scholarly journals Genomic Tools for the Conservation and Genetic Improvement of a Highly Fragmented Breed—The Ramo Grande Cattle from the Azores

Animals ◽  
2020 ◽  
Vol 10 (6) ◽  
pp. 1089
Author(s):  
Andreia J. Amaral ◽  
Ana L. Pavão ◽  
Luis T. Gama
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Genome Wide Association Study ◽  
Cattle Breed ◽  
Production Traits ◽  
Effective Population ◽  
Age At First Calving ◽  
Large Effective Population Size ◽  
Genomic Inbreeding ◽  
Genomic Regions

Ramo Grande is a local cattle breed raised in the archipelago of Azores, with a small and dispersed census, where inbreeding control is of utmost importance. A single nucleotide polymorphism (SNP) Beadchip array was used to assess inbreeding, by analysis of genomic regions harboring contiguous homozygous genotypes named runs of homozygosity (ROH), and to estimate past effective population size by analysis of linkage disequilibrium (LD). Genetic markers associated with production traits were also investigated, exploiting the unique genetic and adaptation features of this breed. A total of 639 ROH with length >4 Mb were identified, with mean length of 14.96 Mb. The mean genomic inbreeding was 0.09, and long segments of ROH were common, indicating recent inbred matings. The LD pattern indicates a large effective population size, suggesting the inflow of exotic germplasm in the past. The genome-wide association study identified novel markers significantly affecting longevity, age at first calving and direct genetic effects on calf weight. These results provide the first evidence of the association of longevity with genes related with DNA recognition and repair, and the association of age at first calving with aquaporin proteins, which are known to have a crucial role in reproduction.

scholarly journals Genome-Wide Patterns of Homozygosity and Relevant Characterizations on the Population Structure in Piétrain Pigs

Genes ◽  
2020 ◽  
Vol 11 (5) ◽  
pp. 577
Author(s):  
Huiwen Zhan ◽  
Saixian Zhang ◽  
Kaili Zhang ◽  
Xia Peng ◽  
Shengsong Xie ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Average Length ◽  
The Other ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
Inbreeding Coefficients ◽  
Genome Wide ◽  
Genomic Regions

Investigating the patterns of homozygosity, linkage disequilibrium, effective population size and inbreeding coefficients in livestock contributes to our understanding of the genetic diversity and evolutionary history. Here we used Illumina PorcineSNP50 Bead Chip to identify the runs of homozygosity (ROH) and estimate the linkage disequilibrium (LD) across the whole genome, and then predict the effective population size. In addition, we calculated the inbreeding coefficients based on ROH in 305 Piétrain pigs and compared its effect with the other two types of inbreeding coefficients obtained by different calculation methods. A total of 23,434 ROHs were detected, and the average length of ROH per individual was about 507.27 Mb. There was no regularity on how those runs of homozygosity distributed in genome. The comparisons of different categories suggested that the formation of long ROH was probably related with recent inbreeding events. Although the density of genes located in ROH core regions is lower than that in the other genomic regions, most of them are related with Piétrain commercial traits like meat qualities. Overall, the results provide insight into the way in which ROH is produced and the identified ROH core regions can be used to map the genes associated with commercial traits in domestic animals.

Pedigree analysis of the Afrikaner cattle breed

2015 ◽  
Vol 57 ◽  
pp. 51-56 ◽  
Author(s):  
L. Pienaar ◽  
F.W.C. Neser ◽  
J.P. Grobler ◽  
M.M. Scholtz ◽  
M.D. MacNeil
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Cattle Breed ◽  
Pedigree Analysis ◽  
Rate Of Change ◽  
Full Potential ◽  
Effective Population ◽  
Indigenous Cattle ◽  
Sanga Cattle

SummaryThe reduction of genetic variability in beef cattle has been extensively researched on a global scale. However, the genetic variability and inbreeding of indigenous cattle breeds of Southern Africa, referred to as Sanga cattle, has been less well characterized. Breeds of Sanga cattle include Afrikaner, Drakensberger and Nguni breeds. In recent years, the number of Afrikaner cattle and herds has decreased. Our objective was to determine the mean level of inbreeding (F), effective population size (Ne) and generation intervals of Afrikaner cattle using their recorded pedigree. A total of 244 718 records extending from 1940 until 2011 were analysed. The average inbreeding coefficient was 1.83 percent and the effective population size was 167.54. The average generation interval was calculated as 6.6 ± 3.9 years. Pedigree analysis on the Afrikaner cattle population yielded levels of inbreeding that appear to be both acceptable and manageable. By implication, the largeNeresults in a low rate of change inF. Current results study can be utilized by farmers and the breeders’ society to conserve the Afrikaner and utilize the breed to its full potential in the era of climate change.

