Principal component analysis of phenotypic and breeding value data for semen traits in Egyptian buffalo bulls.

Buffalo bull semen traits are economically important traits that influence farm fertility and profitability. Genetic improvement of semen characteristics is an important detail of the genetic improvement. This study was conducted to assess the relationship between the breeding values as well as the phenotypic values for semen traits (VOL, MM, LS, AS and CONC) of the Egyptian buffalo bulls. A total of 7761 normal semen ejaculates were collected and characterized at ILMTC laboratory from 26 bulls from 2009 to 2019. For VOL, MM, LS, AS, and CONC, the actual means were 3.89 mL, 62.37%, 60.64%, 3.94%, and 0.67 × 109 sperm/mL, respectively. The prediction of breeding values for semen traits was estimated using a Bayesian procedure. The estimated standardized EBVs and phenotypic values were used in the principal component analysis (PCA). Of five PCs, one PC (PC1) had > 1 eigenvalues that was responsible for 87.19% of the total variation of SEBV, and two PCs had > 1 eigenvalues that were responsible for 59.61% and 21.35% of the total variation of the phenotypic values. Together, PC1 and PC2 accounted for 97.97% of the total variance of SEBV and 80.96% of the total variance of phenotypic values. A graphs of the first two components showed the traits separated into two different directions by group. This indicates each group was under similar genetic influence. Therefore, selection can be done separately for each group without influencing the other. Principal component analysis reduced variables to describe the key information in buffalo semen data.

A Single-Step Genome-Wide Association Study for Semen Traits of Egyptian Buffalo Bulls.

The present study aimed to contribute to the limited research on buffalo (Bubalus bubalis) semen traits by incorporating genomic data. A total of 8465 ejaculates were collected. The genotyping procedure was conducted using the Axiom® Buffalo Genotyping 90 K array designed by the Affymetrix Expert Design Program. After conducting a quality assessment, we utilized 67,282 SNPs genotyped in 192 animals. We identified several genomic loci explaining high genetic variance by employing single-step genomic evaluation. The aforementioned regions were located on buffalo chromosomes no. 3, 4, 6, 7, 14, 16, 20, 22, and the X-chromosome. The X-chromosome exhibited substantial influence, accounting for 4.18, 4.59, 5.16, 5.19, and 4.31% of the genomic variance for ejaculate volume, mass motility, livability, abnormality, and concentration, respectively. In the examined genomic regions, we identified five novel candidate genes linked to male fertility and spermatogenesis, four in the X-chromosome and one in chromosome no. 16. Additional extensive research with larger sample sizes and datasets is imperative to validate these findings and evaluate their applicability for genomic selection.

Genome-Wide Association Study of Maternal Genetic Effects on Intramuscular Fat and Fatty Acid Composition in Rabbits.

Maternal genetic effects (MGE) could affect meat quality traits such as intramuscular fat (IMF) and its fatty acid composition. However, it has been scarcely studied, especially in rabbits. The objectives of the present study were, first, to assess the importance of MGE on intramuscular fat and fatty acid composition by applying a Bayesian maternal animal model in two rabbit lines divergently selected for IMF. The second objective was to identify genomic regions and candidate genes of MGE that are associated with the traits of these offspring, using Bayesian methods in a Genome Wide Association Study (GWAS). Quantitative analyses were performed using data from 1982 rabbits, and 349 animals from the 9th generation and 76 dams of the 8th generation with 88,512 SNPs were used for the GWAS. The studied traits were IMF, saturated fatty acids (total SFA, C14:0; myristic acid, C16:0; palmitic acid and C18:0; stearic acid), monounsaturated fatty acids (total MUFA, C16:1n-7; palmitoleic acid and C18:1n-9; oleic acid), polyunsaturated fatty acids (total PUFA, C18:2n-6; linoleic acid, C18:3n-3; α-linolenic acid and C20:4n-6; arachidonic acid), MUFA/SFA and PUFA/SFA. The proportion of phenotypic variance explained by the maternal genetic effect ranged from 8 to 22% for IMF, depending on the model. For fatty acid composition, the proportion of phenotypic variance explained by maternal genetic effects varied from 10% (C18:0) to 46% (MUFA) in a model including both direct and additive maternal genetic effects, together with the common litter effect as a random variable. In particular, there were significant direct maternal genetic correlations for C16:0, C18:1n9, C18:2n6, SFA, MUFA, and PUFA with values ranging from -0.53 to -0.89. Relevant associated genomic regions were located on the rabbit chromosomes (OCU) OCU1, OCU5 and OCU19 containing some relevant candidates (TANC2, ACE, MAP3K3, TEX2, PRKCA, SH3GL2, CNTLN, RPGRIP1L and FTO) related to lipid metabolism, binding, and obesity. These regions explained about 1.2 to 13.9% of the total genomic variance of the traits studied. Our results showed an important maternal genetic effect on IMF and its fatty acid composition in rabbits and identified promising candidate genes associated with these traits.

