Research Note: Genetic parameters estimation of egg quality traits in Rhode Island Red and White Leghorn chickens.

The continuous increasing demand for egg quality and quantity, and the expanding market share have enabled the egg industry to achieve significant benefits through genetic improvement. This study aims to estimate the genetic parameters and explore selectable breeding traits in the purebred Rhode Island Red (RIR) and White Leghorn (WL), which are 2 high-yielding layer breeds, and better understand their underlying genetic basis and accelerate genetic progress. The DMU software was utilized to analyze 12 egg quality traits, including egg length (EL), egg width (EW), egg shape index (ESI), egg weight (EWT), albumen height (AH), yolk color (YC), Haugh unit (HU), yolk weight (YW), albumen weight (AW), albumen-to-egg weight ratio (AWR), yolk-to-albumen ratio (YAR), and yolk-to-egg weight ratio (YWR). In RIR, the heritability of egg quality traits ranged from 0.196 to 0.427, while the repeatability ranged from 0.395 to 0.668. In WL, the heritability of egg quality traits ranged from 0.203 to 0.347, and the repeatability ranged from 0.424 to 0.656. In both RIR and WL, highly strong genetic correlations were observed between AW and EW, as well as between AW and EWT. The genetic correlations for AW and EW were 0.902 in RIR and 0.864 in WL, while the genetic correlations for AW and EWT were 0.981 in RIR and 0.960 in WL. The egg quality traits in both breeds showed moderate heritability, indicating great genetic potential for improvement through selective breeding. This can help breeders meet the increasingly diverse egg preferences of consumers through genetic selection. Additionally, there is a highly strong correlation between egg width/egg weight, and albumen weight in both breeds. In practical production, it is feasible to estimate albumen weight by measuring egg width and egg weight, which can simplify the method for measuring albumen weight. In conclusions, our finding provided valuable insights into the genetic architecture of egg quality traits in RIR and WL chickens. They help our understanding of the potential for genetic improvement of these traits through selective breeding programs.

Effect of heat stress on semen characteristics and genetics in Thai native grandparent roosters.

Grandparent roosters are crucial in poultry breeding programs and significantly influence future bird generations' genetic makeup and performance. However, these roosters face considerable challenges from heat stress, which can adversely affect their reproductive performance, semen quality, and overall health and welfare. Our study aimed to investigate the effects of heat stress on the genetics of semen characteristics, identify the appropriate temperature and humidity indices (THI), and determine the threshold point of heat stress to prevent thermal stress. We analyzed data from 3,895 records of 242 Thai native grandparent roosters in conjunction with the THI using 7 THI functions and the regression method. The threshold point of heat stress, genetic parameters, rate of decline of semen characteristics per level of THI, estimated breeding values and selection index values were analyzed using the multivariate test-day model in the AIREML and BLUPF90 programs. Based on the regression coefficient and statistical criteria of the lowest -2logL and AIC values, the results showed that a THI of 78 was considered the threshold point of heat stress. The estimated heritability values ranged from 0.023 to 0.032, 0.066 to 0.069, 0.047 to 0.057, and 0.022 to 0.024 for mass movement, semen volume, sperm concentration, and the semen index, respectively. The reduction rates of mass movement, semen volume, sperm concentration, and semen index at a THI of 78 were -0.009, -0.003, -0.170, and -0.083 per THI, respectively. The genetic correlations among the semen traits were moderately to strongly positive and ranged from 0.562 to 0.797. The genetic correlations between semen traits and heat stress were negative and ranged from -0.437 to -0.749. The permanent environmental correlations among the semen traits (0.648-0.929) were positive and greater than the genetic correlations. Permanent environmental correlations between semen traits and heat stress were negative and ranged from -0.539 to -0.773. The results of the selection indices showed that the higher the selection intensity was, the greater the degree to which the selection index corresponded to genetic progress. The recommendation for animal genetic selection is that the top 10% is appropriate because it seems most preferred. Therefore, using a multivariate test-day model and selection index for the high genetic potential of semen traits and heat tolerance in Thai native grandparent roosters makes it possible to achieve genetic assessment in a large population.

Estimation of Genetic Parameters of Early Growth Traits in Dumeng Sheep.

