Single-step genome-wide association analyses for milk urea concentration in Walloon Holstein cows

The aims of this study were to conduct a single-step genome-wide association to identify genomic regions associated with milk urea (MU) and to estimate genetic correlations between MU and milk yield (MY), milk composition (calcium content [CC], fat percentage [FP], protein percentage [PP], and casein percentage [CNP]), and cheese-making properties (CMP; coagulation time [CT], curd firmness after 30 min from rennet addition [a30], and titratable acidity [TA]). The used data have been collected from 2015 to 2020 on 78,073 first-parity (485,218 test-day records) and 48,766 second-parity (284,942 test-day records) Holstein cows distributed in 671 herds in the Walloon Region of Belgium. Data of 565,533 SNP located on 29 BTA of 6,617 animals (1,712 males) 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 50 consecutive SNPs (with an average size of ∼216 kb) was calculated, and the top-3 genomic regions explaining the largest rate of the genetic variance were considered promising regions and used to identify potential candidate genes. Mean (SD) MU was 25.38 (8.02) mg/dL and 25.03 (8.06) mg/dL in the first and second lactation, respectively. Mean heritability estimates for daily MU were 0.21 and 0.23 for the first and second lactation, respectively. The genetic correlations estimated between MU and MY, milk composition, and CMP were quite low (ranged from -0.10 [CC] to 0.10 [TA] and -0.05 [CT] to 0.13 [TA] for the first and second lactations, respectively). The top-3 regions associated with MU were located from 80.61 to 80.74 Mb on BTA6, 103.26 to 103.41 Mb on BTA11, and 1.59 to 2.15 Mb on BTA14. Genes including KCNT1, MROH1, SHARPIN, TSSK5, CPSF1, HSF1, TONSL, DGAT1, SCX, and MAF1 were identified as positional candidate genes for MU. The findings of this study can be used for a better understanding of the genomic architecture underlying MU in Holstein cattle.

Genetic analysis of milk citrate predicted by milk mid-infrared spectra of Holstein cows in early lactation

Milk citrate is regarded as an early biomarker of negative energy balance in dairy cows during early lactation and serves as a suitable candidate phenotype for genomic selection due to its wide availability across a large number of cows through milk mid-infrared spectra prediction. However, its genetic background is not well known. Therefore, the objectives of this study were to (1) analyze the genetic parameters of milk citrate; (2) identify genomic regions associated with milk citrate; and (3) analyze the functional annotation of candidate genes and quantitative trait loci (QTL) related to milk citrate in Walloon Holstein cows. In total, 134,517 test-day milk-citrate phenotypes (mmol/L) collected within the first 50 d in milk on 52,198 Holstein cows were used. These milk-citrate phenotypes, predicted by milk mid-infrared spectra, were divided into 3 traits according to the first (citrate1), second (citrate2), and third to fifth parity (citrate3+). Genomic information for 566,170 SNPs was available for 4,479 animals. A multiple-trait repeatability model was used to estimate genetic parameters. A single-step GWAS was used to identify candidate genes for citrate and post-GWAS analysis was done to investigate the relationship and function of the identified candidate genes. The heritabilities estimated for citrate1, citrate2, and citrate3+ were 0.40, 0.37, and 0.35, respectively. The genetic correlations among the 3 traits ranged from 0.98 to 0.99. The genomic correlations among the 3 traits were also close to 1.00 across the genomic regions (1 Mb) in the whole genome, which means that citrate can be considered as a single trait in the first 5 parities. In total, 603 significant SNPs located on 3 genomic regions (chromosome 7, 68.569-68.575 Mb; chromosome 14, 0.15-1.90 Mb; and chromosome 20, 54.00-64.28 Mb), were identified to be associated with milk citrate. We identified 89 candidate genes including GPT, ANKH, PPP1R16A, and 32 QTL reported in the literature related to the identified significant SNPs. These identified QTL were mainly reported associated with milk fatty acids and metabolic diseases in dairy cows. This study suggests that milk citrate in Holstein cows is highly heritable and has the potential to be used as an early proxy for the negative energy balance of Holstein cows in a breeding objective.

Estimation of genetic parameters and single-step genome-wide association studies for eating time and rumination time in Holstein dairy cows

The aims of this study were to estimate genetic parameters and to identify genomic regions associated with eating time (ET) and rumination time (RUT) in Holstein dairy cows. Genetic correlations among ET, RUT, and milk yield traits were also estimated. The data were collected from 2019 to 2022 in 6 dairy herds located in the Walloon Region of Belgium. The dataset consisted of daily ET and RUT records on 284 Holstein cows, from which 41 cows had records only for the first parity (P1), 101 cows had records from both the first and second parities, and 142 cows had records only for the second parity (P2). The number of daily ET and RUT records in the P1 and P2 cows were 18,569 (on 142 cows) and 34,464 (on 243 cows), respectively. Data on 28,994 SNPs located on 29 Bos taurus autosomes (BTA) of 747 animals (435 males) 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 20-SNP sliding window (with an average size of 1.52 Mb) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for candidate genes. Mean (standard deviation; SD) averaged daily ET and RUT were 327.0 (85.66) and 559.4 (77.69) min/d for cows in P1 and 316.0 (82.24) and 574.2 (75.42) min/d for cows in P2, respectively. Mean (standard deviation; SD) heritability estimates for daily ET and RUT were 0.42 (0.09) and 0.45 (0.06) for cows in P1 and 0.45 (0.04) and 0.43 (0.02) for cows in P2, respectively. Mean (SD) daily genetic correlations between daily ET and RUT were 0.27 (0.07) for P1 and 0.34 (0.08) for P2. Genome-wide association analyses identified 6 genomic regions distributed over 5 chromosomes (BTA1, BTA4, BTA11, 2 regions of BTA14, and BTA17) associated with ET or RUT. The findings of this study increase our preliminary understanding of the genetic background of feeding behavior in dairy cows; however, larger datasets are needed to determine whether ET and RUT might have the potential to be used in selection programs.

Lactation performances in primiparous Holstein cows following short and normal gestation lengths

Despite decades of research, little is known regarding physiologic temporal limits for initiation of lactation in pregnant non-lactating cattle the aim of this study was to compare the lactation performances in primiparous Holstein cows after a short gestation length (GL) or abortion to those after a normal GL. The data were collected using an automated data collection system. The 94 herds evaluated were located in Belgium, France, Italy, the Netherlands and Germany. Data from a wide range of physiological cow-life events including birth and calving events, reproduction events (insemination, pregnancy checks, and abortions), and milking events were collected. The GL was defined as the interval between the last insemination and the subsequent calving (or abortion) within a range of 150-297 days. Animals were categorized into one of five categories based on GL quantiles (C-I to C-V). Lactation curve parameters including the scale, ramp, and decay were estimated using the Milkbot model. Then, the derived 305-day milk yield (M305-d), peak yield, and time to peak were compared between different GL categories. Of 13,732 lactations, 15 (0.11%) were found with a GL shorter than 210 days (ranging from 158 to 208 days). The 305-day milk yield was significantly lower in the C-I (7,566 ± 186) and C-II groups (7,802 ± 136 kg), compared to the C-III (8,254 ± 116 kg), C-IV (8,148 ± 119 kg), and C-V (8,255 ± 117 kg) groups. The same trends were found for the scale and peak yield of the lactation; the lowest scale were found for the C-I (31.5 ± 0.73) and C-II (32.8 ± 0.53) groups, and the highest were found for the C-III (34.5 ± 0.46), C-IV (34.9 ± 0.45), and C-V (35.0 ± 0.45) groups. Peak yield increased significantly from C-I (27.8 ± 0.66 kg) and C-II group (28.8 ± 0.48 kg) to the C-III (30.2 ± 0.42 kg) and further to the C-IV (30.6 ± 0.40 kg) and C-V (30.6 ± 0.41 kg) groups. Moreover, primiparous cows in the C-II GL category showed a higher milk yield persistency (decay of 1.30E-4 ± 3.55E-5) compared to those belonging to the C-IV (decay of 1.38E-4 ± 2.51E-5) and C-V (decay of 1.38E-4 ± 2.58E-5) group. In conclusion, results showed that primiparous cows with a shorter GL produced significantly less 305-day milk and peak yields, had a higher lactation persistency, and showed a lower upward slope of the lactation curve compared to those with a normal GL.

