Mapping genomic regions for reproductive traits in beef cattle: Inclusion of the X chromosome

Abstract Background Genomic regions with a high frequency of runs of homozygosity (ROH) are related to important traits in farm animals. We carried out a comprehensive analysis of ROH and evaluated their association with production traits using the BovineHD (770 K) SNP array in Chinese Simmental beef cattle. Results We detected a total of 116,953 homozygous segments with 2.47Gb across the genome in the studied population. The average number of ROH per individual was 99.03 and the average length was 117.29 Mb. Notably, we detected 42 regions with a frequency of more than 0.2. We obtained 17 candidate genes related to body size, meat quality, and reproductive traits. Furthermore, using Fisher’s exact test, we found 101 regions were associated with production traits by comparing high groups with low groups in terms of production traits. Of those, we identified several significant regions for production traits (P < 0.05) by association analysis, within which candidate genes including ECT2, GABRA4, and GABRB1 have been previously reported for those traits in beef cattle. Conclusions Our study explored ROH patterns and their potential associations with production traits in beef cattle. These results may help to better understand the association between production traits and genome homozygosity and offer valuable insights into managing inbreeding by designing reasonable breeding programs in farm animals.

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Influence of X-chromosome markers on reproductive traits of beef cattle

Livestock Science ◽

10.1016/j.livsci.2018.12.021 ◽

2019 ◽

Vol 220 ◽

pp. 152-157 ◽

Cited By ~ 3

Author(s):

Caio Victor Damasceno Carvalho ◽

Isis da Costa Hermisdorff ◽

Isadora Saraiva Souza ◽

Gleb Strauss Borges Junqueira ◽

Ana Fabricia Braga Magalhães ◽

...

Keyword(s):

Beef Cattle ◽

X Chromosome ◽

Reproductive Traits ◽

Chromosome Markers

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Effect of the X chromosome in genomic evaluations of reproductive traits in beef cattle

Animal Reproduction Science ◽

10.1016/j.anireprosci.2020.106682 ◽

2021 ◽

Vol 225 ◽

pp. 106682

Author(s):

Iara Del Pilar Solar Diaz ◽

Gregório Miguel Ferreira de Camargo ◽

Valdecy Aparecida Rocha da Cruz ◽

Isis da Costa Hermisdorff ◽

Caio Victor Damasceno Carvalho ◽

...

Keyword(s):

Beef Cattle ◽

X Chromosome ◽

Reproductive Traits

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Important effect of the X chromosome in genomic evaluations of reproductive traits in beef cattle

10.1101/2020.06.30.178558 ◽

2020 ◽

Author(s):

Iara Del Pilar Solar Diaz ◽

Gregório Miguel Ferreira de Camargo ◽

Valdecy Aparecida Rocha da Cruz ◽

Isis da Costa Hermisdorff ◽

Caio Victor Damasceno Carvalho ◽

...

Keyword(s):

Beef Cattle ◽

X Chromosome ◽

Reproductive Traits ◽

Breeding Value ◽

Prediction Ability ◽

Genomic Breeding ◽

Breeding Values ◽

Scrotal Circumference ◽

The Mean ◽

Genomic Breeding Value

AbstractThe aim of this study was to evaluate the efficiency of inclusion and the prediction ability of the X chromosome for reproductive (occurrence of early pregnancy – P16 and age at first calving - AFC) and andrological traits (scrotal circumference -SC) in a herd of Nellore beef cattle herd. 3,263 genotypes of females and males were used. Genomic prediction for SC, AFC and P16 was carried out considering two scenarios: 1) only autosomal markers or 2) autosomal + X chromosome markers. To evaluate the effect of inclusion of the X chromosome on selection, the responses to the selection performed were compared including or not the X chromosome in the evaluation of the traits. Higher heritability estimates were obtained for SC (0.40 and 0.31), AFC (0.11 and 0.09) and P16 (0.43 and 0.38) for the analyses including the X chromosome compared to those without. The percent reduction on mean genomic breeding values when selection was based on the results of analysis that did not include the X chromosome to 1, 5 and 10% of the top males, was for SC slightly more than 7% of the mean genomic breeding value of the selected animals. For P16, the loss can reach more than 4%, while this loss does not seem to be as important for AFC. Average predictive correlation of 0.79, 0.98 and 0.84 for SC, AFC and P16 was obtained, respectively. These estimates demonstrate that inclusion of the X chromosome in the analysis can improve the prediction of genomic breeding values, especially for SC.

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

Journal of Animal Science ◽

10.1093/jas/skab235.042 ◽

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.

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Estimates of heritability and repeatability for reproductive traits in Australian beef cattle

Livestock Production Science ◽

10.1016/0301-6226(90)90038-8 ◽

1990 ◽

Vol 25 (1-2) ◽

pp. 15-30 ◽

Cited By ~ 82

Author(s):

K Meyer ◽

K Hammond ◽

P.F Parnell ◽

M.J MacKinnon ◽

S Sivarajasingam

Keyword(s):

Beef Cattle ◽

Reproductive Traits

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Genomic Approaches Reveal Pleiotropic Effects in Crossbred Beef Cattle

Frontiers in Genetics ◽

10.3389/fgene.2021.627055 ◽

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.

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

Journal of Animal Science ◽

10.1093/jas/skab235.021 ◽

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.

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