scholarly journals Evaluating the use of ABBA-BABA statistics to locate introgressed loci

2013 ◽  
Author(s):  
Simon H. Martin ◽  
John W. Davey ◽  
Chris D. Jiggins
Keyword(s):  
Population Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Ancestral Population ◽  
Whole Genome ◽  
Effective Population ◽  
Genome Data ◽  
Genome Wide ◽  
A Genome ◽  
Genomic Regions

Several methods have been proposed to test for introgression across genomes. One method tests for a genome-wide excess of shared derived alleles between taxa using Patterson?s D statistic, but does not establish which loci show such an excess or whether the excess is due to introgression or ancestral population structure. Several recent studies have extended the use of D by applying the statistic to small genomic regions, rather than genome-wide. Here, we use simulations and whole genome data from Heliconius butterflies to investigate the behavior of D in small genomic regions. We find that D is unreliable in this situation as it gives inflated values when effective population size is low, causing D outliers to cluster in genomic regions of reduced diversity. As an alternative, we propose a related statistic f̂d, a modified version of a statistic originally developed to estimate the genome-wide fraction of admixture. f̂d is not subject to the same biases as D, and is better at identifying introgressed loci. Finally, we show that both D and f̂d outliers tend to cluster in regions of low absolute divergence (dXY), which can confound a recently proposed test for differentiating introgression from shared ancestral variation at individual loci.

scholarly journals Natural selection does not affect the estimates of effective population size based on linkage disequilibrium

2021 ◽  
Author(s):  
Irene Novo ◽  
Armando Caballero ◽  
Enrique Santiago
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Recombination Rate ◽  
Nucleotide Diversity ◽  
Loss Of Function ◽  
Effective Population ◽  
Genomic Regions ◽  
The Relationship ◽  
Key Parameter

The effective population size ( N e ) is a key parameter to quantify the magnitude of genetic drift and inbreeding, with important implications in human evolution. The increasing availability of high-density genetic markers allows the estimation of historical changes in N e across time using measures of genome diversity or linkage disequilibrium between markers. Selection is expected to reduce diversity and N e , and this reduction is modulated by the heterogeneity of the genome in terms of recombination rate. Here we investigate by computer simulations the consequences of selection (both positive and negative) and of recombination rate heterogeneity in the estimation of historical N e . We also investigate the relationship between diversity parameters and N e across the different regions of the genome using human marker data. We show that the estimates of historical N e obtained from linkage disequilibrium between markers ( N e LD ) are virtually unaffected by selection. In contrast, those estimates obtained by coalescence mutation-recombination-based methods can be strongly affected by it, what could have important consequences for the estimation of human demography. The simulation results are supported by the analysis of human data. The estimates of N e LD obtained for particular genomic regions do not correlate with recombination rate, nucleotide diversity, polymorphism, background selection statistic, minor allele frequency of SNPs, loss of function and missense variants and gene density. This suggests that N e LD measures are merely indicative of demographic changes in population size across generations.

scholarly journals The evaluation of genomic diversity and selection signals in the autochthonous Slovak Spotted cattle  

2021 ◽  
Author(s):  
Radovan Kasarda ◽  
Nina Moravčíková ◽  
Barbora Olšanská ◽  
Gábor Mészáros ◽  
Luboš Vostrý ◽  
...  
Keyword(s):  
Population Size ◽  
Effective Population Size ◽  
Coat Colour ◽  
Genomic Diversity ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
Dual Purpose ◽  
High Selection ◽  
Genomic Regions

