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A hybrid zone between Bathymodiolus mussel lineages from eastern Pacific hydrothermal vents ArchiMer
Johnson, Shannon B.; Won, Yong-jin; Harvey, Julio B. J.; Vrijenhoek, Robert C..
Background: The inhabitants of deep-sea hydrothermal vents occupy ephemeral island-like habitats distributed sporadically along tectonic spreading-centers, back-arc basins, and volcanically active seamounts. The majority of vent taxa undergo a pelagic larval phase, and thus varying degrees of geographical subdivision, ranging from no impedance of dispersal to complete isolation, often exist among taxa that span common geomorphological boundaries. Two lineages of Bathymodiolus mussels segregate on either side of the Easter Microplate, a boundary that separates the East Pacific Rise from spreading centers connected to the Pacific-Antarctic Ridge. Results: A recent sample from the northwest flank of the Easter Microplate contained an admixture of northern...
Tipo: Text Palavras-chave: Bathymodiolus antarcticus n. sp; Hybridization; Recombination; Linkage disequilibrium; Deep-sea; Hydrothermal vent; Bathymodiolus thermophilus.
Ano: 2013 URL: http://archimer.ifremer.fr/doc/00185/29626/28000.pdf
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Assessment of the association between SMAD1 and HHIP gene variation and non-syndromic cleft-lip palate in Chilean case-parent trios Genet. Mol. Biol.
Suazo,José; Santos,José Luis; Jara,Lilian; Blanco,Rafael.
Nonsyndromic cleft lip/palate (NSCLP) is a congenital malformation with features of a complex genetic trait. Several studies have reported positive association and linkage between NSCLP and microsatellite markers in the 4q28-4q33 region particularly with the D4S192 (4q31) marker. We hypothesized that the candidate genes SMAD1 and HHIP (4q31) could be involved in the etiology of NSCLP based on previous positive linkage results and their important role in maxillofacial development. We evaluated the possible association between microsatellite markers located at less than 1 cM from these genes and NSCLP using a sample of 58 Chilean case-parent trios. Microsatellite markers were analyzed using the polymerase chain reaction (PCR) with fluorescent labeled...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Candidate genes; Case-parents trio design; Linkage disequilibrium; Nonsyndromic cleft lip/palate.
Ano: 2008 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000400006
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Demarcation of informative chromosomes in tropical sweet corn inbred lines using microsatellite DNA markers Genet. Mol. Biol.
Kashiani,Pedram; Saleh,Ghizan; Panandam,Jothi Malar; Abdullah,Nur Ashikin Psyquay; Selamat,Ahmad.
A study of genetic variation among 10 pairs of chromosomes extracted from 13 tropical sweet corn inbred lines, using 99 microsatellite markers, revealed a wide range of genetic diversity. Allelic richness and the number of effective alleles per chromosome ranged from 2.78 to 4.33 and 1.96 to 3.47, respectively, with respective mean values of 3.62 and 2.73. According to the Shannon's information index (I) and Nei's gene diversity coefficient (Nei), Chromosome 10 was the most informative chromosome (I = 1.311 and Nei = 0.703), while Chromosome 2 possessed the least (I = 0.762 and Nei = 0.456). Based on linkage disequilibrium (LD) measurements for loci less than 50 cM apart on the same chromosome, all loci on Chromosomes 1, 6 and 7 were in equilibrium. Even...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Microsatellite; Inbred line; Chromosome; Genetic variation; Linkage disequilibrium.
Ano: 2012 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572012000400012
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Estimating effective population size of large marine populations, is it feasible? ArchiMer
Marandel, Florianne; Lorance, Pascal; Berthele, Olivier; Trenkel, Verena; Waples, Robin S.; Lamy, Jean-baptiste.
stainable exploitation of marine populations is a challenging task relying on information about their current and past abundance. Fisheries‐related data can be scarce and unreliable making them unsuitable for quantitative modelling. One fishery independent method that has attracted attention in this context consists in estimating the effective population size (Ne), a concept founded in population genetics. We reviewed recent empirical studies on Ne and carried out a simulation study to evaluate the feasibility of estimating Ne in large fish populations with the currently available methods. The detailed review of 26 studies found that published empirical Ne values were very similar despite differences in species and total population sizes (N). Genetic...