This study aimed to estimate the genetic and non-genetic factors that affect the nine early growth traits of Dumeng sheep, as well as to estimate the variance components and genetic parameters associated with these traits. A dataset containing detailed information on 17,896 preweaning trait records of 4474 lambs was collected. In addition, 5015 postweaning trait records of 1003 lambs were documented. The effects of recipient dam age, sex, year, season, and herd on the early growth traits were assessed using the general linear model procedure of the statistical analysis system, revealing different levels of significance across different traits. To determine the most suitable model for estimating the genetic parameters, the likelihood ratio (LR) test was employed, fitting six animal models that either excluded or included maternal genetic and maternal permanent environmental effects within the average information restricted maximum likelihood (AIREML) framework using WOMBAT software (Version: 23/11/23). The model incorporating direct additive genetic effects, maternal genetic effects, and maternal permanent environment effects as random effects (model 6) provided the best fit for birth weight (BW) estimation. In contrast, the model combining direct additive genetic effects and maternal permanent environment effects as random effects (model 2) demonstrated a superior fit for estimating the genetic parameters of weaning weight (WW), average daily gain weight from birth to weaning (ADG1), and Kleiber ratio from birth to weaning (KR1). With regard to the genetic parameters of body weight at 6 months of age (6MW), average daily gain weight from weaning to 6 months (ADG2), average daily gain weight from birth to 6 months (ADG3), Kleiber ratio from weaning to 6 months (KR2), and Kleiber ratio from birth to 6 months (KR3), model 1, which incorporates only direct additive genetic effects, was identified as the optimal choice. With the optimal model, the heritability estimates ranged from 0.010 ± 0.033 for 6MW to 0.1837 ± 0.096 for KR3. The bivariate analysis method was employed to estimate the correlation between various traits using the most suitable model. The absolute values of genetic correlation coefficients among the traits spanned a range from 0.1460 to 0.9998, highlighting both weak and strong relationships among the studied traits. Specifically, the estimated genetic correlations between WW and ADG1, ADG3, KR1, and KR3 were 0.9859, 0.9953, 0.9911, and 0.9951, respectively, while the corresponding phenotypic correlations were 0.9752, 0.7836, 0.8262, and 0.5767. These findings identified that WW could serve as an effective selection criterion for enhancing early growth traits.

ASReml-based estimation of early genetic parameters in hybrid mutton sheep populations.

The aim of this study was to analyze the effects of non-genetic factors on the estimation of genetic parameters of early growth traits in hybrid mutton sheep using ASReml software, in order to provide theoretical basis for screening the optimal hybriding combinations and accelerating the breeding process of new breeds of specialized housed-feeding mutton sheep. We selected the wellgrown hybrid Southhu (Southdown × Hu sheep) and Dorhu (Dorset × Hu sheep) sheep as the research objects, constructed weight correction formulae for SH and DH sheep at 60 and 180 days; and used ASReml software to investigate the effects of non-genetic factors on the estimation of genetic parameters of early growth traits in hybrid sheep. The results showed that the birth month and birth type were found significant for all traits (p < 0.001); the heritability of maternal effects ranged from 0.0709 to 0.1859. It was found that both SH and DH sheep emerged the potential for rapid early growth and development, early growth traits are significantly affected by maternal genetic effects, thereby the maternal effect should be taken into consideration for the purpose of improving accuracy in parameter estimations and therefore increasing the success of breeding programs.

Genetic relationship of energy balance predicted from milk traits with fertility in Japanese Holsteins.

We predicted the energy balance of cows from milk traits and estimated the genetic correlations of predicted energy balance (PEB) with fertility traits for the first three lactations. Data included 9,646,606 test-day records of 576,555 Holstein cows in Japan from 2015 to 2019. Genetic parameters were estimated with a multiple-trait model in which the records among lactation stages and parities were treated as separate traits. Fertility traits were conception rate at first insemination (CR), number of inseminations (NI), and days open (DO). Heritability estimates of PEB were 0.28-0.35 (first lactation), 0.15-0.29 (second), and 0.09-0.23 (third). Estimated genetic correlations among lactation stages were 0.85-1.00 (first lactation), 0.73-1.00 (second), and 0.64-1.00 (third). Estimated genetic correlations among parities were 0.82-0.96 (between first and second), 0.97-0.99 (second and third), and 0.69-0.92 (first and third). Estimated genetic correlations of PEB in early lactation with fertility were 0.04 to 0.19 for CR, -0.03 to -0.19 for NI, and -0.01 to -0.24 for DO. Genetic improvement of PEB is possible. Lower PEB in early lactation was associated with worse fertility, suggesting that improving PEB in early lactation may improve reproductive performance.

