Low Estimated Breeding Values Research Articles

Reducing fecal egg count through selective breeding alters dorper lamb response to Haemonchus contortus in an artificial challenge trial

Infection by gastrointestinal nematodes (GIN), particularly Haemonchus contortus, can be detrimental to sheep health and performance. Genetic susceptibility to GIN varies between breeds, with those lacking high levels of natural resistance often requiring frequent anthelmintic treatment when facing parasitic challenge. Genetic technology can serve as a tool to decrease GIN susceptibility via selection for sheep with reduced fecal egg count (FEC) estimated breeding values (EBVs). However, the physiological changes that result from implementation of this strategy are not well described. Additionally, there is a need for comparison of animals from recent selective breeding against breeds with inherent GIN resistance. In this study we administered a challenge of H. contortus to Dorper x White Dorper (DWD; n = 92) lambs that have been genetically selected for either low (DWD-) or high (DWD+) FEC EBVs and Barbados Blackbelly x Mouflon (BBM; n = 19) lambs from a genetically resistant breed backgrounds. Lamb FEC, packed-cell volume (PCV) and serum IgG were measured at intermittent levels over 5 weeks. At day 21 and day 35, the selectively bred DWD- had a lower mean FEC compared to DWD+, but were higher than BBM. Reductions in both PCV and serum IgG from initial day 0 levels were observed in DWD lambs, but not in BBM. Furthermore, from a subset of lambs (n = 24) harvested at day 21, DWD- only tended (p = 0.056) to have lower mean worm counts than DWD+, with BBM having the lowest mean worm count. Differentially expressed genes (DEGs) identified via RNA-sequencing of abomasal tissue at day 21 indicate a more pronounced Th2 immune response and more rapid worm expulsion occurred in iBBM than iDWD- and iDWD+ lambs. However, gene expression in DWD- suggests an association between reduced FEC EBV and gastric acid secretion and the ability to limit worm fecundity. Ultimately, selection of Dorper sheep for low FEC EBV can reduce susceptibility to GIN, but it will likely require multiple generations with this trait as a breeding priority before presenting a similar resistance level to Caribbean breeds.

Genetic factors underlying host resistance to Rhipicephalus microplus tick infestation in Braford cattle: a systems biology perspective.

Approximately 80% of the world's cattle are raised in regions with a high risk of tick-borne diseases, resulting in significant economic losses due to parasitism by Rhipicephalus (Boophilus) microplus. However, the lack of a systemic biology approach hampers a comprehensive understanding of tick-host interactions that mediate tick resistance phenotypes. Here, we conducted a genome-wide association study (GWAS) of 2933 Braford cattle and found 340 single-nucleotide polymorphisms (SNPs) associated with tick counts. Gene expression analyses were performed on skin samples obtained from previously tick-exposed heifers with extremely high or low estimated breeding values for R. microplus counts. Evaluations were performed both before and after artificial infestation with ticks. Differentially expressed genes were found within 1-Mb windows centered at significant SNPs from GWAS. A total of 330 genes were related to the breakdown of homeostasis that was induced by larval attachment to bovine skin. Enrichment analysis pointed to a key role of proteolysis and signal transduction via JAK/STAT, NFKB and WNT/beta catenin signaling pathways. Integrative analysis on matrixEQTL revealed two cis-eQTLs and four significant SNPs in the genes peptidyl arginine deiminase type IV (PADI4) and LOC11449251. The integration of genomic data from QTL maps and transcriptome analyses has identified a set of twelve key genes that show significant associations with tick loads. These genes could be key candidates to improve the accuracy of genomic predictions for tick resistance in Braford cattle.

66 Effect of copper oxide wire particles on parasitism and growth in Katahdin lambs divergently selected for fecal egg count estimated breeding value