Tipo: Text Palavras-chave: Census population size; Effective population size; Fish; Linkage disequilibrium; Management; Simulation.
Ano: 2019 URL: https://archimer.ifremer.fr/doc/00470/58162/60678.pdf
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Estimating effective population size using RADseq: Effects of SNP selection and sample size ArchiMer
Marandel, Florianne; Charrier, Gregory; Lamy, Jean-baptiste; Le Cam, Sabrina; Lorance, Pascal; Trenkel, Verena.
Effective population size (Ne) is a key parameter of population genetics. However, Ne remains challenging to estimate for natural populations as several factors are likely to bias estimates. These factors include sampling design, sequencing method, and data filtering. One issue inherent to the restriction site‐associated DNA sequencing (RADseq) protocol is missing data and SNP selection criteria (e.g., minimum minor allele frequency, number of SNPs). To evaluate the potential impact of SNP selection criteria on Ne estimates (Linkage Disequilibrium method) we used RADseq data for a nonmodel species, the thornback ray. In this data set, the inbreeding coefficient FIS was positively correlated with the amount of missing data, implying data were missing...
Tipo: Text Palavras-chave: Effective population size; Linkage disequilibrium; NeEstimator; RADseq; Skates and rays.
Ano: 2020 URL: https://archimer.ifremer.fr/doc/00607/71934/70628.pdf
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Evaluation of genetic diversity and linkage disequilibrium in Korean-bred rice varieties using SSR markers Electron. J. Biotechnol.
Wang,Xiao-Qiang; Kwon,Soon-Wook; Park,Yong-Jin.
Background: In order to evaluate the variation among different rice types, the genetic diversity in a rice collection composed by 59 breeding lines, 23 landraces, 18 weedy rice lines, and 35 introduced lines that collected from countries worldwide was analyzed using 134 simple sequence repeat markers. Results: In total, 1264 alleles were identified (average, 9.43 per locus). Rare alleles made up a large portion (58.4%) of the detected alleles, and 29 unique alleles associated with rice accessions were also discovered. A model-based structural analysis revealed the presence of three subpopulations. The genetic relationships revealed by the neighbour-joining tree method were fairly consistent with the structure-based membership assignments for most of the...
Tipo: Journal article Palavras-chave: Landraces; Linkage disequilibrium; Population structure; Rice; Simple sequence repeats.
Ano: 2013 URL: http://www.scielo.cl/scielo.php?script=sci_arttext&pid=S0717-34582013000500011
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Evaluation of imputed genomic data in discrete traits using Random forest and Bayesian threshold methodsb Animal Sciences
Sadeghi, Saadat; Rafat, Seyed Abbas; Alijani, Sadegh.
The objectives of this study were (1) to quantify imputation accuracy and to assess the factors affecting it; and (2) to evaluate the accuracy of threshold BayesA (TBA), Bayesian threshold LASSO (BTL) and random forest (RF) algorithms to analyze discrete traits. Genomic data were simulated to reflect variations in heritability (h2 = 0.30 and 0.10), number of QTL (QTL = 81 and 810), number of SNP (10 K and 50 K) and linkage disequilibrium (LD=low and high) for 27 chromosomes. For real condition simulating, we randomly masked markers with 90% missing rate for each scenario; afterwards, hidden markers were imputed using FImpute software. In imputed genotypes, a wide range of accuracy was observed for RF (0.164-0.512) compared to TBA (0.283-0.469) and BTL...
Tipo: Info:eu-repo/semantics/article Palavras-chave: PhD candidate of animal breeding accuracy; Genomic architecture; Linkage disequilibrium; Machine learning; Masked genotypes..
Ano: 2018 URL: http://periodicos.uem.br/ojs/index.php/ActaSciAnimSci/article/view/39007
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Genetic association of SNPs in the FTO gene and predisposition to obesity in Malaysian Malays BJMBR
Apalasamy,Y.D.; Ming,M.F.; Rampal,S.; Bulgiba,A.; Mohamed,Z..
