This study aims to evaluate the genetics of imported semen and assess the
genetic trend of production traits in Holstein cows during their first
lactation in Iran. The data was collected from 28 ...different herds in Isfahan
province between 2011 and 2020. Variance-covariance components were
estimated by the restricted maximum likelihood method and the single and
multi-trait animal model. The correlation between breeding values for bulls
reported in catalogs and estimated in this was calculated. The mean of the
least squares by countries shows that the daughters of Spanish bulls have
the highest average for milk production, and the daughters of German,
French, Spanish, and American bulls have the highest average percentage of
fat and protein and the amount of fat and protein, respectively. Estimated
heritability for milk production, fat, and protein percentage, and the
amount of fat and protein were 0.34?0.011, 0.48?0.021, 0.41?0.016,
0.40?0.090, and 0.39?0.010 respectively. The mean genetic trend of milk
production, fat percentage, protein percentage, fat content, and protein
content were 92, 0.010, 0.004, 1.73, and 2.52, respectively. The correlation
between the estimated and reported breeding value of bulls for milk
production trait, percentage of fat and protein, and the amount of fat and
protein was estimated at 0.48, 0.67, 0.69, 0.14, and 0.26, and all of the
estimated correlations are statistically significant at the level of 0.05.
Based on the results for the most critical production trait in Isfahan
herds, milk production, American bulls have the best performance and genetic
trend.
Pyruvate kinase (PKLR) is a potential candidate gene for milk production traits in cows. The main aim of this work is to investigate the potentially deleterious non-synonymous single nucleotide ...polymorphisms (nsSNPs) in the PKLR gene by using several computational tools. In silico tools including SIFT, Polyphen-2, SNAP2 and Panther indicated only 18 nsSNPs out of 170 were considered deleterious. The analysis of proteins' stability change due to amino acid substitution performed by the use of the I-mutant, MUpro, CUPSTAT, SDM and Dynamut confirmed that 9 nsSNPs decreased protein stability. ConSurf analysis predicted that all 18 nsSNPs were evolutionary moderately or highly conserved. Two different domains of PKLR protein were revealed by the InterPro tool with 12 nsSNPs positioned in the Pyruvate Kinase barrel domain and 6 nsSNP present in the Pyruvate Kinase C Terminal. The PKLR 3D model was predicted by MODELLER software and validated via Ramachandran plot and Prosa which indicated a good quality model. The analysis of energy minimizations for the native and mutated structures was performed by SWISS PDB viewer with GROMOS 96 program and showed that 3 structural and 4 functional residues had total energy higher than the native model. These findings indicate that these mutant structures (rs441424814, rs449326723, rs476805413, rs472263384, rs474320860, rs475521477, rs441633284) were less stable than the native model. Molecular Dynamics simulations were performed to confirm the impact of nsSNPs on the protein structure and function. The present study provides useful information about functional SNPs that have an impact on PKLR protein in cattle.
Communicated by Ramaswamy H. Sarma
Inbreeding, by virtue of its consequence on traits of interest, is a topic of major interest for geneticists and animal breeders. Based on meta‐analysis conducted on 57 studies and seven livestock ...species considering a wide variety of selected traits, it was estimated that inbreeding depression corresponds to on average a decrease of 0.137 percent of the mean of a trait per 1 percent of inbreeding. The decrease was larger for production traits (reduction of 0.351%) than for other trait categories. For populations raised as purebreds, inbreeding depression may impact the economic income of breeders. There is a need for studies assessing the existence of an inbreeding purge phenomenon as well as the impact of inbreeding on adaptation capacities of livestock species. Promises brought by the development of dense genotyping as well as functional genomics will increase the capacities to improve our understanding and management of the phenomenon.
High resilience against diseases, changing environmental conditions, and other stress factors and the ability to efficiently recover to normal status, is becoming increasingly important in pig ...production. Finding new phenotypes that relate to resilience is a crucial step for improving the resilience of pigs through selection. The objective of this study was to extract resilience-related phenotypes based on fluctuations in daily feed intake (DFI, g) and time spent in feeding per day (TPD, min) and to estimate the heritability of these traits and genetic correlations with production traits (PT). Resilience-related traits with high enough heritability and with either favorable or neutral genetic correlation with PT could be used in the selection program to improve the productivity and welfare of pigs. In this study, we used data from 7,347 Finnish Yorkshire, Landrace, and crossbred pigs raised at the test station. Six pig-specific resilience-related phenotypes were extracted from the individual DFI and TPD: root mean square error (RMSE), quantile regression (QR), and coefficient of variation (CV). RMSE was calculated from the differences between the actual DFI (or TPD) and the pig-specific predicted values. QR was based on the number of days that a pig belonged to the group with the lowest 5% of pigs based on DFI (or TPD), and CV was calculated over the daily observations of DFI (or TPD). PT included average daily gain (ADG, g), backfat thickness (BF, mm), and feed conversion rate (FCR, g/g). The heritability estimates for resilience-related traits varied between 0.07 ± 0.02 (QRDFI) and 0.20 ± 0.03 (RMSETPD). The genetic correlations between resilience-related traits and PT were mostly neutral, but for example, RMSEDFI had a favorable genetic correlation with FCR and BF but an unfavorable correlation with ADG. Lastly, we observed that pigs belonging to the lowest 10% group based on their breeding value (BV) for QRTPD had a lower proportion (10% incidence) of sick days compared to the highest 10% BV group (30% incidence). Therefore, pigs exhibiting small TPD variation (related to high resilience) tend to be less susceptible to sickness than pigs with large TPD variation (related to low resilience). Given its moderate heritability, neutral genetic correlation with PT, and positive effect on health, QRTPD can be considered the most promising resilience-related trait in the Finnish production system.