Abstract Internal parasites are one of the greatest threats to small ruminant production across the United States and parasitic resistance to anthelmintics continues to increase. Genetic selection and copper oxide wire particles (COWP) are two tools that could help reduce effects of parasites in small ruminants. The objective of this project was to determine the effects and interactions of COWP and genetic selection based on fecal egg count (FEC) estimated breeding value (EBV) on gastrointestinal nematode (GIN) infection and performance in naturally infected Katahdin lambs. Spring-born Katahdin ram lambs (n = 52) selected for extremely high FEC EBV (HighFEC, PFEC EBV = +100%) or low FEC EBV (LowFEC, PFEC EBV = -81%) were managed on a fescue-based pasture at the Southwest Virginia Agricultural Research and Extension Center (Glade Spring, VA). At weaning (June 29), lambs were dewormed with a three-combination treatment and rested for 21 d. At the start of the project (July 18), a random subset of lambs (HighFEC, n = 11; LowFEC, n = 15) were given a 2 g copper oxide wire particle bolus, while an equal number of remaining lambs were managed as controls without a copper bolus. All lambs were managed as one contemporary group. Fecal egg counts, FAMACHA scores, body weights, and packed cell volume (PCV) were measured bi-weekly for 10 weeks. Statistical analysis was performed using PROC Mixed Procedure of SAS (SAS Institute, Cary, NC) and FEC data were log transformed for normality. There were no effects of COWP treatment on FEC (P = 0.18). However, LowFEC-selected lambs had less FEC than HighFEC-selected lambs (230 vs. 565 eggs/g, respectively; P < 0.01). There was no interaction of COWP treatment and FEC genotype (P = 0.37). Copper oxide wire particle treatment had no effect on lamb body weight (P = 0.21), PCV (P = 0.69), FAMACHA score (P = 0.41), or overall ADG (P = 0.12). Lamb FEC genotype did not affect FAMACHA score or overall ADG (P = 0.10 and P = 0.22, respectively). LowFEC-selected lambs had lighter body weights (27.7 vs. 30.6 kg, respectively) and PCV (29.2% vs. 30.4%, respectively) than the HighFEC-selected lambs (P < 0.05). None of the 52 lambs met the requirement for deworming (FAMACHA ≥ 3) during the study. These results indicate that lamb FEC genotype may have a greater effect on parasitism than COWP treatment when given once during the post-weaning period. Even so, multiple tools should be considered, in addition to selection, for an integrated parasite management plan.

Effect of sire fecal egg count estimated breeding value on parasite resistance traits in Haemonchus contortus infected Katahdin lambs

In the midst of anthelmintic resistance, genetic resistance to gastrointestinal nematodes (GIN) in lambs could reduce anthelmintic requirements; therefore, the fecal egg count (FEC) estimated breeding value (EBV) was developed as a measure of genetic merit for parasite burden. One of the first breeds to effectively implement the FEC EBV was Katahdin. To better understand the relationship between the FEC EBV and Haemonchus contortus (Hc) challenge infection, a divergent mating scheme was established with extremely high (High FEC, n = 5) or extremely low (Low FEC, n = 5) FEC EBV Katahdin rams over 2 years. Purebred lambs sired by these rams were born beginning in mid-March and managed on pasture until approximately 120 days of age. A primary infection was established based on FEC during this period. At this point, lambs (n = 109 in Year 1, n = 114 in Year 2) were removed from pasture, treated with an anthelmintic to reduce FEC and transported to the Animal Sciences Farm at West Virginia University. After a rest period, lambs were given 10,000 (Year 1) or 5000 (Year 2) Hc L3. Body weights, FEC, and packed cell volume were collected weekly. Lambs were harvested (n = 60/year) at 5 weeks post-infection. Abomasum worm counts were determined, and worm length was measured using Image J. Statistical analysis was performed by year using the Mixed Model procedure of SAS (SAS Institute, Cary, NC) with fixed effects of sire EBV type. Change in FEC after the prepatent period was greater in Year 1 High FEC-sired lambs compared to Low FEC-sired lambs (210 vs. 34 eggs/g, respectively; P < 0.05). At harvest in Year 2, a greater proportion of Low FEC- than High FEC-sired lambs had worm counts of zero (P < 0.05). Worm fecundity was lower in lambs sired by Low FEC rams (P < 0.05). Taken together, sire selection for low FEC EBV will lower FEC and worm count and improve GIN resistance in progeny.

The association of immune response and colostral immunoglobulin G in Canadian and US Holstein-Friesian dairy cows

In cattle, maternal immunoglobulins are transferred through colostrum to provide passive immunity to the neonatal calf once they are absorbed into circulation. Cows can be assessed for antibody- and cell-mediated immune responses (AMIR and CMIR, respectively), and through estimated breeding values (EBV) and genomic parent averages (GPA), cows can be classified as having high, average, or low immune response (IR). The objective of this study was to identify associations of colostral IgG concentrations with IR in dairy cows. High IR dairy cows identified by GPA or EBV were hypothesized to produce higher colostral IgG concentrations than cows with average or low IR. Colostrum was collected from Holstein dairy cows from 3 large commercial herds (n = 590) in the United States and 1 research herd at the Ontario Dairy Research Centre (n = 275) in Canada. For the US herds, IR GPA were available through genotyping. For the Canadian herd, IR EBV were available through phenotyping and pedigree information. Colostral IgG concentrations were measured by radial immunodiffusion and analyzed using general linear models in SAS. Based on a prediction equation, cows in US herds with a CMIR GPA of 1 would have colostral IgG concentrations 6.3 g/L higher on average than cows with a CMIR GPA of 0. High CMIR cows produced statistically greater colostral IgG concentrations (least squares mean ± standard error of the mean, 107.5 ± 7.7 g/L) than low CMIR cows (91.4 ± 7.1 g/L), with intermediate values for average CMIR cows (105.1 ± 5.6 g/L). No differences were found among AMIR categories in US cows. The Canadian herd showed a trend for cows with high CMIR EBV (continuous variable) to produce greater colostral IgG. No differences were observed among high, average, and low AMIR EBV classifications in Canadian cows. The findings suggest that selective breeding of Holstein cows to enhance CMIR could contribute to higher-quality colostrum in succeeding generations.