Estimation of genetic parameters for semen traits in Egyptian buffalo bulls.

This study was conducted to characterize semen traits (ejaculate volume (VOL), mass motility (MM), sperm livability (LS), percentage of abnormal sperms (AS), and sperm concentration (CONC)) of Egyptian buffalo bulls and evaluate the importance of some nongenetic factors (year (YC) and season (SC) of semen collection and age of bull genetically and environmentally at collection (ABC)) affecting the investigated traits. A total of 7761 normal semen ejaculates were collected from 26 bulls from 2009 to 2019. Single-trait and bivariate repeatability animal models using Bayesian methods were used to estimate variance components, heritability, repeatability, and genetic correlations among the investigated semen traits. YC and ABC exerted significant effects on most semen traits, whereas SC exerted no significant effect on all the investigated semen traits. Heritability estimates were 0.08, 0.52, 0.51, 0.04, and 0.49 for VOL, MM, LS, AS, and CONC, respectively. Repeatability estimates were 0.14, 0.82, 0.79, 0.06, and 0.78 for VOL, MM, LS, AS, and CONC, respectively. The genetic correlations between MM and each of LS and CONC were highly significant (0.99 ± 0.01 and 0.95 ± 0.14, respectively), and that between LS and CONC was also highly significant (0.92 ± 0.20). The high heritability estimates for MM, LS, and CONC combined with the favorable high significant genetic correlations between these traits indicated that direct selection for MM may be an effective method to enhance semen quality in Egyptian buffalo bulls and consequently improve fertility.

Genetic analysis of post-weaning growth traits in a simple crossbreeding experiment between Gabali and Hyplus line rabbits.

A simple crossbreeding experiment between Gabali (G) bucks and Hyplus (H) does was performed to estimate crossbreeding effects for post-weaning growth traits (body weight at 5 (BW5), 7 (BW7), 9 (BW9), 11 (BW11), and 13 (BW13) weeks of age and daily weight gains (DG) during (DG5-7), (DG7-9), (DG9-11), (DG11-13) and (DG5-13), weeks of age). Estimates of heritability were mostly low or moderate for growth traits and ranged from 0.12 to 0.35 for body weights and 0.05 to 0.66 for daily weight gains. The percentages of direct additive genetic effects on body weights favored (p ≤ 0.01) the Gabali breed by 22.1, 31.2, 32.8, 31.1, and 25.2% at 5, 7, 9, 11, and 13 weeks and by 35.4, 38.1, 21.9, 3.7, and 27% for DG5-7, DG7-9, DG9-11, DG11-13, and DG5-13, respectively. The percentages of maternal effects ranged from 22 to 34.8% for body weights and ranged from 4.7 to 43.4% for daily weight gains. The percentages of direct heterosis were significantly positive by 11, 19.1, 20.3, 19.7, and 16.5% for body weights at 5, 7, 9, 11, and 13 weeks and by 25.6, 27.2, 17.3, 3.5, and 17.9% for DG5-7, DG7-9, DG9-11, DG11-13, and DG5-13, respectively. These results suggest that the Gabali breed could be used as a sire-group and the Hyplus line could be used as a dam-group to create new high growth rabbit lines in Egypt.

Dietary Supplementation of Silybum marianum Seeds Improved Growth Performance and Upregulated Associated Gene Expression of Muscovy Ducklings (Cairina moschata).

The effect of feeding on diets supplemented with Silybum marianum L. dry seeds (SMS) on growth performance, mortality percentage, biochemical parameters, the expression profile of related genes, and genotoxic effect in Muscovy ducklings was evaluated during a brooding period of 4 weeks. Two hundred and forty one-day-old Muscovy ducks were randomly assigned to four treatment groups (60 ducklings/group), the first group fed on basal diet with no additives (control), and the second (4 g kg-1), third (8 g kg-1), and fourth (12 g kg-1) groups fed the basal diet supplemented with 0, 4, 8, and 12 g kg-1 diet SMS, respectively. A substantial improvement in live body weight (LBW), body weight gain (BWG), and growth rate (GR), and a decrease in feed conversion ratios (FCR) and mortality rate were shown in ducks fed a diet supplemented with either 8 g kg-1 or 12 g kg-1 SMS compared to the other groups. Relevant improvements in liver function, oxidative stress markers, purinergic cell energy, and brain appetite were recorded on ducklings fed diets supplemented with SMS. Moreover, diets which included 8 or 12 g kg-1 SMS positively upregulated the expression of growth hormone gene (GH) and antioxidant genes (SOD1, SOD2, and CAT). These results are consistent with the increase in liver activity SOD and CAT enzymes, resulting in less DNA fragmentation. Consequently, all the aforementioned improvements in biochemical parameters and gene expression profiling may explain the superiority of the treated ducklings compared with the control group. Conclusively, the SMS could be used as a natural feed additive to promote health status and improve the growth performance of small grower ducks during the brooding period.

