20/2022]
Abstract
In this study, 2 procedures were used to analyze a data set from a whole-genome scan, one based on linkage analysis information and the other combing linkage disequilibrium and linkage analysis (LDLA), to determine the quantitative trait loci (QTL) influencing milk production traits in sheep. A total of 1,696 animals from 16 half-sib families were genotyped using the OvineSNP50 BeadChip (Illumina Inc., San Diego, CA) and analysis was performed using a daughter design. Moreover, the same data set has been previously investigated through a genome-wide association (GWA) analysis and a comparison of results from the 3 methods has been possible. The linkage analysis and LDLA methodologies yielded different results, although some significantly associated regions were common to both procedures. The linkage analysis detected 3 overlapping genome-wise significant QTL on sheep chromosome (OAR) 2 influencing milk yield, protein yield, and fat yield, whereas 34 genome-wise significant QTL regions were detected using the LDLA approach. The most significant QTL for protein and fat percentages was detected on OAR3, which was reported in a previous GWA analysis. Both the linkage analysis and LDLA identified many other chromosome-wise significant associations across different sheep autosomes. Additional analyses were performed on OAR2 and OAR3 to determine the possible causality of the most significant polymorphisms identified for these genetic effects by the previously reported GWA analysis. For OAR3, the analyses demonstrated additional genetic proof of the causality previously suggested by our group for a single nucleotide polymorphism located in the α-lactalbumin gene (LALBA). In summary, although the results shown here suggest that in commercial dairy populations, the LDLA method exhibits a higher efficiency to map QTL than the simple linkage analysis or linkage disequilibrium methods, we believe that comparing the 3 analysis methods is the best approach to obtain a global picture of all identifiable QTL segregating in the population at both family-based and population-based levels.
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Affiliation(s)
- E Garcia-Gámez
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, 24071 León, Spain
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Abo-Ismail MK, Kelly MJ, Squires EJ, Swanson KC, Bauck S, Miller SP. Identification of single nucleotide polymorphisms in genes involved in digestive and metabolic processes associated with feed efficiency and performance traits in beef cattle1,2. J Anim Sci 2013; 91:2512-29. [DOI: 10.2527/jas.2012-5756] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- M. K. Abo-Ismail
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada, N1G 2W0
- Department of Animal and Poultry Science, Damanhour University, Damanhour, Egypt
| | - M. J. Kelly
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada, N1G 2W0
- Queensland Alliance for Agriculture and Food Innovation University of Queensland, St Lucia, QLD 4072, Australia
| | - E. J. Squires
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada, N1G 2W0
| | - K. C. Swanson
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada, N1G 2W0
- Animal Sciences Department, North Dakota State University, Fargo 58108-6050
| | - S. Bauck
- GeneSeek, 4665 Innovation Drive, Suite 120, Lincoln, NE 68521
| | - S. P. Miller
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada, N1G 2W0
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Enlarging a training set for genomic selection by imputation of un-genotyped animals in populations of varying genetic architecture. Genet Sel Evol 2013; 45:12. [PMID: 23621897 PMCID: PMC3652763 DOI: 10.1186/1297-9686-45-12] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Accepted: 03/24/2013] [Indexed: 02/02/2023] Open
Abstract
Background The most common application of imputation is to infer genotypes of a high-density panel of markers on animals that are genotyped for a low-density panel. However, the increase in accuracy of genomic predictions resulting from an increase in the number of markers tends to reach a plateau beyond a certain density. Another application of imputation is to increase the size of the training set with un-genotyped animals. This strategy can be particularly successful when a set of closely related individuals are genotyped. Methods Imputation on completely un-genotyped dams was performed using known genotypes from the sire of each dam, one offspring and the offspring’s sire. Two methods were applied based on either allele or haplotype frequencies to infer genotypes at ambiguous loci. Results of these methods and of two available software packages were compared. Quality of imputation under different population structures was assessed. The impact of using imputed dams to enlarge training sets on the accuracy of genomic predictions was evaluated for different populations, heritabilities and sizes of training sets. Results Imputation accuracy ranged from 0.52 to 0.93 depending on the population structure and the method used. The method that used allele frequencies performed better than the method based on haplotype frequencies. Accuracy of imputation was higher for populations with higher levels of linkage disequilibrium and with larger proportions of markers with more extreme allele frequencies. Inclusion of imputed dams in the training set increased the accuracy of genomic predictions. Gains in accuracy ranged from close to zero to 37.14%, depending on the simulated scenario. Generally, the larger the accuracy already obtained with the genotyped training set, the lower the increase in accuracy achieved by adding imputed dams. Conclusions Whenever a reference population resembling the family configuration considered here is available, imputation can be used to achieve an extra increase in accuracy of genomic predictions by enlarging the training set with completely un-genotyped dams. This strategy was shown to be particularly useful for populations with lower levels of linkage disequilibrium, for genomic selection on traits with low heritability, and for species or breeds for which the size of the reference population is limited.