Genetic Selection Approach for Semen Characteristics in Thai Native Grandparent Roosters (Pradu Hang Dum) Using Random Regression Test-Day Models and Selection Indices.

The aim of this study was to analyze suitable genetic models and selection indices to estimate the genetic parameters and breeding values of native Thai roosters. A total of 3475 records of seven semen traits (mass movement, semen pH, semen color, volume, sperm viability, sperm abnormalities, and sperm concentration) from 242 Thai native grandparent roosters were analyzed. Multiple-trait random regression test-day models with five covariance functions were used to analyze the variance components, genetic parameters, and breeding values. The selection index (SI) was calculated to determine the optimal genetic value for different selection percentages. The results showed that a multiple-trait random regression test-day model with a second-order Legendre polynomial function was the most appropriate genetic model for this population. The estimated heritability values were low to moderate, ranging from 0.110 to 0.112 (mass movement), 0.040 to 0.051 (semen pH), 0.092 to 0.097 (semen color), 0.220 to 0.225 (semen volume), 0.067 to 0.083 (sperm viability), 0.086 to 0.099 (sperm abnormalities), and 0.134 to 0.138 (sperm concentration). The repeatability values exceeded the heritability values and were within the range of 0.133 to 0.688. The genetic correlations among semen traits ranged from -0.332 to 0.677, and phenotypic correlations ranged from -0.260 to 0.460. When considering heritability and genetic correlation values, semen volume, sperm concentration, and mass movement were the top three priority semen traits calculated as selection indices. Finally, the top 10% of the selection index was recommended for creating the next generation. Our findings provide useful information on genetic parameters and an appropriate selection index of semen traits for selecting the genetics of individual Thai native grandparent roosters. The heritability estimates for semen traits reported here suggest an adequate response to selection through a genetic evaluation approach. Our results indicate that it is possible to select grandparent roosters with better reproductive performance.

Integrative Meta-Analysis: Unveiling Genetic Factors in Meat Sheep Growth and Muscular Development through QTL and Transcriptome Studies.

OBJECTIVE: The study aimed to investigate the effects of castration on performance, carcass characteristics, and meat quality in sheep, as well as explore the expression of key genes related to metabolic pathways and muscle growth following castration. METHODS: A meta-analysis approach was utilized to analyze data from multiple studies to compare the performance, carcass characteristics, and meat quality of castrated sheep (wethers) with intact rams. Additionally, protein-protein interaction (PPI) networks, differential gene expression (DEG) interactions, Gene Ontology (GO) terms, and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were examined to identify molecular mechanisms associated with fat metabolism and muscle development in sheep tails. RESULTS: The analysis revealed that castrated sheep (wethers) exhibited improved average daily gain, increased tenderness, lower backfat thickness, and a tendency for greater loin muscle area compared to intact rams. This suggests that castration promotes faster growth and results in leaner carcasses with potentially higher muscle content. Furthermore, the identification of downregulated DEGs like ACLY, SLC27A2, and COL1A1 and upregulated DEGs such as HOXA9, PGM2L1, and ABAT provides insights into the molecular mechanisms underlying fat deposition and muscle development in sheep. CONCLUSIONS: The findings support the practice of castration in sheep production as it enhances growth performance, leads to leaner carcasses with higher muscle content, and improves meat tenderness. The identified changes in gene expression offer valuable insights for further research into understanding the impact of castration on muscle development and fat metabolism in sheep. This meta-analysis contributes to the knowledge of molecular mechanisms involved in fat deposition in sheep, opening avenues for future investigations in livestock fat metabolism research.

Incorporating body measurement traits to increase genetic gain of feed efficiency and carcass traits in Japanese Black steers.

