Association study between SNP markers located in meat quality candidate genes with intramuscular fat content in an endangered dual-purpose cattle population

The aim of this study was to associate single nucleotide polymorphisms (SNP) of the bovine calcium-activated neutral protease µ-calpain, calpastatin, diacylglycerol-O-acyltransferase, adipose fatty acid binding protein, retinoic acid receptor-related orphan receptor C (RORC), and thyroglobulin (TG) gene with intramuscular fat content (IMF). Therefore, 542 animals of the cattle breed "Rotes Höhenvieh" (RHV) were phenotyped for IMF. Genotyping of the animals was performed using polymerase chain reaction-restriction fragment length polymorphism tests for six SNP from candidate genes for meat quality traits. In addition, we calculated allele substitution and dominance effects on IMF. A subgroup of animals (n = 44, reduced dataset) with extraordinary high IMF was analyzed separately. The mean IMF content was 2.5% (SD: 2.8) but ranged from 0.02% to 23.9%, underlining the breeds' potential for quality meat production. Allele and genotype frequencies for all SNP were similar in the complete and reduced dataset. Association analyses in the complete dataset revealed the strongest effects of RORC on IMF (P = 0.075). The log-transformed least-squares mean for IMF of genotype g.3290GG was 0.45 ± 0.16, 0.26 ± 0.14 for genotype g.3290GT, and 0.32 ± 0.14 for genotype g.3290TT. In the reduced dataset, we found a significant effect (P < 0.05) of the g.422C>T-SNP of TG on IMF, with highest IMF for genotype CT (0.91 ± 0.17), lowest IMF for genotype TT (0.37 ± 0.25), and medium IMF for genotype CC (0.59 ± 0.16; log-transformed values). Compared to the complete dataset, allele substitution effects increased in the reduced dataset for most of the SNP, possibly due to the selective genotyping strategy, with focus on animals with highest IMF implying strong phenotypic IMF contrast. Dominance effects were small in both datasets, related to the high heritability of IMF. Results indicated RHV breed particularities regarding the effects of meat quality genes on IMF. An explanation might be the breeding history of RHV with focus on adaptation and resilience in harsh outdoor systems. Consequently, it is imperative to develop breed-specific selection strategies. Allele substitution and dominance effects were in a similar direction in both datasets, suggesting the same breeding approaches for different RHV strains in different regions. Nevertheless, a selective genotyping approach (reduced dataset), contributed to more pronounced genotype effect differences on IMF and dominance values.

Single-step genome-wide association for selected milk fatty acids in Dual-Purpose Belgian Blue cows

The aim of this study was to estimate genetic parameters and identify genomic regions associated with selected individual and groups of milk fatty acids (FA) predicted by milk mid-infrared spectrometry in Dual-Purpose Belgian Blue cows. The used data were 69,349 test-day records of milk yield, fat percentage, and protein percentage along with selected individual and groups FA of milk (g/dL milk) collected from 2007 to 2020 on 7,392 first-parity (40,903 test-day records), and 5,185 second-parity (28,446 test-day records) cows distributed in 104 herds in the Walloon Region of Belgium. Data of 28,466 SNPs, located on 29 Bos taurus autosomes (BTA), of 1,699 animals (639 males and 1,060 females) were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic best linear unbiased prediction approach. The proportion of genetic variance explained by each 25-SNP sliding window (with an average size of ~2 Mb) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for candidate genes. Average daily heritability estimated for the included milk FA traits ranged from 0.01 (C4:0) to 0.48 (C12:0) and 0.01 (C4:0) to 0.42 (C12:0) in the first and second parities, respectively. Genetic correlations found between milk yield and the studied individual milk FA, except for C18:0, C18:1 trans, C18:1 cis-9, were positive. The results showed that fat percentage and protein percentage were positively genetically correlated with all studied individual milk FA. Genome-wide association analyses identified 11 genomic regions distributed over 8 chromosomes [BTA1, BTA4, BTA10, BTA14 (4 regions), BTA19, BTA22, BTA24, and BTA26] associated with the studied FA traits, though those found on BTA14 partly overlapped. The genomic regions identified differed between parities and lactation stages. Although these differences in genomic regions detected may be due to the power of quantitative trait locus detection, it also suggests that candidate genes underlie the phenotypic expression of the studied traits may vary between parities and lactation stages. These findings increase our understanding about the genetic background of milk FA and can be used for the future implementation of genomic evaluation to improve milk FA profile in Dual-Purpose Belgian Blue cows.