Copy number variation (CNV) is a major type of genomic structural variation. We investigated their impacts on goat dairy traits using the CaprineSNP50 array. From 120 samples of five dairy goat ...breeds, we totally identified 42 CNVs ranging from 56,044 bp to 4,337,625 bp. We found significant associations between two CNVs (CNV5 and CNV25) and two milk production traits (mean of milk fat yield and mean of milk protein yield) after false discovery rate (FDR) correction (P < 0.05). CNV5 overlaps the ADAMTS20 gene, which is involved in the differentiation of mammary cell and plays a crucial role in lactogenic activity of bovine mammary epithelial cells. CNV25 overlaps with PAPPA2, which has been found to be associated with bovine reproduction and milk production traits. Our results revealed that CNVs overlapped with ADAMTS20 and PAPPA2 could be involved in goat dairy traits and function as candidate markers for further genetic selection.
Selection is an important part of animal breeding and is usually performed on the basis of a set of traits,
each of them characterized by its BV (breeding value) and EV (economic value). Different ...approaches have been
used in recent years for the calculation of the economic values of traits - simple profit functions and more complex
bio-economic models. The most common approach nowadays is the bio-economic modeling of the production system
due to its precision, flexibility, the inclusion of many biological details reflecting the changes in genetic values on overall
profitability. The objective of this review is to present and summarize research on calculation of economic values
for dairy, meat and indigenous (multipurpose) sheep breeds using bio-economic models. According to the type of
sheep production, various productive and functional characteristics have been studied. Of particular importance for the
predominance of a particular trait over others in terms of its contribution to profit on farms are the breed, production
system, climatic conditions, market determinants, demand and supply of sheep products, etc., which may undergo
changes over time. For this reason, a recalculation of the economic importance of profit-related traits in sheep is
needed for the adaptation of the breeding objectives of the enterprises according to their economic importance.
This research investigated the growth and other production traits of four distinct lines (L1, L2, L3, and L4) of Japanese quail (Cortunix japanoica) kept in the tropical climate of Tamil Nadu, India. ...The traits related to body weight at different weeks and weight gain were measured in 180 birds (90 males and 90 females) per line up to the fifth week of age, and then 90 birds (females only) from the sixth to the 16th week of age, with egg production and feed efficiency parameters measured in 10 observations per line. The traits were analysed using the General Linear Model procedure, and Tukey's HSD was used to test for statistical differences (
< 0.05) between the means for subclasses under a specific effect. The results revealed a highly significant difference (
< 0.01) in body weight from hatch to fifth week of age. At 5th week of age, the L3 and L2 did not differ (
> 0.05) based on Tukey test; therefore, both presented the highest values and were statistically significant (
< 0.01) with L4 with a lowest value of 203.62 g. The cumulative fifth week feed conversion ratio showed non-significant difference (
> 0.05) at first and second week, and highly significant difference (
< 0.01) from third to fifth week of age. The age at 50 per cent egg production was 60.2 (L4), 61.4 (L2), 65.1 (L3) and 66.0 (L1) days and the L1 egg production differed significantly (
< 0.01) from L4 line. The highest bodyweight (g) during the laying period (at 15 weeks of age) was observed in L2 (327.08) and L3 (326.54) and differed significantly (
< 0.01) from L1 (309.24) as well as L4 (288.69) lines. The mean egg weight (g) of different lines showed non-significant difference (
> 0.05) at all weeks, except at 11th week of age (
< 0.01). The mean feed consumption (g)/bird/day differed significantly (
< 0.01) from 6th to 16th week of age, except at sixth and eighth week of age, where it was non-significant (
> 0.05). The overall feed efficiency/dozen of eggs (from 6th to 16th weeks) ranged from 1.33 (L1) to 1.98 (L3). The livability from 6 to 16 weeks of age was 100 per cent in all the lines. In order to boost Japanese quail production in the tropics, L3 and L4 may be selected for body weight and egg production, respectively.
Avian Leukosis Virus subgroup E (ALVE) integrations are endogenous retroviral elements found in the chicken genome. The presence of ALVE has been reported to have negative impacts on multiple traits, ...including egg production and body weight. The recent development of rapid, inexpensive and specific ALVE detection methods has facilitated their characterization in elite commercial egg production lines across multiple generations. The presence of 20 ALVE was examined in 8 elite lines, from 3 different breeds. Seventeen of these ALVE (85%) were informative and found to be segregating in at least one of the lines. To test for an association between specific ALVE inserts and traits, a large genotype by phenotype study was undertaken. Genotypes were obtained for 500 to 1500 males per line, and the phenotypes used were sire-daughter averages. Phenotype data were analyzed by line with a linear model that included the effects of generation, ALVE genotype and their interaction. If genotype effect was significant, the number of ALVE copies was fitted as a regression to estimate additive ALVE gene substitution effect. Significant associations between the presence of specific ALVE inserts and 18 commercially relevant performance and egg quality traits, including egg production, egg weight and albumen height, were observed. When an ALVE was segregating in more than one line, these associations did not always have the same impact (negative, positive or none) in each line. It is hypothesized that the presence of ALVE in the chicken genome may influence production traits by 3 mechanisms: viral protein production may modulate the immune system and impact overall production performance (virus effect); insertional mutagenesis caused by viral integration may cause direct gene alterations or affect gene regulation (gene effect); or the integration site may be within or adjacent to a quantitative trait region which impacts a performance trait (linkage disequilibrium, marker effect).
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