Exploring and Identifying Candidate Genes and Genomic Regions Related to Economically Important Traits in Hanwoo Cattle

The purpose of the current review was to explore and summarize different studies concerning the detection and characterization of candidate genes and genomic regions associated with economically important traits in Hanwoo beef cattle. Hanwoo cattle, the indigenous premium beef cattle of Korea, were introduced for their marbled fat, tenderness, characteristic flavor, and juiciness. To date, there has been a strong emphasis on the genetic improvement of meat quality and yields, such as backfat thickness (BFT), marbling score (MS), carcass weight (CW), eye muscle area (EMA), and yearling weight (YW), as major selection criteria in Hanwoo breeding programs. Hence, an understanding of the genetics controlling these traits along with precise knowledge of the biological mechanisms underlying the traits would increase the ability of the industry to improve cattle to better meet consumer demands. With the development of high-throughput genotyping, genomewide association studies (GWAS) have allowed the detection of chromosomal regions and candidate genes linked to phenotypes of interest. This is an effective and useful tool for accelerating the efficiency of animal breeding and selection. The GWAS results obtained from the literature review showed that most positional genes associated with carcass and growth traits in Hanwoo are located on chromosomes 6 and 14, among which LCORL, NCAPG, PPARGC1A, ABCG2, FAM110B, FABP4, DGAT1, PLAG1, and TOX are well known. In conclusion, this review study attempted to provide comprehensive information on the identified candidate genes associated with the studied traits and genes enriched in the functional terms and pathways that could serve as a valuable resource for future research in Hanwoo breeding programs.

MOET Efficiency in a Spanish Herd of Japanese Black Heifers and Analysis of Environmental and Metabolic Determinants

Multiple ovulation and embryo transfer (MOET) systems have been intensively implemented in Japanese Black cattle in Japan and to create Japanese Black herds out of these areas. Environmental conditions influence MOET efficiency. Thus, we describe results of 137 in vivo, non-surgical embryo flushings performed between 2016-2020, in a full-blood Japanese Black herd kept in Spain and the possible effects of heat, year, bull, donor genetic value, and metabolic condition. Additionally, 687 embryo transfers were studied for conception rate (CR) and recipient related factors. A total of 71.3% of viable embryos (724/1015) were obtained (5.3 ± 4.34/flushing). Donor metabolites did not affect embryo production (p > 0.1), although metabolite differences were observed over the years, and by flushing order, probably related to the donor age. CR was not affected by embryo type (fresh vs. frozen), recipient breed, and whether suckling or not suckling (p > 0.1). CR decreased significantly with heat (44.3 vs. 49.2%; (p = 0.042)) and numerically increased with recipient parity and ET-number. Pregnant recipients showed significantly higher levels of cholesterol-related metabolites, glucose, and urea (p < 0.05). Therefore, adequate MOET efficiency can be achieved under these conditions, and heat stress should be strongly avoided during Japanese Black embryo transfers. Moreover, recipients' metabolites are important to achieve pregnancy, being probably related to better nutrient availability during pregnancy.

Single nucleotide polymorphisms of leptin gene in five Ethiopian indigenous cattle breeds and the Korean Hanwoo breed

Considering the escalating number of scientific reports on the association between the leptin gene and diverse physiological traits and performance of cattle populations, this study was directed towards identifying SNPs in the leptin gene among five indigenous cattle breeds of Ethiopia. DNA samples were extracted from the nasal swabs of the Ethiopian indigenous cattle breeds: Arsi (n = 18), Horro (n = 20), Begait (n = 21), Boran (n = 19), and Fogera (n = 17) and the Korean Hanwoo (a representative taurine breed) (n = 20), followed by PCR amplification of exon 2 and exon 3 regions of the leptin gene and sequence analysis of the PCR products. Five SNPs, two (generating missense mutations) on exon 2 and three (generating silent mutations) on exon 3 regions, were explicated in this study. Allele frequency and genotype frequency distribution pertaining to the SNPs were recorded for the studied cattle breeds besides the minor allele frequency and deviation from the Hardy-Weinberg equilibrium. Positive F_IS index values were recorded for all the markers except SNP2, illustrative of heterozygote deficiency. MEGA X software-based evolutionary divergence analysis of the phylogenetic tree based on the SNP data revealed that the large-sized breeds, Hanwoo, Begait, Boran, and Fogera, were more closely clustered compared to the small-sized Arsi breed. Among the seven haplotypes documented from the various breeds, sequence analysis was suggestive of haplotypes 1 and 2 to be ancestral haplotypes for the leptin gene. This study is envisaged to accelerate molecular breeding programs for the genetic improvement of the Ethiopian cattle breeds.