The common variants in the fat mass- and obesity-associated (FTO) gene have been previously found to be associated with obesity in various adult populations. The objective of the present study was to investigate whether the single nucleotide polymorphisms (SNPs) and linkage disequilibrium (LD) blocks in various regions of the FTO gene are associated with predisposition to obesity in Malaysian Malays. Thirty-one FTO SNPs were genotyped in 587 (158 obese and 429 non-obese) Malaysian Malay subjects. Obesity traits and lipid profiles were measured and single-marker association testing, LD testing, and haplotype association analysis were performed. LD analysis of the FTO SNPs revealed the presence of 57 regions with complete LD (D’ = 1.0). In addition, we...
Tipo: Info:eu-repo/semantics/article Palavras-chave: FTO gene; SNP; Obesity; Linkage disequilibrium; Haplotypes.
Ano: 2012 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2012001200003
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Genome selection in fruit breeding: application to table grapes Scientia Agricola
Viana,Alexandre Pio; Resende,Marcos Deon Vilela de; Riaz,Summaira; Walker,Michael Andrew.
ABSTRACT Genomic selection (GS) has recently been proposed as a new selection strategy which represents an innovative paradigm in crop improvement, now widely adopted in animal breeding. Genomic selection relies on phenotyping and high-density genotyping of a sufficiently large and representative sample of the target breeding population, so that the majority of loci that regulate a quantitative trait are in linkage disequilibrium with one or more molecular markers and can thus be captured by selection. In this study we address genomic selection in a practical fruit breeding context applying it to a breeding population of table grape obtained from a cross between the hybrid genotype D8909-15 (Vitis rupestris × Vitis arizonica/girdiana), which is resistant...
Tipo: Info:eu-repo/semantics/article Palavras-chave: MAS; SSR markers; Linkage disequilibrium; Genomic selection.
Ano: 2016 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-90162016000200142
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Genome-wide association for mapping QTLs linked to protein and oil contents in soybean PAB
Dias,Douglas Antônio; Polo,Leandra Regina Texeira; Lazzari,Fabiane; Silva,Glacy Jaqueline da; Schuster,Ivan.
Abstract: The objective of this work was to identify single-nucleotide polymorphism (SNP) markers linked with quantitative trait loci (QTLs) associated with increased contents of protein and oil in soybean. A total of 169 Brazilian soybean varieties, genotyped with 6,000 SNP markers, were evaluated. Protein and oil contents were obtained with the near-infrared reflectance method. Correlation and multiple linear regression analyses were used to identify linkage disequilibrium between SNP markers and the QTLs associated with the two characteristics. Seven QTLs were found to be associated with protein content, on six chromosomes (2, 6, 11, 12, 13, and 16), explaining 60.9% of the variation in this trait. For oil content, eight QTLs were identified on six...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Glycine max; Association genetics; Genomic selection; Grain quality; Linkage disequilibrium; Marker-assisted selection..
Ano: 2017 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-204X2017001000896
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Genome-wide association study of pre-harvest sprouting resistance in Chinese wheat founder parents Genet. Mol. Biol.
Lin,Yu; Liu,Shihang; Liu,Yaxi; Liu,Yujiao; Chen,Guoyue; Xu,Jie; Deng,Mei; Jiang,Qiantao; Wei,Yuming; Lu,Yanli; Zheng,Youliang.
Abstract Pre-harvest sprouting (PHS) is a major abiotic factor affecting grain weight and quality, and is caused by an early break in seed dormancy. Association mapping (AM) is used to detect correlations between phenotypes and genotypes based on linkage disequilibrium (LD) in wheat breeding programs. We evaluated seed dormancy in 80 Chinese wheat founder parents in five environments and performed a genome-wide association study using 6,057 markers, including 93 simple sequence repeat (SSR), 1,472 diversity array technology (DArT), and 4,492 single nucleotide polymorphism (SNP) markers. The general linear model (GLM) and the mixed linear model (MLM) were used in this study, and two significant markers (tPt-7980 and wPt-6457) were identified. Both markers...
Tipo: Info:eu-repo/semantics/article Palavras-chave: General linear model; Linkage disequilibrium; Marker-trait associations; Mixed linear model; Seed dormancy.
Ano: 2017 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572017000400620
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Identification and characterization of polymorphisms at the HSA alpha1-acid glycoprotein (ORM*) gene locus in Caucasians Genet. Mol. Biol.
Owczarek,Catherine M.; Owczarek,Aleksander L.; Board,Philip G..
