SABIIA - Sistema Aberto e Integrado de Informação em Agricultura (Sabiia)

A hybrid zone between Bathymodiolus mussel lineages from eastern Pacific hydrothermal vents

SOMAVILLA, A. L.; SONSTEGARD, T. S.; HIGA, R. H.; ROSA, A. do N.; SIQUEIRA, F.; SILVA, L. O. C. da; TORRES JUNIOR, R. A. de A.; COUTINHO, L. L.; MUDADU, M. de A.; ALENCAR, M. M. de; REGITANO, L. C. de A..

Brazilian Nellore cattle (Bos indicus) have been selected for growth traits for over more than four decades. In recent years, reproductive and meat quality traits have become more important because of increasing consumption, exports and consumer demand. The identification of genome regions altered by artificial selection can potentially permit a better understanding of the biology of specific phenotypes that are useful for the development of tools designed to increase selection efficiency. Therefore, the aims of this study were to detect evidence of recent selection signatures in Nellore cattle using extended haplotype homozygosity methodology and BovineHD marker genotypes (>777 000 single nucleotide polymorphisms) as well as to identify corresponding...

Tipo: Artigo de periódico

Palavras-chave: Single nucleotid; Relative extended haplotype homozygosity; Single nucleotide polymorphisms; Bos Indicus; Beef cattle; Genotyping; Linkage disequilibrium.

Ano: 2014

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/998406

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

An insight into the linkage disequilibrium map of the Canchim beef cattle breed.

MOKRY, F. B.; LIMA, A. O. de; MUDADU, M. A.; HIGA, R. H.; MEIRELLES, S. L. C.; REGITANO, L. C. de A..

The development of linkage disequilibrium (LD) maps is very important for understanding the nature of non-linear association between phenotypes and genes, as LD can be defined as the non-random segregation of a pair of alleles at polymorphic sites. Canchim is a composite beef cattle breed which was developed in the 1960's by the crossing of Bos indicus (3/8) x Charolais (5/8) animals. The objective in this study was to analyze the extension of LD maps from a Canchim beef cattle population.

Aplicação da metodologia de homozigose do haplótipo estendido (EHH) para genes relacionados com crescimento e deposição de gordura em bovinos da raça Nelore.

Palavras-chave: Desequilíbrio de ligação.; Gado.; Linkage disequilibrium; Cattle; Zebu; Haplotypes.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/946432

SOMAVILLA, A. L.; HIGA, R. H.; MUDADU, M. de A.; ALENCAR, M. M. de; REGITANO, L. C. de A.; REDE BIFEQUALI.

Resumo: O rebanho bovino brasileiro destinado à produção de carne vem sendo selecionado há décadas, por programas de melhoramento genético, para diversas características de crescimento e, mais recentemente, de deposição de gordura. A seleção artificial resulta em alterações no genoma, que podem ser detectadas, por exemplo, por diferenças nos padrões de homozigose dos indivíduos de uma população, permitindo a identificação de regiões do genoma que controlam características sob seleção. Com o objetivo de avaliar a presença de assinaturas de seleção do genoma de bovinos Nelore que continham genes candidatos relacionados com crescimento e deposição de gordura, foram genotipados 796 indivíduos com o chip Illumina BovineHD BeadChip e, posteriormente, inferida a...

Assessing signatures of selection through variation in linkage disequilibrium between taurine and indicine cattle.

Palavras-chave: Assinaturas de seleção; Deposição muscular; Desequilíbrio de ligação; Acabamento; Muscle deposition; Selection signatures.; Gado de Corte.; Linkage disequilibrium; Beef cattle; Finishing.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/946741

Assessment of the association between SMAD1 and HHIP gene variation and non-syndromic cleft-lip palate in Chilean case-parent trios

O'BRIEN, A. M. P.; UTSUNOMIYA, Y. T.; MÉSZÁROS, G.; BICKHART, D. M.; LIU, G. E.; TASSEL, C. P. V.; SONSTEGARD, T. S.; SILVA, M. V. G. B.; GARCIA, J. F.; SÖLKNER, J..