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Fine-mapping quantitative trait loci with a medium density marker panel: efficiency of population structures and comparison of linkage disequilibrium linkage analysis models. Genet Res (Camb) 2013; 94:223-34. [PMID: 22950902 PMCID: PMC3487687 DOI: 10.1017/s0016672312000407] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
Recently, a Haley–Knott-type regression method using combined linkage disequilibrium and linkage analyses (LDLA) was proposed to map quantitative trait loci (QTLs). Chromosome of 5 and 25 cM with 0·25 and 0·05 cM, respectively, between markers were simulated. The differences between the LDLA approaches with regard to QTL position accuracy were very limited, with a significantly better mean square error (MSE) with the LDLA regression (LDLA_reg) in sparse map cases; the contrary was observed, but not significantly, in dense map situations. The computing time required for the LDLA variance components (LDLA_vc) model was much higher than the LDLA_reg model. The precision of QTL position estimation was compared for four numbers of half-sib families, four different family sizes and two experimental designs (half-sibs, and full- and half-sibs). Regarding the number of families, MSE values were lowest for 15 or 50 half-sib families, differences not being significant. We observed that the greater the number of progenies per sire, the more accurate the QTL position. However, for a fixed population size, reducing the number of families (e.g. using a small number of large full-sib families) could lead to less accuracy of estimated QTL position.
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Alhaddad H, Khan R, Grahn RA, Gandolfi B, Mullikin JC, Cole SA, Gruffydd-Jones TJ, Häggström J, Lohi H, Longeri M, Lyons LA. Extent of linkage disequilibrium in the domestic cat, Felis silvestris catus, and its breeds. PLoS One 2013; 8:e53537. [PMID: 23308248 PMCID: PMC3538540 DOI: 10.1371/journal.pone.0053537] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2012] [Accepted: 12/03/2012] [Indexed: 01/21/2023] Open
Abstract
Domestic cats have a unique breeding history and can be used as models for human hereditary and infectious diseases. In the current era of genome-wide association studies, insights regarding linkage disequilibrium (LD) are essential for efficient association studies. The objective of this study is to investigate the extent of LD in the domestic cat, Felis silvestris catus, particularly within its breeds. A custom illumina GoldenGate Assay consisting of 1536 single nucleotide polymorphisms (SNPs) equally divided over ten 1 Mb chromosomal regions was developed, and genotyped across 18 globally recognized cat breeds and two distinct random bred populations. The pair-wise LD descriptive measure (r2) was calculated between the SNPs in each region and within each population independently. LD decay was estimated by determining the non-linear least-squares of all pair-wise estimates as a function of distance using established models. The point of 50% decay of r2 was used to compare the extent of LD between breeds. The longest extent of LD was observed in the Burmese breed, where the distance at which r2 ≈ 0.25 was ∼380 kb, comparable to several horse and dog breeds. The shortest extent of LD was found in the Siberian breed, with an r2 ≈ 0.25 at approximately 17 kb, comparable to random bred cats and human populations. A comprehensive haplotype analysis was also conducted. The haplotype structure of each region within each breed mirrored the LD estimates. The LD of cat breeds largely reflects the breeds’ population history and breeding strategies. Understanding LD in diverse populations will contribute to an efficient use of the newly developed SNP array for the cat in the design of genome-wide association studies, as well as to the interpretation of results for the fine mapping of disease and phenotypic traits.
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Affiliation(s)
- Hasan Alhaddad
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Razib Khan
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Robert A. Grahn
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - Barbara Gandolfi
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
| | - James C. Mullikin
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Shelley A. Cole
- Department of Genetics, Texas Biomedical Research Institute, San Antonio, Texas, United States of America
| | - Timothy J. Gruffydd-Jones
- The Feline Centre, School of Veterinary Science, University of Bristol, Langford, Bristol, United Kingdom
| | - Jens Häggström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Hannes Lohi
- Department of Veterinary Biosciences, Research Programs Unit, Molecular Medicine, University of Helsinki, and The Folkhälsan Research Center, Helsinki, Finland
| | - Maria Longeri
- Dipartimento di Scienze Veterinarie e Sanità Pubblica, Università di Milano, Milano, Italy
| | - Leslie A. Lyons
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, California, United States of America
- * E-mail:
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Sallé G, Jacquiet P, Gruner L, Cortet J, Sauvé C, Prévot F, Grisez C, Bergeaud JP, Schibler L, Tircazes A, François D, Pery C, Bouvier F, Thouly JC, Brunel JC, Legarra A, Elsen JM, Bouix J, Rupp R, Moreno CR. A genome scan for QTL affecting resistance to Haemonchus contortus in sheep1. J Anim Sci 2012; 90:4690-705. [DOI: 10.2527/jas.2012-5121] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- G. Sallé