The objective of the present study was to comprehensively evaluate whether body measurement traits, including body weight and body size, could be used as indicators of genetic selection for feed efficiency and carcass traits in Japanese Black steers. First, we estimated the genetic parameters for body measurements, feed efficiency, and carcass traits. Second, we estimated the correlated responses in feed efficiency and carcass traits when selection was applied to one or multiple-body measurement traits. In total, 4,578 Japanese Black steers with phenotypic values of residual feed intake (RFI) and residual body weight gain (RG) as feed efficiency traits and carcass weight (CWT) and beef marbling standard (BMS) as carcass traits were used. Eleven body measurement traits were measured at the start and finish of the fattening periods (BMT1 and BMT2, respectively), and their growth during the fattening period (BMT3) was used for genetic analyses. The results of genetic parameters showed that the heritability estimates were low to moderate (0.10 to 0.66), and the genetic correlations among body measurement traits were also estimated to be positively moderate to high in each measuring point (0.23 to 0.99). The genetic correlations of body measurement traits with RFI and BMS were estimated to be low (-0.14 to 0.30 and -0.17 to 0.35, respectively), but those with CWT were positively low to high (0.12 to 0.97). The genetic correlation estimates between BMT3 and RG were moderate to high (0.38 to 0.78). Second, correlated responses were estimated under positive selection for body measurement traits. Positive selection for BMT2 and BMT3 increased CWT and RG; however, positive selection for body measurement traits resulted in no change in RFI and BMS. Favorable directions of genetic gains, which were positive for RG, CWT, and BMS and negative for RFI, were obtained by selection indices, including multiple traits in BMT1. Our results suggest that using only one-body measurement trait as an indicator of genetic selection for RFI is difficult. However, body measurement traits can be indirect indicators of improved RG. Our results also suggest that genetic improvement of both RFI and RG without reducing CWT and BMS could be achieved using selection indices that account for a balance of body conformation using multiple-body measurement traits in Japanese Black cattle.

Improving feed efficiency is a key objective in the beef cattle industry. Still, high costs and logistical efforts make measuring daily feed intake per animal in many cattle difficult. Here, we focused on body measurement traits, including body weight and body size, as indirect indicators of feed efficiency in Japanese Black cattle, as measuring these traits is easy and inexpensive. When selection was applied to one- or multiple-body measurement traits, we estimated the correlated responses in feed efficiency and carcass traits. We also estimated the genetic relationships of body measurement traits with feed efficiency and carcass traits. Our results showed body measurement traits were heritable and had weak genetic relationships with residual feed intake. Regarding the possibility of genetic selection for residual feed intake using body measurement traits as indirect indicators, our results suggest that using a single body measurement trait as an indicator is difficult. However, our results also suggest that the genetic improvement of residual feed intake could be possible using selection indices that account for a balance of body conformation using multiple-body measurement traits in Japanese Black cattle.

Stability and performance analysis of storage root yield in a dataset of sweet potato varieties (Ipomoea batatas L.).

The dataset focuses on evaluating the performance of 17 sweet potato varieties (G) released by the Bangladesh Agricultural Research Institute (BARI) in terms of storage root yield and stability across five locations (E) in Bangladesh-Gazipur, Bogura, Jamalpur, Jashore, and Chattogram. The result revealed that BARI Mistialu-12 exhibited the highest average storage root yield at 45.35 t/ha, closely followed by BARI Mistialu-16 at 44.64 t/ha. Conversely, BARI Mistialu-1 had the lowest mean yield of 25.99 t/ha. Among the locations, Bogura recorded the highest mean root yield at 37.05 t/ha, while Chattogram exhibited the lowest at 31.27 t/ha. A combined analysis of variance revealed the presence of variability in storage root yield attributed to the genotype-location (environment) interaction (GEI). To delve deeper into this interaction, additive and multiplicative interaction effect models (AMMI) along with a linear mixed model (LMM) were employed for further investigations to confirm the significant contribution of GEI variance to root yield. The LMM results showed genetic variance (%), heritability (%), selection accuracy (%), and GEI correlation coefficients of 52.27, 54, 94, and 30, respectively. The AMMI analysis indicated that the first two principal components accounted for 74.60 % of GEI, with 20.16 % attributed to it. Assessing significant Interaction Principal Component Analyses (IPCAs) through the Weighted Average of Absolute Scores (WAAS) indicated that BARI Mistialu-12 is the most stable genotype, followed by BARI Mistialu-16 and BARI Mistialu-8, all displaying above-average root yield. The mega-environment analysis associated the highest root production of BARI Mistialu-11 and BARI Mistialu-2 with the Jamalpur location, while Gazipur, Bogura, and Jashore were linked with the superior performance of BARI Mistialu-12 and BARI Mistialu-16 genotypes. These findings are crucial for future breeding programs and the rapidly growing sweet potato industry, given the stable high-yield potential across diverse agro-ecological conditions. However, it is imperative to repeat the study to ensure reliable outcomes.

Reaction-norm animal model analysis of average daily gain heat tolerance in purebred Duroc pigs.

