Overlapping haplotype blocks indicate shared genomic regions between a composite beef cattle breed and its founder breeds

2021 ◽  
pp. 104747
Author(s):  
Marcos Eli Buzanskas ◽  
Maria Victória Henrique Genuíno ◽  
Igor Nelson Herculano Duarte ◽  
Ayrton Fernandes de Oliveira Bessa ◽  
Luciana Diniz Rola ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Cattle Breed ◽  
Haplotype Blocks ◽  
Genomic Regions

46 Footprints of Selection in Angus and Hanwoo Beef Cattle Using Imputed Whole Genome Sequence Data

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 25-25
Author(s):  
Muhammad Yasir Nawaz ◽  
Rodrigo Pelicioni Savegnago ◽  
Cedric Gondro
Keyword(s):  
Beef Cattle ◽  
Genome Sequence ◽  
Sequence Data ◽  
Whole Genome Sequence ◽  
Fixation Index ◽  
Whole Genome ◽  
Extended Haplotype Homozygosity ◽  
Extended Haplotype ◽  
Genome Sequence Data ◽  
Genomic Regions

Abstract In this study, we detected genome wide footprints of selection in Hanwoo and Angus beef cattle using different allele frequency and haplotype-based methods based on imputed whole genome sequence data. Our dataset included 13,202 Angus and 10,437 Hanwoo animals with 10,057,633 and 13,241,550 imputed SNPs, respectively. A subset of data with 6,873,624 common SNPs between the two populations was used to estimate signatures of selection parameters, both within (runs of homozygosity and extended haplotype homozygosity) and between (allele fixation index, extended haplotype homozygosity) the breeds in order to infer evidence of selection. We observed that correlations between various measures of selection ranged between 0.01 to 0.42. Assuming these parameters were complementary to each other, we combined them into a composite selection signal to identify regions under selection in both beef breeds. The composite signal was based on the average of fractional ranks of individual selection measures for every SNP. We identified some selection signatures that were common between the breeds while others were independent. We also observed that more genomic regions were selected in Angus as compared to Hanwoo. Candidate genes within significant genomic regions may help explain mechanisms of adaptation, domestication history and loci for important traits in Angus and Hanwoo cattle. In the future, we will use the top SNPs under selection for genomic prediction of carcass traits in both breeds.

scholarly journals Genomic Approaches Reveal Pleiotropic Effects in Crossbred Beef Cattle

2021 ◽  
Vol 12 ◽  
Author(s):  
Fernanda M. Rezende ◽  
Eduardo Rodriguez ◽  
Joel D. Leal-Gutiérrez ◽  
Mauricio A. Elzo ◽  
Dwain D. Johnson ◽  
...  
Keyword(s):  
Beef Cattle ◽  
Genomic Selection ◽  
Meat Quality ◽  
Additive Genetic Variance ◽  
Cytoskeletal Proteins ◽  
Pleiotropic Effects ◽  
Genome Wide Association Studies ◽  
Quality Traits ◽  
Meat Quality Traits ◽  
Genomic Regions

Carcass and meat quality are two important attributes for the beef industry because they drive profitability and consumer demand. These traits are of even greater importance in crossbred cattle used in subtropical and tropical regions for their superior adaptability because they tend to underperform compared to their purebred counterparts. Many of these traits are challenging and expensive to measure and unavailable until late in life or after the animal is harvested, hence unrealistic to improve through traditional phenotypic selection, but perfect candidates for genomic selection. Before genomic selection can be implemented in crossbred populations, it is important to explore if pleiotropic effects exist between carcass and meat quality traits. Therefore, the objective of this study was to identify genomic regions with pleiotropic effects on carcass and meat quality traits in a multibreed Angus–Brahman population that included purebred and crossbred animals. Data included phenotypes for 10 carcass and meat quality traits from 2,384 steers, of which 1,038 were genotyped with the GGP Bovine F-250. Single-trait genome-wide association studies were first used to investigate the relevance of direct additive genetic effects on each carcass, sensory and visual meat quality traits. A second analysis for each trait included all other phenotypes as covariates to correct for direct causal effects from identified genomic regions with pure direct effects on the trait under analysis. Five genomic windows on chromosomes BTA5, BTA7, BTA18, and BTA29 explained more than 1% of additive genetic variance of two or more traits. Moreover, three suggestive pleiotropic regions were identified on BTA10 and BTA19. The 317 genes uncovered in pleiotropic regions included anchoring and cytoskeletal proteins, key players in cell growth, muscle development, lipid metabolism and fat deposition, and important factors in muscle proteolysis. A functional analysis of these genes revealed GO terms directly related to carcass quality, meat quality, and tenderness in beef cattle, including calcium-related processes, cell signaling, and modulation of cell–cell adhesion. These results contribute with novel information about the complex genetic architecture and pleiotropic effects of carcass and meat quality traits in crossbred beef cattle.