- INRA, UR631, Station d'Amélioration Génétique des Animaux, BP 27, F-31326, Castanet-Tolosan, France
- INRA, UMR1225, Interactions Hôtes—Agents Pathogènes, BP 87614, F-31076 Toulouse, France
| | - P. Jacquiet
- INRA, UMR1225, Interactions Hôtes—Agents Pathogènes, BP 87614, F-31076 Toulouse, France
| | - L. Gruner
- INRA, UR1282, Infectiologie Animale et Santé Publique, F-37880 Nouzilly, France
| | - J. Cortet
- INRA, UR1282, Infectiologie Animale et Santé Publique, F-37880 Nouzilly, France
| | - C. Sauvé
- INRA, UR1282, Infectiologie Animale et Santé Publique, F-37880 Nouzilly, France
| | - F. Prévot
- INRA, UMR1225, Interactions Hôtes—Agents Pathogènes, BP 87614, F-31076 Toulouse, France
| | - C. Grisez
- INRA, UMR1225, Interactions Hôtes—Agents Pathogènes, BP 87614, F-31076 Toulouse, France
| | - J. P. Bergeaud
- INRA, UMR1225, Interactions Hôtes—Agents Pathogènes, BP 87614, F-31076 Toulouse, France
| | - L. Schibler
- INRA, UMR1313, Laboratoire de Génétique Biochimique et de Cytogénétique, F-78252 Jouy-en-Josas, France
| | - A. Tircazes
- INRA, UR631, Station d'Amélioration Génétique des Animaux, BP 27, F-31326, Castanet-Tolosan, France
| | - D. François
- INRA, UR631, Station d'Amélioration Génétique des Animaux, BP 27, F-31326, Castanet-Tolosan, France
| | - C. Pery
- INRA, UE332, Domaine de la Sapinière, F-18390, Osmoy, France
| | - F. Bouvier
- INRA, UE332, Domaine de la Sapinière, F-18390, Osmoy, France
| | - J. C. Thouly
- INRA, UE332, Domaine de la Sapinière, F-18390, Osmoy, France
| | - J. C. Brunel
- INRA, UE332, Domaine de la Sapinière, F-18390, Osmoy, France
| | - A. Legarra
- INRA, UR631, Station d'Amélioration Génétique des Animaux, BP 27, F-31326, Castanet-Tolosan, France
| | - J. M. Elsen
- INRA, UR631, Station d'Amélioration Génétique des Animaux, BP 27, F-31326, Castanet-Tolosan, France
| | - J. Bouix
- INRA, UR631, Station d'Amélioration Génétique des Animaux, BP 27, F-31326, Castanet-Tolosan, France
| | - R. Rupp
- INRA, UR631, Station d'Amélioration Génétique des Animaux, BP 27, F-31326, Castanet-Tolosan, France
| | - C. R. Moreno
- INRA, UR631, Station d'Amélioration Génétique des Animaux, BP 27, F-31326, Castanet-Tolosan, France
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Aslam ML, Bastiaansen JWM, Elferink MG, Megens HJ, Crooijmans RPMA, Blomberg LA, Fleischer RC, Van Tassell CP, Sonstegard TS, Schroeder SG, Groenen MAM, Long JA. Whole genome SNP discovery and analysis of genetic diversity in Turkey (Meleagris gallopavo). BMC Genomics 2012; 13:391. [PMID: 22891612 PMCID: PMC3496629 DOI: 10.1186/1471-2164-13-391] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Accepted: 08/09/2012] [Indexed: 11/23/2022] Open
Abstract
Background The turkey (Meleagris gallopavo) is an important agricultural species and the second largest contributor to the world’s poultry meat production. Genetic improvement is attributed largely to selective breeding programs that rely on highly heritable phenotypic traits, such as body size and breast muscle development. Commercial breeding with small effective population sizes and epistasis can result in loss of genetic diversity, which in turn can lead to reduced individual fitness and reduced response to selection. The presence of genomic diversity in domestic livestock species therefore, is of great importance and a prerequisite for rapid and accurate genetic improvement of selected breeds in various environments, as well as to facilitate rapid adaptation to potential changes in breeding goals. Genomic selection requires a large number of genetic markers such as e.g. single nucleotide polymorphisms (SNPs) the most abundant source of genetic variation within the genome. Results Alignment of next generation sequencing data of 32 individual turkeys from different populations was used for the discovery of 5.49 million SNPs, which subsequently were used for the analysis of genetic diversity among the different populations. All of the commercial lines branched from a single node relative to the heritage varieties and the South Mexican turkey population. Heterozygosity of all individuals from the different turkey populations ranged from 0.17-2.73 SNPs/Kb, while heterozygosity of populations ranged from 0.73-1.64 SNPs/Kb. The average frequency of heterozygous SNPs in individual turkeys was 1.07 SNPs/Kb. Five genomic regions with very low nucleotide variation were identified in domestic turkeys that showed state of fixation towards alleles different than wild alleles. Conclusion The turkey genome is much less diverse with a relatively low frequency of heterozygous SNPs as compared to other livestock species like chicken and pig. The whole genome SNP discovery study in turkey resulted in the detection of 5.49 million putative SNPs compared to the reference genome. All commercial lines appear to share a common origin. Presence of different alleles/haplotypes in the SM population highlights that specific haplotypes have been selected in the modern domesticated turkey.
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Affiliation(s)
- Muhammad L Aslam
- Animal Breeding and Genomics Centre, Wageningen University, De Elst 1, 6708WD Wageningen, The Netherlands.