161 Effect of High- and low-Fiber Diets on Growth Performance in Growing-Finishing Pigs Selected for low or High Feed Efficiency

Abstract Understanding the effects of high- and low-fiber diets on the growth performance of pigs with different feed efficiencies will help the livestock industry develop new strategies to reduce the costs of pig production. In this study, 18 Landrace × Large White sows with high and low estimated breeding value on feed conversion ratio (EBV-FCR) were inseminated with semen from Large White with known EBV-FCR to produce 9 litters of low feed efficiency pigs and 9 litters of high feed efficiency pigs. A total of 94 growing pigs with low or high feed efficiency were fed a low-fiber (3% crude fiber) or high-fiber (6% crude fiber) content diet in a 2 × 2 factorial arrangement for 70 days. Pigs fed a high-fiber diet presented higher body weight (BW) on day 70 (P &amp;lt; 0.05). High feed efficiency pigs presented lower average daily feed intake (ADFI) and feed conversion ratio (FCR) than low feed efficiency pigs from day 0 to 70 (P&amp;lt; 0.05). There was an interaction between fiber and feed efficiency group on average daily gain (ADG;P &amp;lt; 0.05) and FCR (P &amp;lt; 0.05) from day 0 to 35. High feed efficiency pigs fed a high-fiber diet presented lower FCR than low feed efficiency pigs fed a low-fiber diet (P&amp;lt; 0.05). Low feed efficiency pigs fed a low-fiber diet showed the lowest ADG (P&amp;lt; 0.05). Regardless of efficiency groups, pigs fed a high-fiber diet presented higher ADG and lower FCR than pigs fed a low-fiber diet from day 42 to 70 (P&amp;lt; 0.05). These results suggest that high feed efficiency pigs can present lower FCR and ADFI without reducing final BW and ADG. Feeding a high-fiber diet can increase ADG and reduce FCR in the later stages of the experiment.

Could serum glucose be a selection criterion in Nile tilapia breeding programs?

Consumers, researchers, and organizations worldwide have expressed increasing concern about the conditions under which farm animals are raised and handled. The development of tools for selecting animals better conditioned to their environment is a strategy to increase animal wellbeing. This study investigated the use of blood glucose as possible selection criteria to achieve better conditioning of fish to the farming environment. We carried out four experiments. The first experiment evaluated serum glucose levels during a 24 h fasting period. Then, heritability estimates and other genetic parameters for blood glucose level (GL) and live weight (LW) were determined (Experiment II). Using the genetic parameters it was possible to identify two distinct groups: animals with a low estimated breeding value (EBV) for GL and those with a high EBV for GL. The expression of genes encoding catalase (CAT) and glucose transport 1 (GLUT1) were assessed and compared between groups (Experiment III). In the fourth experiment, the response of genetic groups to handling stress was assessed. The heritability estimate of GL (0.26) and the positive and significant correlation between GL and LW (0.32) indicated that GL has sufficient genetic variability for use as a selection criterion. Genetic gains in both traits were evidenced by good responses to direct and correlated selection. CAT expression did not differ between groups (Low and High EBV for GL). On the other hand, GLUT1 expression was higher in the high EBV (0.013 AU) than in the low EBV group (0.005 AU). As shown by their good response to handling stress and high performance, fish in the high EBV group were better conditioned to the environment. The relationships between animal performance, the environment, and blood glucose observed in this study indicate that Glucose can be use as a indicator of better use of glucose and better adaptation to stress situations in Nile tilapia.

The effects of birth weight and estimated breeding value for protein deposition on nitrogen efficiency in growing pigs.