Genetic analysis of prolificacy, milk production and composition traits in Egyptian Zaraibi goats.

This study was conducted to genetically and environmentally characterize prolificacy (litter size and weight at birth; LSB and LWB and litter size and weight at weaning; LSW and LWW, respectively), milk yield at the 7th (MY7), 15th (MY15), 30th (MY30), 60th (MY60), 90th (MY90) day of lactation and monthly milk yield (MMY) and milk composition traits in Egyptian Zaraibi goats. A total of 443 and 421 records produced by 121 Zaraibi lactating goats were used to assess prolificacy and milk production traits, respectively. The milk composition traits were measured using 371 milk samples obtained at random from 53 goats. The fourth parity showed the highest values for LWB, LWW, and MMY (3.62, 18.15, and 28.99 kg, respectively). Milk composition traits revealed an inverse tendency, decreasing until the second month and then increasing until the seventh month. The heritability estimates ranged from 0.07 to 0.13, from 0.04 to 0.39, and from 0.07 to 0.33 for prolificacy, milk yield, and milk composition traits, respectively. Negatively high genetic correlations between MMY and all milk composition traits were found. MMY had the highest estimate of heritability (0.39 ± 0.07), this means that the genetic improvement of this trait could be achieved through direct selection.

Functional longevity in five rabbit lines founded on different criteria: Comparison at foundation and at fixed times after selection.

The enhancement of rabbit female functional longevity, that is the ability to avoid voluntary culling, is a paramount aspect for the sustainability of meat rabbit production; this trait represents a direct indicator of female robustness. The objective of our study was to compare the functional longevity of five rabbit lines at their foundation and at fixed times during their selection processes. Four of them are maternal lines (A, V, H and LP) selected for litter size at weaning. The fifth line is the paternal line R, founded and selected for post-weaning daily gain from 28 to 63 days. The comparison at foundation involved the complete data set (from March 1980 to March 2013; records of 15,670 does) and pedigree (19,405 animals). Latter comparisons were made when all lines shared the same environmental and management conditions, from March 1997 to September 1998 and from March 2011 to September 2012. In these second comparisons, the same model as that used in the comparison at foundation was used, but now the additive effect was excluded, only data from the corresponding periods were considered. At their foundation, lines V, H and LP showed larger functional longevity than lines A and R, being LP line that with the longest productive life. In the latter comparisons, lines A and R still showing the lowest functional longevities. However, as the selection process evolves, the differences between these two lines and the others were reduced. It could be concluded that the average longevity of a population greatly depends on the criteria followed for its foundation. In addition, along the selection for litter size, the differences of longevity between lines tend to decrease, this is due to an unintended selection for functional longevity, since only offspring from females reaching three parturitions are selected as breeding animals for the next generation.

Factors affecting calving ease in Egyptian buffalo.

Calving ease (CE) is a trait of economic importance that affects animal welfare and farm profitability. The objective of present study was to investigate genetic and environmental factors affecting CE among Primiparous (PP) and multiparous (MP) buffaloes. A total of 9,627 records from 1999 MP and 2,110 PP recorded during the period from 1988 to 2018 were considered. Herd, season of calving, year of calving, birth weight, parity order and gestation length significantly affected CE rate, while age at first calving and sex of calf had no significant effects. Direct and maternal heritabilities of CE in PP and MP were 0.06 and 0.01, respectively. The low heritability of CE indicated that direct selection may not be an effective method to improve CE trait in Egyptian buffalo.

Genetic analysis of functional longevity in a complete diallel crossing experiment involving four maternal rabbit lines.

In a diallel cross between four maternal lines of rabbits, the four maternal lines and the corresponding crossbred females (does) were evaluated concerning functional longevity, estimating their crossbreeding components. Sixteen genetic groups were produced by using four maternal lines of rabbit (A, V, H and LP (L)). The groups were distributed over 4 Spanish farms. In all farms, the V line was present as the reference group. A total of 7,211 does' longevity records were recorded. Using a Cox proportional hazard model of fixed effects, survival analysis was performed to study longevity analysing the hazard of death or culling. Does from lines A, H and V had similar risks of death or of being culled, and they were more susceptible compared with those from line L. The lowest hazard was associated with L line does. No significant differences were found between the average of all crosses and the V line except when comparing the V line to the cross between A and H lines, favouring the former (1.30 higher risk of replacement for AH animals). Significant differences between reciprocal crosses were observed between VH and HV, in favour of HV (0.72 of relative risk of replacement) and between LH and HL, in favour of HL (0.76 of relative risk). Line V had the highest risk due to the direct genetic effects, and these differences were significant with the lines H (1.40 of relative risk) and L (1.43 of relative risk). The differences in maternal genetic effects were small and not significant except between lines H and V in favour of V line (0.75 of relative risk). The estimated direct heterosis effects do not always follow the same trend but they showed the importance of the crossing between specialized lines to produce crossbred does for intensive meat rabbit production.