scholarly journals Analysis of selection signatures in the beef cattle genome

2019 ◽  
Vol 64 (No. 12) ◽  
pp. 491-503 ◽  
Author(s):  
Nina Moravčíková ◽  
Radovan Kasarda ◽  
Luboš Vostrý ◽  
Zuzana Krupová ◽  
Emil Krupa ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Beef Cattle ◽  
Muscle Development ◽  
Genome Structure ◽  
Coat Colour ◽  
Meat Tenderness ◽  
Selection Signatures ◽  
Genetic Progress ◽  
Genomic Regions ◽  
The Impact

This study aimed to evaluate the impact of selection on the genome structure of beef cattle through identification of selection signatures reflecting the breeding standard of each breed and to discover potential functional genetic variants to improve performance traits. Genotyping data of six beef breeds (Aberdeen Angus, Hereford, Limousin, Charolais, Piedmontese and Romagnola) were used to perform genome-wide scans for selection signatures. The approaches applied were based on an assumption that selection leads to linkage disequilibrium or to a decrease of genetic variability in genomic regions containing genotypes connected with favourable phenotypes. Thus, the selection signatures were analysed based on Wright’s F<sub>ST</sub> index, distribution of runs of homozygosity segments in the beef genome and determination of linkage disequilibrium variability between breeds. The number and length of detected selection signals were different depending on the breeds and methodological approaches. As expected due to the breeding goals of analysed breeds, common signals were located on autosomes 2, 6, 7, 13 and 20 close to the genes associated with coat colour (KIT, KDR), muscle development (GDF9, GHRH, GHR), double muscling (MSTN), meat tenderness (CAST) and intramuscular fat content (SCD). But, across the genomes of analysed breeds, unique selection signals were found as well. The subsequent analysis of those single nucleotide polymorphism markers can be beneficial for the genetic progress of studied breeds in future.

Identification of genomic regions related to tenderness in Nellore beef cattle

2017 ◽  
Vol 8 (s1) ◽  
pp. s42-s44 ◽  
Author(s):  
M. E. Carvalho ◽  
F. S. Baldi ◽  
M. H. A. Santana ◽  
R. V. Ventura ◽  
G. A. Oliveira ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Genome Wide Association Study ◽  
Additive Genetic Variance ◽  
Single Step ◽  
Meat Tenderness ◽  
Beef Tenderness ◽  
Genome Wide ◽  
Quality Grade ◽  
Nellore Cattle ◽  
Genomic Regions

The aim of this study was to identify genomic regions that associated with beef tenderness in Nellore cattle. Phenotypes were obtained according to the standard USDA Quality Grade (1999). Data from 909 genotyped Nellore bulls were used in the Genome-Wide Association Study (GWAS) undertaken using a single-step approach including also a pedigree file composed of 6276 animals. The analyses were performed using the Blupf90 software, estimating the effect of genomic windows of 10 consecutive markers. The GWAS results identified 18 genomic regions located on 14 different chromosomes (1, 4, 6, 7, 8, 10, 18, 19, 20, 21, 22, 25, 26 and 29), which explained more than 1% of the total additive genetic variance; several candidate genes were located in these regions including SLC2A9, FRAS1, ANXA3, FAM219A, DNAI, AVEN, SHISA7, UBE2S, CDC42EP5, CNTN3, C16orf96, UBALD1, MGRN1 and SNORA1 With the single-step GWAS, it was possible to identify regions and genes related to meat tenderness in Nellore beef cattle.

scholarly journals Genomic measures of inbreeding coefficients and genome-wide scan for runs of homozygosity islands in Iranian river buffalo, Bubalus bubalis

2019 ◽  
Author(s):  
Seyed Mohammad Ghoreishifar ◽  
Hossein Moradi-Shahrbabak ◽  
Mohammad Hossein Fallahi ◽  
Ali Jalil-Sarghaleh ◽  
Mohammad Moradi-Shahrbabak ◽  
...  
Keyword(s):  
Muscle Development ◽  
Bone Development ◽  
Coat Colour ◽  
Genomic Relationship Matrix ◽  
Relationship Matrix ◽  
River Buffalo ◽  
Runs Of Homozygosity ◽  
Effective Population ◽  
Genomic Inbreeding ◽  
Genomic Regions

