Genome-wide association for growth traits in Canchim beef cattle.
ABSTRACT: Studies are being conducted on the applicability of genomic data to improve the accuracy of the selection process in livestock, and genome-wide association studies (GWAS) provide valuable information to enhance the understanding on the genetics of complex traits. The aim of this study was to identify genomic regions and genes that play roles in birth weight (BW), weaning weight adjusted for 210 days of age (WW), and long-yearling weight adjusted for 420 days of age (LYW) in Canchim cattle. GWAS were performed by means of the Generalized Quasi-Likelihood Score (GQLS) method using genotypes from the BovineHD BeadChip and estimated breeding values for BW, WW, and LYW. Data consisted of 285 animals from the Canchim breed and 114 from the MA genetic group (derived from crossings between Charolais sires and ½ Canchim + ½ Zebu dams). After applying a false discovery rate correction at a 10% significance level, a total of 4, 12, and 10 SNPs were significantly associated with BW, WW, and LYW, respectively. These SNPs were surveyed to their corresponding genes or to surrounding genes within a distance of 250 kb. The genes DPP6 (dipeptidyl-peptidase 6) and CLEC3B (C-type lectin domain family 3 member B) were highlighted, considering its functions on the development of the brain and skeletal system, respectively. The GQLS method identified regions on chromosome associated with birth weight, weaning weight, and long-yearling weight in Canchim and MA animals. New candidate regions for body weight traits were detected and some of them have interesting biological functions, of which most have not been previously reported. The observation of QTL reports for body weight traits, covering areas surrounding the genes (SNPs) herein identified provides more evidence for these associations. Future studies targeting these areas could provide further knowledge to uncover the genetic architecture underlying growth traits in Canchim cattle.
Project description:<b>Objective:</b> Body weight is an important economic trait for a goat, which greatly affects animal growth and survival. The purpose of this study was to identify genes associated with birth weight (BW), weaning weight (WW), and yearling weight (YW). <b>Materials and Methods:</b> In this study, a genome-wide association study (GWAS) of BW, WW, and YW was determined using the GGP_Goat_70K single-nucleotide polymorphism (SNP) chip in 1,920 Inner Mongolia cashmere goats. <b>Results:</b> We discovered that 21 SNPs were significantly associated with BW on the genome-wide levels. These SNPs were located in 10 genes, e.g., Mitogen-Activated Protein Kinase 3 (<i>MAPK3</i>), LIM domain binding 2 (<i>LDB2</i>), and low-density lipoprotein receptor-related protein 1B (<i>LRP1B</i>), which may be related to muscle growth and development in Inner Mongolia Cashmere goats. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these genes were significantly enriched in the regulation of actin cytoskeleton and phospholipase D signaling pathway etc. <b>Conclusion:</b> In summary, this study will improve the marker-assisted breeding of Inner Mongolia cashmere goats and the molecular mechanisms of important economic traits.
Project description:<h4>Background</h4>Single nucleotide polymorphism (SNP) arrays have facilitated discovery of genetic markers associated with complex traits in domestic cattle; thereby enabling modern breeding and selection programs. Genome-wide association analyses (GWAA) for growth traits were conducted on 10,837 geographically diverse U.S. Gelbvieh cattle using a union set of 856,527 imputed SNPs. Birth weight (BW), weaning weight (WW), and yearling weight (YW) were analyzed using GEMMA and EMMAX (via imputed genotypes). Genotype-by-environment (GxE) interactions were also investigated.<h4>Results</h4>GEMMA and EMMAX produced moderate marker-based heritability estimates that were similar for BW (0.36-0.37, SE?=?0.02-0.06), WW (0.27-0.29, SE?=?0.01), and YW (0.39-0.41, SE?=?0.01-0.02). GWAA using 856K imputed SNPs (GEMMA; EMMAX) revealed common positional candidate genes underlying pleiotropic QTL for Gelbvieh growth traits on BTA6, BTA7, BTA14, and BTA20. The estimated proportion of phenotypic variance explained (PVE) by the lead SNP defining these QTL (EMMAX) was larger and most similar for BW and YW, and smaller for WW. Collectively, GWAAs (GEMMA; EMMAX) produced a highly concordant set of BW, WW, and YW QTL that met a nominal significance level (P???1e-05), with prioritization of common positional candidate genes; including genes previously associated with stature, feed efficiency, and growth traits (i.e., PLAG1, NCAPG, LCORL, ARRDC3, STC2). Genotype-by-environment QTL were not consistent among traits at the nominal significance threshold (P???1e-05); although some shared QTL were apparent at less stringent significance thresholds (i.e., P???2e-05).<h4>Conclusions</h4>Pleiotropic QTL for growth traits were detected on BTA6, BTA7, BTA14, and BTA20 for U.S. Gelbvieh beef cattle. Seven QTL detected for Gelbvieh growth traits were also recently detected for feed efficiency and growth traits in U.S. Angus, SimAngus, and Hereford cattle. Marker-based heritability estimates and the detection of pleiotropic QTL segregating in multiple breeds support the implementation of multiple-breed genomic selection.