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García-Gámez E, Sahana G, Gutiérrez-Gil B, Arranz JJ. Linkage disequilibrium and inbreeding estimation in Spanish Churra sheep. BMC Genet 2012; 13:43. [PMID: 22691044 PMCID: PMC3431250 DOI: 10.1186/1471-2156-13-43] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2012] [Accepted: 06/12/2012] [Indexed: 02/02/2023] Open
Abstract
Background Genomic technologies, such as high-throughput genotyping based on SNP arrays, have great potential to decipher the genetic architecture of complex traits and provide background information concerning genome structure in domestic animals, including the extent of linkage disequilibrium (LD) and haplotype blocks. The objective of this study was to estimate LD, the population evolution (past effective population size) and the level of inbreeding in Spanish Churra sheep. Results A total of 43,784 SNPs distributed in the ovine autosomal genome was analyzed in 1,681 Churra ewes. LD was assessed by measuring r2 between all pairs of loci. For SNPs up to 10 kb apart, the average r2 was 0.329; for SNPs separated by 200–500 kb the average r2 was 0.061. When SNPs are separated by more than 50 Mbp, the average r2 is the same as between non-syntenic SNP pairs (0.003). The effective population size has decreased through time, faster from 1,000 to 100 years ago and slower since the selection scheme started (15–25 generations ago). In the last generation, four years ago, the effective population size was estimated to be 128 animals. Inbreeding coefficients, although differed depending on the estimation approaches, were generally low and showed the same trend, which indicates that since 2003, inbreeding has been slightly increasing in the studied resource population. Conclusions The extent of LD in Churra sheep persists over much more limited distances than reported in dairy cattle and seems to be similar to other ovine populations. Churra sheep show a wide genetic base, with a long-term viable effective population size that has been slightly decreasing since selection scheme began in 1986. The genomic dataset analyzed provided useful information for identifying low-level inbreeding in the sample, whereas based on the parameters reported here, a higher marker density than that analyzed here will be needed to successfully conduct accurate mapping of genes underlying production traits and genomic selection prediction in this sheep breed. Although the Ovine Assembly development is still in a draft stage and future refinements will provide a more accurate physical map that will improve LD estimations, this work is a first step towards the understanding of the genetic architecture in sheep.
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Arumugasundaram S, Ghosh M, Veerasamy S, Ramasamy Y. Species discrimination, population structure and linkage disequilibrium in Eucalyptus camaldulensis and Eucalyptus tereticornis using SSR markers. PLoS One 2011; 6:e28252. [PMID: 22163287 PMCID: PMC3233572 DOI: 10.1371/journal.pone.0028252] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Accepted: 11/04/2011] [Indexed: 12/19/2022] Open
Abstract
Eucalyptus camaldulensis and E. tereticornis are closely related species commonly cultivated for pulp wood in many tropical countries including India. Understanding the genetic structure and linkage disequilibrium (LD) existing in these species is essential for the improvement of industrially important traits. Our goal was to evaluate the use of simple sequence repeat (SSR) loci for species discrimination, population structure and LD analysis in these species. Investigations were carried out with the most common alleles in 93 accessions belonging to these two species using 62 SSR markers through cross amplification. The polymorphic information content (PIC) ranged from 0.44 to 0.93 and 0.36 to 0.93 in E. camaldulensis and E. tereticornis respectively. A clear delineation between the two species was evident based on the analysis of population structure and species-specific alleles. Significant genotypic LD was found in E. camaldulensis, wherein out of 135 significant pairs, 17 pairs showed r2≥0.1. Similarly, in E. tereticornis, out of 136 significant pairs, 18 pairs showed r2≥0.1. The extent of LD decayed rapidly showing the significance of association analyses in eucalypts with higher resolution markers. The availability of whole genome sequence for E. grandis and the synteny and co-linearity in the genome of eucalypts, will allow genome-wide genotyping using microsatellites or single nucleotide polymorphims.
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Affiliation(s)
| | - Modhumita Ghosh
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, Coimbatore, Tamilnadu, India
| | - Sivakumar Veerasamy
- Division of Genetics and Tree Breeding, Institute of Forest Genetics and Tree Breeding, Coimbatore, Tamilnadu, India
| | - Yasodha Ramasamy
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, Coimbatore, Tamilnadu, India
- * E-mail:
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Whiteley AR, Bhat A, Martins EP, Mayden RL, Arunachalam M, Uusi-Heikkilä S, Ahmed ATA, Shrestha J, Clark M, Stemple D, Bernatchez L. Population genomics of wild and laboratory zebrafish (Danio rerio). Mol Ecol 2011; 20:4259-76. [PMID: 21923777 PMCID: PMC3627301 DOI: 10.1111/j.1365-294x.2011.05272.x] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Understanding a wider range of genotype–phenotype associations can be achieved through ecological and evolutionary studies of traditional laboratory models. Here, we conducted the first large-scale geographic analysis of genetic variation within and among wild zebrafish (Danio rerio) populations occurring in Nepal, India, and Bangladesh, and we genetically compared wild populations to several commonly used lab strains. We examined genetic variation at 1832 polymorphic EST-based single nucleotide polymorphisms (SNPs) and the cytb mitochondrial gene in 13 wild populations and three lab strains. Natural populations were subdivided into three major mitochondrial DNA clades with an average among-clade sequence divergence of 5.8%. SNPs revealed five major evolutionarily and genetically distinct groups with an overall FST of 0.170 (95% CI 0.105–0.254). These genetic groups corresponded to discrete geographic regions and appear to reflect isolation in refugia during past climate cycles. We detected 71 significantly divergent outlier loci (3.4%) and nine loci (0.5%) with significantly low FST values. Valleys of reduced heterozygosity, consistent with selective sweeps, surrounded six of the 71 outliers (8.5%). The lab strains formed two additional groups that were genetically distinct from all wild populations. An additional subset of outlier loci was consistent with domestication selection within lab strains. Substantial genetic variation that exists in zebrafish as a whole is missing from lab strains that we analysed. A combination of laboratory and field studies that incorporates genetic variation from divergent wild populations along with the wealth of molecular information available for this model organism provides an opportunity to advance our understanding of genetic influences on phenotypic variation for a vertebrate species.