Abstract Background: Consecutive homozygous fragments of the genome inherited from a common ancestor to offspring are known as runs of homozygosity (ROH). ROH can be used to calculate genomic inbreeding and to identifying genomic regions that are potentially under historical selection pressure. The dataset of our study consisted of 254 Azeri (AZ) and 115 Khuzestani (KHZ) river buffalo genotyped for ~65000 SNPs for the following two purposes: 1) to estimate and compare inbreeding calculated using ROH (FROH), excess of homozygosity (FHOM), correlation between uniting gametes (FUNI), and diagonal elements of the genomic relationship matrix (FGRM); 2) to identify frequently occurring ROH (i.e. ROH islands) for our selection signature and gene enrichment studies. Results: In this study, 9102 ROH were identified, with an average number of 21.2±13.1 and 33.2±15.9 segments per animal in AZ and KHZ breeds, respectively. On average in AZ, 4.35% (108.8±120.3 Mb), and in KHZ, 5.96% (149.1±107.7 Mb) of the genome was autozygous. The estimated inbreeding values based on FHOM, FUNI and FGRM were higher in AZ than they were in KHZ, which was in contrast to the FROH estimates. We identified 11 ROH islands (four in AZ and seven in KHZ). In the KHZ breed, the genes located in ROH islands were enriched for multiple Gene Ontology (GO) terms (P<0.05). The genes located in ROH islands were associated with diverse biological functions and traits such as body size and muscle development (BMP2), immune response (CYP27B1), milk production and components (MARS, ADRA1A, and KCTD16), coat colour and pigmentation (PMEL and MYO1A), reproductive traits (INHBC, INHBE, STAT6 and PCNA), and bone development (SUOX). Conclusion: The calculated FROH was in line with expected higher inbreeding in KHZ than in AZ because of the smaller effective population size of KHZ. Thus, we find that FROH can be used as a robust estimate of genomic inbreeding. Further, the majority of ROH peaks were overlapped with or in close proximity to the previously reported genomic regions with signatures of selection. This tells us that it is likely that the genes in the ROH islands have been subject to artificial and/or natural selection.

scholarly journals Detection and Visualization of Heterozygosity-Rich Regions and Runs of Homozygosity in Worldwide Sheep Populations

Animals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 2696
Author(s):  
Alana Selli ◽  
Ricardo V. Ventura ◽  
Pablo A. S. Fonseca ◽  
Marcos E. Buzanskas ◽  
Lucas T. Andrietta ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Business Intelligence ◽  
Muscle Development ◽  
Strong Association ◽  
High Linkage Disequilibrium ◽  
Detection Methods ◽  
Future Research ◽  
Runs Of Homozygosity ◽  
Brain Functions ◽  
The Impact

In this study, we chose 17 worldwide sheep populations of eight breeds, which were intensively selected for different purposes (meat, milk, or wool), or locally-adapted breeds, in order to identify and characterize factors impacting the detection of runs of homozygosity (ROH) and heterozygosity-rich regions (HRRs) in sheep. We also applied a business intelligence (BI) tool to integrate and visualize outputs from complementary analyses. We observed a prevalence of short ROH, and a clear distinction between the ROH profiles across populations. The visualizations showed a fragmentation of medium and long ROH segments. Furthermore, we tested different scenarios for the detection of HRR and evaluated the impact of the detection parameters used. Our findings suggest that HRRs are small and frequent in the sheep genome; however, further studies with higher density SNP chips and different detection methods are suggested for future research. We also defined ROH and HRR islands and identified common regions across the populations, where genes related to a variety of traits were reported, such as body size, muscle development, and brain functions. These results indicate that such regions are associated with many traits, and thus were under selective pressure in sheep breeds raised for different purposes. Interestingly, many candidate genes detected within the HRR islands were associated with brain integrity. We also observed a strong association of high linkage disequilibrium pattern with ROH compared with HRR, despite the fact that many regions in linkage disequilibrium were not located in ROH regions.