Signatures of selection are regions in the genome that have been preferentially increased in frequency and fixed in a population because of their functional importance in specific processes. These regions can be detected because of their lower genetic variability and specific regional linkage disequilibrium (LD) patterns. By comparing the differences in regional LD variation between dairy and beef cattle types, and between indicine and taurine subspecies, we aim at finding signatures of selection for production and adaptation in cattle breeds. The VarLD method was applied to compare the LD variation in the autosomal genome between breeds, including Angus and Brown Swiss, representing taurine breeds, and Nelore and Gir, representing indicine breeds. The...

Tipo: Separatas

Palavras-chave: Cattle - genetic improvement; Indicine; Minor allele frequency.; Linkage disequilibrium; Taurine..

Ano: 2014

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1006605

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...

Caracterização de haplótipos e identificação de assinaturas de seleção em bovinos da raça Nelore.

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

SOMAVILLA, A. L.; HIGA, R. H.; MUDADU, M. de A.; ALENCAR, M. M. de; REGITANO, L. C. de A..

A identificação de regiões do genoma que controlam características de interesse econômico e que estejam sob seleção é possível por conta da disponibilidade da genotipagem em plataformas de altas densidades de polimorfismos de único nucleotídeo (SNPs). A busca por assinaturas de seleção avalia, principalmente, altas e não usuais frequências alélicas dos loci adjacentes às mutações favoráveis. Com o objetivo de detectar evidências de assinaturas de seleção recente no genoma de bovinos da raça Nelore, foram genotipados 796 indivíduos com o chip Illumina BovineHD BeadChip, que possui mais de 777 mil SNPs e, posteriormente, inferida a fase de ligação dos SNPs e a reconstrução dos blocos de desequilíbrio de ligação (haplótipos). A detecção de assinaturas de...

Demarcation of informative chromosomes in tropical sweet corn inbred lines using microsatellite DNA markers

Palavras-chave: Desequilíbrio de ligação; Genotipagem.; Bos Indicus.; Zebu; Genotype; Single nucleotide polymorphism; Linkage disequilibrium.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/946719

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...

Descriptive analysis of haplotypes in a population of Canchim beef cattle.

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

MOKRY, F. B.; LIMA, A. O.; MUDADU, M. A.; HIGA, R. H.; MEIRELLES, S. L. C.; SILVA, M. V. B.; CARDOSO, F. F.; NICIURA, S. C. M.; ALENCAR, M. M.; REGITANO, L. C. A..

The aim in this study was to descriptively analyze haplotypes from a Canchim beef cattle population.

Descriptive analysis of haplotypes in a population of Canchim beef cattle.

Palavras-chave: Desequilíbrio de ligação.; Gado.; Cattle; Linkage disequilibrium; Single nucleotide polymorphism.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/946423

Estimating effective population size of large marine populations, is it feasible?

MOKRY, F. B.; LIMA, A. O.; MUDADU, M. A.; HIGA, R. H.; MEIRELLES, S. L. C.; SILVA, M. V. B.; CARDOSO, F. F.; NICIURA, S. C. M.; ALENCAR, M. M.; REGITANO, L. C. A..

The aim in this study was to descriptively analyze haplotypes from a Canchim beef cattle population.

Tipo: Parte de livro

Palavras-chave: Desequilíbrio de ligação.; Gado.; Cattle; Linkage disequilibrium; Single nucleotide polymorphism.

Ano: 2012

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/967077

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

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

Estimation of linkage disequilibrium, persistence of phase and effective population size of Brazilian Hereford and Braford breeds.

BIEGELMEYER, P.; OLIVEIRA, M. M.; CARDOSO, L. L.; GOMES, C. C. G.; HIGA, R. H.; DIONELLO, N. J. L.; CAETANO, A. R.; STEIBEL, J. P.; CARDOSO, F. F..