scholarly journals SELEKSI BOBOT BADAN INDUK DAN EVALUASI KESULITAN PARTUS ANAK (Dystocia) SAPI BALI HASIL PERSILANGAN PEJANTAN SAPI LOKAL UNGGUL SULAWESI UTARA

ZOOTEC ◽  
2019 ◽  
Vol 39 (2) ◽  
pp. 486
Author(s):  
Umar Paputungan ◽  
Manopo Jouke Hendrik ◽  
Surtijono Edmundus Siswosubroto
Keyword(s):  
Beef Cattle ◽  
Rural Areas ◽  
Cattle Breed ◽  
Live Weight ◽  
Nonparametric Test ◽  
Body Dimensions ◽  
North Sulawesi ◽  
Numerical Order ◽  
Female Cattle ◽  
Calving Difficulty

BODY WEIGHT SELECTION AND EVALUATION OF CALVING DIFFICULTY (Dystocia) IN BALI BREED FEMALE CATTLE MATED WITH OUTSTANDING LOCAL BULL OF NORTH SULAWESI. Records on calving performances of 217 parental dams of Bali beef cattle breed including their calves were used to study calving difficulty of Bali beef cattle breed heifers and cows with experiencing in delivery of more than one generation of calving. The difficulties of calving were scored into calving difficulty scores of six scores, initiated at score 0 indicating normal calving to score 5 indicating the most difficult calving delivery requiring surgery. The parental heifers and adult cows as well as their calves grazed onto places within local grass pasture all days starting at 07.00 a.m. to 17.30 p.m. without supplementary feeds of concentrate as the main management system practiced by 104 farmers as the animal owners at rural areas. Differences of calving difficulties in both Bali beef cattle breed groups of heifers and cows were analyzed by nonparametric test of “The Mann-Whitney U test”, using ranks of data based on the incidence frequencies of calving difficulty scores. Data of calving difficulty scores of both Bali beef cattle breed heifer group and cow group were ranked in to the numerical rank initiated from the lowest to largest numerical order. The calculated z value in this study indicating the incidence frequencies of calving difficulty in heifer group was significantly higher than those in cow group. Frequencies of calving difficulty on the category score basis in Bali beef cattle breed heifer group were significantly higher compared with those in Bali beef cattle breed cow group. Low live weights and body dimensions of heifer group highly tended to experience in the incidence and severity of calving difficulty compared with those of cow group. Selection of heifers with relatively well developed body dimensions and live weight relative to expected calf birth weight would be recommended to reduce calving difficulty.Keywords: Bali beef cattle breed, dam and calf body measurements, calving difficulty

21 Unravelling Transmission Ratio Distortion Across the Genome of a Crossbreed Beef Cattle Population

2021 ◽  
Vol 99 (Supplement_3) ◽  
pp. 12-13
Author(s):  
Daiane C Becker Scalez ◽  
Samir Id-Lahoucine ◽  
Pablo A S Fonseca ◽  
Joaquim Casellas ◽  
Angela Cánovas
Keyword(s):  
Beef Cattle ◽  
Bayes Factor ◽  
Null Distribution ◽  
Transmission Ratio Distortion ◽  
Transmission Ratio ◽  
Snp Analysis ◽  
Cattle Population ◽  
Empirical Null Distribution ◽  
Ratio Distortion ◽  
Genomic Regions

