Post-partum anoestrus in tropical beef cattle: A systems approach combining gene expression and genome-wide association results

Fortes, M. R. S.; Suhaimi, A. H. M. S.; Porto-Neto, Laércio R.; McWilliam, Sean M.; Flatscher-Bader, Trudi; Moore, S. S.; D’Occhio, Michael J.; Meira, Camila Tângari; Thomas, M. G.; Snelling, W. M.; Reverter, Antônio; Lehnert, S. A.

doi:10.1016/j.livsci.2014.06.017

Cited by 13 publications

(11 citation statements)

References 42 publications

(42 reference statements)

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“…Some of the regions identified here have also been detected in other studies investigating reproductive traits in cattle, such as regions Chr05/8.89–10.12Mb [ 45 – 47 ], Chr07/3.12–3.85Mb and Chr07/41.29–42.03Mb [ 46 ], and Chr21/0.01–3.02Mb [ 46 , 47 ]. Taken together, these findings demonstrate that cattle breeds share regions that exert a great influence on reproductive traits.…”

Section: Resultssupporting

confidence: 73%

Genome-Wide Association Study for Indicator Traits of Sexual Precocity in Nellore Cattle

et al. 2016

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The objective of this study was to perform a genome-wide association study (GWAS) to detect chromosome regions associated with indicator traits of sexual precocity in Nellore cattle. Data from Nellore animals belonging to farms which participate in the DeltaGen® and Paint® animal breeding programs, were used. The traits used in this study were the occurrence of early pregnancy (EP) and scrotal circumference (SC). Data from 72,675 females and 83,911 males with phenotypes were used; of these, 1,770 females and 1,680 males were genotyped. The SNP effects were estimated with a single-step procedure (WssGBLUP) and the observed phenotypes were used as dependent variables. All animals with available genotypes and phenotypes, in addition to those with only phenotypic information, were used. A single-trait animal model was applied to predict breeding values and the solutions of SNP effects were obtained from these breeding values. The results of GWAS are reported as the proportion of variance explained by windows with 150 adjacent SNPs. The 10 windows that explained the highest proportion of variance were identified. The results of this study indicate the polygenic nature of EP and SC, demonstrating that the indicator traits of sexual precocity studied here are probably controlled by many genes, including some of moderate effect. The 10 windows with large effects obtained for EP are located on chromosomes 5, 6, 7, 14, 18, 21 and 27, and together explained 7.91% of the total genetic variance. For SC, these windows are located on chromosomes 4, 8, 11, 13, 14, 19, 22 and 23, explaining 6.78% of total variance. GWAS permitted to identify chromosome regions associated with EP and SC. The identification of these regions contributes to a better understanding and evaluation of these traits, and permits to indicate candidate genes for future investigation of causal mutations.

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Section: Resultssupporting

confidence: 73%

Genome-Wide Association Study for Indicator Traits of Sexual Precocity in Nellore Cattle

et al. 2016

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“…Using part of the data from the study of Hawken et al (2012), Fortes et al (2012) identified SNPs and chromosome regions that are directly associated with age at puberty of females and scrotal circumference in bulls. There have been some studies related to reproductive traits in zebu cattle such as: genome-wide association studies using 777k SNP panels (Irano et al, 2016;Nascimento et al, 2015;Costa et al, 2015), candidate gene/SNP studies (Fortes et al, 2013a,b), and combinations of methodologies (SNP association and gene expression; Fortes et al, 2014). The use of these technologies is being developed especially in tropical regions due to the importance of female performance in beef production profitability.…”

Section: Introductionmentioning

confidence: 99%

Association between single nucleotide polymorphisms and sexual precocity in Nellore heifers

Regatieri

Boligon

Costa

et al. 2017

Animal Reproduction Science

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The aim of this study was to determine the extent (r) of linkage disequilibrium (LD) in the genome of Nellore cattle, and to examine associations between single nucleotide polymorphisms (SNP) and age at first calving (AFC) and early pregnancy (EP) using a panel of high-density SNPs and data from 1182 Nellore females. A total of 13 contemporary groups (CG) were used consisting of farm, season, and year of birth. For genome-wide association analysis, SNPs with a minor allele frequency (MAF)<0.05 and animals with a call rate<0.90 were excluded, totaling 431,885 SNPs. For statistical analysis, a linear model was used for AFC and a threshold model for EP. To estimate the significance of the associations for the two traits, the model included the categorical fixed effects of CG, SNPs, and sire. In addition, the polygenic effect was included in the analysis. The additive effects and dominance deviations of Bonferroni-adjusted significant SNPs for AFC and EP were estimated using orthogonal contrasts. The average estimate of r for all autosomes was 0.18 at a distance of 4.8kb and the mean MAF was 0.25±0.13. The LD decreased as the distance between markers increased: 0.35 (1kb) to 0.12 (100kb). Eleven significant associations were detected in seven different chromosomes. Seven SNPs were associated with AFC and four were associated with EP. Three SNPs were significant for both traits. The identification of SNPs associated with AFC and EP may contribute for selecting sexually precocious animals.

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“…In breeding programs, causal mutations might be important and could aid genomic selection and genetic gain . According to Fortes et al (2014), causal mutations have an advantage in comparison to random SNP: they are not dependent on LD, and so they can be used for selection over generations, across breeds, and in breeds that were not in the reference population.…”

Section: Principles Underlying Multi-breed Genomic Selectionmentioning

confidence: 99%

Genomic selection in multi-breed dairy cattle populations

Cole

Silva

2016

R. Bras. Zootec.

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-Genomic selection has been a valuable tool for increasing the rate of genetic improvement in purebred dairy cattle populations. However, there also are many large populations of crossbred dairy cattle in the world, and multi-breed genomic evaluations may be a valuable tool for improving rates of genetic gain in those populations. Multi-breed models are an extension of single-breed genomic models in which a genomic relationship matrix is used to account for the breed origin of alleles in the population, as well as allele frequency differences between breeds. Most studies have found little benefit from multi-breed evaluations for pure breeds that have large reference populations. However, breeds with small reference populations may benefit from inclusion in a multi-breed evaluation without adversely affecting evaluations for purebred performance. Most research has been conducted in taurine breeds, so additional research is needed to determine the value of multi-breed reference populations for composite and synthetic breeds that include both indicine and taurine cattle adapted to tropical climates.

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Post-partum anoestrus in tropical beef cattle: A systems approach combining gene expression and genome-wide association results

Cited by 13 publications

References 42 publications

Genome-Wide Association Study for Indicator Traits of Sexual Precocity in Nellore Cattle

Genome-Wide Association Study for Indicator Traits of Sexual Precocity in Nellore Cattle

Association between single nucleotide polymorphisms and sexual precocity in Nellore heifers

Genomic selection in multi-breed dairy cattle populations

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