The present study aimed to genetically improve growth performance under high-heat environments by specifically designing a reaction-norm animal model (RNAM) for purebred Duroc pigs in Japan. A total of 54,750 records of average daily gain (ADG) measured for pigs reared at four farms in different prefectures were analyzed. Estimated maximum daily temperatures at the respective farm locations were used to calculate the average cumulative thermal load (TL). The TL values served as an indicator of high-heat environments for pigs. The plausible cumulative period length and threshold temperature for calculating TL were determined to be 8 weeks until just before shipping and 25°C, respectively. Variance components were estimated via RNAM analysis using TL as a linear covariate. The estimated additive genetic variances under both responsive and non-responsive to TL were found to be significant. Moreover, the estimated heritability of ADG ranged from 0.38 to 0.73 for TL values of 0-8. These results suggest that the RNAM developed holds the potential for improving the genetic ability of growth under high-heat environments in pigs.

Genetic analysis of feed efficiency and novel feeding behavior traits measured in group-housed broilers using electronic feeders.

This study aimed to estimate genetic parameters for feeding behavior (FB) traits and to assess their genetic relationship with performance traits in group-housed broilers. In total, 99,472,151 visits were recorded for 95,711 birds between 2017 and 2022 using electronic feeders. The visits were first clustered into 2,667,617 daily observations for ten FB traits: daily feed intake (DFI), daily number of visits (NVIS), time spent at the feeders (TSF), number of visited feeders (NVF), visiting activity interval (VAI), feeding rate (FR), daily number of meals (NMEAL), average intake per meal (INTMEAL), number of visits per meal (VISMEAL) and interval between meals (MEALIVL). All FB traits were then considered as the average per bird across the feeding test period. Three growth traits (body weight at the start - SBW and at the end of the feeding test - FBW, and weight gain over the test period - BWG), and 2 feed efficiency (FE) traits (Feed Conversion Rate - FCR and Residual Feed Intake - RFI) were also recorded. The (co)variance components were estimated using multitrait animal mixed models. For growth and FE, the heritability (h2) estimates were moderate, ranging from 0.20 ± 0.01 (BWG) to 0.32 ± 0.02 (RFI). Overall, the h2 estimates for FB traits were higher than for productive traits, ranging from 0.31 ± 0.01 (DFI) to 0.56 ± 0.02 (TSF). DFI presented high genetic correlations (0.53-0.86) with all performance traits. Conversely, the remaining FB traits presented null to moderate genetic correlations with these traits, ranging from -0.38 to 0.42 for growth traits and between -0.14 and 0.25 for FE traits. Genetic selection for favorable feeding behavior is expected to exhibit a fast genetic response. The results suggest that it is possible to consider different feeding strategies without compromising the genetic progress of FE. Conversely, breeding strategies prioritizing a higher bird activity might result in lighter broiler lines in the long term, given the negative genetic correlations between visit-related traits (NV, NVF, and NMEAL) and growth traits (SBW and FBW).

Risk Factor Analysis and Genetic Parameter Estimation for Pre-Weaning Mortality Traits in Boer, Spanish, and Crossbred Goat Kids.

The objectives of this study were to evaluate fixed risk factors associated with PWM and to estimate genetic parameters for PWM. A total of 927 birth records from a mixed population of purebred and crossbred Boer and Spanish goats born between 2016 and 2023 at the International Goat Research Center (IGRC) were used for this study. Four binary traits were studied: D0-3 (death within 3 days after birth), D4-60 (death between 4 and 60 days), D61-90 (death between 61 and 90 days), and D0-90 (death within 90 days). Logistic regression models were used to evaluate the risk factors associated with PWM traits. Bayesian threshold models and Gibbs sampling were used to estimate the genetic parameters. Birth weight, season, litter size, sex, dam age, breed, and heterosis were found to be significantly associated with at least one of the PWM traits. Heritability estimates were 0.263, 0.124, 0.080, and 0.207, for D0-3, D4-60, D61-90, and D0-90, respectively. The genetic correlations between the studied traits ranged from 0.892 (D0-3 and D0-90) to 0.999 (D0-3 and D61-90). These results suggest that PWM in goats is influenced by both non-genetic and genetic factors and can be reduced by management, genetic selection, and crossbreeding approaches.

Evaluation of Genetic Parameters and Comparison of Stress Tolerance Traits in Different Strains of Litopenaeus vannamei.