The effects of birth weight (BiW; low BiW [LBW] vs. high BiW [HBW]) and estimated breeding value (EBV) for protein deposition (low EBV [LBV] vs. high EBV [HBV]) on N retention, N efficiency, and concentrations of metabolites in plasma and urine related to N efficiency in growing pigs were studied. At an age of 14 wk, 10 LBW–LBV (BiW: 1.07 ± 0.09 [SD] kg; EBV: −2.52 ± 3.97 g/d, compared with an average crossbred pig with a protein deposition of 165 g/d), 10 LBW–HBV (BiW: 1.02 ± 0.13 kg; EBV: 10.47 ± 4.26 g/d), 10 HBW–LBV (BiW: 1.80 ± 0.13 kg; EBV: −2.15 ± 2.28 g/d), and 10 HBW–HBV (BiW: 1.80 ± 0.15 kg; EBV: 11.18 ± 3.68 g/d) male growing pigs were allotted to the experiment. The pigs were individually housed in metabolism cages and were subjected to an N balance study in two sequential periods of 5 d, after an 11-d dietary adaptation period. Pigs were assigned to a protein adequate (A) or protein restricted (R, 70% of A) regime in a change-over design. Pigs were fed 2.8 times the energy requirements for maintenance. Nontargeted metabolomics analyses were performed in urine and blood plasma samples. The N retention (in g/d) was higher in the HBW than in the LBW pigs (P < 0.001). The N retention (in g/[kg metabolic body weight (BW0.75) · d]) and N efficiency, however, were not affected by the BiW of the pigs. The N retention (P = 0.04) and N efficiency (P = 0.04) were higher in HBV than in LVB pigs on the A regime but were not affected by EBV in pigs on the R regime. Restricting the dietary protein supply with 30% decreased the N retention (P < 0.001) but increased the N efficiency (P = 0.003). Nontargeted metabolomics showed that a hexose, free amino acids (AA), and lysophosphatidylcholines were the most important metabolites in plasma for the discrimination between HBV and LBV pigs, whereas metabolites of microbial origin contributed to the discrimination between HBV and LBV pigs in urine. This study shows that BiW does not affect N efficiency in the later life of pigs. Nitrogen efficiency and N retention were higher in HBV than in LBV pigs on the A regime but similar in HBV and LBV pigs on the R regime. In precision feeding concepts aiming to further optimize protein and AA efficiency in pigs, the variation in EBV for protein deposition of pigs should be considered as a factor determining N retention, growth performance, and N efficiency.

159 The effect of sire FEC EBV on parasitism and survivability in grazing Katahdin lambs

Abstract Selection for reduced fecal egg count (FEC) is an important management tool to combat anthelmintic resistance in worm populations. To understand consequences of selection for parasite resistance, a divergent mating scheme was established whereby Katahdin rams with high (HiFEC; n = 4) or low fecal egg count (LoFEC; n = 4) estimated breeding values (EBV) were randomly mated to ewes at the Southwest Virginia AREC. Mid-March born lambs (n = 199) were managed as one group until approximately 120 days of age (Weaning: June 4). Beginning at 45 days of age, BW and FAMACHA scores were collected weekly. Deworming occurred as necessary (FAMACHA ≥ 3) and fecal egg counts were taken biweekly. Statistical analysis was performed using SAS with fixed effects of sire EBV type. Fecal egg count was significantly higher in HiFEC-sired lambs one week prior to weaning (665 vs. 427 eggs/g, P &amp;lt; 0.05) and again at three (3398 vs. 2175 eggs/g, P &amp;lt; 0.01) and five (3596 vs. 2209 eggs/g, P &amp;lt; 0.01) weeks post-weaning. These FEC differences corresponded to differences in lamb weaning and post-weaning FEC EBV (43% vs. -43%, P &amp;lt; 0.05 and 82% vs. -66%, P &amp;lt; 0.01; respectively). Lambs sired by HiFEC-rams required more anthelmintic treatment than LoFEC-selected lambs (76% vs. 61%, P &amp;lt; 0.05). The weaning and post-weaning FEC EBV of HiFEC-sired lambs was greater in lambs that died than those that survived to 120 d (37% vs. 83%, P &amp;lt; 0.01 and 73% vs. 138%, P &amp;lt; 0.01; respectively); however, this phenomenon did not occur in LoFEC-sired lambs. Taken together, these data indicate that LoFEC-sired lambs have reduced parasite burden and are more likely to survive to weaning. Thus, sire selection for low FEC EBV can have indirect effects on lamb survival and general immunity.