scholarly journals Genome-Wide Analysis Reveals Selection Signatures Involved in Meat Traits and Local Adaptation in Semi-Feral Maremmana Cattle

2021 ◽  
Vol 12 ◽  
Author(s):  
Slim Ben-Jemaa ◽  
Gabriele Senczuk ◽  
Elena Ciani ◽  
Roberta Ciampolini ◽  
Gennaro Catillo ◽  
...  
Keyword(s):  
Muscle Development ◽  
Single Nucleotide Polymorphism Array ◽  
Reference Population ◽  
Selection Signatures ◽  
Genomic Signatures ◽  
Genome Wide ◽  
Parasite Infections ◽  
Breeding Schemes ◽  
Candidate Regions ◽  
Genomic Regions

The Maremmana cattle is an ancient Podolian-derived Italian breed raised in semi-wild conditions with distinctive morphological and adaptive traits. The aim of this study was to detect potential selection signatures in Maremmana using medium-density single nucleotide polymorphism array. Putative selection signatures were investigated combining three statistical approaches designed to quantify the excess of haplotype homozygosity either within (integrated haplotype score, iHS) or among pairs of populations (Rsb and XP-EHH), and contrasting the Maremmana with a single reference population composed of a pool of seven Podolian-derived Italian breeds. Overall, the three haplotype-based analyses revealed selection signatures distributed over 19 genomic regions. Of these, six relevant candidate regions were identified by at least two approaches. We found genomic signatures of selective sweeps spanning genes related to mitochondrial function, muscle development, growth, and meat traits (SCIN, THSD7A, ETV1, UCHL1, and MYOD1), which reflects the different breeding schemes between Maremmana (semi-wild conditions) and the other Podolian-derived Italian breeds (semi-extensive). We also identified several genes linked to Maremmana adaptation to the environment of the western-central part of Italy, known to be hyperendemic for malaria and other tick-borne diseases. These include several chemokine (C-C motif) ligand genes crucially involved in both innate and adaptive immune responses to intracellular parasite infections and other genes playing key roles in pulmonary disease (HEATR9, MMP28, and ASIC2) or strongly associated with malaria resistance/susceptibility (AP2B1). Our results provide a glimpse into diverse selection signatures in Maremmana cattle and can be used to enhance our understanding of the genomic basis of environmental adaptation in cattle.

Embryo manipulation in cattle breeding and production

1989 ◽  
Vol 48 (1) ◽  
pp. 3-30 ◽  
Author(s):  
J. A. Woolliams ◽  
I. Wilmut
Keyword(s):  
Gene Transfer ◽  
Beef Cattle ◽  
Embryo Transfer ◽  
Nuclear Transfer ◽  
Progeny Testing ◽  
Genetic Progress ◽  
Embryo Recovery ◽  
Multiple Ovulation ◽  
The Impact

ABSTRACTDevelopments, both recent and potential, in procedures for manipulating embryos are described. The procedures considered include: embryo transfer, multiple ovulation and embryo recovery, recovery of oocytes, in vitro maturation (IVM) and fertilization (IVF) of oocytes, in vitro culture of zygotes, embryo splitting and nuclear transfer, embryo storage, embryo sexing, gene transfer and embryo stem cells. The impact of these procedures on breeding strategies such as multiple ovulation and embryo transfer (MOET) nucleus breeding schemes and progeny testing are discussed for both dairy and beef cattle.For MOET nucleus schemes all these procedures have potential applications in producing maximal rates of genetic progress for a fixed rate of inbreeding. With the current effectiveness of the procedures, embryo sexing and nuclear transfer would have the most impact. The potential for increasing genetic progress through progeny testing is enhanced using multiple ovulation, embryo recovery and transfer in cows to breed bulls, but no other procedures appeared to offer major benefits. The efficiency of beef production from the dairy herd could be increased either by using IVM and IVF to produce more beef-type calves or, potentially, by cloning and embryo transfer, to produce pure beef calves. Procedures leading to the production of clone families would make an impact on the evaluation of genotypes and environments. Gene transfer may be used to modify the composition of milk including the production of pharmaceutical proteins, and to increase milk yield or the efficiency of lean meat production.It is concluded that, although much further research is required, the procedures discussed will have major implications for the structure and organization of dairy and beef cattle herds over the next decade.