Validating genomic prediction for nitrogen efficiency index and its composition traits of Holstein cows in early lactation

Nitrogen (N) use efficiency (NUE) is an economically important trait for dairy cows. Recently, we proposed a new N efficiency index (NEI), that simultaneously considers both NUE and N pollution. This study aimed to validate the genomic prediction for NEI and its composition traits and investigate the relationship between SNP effects estimated directly from NEI and indirectly from its composition traits. The NEI composition included genomic estimated breeding value of N intake (NINT), milk true protein N (MTPN) and milk urea N yield. The edited data were 132,899 records on 52,064 cows distributed in 773 herds. The pedigree contained 122,368 animals. Genotypic data of 566,294 SNP was available for 4514 individuals. A total of 4413 cows (including 181 genotyped) and 56 bulls (including 32 genotyped) were selected as the validation populations. The linear regression method was used to validate the genomic prediction of NEI and its composition traits using best linear unbiased prediction (BLUP) and single-step genomic BLUP (ssGBLUP). The mean theoretical accuracies of validation populations obtained from ssGBLUP were higher than those obtained from BLUP for both NEI and its composition traits, ranging from 0.57 (MTPN) to 0.72 (NINT). The highest mean prediction accuracies for NEI and its composition traits were observed for the genotyped cows estimated under ssGBLUP, ranging from 0.48 (MTPN) to 0.66 (NINT). Furthermore, the SNP effects estimated from NEI composition traits, multiplied by the relative weight were the same as those estimated directly from NEI. This study preliminary showed that genomic prediction can be used for NEI, however, we acknowledge the need for further validation of this result in a larger dataset. Moreover, the SNP effects of NEI can be indirectly calculated using the SNP effects estimated from its composition traits. This study provided a basis for adding genomic information to establish NEI as part of future routine genomic evaluation programs.

Single-step genome-wide association analyses for selected infrared-predicted cheese-making traits in Walloon Holstein cows

This study aimed to perform genome-wide association study to identify genomic regions associated with milk production and cheese-making properties (CMP) in Walloon Holstein cows. The studied traits were milk yield, fat percentage, protein percentage, casein percentage (CNP), calcium content, somatic cell score (SCS), coagulation time, curd firmness after 30 min from rennet addition, and titratable acidity. The used data have been collected from 2014 to 2020 on 78,073 first-parity (485,218 test-day records), 48,766 second-parity (284,942 test-day records), and 21,948 third-parity (105,112 test-day records) Holstein cows distributed in 671 herds in the Walloon Region of Belgium. Data of 565,533 single nucleotide polymorphisms (SNP), located on 29 Bos taurus autosomes (BTA) of 6,617 animals (1,712 males), 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 50 consecutive SNPs (with an average size of ∼216 KB) was calculated, and regions accounting for at least 1.0% of the total additive genetic variance were used to search for positional candidate genes. Heritability estimates for the studied traits ranged from 0.10 (SCS) to 0.53 (CNP), 0.10 (SCS) to 0.50 (CNP), and 0.12 (SCS) to 0.49 (CNP) in the first, second, and third parity, respectively. Genome-wide association analyses identified 6 genomic regions (BTA1, BTA14 [4 regions], and BTA20) associated with the considered traits. Genes including the SLC37A1 (BTA1), SHARPIN, MROH1, DGAT1, FAM83H, TIGD5, MROH6, NAPRT, ADGRB1, GML, LYPD2, JRK (BTA14), and TRIO (BTA20) were identified as positional candidate genes for the studied CMP. The findings of this study help to unravel the genomic background of a cow's ability for cheese production and can be used for the future implementation and use of genomic evaluation to improve the cheese-making traits in Walloon Holstein cows.

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.

Genome-wide association study and functional annotation analyses for nitrogen efficiency index and its composition traits in dairy cattle

The aims of this study were (1) to identify genomic regions associated with a N efficiency index (NEI) and its composition traits and (2) to analyze the functional annotation of identified genomic regions. The NEI included N intake (NINT1), milk true protein N (MTPN1), milk urea N yield (MUNY1) in primiparous cattle, and N intake (NINT2+), milk true protein N (MTPN2+), and milk urea N yield (MUNY2+) in multiparous cattle (2 to 5 parities). The edited data included 1,043,171 records on 342,847 cows distributed in 1,931 herds. The pedigree consisted of 505,125 animals (17,797 males). Data of 565,049 SNPs were available for 6,998 animals included in the pedigree (5,251 females and 1,747 males). The SNP effects were estimated using a single-step genomic BLUP approach. The proportion of the total additive genetic variance explained by windows of 50 consecutive SNPs (with an average size of about 240 kb) was calculated. The top 3 genomic regions explaining the largest rate of the total additive genetic variance of the NEI and its composition traits were selected for candidate gene identification and quantitative trait loci (QTL) annotation. The selected genomic regions explained from 0.17% (MTPN2+) to 0.58% (NEI) of the total additive genetic variance. The largest explanatory genomic regions of NEI, NINT1, NINT2+, MTPN1, MTPN2+, MUNY1, and MUNY2+ were Bos taurus autosome 14 (1.52-2.09 Mb), 26 (9.24-9.66 Mb), 16 (75.41-75.51 Mb), 6 (8.73-88.92 Mb), 6 (8.73-88.92 Mb), 11 (103.26-103.41 Mb), 11 (103.26-103.41 Mb). Based on the literature, gene ontology, Kyoto Encyclopedia of Genes and Genomes, and protein-protein interaction, 16 key candidate genes were identified for NEI and its composition traits, which are mainly expressed in the milk cell, mammary, and liver tissues. The number of enriched QTL related to NEI, NINT1, NINT2+, MTPN1, and MTPN2+ were 41, 6, 4, 11, 36, 32, and 32, respectively, and most of them were related to the milk, health, and production classes. In conclusion, this study identified genomic regions associated with NEI and its composition traits, and identified key candidate genes describing the genetic mechanisms of N use efficiency-related traits. Furthermore, the NEI reflects not only its composition traits but also the interactions among them.

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.