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Affiliation(s)
- Andrew R Whiteley
- Department of Environmental Conservation, University of Massachusetts, Amherst, MA 01003, USA.
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Vangestel C, Mergeay J, Dawson DA, Vandomme V, Lens L. Developmental stability covaries with genome-wide and single-locus heterozygosity in house sparrows. PLoS One 2011; 6:e21569. [PMID: 21747940 PMCID: PMC3128584 DOI: 10.1371/journal.pone.0021569] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2010] [Accepted: 06/03/2011] [Indexed: 11/19/2022] Open
Abstract
Fluctuating asymmetry (FA), a measure of developmental instability, has been hypothesized to increase with genetic stress. Despite numerous studies providing empirical evidence for associations between FA and genome-wide properties such as multi-locus heterozygosity, support for single-locus effects remains scant. Here we test if, and to what extent, FA co-varies with single- and multilocus markers of genetic diversity in house sparrow (Passer domesticus) populations along an urban gradient. In line with theoretical expectations, FA was inversely correlated with genetic diversity estimated at genome level. However, this relationship was largely driven by variation at a single key locus. Contrary to our expectations, relationships between FA and genetic diversity were not stronger in individuals from urban populations that experience higher nutritional stress. We conclude that loss of genetic diversity adversely affects developmental stability in P. domesticus, and more generally, that the molecular basis of developmental stability may involve complex interactions between local and genome-wide effects. Further study on the relative effects of single-locus and genome-wide effects on the developmental stability of populations with different genetic properties is therefore needed.
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Affiliation(s)
- Carl Vangestel
- Terrestrial Ecology Unit, Department of Biology, Ghent University, Ghent, Belgium.
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Amaral AJ, Ferretti L, Megens HJ, Crooijmans RPMA, Nie H, Ramos-Onsins SE, Perez-Enciso M, Schook LB, Groenen MAM. Genome-wide footprints of pig domestication and selection revealed through massive parallel sequencing of pooled DNA. PLoS One 2011; 6:e14782. [PMID: 21483733 PMCID: PMC3070695 DOI: 10.1371/journal.pone.0014782] [Citation(s) in RCA: 99] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Accepted: 01/29/2011] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Artificial selection has caused rapid evolution in domesticated species. The identification of selection footprints across domesticated genomes can contribute to uncover the genetic basis of phenotypic diversity. METHODOLOGY/MAIN FINDINGS Genome wide footprints of pig domestication and selection were identified using massive parallel sequencing of pooled reduced representation libraries (RRL) representing ∼2% of the genome from wild boar and four domestic pig breeds (Large White, Landrace, Duroc and Pietrain) which have been under strong selection for muscle development, growth, behavior and coat color. Using specifically developed statistical methods that account for DNA pooling, low mean sequencing depth, and sequencing errors, we provide genome-wide estimates of nucleotide diversity and genetic differentiation in pig. Widespread signals suggestive of positive and balancing selection were found and the strongest signals were observed in Pietrain, one of the breeds most intensively selected for muscle development. Most signals were population-specific but affected genomic regions which harbored genes for common biological categories including coat color, brain development, muscle development, growth, metabolism, olfaction and immunity. Genetic differentiation in regions harboring genes related to muscle development and growth was higher between breeds than between a given breed and the wild boar. CONCLUSIONS/SIGNIFICANCE These results, suggest that although domesticated breeds have experienced similar selective pressures, selection has acted upon different genes. This might reflect the multiple domestication events of European breeds or could be the result of subsequent introgression of Asian alleles. Overall, it was estimated that approximately 7% of the porcine genome has been affected by selection events. This study illustrates that the massive parallel sequencing of genomic pools is a cost-effective approach to identify footprints of selection.