scholarly journals PSI-B-14 Late-Breaking: Evaluation of mRNA isoforms expression profile using two approaches to measure meat tenderness from Longissimus thoracis muscle in beef cattle

2019 ◽  
Vol 97 (Supplement_3) ◽  
pp. 318-319
Author(s):  
Maria Malane M Muniz ◽  
Angela Cánovas ◽  
Larissa Fernanda Simielli Fonseca ◽  
Danielly Beraldo dos Santos Silva ◽  
Ana Fabrícia Braga Magalhães ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Beef Cattle ◽  
Muscle Development ◽  
Trinucleotide Repeat ◽  
Biological Marker ◽  
Differentially Expressed ◽  
Meat Tenderness ◽  
Mrna Isoforms ◽  
Beef Tenderness ◽  
Mrna Isoform

Abstract The Warner-Bratzler shear force (WBSF) and myofibrillar fragmentation index (MFI) are complementary methodologies commonly used to measure beef tenderness. To identify mRNA isoforms differentially expressed became an important tool to provide new insights to better understand the transcripts involved in the regulation of the meat tenderness, using MFI and WBSF measures in Nellore beef cattle. Longissimus thoracis muscle samples from the 20 most extreme bulls (out of 80 bulls set) for WBSF [tender (n = 9) and tough (n = 10) groups] and MFI [high (n = 10) and low (n = 10) groups] traits were collected to perform transcriptomic analysis using RNA-Sequencing. The CLC Genomics Workbench v.12.0 was used to align the fragments of each sample to the bovine reference genome ARS.UCD1.2. An average of 37 million transcripts were expressed in the Nellore muscle transcriptome. A total of 41 and 31 mRNA isoforms were differentially expressed (q≤0.05 and Fold Change greater than 2) between the two groups of divergent bulls for WBSF and MFI traits, respectively. The RPL14-202 mRNA isoform was the only isoform differentially expressed in common between both traits and is one of two known transcripts of the RPL14 gene. The RPL14 gene contains a trinucleotide repeat tract whose length is highly polymorphic and has several biochemical functions. Bulls with tender meat have one base insertion inside this region and possibly has splice site disruption effects. The RPL14-202 mRNA isoform could be used as potential biological marker for beef tenderness. The identified differentially expressed mRNA isoforms (ACTA1-202, ACTN3-201, MYL6-202, MYL6-201, MYBPC2-202) were involved with skeletal muscle cell differentiation, negative regulation of sarcomere organization and regulation of skeletal muscle contraction. mRNA isoforms directly associated with muscle development were identified using different approaches to measure beef tenderness suggesting potential key regulator genes and biomarkers associated with an important consumer valued trait for the beef industry.

scholarly journals High density genome scan for selection signatures in French sheep reveals allelic heterogeneity and introgression at adaptive loci

2017 ◽  
Author(s):  
Christina Marie Rochus ◽  
Flavie Tortereau ◽  
Florence Plisson-Petit ◽  
Gwendal Restoux ◽  
Carole Moreno ◽  
...  
Keyword(s):  
Environmental Conditions ◽  
Evolutionary History ◽  
Coat Colour ◽  
Phenotypic Trait ◽  
Southern Population ◽  
Selection Signatures ◽  
Adaptive Mutations ◽  
Livestock Species ◽  
History Of ◽  
Genomic Regions