Defining a nitrogen efficiency index in Holstein cows and assessing its potential effect on the breeding program of bulls

The purposes of this study were (1) to explore the relationship between 3 milk mid-infrared predicted features including nitrogen intake (NINT), milk true protein N (MTPN), and milk urea-N yield (MUNY); (2) to integrate these 3 features into an N efficiency index (NEI) and analyses approximate genetic correlations between the NEI and 37 traits (indices) of interest; and (3) to assess the potential effect of including the NEI into breeding programs of bulls. The edited data were 1,043,171 test-day records on 342,847 cows in 1,931 herds and 143,595 test-day records on 53,660 cows in 766 herds used for estimating breeding values (EBV) and variance components, respectively. The used records were within 5 to 50 d in milk. The records were grouped into primiparous and multiparous. The genetic parameters for the included mid-infrared features and EBV of the animals included in the pedigree were estimated using a multiple-trait repeatability animal model. Then, the EBV of the NINT, MTPN, MUNY were integrated into the NEI using a selection index assuming weights based on the N partitioning. The approximate genetic correlations between the NEI and 37 traits of interest were estimated using the EBV of the selected bulls. The bulls born from 2011 to 2014 with NEI were selected and the NEI distribution of these bulls having EBV for the 8 selected traits (indices) was checked. The heritability and repeatability estimates for NINT, MTPN, and MUNY ranged from 0.09 to 0.13, and 0.37 to 0.65, respectively. The genetic and phenotypic correlations between NINT, MTPN, and MUNY ranged from -0.31 to 0.87, and -0.02 to 0.42, respectively. The NEI ranged from -13.13 to 12.55 kg/d. In total, 736 bulls with reliability ≥0.50 for all included traits (NEI and 37 traits) and at least 10 daughters distributed in at least 10 herds were selected to investigate genetic aspects of the NEI. The NEI had positive genetic correlations with production yield traits (0.08-0.46), and negative genetic correlations with the investigated functional traits and indices (-0.71 to -0.07), except for the production economic index and functional type economic index. The daughters of bulls with higher NEI had lower NINT and MUNY, and higher MTPN. Furthermore, 26% of the bulls (n = 50) with NEI born between 2011 to 2014 had higher NEI and global economic index than the average in the selected bulls. Finally, the developed NEI has the advantage of large-scale prediction and therefore has the potential for routine application in dairy cattle breeding in the future.

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 for Lactation Performance in the Early and Peak Stages of Lactation in Holstein Dairy Cows

Simple Summary

Although genome-wide association studies (GWAS) have been carried out within a variety of cattle breeds, they are mainly based on the accumulated 305-day lactation yield traits estimated by summing the test-day recorded every day during the lactation period, or combining the weekly or monthly test-day records by linear interpolation. Since the additive genetic variance for milk yield and composition changes during lactation, the genetic effects of QTL related to these traits are not constant during the lactation period. Therefore, a better understanding of the genetic architecture of milk production traits in different lactation stages (e.g., beginning, peak, and end stages of lactation) is needed. The aim of this study was to detect genomic loci associated with lactation performance during 9 to 50 days in milk (DIM) in Holstein dairy cows. Candidate genes identified for milk production traits showed contrasting results between the EARLY and PEAK stages of lactation. Based on the results of this study, it can be concluded that in any genomic study it should be taken into account that the genetic effects of genes related to the lactation performance are not constant during the lactation period.

Abstract

This study aimed to detect genomic loci associated with the lactation performance during 9 to 50 days in milk (DIM) in Holstein dairy cows. Daily milk yield (MY), fat yield (FY), and protein yield (PY) during 9 to 50 DIM were recorded on 134 multiparous Holstein dairy cows distributed in four research herds. Fat- and protein-corrected milk (FPCM), fat-corrected milk (FCM), and energy-corrected milk (ECM) were predicted. The records collected during 9 to 25 DIM were put into the early stage of lactation (EARLY) and those collected during 26 to 50 DIM were put into the peak stage of lactation (PEAK). Then, the mean of traits in each cow included in each lactation stage (EARLY and PEAK) were estimated and used as phenotypic observations for the genome-wide association study. The included animals were genotyped with the Illumina BovineHD Genotyping BeadChip (Illumina Inc., San Diego, CA, USA) for a total of 777,962 single nucleotide polymorphisms (SNPs). After quality control, 585,109 variants were analyzed using GEMMA software in a mixed linear model. Although there was no SNP associated with traits included at the 5% genome-wide significance threshold, 18 SNPs were identified to be associated with milk yield and composition at the suggestive genome-wide significance threshold. Candidate genes identified for milk production traits showed contrasting results between the EARLY and PEAK stages of lactation. This suggests that differential sets of candidate genes underlie the phenotypic expression of the considered traits in the EARLY and PEAK stages of lactation. Although further functional studies are needed to validate our findings in independent populations, it can be concluded that in any genomic study it should be taken into account that the genetic effects of genes related to the lactation performance are not constant during the lactation period.

Systems Biology–Derived Genetic Signatures of Mastitis in Dairy Cattle: A New Avenue for Drug Repurposing

Simple Summary

Therapeutic success of bovine mastitis depends mainly on accurately diagnosing the type of pathogen involved. Despite the development prospects for bovine mastitis diagnosis, including new biomarker discovery to target specific pathogens with high sensitivity and specificity, treatment studies have shown controversial results, and the most efficient, safe, and economical treatments for mastitis are still topics of scientific debate. The goal of this research is the integration of different levels of systems biology data to predict candidate drugs for the control and management of E. coli mastitis. We propose that the novel drugs could be used by pharmaceutical scientists or veterinarians to find commercially efficacious medicines.

Abstract

Mastitis, a disease with high incidence worldwide, is the most prevalent and costly disease in the dairy industry. Gram-negative bacteria such as Escherichia coli (E. coli) are assumed to be among the leading agents causing acute severe infection with clinical signs. E. Coli, environmental mastitis pathogens, are the primary etiological agents of bovine mastitis in well-managed dairy farms. Response to E. Coli infection has a complex pattern affected by genetic and environmental parameters. On the other hand, the efficacy of antibiotics and/or anti-inflammatory treatment in E. coli mastitis is still a topic of scientific debate, and studies on the treatment of clinical cases show conflicting results. Unraveling the bio-signature of mastitis in dairy cattle can open new avenues for drug repurposing. In the current research, a novel, semi-supervised heterogeneous label propagation algorithm named Heter-LP, which applies both local and global network features for data integration, was used to potentially identify novel therapeutic avenues for the treatment of E. coli mastitis. Online data repositories relevant to known diseases, drugs, and gene targets, along with other specialized biological information for E. coli mastitis, including critical genes with robust bio-signatures, drugs, and related disorders, were used as input data for analysis with the Heter-LP algorithm. Our research identified novel drugs such as Glibenclamide, Ipratropium, Salbutamol, and Carbidopa as possible therapeutics that could be used against E. coli mastitis. Predicted relationships can be used by pharmaceutical scientists or veterinarians to find commercially efficacious medicines or a combination of two or more active compounds to treat this infectious disease.

The pattern of linkage disequilibrium in Dual-Purpose Belgian Blue cattle

Quantifying the level of linkage disequilibrium (LD), non-random association of alleles at two or more loci, is important to determine the number of markers needed for genomic selection. The aims of this study were to evaluate the extent of LD in Dual-Purpose Belgian Blue (DPBB) and to compare the level of LD in DPBB with that of Walloon Holstein. Data of 28,427 single nucleotide polymorphisms (SNP), located on 29 Bos taurus autosomes (BTA), of 639 DPBB and 398 Holstein bulls were used. The level of LD between pairwise SNPs separated by up to 10 Mb was evaluated, separately for each breed, using the squared correlation of the alleles at two loci. The analysis of molecular variance showed that the percentage of variation within populations (85.48%) was higher than between populations (14.52%). However, permutation tests showed a significant genetic differentiation between the two studied populations (p < .01). The average LD found between adjacent SNP pairs in DPBB (0.16 (SD = 0.22)) was generally lower than in Holstein (0.23 (SD = 0.27)). The proportion of SNPs in useful LD (r²  > 0.30) within a genomic distance of ≤0.10 Mb between SNPs was 18.58% and 28.23% in DPBB and Holstein bulls, respectively. In both breeds, the effective population size decreased over generations; however, the decline was greater in DPBB than that in Holstein. Based on results, it can be concluded that at least 68,000 SNPs are needed for implementing genomic selection in DPBB cattle with enough accuracy.