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Affiliation(s)
- Andreia J. Amaral
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - Luca Ferretti
- Department of Animal Science and Food Technology, Universitat Autonoma de Barcelona, Bellaterra, Spain
- Animal Science Department, Centre for Research in Agricultural Genomics, Bellaterra, Spain
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | | | - Haisheng Nie
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - Sebastian E. Ramos-Onsins
- Department of Animal Science and Food Technology, Universitat Autonoma de Barcelona, Bellaterra, Spain
- Animal Science Department, Centre for Research in Agricultural Genomics, Bellaterra, Spain
| | - Miguel Perez-Enciso
- Department of Animal Science and Food Technology, Universitat Autonoma de Barcelona, Bellaterra, Spain
- Animal Science Department, Centre for Research in Agricultural Genomics, Bellaterra, Spain
- Life and Medical Sciences, Institució Catalana de Recerca i Estudis Avançats, Barcelona, Spain
| | - Lawrence B. Schook
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Martien A. M. Groenen
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
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Zhang C, Plastow G. Genomic Diversity in Pig (Sus scrofa) and its Comparison with Human and other Livestock. Curr Genomics 2011; 12:138-46. [PMID: 21966252 PMCID: PMC3129048 DOI: 10.2174/138920211795564386] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 01/21/2011] [Accepted: 01/22/2011] [Indexed: 11/22/2022] Open
Abstract
We have reviewed the current pig (Sus scrofa) genomic diversity within and between sites and compared them with human and other livestock. The current Porcine 60K single nucleotide polymorphism (SNP) panel has an average SNP distance in a range of 30 - 40 kb. Most of genetic variation was distributed within populations, and only a small proportion of them existed between populations. The average heterozygosity was lower in pig than in human and other livestock. Genetic inbreeding coefficient (F(IS)), population differentiation (F(ST)), and Nei's genetic distance between populations were much larger in pig than in human and other livestock. Higher average genetic distance existed between European and Asian populations than between European or between Asian populations. Asian breeds harboured much larger variability and higher average heterozygosity than European breeds. The samples of wild boar that have been analyzed displayed more extensive genetic variation than domestic breeds. The average linkage disequilibrium (LD) in improved pig breeds extended to 1 - 3 cM, much larger than that in human (~ 30 kb) and cattle (~ 100 kb), but smaller than that in sheep (~ 10 cM). European breeds showed greater LD that decayed more slowly than Asian breeds. We briefly discuss some processes for maintaining genomic diversity in pig, including migration, introgression, selection, and drift. We conclude that, due to the long time of domestication, the pig possesses lower heterozygosity, higher F(IS), and larger LD compared with human and cattle. This implies that a smaller effective population size and less informative markers are needed in pig for genome wide association studies.
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Affiliation(s)
| | - Graham Plastow
- 1400 College Plaza, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2C8, Canada
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Belamkar V, Selvaraj MG, Ayers JL, Payton PR, Puppala N, Burow MD. A first insight into population structure and linkage disequilibrium in the US peanut minicore collection. Genetica 2011; 139:411-29. [PMID: 21442404 DOI: 10.1007/s10709-011-9556-2] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 01/25/2011] [Indexed: 12/13/2022]
Abstract
Knowledge of genetic diversity, population structure, and degree of linkage disequilibrium (LD) in target association mapping populations is of great importance and is a prerequisite for LD-based mapping. In the present study, 96 genotypes comprising 92 accessions of the US peanut minicore collection, a component line of the tetraploid variety Florunner, diploid progenitors A. duranensis (AA) and A. ipaënsis (BB), and synthetic amphidiploid accession TxAG-6 were investigated with 392 simple sequence repeat (SSR) marker bands amplified using 32 highly-polymorphic SSR primer pairs. Both distance- and model-based (Bayesian) cluster analysis revealed the presence of structured diversity. In general, the wild-species accessions and the synthetic amphidiploid grouped separately from most minicore accessions except for COC155, and were eliminated from most subsequent analyses. UPGMA analysis divided the population into four subgroups, two major subgroups representing subspecies fastigiata and hypogaea, a third group containing individuals from each subspecies or possibly of mixed ancestry, and a fourth group, either consisting of COC155 alone if wild species were excluded, or of COC155, the diploid species, and the synthetic amphidiploid. Model-based clustering identified four subgroups- one each for fastigiata and hypogaea subspecies, a third consisting of individuals of both subspecies or of mixed ancestry predominantly from Africa or Asia, and a fourth group, consisting of individuals predominantly of var fastigiata, peruviana, and aequatoriana accessions from South America, including COC155. Analysis of molecular variance (AMOVA) revealed statistically-significant (P < 0.0001) genetic variance of 16.87% among subgroups. A total of 4.85% of SSR marker pairs revealed significant LD (at r(2) ≥ 0.1). Of the syntenic marker pairs separated by distances < 10 cM, 11-20 cM, 21-50 cM, and > 50 cM, 19.33, 5.19, 6.25 and 5.29% of marker pairs were found in strong LD (P ≤ 0.01), in accord with LD extending to great distances in self pollinated crops. A threshold value of r(2) > 0.035 was found to distinguish mean r(2) values of linkage distance groups statistically from the mean r(2) values of unlinked markers; LD was found to extend to 10 cM over the entire minicore collection by this criterion. However, there were large differences in r(2) values among marker pairs even among tightly-linked markers. The implications of these findings with regard to the possibility of using association mapping for detection of genome-wide SSR marker-phenotype association are discussed.