Genomic selection for white spot syndrome virus resistance in whiteleg shrimp boosts survival under an experimental challenge test

White spot syndrome virus (WSSV) causes major worldwide losses in shrimp aquaculture. The development of resistant shrimp populations is an attractive option for management of the disease. However, heritability for WSSV resistance is generally low and genetic improvement by conventional selection has been slow. This study was designed to determine the power and accuracy of genomic selection to improve WSSV resistance in Litopenaeus vannamei. Shrimp were experimentally challenged with WSSV and resistance was evaluated as dead or alive (DOA) 23 days after infestation. All shrimp in the challenge test were genotyped for 18,643 single nucleotide polymorphisms. Breeding candidates (G0) were ranked on genomic breeding values for WSSV resistance. Two G1 populations were produced, one from G0 breeders with high and the other with low estimated breeding values. A third population was produced from “random” mating of parent stock. The average survival was 25% in the low, 38% in the random and 51% in the high-genomic breeding value groups. Genomic heritability for DOA (0.41 in G1) was high for this type of trait. The realised genetic gain and high heritability clearly demonstrates large potential for further genetic improvement of WSSV resistance in the evaluated L. vannamei population using genomic selection.

Genomic prediction using pooled data in a single-step genomic best linear unbiased prediction framework.

Economically relevant traits are routinely collected within the commercial segments of the beef industry but are rarely included in genetic evaluations because of unknown pedigrees. Individual relationships could be resurrected with genomics, but this would be costly; therefore, pooling DNA and phenotypic data provide a cost-effective solution. Pedigree, phenotypic, and genomic data were simulated for a beef cattle population consisting of 15 generations. Genotypes mimicked a 50k marker panel (841 quantitative trait loci were located across the genome, approximately once per 3 Mb) and the phenotype was moderately heritable. Individuals from generation 15 were included in pools (observed genotype and phenotype were mean values of a group). Estimated breeding values (EBV) were generated from a single-step genomic best linear unbiased prediction model. The effects of pooling strategy (random and minimizing or uniformly maximizing phenotypic variation within pools), pool size (1, 2, 10, 20, 50, 100, or no data from generation 15), and generational gaps of genotyping on EBV accuracy (correlation of EBV with true breeding values) were quantified. Greatest EBV accuracies of sires and dams were observed when there was no gap between genotyped parents and pooled offspring. The EBV accuracies resulting from pools were usually greater than no data from generation 15 regardless of sire or dam genotyping. Minimizing phenotypic variation increased EBV accuracy by 8% and 9% over random pooling and uniformly maximizing phenotypic variation, respectively. A pool size of 2 was the only scenario that did not significantly decrease EBV accuracy compared with individual data when pools were formed randomly or by uniformly maximizing phenotypic variation (P > 0.05). Pool sizes of 2, 10, 20, or 50 did not generally lead to statistical differences in EBV accuracy than individual data when pools were constructed to minimize phenotypic variation (P > 0.05). Largest numerical increases in EBV accuracy resulting from pooling compared with no data from generation 15 were seen with sires with prior low EBV accuracy (those born in generation 14). Pooling of any size led to larger EBV accuracies of the pools than individual data when minimizing phenotypic variation. Resulting EBV for the pools could be used to inform management decisions of those pools. Pooled genotyping to garner commercial-level phenotypes for genetic evaluations seems plausible although differences exist depending on pool size and pool formation strategy.

Realization of breeding values for milk fatty acids in relation to seasonal variation in organic milk

Prediction of detailed milk fatty acid (FA) composition by mid-infrared spectroscopy (MIRS) offers possibilities for high-throughput indirect measurements of detailed milk compositional parameters through the milk testing system, which can be used to differentiate the FA profile by genetics or specific management or on dairies for milk quality evaluation. Since 2015, milk samples from all Danish dairy cows under milk testing have been recorded using MIRS. The MIRS software from the FOSS Application Note 64 was used to predict contents of 7 FA groups and 4 individual FA. Data generated from the application note have been used to estimate breeding values for sires for percentage of saturated fat (SFA%) in milk. To investigate whether extreme SFA% breeding values of sires were reflected in the detailed milk FA profile from their daughters, milk samples from 194 cows in 7 organic herds were collected and the detailed FA composition measured by gas chromatography. From each cow, milk samples were collected twice to explore specific seasonal effects of pasture-based diets in relation to sires' estimated breeding value (EBV) for MIRS-predicted SFA% (MIRS-SFA%). The results showed a significant difference in SFA% measured from GC (GC-SFA%) in milk from daughters of sires having high SFA% EBV compared with daughters of sires having low SFA% EBV. The EBV group (low or high) also significantly affected most FA except C13:0, C15:0, C17:0, and C18:1 trans-11. Contents of SFA with even chain-lengths were all higher in the high EBV group, whereas C14:1, C16:1, and the other unsaturated C18 FA had a higher content in the low EBV group. All FA were significantly affected by season. The SFA% decreased from indoor spring feeding to summer pasture, as did FA with chain length ≤16 carbons, whereas long-chain FA (>C17) all increased during summer pasture. The results show that use of MIRS-predicted EBV for SFA% will most likely display a correlated response on the detailed FA composition in milk. In the current study, the combined action of feeding and genetics resulted in a 10 percentage-point difference on average when comparing milk SFA% from daughters of high SFA% EBV sires during indoor spring feeding from one farm to milk SFA% from daughters of low SFA% EBV sires during summer from another farm.