Genetic analysis of milk urea concentration and its genetic relationship with selected traits of interest in dairy cows

The aim of this study was to estimate genetic parameters of milk urea concentration (MU) and its genetic correlations with milk production traits, longevity, and functional traits in the first 3 parities in dairy cows. The edited data set consisted in 9,107,349 MU test-day records from the first 3 parities of 560,739 cows in 2,356 herds collected during the years 1994 to 2020. To estimate the genetic parameters of MU, data of 109 randomly selected herds, with a total of 770,016 MU test-day records, were used. Genetic parameters and estimated breeding values were estimated using a multiple-trait (parity) random regression model. Herd-test-day, age-year-season of calving, and days in milk classes (every 5 d as a class) were used as fixed effects, whereas effects of herd-year of calving, permanent environment, and animal were modeled using random regressions and Legendre polynomials of order 2. The average daily heritability and repeatability of MU during days in milk 5 to 365 in the first 3 parities were 0.19, 0.22, 0.20, and 0.48, 0.48, 0.47, respectively. The mean genetic correlation estimated among MU in the first 3 parities ranged from 0.96 to 0.97. The average daily estimated breeding values for MU of the selected bulls (n = 1,900) ranged from -9.09 to 7.37 mg/dL. In the last 10 yr, the genetic trend of MU has gradually increased. The genetic correlation between MU and 11 traits of interest ranged from -0.28 (milk yield) to 0.28 (somatic cell score). The findings of this study can be used as the first step for development of a routine genetic evaluation for MU and its inclusion into the genetic selection program in the Walloon Region of Belgium.

Reproductive and embryological toxicity of lead acetate in male mice and their offspring and mitigation effects of quercetin

Exposure to heavy metals not only impacts on fertility in males, it may also affect the offspring. The aim of the present study was to examine the toxic effects of lead acetate on fertility in male mice and their offspring, and the potential effect of quercetin on mitigating the likely effects. Experimental mice were randomly divided into three groups and administered with (i) distilled water (control); (ii) lead acetate (150 mg/kg BW/day); (iii) lead acetate (150 mg/kg BW/day) with quercetin (75 mg/kg BW/day). Lead acetate administration in male mice adversely affected their fertility through changes in sperm motility, viability, morphology, maturity, membrane integrity, and intracellular reactive oxygen species (P <  0.05). Similar findings were observed in the offspring of the lead-treated male mice. Early embryonic development and implantation rate were also adversely influenced in both the sires and offspring when male mice were treated with lead acetate (P <  0.05). The data demonstrated that down-regulation of Cks2 (CDC28 protein kinase regulatory subunit-2) in sperm had an association with early embryonic development in lead acetate treated group. In conclusion, lead acetate administration adversely impacted on the fertility of the male mice and their male offspring fertility; on the other hand, paternal quercetin co-administration somewhat ameliorated the adverse effects of lead on male mice and their offspring.

Genetic parameters for milk urea and its relationship with milk yield and compositions in Holstein dairy cows

The aim was to estimate genetic parameters for milk urea (MU) concentration and its relationship with milk yield and compositions in Holstein dairy Cows. Edited data were 90,594 test-day records of milk yield and composition collected during 2015 to 2018 on 13,737 lactations obtained from 7,850 Holstein cows in 50 herds. Random regression test-day model was used to estimate genetic parameters. (Co)variance components were estimated with the Bayesian Gibbs sampling method using a single chain of 400,000 iterates. The first 50,000 iterates of each chain were regarded as a burn-in period. Mean (SD) of MU was 23.03 (5.99) and 22.41 (5.74) mg/dl in primiparous and multiparous cows, respectively. Average heritability estimates for daily MU was 0.33 (SD = 0.02) ranged 0.29 to 0.36 and 0.32 (SD = 0.03) ranged 0.27 to 0.34, respectively, for primiparous and multiparous cows. The mean (SD) genetic correlation between MU and milk yield, fat yield, protein yield, lactose yield, fat percentage, protein percentage, lactose percentage, and somatic cell score was, respectively, -0.02 (0.03), -0.02 (0.01), 0.01 (0.04), 0.01 (0.03), 0.00 (0.07), -0.03 (0.04), 0.00 (0.01), -0.11 (0.06) in primiparous cows. The corresponding values in multiparous cows were -0.01 (0.02), -0.01 (0.03), -0.04 (0.04), -0.04 (0.04), 0.04 (0.04), 0.04 (0.07), -0.03 (0.09), 0.06 (0.11), respectively. The results indicate that selection on MU is possible with no effect on milk yield or compositions, however, relationships between MU and other important traits such as longevity, metabolic diseases, and fertility are needed.

Association between age at first calving and lactation performance, lactation curve, calving interval, calf birth weight, and dystocia in Holstein dairy cows

In the present study, records on 115,291 heifers distributed in 113 herds were used to investigate the association between age at the first calving (AFC) and lactation performance, lactation curve, the length of the first calving interval (CI), calf birth weight (CBW), and the incidence of dystocia in Holstein heifers in Iran. Based on the AFC, the heifers were classified into eight classes: AFC of 541 to 690 d, 691 to 720 d, 721 to 750 d, 751 to 780 d, 781 to 810 d, 811 to 840 d, 841 to 900 d, and 901 to 1200 d (AFC1 to AFC8, respectively). Multiple regression mixed models were used to investigate the association between AFC and lactation curve parameters, partial and 305-d lactation performance, 100- and 305-d SCS, and the length of the first calving (CI) interval. The mean (SD) and median AFC across all heifers was 760.2 (74.01) and 750 d, respectively. Of 115,291 heifers included, 28,192 and 7,602 heifers were, respectively, ≤ 720 and > 900 d when calving for the first time. More than 44% of the heifers were at 691 to 750 d (23 to 25 months) of age when calving for the first time. An increased AFC was associated with increased partial and 305-d lactation performance, 100- and 305-d SCS, initial milk yield, milk production at the peak of lactation, upward and downward slopes of the lactation curve. The 305-d fat percentage was associated with AFC; however, there was no association between AFC and 305-d protein percentage. An increased AFC was also associated with decreased milk production persistency, delayed peak time, longer CI, and higher calf birth weight. Compared to heifers calving for the first time between 691 to 780 d (23 to 26 months) of age, both increasing and decreasing AFC were associated with increased risk of dystocia. Controlling AFC is an important management factor in achieving a lower risk of dystocia, higher lactation performance, lower SCS, and shorter length of the calving interval.