Project description:Data on calving ease (CE) and birth, weaning weight (WW), and yearling weight (YW) were obtained from the American Simmental Association (ASA) and included pedigree and performance information on 11,640,735 animals. Our objective was to quantify differential response from selection for high CE vs. low birth weight (LBW) in first-calf Simmental heifers. We hypothesized that direct selection for CE should be used as the primary approach to reduce dystocia and mitigate losses in growth-related traits. WW and YW were adjusted to 205 and 365 d of age, respectively. Sire and maternal grandsire (co)variance components for CE, birth weight (BW), and 205-d weaning weight (205-d WW), and sire covariance components for 160-d postweaning gain (160-d gain) were estimated using a sire-maternal grandsire model. Direct and maternal expected progeny differences (EPD) for CE, BW, and 205-d WW and direct EPD for 160-d gain and 365-d yearling weight (365-d YW) for first-calf Simmental heifers population (465,710 animals) were estimated using a threshold-linear multivariate maternal animal model. This population was used to estimate genetic trends and as a selection pool (control) for various selection scenarios. Selection scenarios were high CE (HCE), LBW, the all-purpose selection index (API = -1.8 BW + 1.3 CE + 0.10 WW + 0.20 YW) of the ASA and its two derived subindices: (API1 = 1.3 CE + 0.20 YW) and (API2 = -1.8 BW + 0.20 YW), and lastly Dickerson's selection index (DSI = -3.2 BW + YW). Data for each selection scenario were created by selecting sires with EPD greater than or equal to the average along with the top 75% of dams. Comparison between selection scenarios involved evaluating the direct and maternal genetic trends from these scenarios. Direct heritabilities for CE, BW, 205-d WW, 160-d gain, and 365-d YW of Simmental cattle were 0.23, 0.52, 0.28, 0.21, and 0.33, respectively. The single trait, HCE, selection scenario, as opposed to LBW, increased the intercept for CE by 57.7% and the slopes (P < 0.001) for BW, 205-d WW, 160-d gain, and 365-d YW by 27.9%, 37.5%, 16%, and 28%, respectively. Comparisons of various selection scenarios revealed that the CE-based selection scenarios (HCE, API, and API1) had a greater response for CE and growth traits.
Project description:<h4>Background</h4>Beef cattle breeding programs in Brazil have placed greater emphasis on the genomic study of reproductive traits of males and females due to their economic importance. In this study, genome-wide associations were assessed for scrotal circumference at 210 d of age, scrotal circumference at 420 d of age, age at first calving, and age at second calving, in Canchim beef cattle. Data quality control was conducted resulting in 672,778 SNPs and 392 animals.<h4>Results</h4>Associated SNPs were observed for scrotal circumference at 420 d of age (435 SNPs), followed by scrotal circumference at 210 d of age (12 SNPs), age at first calving (six SNPs), and age at second calving (four SNPs). We investigated whether significant SNPs were within genic or surrounding regions. Biological processes of genes were associated with immune system, multicellular organismal process, response to stimulus, apoptotic process, cellular component organization or biogenesis, biological adhesion, and reproduction.<h4>Conclusions</h4>Few associations were observed for scrotal circumference at 210 d of age, age at first calving, and age at second calving, reinforcing their polygenic inheritance and the complexity of understanding the genetic architecture of reproductive traits. Finding many associations for scrotal circumference at 420 d of age in various regions of the Canchim genome also reveals the difficulty of targeting specific candidate genes that could act on fertility; nonetheless, the high linkage disequilibrium between loci herein estimated could aid to overcome this issue. Therefore, all relevant information about genomic regions influencing reproductive traits may contribute to target candidate genes for further investigation of causal mutations and aid in future genomic studies in Canchim cattle to improve the breeding program.