Reduced egg shedding in nematode-resistant ewes and projected epidemiological benefits under climate change

Global livestock production is facing serious new challenges, including climate-driven changes in parasite epidemiology, and anthelmintic resistance, driving a need for non-chemotherapeutic methods of parasite control. Selecting for genetic resistance to gastrointestinal nematode infection could reduce reliance on chemical intervention and mitigate increases in parasite challenge due to climate change. Ewes of the composite Exlana breed with a range of estimated breeding values (EBVs) based on nematode faecal egg counts (FECs) were monitored during the peri-parturient period on two farms in southwestern England. Ewes with low EBVs (“resistant”) had lower FECs during the peri-parturient period than those with high EBVs (“susceptible”): the mean FEC was reduced by 23% and 34% on Farms 1 and 2, respectively, while the peak FEC was reduced by 30% and 37%, respectively. Neither EBV nor FEC were correlated with key performance indicators (estimated milk yield, measured indirectly using 8 week lamb weight, and ewe weight loss during lactation). Simulations predict that the reduced FECs of resistant ewes would result in a comparable reduction in infection pressure (arising from eggs shed by ewes) for their lambs. Furthermore, although the reduced FECs observed were modest, simulations predicted that selecting for nematode resistance in ewes could largely offset predicted future climate-driven increases in pasture infectivity arising from eggs contributed by these ewes. Selective breeding of the maternal line for nematode resistance therefore has potential epidemiological benefits by reducing pasture infectivity early in the grazing season and alleviating the need for anthelmintic treatment of ewes during the peri-parturient period, thus reducing selection pressure for anthelmintic resistance. These benefits are magnified under predicted future climate change. The maternal line warrants more attention in selective breeding programmes for nematode resistance.

SNV discovery and functional candidate gene identification for milk composition based on whole genome resequencing of Holstein bulls with extremely high and low breeding values.

We have sequenced the whole genomes of eight proven Holstein bulls from the four half-sib or full-sib families with extremely high and low estimated breeding values (EBV) for milk protein percentage (PP) and fat percentage (FP) using Illumina re-sequencing technology. Consequently, 2.3 billion raw reads were obtained with an average effective depth of 8.1×. After single nucleotide variant (SNV) calling, total 10,961,243 SNVs were identified, and 57,451 of them showed opposite fixed sites between the bulls with high and low EBVs within each family (called as common differential SNVs). Next, we annotated the common differential SNVs based on the bovine reference genome, and observed that 45,188 SNVs (78.70%) were located in the intergenic region of genes and merely 11,871 SNVs (20.67%) located within the protein-coding genes. Of them, 13,099 common differential SNVs that were within or close to protein-coding genes with less than 5 kb were chosen for identification of candidate genes for milk compositions in dairy cattle. By integrated analysis of the 2,657 genes with the GO terms and pathways related to protein and fat metabolism, and the known quantitative trait loci (QTLs) for milk protein and fat traits, we identified 17 promising candidate genes: ALG14, ATP2C1, PLD1, C3H1orf85, SNX7, MTHFD2L, CDKN2D, COL5A3, FDX1L, PIN1, FIG4, EXOC7, LASP1, PGS1, SAO, GPLD1 and MGEA5. Our findings provided an important foundation for further study and a prompt for molecular breeding of dairy cattle.

Determination of genetic associations between indels in 11 candidate genes and milk composition traits in Chinese Holstein population

BackgroundWe have previously identified 11 promising candidate genes for milk composition traits by resequencing the whole genomes of 8 Holstein bulls with extremely high and low estimated breeding values for milk protein and fat percentages (high and low groups), including FCGR2B, CENPE, RETSAT, ACSBG2, NFKB2, TBC1D1, NLK, MAP3K1, SLC30A2, ANGPT1 and UGDH those contained 25 indels between high and low groups. In this study, the purpose was to further examine whether these candidates have significant genetic effects on milk protein and fat traits.ResultsWith PCR product sequencing, 13 indels identified by whole genome resequencing were successfully genotyped. With association analysis in 769 Chinese Holstein cows, we found that the indel in FCGR2B was significantly associated with milk yield, protein yield and protein percentage (P = 0.0041 to 0.0297); five indels in CENPE and one indel in MAP3K1 were markedly relevant to milk yield, fat yield and protein yield (P < 0.0001 to 0.0073); polymorphism in RETSAT was evidently associated with milk yield, fat yield, protein yield and protein percentage (P = 0.0001 to 0.0237); variant in ACSBG2 affected fat yield and protein percentage (P = 0.0088 and 0.0052); one indel in TBC1D1 was with respect to fat percentage and protein percentage (P = 0.0224 and 0.0209). Significant associations were shown between indels in NLK and protein yield and protein percentage (P = 0.0012 to 0.0257); variant in UGDH was related to the milk yield (P = 0.0312). The two exonic indels in FCGR2B and CENPE were predicted to change the mRNA and protein secondary structures, and resulted in the corresponding protein dysfunction.ConclusionOur findings presented here provide the first evidence for the associations of eight functional genes with milk yield and composition traits in dairy cattle.