Genome-wide association for metabolic clusters in early-lactation Holstein dairy cows

The aim of this study was to detect the genomic region or regions associated with metabolic clusters in early-lactation Holstein cows. This study was carried out in 2 experiments. In experiment I, which was carried out on 105 multiparous Holstein cows, animals were classified through k-means clustering on log-transformed and standardized concentrations of blood glucose, insulin-like growth factor I, free fatty acids, and β-hydroxybutyrate at 14 and 35 d in milk (DIM), into metabolic clusters, either balanced (BAL) or other (OTR). Forty percent of the animals were categorized in the BAL group, and the remainder were categorized as OTR. The cows were genotyped for a total of 777,962 SNP. A genome-wide association study was performed, using a case-control approach through the GEMMA software, accounting for population structure. We found 8 SNP (BTA11, BTA23, and BTAX) associated with the predicted metabolic clusters. In experiment II, carried out on 4,267 second-parity Holstein cows, milk samples collected starting from the first week until 50 DIM were used to determine Fourier-transform mid-infrared (FT-MIR) spectra and subsequently to classify the animals into the same metabolic clusters (BAL vs. OTR). Twenty-eight percent of the animals were categorized in the BAL group, and the remainder were classified in the OTR category. Although daily milk yield was lower in BAL cows, we found no difference in daily fat- and protein-corrected milk yield in cows from the BAL metabolic cluster compared with those in the OTR metabolic cluster. In the next step, a single-step genomic BLUP was used to identify the genomic region(s) associated with the predicted metabolic clusters. The results revealed that prediction of metabolic clusters is a highly polygenic trait regulated by many small-sized effects. The region of 36,258 to 36,295 kb on BTA27 was the highly associated region for the predicted metabolic clusters, with the closest genes to this region (ANK1 and miR-486) being related to hematopoiesis, erythropoiesis, and mammary gland development. The heritability for metabolic clustering was 0.17 (SD 0.03), indicating that the use of FT-MIR spectra in milk to predict metabolic clusters in early-lactation across a large number of cows has satisfactory potential to be included in genetic selection programs for modern dairy cows.

29 Time-lapse analysis of bovine embryos derived after invitro fertilization from vitrified and fresh oocytes

Oocyte vitrification enables the long-term conservation of female genetic resources. However, obtaining viable bovine embryos from vitrified oocytes has proven to be difficult. Embryo development is a dynamic process, and critical stages can go unnoticed with the use of traditional morphologic assessments. Therefore, the aim was to evaluate morphokinetic parameters in embryos derived from fresh versus vitrified oocytes. After 22h of IVM, oocytes were divided into (1) oocytes surrounded by multiple layers of cumulus cells (COCs; n=275) and (2) oocytes partially denuded, leaving only corona radiata (CR; n=178). Then, two-thirds of the CR oocytes were subjected to one of two vitrification protocols as follows: high concentration of cryoprotectants (CR-H; n=171; Ortiz-Escribano et al. 2016 Theriogenology 86, 635-641) and low concentration of cryoprotectants (CR-L; n=163; Ishii et al. 2018 J. Reprod. Develop. 6). After warming, vitrified oocytes were incubated ~2h in maturation medium. Invitro fertilization and culture were performed simultaneously for all groups. Four to eight zygotes from each group were assigned randomly to time lapse (Primo Vision; Vitrolife), and group culture was performed in leftovers as a control. Differences between groups in survival (intact zygotes after IVF), cleavage, and blastocyst rates were evaluated by logistic regression. Morphokinetic data (time to reach first (1-2 cells), second (3-4 cells), third (5-8), fourth (9-16 cells), fifth (&gt;16 cells), cleavage, and blastocyst stage, and time in lag phase) were investigated. Survival rates in COCs (98%) and CR (96%) groups were not different; CR-H (87%) showed lower survival than COCs but similar survival to that of CR. Group CR-L (82%) had a lower survival rate than the rest of the groups (P&lt;0.05). Higher cleavage rate (83%) was found in COCs compared with the rest of the groups. The CR and CR-H groups showed similar cleavage rate (65 and 55%, respectively), whereas CR-L had a lower cleavage rate (42%) than other groups (P&lt;0.05). As expected, both vitrified groups showed lower blastocyst rates (4% for CR-H and 10% for CR-L) than fresh COCs (44%; P&lt;0.05). Morphokinetics measures were affected by the treatments: time to reach first cleavage was similar for COCs (35.3h), CR (38.4h), and CR-L (34.8h), whereas CR-H was slower (42.4h). However, the fourth division was reached earlier by CR-H (51.7h), which was significantly faster than for CR-L (88.8 h; P&lt;0.05) but similar for COCs (71.3h) and CR (60.7h). In conclusion, more morphokinetic data are needed to compare different vitrification methods and confirm whether time-lapse analysis can be used to predict blastocyst outcome after oocyte vitrification.

Association between gestation length and lactation performance, lactation curve, calf birth weight and dystocia in Holstein dairy cows in Iran

In this study, 252,798 lactations on 108,077 cows in 433 herds were used to determine the association between gestation length (GL) and lactation performance, lactation curve, calf birth weight and dystocia in Holstein dairy cows in Iran. The GL averaged 278.1 ± 5.41 d, was categorized as short (SGL; at 1 SD below the population mean), average (AGL; the population mean ± 1 SD), or long (LGL; at least 1 SD above the population mean). Factors including parity, calf gender and calving season were associated with the GL. Primiparous cows with SGL had less lactation performance than those with longer GL; however, there was no difference between those with AGL and LGL. Multiparous cows with longer GL always had more partial and 305-d lactation performance. Primiparous cows with SGL produced less milk at the beginning of lactation and at the peak than those with AGL or LGL; inverse trends were found for lactation persistency, upward and downward slopes of the lactation curve. Within multiparous, a direct relationship was found between GL and the peak yield, where cows with longer GL always produced more milk at the peak. Multiparous cows with SGL produced less milk at the beginning of lactation, reached their peaks later, had higher lactation persistency and showed a lower upward slope of lactation curve than those with AGL or LGL. There was a direct relationship between GL and calf birth weight, where cows with longer GL had calves with more weight at the birth. Within primiparous, cows with SGL had the lowest and those with LGL had the highest rate of dystocia. However, multiparous cows with AGL had a lower rate of dystocia than those with SGL or LGL. Although there was a direct relationship between GL and lactation performance, intermediate GL seems optimal when considering dystocia.

Genome-wide association for milk production and lactation curve parameters in Holstein dairy cows

The aim of this study was to identify genomic regions associated with 305‐day milk yield and lactation curve parameters on primiparous (n = 9,910) and multiparous (n = 11,158) Holstein cows. The SNP solutions were estimated using a weighted single‐step genomic BLUP approach and imputed high‐density panel (777k) genotypes. The proportion of genetic variance explained by windows of 50 consecutive SNP (with an average of 165 Kb) was calculated, and regions that accounted for more than 0.50% of the variance were used to search for candidate genes. Estimated heritabilities were 0.37, 0.34, 0.17, 0.12, 0.30 and 0.19, respectively, for 305‐day milk yield, peak yield, peak time, ramp, scale and decay for primiparous cows. Genetic correlations of 305‐day milk yield with peak yield, peak time, ramp, scale and decay in primiparous cows were 0.99, 0.63, 0.20, 0.97 and −0.52, respectively. The results identified three windows on BTA14 associated with 305‐day milk yield and the parameters of lactation curve in primi‐ and multiparous cows. Previously proposed candidate genes for milk yield supported by this work include GRINA, CYHR1, FOXH1, TONSL, PPP1R16A, ARHGAP39, MAF1, OPLAH and MROH1, whereas newly identified candidate genes are MIR2308, ZNF7, ZNF34, SLURP1, MAFA and KIFC2 (BTA14). The protein lipidation biological process term, which plays a key role in controlling protein localization and function, was identified as the most important term enriched by the identified genes.