Project description:In beef cattle farming, growth and carcass traits are important for genetic breeding programs. Molecular markers can be used to assist selection and increase genetic gain. The ADIPOQ, OLR1 and PPARGC1A genes are involved in lipid synthesis and fat accumulation in adipose tissue. The objective of this study was to identify polymorphisms in these genes and to assess the association with growth and carcass traits in Nelore cattle. A total of 639 animals were genotyped by PCR-RFLP for rs208549452, rs109019599 and rs109163366 in ADIPOQ, OLR1 and PPARGC1A gene, respectively. We analyzed the association of SNPs identified with birth weight, weaning weight, female yearling weight, female hip height, male yearling weight, male hip height, loin eye area, rump fat thickness, and backfat thickness. The OLR1 marker was associated with rump fat thickness and weaning weight (P < 0.05) and the PPARGC1 marker was associated with female yearling weight.
Project description:BACKGROUND: Meat quality involves many traits, such as marbling, tenderness, juiciness, and backfat thickness, all of which require attention from livestock producers. Backfat thickness improvement by means of traditional selection techniques in Canchim beef cattle has been challenging due to its low heritability, and it is measured late in an animal's life. Therefore, the implementation of new methodologies for identification of single nucleotide polymorphisms (SNPs) linked to backfat thickness are an important strategy for genetic improvement of carcass and meat quality. RESULTS: The set of SNPs identified by the random forest approach explained as much as 50% of the deregressed estimated breeding value (dEBV) variance associated with backfat thickness, and a small set of 5 SNPs were able to explain 34% of the dEBV for backfat thickness. Several quantitative trait loci (QTL) for fat-related traits were found in the surrounding areas of the SNPs, as well as many genes with roles in lipid metabolism. CONCLUSIONS: These results provided a better understanding of the backfat deposition and regulation pathways, and can be considered a starting point for future implementation of a genomic selection program for backfat thickness in Canchim beef cattle.
Project description:Improving the genetic process of growth traits is one of the major goals in the beef cattle industry, as it can increase meat production and reduce the cost of raising animals. Although several quantitative trait loci affecting growth traits in beef cattle have been identified, the genetic architecture of these economically important traits remains elusive. This study aims to map single nucleotide polymorphisms (SNPs) and genes associated with birth weight (BW), yearling weight (YW), average daily gain from birth to yearling (BYADG), and body weight at the age of 18 months (18MW) in a Chinese Simmental beef cattle population using a weighted, single-step, genome-wide association study (wssGWAS). Phenotypic and pedigree data from 6022 animals and genotypes from 744 animals (596,297 SNPs) were used for an association analysis. The results showed that 66 genomic windows explained 1.01-20.15% of the genetic variance for the four examined traits, together with the genes near the top SNP within each window. Furthermore, the identified genomic windows (>1%) explained 50.56%, 57.71%, 61.78%, and 37.82% of the genetic variances for BW, YW, BYADG, and 18MW, respectively. Genes with potential functions in muscle development and regulation of cell growth were highlighted as candidates for growth traits in Simmental cattle (SQOR and TBCB for BW, MYH10 for YW, RLF for BYADG, and ARHGAP31 for 18MW). Moreover, we found 40 SNPs that had not previously been identified as being associated with growth traits in cattle. These findings will further advance our understanding of the genetic basis for growth traits and will be useful for the molecular breeding of BW, YW, BYADG, and 18MW in the context of genomic selection in beef cattle.