Genetic background and embryonic temperature affect DNA methylation and expression of myogenin and muscle development in Atlantic salmon (Salmo salar).

The development of ectothermic embryos is strongly affected by incubation temperature, and thermal imprinting of body growth and muscle phenotype has been reported in various teleost fishes. The complex epigenetic regulation of muscle development in vertebrates involves DNA methylation of the myogenin promoter. Body growth is a heritable and highly variable trait among fish populations that allows for local adaptations, but also for selective breeding. Here we studied the epigenetic effects of embryonic temperature and genetic background on body growth, muscle cellularity and myogenin expression in farmed Atlantic salmon (Salmo salar). Eggs from salmon families with either high or low estimated breeding values for body growth, referred to as Fast and Slow genotypes, were incubated at 8°C or 4°C until the embryonic ‘eyed-stage’ followed by rearing at the production temperature of 8°C. Rearing temperature strongly affected the growth rates, and the 8°C fish were about twice as heavy as the 4°C fish in the order Fast8>Slow8>Fast4>Slow4 prior to seawater transfer. Fast8 was the largest fish also at harvest despite strong growth compensation in the low temperature groups. Larval myogenin expression was approximately 4–6 fold higher in the Fast8 group than in the other groups and was associated with relative low DNA methylation levels, but was positively correlated with the expression levels of the DNA methyltransferase genes dnmt1, dnmt3a and dnmt3b. Juvenile Fast8 fish displayed thicker white muscle fibres than Fast4 fish, while Slow 8 and Slow 4 showed no difference in muscle cellularity. The impact of genetic background on the thermal imprinting of body growth and muscle development in Atlantic salmon suggests that epigenetic variation might play a significant role in the local adaptation to fluctuating temperatures over short evolutionary time.

CNV discovery for milk composition traits in dairy cattle using whole genome resequencing

BackgroundCopy number variations (CNVs) are important and widely distributed in the genome. CNV detection opens a new avenue for exploring genes associated with complex traits in humans, animals and plants. Herein, we present a genome-wide assessment of CNVs that are potentially associated with milk composition traits in dairy cattle.ResultsIn this study, CNVs were detected based on whole genome re-sequencing data of eight Holstein bulls from four half- and/or full-sib families, with extremely high and low estimated breeding values (EBVs) of milk protein percentage and fat percentage. The range of coverage depth per individual was 8.2–11.9×. Using CNVnator, we identified a total of 14,821 CNVs, including 5025 duplications and 9796 deletions. Among them, 487 differential CNV regions (CNVRs) comprising ~8.23 Mb of the cattle genome were observed between the high and low groups. Annotation of these differential CNVRs were performed based on the cattle genome reference assembly (UMD3.1) and totally 235 functional genes were found within the CNVRs. By Gene Ontology and KEGG pathway analyses, we found that genes were significantly enriched for specific biological functions related to protein and lipid metabolism, insulin/IGF pathway-protein kinase B signaling cascade, prolactin signaling pathway and AMPK signaling pathways. These genes included INS, IGF2, FOXO3, TH, SCD5, GALNT18, GALNT16, ART3, SNCA and WNT7A, implying their potential association with milk protein and fat traits. In addition, 95 CNVRs were overlapped with 75 known QTLs that are associated with milk protein and fat traits of dairy cattle (Cattle QTLdb).ConclusionsIn conclusion, based on NGS of 8 Holstein bulls with extremely high and low EBVs for milk PP and FP, we identified a total of 14,821 CNVs, 487 differential CNVRs between groups, and 10 genes, which were suggested as promising candidate genes for milk protein and fat traits.

CNV Analysis of Host Responses to Porcine Reproductive and Respiratory Syndrome Virus Infection.