Human alpha1-acid glycoprotein (AGP) or orosomucoid (ORM) is a major acute phase protein that is thought to play a crucial role in maintaining homeostasis. Human AGP is the product of a cluster of at least two adjacent genes located on HSA chromosome 9. Using a range of restriction endonucleases we have investigated DNA variation at the locus encoding the AGP genes in a panel of healthy Caucasians. Polymorphisms were identified using BamHI, EcoRI, BglII, PvuII, HindIII, TaqI and MspI. Non-random associations were found between the BamHI, EcoRI, BglII RFLPs. The RFLPs detected with PvuII, TaqI and MspI were all located in exon 6 of both AGP genes. The duplication of an AGP gene was observed in 11% of the indiviuals studied and was in linkage disequilibrium...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Human alpha1-acid glycoprotein; RFLP; Linkage disequilibrium.
Ano: 2002 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572002000100004
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Linkage disequilibrium and diversity for three genomic regions in Azoreans and mainland Portuguese Genet. Mol. Biol.
Branco,Claudia C.; Pacheco,Paula R.; Cabrol,Ester; Cabral,Rita; Vicente,Astrid M.; Mota-Vieira,Luisa.
Studies on linkage disequilibrium (LD) across the genome and populations have been used in recent years with the main objective of improving gene mapping of complex traits. Here, we characterize the patterns of genetic diversity of HLA loci and evaluate LD (D') extent in three genomic regions: Xq13.3, NRY and HLA. In addition, we examine the distribution of DXS1225-DXS8082 haplotype diversity in Azoreans and mainland Portuguese. Allele distribution has demonstrated that the São Miguel population is genetically very diverse; haplotype analysis revealed 100% discriminatory power for X- and Y-markers and 94.3% for HLA markers. Standardized multiallelic D' in these three genomic regions shows values lower than 0.33, thereby suggesting there is no extensive LD...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Linkage disequilibrium; X-chromosome; Y-chromosome; HLA; São Miguel; Azores.
Ano: 2009 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572009000200003
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Linkage disequilibrium and past effective population size in native Tunisian cattle Genet. Mol. Biol.
Jemaa,Slim Ben; Thamri,Nejia; Mnara,Sofiane; Rebours,Emmanuelle; Rocha,Dominique; Boussaha,Mekki.
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...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Tunisian cattle; Conservation; Linkage disequilibrium; Effective population size; Single nucleotide polymorphism.
Ano: 2019 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572019000100052
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Linkage disequilibrium, genetic association mapping and gene localization in crop plants Genet. Mol. Biol.
Sorkheh,Karim; Malysheva-Otto,Lyudmyla V.; Wirthensohn,Michelle G.; Tarkesh-Esfahani,Saeed; Martínez-Gómez,Pedro.
DNA-based molecular markers have been extensively utilized for a variety of studies in both plant and animal systems. One of the major uses of these markers is the construction of genome-wide molecular maps and the genetic analysis of simple and complex traits. However, these studies are generally based on linkage analysis in mapping populations, thus placing serious limitations in using molecular markers for genetic analysis in a variety of plant populations. Therefore, alternative approach has been suggested, linkage disequilibrium-based association analysis which detects and locates quantitative trait loci (QTL) by the strength of the correlation between a trait and a marker. Although association analysis has already been used for studies on genetics of...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Linkage disequilibrium; LD; Association mapping; Population structure; QTLs; Localization of genes; Marker-trait associations.
Ano: 2008 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572008000500001
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Linkage disequilibrium levels and allele frequency distribution in Blanco Orejinegro and Romosinuano Creole cattle using medium density SNP chip data Genet. Mol. Biol.
Bejarano,Diego; Martínez,Rodrigo; Manrique,Carlos; Parra,Luis Miguel; Rocha,Juan Felipe; Gómez,Yolanda; Abuabara,Yesid; Gallego,Jaime.
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...
Tipo: Info:eu-repo/semantics/article Palavras-chave: Creole breeds; BovineSNP50; Linkage disequilibrium; Minor allele frequency.
Ano: 2018 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572018000300426
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Population analysis of the GLB1 gene in South Brazil Genet. Mol. Biol.
Baiotto,Cléia; Sperb,Fernanda; Matte,Ursula; Silva,Cláudia Dornelles da; Sano,Renata; Coelho,Janice Carneiro; Giugliani,Roberto.