Litopenaeus vannamei stands out globally in aquaculture for its fast growth, broad salt tolerance, disease resistance, and high protein levels. Selective breeding requires the precise estimation of the variance components and genetic parameters for important traits. This study formed lineages from 20 full sibling families of L. vannamei, with progenitors from Thailand and the USA. We then assessed the genetic resilience traits of juvenile shrimp from these families to high ammonia-N, high pH, and low salinity by performing a 96 h acute toxicity test. Mortality rates for the families under 96 h exposure to high ammonia-N, high pH, and low salinity were 19.52-92.22%, 23.33-92.22%, and 19.33-80.00%, respectively, showing significant variance in stress tolerance among families (p < 0.05). Survival heritability estimates, using threshold male and female models, were 0.44 ± 0.12 in high ammonia-N, 0.41 ± 0.12 in high pH, and 0.27 ± 0.08 in low salinity, respectively. Genetic correlations between growth and stress resistance traits varied from 0.0137 ± 0.2406 to 0.8327 ± 0.0781, and phenotypic correlations ranged from 0.0019 ± 0.0590 to 0.6959 ± 0.0107, indicating a low-to-high positive correlation significant at (p < 0.05). It was found that the survival rate of families No. 2 and No. 9 was higher under high ammonia-N and high pH stresses, while the survival rate of family No. 10 was higher under low salinity stress after comparing two selection criteria, the breeding values and phenotypic values. Thus, these three families are identified as potential breeding program candidates. Through the creation of a genetic parameter estimation model, the genetic variances across mating combinations for stress resistance traits were obtained and families with heightened stress resistance were identified, laying the groundwork for enhanced genetic selection of L. vannamei.

Estimation of genetic parameters for growth traits and kleiber ratio in dorper sheep breed.

The study aimed to estimate genetic and phenotypic parameters for growth traits and Kleiber ratio in Dorper sheep breed. Data used in this study were collected over 12 years (2012-2023) at Debre Birhan Agricultural Research Center sheep research station in Ethiopia. Studied traits were body weights at birth (WT0), weaning (WT3), six month (WT6), and yearling (WT12) age; average daily gains from birth to weaning (ADG0-3), from weaning to six months (ADG3-6), from six months to yearling (ADG6-12); and Kleiber ratios from birth to weaning (KR1) and from weaning to six months (KR2). The (co)variance components were estimated with different animal models using Average Information Restricted Maximum Likelihood (AI-REML) procedure. The best-fitted model for each trait was determined using likelihood ratio tests. Phenotypic performance for WT3, WT6, WT12, ADG0-3 and ADG3-6 showed a decline trend at a rate of 0.216 kg, 0.794 kg, 0.671 kg, 2.601 g and 4.865 g over years respectively. However, WT3, WT6, WT12, ADG0-3 showed a positive genetic improvement trend at a rate of 0.029 kg, 0.043 kg, 0.049 kg and 0.257 g over years respectively. Year of birth had a significant effect (P < 0.001) on all studied traits. Model including direct genetic as well as permanent environmental effect (Model 2) was chosen as the most appropriate model for WT0. Model which included only direct genetic effect (Model 1) was the best-fit model for all other studied traits. Direct heritability estimates based on suitable models were 0.07 ± 0.06, 0.11 ± 0.06, 0.09 ± 0.07, 0.11 ± 0.09 0.11 ± 0.06, 0.00 ± 0.04, 0.15 ± 0.07 and 0.00 ± 0.04 for WT0, WT3, WT6, WT12, ADG0-3, ADG3-6, KR1 and KR2 respectively. The variance ratio for the permanent environmental effect was 0.13 ± 0.04 for WT0. Genetic correlations among the traits ranged from negative (-0.39) for WT0-KR1 to high (0.99) for WT3-ADG0-3 and phenotypic correlations ranged from negative (-0.31) for WT0-KR1 to high (0.98) for WT3-ADG0-3. The low direct heritability estimates for the studied traits indicated that genetic improvement by direct selection might be difficult. Further investigation for the unexpected declined trend of phenotypic performance over years need to be required.

Estimation of genetic parameters for visceral diseases of fattening Japanese Black cattle in Shimane Prefecture, Japan.