Porcine reproductive and respiratory syndrome (PRRS) is a devastating disease with a significant impact on the swine industry causing major economic losses. The objective of this study is to examine copy number variations (CNVs) associated with the group-specific host responses to PRRS virus infection. We performed a genome-wide CNV analysis using 660 animals genotyped with on the porcine SNP60 BeadChip and discovered 7097 CNVs and 271 CNV regions (CNVRs). For this study, we used two established traits related to host response to the virus, i.e. viral load (VL, area under the curve of log-transformed serum viremia from 0 to 21 days post infection) and weight gain (WG42 from 0 to 42 days post infection). To investigate the effects of CNVs on differential host responses to PRRS, we compared groups of animals with extreme high and low estimated breeding values (EBVs) for both traits using a case-control study design. For VL, we identified 163 CNVRs (84 Mb) from the high group and 159 CNVRs (76 Mb) from the low group. For WG42, we detected 126 (68 Mb) and 156 (79 Mb) CNVRs for high and low groups, respectively. Based on gene annotation within group-specific CNVRs, we performed network analyses and observed some potential candidate genes. Our results revealed these group-specific genes are involved in regulating innate and acquired immune response pathways. Specifically, molecules like interferons and interleukins are closely related to host responses to PRRS virus infection.

Whole-Genome Resequencing of Holstein Bulls for Indel Discovery and Identification of Genes Associated with Milk Composition Traits in Dairy Cattle.

The use of whole-genome resequencing to obtain more information on genetic variation could produce a range of benefits for the dairy cattle industry, especially with regard to increasing milk production and improving milk composition. In this study, we sequenced the genomes of eight Holstein bulls from four half- or full-sib families, with high and low estimated breeding values (EBVs) of milk protein percentage and fat percentage at an average effective depth of 10×, using Illumina sequencing. Over 0.9 million nonredundant short insertions and deletions (indels) [1–49 base pairs (bp)] were obtained. Among them, 3,625 indels that were polymorphic between the high and low groups of bulls were revealed and subjected to further analysis. The vast majority (76.67%) of these indels were novel. Follow-up validation assays confirmed that most (70%) of the randomly selected indels represented true variations. The indels that were polymorphic between the two groups were annotated based on the cattle genome sequence assembly (UMD3.1.69); as a result, nearly 1,137 of them were found to be located within 767 annotated genes, only 5 (0.138%) of which were located in exons. Then, by integrated analysis of the 767 genes with known quantitative trait loci (QTL); significant single-nucleotide polymorphisms (SNPs) previously identified by genome-wide association studies (GWASs) to be associated with bovine milk protein and fat traits; and the well-known pathways involved in protein, fat synthesis, and metabolism, we identified a total of 11 promising candidate genes potentially affecting milk composition traits. These were FCGR2B, CENPE, RETSAT, ACSBG2, NFKB2, TBC1D1, NLK, MAP3K1, SLC30A2, ANGPT1 and UGDH. Our findings provide a basis for further study and reveal key genes for milk composition traits in dairy cattle.

Additive genetic variation in resistance of Nile tilapia (Oreochromis niloticus) to Streptococcus iniae and S. agalactiae capsular type Ib: Is genetic resistance correlated?

Streptococcus iniae and S. agalactiae are both economically important Gram positive bacterial pathogens affecting the globally farmed tilapia (Oreochromis spp.). Historically, control of these bacteria in tilapia culture has included biosecurity, therapeutants and vaccination strategies. Genetic gains in performance traits have been realized for Nile tilapia (Oreochromis niloticus) and interest in breeding for disease resistance has recently received attention. The goal of this study was three fold: 1) to verify previous results demonstrating heritability of S. iniae resistance in Nile tilapia families using increased numbers of fish per family; 2) to determine if realized genetic gain in resistance and/or susceptibility to S. iniae can be obtained following positive assortative mating between parents with high or low estimated breeding values (EBV); and 3) to determine if resistance to S. iniae and S. agalactiae capsular type Ib is genetically correlated. A total of 144 and 130 full sib families were challenged intraperitoneally with S. iniae and intramuscularly with S. agalactiae Ib, respectively. Cumulative mortality at test end was 46% for S. iniae and 68% for S. agalactiae. There was a high additive genetic component found for survival in fish injected with S. iniae (estimated heritability 0.52±0.12) and with S. agalactiae (estimated heritability 0.38±0.11). The S. iniae challenge results confirmed additive genetic variation in resistance of Nile tilapia to S. iniae. We also demonstrated via assortative mating that genetic gain for survival to S. iniae is possible. The genetic correlation between resistance to S. iniae and S. agalactiae Ib was not significantly different from zero (rg=−0.30±0.19). The lack of correlation suggests if resistance to both Streptococcus sp. is desired, selection for both traits must be simultaneous. Selection of fish to improve survival to Streptococcus sp. may require a thorough understanding of the type of pathogen prevalent in the region so that custom genetic material may be tailored to meet the needs of the individual farm and/or region.