Correlations between circulating leptin concentrations and growth performance, carcass traits, and meat quality indexes in finishing Simmental × Luxi bulls fed high-concentrate diets

Circulating leptin concentrations could potentially be used as a predictor of production traits in cattle. This study aimed to clarify the correlations between circulating leptin concentrations and growth performance, carcass traits, and meat quality indexes in finishing bulls fed high-concentrate diets (concentrate-to-forage ratio 70:30). Fifty-seven Simmental × Luxi F1 crossbred bulls were used for 112-day finishing experiment. Circulating leptin concentrations and relevant indexes of growth performance, and carcass traits and meat quality were measured during or after finishing trail. The results indicated that the leptin concentrations tended to be negatively correlated with dry matter intake (DMI) (r = -.233, p = .081), and were positively correlated with 12th-rib fat thickness (r = .330, p = .012), marbling score (r = .336, p = .011), and intramuscular fat content (r = .368, p = .021). Moreover, the leptin concentrations were negatively correlated with cholesterol content (r = -.339, p = .037) and were not correlated with sensory indexes including tenderness, juiciness, and like flavor (p > .05). In conclusion, circulating leptin concentrations may potentially be used as a predictor of carcass traits related to content of fat and beef quality traits related to content of cholesterol in finishing bulls fed high-concentrate diets.

Evaluation of candidate genotype of leptin gene associated with fertility and production traits in Hardhenu (Bos taurus × Bos indicus) cattle

The present study was conducted on Hardhenu cattle to screen genomic region of leptin gene with an objective to find the association of genotypes with fertility and production traits. The association analysis with traits under study was analysed by least squares analysis of variance by taking SNPs genotype as fixed effects in the statistical model. The genotypic frequencies with respect to targeted loci g.92450765 G > A indicated that AG (0.54) genotype was highest in Hardhenu cattle. Chi-squared tests showed that g.92450765G > A SNP meet with the Hardy-Weinberg equilibrium (p > .05).The association analysis revealed significant association of genotypes with total milk yield (TMY) and 305 days milk yield (MY) (p < .05). Service period (SP) and calving interval (CI) were also found significantly associated with genotypes (p < .05). Whereas, lactation length (LL), dry days (DD) and age at first calving (AFC) did not divulge any significant association with genotype. The AG and GG genotypes were associated with higher milk yields as compared to AA genotype, indicating that allele G was associated with superior milk performance. However, AA genotyped cattle found to be favourable with SP, CI and artificial insemination (AI) per conception compared to AG and GG genotyped cows. Chi-square analysis revealed that genetic variants of g.92450765 G > A SNP of leptin gene differ significantly with regard to reproductive disorders incidence (p < .05). The frequency of GG genotype (88.89%) in the affected animal group was very high followed by AG. The animals with GG genotype were found to be more susceptible to reproductive disorders as suggested by the higher odd ratio value (16.00) in logistic model. These observations and their differential association with the fertility and production traits can be utilized as an aid to selection for genetic improvement of antagonistic traits in dairy cows.

Associations between UASMS2 polymorphism in leptin gene and growth, carcass and meat quality traits of cattle: a meta-analysis

Although numerous studies investigated the effect of UASMS2 polymorphism in leptin gene on cattle production, a consensus has not yet been reached. Therefore, we reviewed and meta-analyzed the effects of UASMS2 on cattle. We searched potentially relevant studies from seven databases (to December 25, 2019). Standard mean difference along with 95% confidence intervals was calculated to assess the strength of association through the random-effects model. Six published articles containing 1378 cattle samples were included in our meta-analysis. We found UASMS2 was not related to carcass weight, dressing percentage and loin muscle area in the recessive genetic model, but there was a significant association between UASMS2 and average daily weight gain, dry matter intake, body weight, marbling score, and backfat thickness. This meta-analysis indicated that UASMS2 was associated with growth and meat quality traits of cattle, implying that this SNP can be used reliably in beef cattle breeding. This study may provide valuable information on improving beef yield and quality in cattle production.