Genetic parameters for milk yield and lactation persistency in the three first parities of Iranian Holstein cows

Background: Lactation persistency influences cow health and reproduction and has an impact on the feed costs of dairy farms. Objective: To estimate (co)variance components and genetic parameters of 100- and 305-d milk yield, and lactation persistency in Holstein cows in Iran. Methods: Records collected from January 2000 to December 2012 by the Animal Breeding Center of Iran (Karaj, Iran) were used. The following four measures of lactation persistency were used: P21: Ratio of milk yield in the second 100-d in milk (DIM) divided by that of the first 100-d. P31: Ratios of milk yield in the third100-d divided by that of the first 100-d. PW: The persistency measure derived from the incomplete gamma function. PJ: The difference between milk yield in day 60th and 280th of lactation. Results: The estimated heritability of lactation persistency for the three first parities (first, second, and third lactation) ranged from 0.01 to 0.06, 0.02 to 0.10, and 0.01 to 0.12, respectively. Genetic correlations among lactation persistency measures for the three first parities ranged from 0.77 to 0.98, 0.65 to 0.98, and 0.58 to 0.98, respectively; while corresponding values for genetic correlations among lactation persistency with 305-d milk production ranged from 0.18 to 0.63, 0.32 to 0.75, and 0.41 to 0.71, respectively. The estimated repeatability for lactation persistency measures ranged from 0.06 to 0.20. Conclusion: The moderate positive genetic correlation between lactation persistency and 305-d milk yield indicates that selection for increasing milk yield can slightly improve lactation persistency.Key words: dairy cattle, heritability, lactation curve, milk yield, persistency, repeatability. ResumenAntecedentes: La persistencia de la lactancia tiene una gran influencia en la salud, la reproducción y los costos de alimentación de las granjas lecheras. Objetivo: Estimar los componentes de (co)varianza y los parámetros genéticos de la producción de leche a 100 y 305 d, asi como la persistencia de la lactancia en vacas Holstein en Irán. Métodos: Se utilizaron registros recopilados entre enero de 2000 y diciembre de 2012 por el Centro de cría de animales de Irán (Karaj, Irán). Se utilizaron las siguientes cuatro medidas de persistencia de la lactancia: P21: Proporción de producción de leche en los segundos 100-d en leche (DIM) dividida por la de los primeros 100-d. P31: Proporcion de producción de leche en los terceros 100-d dividido por el de los primeros 100-d. PW: medida de persistencia derivada de la función gamma incompleta. PJ: diferencia entre el rendimiento de leche en el 60 y el 280 día de lactancia. Resultados: La heredabilidad estimada de la persistencia de la lactancia para los tres primeros partos (primera, segunda y tercera lactancia) varió de 0,01 a 0,06; 0,02 a 0,10; y 0,01 a 0,12, respectivamente. Las correlaciones genéticas entre las medidas de persistencia de lactancia para los tres primeros partos variaron de 0,77 a 0,98; 0,65 a 0,98; y 0,58 a 0,98, respectivamente; mientras que los valores correspondientes para las correlaciones genéticas entre la persistencia de la lactancia con la producción de leche a 305 d variaron de 0,18 a 0,63; 0,32 a 0,75; y 0,41 a 0,71, respectivamente. La repetibilidad estimada para las medidas de persistencia de la lactancia varió de 0,06 a 0,20. Conclusión: La correlación genética positiva moderada entre la persistencia de la lactancia y la producción de leche a 305-d indica que la selección para aumentar la producción de leche puede mejorar ligeramente la persistencia de la lactancia.Palabras clave: curva de lactancia, ganado lechero, heredabilidad, persistencia, producción de leche, repetibilidad. ResumoAntecedentes: A persistência da lactação tem grande influência nos custos de saúde, reprodução e alimentação em fazendas leiteiras. Objetivo: Estimar os componentes da variância (co)variância e os parâmetros genéticos da produção de leite de 100 e 305 d e a persistência da lactação em vacas Holandesas no Irã. Métodos: Os dados utilizados foram registros coletados de janeiro de 2000 a dezembro de 2012 pelo Centro de Criação de Animais do Irã (Karaj, Irã). As seguintes quatro medidas de persistência de lactação foram utilizadas: P21: Razão da produção de leite no segundo 100-d em leite (DIM) dividido pelo primeiro 100-d. P31: Razões da produção de leite na terceira 100d dividida pela da primeira 100-d. PW: A medida de persistência derivada da função gama incompleta. PJ: A diferença entre a produção de leite no 60º e 280º dia de lactação. Resultados: A hereditariedade estimada da persistência da lactação para as três primeiras paridades (primeira, segunda e terceira lactação) variou de 0,01 a 0,06; 0,02 a 0,10; e 0,01 a 0,12, respectivamente. As correlações genéticas entre as medidas de persistência da lactação para as três primeiras paridades variaram de 0,77 a 0,98; 0,65 a 0,98; e 0,58 a 0,98, respectivamente; enquanto os valores correspondentes para correlações genéticas entre a persistência da lactação com produção de leite de 305d variaram de 0,18 a 0,63; 0,32 a 0,75; e 0,41 a 0,71, respectivamente. A repetibilidade estimada para medidas de persistência de lactação variou de 0,06 a 0,20. Conclusão: A correlação genética positiva moderada entre a persistência da lactação e a produção de leite de 305d indicou que a seleção para aumentar a produção de leite melhoraria ligeiramente a persistência da lactação.Palavras-chave: curva de lactação, gado de leite, hereditariedade, persistência, produção de leite, repetibilidade.

Variant <i>GDF9</i> mRNA is likely not the main cause of larger litter size in Iranian Lori-Bakhtyari, Shal, Ghezel, and Afshari sheep breeds

Abstract. This study was carried out to screen the GDF9 gene and evaluate the polymorphism effect on litter size of four Iranian sheep breeds using the PCR-RFLP and PCR-SSCP methods. First, sequencing of the GDF9 gene in 16 twin-birth, 4 triplet-birth, and 2 infertile ewes showed that, in addition to G2, G3, G4, G5, and G6 mutations that have been previously reported in other breeds, a new G0 mutation, called C25T, exists in the GDF9 sequence of 1 out of 22 ewes and causes L9F substitution in the signal peptide region. None of the triplet-birth or infertile ewes carried G1, G4, G7, FecGE, G8, or FecGT mutations. In the second experiment, a large dataset was used: 605 individuals including 496 ewes (145 Afshari, 54 Shal, 126 Ghezel, and 171 Lori-Bakhtyari sheep), and 109 rams (26 Afshari, 23 Shal, 10 Ghezel, and 50 Lori-Bakhtyari sheep. There were no sheep carrying the G7, G8, or Thoka mutations. Among all 109 rams that were used in this study, none of them were homozygous for the G1 mutation. Moreover, abundance of heterozygote rams (G1/G+) varied from 0.0 (Afshari) to 28.6 % (Lori-Bakhtyari and Ghezel). The highest and the lowest frequencies of the G4 mutation were 30.6 and 3.0 % in Shal and Afshari breeds, respectively. Moreover, G4 abundance varied from 0.0 to 42.3 %, from 3.0 to 26.9, and from 3.0 to 30.6 % in rams, ewes, and overall, respectively. There was a significant difference in the abundance of G1 and G4 mutations between breeds. However, neither the G1 nor the G4 mutation was associated with litter size in Afshari, Ghezel, Lori-Bakhtyari, or Shal sheep breeds. In conclusion, the results of this study showed that GDF9 G1 and G4 mutations are not the reason for higher litter size in Iranian sheep. Moreover, the GDF9 G0 and G6 mutations do not cause triplet births or infertility in Iranian ewes. Therefore, it is unlikely that variant GDF9 mRNA induces larger litter size or infertility in Iranian ewes.