Does Gender Impact Technology Adoption in Dual-Purpose Cattle in Mexico?

This paper examines the role of women in the dual-purpose livestock system (DP) in Mexico through their technological adoption patterns and aims to evaluate whether there are significant differences between the technology adoption networks of men and women farmers. The sample was composed of 383 DP small farms with 20 or fewer cows and a high level of vulnerability. Social Network Analysis (SNA) was applied, and the centrality measures were calculated for the technological areas of management, feeding, genetics, reproduction, and animal health. Significant differences were found in reproduction levels between men and women farmers. Therefore, SNA was developed in this technological area where men mainly occupied central positions (brokers) while women were just close to the leaders in the network. The results have shown that farms run by women were smaller and presented higher levels of specialization and milk productivity (20% higher), and women prioritized those technologies linked to female reproductive efficiency. Moreover, women were deeply embedded in men's networks through numerous ties and were capable of building connections with groups of farmers outside of their own group.

Genome-wide association study for selected cheese-making properties in Dual-Purpose Belgian Blue cows

This study aimed to estimate genetic parameters and identify genomic region(s) associated with selected cheese-making properties (CMP) in Dual-Purpose Belgian Blue (DPBB) cows. Edited data were 46,301 test-day records of milk yield, fat percentage, protein percentage, casein percentage, milk calcium content (CC), coagulation time (CT), curd firmness after 30 min from rennet addition (a30), and milk titratable acidity (MTA) collected from 2014 to 2020 on 4,077 first-parity (26,027 test-day records), and 3,258 second-parity DPBB cows (20,274 test-day records) distributed in 124 herds in the Walloon Region of Belgium. Data of 28,266 SNP, located on 29 Bos taurus autosomes (BTA) of 1,699 animals were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method. The SNP solutions were estimated using a single-step genomic BLUP approach. The proportion of the total additive genetic variance explained by windows of 25 consecutive SNPs (with an average size of ∼2 Mb) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for candidate genes. Heritability estimates for the included CMP ranged from 0.19 (CC) to 0.50 (MTA), and 0.24 (CC) to 0.41 (MTA) in the first and second parity, respectively. The genetic correlation estimated between CT and a30 varied from -0.61 to -0.41 and from -0.55 to -0.38 in the first and second lactations, respectively. Negative genetic correlations were found between CT and milk yield and composition, while those estimated between curd firmness and milk composition were positive. Genome-wide association analyses results identified 4 genomic regions (BTA1, BTA3, BTA7, and BTA11) associated with the considered CMP. The identified genomic regions showed contrasting results between parities and among the different stages of each parity. It suggests that different sets of candidate genes underlie the phenotypic expression of the considered CMP between parities and lactation stages of each parity. The findings of this study can be used for future implementation and use of genomic evaluation to improve the cheese-making traits in DPBB cows.

Genome-wide association for milk urea concentration in Dual-Purpose Belgian Blue cows

