Genomic inbreeding
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Part 1 book "Advances in breeding of dairy cattle" includes content: Genetic and phenotypic improvements in temperate dairy systems, assessing inbreeding and genetic diversity in the holstein breed using pedigree and genomic approaches, genetic diversity in dairy cattle - variation within and between breeds, the use of genomic information to improve selection response while controlling inbreeding in dairy cattle breeding programs.... and other contents.
315p oursky04 14-09-2023 5 3 Download
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Relationships between individuals and inbreeding coefficients are commonly used for breeding decisions, but may be affected by the type of data used for their estimation. The proportion of variants with low Minor Allele Frequency (MAF) is larger in whole genome sequence (WGS) data compared to Single Nucleotide Polymorphism (SNP) chips.
12p vinarcissa 21-03-2023 2 1 Download
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Levels of inbreeding in cattle populations have increased in the past due to the use of a limited number of bulls for artificial insemination. High levels of inbreeding lead to reduced genetic diversity and inbreeding depression. Various estimators based on different sources, e.g., pedigree or genomic data, have been used to estimate inbreeding coefficients in cattle populations.
11p vinarcissa 21-03-2023 6 1 Download
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Consecutive homozygous fragments of a genome inherited by offspring from a common ancestor are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identify genomic regions that are potentially under historical selection pressure.
12p vihagrid 30-01-2023 7 3 Download
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The pathogenicity of many Mendelian variants has been challenged by large-scale sequencing efforts. However, many rare and benign “disease mutations” are difficult to analyze due to their rarity. The Saudi Arabian variome is enriched for homozygosity due to inbreeding, a key advantage that can be exploited for the critical examination of previously published variants.
7p vialfrednobel 29-01-2022 18 0 Download
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If unmanaged, high rates of inbreeding in livestock populations adversely impact their reproductive fitness. In beef cattle, historical selection strategies have increased the frequency of several segregating fatal autosomal recessive polymorphisms. Selective breeding has also decreased the extent of haplotypic diversity genome-wide. By identifying haplotypes for which homozygotes are not observed but would be expected based on their frequency, candidates for developmentally lethal recessive loci can be localized.
11p vilarryellison 29-10-2021 8 1 Download
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Runs of homozygosity (ROH) are continuous homozygous segments of the DNA sequence. They have been applied to quantify individual autozygosity and used as a potential inbreeding measure in livestock species.
13p vilarryellison 29-10-2021 17 1 Download
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The effects of different selection methods on ROH patterns were also compared. Furthermore, inbreeding coefficients were estimated in a sample of genotyped North American Holstein animals born from 1990 to 2016 using 50 k chip data and ROH patterns were assessed before and after genomic selection.
12p vibeauty 23-10-2021 11 1 Download
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Maintaining maximum genetic diversity and preserving breed viability in conserved populations necessitates the rigorous evaluation of conservation schemes. Three chicken breeds (Baier Yellow Chicken (BEC), Beijing You Chicken (BYC) and Langshan Chicken (LSC)) are currently in conservation programs in China. Changes in genetic diversity were measured by heterozygosity, genomic inbreeding coefficients, and autozygosity, using estimates derived from runs of homozygosity (ROH) that were identified using SNPs.
12p vitzuyu2711 29-09-2021 16 1 Download
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The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED).
14p vitzuyu2711 29-09-2021 9 1 Download
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Quantitative trait loci (QTL) mapping provides a powerful tool to unravel the genetic bases of cotton yield and its components, as well as their heterosis. In the present study, the genetic basis underlying inbreeding depression and heterosis for yield and yield components of upland cotton was investigated in recombinant inbred line (RIL), immortalized F2 (IF2), and two backcross (BCF1) populations based on a high-density SNP linkage map across four environments.
16p viseulgi2711 31-08-2021 11 1 Download
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PLINK is probably the most used program for analyzing SNP genotypes and runs of homozygosity (ROH), both in human and in animal populations. The last decade, ROH analyses have become the state-of-the-art method for inbreeding assessment.
14p vijeeni2711 24-07-2021 13 0 Download
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Achieving rapid genetic progress while maintaining adequate genetic diversity is one of the main challenges facing the dairy industry. The increase in inbreeding can be used to monitor the loss of genetic diversity
9p vijeeni2711 24-07-2021 16 0 Download
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Although inbreeding caused by the mating of animals related through a recent common ancestor is expected to have more harmful effects on phenotypes than ancient inbreeding (old inbreeding), estimating these effects requires a clear definition of recent (new) and ancient (old) inbreeding.
17p vijeeni2711 24-07-2021 5 0 Download
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Phenotypic performances of livestock animals decline with increasing levels of inbreeding, however, the noticeable decline known as inbreeding depression, may not be due only to the total level of inbreeding, but rather could be distinctly associated with more recent or more ancient inbreeding.
15p vijeeni2711 30-06-2021 10 2 Download
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Genome-wide association studies (GWASs) have identified several single-nucleotide polymorphisms (SNPs) influencing the risk of thyroid cancer (TC). Most cancer predisposition genes identified through GWASs function in a co-dominant manner, and studies have not found evidence for recessively functioning disease loci in TC.
11p vinaypyidaw2711 26-08-2020 12 2 Download
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Inbreeding among farm animals is common practice to maintain purity of a specific population and also is unavoidable due to use of few male animals compared to large number of females in any animal breeding farm. Level of inbreeding practiced in a farm is very crucial as the inbreeding depression causes loss of productivity and vitality of the breeding animals. Measuring inbreeding coefficient needs pedigree of each animal which is often not maintained in most of farms, or is incorrect and limited to a very few generations.
6p cothumenhmong5 17-05-2020 14 1 Download
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Foxtail millet (Setaria italica L. P. Beauv) has been considered as a tractable model crop in recent years due to its short growing cycle, lower amount of repetitive DNA, inbreeding nature, small diploid genome, and outstanding abiotic stress-tolerance characteristics.
19p vishikamaru2711 29-04-2020 9 0 Download