Effect of thymol and carvacrol on nutrient digestibility in rams fed high or low concentrate diets

Published data on the effects of essential oils (EO) on in vivo nutrient digestibility in sheep are contradictory. In 2 experiments, the effect of thymol and carvacrol on nutrient digestibility was studied in sheep fed with high (70%) or low (52%) concentrate diets, using incomplete Latin Square designs. The essential oils were mixed with the concentrate portion of the diet at the rate of 0.0, 0.3, or 0.6 g per kg dry matter (DM) diet. Supplementation of thymol had no significant effect on digestibility of dry matter (DM), organic matter (OM), crude protein (CP) and acid detergent fiber (ADF). The main effect of thymol on neutral detergent fiber (NDF) and ether extract (EE) digestibility and on nitrogen balance (NB) was significant (P<0.05), but within each level of dietary concentrate no significant differences were observed for these measurements. Overall, ruminal ammonia concentration was higher (P<0.05) in both HCD and LCD lambs receiving 0.3 mg thymol per kg diet. Supplementation of carvacrol had no significant effect on nutrient digestibility. The main effect of carvacrol on ruminal ammonia levels and NB was significant, but within each level of dietary concentrate no significant differences were observed in ammonia levels and NB. Inclusion of 0.3 g/kg diet DM of carvacrol or thyme was more effective than 0.6 g/kg diet DM in terms of NB but neither dose affected nutrient digestibility. Future research should determine the long-term effects of essential oils on digestibility and performance in sheep, before recommendation can be made for their use under practical husbandry conditions.

The relationship between growth hormone polymorphism and growth hormone receptor genes with milk yield and reproductive performance in Holstein dairy cows

The aim of this study was to investigate the potential association between growth hormone GH/AluI and growth hormone receptor GHR/AluI polymorphisms with milk yield and reproductive performances in Holstein dairy cows in Iran. Blood samples of 150 Holstein cows were collected and their genomic DNA was extracted using Gene-Fanavaran DNA extracting kit. Fragments of the 428 bp of exon 5 growth hormone (GH) gene and the 342 bp of exon 10 growth hormone receptor (GHR) gene were amplified using the polymerase chain reaction (PCR) method. PCR products were digested by the AluI restriction enzyme and electrophoresed on 3% agarose gel. Continuous and categorical data were analyzed using linear mixed models through Proc MIXED and logistic regression models through Proc GENMOD of SAS software, respectively. The results showed no relationship between the examined traits and GH/AluI or GHR/AluI genes. A significant relationship was found between GH/AluI polymorphism and dystocia, but the presence of the GH-L allele reduced the incidence of dystocia. The results suggest that the GH-LL genotype reduces dystocia probably by affecting the release of growth hormone; nevertheless, further studies will be needed to examine the relationship between dystocia and GH genotypes.

Prevalence, risk factors and consequent effect of dystocia in holstein dairy cows in iran

The objective of this research was to determine the prevalence, risk factors and consequent effect of dystocia on lactation performance in Holstein dairy cows in Iran. The data set consisted of 55,577 calving records on 30,879 Holstein cows in 30 dairy herds for the period March 2000 to April 2009. Factors affecting dystocia were analyzed using multivariable logistic regression models through the maximum likelihood method in the GENMOD procedure. The effect of dystocia on lactation performance and factors affecting calf birth weight were analyzed using mixed linear model in the MIXED procedure. The average incidence of dystocia was 10.8% and the mean (SD) calf birth weight was 42.13 (5.42) kg. Primiparous cows had calves with lower body weight and were more likely to require assistance at parturition (p<0.05). Female calves had lower body weight, and had a lower odds ratio for dystocia than male calves (p<0.05). Twins had lower birth weight, and had a higher odds ratio for dystocia than singletons (p<0.05). Cows which gave birth to a calf with higher weight at birth experienced more calving difficulty (OR (95% CI) = 1.1(1.08–1.11). Total 305-d milk, fat and protein yield was 135 (23), 3.16 (0.80) and 6.52 (1.01) kg less, in cows that experienced dystocia at calving compared with those that did not (p<0.05).

Association between dry period length and lactation performance, lactation curve, calf birth weight, and dystocia in Holstein dairy cows in Iran

In this study, 65,971 lactations on 41,842 cows in 64 herds were used to determine the association between dry period length (DPL) and lactation performance, lactation curve, calf birth weight, and the incidence of calving difficulty during the subsequent parity in Holstein dairy cows in Iran. The length of the dry period was classified into 7 categories: 0 to 35d, 36 to 50d, 51 to 60d, 61 to 70d, 71 to 85d, 86 to 110d, and 111 to 160d. Cows with the standard DPL (51 to 60d) produced more 305-d milk, fat, and protein over the next lactation compared with those with shorter dry periods. Shorter dry periods (0 to 35d and 36 to 50d) were associated with lower initial milk yield, steeper inclining and declining slopes of the lactation curve, and higher milk persistency compared with dry period length of 51 to 60d. Peak lactation was achieved later in cows with 0- to 35-d and 36- to 50-d dry period length than in those with dry period length of 51 to 60d. We also observed a relationship between DPL and calf birth weight: smaller calf birth weight was recorded with a dry period of 51 to 60d compared with longer dry periods. The incidence of calving difficulty did not differ in cows with 51- to 60-d dry period compared with cows with 0- to 35-d and 36- to 50-d dry periods. In conclusion, the results of this study did not support previous findings that suggested a shorter dry period could be beneficial to dairy production.

Growth performance and intestinal morphology in broiler chickens produced from hyperthyroid breeder hens

An association between induced maternal hyperthyroidism and a decreased incidence of cold-induced ascites in broiler chickens has been reported recently. There are also reports suggesting that thyroid hormones have an effect on intestine, a high oxygen-demanding organ. The present study aimed to determine whether the ascites-attenuating effect of maternal hyperthyroidism is associated with morphological changes in intestine and with probable adverse effects on growth performance in progeny chicks. Eighty-eight broiler breeder hens were allotted to control or hyperthyroid [HYPER; thyroxine-treated] groups, and artificially inseminated. Hatching eggs (n = 924) were incubated and day-old male chicks (n = 288) were reared for 42 days under standard or low ambient temperature. Plasma thyroxine was higher in the HYPER hens and their embryos at internal pipping. Maternal hyperthyroidism did not adversely affect the feed : gain ratio and carcass weight, whereas cold stress impaired them. A higher relative weight was found at 42 days of age for all intestinal regions at low ambient temperature. The duodenal and jejunal crypt depths (CD) were lower in HYPER group at 7 days of age. Cold exposure decreased the duodenal and jejunal villus height and CD, and increased the ileal goblet cell number at 21 days. On Day 42, higher values were recorded for CD, goblet cell number, and epithelial thickness of different intestinal regions in cold-exposed birds. In conclusion, growth performance was not adversely influenced by maternal hyperthyroidism and its minimal early effect on intestinal morphology does not appear to be the underlying mechanism for decreased incidence of ascites in broilers.