The objectives of this study were to estimate genetic parameters and identify genomic regions associated with milk urea concentration (MU) in Dual-Purpose Belgian Blue (DPBB) cows. The data were 29,693 test-day records of milk yield (MY), fat yield (FY), protein yield (PY), fat percentage (FP), protein percentage (PP) and MU collected between 2014 and 2020 on 2498 first parity cows (16,935 test-day records) and 1939 second-parity cows (12,758 test-day records) from 49 herds in the Walloon Region of Belgium. Data of 28,266 single nucleotide polymorphisms (SNP), located on 29 Bos taurus autosomes (BTA), on 1699 animals (639 males and 1060 females) were used. Random regression test-day models were used to estimate genetic parameters through the Bayesian Gibbs sampling method using a single chain of 100,000 iterations after a burn-in period of 20,000. SNP solutions were estimated using a single-step genomic best linear unbiased prediction approach. The proportion of genetic variance explained by windows of 25 consecutive SNPs (with an average size of ~2 Mb) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for candidate genes. The mean (SD) of MU was 22.89 (10.07) and 22.35 (10.07) mg/dl for first and second parity, respectively. The mean (SD) heritability estimates for daily MU were 0.18 (0.01) and 0.22 (0.02), for first and second parity, respectively. The mean (SD) genetic correlations between daily MU and MY, FY, PY, FP and PP were -0.05 (0.09), -0.07 (0.11), -0.03 (0.13), -0.05 (0.08) and -0.03 (0.11) for first parity, respectively. The corresponding values estimated for second parity were 0.02 (0.10), -0.02 (0.09), 0.02 (0.08), -0.08 (0.06) and -0.05 (0.05). The genome-wide association analyses identified three genomic regions (BTA2, BTA3 and BTA13) associated with MU. The identified regions showed contrasting results between parities and among different stages within each parity. This suggests that different groups of candidate genes underlie the phenotypic expression of MU between parities and among different lactation stages within a parity. The results of this study can be used for future implementation and use of genomic evaluation to reduce MU in DPBB cows.

Genome-Wide Association Study Using Whole-Genome Sequence Data for Fertility, Health Indicator, and Endoparasite Infection Traits in German Black Pied Cattle

This genome-wide association study (GWAS) aimed to identify sequence variants (SVs) and candidate genes associated with fertility and health in endangered German Black Pied cattle (DSN) based on whole-genome sequence (WGS) data. We used 304 sequenced DSN cattle for the imputation of 1797 genotyped DSN to WGS. The final dataset included 11,413,456 SVs of 1886 cows. Cow traits were calving-to-first service interval (CTFS), non-return after 56 days (NR56), somatic cell score (SCS), fat-to-protein ratio (FPR), and three pre-corrected endoparasite infection traits. We identified 40 SVs above the genome-wide significance and suggestive threshold associated with CTFS and NR56, and three important potential candidate genes (ARHGAP21, MARCH11, and ZNF462). For SCS, most associations were observed on BTA 25. The GWAS revealed 61 SVs, a cluster of 10 candidate genes on BTA 13, and 7 pathways for FPR, including key mediators involved in milk fat synthesis. The strongest associations for gastrointestinal nematode and Dictyocaulus viviparus infections were detected on BTA 8 and 24, respectively. For Fasciola hepatica infections, the strongest associated SVs were located on BTA 4 and 7. We detected 200 genes for endoparasite infection traits, related to 16 pathways involved in host immune response during infection.

Heat stress during late pregnancy and postpartum influences genetic parameter estimates for birth weight and weight gain in dual-purpose cattle offspring generations

Impact of direct heat stress (HS) on genetic parameter estimates, i.e., HS close to the trait recording date, was verified in several previous studies conducted in dairy and beef cattle populations. The aim of the present study was to analyze the impact of time-lagged HS at different recording periods during late pregnancy (a.p.) and postpartum (p.p.) on genetic parameter estimates for birth weight (BWT) and weight gain traits (200 d- and 365 d-weight gain (200dg, 365dg)) in offspring of the dual-purpose cattle breed "Rotes Höhenvieh" (RHV). Furthermore, we estimated genetic correlations within traits across time-lagged climatic indicators, in order to proof possible genotype by environment interactions (G×E). Trait recording included 5,434 observations for BWT, 3,679 observations for 200dg and 2,998 observations for 365dg. Time-lagged climatic descriptors were classes for the mean temperature humidity index (mTHI) and number of HS days (nHS) from the following periods: 7 d-period a.p. (BWT), 56 d-period a.p., and 56 d-period p.p. (200dg and 365dg). Genetic parameters were estimated via 2-trait animal models, i.e., defining the same trait in different climatic environments as different traits. Genetic variances and heritabilities for all traits increased with increasing mTHI- and nHS-classes for all recording periods, indicating pronounced genetic differentiation with regard to time-lagged in utero HS and HS directly after birth. Similarly, in low mTHI- and nHS-classes indicating cold stress, genetic variances, and heritabilities were larger than for temperate climates. Genetic correlations substantially smaller than 0.80 indicating G × E were observed when considering same traits from mTHI- and nHS-classes in greater distance. Estimated breeding values (EBV) of the 10 most influential sires with the largest number of offspring records fluctuated across mTHI- and nHS-classes. Correlations between sire EBV for same traits from distant climatic classes confirmed the genetic correlation estimates. Sires displaying stable EBV with climatic alterations were also identified. Selection of those sires might contribute to improved robustness in the RHV outdoor population genetically.