AbstractSheep was one of the first domesticated livestock species in the Anatolia region of contemporary Iran and eventually spread world-wide. Previous studies have shown that French sheep populations likely harbour a large part of European domesticated sheep diversity in a relatively small geographical region, offering a powerful model for the study of adaptation. We studied the diversity of 27 French sheep populations by genotyping 542 individuals for more than 500 000 SNPs. We found that French sheep breeds were divided into two main groups, corresponding to northern and southern origins and additionally we identified admixture events between northern and southern populations. The genetic diversity of domesticated animals results from adaptation of populations to constraints imposed by farmers and environmental conditions. We identified 126 genomic regions likely affected by selection. In many cases, we found evidence for parallel selection events in different genetic backgrounds, most likely for different mutations. Some of these regions harbour genes potentially involved in morphological traits (SOCS2, NCAPG/LCORL, MSRB3), coat colour (MC1R) and adaptation to environmental conditions (ADAMTS9). Closer inspection of two of these regions clarified their evolutionary history: at the LCORL/NCAPG locus we found evidence for introgression of an adaptive allele from a southern population into northern populations and by resequencing MC1R in some breeds we confirmed different mutations in this gene are responsible for the same phenotypic trait. Our study illustrates how dense genetic data in multiple populations allows the deciphering of evolutionary history of populations and of their adaptive mutations.

scholarly journals Review: Impacts of shade on cattle well-being in the beef supply chain

2020 ◽  
Author(s):  
Lily N Edwards-Callaway ◽  
M Caitlin Cramer ◽  
Caitlin N Cadaret ◽  
Elizabeth J Bigler ◽  
Terry E Engle ◽  
...  
Keyword(s):  
Supply Chain ◽  
Heat Stress ◽  
Beef Cattle ◽  
Production Systems ◽  
Construction Materials ◽  
Well Being ◽  
Third Party ◽  
Ambient Temperatures ◽  
Stress Susceptibility ◽  
The Impact

ABSTRACT Shade is a mechanism to reduce heat load providing cattle with an environment supportive of their welfare needs. Although heat stress has been extensively reviewed, researched, and addressed in dairy production systems, it has not been investigated in the same manner in the beef cattle supply chain. Like all animals, beef cattle are susceptible to heat stress if they are unable to dissipate heat during times of elevated ambient temperatures. There are many factors that impact heat stress susceptibility in beef cattle throughout the different supply chain sectors, many of which relate to the production system, i.e. availability of shade, microclimate of environment, and nutrition management. The results from studies evaluating the effects of shade on production and welfare are difficult to compare due to variation in structural design, construction materials used, height, shape, and area of shade provided. Additionally, depending on operation location, shade may or may not be beneficial during all times of the year, which can influence the decision to make shade a permanent part of management systems. Shade has been shown to lessen the physiologic response of cattle to heat stress. Shaded cattle exhibit lower respiration rates, body temperatures, and panting scores compared to un-shaded cattle in weather that increases the risk of heat stress. Results from studies investigating the provision of shade indicate that cattle seek shade in hot weather. The impact of shade on behavioral patterns is inconsistent in the current body of research, some studies indicating shade provision impacts behavior and other studies reporting no difference between shaded and un-shaded groups. Analysis of performance and carcass characteristics across feedlot studies demonstrated that shaded cattle had increased ADG, improved feed efficiency, HCW, and dressing percentage when compared to cattle without shade. Despite the documented benefits of shade, current industry statistics, although severely limited in scope, indicate low shade implementation rates in feedlots and data in other supply chain sectors do not exist. Industry guidelines and third party on-farm certification programs articulate the critical need for protection from extreme weather but are not consistent in providing specific recommendations and requirements. Future efforts should include: updated economic analyses of cost versus benefit of shade implementation, exploration of producer perspectives and needs relative to shade, consideration of shade impacts in the cow-calf and slaughter plant segments of the supply chain, and integration of indicators of affective (mental) state and preference in research studies to enhance the holistic assessment of cattle welfare.

scholarly journals Trends in genetic diversity and the effect of inbreeding in American Angus cattle under genomic selection

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Emmanuel A. Lozada-Soto ◽  
Christian Maltecca ◽  
Duc Lu ◽  
Stephen Miller ◽  
John B. Cole ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Beef Cattle ◽  
Genomic Selection ◽  
Inbreeding Depression ◽  
Growth Traits ◽  
Effective Population ◽  
Angus Cattle ◽  
Genomic Inbreeding ◽  
Chromosome Segments ◽  
The Impact