Abstract Transmission ratio distortion (TRD) is a process when one allele from either parent is preferentially transmitted to the offspring. The identification of genomic regions affected by TRD might help in the detection of lethal alleles or potential genes affecting reproduction. Here, we investigated TRD in crossbreed beef cattle population aiming to identify genomic regions showing altered deviations in segregation that could be affecting reproduction performance. A total of 237 genotyped animals were used including 46 sires, 80 dams, and 111 parent-offspring (trios). The predominant breeds of these animals were Angus (61.83%), Simmental (18.99%), Gelbvieh (6.12%), Charolais (3.65%), Hereford (2.46%) and Limousin (1.57%). After excluding SNPs with minor allele frequency lower than 0.05 and call-rate lower than 0.90, a total of 369,902 autosomal SNPs were retained for further analyses. The SNP-by-SNP analysis was performed within a Bayesian framework using TRDscanv.2.0 software, using 100,000 iterations, with 10,000 iterations being discarded as burn-in. As table 1 shows, 33 SNPs were identified with TRD, considering a Bayes Factor (BF)≥100 and the approximate empirical null distribution of TRD at 0.01% margin error. Among them, 26 SNPs were parent-unspecific and 7 SNPs were parent-specific TRD. For parent-specific TRD, 214 were identified for sire- and 162 for dam-TRD (BF≥100). Among them, 4 SNPs were detected with sire- and dam-TRD in opposite direction of preference of transmission. Preliminary functional and positional analysis was performed using the list of TRD regions with BF≥100 and the approximate empirical null distribution of TRD at 0.01% margin error. For sire-TRD, 14% of the identified QTL (n = 254) were related to non-return rate. For dam-TRD, 21 regions related to conception rate were found (1.5%) and 13 regions related to stillbirth (0.93%). Haplotype analysis is in progress to identify additional candidate regions and alleles with TRD to better understand this phenomenon in a crossbreed beef population.

132 OVERVIEW OF FERTILITY TRAITS IN RUSSIAN HOLSTEIN BULLS USING GENOME-WIDE ASSOCIATION

2017 ◽  
Vol 29 (1) ◽  
pp. 174 ◽  
Author(s):  
A. A. Sermyagin ◽  
E. N. Naryshkina ◽  
E. A. Gladyr ◽  
I. N. Yanchukov ◽  
G. Brem ◽  
...  
Keyword(s):  
Semen Quality ◽  
Additive Genetic Variance ◽  
Sperm Concentration ◽  
Cattle Breed ◽  
Ministry Of Education ◽  
Data Set ◽  
Scientific Organizations ◽  
Estimated Breeding Values ◽  
Genomic Regions ◽  
Fertility Traits