Time-lagged and acute impact of heat stress on production and fertility traits in the local dual-purpose cattle breed "Rotes Höhenvieh" under pasture-based conditions

Climate change causes rising temperatures and extreme weather events worldwide, with possible detrimental time-lagged and acute impact on production and functional traits of cattle kept in outdoor production systems. The aim of the present study was to infer the influence of mean daily temperature humidity index (mTHI) and number of heat stress days (nHS) from different recording periods on birth weight (BWT), 200 d- and 365 d-weight gain (200 dg, 365 dg) of calves, and on the probability of stillbirth (SB), and calving interval (CINT) of their dams. Data recording included 4,362 observations for BWT, 3,136 observations for 200 dg, 2,502 observations for 365 dg, 9,293 observations for the birth status, and 2,811 observations for CINT of the local dual-purpose cattle breed "Rotes Höhenvieh" (RHV). Trait responses on mTHI and nHS were studied via generalized linear mixed model applications with identity link functions for Gaussian traits (BWT, 200 dg, 365 dg, CINT) and logit link functions for binary SB. High mTHI and high nHS before autumn births had strongest detrimental impact on BWT across all antepartum- (a.p.) periods (34.4 ± 0.79 kg maximum). Prolonged CINT was observed when cows suffered heat stress (HS) before or after spring calvings, with maximum length of 391.6 ± 3.82 d (56 d a.p.-period). High mTHI and high nHS during the 42 d- and 56 d a.p.-period implied increased probabilities for SB. We found a significant (P < 0.05) seasonal effect on SB in model 3 across all a.p.-periods, with the highest probability in autumn (maximum of 5.4 ± 0.82% in the 7 d a.p.-period). Weight gains of calves (200 dg and 365 dg) showed strongest HS response for mTHI and nHS measurements from the long-term postnatal periods (42 d- and 56 d-periods), with minimum 200 dg of 194.2 ± 4.15 kg (nHS of 31 to 42 d in the 42 d-period) or minimum 365 dg of 323.8 ± 3.82 kg (mTHI ≥ 60 in the 42 d-period). Calves born in summer, combined with high mTHI or high nHS pre- or postnatal, had lower weight gains, compared with calves born in other calving seasons or under cooler conditions. Highest BWT, weight gains, and shortest CINT mostly were detected under cool to moderate climate conditions for mTHI, and small to moderate nHS. Results indicate acute and time-lagged HS effects and address possible HS-induced epigenetic modifications of the bovine genome across generations and limited acclimatization processes to heat, especially when heat occurs during the cooler spring and autumn months.

Genomic and single-step evaluations of carcass traits of young bulls in dual-purpose cattle

Genetic evaluations for carcass traits of young bulls in Normande and Montbeliarde breeds are currently being developed in France. In order to determine a suitable genomic evaluation for three carcass traits of young bulls, genomic breeding values were estimated for young candidates to selection using different approaches. Records of 111,789 Normande and 118,183 Montbeliarde were used. Average progeny pre-adjusted performances (DYD) were calculated for sires. Evaluation approaches were compared based on an assessment of their accuracy (correlation between DYD and estimated breeding values [EBVs]) and bias (regression coefficient of DYD on EBVs) on the 20% youngest AI sires. All genomic approaches were generally more accurate than BLUP (+.045 to +.116 correlation points), except for age at slaughter where single-step GBLUP (SSGBLUP) was the only genomic method leading to a greater accuracy (+.038 to +.126 points). The best setting of the SSGBLUP relationship matrix was characterized by a weight of 30% for pedigree information in the genomic relationship matrix. SSGBLUP was the most valuable evaluation approach for the evaluation of carcass traits of Normande and Montbeliarde young bulls.