Comprehensive assessment of candidate genes associated with fattening performance in Holstein-Friesian bulls

The objective of this study was to determine the association of single nucleotide polymorphisms (SNPs) in selected candidate genes with fattening performance traits in a commercial cattle herd. Fifteen SNPs in 12 candidate genes (LEP, FABP4, DGAT1, TG, IGF1, IGF1R, MYF5, LGB, CAPN1, CAST, GHR, and OLR1) were evaluated in 296 purebred Holstein-Friesian bulls using PCR-RFLP (polymerase chain reaction - restriction fragment length polymorphism). Associations between each segregating SNP and genetic merit for fattening performance were quantified using linear mixed models. Traits included in the study were fattening period, final weight, dry matter intake, feed conversion rate, and average daily weight gain. Apart from the general determination of the above-mentioned traits, each trait was evaluated based on the fattening periods between five selected target body weights (W1  =  100 kg, W2  =  200 kg, W3  =  300 kg, W4  =  400 kg, W5  =  450 kg). All markers with the exception of CAPN1 530, IGF1R, TG, and DGAT1 were associated with at least one of the traits. Furthermore, novel associations were observed for LEP  ×  GHR, IGF1  ×  LEP, FABP4 3691  ×  FABP4 2834, and FAP4 3533  ×  LEP interactions. The results of this study confirm some previously reported associations. Moreover, novel associations have been identified, which may be incorporated into breeding programs to improve fattening performance.

Effects of polymorphisms at <i>LEP</i>, <i>CAST</i>, <i>CAPN1</i>, <i>GHR</i>, <i>FABP4</i> and <i>DGAT1</i> genes on fattening performance and carcass traits in Simmental bulls

Abstract. The aim of this study was to investigate the effects of single nucleotide polymorphisms (SNPs) at six candidate genes (LEP, CAST, CAPN1, GHR, FABP4 and DGAT1) on fattening performance and carcass traits of Simmental bulls in Turkey. The analysis covered a total of 81 Simmental bulls grown on a private farm that were randomly selected for their fattening period for use in this study. Genotyping was performed using the PCR-RFLP method. The S20T polymorphism at the CAST gene and the G316A polymorphism at the CAPN1 gene were associated with variation in final weight, fattening period, weight gain and average daily gain (P < 0.05). In addition, LEP A80V had a significant effect on hot and chilled carcass weight and dressing percentage (P < 0.05). There was no association between GHR S555G, FABP4 V110M and DGAT1 K232A markers with the traits analysed. These results suggested that focusing on the novel effects of LEP, CAST and CAPN1 gene polymorphisms on meat production traits might be useful for marker-assisted selection in Simmental cattle.

Identification of leptin gene polymorphisms associated with carcass traits and fatty acid composition in Japanese Black cattle

Previous studies have indicated that some leptin gene polymorphisms were associated with economically important traits in cattle breeds. However, polymorphisms in the leptin gene have not been reported thus far in Japanese Black cattle. Here, we aimed to identify the leptin gene polymorphisms which are associated with carcass traits and fatty acid composition in Japanese Black cattle. We sequenced the full-length coding sequence of leptin gene for eight Japanese Black cattle. Sequence comparison revealed eight single nucleotide polymorphisms (SNPs). Three of these were predicted to cause amino acid substitutions: Y7F, R25C and A80V. Then, we genotyped these SNPs in two populations (JB1 with 560 animals and JB2 with 450 animals) and investigated the effects on the traits. Y7F in JB1 and A80V in JB2 were excluded from statistical analysis because the minor allele frequencies were low (< 0.1). Association analysis revealed that Y7F had a significant effect on the dressed carcass weight in JB2; R25C had a significant effect on C18:0 and C14:1 in JB1 and JB2, respectively; and A80V had a significant effect on C16:0, C16:1, C18:1, monounsaturated fatty acid and saturated fatty acid in JB1. The results suggested that these SNPs could be used as an effective marker for the improvement of Japanese Black cattle.