The aim of this study was to evaluate the effective population size based on linkage disequilibrium and the trend of inbreeding derived from runs of homozygosity (ROH) in the Slovak Spotted cattle. The ROH segments longer than 4 Mb were then analysed to identify selection signals. Eighty-five individuals were genotyped using the ICBF International Dairy and Beef chip (dams of sires) and Illumina BovineSNP50 BeadChip (sires). The ROH segments > 1 Mb occurred most often in the autosomal genome with an average number of 16.75 ± 7.23. The ROH segments > 16 Mb covering 0.41% of the genome pointed to the long-term effort of breeders to reduce inbreeding in the population of Slovak Spotted cattle. However, the average observed heterozygosity indicated a decrease in overall diversity in the current population. The decrease of heterozygosity per generation also confirmed the estimates of historical and recent effective population size (a decrease of 6.88 animals per generation). The predicted current effective population size was 58 animals. Twenty-one regions across 12 different autosomes were fixed due to the high selection pressure. Within these genomic regions were identified various genes associated with reproduction (SLC9C1, PTPN12), milk production (IGF1, ABCG2), beef production (IFRD1, PTPN4), developmental processes (FMNL2, GLI2), immune system (CD96, CSK) and coat colour (KIT). These selection signals detected in the genome of Slovak Spotted cattle confirm the constant effort of breeders to preserve the dual-purpose nature of this breed.

Effective population size of an indigenous Swiss cattle breed estimated from linkage disequilibrium

2010 ◽  
Vol 127 (5) ◽  
pp. 339-347 ◽  
Author(s):  
C. Flury ◽  
M. Tapio ◽  
T. Sonstegard ◽  
C. Drögemüller ◽  
T. Leeb ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Population Size ◽  
Effective Population Size ◽  
Cattle Breed ◽  
Effective Population

scholarly journals Genetic Background and Inbreeding Depression in Romosinuano Cattle Breed in Mexico

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 321
Author(s):  
Jorge Hidalgo ◽  
Alberto Cesarani ◽  
Andre Garcia ◽  
Pattarapol Sumreddee ◽  
Neon Larios ◽  
...  
Keyword(s):  
Genetic Variability ◽  
Population Size ◽  
Effective Population Size ◽  
Genetic Background ◽  
Cattle Breed ◽  
Pedigree Information ◽  
Runs Of Homozygosity ◽  
Genomic Information ◽  
Effective Population ◽  
Genetic Progress

The ultimate goal of genetic selection is to improve genetic progress by increasing favorable alleles in the population. However, with selection, homozygosity, and potentially harmful recessive alleles can accumulate, deteriorating genetic variability and hampering continued genetic progress. Such potential adverse side effects of selection are of particular interest in populations with a small effective population size like the Romosinuano beef cattle in Mexico. The objective of this study was to evaluate the genetic background and inbreeding depression in Mexican Romosinuano cattle using pedigree and genomic information. Inbreeding was estimated using pedigree (FPED) and genomic information based on the genomic relationship matrix (FGRM) and runs of homozygosity (FROH) of different length classes. Linkage disequilibrium (LD) was evaluated using the correlation between pairs of loci, and the effective population size (Ne) was calculated based on LD and pedigree information. The pedigree file consisted of 4875 animals born between 1950 and 2019, of which 71 had genotypes. LD decreased with the increase in distance between markers, and Ne estimated using genomic information decreased from 610 to 72 animals (from 109 to 1 generation ago), the Ne estimated using pedigree information was 86.44. The reduction in effective population size implies the existence of genetic bottlenecks and the decline of genetic diversity due to the intensive use of few individuals as parents of the next generations. The number of runs of homozygosity per animal ranged between 18 and 102 segments with an average of 55. The shortest and longest segments were 1.0 and 36.0 Mb long, respectively, reflecting ancient and recent inbreeding. The average inbreeding was 2.98 ± 2.81, 2.98 ± 4.01, and 7.28 ± 3.68% for FPED, FGRM, and FROH, respectively. The correlation between FPED and FGRM was −0.25, and the correlations among FPED and FROH of different length classes were low (from 0.16 to 0.31). The correlations between FGRM and FROH of different length classes were moderate (from 0.44 to 0.58), indicating better agreement. A 1% increase in population inbreeding decreased birth weight by 0.103 kg and weaning weight by 0.685 kg. A strategy such as optimum genetic contributions to maximize selection response and manage the long-term genetic variability and inbreeding could lead to more sustainable breeding programs for the Mexican Romosinuano beef cattle breed.

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