Abstract Background While the adoption of genomic evaluations in livestock has increased genetic gain rates, its effects on genetic diversity and accumulation of inbreeding have raised concerns in cattle populations. Increased inbreeding may affect fitness and decrease the mean performance for economically important traits, such as fertility and growth in beef cattle, with the age of inbreeding having a possible effect on the magnitude of inbreeding depression. The purpose of this study was to determine changes in genetic diversity as a result of the implementation of genomic selection in Angus cattle and quantify potential inbreeding depression effects of total pedigree and genomic inbreeding, and also to investigate the impact of recent and ancient inbreeding. Results We found that the yearly rate of inbreeding accumulation remained similar in sires and decreased significantly in dams since the implementation of genomic selection. Other measures such as effective population size and the effective number of chromosome segments show little evidence of a detrimental effect of using genomic selection strategies on the genetic diversity of beef cattle. We also quantified pedigree and genomic inbreeding depression for fertility and growth. While inbreeding did not affect fertility, an increase in pedigree or genomic inbreeding was associated with decreased birth weight, weaning weight, and post-weaning gain in both sexes. We also measured the impact of the age of inbreeding and found that recent inbreeding had a larger depressive effect on growth than ancient inbreeding. Conclusions In this study, we sought to quantify and understand the possible consequences of genomic selection on the genetic diversity of American Angus cattle. In both sires and dams, we found that, generally, genomic selection resulted in decreased rates of pedigree and genomic inbreeding accumulation and increased or sustained effective population sizes and number of independently segregating chromosome segments. We also found significant depressive effects of inbreeding accumulation on economically important growth traits, particularly with genomic and recent inbreeding.

scholarly journals A Scan for Linkage Disequilibrium Across the Human Genome

Genetics ◽  
1999 ◽  
Vol 152 (4) ◽  
pp. 1711-1722 ◽  
Author(s):  
Gavin A Huttley ◽  
Michael W Smith ◽  
Mary Carrington ◽  
Stephen J O’Brien
Keyword(s):  
Linkage Disequilibrium ◽  
Human Genome ◽  
Pedigree Analysis ◽  
Exact Test ◽  
Genomic Scale ◽  
Genomic Regions ◽  
Formal Test ◽  
Scale Data ◽  
Short Tandem ◽  
Tandem Repeat Polymorphism

Abstract Linkage disequilibrium (LD), the tendency for alleles of linked loci to co-occur nonrandomly on chromosomal haplotypes, is an increasingly useful phenomenon for (1) revealing historic perturbation of populations including founder effects, admixture, or incomplete selective sweeps; (2) estimating elapsed time since such events based on time-dependent decay of LD; and (3) disease and phenotype mapping, particularly for traits not amenable to traditional pedigree analysis. Because few descriptions of LD for most regions of the human genome exist, we searched the human genome for the amount and extent of LD among 5048 autosomal short tandem repeat polymorphism (STRP) loci ascertained as specific haplotypes in the European CEPH mapping families. Evidence is presented indicating that ∼4% of STRP loci separated by &lt;4.0 cM are in LD. The fraction of locus pairs within these intervals that display small Fisher’s exact test (FET) probabilities is directly proportional to the inverse of recombination distance between them (1/cM). The distribution of LD is nonuniform on a chromosomal scale and in a marker density-independent fashion, with chromosomes 2, 15, and 18 being significantly different from the genome average. Furthermore, a stepwise (locus-by-locus) 5-cM sliding-window analysis across 22 autosomes revealed nine genomic regions (2.2-6.4 cM), where the frequency of small FET probabilities among loci was greater than or equal to that presented by the HLA on chromosome 6, a region known to have extensive LD. Although the spatial heterogeneity of LD we detect in Europeans is consistent with the operation of natural selection, absence of a formal test for such genomic scale data prevents eliminating neutral processes as the evolutionary origin of the LD.

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