Residual feed intake studies in Angus-sired cattle reveal a potential role for hypothalamic gene expression in regulating feed efficiency

Mechanisms underlying variation in residual feed intake (RFI), a heritable feed efficiency measure, are poorly understood while the relationship between RFI and meat quality is uncertain. To address these issues, 2 divergent cohorts consisting of High (HRFI) and Low (LRFI) RFI individuals were created by assessing RFI in 48 Angus-sired steers during a 70 d feeding trial to identify steers with divergent RFI. The association of RFI with indices of meat quality and expression of genes within hypothalamic and adipose tissue was then determined in LRFI and HRFI steers. While on test, feed intake was recorded daily with BW and hip heights recorded at 14 d intervals. Ultrasound measurements of rib eye area (REA) and backfat (BF) were recorded initially and before harvest. Carcass and growth data were analyzed using a mixed model with RFI level (LRFI, HRFI) as the independent variable. The least-square means (lsmeans) for RFI were -1.25 and 1.51 for the LRFI and HRFI cohorts (P < .0001). Dry matter intake was higher for the HRFI individuals versus the LRFI steers (P < .0001) while on test BW gain was not different between the 2 groups (P < 0.73). There were no differences detected in marbling score (P < 0.93), BF (P < 0.61), REA (P < 0.15), yield grade (P < 0.85) or objective Hunter color measures between LRFI and HRFI steers indicating that there was no relationship between RFI and meat quality. Neuropeptide-Y (NPY), relaxin-3 (RLN3), melanocortin 4 receptor (MC4R), and GnRH mRNA expression was 64%, 59%, 58%, 86% lower (P < 0.05), respectively, while gonadotropin inhibiting hormone (GnIH) and pro-opiomelanocortin (POMC) mRNA expression was 198% and 350% higher (P < 0.01) in the arcuate nucleus of LRFI steers. Expression of agouti-related protein (AGRP), relaxin/insulin-like family peptide receptor 1 (RXFP1), and melanocortin 3 receptor mRNA was similar between LRFI and HRFI animals. Pituitary expression of FSHβ (P < 0.03) and LHβ (P < 0.01) was correlated to hypothalamic GnRH levels suggesting that changes in gene expression within the arcuate nucleus had functional consequences. Leptin mRNA expression was 245% higher in the adipose tissue of LRFI steers consistent with lower levels of NPY and higher expression of POMC in their hypothalami. These data support the hypothesis that differences in hypothalamic neuropeptide gene expression underlie variation in feed efficiency in steers while the gonadotropin axis may also influence feed efficiency.

Leptin in farm animals: where are we and where can we go?

Fat affects meat quality, value and production efficiency as well as providing energy reserves for pregnancy and lactation in farm livestock. Leptin, the adipocyte product of the obese (ob) gene, was quickly seen as a predictor of body fat content in animals approaching slaughter and an aid to assessing reproductive readiness in females. Its participation in inflammation and immune responses that help animals survive infection and trauma has clear additional relevance to meat and milk production. Furthermore, almost a decade of discoveries of nucleotide polymorphisms in the leptin and leptin receptor genes has suggested useful applications relating to feed intake regulation, the efficiency of feed use, the composition of growth, the timing of puberty, mammogenesis and mammary gland function and fertility in cattle, pigs and poultry. The current review attempts to summarise where research has taken us in each of these aspects and speculates on where future research might lead.

Whole-genome analysis for backfat thickness in a tropically adapted, composite cattle breed from Brazil

Backfat thickness affects the preservation of the beef carcass after slaughter and confers organoleptic characteristics assessed by the consumer. One of the breeding goals for Canchim, a tropically adapted breed, is to comprehensively increase fat thickness. Our goals were to identify genomic regions associated with backfat in Canchim populations and validate the association of single nucleotide polymorphisms (SNPs) overlapping previously identified QTL regions known to affect fat deposition. Fifteen animals with lower and 15 animals with higher residues for backfat, according to a linear model using the SAS GLM procedure, were selected from a population of 1171 animals and genotyped using the BovineSNP50 BeadChip. Initial analysis revealed more than 100 SNPs that discriminated the tails of phenotypic distribution. One extended region of association included the centromeric region of chromosome (Chr) 14. Because this region overlapped with QTL from previous reports, we developed SNP assays to interrogate two linkage disequilibrium blocks, one in the centromeric region and another in the middle region of Chr 14 to confirm the association. The analysis validated the presence of specific haplotypes affecting fat thickness.

