Genome-wide association study for birth, weaning and yearling weight in Colombian Brahman cattle

Martínez, Rodrigo; Garavito, Diego Hernán Bejarano; Gómez, Yolanda; Dasoneville, Romain; Jiménez, Arturo; Even, Gael; Sölkner, Johann; Mészáros, Gábor

doi:10.1590/1678-4685-gmb-2016-0017

Cited by 28 publications

(19 citation statements)

References 28 publications

(27 reference statements)

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“…In the current study, many QTL regions with genome-wide significance for additive genetic effects were identified [see Additional file 1 : Tables S1, S2 and S3]. For most of the traits studied, peaks for significant additive SNPs across the three datasets were on BTA6 followed by BTA7 and 14 (see Additional file 2 : Figures S13, S14, S15, S16, S17 and S18), which correspond to previously identified QTL [ 3 , 33 – 36 ]. These additive SNPs can contribute to the process of building consensus beef cattle QTL effects and can also provide a starting point for mapping the underlying candidate genes.…”

Section: Discussionsupporting

confidence: 73%

“…Growth traits such as birth weight, weaning weight, pre-weaning daily gain and yearling weight are economically important traits in beef cattle, which are traditionally included in the selection criteria of beef cattle breeding programs [ 48 ] because they are moderately to highly heritable [ 13 ] and are genetically correlated to carcass and meat quality traits [ 49 ]. Several QTL that underlie the variation of growth traits have been detected in several GWAS on different beef cattle populations (Table 2 ) [ 5 , 32 , 34 – 36 ]. SNPS were generally mapped to nearly all of the chromosomes, except BTA3, 9, 10 12, 13, 19, 20 23, 24 and 26 [ 34 – 36 ] and were linked to several candidate genes that differed from those detected in the current study.…”

Section: Discussionmentioning

confidence: 99%

“…Several QTL that underlie the variation of growth traits have been detected in several GWAS on different beef cattle populations (Table 2 ) [ 5 , 32 , 34 – 36 ]. SNPS were generally mapped to nearly all of the chromosomes, except BTA3, 9, 10 12, 13, 19, 20 23, 24 and 26 [ 34 – 36 ] and were linked to several candidate genes that differed from those detected in the current study. These previous studies mainly considered additivity when evaluating effects of SNP genotypes.…”

Section: Discussionmentioning

confidence: 99%

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Genome-wide association scan for heterotic quantitative trait loci in multi-breed and crossbred beef cattle

et al. 2018

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BackgroundHeterosis has been suggested to be caused by dominance effects. We performed a joint genome-wide association analysis (GWAS) using data from multi-breed and crossbred beef cattle to identify single nucleotide polymorphisms (SNPs) with significant dominance effects associated with variation in growth and carcass traits and to understand the mode of action of these associations.MethodsIllumina BovineSNP50 genotypes and phenotypes for 11 growth and carcass traits were available for 6796 multi-breed and crossbred beef cattle. After performing quality control, 42,610 SNPs and 6794 animals were used for further analyses. A single-SNP GWAS for the joint association of additive and dominance effects was conducted in purebred, crossbred, and combined datasets using the ASReml software. Genomic breed composition predicted from admixture analyses was included in the mixed effect model to account for possible population stratification and breed effects. A threshold of 10% genome-wide false discovery rate was applied to declare associations as significant. The significant SNPs with dominance association were mapped to their corresponding genes at 100 kb.ResultsSeven SNPs with significant dominance associations were detected for birth weight, weaning weight, pre-weaning daily gain, yearling weight and marbling score across the three datasets at a false discovery rate of 10%. These SNPs were located on bovine chromosomes 1, 3, 4, 6 and 21 and mapped to six putative candidate genes: U6atac, AGBL4, bta-mir-2888-1, REPIN1, ICA1 and NXPH1. These genes have interesting biological functions related to the regulation of gene expression, glucose and lipid metabolism and body fat mass. For most of the identified loci, we observed over-dominance association with the studied traits, such that the heterozygous individuals at any of these loci had greater genotypic values for the trait than either of the homozygous individuals.ConclusionsOur results revealed very few regions with significant dominance genetic effects across all the traits studied in the three datasets used. Regarding the SNPs that were detected with dominance associations, further investigation is needed to determine their relevance in crossbreeding programs assuming that dominance effects are the main cause of (or contribute usefully to) heterosis.Electronic supplementary materialThe online version of this article (10.1186/s12711-018-0405-y) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 73%

Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

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Genome-wide association scan for heterotic quantitative trait loci in multi-breed and crossbred beef cattle

et al. 2018

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“…The main advantages of BON is that there is a low frequency of dystocia, resistance to diseases and good weight gains despite poor nutritional conditions. Its performance is similar to that of other Creole, Zebu and European breeds in the region ( Vásquez et al, 2006 ; Baldi et al, 2010 ; Martínez et al, 2017 ; Palacios-Espinosa et al, 2019 ). A wide range was found for the different traits, and coefficients of variation were between 10.92 and 15.76, which may be explained by the diverse pasture, the grazing periods and type of pastures used to feed the animals in the different herds.…”

Section: Discussionsupporting

confidence: 70%

Genetic parameters and trends for growth traits in Blanco Orejinegro cattle

Toro

Burgos-Paz

Elzo

et al. 2020

Translational Animal Science

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Since 1940, efforts have been made to preserve the Blanco Orejinegro (BON) cattle breed by maintaining gene banks. Nine years ago, a BON genetic improvement program was implemented to increase genetic gain based on control of productivity and the use of performance tests, polygenic and genomic evaluations, and selection indices. The objective of this study was to estimate genetic parameters and trends for growth traits by using polygenic (PM) and genomic-polygenic (GPM) models. Productive information from years 1980 to 2019 was used. The following data were used: 7304 birth weight (BW) records, 1281 records of body weight adjusted to 120 days (W120), 4791 records of weight adjusted to 240 days (W240), 3339 records of weight adjusted to 480 days (W480), and 1364 records of weight adjusted to 720 days (W720). The relationship matrix included 13612 pure animals belonging to the Colombian Corporation for Agricultural Research - AGROSAVIA and the Producer Network program. A total of 1224 individuals were genotyped with chips of different densities and all were imputed up to 50932 SNPs. Polygenic and genomic-polygenic models were used to estimate genetic parameters and correlations between the genetic values estimated by each model. A generalized additive model with smoothing was used to estimate trends of genetic values from 1980 to 2019. Heritabilities between 0.29 and 0.40, genetic correlations between 0.13 and 0.94, and phenotypic correlations between 0.23 and 0.72 were observed. Close-to-zero genetic growth was observed for BW and W120. Genetic trends for the other traits were positive, with higher growth in the last seven years. The heritabilities observed in this population indicate that the traits measured would respond to selection. Greater genetic progress can be achieved in W240, W480 and W720 by continuing with genetic evaluations and developing performance tests and strategies to make genetic material readily available to producers.

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“…However, Table 2. Top 10 windows explaining the highest proportion of genetic variance for feet and legs binary score (FL1) in Nellore cattle association studies of SNPs for production, carcass and reproductive traits have identified common genomic regions using small population sizes in beef cattle (e.g., Cesar et al, 2014;Martínez et al, 2017;Olivieri et al, 2017;Seabury et al, 2017).…”

Section: Resultsmentioning

confidence: 99%

Genome-wide association study and functional analysis of feet and leg conformation traits in Nellore cattle

Vargas

Neves

Camargo

et al. 2018

Journal of Animal Science

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Feet and leg conformation is evaluated as a subset of conformational structure traits in dairy and beef cattle and is related to the feet and leg quality that can compromise the animals' productive performance and longevity. The aim of this study was to perform a genome-wide association study (GWAS) of two traits related to feet and leg conformation in Nellore cattle to identify chromosomal regions related to the expression of these traits. Phenotypic and pedigree data from 104,725 animals and genotypes from 1,435 animals and 407,730 SNPs were used. Feet and leg structure was evaluated as a binary trait (FL1) to identify yearling animals with feet and leg problems or as categorical score (FL2) to assess the overall quality of their feet and leg. The top ten 1-Mb windows that explained the largest proportion of the total genetic variance were identified and functional enrichment analyses were performed. The 10 windows with large effects obtained for FL1 are located on chromosomes 1, 2, 6, 7, 8, 10, and 14, and together explained 8.96% of the additive genetic variance. For FL2, these windows are located on chromosomes 1, 7, 10, 11, 18, 20, 22, 28, and 29, explaining 8.98% of the additive genetic variance. Several candidate genes were identified, including DLX2 which is associated with osteogenic differentiation, IL-1β and IL-1A associated with some properties of articular cartilage, PiT1 which plays an important role in bone physiology, and CTSL associated with rheumatoid arthritis. The results presented here should contribute to a better understanding of the genetic and physiologic mechanisms regulating both traits, and identifies candidate genes for future investigation of causal mutations.

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Genome-wide association study for birth, weaning and yearling weight in Colombian Brahman cattle

Cited by 28 publications

References 28 publications

Genome-wide association scan for heterotic quantitative trait loci in multi-breed and crossbred beef cattle

Genome-wide association scan for heterotic quantitative trait loci in multi-breed and crossbred beef cattle

Genetic parameters and trends for growth traits in Blanco Orejinegro cattle

Genome-wide association study and functional analysis of feet and leg conformation traits in Nellore cattle

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