Linkage Disequilibrium in Domestic Sheep

McRae, Allan F.; McEwan, J. C.; Dodds, K. G.; Wilson, Theresa; Crawford, A. M.; Slate, Jon

doi:10.1093/genetics/160.3.1113

Cited by 147 publications

(17 citation statements)

References 31 publications

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“…Simulations (Kruglyak, 1999) and empirical analyses based on human data (Dunning et al, 2000) suggest that linkage disequilibrium (LD) extends only a few kilobases (kb) around common SNPs; however, other studies indicate that this distance can be greater than 100 kb (Abecasisi et al, 2001) or even beyond 1 Mb (Taillon-Miller et al 2000). Nevertheless, it is suggested that due to genetic drift, admixture, selection and smaller effective population sizes, which reduce allelic heterogeneity, livestock demonstrate greater LD than humans, and LD can extend over several hundred base pairs (McRae et al 2002).…”

Section: Analysis Of Gene Polymorphismsmentioning

confidence: 99%

The association of gene polymorphisms with milk production and mastitis resistance phenotypic traits in dairy cattle

Bagnicka

Brzozowska

Żukowski

et al. 2023

Annals of Animal Science

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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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Section: Analysis Of Gene Polymorphismsmentioning

confidence: 99%

The association of gene polymorphisms with milk production and mastitis resistance phenotypic traits in dairy cattle

Bagnicka

Brzozowska

Żukowski

et al. 2023

Annals of Animal Science

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“…Overall, the 3 types of Hetian sheep can be clearly distinguished and clustered according to geographical distribution. In LD, when the genetic diversity of the population decreases and the linkage between loci increases, the decay rate of LD is the smallest [22] .…”

Section: Population Linkage Genetic Degreementioning

confidence: 99%

Genetic Diversity and Runs of homozygosity analysis of Hetian Sheep Populations Revealed by Illumina OvineSNP50 BeadChip

Han

Zhou

Zhang

et al. 2022

Preprint

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Background Hetian sheep have a long history, a wide production area and rich genetic resources. Due to the different growing environment and feeding methods, wool, body shape and other traits also have some differences. Hetian sheep can be roughly divided into three groups, but the classification at the genome level is not clear. Results We randomly selected 84 healthy, adult ewes were randomly selected from three different ecological regions in Hetian area of Xinjiang, China. DNA was extracted from Ear tissues using phenol chloroform method to produce Illumina OvineSNP50 BeadChip. The SNP chip data were analyzed by Principal component analysis (PCA), neighbor-joining (NJ) phylogenetic and admixture for the population genetic structure of Hetian sheep, and the degree of population linkage was analyzed based on linkage disequilibrium (LD). Finally, the genetic region selection of Hetian sheep genetic germplasm resource populations in three different ecological environments was obtained by runs of homozygosity (ROH) analysis. The obtained candidate genes were annotated with Oar_v4.0 and enriched by GO and KEGG for analysis.Main screened 31 candidate genes adapting to high altitude environment were obtained in the Mountain type. Among them, Genes related to bone cell generation, differentiation and maintenance of bone homeostasis WNT6, WNT10A, CHSY1, etc. Genes related to tooth and tongue development LEF1, TP63, PRDM16, etc. Hearing and vision-related genes RBP4, ATF6, JAG1, etc. Main screened 22 candidate genes related to economic traits were obtained in the Grass type. Among them, Reproduction-related genes PLA2G4F, ACVR1, ADCY2, etc. Growth-related genes CAPN3, YAP1, FGF9, etc. Conclusions Hetian sheep can be classified into three subtypes at the genomic level: Mountain, Mountain-Grass and Grass types. The Grass type evolved from the Mountain type, and some of the Grass type further evolved into the Mountain-Grass type, and the genetic relationship between the Mountain-Grass type and Grass type was closest. Genetic structure and ROH analysis of Hetian sheep based on genomic microarray technology revealed the Mountain-Grass type strain. We enriched the genetic diversity of Hetian sheep germplasm resources, provided directions for Hetian sheep breed conservation, and found that genes related to multiparous trait exist in Mountain-Grass and Grass types Hetian sheep, which provides ideas for the selection and breeding of multiparous Hetian sheep.

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“…In recent years, there has been a dramatic increase of interest in utilizing LD to infer the evolutionary history and process of human populations (Reich et al, 2001;Ardlie et al, 2002 ;Dawson et al, 2002 ;Gabriel et al, 2002) and to identify genes for disease or yield traits by association analyses with DNA-based markers (Remington et al, 2001 ;Ardlie et al, 2002). The efficacy of LD analysis in population genetic studies and gene mapping depends on the level of LD in the population studied, its distribution and heterogeneity across the genome, and its relationship with genetic or geographic distances (Farnir et al, 2000 ;McRae et al, 2002 ;Liu et al, 2006). The pattern of LD decay is well known in human populations, where the relationship between the LD and physical distance is graphically elucidated to infer the origin and evolution of humans (Tishkoff et al, 1996(Tishkoff et al, , 2001Tishkoff & Williams, 2002).…”

Section: Introductionmentioning

confidence: 99%

An algorithmic model for constructing a linkage and linkage disequilibrium map in outcrossing plant populations

Li¹,

Li²,

Hou³

et al. 2009

Genet. Res.

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A linkage-linkage disequilibrium map that describes the pattern and extent of linkage dis-equilibrium (LD) decay with genomic distance has now emerged as a viable tool to unravel the genetic structure of population differentiation and fine-map genes for complex traits. The prerequisite for constructing such a map is the simultaneous estimation of the linkage and LD between different loci. Here, we develop a computational algorithm for simultaneously estimating the recombination fraction and LD in a natural outcrossing population with multilocus marker data, which are often estimated separately in most molecular genetic studies. The algorithm is founded on a commonly used progeny test with open-pollinated offspring sampled from a natural population. The information about LD is reflected in the co-segregation of alleles at different loci among parents in the population. Open mating of parents will reveal the genetic linkage of alleles during meiosis. The algorithm was constructed within the polynomial-based mixture framework and implemented with the Expectation-Maximization (EM) algorithm. The by-product of the derivation of this algorithm is the estimation of outcrossing rate, a parameter useful to explore the genetic diversity of the population. We performed computer simulation to investigate the influences of different sampling strategies and different values of parameters on parameter estimation. By providing a number of testable hypotheses about population genetic parameters, this algorithmic model will open a broad gateway to understand the genetic structure and dynamics of an outcrossing population under natural selection.

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Linkage Disequilibrium in Domestic Sheep

Cited by 147 publications

References 31 publications

The association of gene polymorphisms with milk production and mastitis resistance phenotypic traits in dairy cattle

The association of gene polymorphisms with milk production and mastitis resistance phenotypic traits in dairy cattle

Genetic Diversity and Runs of homozygosity analysis of Hetian Sheep Populations Revealed by Illumina OvineSNP50 BeadChip

An algorithmic model for constructing a linkage and linkage disequilibrium map in outcrossing plant populations

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