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Affiliation(s)
- Vikas Belamkar
- Center for Biotechnology and Genomics, Texas Tech University, Lubbock, TX 79409, USA
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Miller JM, Poissant J, Kijas JW, Coltman DW. A genome-wide set of SNPs detects population substructure and long range linkage disequilibrium in wild sheep. Mol Ecol Resour 2010; 11:314-22. [PMID: 21429138 DOI: 10.1111/j.1755-0998.2010.02918.x] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The development of genomic resources for wild species is still in its infancy. However, cross-species utilization of technologies developed for their domestic counterparts has the potential to unlock the genomes of organisms that currently lack genomic resources. Here, we apply the OvineSNP50 BeadChip, developed for domestic sheep, to two related wild ungulate species: the bighorn sheep (Ovis canadensis) and the thinhorn sheep (Ovis dalli). Over 95% of the domestic sheep markers were successfully genotyped in a sample of fifty-two bighorn sheep while over 90% were genotyped in two thinhorn sheep. Pooling the results from both species identified 868 single-nucleotide polymorphisms (SNPs), 570 were detected in bighorn sheep, while 330 SNPs were identified in thinhorn sheep. The total panel of SNPs was able to discriminate between the two species, assign population of origin for bighorn sheep and detect known relationship classes within one population of bighorn sheep. Using an informative subset of these SNPs (n=308), we examined the extent of genome-wide linkage disequilibrium (LD) within one population of bighorn sheep and found that high levels of LD persist over 4 Mb.
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Affiliation(s)
- J M Miller
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
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Application of association mapping to understanding the genetic diversity of plant germplasm resources. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2010; 2008:574927. [PMID: 18551188 PMCID: PMC2423417 DOI: 10.1155/2008/574927] [Citation(s) in RCA: 107] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2007] [Accepted: 04/18/2008] [Indexed: 02/05/2023]
Abstract
Compared to the conventional linkage mapping, linkage disequilibrium (LD)-mapping, using the nonrandom associations of loci in haplotypes, is a powerful high-resolution mapping tool for complex quantitative traits. The recent advances in the development of unbiased association mapping approaches for plant population with their successful applications in dissecting a number of simple to complex traits in many crop species demonstrate a flourish of the approach as a “powerful gene tagging” tool for crops in the plant genomics era of 21st century. The goal of this review is to provide nonexpert readers of crop breeding community with (1) the basic concept, merits, and simple description of existing methodologies for an association mapping with the recent improvements for plant populations, and (2) the details of some of pioneer and recent studies on association mapping in various crop species to demonstrate the feasibility, success, problems, and future perspectives of the efforts in plants. This should be helpful for interested readers of international plant research community as a guideline for the basic understanding, choosing the appropriate methods, and its application.
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Novel polymorphisms of the growth hormone gene and their effect on growth traits in Chinese goats. Meat Sci 2010; 86:758-63. [PMID: 20643508 DOI: 10.1016/j.meatsci.2010.06.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Revised: 06/12/2010] [Accepted: 06/15/2010] [Indexed: 11/23/2022]
Abstract
The polymorphisms of the growth hormone (GH) gene were analyzed in 686 individuals from four goat populations, Three haplotypes (A, B and C) and three observed genotypes (AA, AB and AC) were detected at the P2 locus, and three haplotypes (E, F and G) and three observed genotypes (EE, EF and EG) were also detected at the P4 locus. In addition, five single nucleotide polymorphisms (SNPs)-A112G, C142T (Gly>Ser), C214T (P2 locus), C266A (Pro>His) and C214T (P4 locus, Arg>Trp), were identified by GH gene sequencing and PCR-SSCP analysis. The SNPs loci were in Hardy-Weinberg disequilibrium in three goat populations (P<0.05). Association of polymorphisms with growth traits was done in BG, F1 and F1 populations, which were shown to be associated with growth traits in three goat populations. The SNPs in the goat GH gene had significant effects on growth traits (P<0.05). suggesting that the GH gene is a strong candidate gene that affects growth traits in goat.
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Backström N, Forstmeier W, Schielzeth H, Mellenius H, Nam K, Bolund E, Webster MT, Öst T, Schneider M, Kempenaers B, Ellegren H. The recombination landscape of the zebra finch Taeniopygia guttata genome. Genome Res 2010; 20:485-95. [PMID: 20357052 PMCID: PMC2847751 DOI: 10.1101/gr.101410.109] [Citation(s) in RCA: 168] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2009] [Accepted: 12/02/2009] [Indexed: 12/18/2022]
Abstract
Understanding the causes and consequences of variation in the rate of recombination is essential since this parameter is considered to affect levels of genetic variability, the efficacy of selection, and the design of association and linkage mapping studies. However, there is limited knowledge about the factors governing recombination rate variation. We genotyped 1920 single nucleotide polymorphisms in a multigeneration pedigree of more than 1000 zebra finches (Taeniopygia guttata) to develop a genetic linkage map, and then we used these map data together with the recently available draft genome sequence of the zebra finch to estimate recombination rates in 1 Mb intervals across the genome. The average zebra finch recombination rate (1.5 cM/Mb) is higher than in humans, but significantly lower than in chicken. The local rates of recombination in chicken and zebra finch were only weakly correlated, demonstrating evolutionary turnover of the recombination landscape in birds. The distribution of recombination events was heavily biased toward ends of chromosomes, with a stronger telomere effect than so far seen in any organism. In fact, the recombination rate was as low as 0.1 cM/Mb in intervals up to 100 Mb long in the middle of the larger chromosomes. We found a positive correlation between recombination rate and GC content, as well as GC-rich sequence motifs. Levels of linkage disequilibrium (LD) were significantly higher in regions of low recombination, showing that heterogeneity in recombination rates have left a footprint on the genomic landscape of LD in zebra finch populations.