Carcass traits of young bulls in dual-purpose cattle: genetic parameters and genetic correlations with veal calf, type and production traits

The profitability of dual-purpose breeding farms can be increased through genetic improvement of carcass traits. To develop a genetic evaluation of carcass traits of young bulls, breed-specific genetic parameters were estimated in three French dual-purpose breeds. Genetic correlations between these traits and veal calf, type and milk production traits were also estimated. Slaughter performances of 156 226 Montbeliarde, 160 361 Normande and 8691 Simmental young bulls were analyzed with a multitrait animal model. In the three breeds, heritabilities were moderate for carcass weight (0.12 to 0.19±0.01 to 0.04) and carcass conformation (0.21 to 0.26±0.01 to 0.04) and slightly lower for age at slaughter (0.08 to 0.17±0.01 to 0.03). For all three breeds, genetic correlations between carcass weight and carcass conformation were moderate and favorable (0.30 to 0.52±0.03 to 0.13). They were strong and favorable (-0.49 to -0.71±0.05 to 0.15) between carcass weight and age at slaughter. Between age at slaughter and carcass conformation, they were low and unfavorable to moderate and favorable (-0.25 to 0.10±0.06 to 0.18). Heavier young bulls tend to be better conformed and slaughtered earlier. Genetic correlations between corresponding young bulls and veal production traits were moderate and favorable (0.32 to 0.70±0.03 to 0.09), implying that selecting sires for veal calf production leads to select sires producing better young bulls. Genetic correlations between young bull carcass weight and cow size were moderately favorable (0.22 to 0.45±0.04 to 0.10). Young bull carcass conformation had moderate and favorable genetic correlations (0.11 to 0.24±0.04 to 0.10) with cow width but moderate and unfavorable genetic correlations (-0.21 to -0.36±0.03 to 0.08) with cow height. Taller cows tended to produce heavier young bulls and thinner cows to produce less conformed ones. Genetic correlations between carcass traits of young bulls and cow muscularity traits were low to moderate and favorable. Finally, genetic correlations between carcass traits of young bulls and milk production traits were low and unfavorable to moderate and favorable. These results indicate the existence for all three breeds of genetic variability for the genetic improvement of carcass traits of young bulls as well as favorable genetic correlations for their simultaneous selection and no strong unfavorable correlation with milk production traits.

Genetic correlations between type and test-day milk yield in small dual-purpose cattle populations: The Aosta Red Pied breed as a case study

This study aimed at estimating the relationships between linear type traits and milk production in the dual-purpose Aosta Red Pied (ARP) cattle breed, by expressing type traits as factor scores with the same biological meaning of the individual traits. Factor analysis was applied to individual type traits for muscularity and udder of 32,275 first-parity ARP cows, obtaining 3 factor scores for individual muscularity (F1), udder side (F2), and udder conformation (F3). Data from 169,008 test-day records of milk, fat, and protein yield (kg), belonging to the first 3 lactations of 16,605 cows, were also analyzed. After obtaining genetic parameters for both morphological factors and milk production traits through a series of AIREML single-trait models, bivariate analyses were performed on a data set accounting for 201,283 records of 35,530 cows, to assess the phenotypic and genetic correlations among all factor scores and milk yield traits. The heritability estimates obtained proved to be moderate for both groups of traits, ranging from 0.132 (fat) to 0.314 (F1). Muscularity factor showed moderate and negative genetic correlations (ra) with udder size (-0.376) and udder conformation (0.214) factors. A low and negative ra was found between udder factors. Strong and positive ra were found among all the 3 milk production traits and F 0010 (ra≥0.597). Negative ra with milk traits were obtained for both F 0005 and F3, ranging from -0.417 to -0.221. Phenotypic correlations were lower than the genetic ones, and sometimes close to zero. The antagonism between milk production and meat attitude traits suggests that great attention should be paid in assigning proper weight to the traits, comprising functional traits such as udder conformation, included in selection indices for the dual-purpose breed. The ra obtained for factor scores are consistent with previous estimates for the corresponding individual type traits, and this confirms the possible use of factor analysis to improve type traits relevant to beef attitude.