In this study, the genetic parameters of major visceral diseases were estimated using the postmortem inspection records of 9057 fattening Japanese Black cattle in Shimane Prefecture, Japan, and the genetic correlation between visceral diseases and carcass traits was analyzed. There were six visceral diseases with a prevalence of 5% or higher, namely, pleurisy, pneumonia, bovine abdominal fat necrosis (BFN), rumenitis, hemorrhagic hepatitis, and perihepatitis. Variance components were estimated using the Gibbs sampling method, and the heritability of the visceral disease ranged from 0.07 to 0.49 for perihepatitis and BFN, respectively. Significant negative genetic correlations were identified between pleurisy and rib thickness (-0.32), BFN and carcass weight (-0.29), and BFN and rib eye area (-0.22). No significant genetic correlation was observed among the visceral diseases. The least squares analysis of variance suggested that some visceral diseases decrease the value of carcass traits. In particular, carcass weight and rib eye area in individuals with BFN were 11.7 kg and 1.87 cm2 lower than those of healthy cattle, respectively. Thus, it was inferred that genetic factors were involved in the visceral diseases of fattening Japanese Black cattle in Shimane Prefecture.

Evidence of additive genetic variation for major milk proteins in dairy cows: A meta-analysis.

In the past, there have been reports of genetic parameters for milk proteins in various dairy cattle populations. The high variability among genetic parameter estimates has been caused by this. This study aimed to use a random-effects meta-analysis model to compile published estimates of genetic parameter for major milk proteins of α-lactalbumin, ß-lactoglobulin, sum of whey proteins, casein, αs1-casein, αs2-casein, ß-casein, and κ-casein in dairy cows. The study used a total of 140 heritability and 256 genetic correlation estimates from 23 papers published between 2004 and 2022. The estimated range of milk protein heritability is from 0.284 (for α-lactalbumin in milk) to 0.596 (for sum of whey proteins). The genetic correlation estimates between casein and milk yield, milk fat and protein percentages were -0.461, 0.693, and 0.976, respectively (p < 0.05). The genetic correlation estimates between milk proteins expressed as a percentage of milk were significant and varied from 0.177 (between ß-lactoglobulin and κ-casein) to 0.892 (between αs1-casein and αs2-casein). Moderate-to-high heritability estimates for milk proteins and their low genetic associations with milk yield and composition indicated the possibility for improving milk proteins in a genetic selection plan with negligible correlated effects on production traits in dairy cows.

Genetic analysis of milk minerals in dairy cattle: a review.

Mineral composition in milk can affect its nutritional as well as physio-chemical properties of milk and is considered an important trait in the evaluation of milk quality. The composition and concentration of milk minerals could be altered with natural source of variation including nutrition and genetics. The effect of diet on milk minerals is well studied. However, genetic effects on the milk minerals have recently gained the attention. This review provides an overview of the genetic variation of milk minerals, and the genomic regions associated with mineral concentration in the milk are also discussed. The difference of milk minerals between breeds and the genetic parameters including heritability estimates and correlation among minerals indicates that milk minerals are under strong genetic control. Recently, the genome-wide association study (GWAS) has explored several regions associated with milk minerals and thus provides a new genetic source for improving the milk quality through genomics-assisted breeding. Hence, a combination of the qualitative and molecular approaches can be exploited to improving the nutritional quality of cattle milk in terms of its mineral composition.

Optimizing selection strategy for enhancing reproduction efficiency in Indian crossbred goats using milk productivity as a selection criterion.

The present study was aimed at optimizing the selection strategy for enhancing reproductive efficiency and milk productivity of Alpine × Beetal crossbred goats. The data set included 2949 milk trait records across parities and 1389 milk records from first parity and corresponding reproductive traits. The traits included for analysis were 150-day milk yield (150DMY), days in milk (DIM), peak yield (PY) and total milk yield (TMY). The litter size (LS) and litter weight (LW) were used for specifically formulating selection plan using indirect selection. The least squares mean for lactation traits during the first parity were 150DMY: 195.32 ± 2.09 kg, DIM: 236.42 ± 3.04 days, PY: 1.82 ± 0.02 kg, TMY: 269.62 ± 4.52 kg. Notably, Alpine × Beetal goats demonstrated genetic superiority pan India for milk productivity as compared to other native goat breeds. The least squares mean for 150DMY across all parities was 236 ± 3.13 kg. An animal model employing average information restricted maximum likelihood was used for (co)variance component estimation to get the genetic parameters. The analysis revealed total heritability estimates for 150DMY, DIM, PY and TMY as 0.18 ± 0.06, 0.04 ± 0.04, 0.12 ± 0.06 and 0.08 ± 0.05, respectively. Repeatability estimates for 150DMY, DIM, and TMY were 0.28 ± 0.04, 0.21 ± 0.03 and 0.37 ± 0.03, respectively. Bivariate analysis of 150DMY with reproductive traits revealed heritability for LS and LW as 0.05 ± 0.01 and 0.10 ± 0.01, respectively using Gibbs sampling. Strong and positive genetic correlations of 150DMY with other production and reproduction traits was observed, such as DIM (0.72), PY (0.98), TMY (0.88), LS (0.57) and LW (0.33). Moderate heritability and repeatability estimate of 150DMY, along with its positive correlation with production and reproductive traits suggested it as a suitable selection criterion for early selection and overall genetic progress of lactation traits. The genetic trend analysis showed an overall improvement in all these traits, with observed gain of 98.4 g per year for 150DMY, 0.04 days per year for DIM, 0.5 g per year for PY and 220.5 g per year for TMY. We observed that selecting based on 150DMY would lead to a favourable indirect improvement for LW as 79 g and LS 0.04 units per generation. We, therefore, recommend employing 150DMY as the single trait selection criteria to enhance both milk productivity and reproductive potential of Alpine × Beetal goats.