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Affiliation(s)
- Niclas Backström
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Wolfgang Forstmeier
- Max Planck Institute for Ornithology, Department of Behavioural Ecology and Evolutionary Genetics, 82319 Seewiesen, Germany
| | - Holger Schielzeth
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
- Max Planck Institute for Ornithology, Department of Behavioural Ecology and Evolutionary Genetics, 82319 Seewiesen, Germany
| | - Harriet Mellenius
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Kiwoong Nam
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Elisabeth Bolund
- Max Planck Institute for Ornithology, Department of Behavioural Ecology and Evolutionary Genetics, 82319 Seewiesen, Germany
| | - Matthew T. Webster
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
| | - Torbjörn Öst
- Molecular Medicine, Department of Medical Sciences, University Hospital, SE-751 85 Uppsala, Sweden
| | - Melanie Schneider
- Max Planck Institute for Ornithology, Department of Behavioural Ecology and Evolutionary Genetics, 82319 Seewiesen, Germany
| | - Bart Kempenaers
- Max Planck Institute for Ornithology, Department of Behavioural Ecology and Evolutionary Genetics, 82319 Seewiesen, Germany
| | - Hans Ellegren
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
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Xu H, Shen X, Zhou M, Luo C, Kang L, Liang Y, Zeng H, Nie Q, Zhang D, Zhang X. The dopamine D2 receptor gene polymorphisms associated with chicken broodiness. Poult Sci 2010; 89:428-38. [DOI: 10.3382/ps.2009-00428] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Rexroad CE, Vallejo RL. Estimates of linkage disequilibrium and effective population size in rainbow trout. BMC Genet 2009; 10:83. [PMID: 20003428 PMCID: PMC2800115 DOI: 10.1186/1471-2156-10-83] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Accepted: 12/14/2009] [Indexed: 12/19/2022] Open
Abstract
Background The use of molecular genetic technologies for broodstock management and selective breeding of aquaculture species is becoming increasingly more common with the continued development of genome tools and reagents. Several laboratories have produced genetic maps for rainbow trout to aid in the identification of loci affecting phenotypes of interest. These maps have resulted in the identification of many quantitative/qualitative trait loci affecting phenotypic variation in traits associated with albinism, disease resistance, temperature tolerance, sex determination, embryonic development rate, spawning date, condition factor and growth. Unfortunately, the elucidation of the precise allelic variation and/or genes underlying phenotypic diversity has yet to be achieved in this species having low marker densities and lacking a whole genome reference sequence. Experimental designs which integrate segregation analyses with linkage disequilibrium (LD) approaches facilitate the discovery of genes affecting important traits. To date the extent of LD has been characterized for humans and several agriculturally important livestock species but not for rainbow trout. Results We observed that the level of LD between syntenic loci decayed rapidly at distances greater than 2 cM which is similar to observations of LD in other agriculturally important species including cattle, sheep, pigs and chickens. However, in some cases significant LD was also observed up to 50 cM. Our estimate of effective population size based on genome wide estimates of LD for the NCCCWA broodstock population was 145, indicating that this population will respond well to high selection intensity. However, the range of effective population size based on individual chromosomes was 75.51 - 203.35, possibly indicating that suites of genes on each chromosome are disproportionately under selection pressures. Conclusions Our results indicate that large numbers of markers, more than are currently available for this species, will be required to enable the use of genome-wide integrated mapping approaches aimed at identifying genes of interest in rainbow trout.
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Affiliation(s)
- Caird E Rexroad
- USDA/ARS National Center for Cool and Cold Water Aquaculture, Leetown, West Virginia 25430, USA.
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Abstract
Knowledge about the extent and patterns of linkage disequilibrium (LD) can provide important insights into demographic processes and strategies to identify the genetic basis of complex phenotypes in wild populations. However, data on the extent and patterns of LD from non-model vertebrate species from the wild are still scarce. We conducted so far the most extensive and detailed examination of LD in a pedigreed wild bird population using genotypes from 97 autosomal and 6 gonosomal microsatellites and a recently established linkage map of Siberian jays (Perisoreus infaustus). Analysis of syntenic marker pairs showed high levels of LD that extended over tens of centimorgans or several megabases and generally decayed as an increasing function of intermarker distance. In addition, significant LD was also very common between nonsyntenic markers. Patterns of LD varied across different linkage groups possibly because of the differences in chromosomal structure (macro-, micro-, and Z-chromosome). In particular, the level of LD was significantly lower on the Z-chromosome than on the autosomes at comparable genetic distances. In general, the high levels and extent of LD in this population are likely owing to its relatively small size, significant intrapopulation genetic structure, and occurrence of inbreeding. Whatever the cause, the long-range LD between syntenic loci suggests that LD mapping of phenotypic traits in this population using low-density markers maps is feasible. However, the frequent occurrence of LD between nonsyntenic markers suggests that the combined use of linkage and LD methods is needed to reduce the likelihood of false-positive associations between marker loci and traits of ecological and evolutionary interest.
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