Genetic markers of body composition and carcass quality in grazing Brangus steers

The somatotropic axis is a major regulatory pathway of energy metabolism during postnatal growth in mammals. Genes involved in this pathway influence many economically important traits. The association of selected SNPs in these genes with carcass traits was examined in grazing Brangus steers. These traits included final live weight, ultrasound backfat thickness (UBFT), rib-eye area, kidney fat weight, hot carcass weight, and intramuscular fat percentage (%IMF). Genomic DNA (N = 246) was genotyped for a panel of 15 tag SNPs located in the growth hormone receptor (GHR), insulin-like growth factor I, insulin-like growth factor-binding protein 6, pro-melanin-concentrating hormone, suppressor of cytokine signaling 2, and signal transducer and activator of transcription 6 (STAT6) genes. Allelic and haplotype frequencies were compared with those of a sample of European breeds (N = 177 steers). Two tag SNPs in the GHR affected %IMF; one of them (ss86273136) was also strongly associated with UBFT (P < 0.003). The frequency of the most favorable GHR haplotype for %IMF was lower in Brangus steers. Moreover, the haplotype carrying two unfavorable alleles was present at a frequency of 31% in this group. Four tag SNPs on STAT6 had a significant effect on UBFT. One of these, SNP ss115492467, was also associated with %IMF. The STAT6 haplotype, including all the alleles favoring UBFT, was the most abundant variant (34%) in the European cattle, while it had a frequency of 14% in the Brangus steers. The four less favorable variants (absent in the European cattle) were found at a frequency of 38% in the Brangus steers. These results support the association of GHR and STAT6 SNP with carcass traits in composite breeds, such as Brangus, under grazing conditions.

Association of bovine leptin polymorphisms with energy output and energy storage traits in progeny tested Holstein-Friesian dairy cattle sires

Background

Leptin modulates appetite, energy expenditure and the reproductive axis by signalling via its receptor the status of body energy stores to the brain. The present study aimed to quantify the associations between 10 novel and known single nucleotide polymorphisms in genes coding for leptin and leptin receptor with performance traits in 848 Holstein-Friesian sires, estimated from performance of up to 43,117 daughter-parity records per sire.

Results

All single nucleotide polymorphisms were segregating in this sample population and none deviated (P > 0.05) from Hardy-Weinberg equilibrium. Complete linkage disequilibrium existed between the novel polymorphism LEP-1609, and the previously identified polymorphisms LEP-1457 and LEP-580. LEP-2470 associated (P < 0.05) with milk protein concentration and calf perinatal mortality. It had a tendency to associate with milk yield (P < 0.1). The G allele of LEP-1238 was associated (P < 0.05) with reduced milk fat concentration, reduced milk protein concentration, longer gestation length and tended to associate (P < 0.1) with an increase in calving difficulty, calf perinatal mortality and somatic cells in the milk. LEP-963 exhibited an association (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and gestation length. It also tended to associate with milk yield (P < 0.1). The R25C SNP associated (P < 0.05) with milk fat concentration, milk protein concentration, calving difficulty and length of gestation. The T allele of the Y7F SNP significantly associated with reduced angularity (P < 0.01) and reduced milk protein yield (P < 0.05). There was also a tendency (P < 0.1) for Y7F to associate with increased body condition score, reduced milk yield and shorter gestation (P < 0.1). A80V associated with reduced survival in the herd (P < 0.05).

Conclusions

Several leptin polymorphisms (LEP-2470, LEP-1238, LEP-963, Y7F and R25C) associated with the energetically expensive process of lactogenesis. Only SNP Y7F associated with energy storage. Associations were also observed between leptin polymorphisms and calving difficulty, gestation length and calf perinatal mortality. The lack of an association between the leptin variants investigated with calving interval in this large data set would question the potential importance of these leptin variants, or indeed leptin, in selection for improved fertility in the Holstein-Friesian dairy cow.

Effect of ageing and μ-calpain markers on meat quality from Brangus steers finished on pasture

Brangus steers (n=247) finished on pasture were used to evaluate the effects of post-mortem ageing and polymorphism CAPN1 316 and CAPN1 4751 markers on meat tenderness and objective colour measurements (CIEL*a*b*) of m. Longissimus dorsi. Ageing meat for 7 days decreased shear force (SF) by 13.7% and improved a* (8.4%) and b* (10%) compared to ageing for 1 day. No difference between 7 and 14 days of ageing was found for SF, a* and b*. However, L* increased markedly with ageing. Fitting both markers simultaneously, CAPN1 316 showed association with SF and L* and CAPN1 4751 with a* and b*. Fitting the markers individually, CAPN1 4751 affected all traits and CAPN1 316 showed association with SF and L*. Post-mortem ageing and the use of markers represent two independent and alternative tools that could be used for improving quality of meat from Brangus cattle.