Project description:BACKGROUND:Recent technological advances in genomics have allowed the genotyping of cattle through single nucleotide polymorphism (SNP) panels. High-density SNP panels possess greater genome coverage and are useful for the identification of conserved regions of the genome due to selection, known as selection signatures (SS). The SS are detectable by different methods, such as the extended haplotype homozygosity (EHH); and the integrated haplotype score (iHS), which is derived from the EHH. The aim of this study was to identify SS regions in Canchim cattle (composite breed), genotyped with high-density SNP panel. RESULTS:A total of 687,655 SNP markers and 396 samples remained for SS analysis after the genotype quality control. The iHS statistic for each marker was transformed into piHS for better interpretation of the results. Chromosomes BTA5 and BTA14 showed piHS?>?5, with 39 and nine statistically significant SNPs (P?<?0.00001), respectively. For the candidate selection regions, iHS values were computed across the genome and averaged within non-overlapping windows of 500 Kb. We have identified genes that play an important role in metabolism, melanin biosynthesis (pigmentation), and embryonic and bone development. CONCLUSIONS:The observation of SS indicates that the selection processes performed in Canchim, as well as in the founder breeds (i.e. Charolais), are maintaining specific genomic regions, particularly on BTA5 and BTA14. These selection signatures regions could be associated with Canchim characterization.
Project description:This study evaluated heifer post-weaning voluntary feed intake (g/kg BW) classification on performance and reproductive measures, as well as impacts on lifetime productivity of 519 commercial Angus beef females. Heifer post-weaning voluntary feed intake (g/kg BW) was calculated over 80 test days following weaning using GrowSafe units. Heifers were categorized based on voluntary feed intake (g/kg BW) as either low (<-0.50 SD from the mean), average (±0.50 SD from the mean), or high (>0.50 SD from the mean) within year. Cow body weight (BW) and body condition score (BCS) at breeding displayed an age effect (<i>p</i> < 0.001), with 2- and 3-year-old cows having lighter BW and lower BCS than 4-yr-old and older cows. Cow BW at weaning showed significance for age and intake (<i>p</i> < 0.001) with younger cows being lighter than older cows, while low intake classified females had greater BW at weaning compared to average and high intake females. Additionally, calf 205-d weights and calf weaning weights (<i>p</i> < 0.01) were significant for age with calves born from older cows weighing more than younger cows. Weaning weight ratio displayed a linear increase with increasing intake classification (<i>p</i> < 0.01). Heifer yearling BW was significant for intake (<i>p</i> < 0.01) with low and average intake heifer classifications having greater heifer yearling BW than cows that had high intake classification as a heifer. Age and intake classification did not impact (<i>p</i> ≥ 0.22) pregnancy status or AI conception. In summary, heifer post-weaning feed intake classification had only minor impacts compared to age effects on lifetime productivity of Angus beef females.
Project description:As a result of selecting for increased litter size, newborn piglets are being born lighter and have a lower chance of survival. Raising fewer pigs to market weight would have a negative impact on the industry and farmer profitability; thus, understanding the genetics of individual growth performance traits will determine whether these traits will play an important role in pig breeding schemes. This study aimed to estimate genetic parameters for individual birth weight (BW), weaning weight (WW), and probe weight (PW) in Canadian-purebred Yorkshire and Landrace pigs. PW is a live weight taken at the time of the ultrasound measurements, when pigs weigh about 100 kg. Data were collected from 2 large and related breeding herds from 2003 to 2015. Four linear animal models were used, which included the following: Model 1-direct additive genetic effect; Model 2-direct additive genetic and maternal genetic effect; Model 3-direct additive genetic and common litter effect; and Model 4-direct additive genetic, maternal genetic, and common litter effect. The model which included all 3 random effects (Model 4) was determined to be the best fit to the data. Low to moderate direct heritability estimates were observed as follows: 0.15 ± 0.03 for BW, 0.04 ± 0.01 for WW, and 0.33 ± 0.03 for PW for the Yorkshire breed; and 0.05 ± 0.01 for BW, 0.01 ± 0.01 for WW, and 0.27 ± 0.03 for PW in the Landrace breed. As expected, the direct heritability estimates increased with age as a result of decreased maternal influence on the trait. Bivariate animal models were also used to estimate genetic and environmental correlations between traits. Strong direct genetic correlations were observed between BW and WW in both breeds. Based on the estimates of genetic parameters, individual BW could be evaluated and considered in breeding programs aiming to increase BW and improve subsequent performance. Different selection emphasis could also be applied on direct and maternal additive genetic effects on BW to optimize the breeding programs and improve selection efficiency.