Genetic aspects of immunoglobulins and cyclophilin A in milk as potential indicators of mastitis resistance in Holstein cows.

Mastitis is one of the most frequent and costly diseases affecting dairy cattle. Natural antibodies (immunoglobulins) and cyclophilin A (CyPA), the most abundant member of the family of peptidyl prolyl cis/trans isomerases, in milk may serve as indicators of mastitis resistance in dairy cattle. However, genetic information for CyPA is not available, and knowledge on the genetic and nongenetic relationships between these immune-related traits and somatic cell score (SCS) and milk yield in dairy cattle is sparse. Therefore, we aimed to comprehensively evaluate whether immune-related traits consisting of 5 Ig classes (IgG, IgG1, IgG2, IgA, and IgM) and CyPA in the test-day milk of Holstein cows can be used as genetic indicators of mastitis resistance by evaluating the genetic and nongenetic relationships with SCS in milk. The nongenetic factors affecting immune-related traits and the effects of these traits on SCS were evaluated. Furthermore, the genetic parameters of immune-related traits according to health status and genetic relationships under different SCS environments were estimated. All immune-related traits were significantly associated with SCS and directly proportional. Additionally, evaluation using a classification tree revealed that IgA, IgG2, and IgG were associated with SCS levels. Genetic factor analyses indicated that heritability estimates were low for CyPA (0.08) but moderate for IgG (0.37), IgA (0.44), and IgM (0.44), with positive genetic correlations among Ig (0.25-0.96). We also evaluated the differences in milk yield and SCS of cows between the low and high groups according to their sires' estimated breeding value for immune-related traits. In the high group, IgA had a significantly lower SCS in milk at 7 to 30 d compared with that in the low group. Furthermore, the Ig in milk had high positive genetic correlations between healthy and infected conditions (0.82-0.99), suggesting that Ig in milk under healthy conditions could interact with those under infected conditions, owing to the genetic ability based on the level of Ig in milk. Thus, Ig in milk are potential indicators for the genetic selection of mastitis resistance. However, because only the relationship between immune-related traits and SCS was investigated in this study, further study on the relationship between clinical mastitis and Ig in milk is needed before Ig can be used as an indicator of mastitis resistance.

Genetic Parameter and Hyper-Parameter Estimation Underlie Nitrogen Use Efficiency in Bread Wheat.

Estimation and prediction play a key role in breeding programs. Currently, phenotyping of complex traits such as nitrogen use efficiency (NUE) in wheat is still expensive, requires high-throughput technologies and is very time consuming compared to genotyping. Therefore, researchers are trying to predict phenotypes based on marker information. Genetic parameters such as population structure, genomic relationship matrix, marker density and sample size are major factors that increase the performance and accuracy of a model. However, they play an important role in adjusting the statistically significant false discovery rate (FDR) threshold in estimation. In parallel, there are many genetic hyper-parameters that are hidden and not represented in the given genomic selection (GS) model but have significant effects on the results, such as panel size, number of markers, minor allele frequency, number of call rates for each marker, number of cross validations and batch size in the training set of the genomic file. The main challenge is to ensure the reliability and accuracy of predicted breeding values (BVs) as results. Our study has confirmed the results of bias-variance tradeoff and adaptive prediction error for the ensemble-learning-based model STACK, which has the highest performance when estimating genetic parameters and hyper-parameters in a given GS model compared to other models.