A set of 41,241 SNP genotypes from 2,435 Hereford (HH) and Braford (BO) bovines were analyzed to estimate linkage disequilibrium (LD) levels, persistence of phase and effective population size of these populations. LD levels were estimated using the squared correlation of alleles at two loci (r2) at varying distances. Average r2 between adjacent SNP was 0.21 for HH and 0.16 for BO. Average inter-marker distance was 61 kb in both breeds. Useful LD values (r2>0.2) were observed at 0-60 kb bins in HH and 0-20 kb bins in BO. Breeds demonstrated moderate to strong persistence of phase at all distances (range=0.53-0.97). The greatest phase correlations (r>0.9) were found in 0-50 kb bins. LD estimates decreased rapidly with increasing distances between...

Evaluation of genetic diversity and linkage disequilibrium in Korean-bred rice varieties using SSR markers

Palavras-chave: Desequilíbrio de ligação; Tamanho populacional; Persistence of phase; Gado de corte; Beef cattle; Linkage disequilibrium; Population size.

Ano: 2014

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1003699

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

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...

Examining the cause of high inbreeding depression: analysis of whole-genome sequence data in 28 selfed progeny of Eucalyptus grandis.

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

Genetic association of SNPs in the FTO gene and predisposition to obesity in Malaysian Malays

HEDRICK, P. W.; HELLSTEN, U.; GRATTAPAGLIA, D..

Tipo: Separatas

Palavras-chave: Heterozygote advantage; Pseudo-overdominance; Tree.; Eucalyptus Grandis.; Linkage disequilibrium; Heterozygosity; Viability..

Ano: 2016

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1055388

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...

Genome selection in fruit breeding: application to table grapes

Palavras-chave: FTO gene; SNP; Obesity; Linkage disequilibrium; Haplotypes.

Ano: 2012

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0100-879X2012001200003

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...

Genome-wide analyses reveal the genetic architecture and candidate genes of indicine, taurine, synthetic crossbreds, and locally adapted cattle in Brazil.

Palavras-chave: MAS; SSR markers; Linkage disequilibrium; Genomic selection.

Ano: 2016

URL: http://www.scielo.br/scielo.php?script=sci_arttext&pid=S0103-90162016000200142

Genome-wide association for mapping QTLs linked to protein and oil contents in soybean

REGITANO, L. C. de A.; VERARDO, L. L.; SILVA, F. F. e; MACHADO, M. A.; PANETTO, J. C. do C.; REIS, D. R. de L.; OTTO, P. I.; SILVA, M. V. G. B.; ZANELLA, R.; ALBUQUERQUE, M. do S. M.; EGITO, A. A. do; SILVA, L. O. C. da.

Cattle population history, breeding systems, and geographic subdivision may be reflected in runs of homozygosity (ROH), effective population size (Ne), and linkage disequilibrium (LD) patterns. Thus, the assessment of this information has become essential to the implementation of genomic selection on purebred and crossbred cattle breeding programs. In this way, we assessed the genotype of 19 cattle breeds raised in Brazil belonging to taurine, indicine, synthetic crossbreds, and Iberian-derived locally adapted ancestries to evaluate the overall LD decay patterns, Ne, ROH, and breed composition. We were able to obtain a general overview of the genomic architecture of cattle breeds currently raised in Brazil and other tropical countries. We found that, among...

Tipo: Artigo de periódico

Palavras-chave: Rusticidade; Rusticity; Bovino; Gado; Genética Animal; Genoma; Produção Leiteira; Comportamento Animal; Fertilidade Animal; Homozygosity; Population size; Linkage disequilibrium; Milk production; Animal behavior; Animal fertility.

Ano: 2021

URL: http://www.alice.cnptia.embrapa.br/alice/handle/doc/1133730

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...