Holsteins are the most widely distributed cattle breed in Russia. To achieve improvement of both milk production and fertility traits, principles were elaborated to use genomic approaches together with breeding strategies to develop a common breeding index. Combining semen-quality measures for sires with the cows’ reproduction records makes it possible to resolve the problems with decreased conception rates and semen production. Our objective was to search the genomic regions and associated markers for bulls’ fertility traits in Russian Holstein cattle. For the first step, 282 bulls were genotyped using the Bovine SNP50 BeadChip (Illumina Inc., San Diego, CA, USA). The data set originated from the Moscow AI station including records for semen volume (SV), sperm concentration (SC), average SV for multiple ejaculates collected from one sire (ASV), motility (Mt), and number of spermatozoa (NS). The data set consisted of 14,490 records, which varied between 10 and 328 per animal, with 104 sires in the data set. The average age of sires was 80.1 ± 0.3 months. For sires with own records, the deregressed estimated breeding values were calculated using BLUP AM, whereas for the sires without records direct genomic values (DGV) were calculated through GBLUP. The DGV values were used as the animal’s pseudo-phenotypes for a common data set. After quality check in Plink 1.07, 41,435 SNP were taken. Bonferroni correction test for detection of significant associations was applied as P < 1.21 × 10−6. The values for the heritability were 0.322, 0.202, 0.366, 0.014, and 0.169 for SV, SC, ASV, Mt, and NS, respectively. The SNP with a direct significant effect on SV and ASV were identified: ARS-BFGL-NGS-100206 (P = 1.5 × 10−7), BTA-89872-no-rs (P = 6.0 × 10−8), ARS-BFGL-NGS-33119 (P = 2.7 × 10−7), Hapmap26947-BTA-133787 (P = 5.0 × 10−7), BTA-30092-no-rs (P = 9.8 × 10−7), ARS-BFGL-BAC-6515 (P = 1.0 × 10−7), and BTB-01625220 (P = 4.2 × 10−8). For SC and NS traits, the polymorphisms ARS-BFGL-NGS-57433 (P = 7.4 × 10−7) and ARS-BFGL-NGS-12662 (P = 5.1 × 10−7) were found. Two QTL for Mt including 11 SNP were detected on BTA1 (146.3–146.9 Mb) and BTA9 (76.9–77.1 Mb). The DGV effect of SNP (R2) ranged from 8.0 to 10.4% of additive genetic variance. The genes SOX5 (BTA12), PERP (BTA9), and EPT1 (BTA11) were associated with embryonic development, cell death, or apoptosis and synthesis of selenoproteins. Our results may be used to select donor cows for oocytes or embryo collection in the focus of genomic selection. Supported by the Federal Agency for Scientific Organizations #0600–2014–0007.6 and by the Russian Ministry of Education and Science #RFMEFI60414X0062.

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.

P1036 A reduced panel to determine beef cattle breed composition

2016 ◽  
Vol 94 (suppl_4) ◽  
pp. 32-32
Author(s):  
L. A. Kuehn ◽  
W. M. Snelling ◽  
A. K. Lindholm-Perry
Keyword(s):  
Beef Cattle ◽  
Cattle Breed

scholarly journals CALVING AND PREWEANING PERFORMANCE OF CROSSBRED PROGENY OF SOME FOREIGN AND DOMESTIC BEEF CATTLE BREEDS

1985 ◽  
Vol 65 (3) ◽  
pp. 583-593 ◽  
Author(s):  
J. A. NEWMAN ◽  
A. K. W. TONG ◽  
H. T. FREDEEN ◽  
G. W. RAHNEFELD
Keyword(s):  
Beef Cattle ◽  
Cattle Breed ◽  
Gestation Length ◽  
Beef Cow ◽  
Calving Ease ◽  
Postnatal Mortality ◽  
Beef Cattle Breeds ◽  
Calving Difficulty ◽  
Calving Traits ◽  
Intermediate Performance

Charolais-, Simmental- and Limousin-sired calves are compared for calving traits and preweaning growth based on observations of 3939 calves born in 48 western Canadian beef cow herds of Hereford, Angus and Shorthorn breeding during the period 1970–1972. Hereford cows produced calves with longer gestation lengths, higher birth weights, slower preweaning growth, and lower weaning weights than Angus cows. Shorthorn cows produced progeny with the shortest gestation lengths and intermediate performance in other traits. Limousin sires produced calves with the longest gestation lengths, the least calving difficulty, the lightest birth weights, the lowest birth-to-weaning mortality, and the slowest preweaning growth. Charolais-sired and Simmental-sired calves did not differ significantly in gestation length, postnatal mortality or preweaning growth rate, but Simmental-sired calves were lighter at birth and calved more easily. Breed-of-sire effects interacted with breed-of-dam effects for birth weight and with sex-of-calf effects for calving ease and most measurement traits, but these interactions did not generally involve a re-ranking of sire breeds. The economic impact of the results is briefly discussed. Key words: Beef cattle, breed effects, preweaning traits

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