Infantile GM1 gangliosidosis is caused by the absence or reduction of lysosomal beta-galactosidase activity. Studies conducted in Brazil have indicated that it is one of the most frequent lysosomal storage disorders in the southern part of the country. To assess the incidence of this disorder, 390 blood donors were tested for the presence of two common mutations (1622-1627insG and R59H) in the GLB1 gene. Another group, consisting of 26 GM1 patients, and the blood donors were tested for the presence of two polymorphisms (R521C and S532G), in an attempt to elucidate whether there is a founder effect. The frequencies of the R59H and 1622-1627insG mutations among the GM1 patients studied were 19.2% and 38.5%, respectively. The frequency of polymorphism S532G...
Tipo: Info:eu-repo/semantics/article Palavras-chave: GM1 gangliosidosis; Beta-galactosidase; GLB1 gene; Founder effect; Linkage disequilibrium.
Ano: 2011 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572011000100009
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Prevalence of estrogen receptor alpha PvuII (c454-397T>C) and XbaI (c454A>G) polymorphisms in a population of Brazilian women BABT
Araújo,Karine Lourenzone; Rezende,Lucas Cunha Dias de; Souza,Letícia Soncini; Daltoé,Renata Dalmaschio; Madeira,Klesia Pirola; Paes,Marcela Ferreira; Herkenhoff,Fernando Luiz; Rangel,Letícia Batista Azevedo; Silva,Ian Victor.
The aim of this work was to study the estrogen receptor alpha (ERS1) PvuII and XbaI gene polymorphisms prevalence in randomly selected women population from Rio de Janeiro and Espírito Santo states in Brazil by polymerase chain reaction restriction fragment lengths polymorphism (PCR_RFLP) methodology. It was shown that Rio de Janeiro women exhibited a significantly different prevalence of XbaI polymorphism comparing to Espirito Santo women. Nonetheless, similar prevalence of PvuII polymorphism was found in both women´s populations. Moreover, a strong linkage disequilibrium was observed between these SNPs reinforcing the hypothesis of differential pattern of inheritance observed on such populations.
Tipo: Info:eu-repo/semantics/article Palavras-chave: Polymorphism; Estrogen Receptor; Brazilian Women; Prevalence; Linkage disequilibrium.
Ano: 2011 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1516-89132011000600010
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TaqI B1/B2 and -629A/C cholesteryl ester transfer protein (CETP) gene polymorphisms and their association with CETP activity and high-density lipoprotein cholesterol levels in a Tehranian population. Part of the Tehran Lipid and Glucose Study (TLGS) Genet. Mol. Biol.
Daneshpour,Maryam S; Hedayati,Mehdi; Azizi,Fereidoun.
We examined the cholesteryl ester transfer protein (CETP) gene TaqI intron 1 B1/B2 polymorphism and the -629A/C CETP promoter polymorphism in respect to high-density lipoprotein cholesterol (HDL-C) in a healthy Iranian population taken from the Tehran Lipid and Glucose Study (TLGS). The relationship between CETP activity and HDL-C level was also determined along with body mass index, blood pressure and tobacco smoking status. PCR-RFLP used to amplify a segment of the CETP intron 1 TaqI (B2/B1) polymorphism from 1021 individuals and we selected 345 individuals from the lowest, middle and highest HDL-C deciles and investigated the -629A/C polymorphism. We also evaluated the CETP activity of 103 of these individuals, each with at least one homozygous allele....
Tipo: Info:eu-repo/semantics/article Palavras-chave: Cholesteryl ester transfer protein (CETP); Hardy-Weinberg equilibrium; Linkage disequilibrium; Polymorphisms.
Ano: 2007 URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S1415-47572007000600001
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The extent of linkage disequilibrium in a large cattle population of western Africa and its consequences for association studies Inra
Thévenon; Dayo, K.; Sylla; Sidibe; Berthier; Legros; BOICHARD, D.. (Directeur); EGGEN, A.; GAUTIER, M..
Tipo: Journal Article Palavras-chave: Cattle; Effective population size; Linkage disequilibrium; Microsatellites; Population history.
Ano: 2007 URL: http://www.prodinra.inra.fr/prodinra/pinra/doc.xsp?id=PROD20073000283a&uri=/notices/prodinra1/2007/08/
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