Seminal characteristics, sperm fatty acids, and blood biochemical attributes in breeder roosters orally administered with sage (Salvia officinalis) extract

Seminal characteristics and blood biochemical attributes were studied in breeder roosters orally administered with sage extract (SG), an herbal extract well known to have potent antioxidant activities. Sixty roosters (34 weeks old) were randomly allotted to five treatment groups to receive no SG, or orally administered with 110, 210, 320, or 420 mg SG/kg liveweight for 8 weeks. Semen samples were evaluated weekly. Blood samples were taken fortnightly and a total of 21 biochemical indices were measured to unmask the effects of SG (especially the adverse ones) on the clinical profile. Excluding the sperm concentration and seminal content of thiobarbituric acid reactive substances (sperm membrane lipid peroxidation index), other seminal traits exhibited one of the linear, quadratic, or cubic responses to the various levels of SG. The most improvements in total live sperm number and sperm membrane integrity (as determined by the hypoosmotic swelling test) were observed in birds receiving 210 and 320 mg SG/kg liveweight, respectively. Serum testosterone level was generally higher (cubically, P = 0.015), but serum copper was lower (linearly, P = 0.014) in SG-administered birds. Birds receiving 320 and 420 mg SG showed a decreased content of C18 : 2(n-6) in sperm plasma membrane. Other biochemical attributes or sperm fatty acids were not affected. It seems that most improvement in the seminal characteristics could be achieved 5–6 weeks following the administration of 210 and 320 mg SG/kg liveweight without any apparent adverse effect on the blood biochemical indices. The improvements, however, could not be attributed to the antioxidative effect of SG. Although it is hypothesised that an increased serum testosterone might have been involved, the underlying mechanism(s) remain(s) to be clarified.

Effect of twinning and stillbirth on the shape of lactation curve in Holstein dairy cows of Iran

Abstract. The aims of this study were to estimate the effects of twinning and stillbirth on the lactation curve traits in Holstein cows in Iran. Data from March 2000 to April 2009 comprising of 862 109 test-day milk records corresponding to 115 805 lactations of 58 756 cows in 27 herds were used. The lowest peak and total lactation yield but the highest days in milk (DIM) until peak yield, persistency and cumulative milk yield from calving up to DIM at peak production were found during the first lactation (P<0.05). Consequential effect of stillbirth and twinning on lactation curve traits, except for the factors associated with the downward slopes of the curve, were significant (P<0.05). Stillbirth affected the 100-d, 200-d and 305-d milk yields. Cows with stillborn calves had longer days to peak yield and higher persistency, but lower peak yield, than those with live calves (P<0.05). Number of days to peak yield, the persistency and total lactation yield from calving up to peak of lactation were higher for twin birth than for single birth calvings (P<0.05). The estimated correlation between peak yield and lactation yield was high (68%) indicating that peak yield is very important in determining the lactation yield.

Genetic relationship of conformation traits with average somatic cell score at 150 and 305 days in milk in Holstein cows of Iran

Genetic, environmental, and phenotypic correlations among average somatic cell score (SCS) at different stages of lactation and conformation traits were estimated. Data consisted of the lactational average of SCS at 150 (SCS(150)) and 305 (SCS(305)) d in milk and 19 conformation traits recorded on 57,154 primiparous Holstein cows, that calved from 1996 to 2009 in 119 herds in Iran. Variance components were estimated using the restricted maximum likelihood procedure based on multiple-trait animal models. Udder depth (-0.32), fore udder attachment (-0.22), and udder width (0.34) showed moderate genetic correlation with SCS(150). Heart girth (0.17), body depth (0.14), chest width (0.26), and angularity (0.19), showed modest genetic correlation with SCS(150). The estimated heritabilities for SCS(150) and SCS(305) were 0.06 and 0.08, respectively. The heritability of the conformation traits ranged from 0.09 to 0.29. Genetic and environmental correlations between SCS(150) and SCS(305) were very high (means ± SE; 0.99±0.01 and 0.89±0.01, respectively), which indicates that recording SCS over a shorter period of lactation is an alternative approach for involving many herds in SCS data collection. The low heritability of SCS indicated that indirect selection for some of udder and body traits might be helpful to reduce the SCS. Additionally, selection for udder traits may help reduce SCS in developing countries where SCS data are sparsely recorded.

Trends in the reproductive performance of Holstein dairy cows in Iran

The study was undertaken to determine the trends in the reproductive performance of Holstein dairy cows in Iran during 1994 to 2008. Reproductive performance data for 528,034 lactations of 246,132 cows in 1,822 Holstein dairy herds of Iran were used. The potential effect of calving season, herd, parity, calving year, as well as herd size and 305-day milk production on reproductive performance traits was investigated using multiple regression models. The least squares means of age at first calving decreased by 3.1 (± 0.06) days per year from 806.5 (± 96.3) days in 1994 to 788 (± 89.9) days in 2008. The least squares means of calving interval increased 1.02 (± 0.03) days per year from 394.1 (± 65) days in 1994 to 413.2 (± 81) days in 2008. Greater 305-day milk production was associated with an average increase of 6.55 (± 0.08) days in calving interval per 1,000-kg increase in milk yield. Larger herd size was associated with an average decrease of 0.22 (± 0.02) days in calving interval per 50 cows per herd. The mean number of days dry was 88.6 (± 51.3) days and increased by 0.82 (± 0.02) days per year. In conclusion, reproductive performance in Holstein dairy herds has generally decreased, whereas herd size and milk production have increased over time. Producers may make significant improvements in herd reproduction by reviewing management strategies including the sire selection, reproductive management, inseminator training and techniques, and improved estrous detection. Moreover, it may be advisable for the fertility traits to be included in the genetic selection indices to reduce the rate of reproductive decline.

Preparations of PAN-based adsorbers for separation of cesium and cobalt from radioactive wastes

Ion-exchange adsorbers are widely used for radioisotope separation, as well as for the removal of hazardous fission products from aqueous waste prior to discharge to the environment. Inorganic exchangers are of particular interest because of their resistance to radiolytic damage and selectivity for specific fission products. Composite inorganic-organic adsorbers represent a group of inorganic ion exchangers modified by using binding organic material, polyacrylonitrile, for preparation of larger size particles with higher granular strength. At the same time, kinetics of ion exchange and sorption capacity of such composite adsorbers are not influenced by the binding polymer. The contents of active component in composite adsorber were varied over a very broad range of 5-95% of the dry weight of the composite adsorber, and tested for separation and concentration of various stimulated wastes. Three different inorganic sorbents, granular hexacyanoferrate-based ion exchanger, were developed for the removal of Cs and Co ions from waste solutions containing different complexing agents as detergents. Radiation and thermal stability studies show that these adsorbents can be used for medium-active waste treatment.

The application and properties of composite sorbents of inorganic ion exchangers and polyacrylonitrile binding matrix

A description is given of the preparation and properties of potassium hexacyanocobalt (II) ferrate (II) (KCFC) and the composite, potassium hexacyanocobalt (II) ferrate (II)-polyacrylonitrile (KCFC-PAN). The materials were dried at high temperatures and characterized by chemical analysis, scanning electron microscope, X-ray diffraction, inductively coupled plasma and infrared. The ion exchange of alkaline earth metals and molybdenum on a nonstoichiometric compound K(2)[CoFe(CN)(6)] and its PAN based absorber was examined by batch methods. The adsorption of molybdenum from aqueous solutions on KCFC-PAN was investigated and optimized as a function of equilibration time and pH. The materials which were dried at optimum high temperature of 110 degrees C were found to be stable in water, dilute acids, alkaline solutions and relatively high temperature. The distribution coefficient values K(d) for alkaline earth metals, followed the same trend of increase for both sets of absorbers studied, i.e. Ba(2+)>Sr(2+)>Ca(2+)>Mg(2+), which closely resembles to the order of the size of the hydrated cations. However, the K(d) values show a significant increase for PAN based absorbers in comparison to KCFC absorbers.