Low Breeding Values Research Articles

Improvement of dairy characters in farms and breeding value of the breeding bulls when assessing the quality of offspring

The article presents studies on comparison of the levels of precocity and milk productivity indicators of the daughters of Holstein bulls, who are evaluated for the quality of offspring simultaneously in two breeding plants of the Moscow region. According to the official ratings of breeding values, the bulls were divided into groups of "improving" and "worsening". The ratio of the daughters of the "best" and "worst" breeding bulls was 511:568 and 160:127 heads over the farms. It was determined which values of the differences in the "daughter – mother" indicators were increased in groups of officially evaluated bulls that received ratings of "improvers" and "deteriorators" according to the characteristics in these two breeding plants. The bulls being tested were fixed individually, and according to the number of pairs as the main ones. At the first insemination, the daughters of the "improving" group of bulls had 6.5–8.5 kg increased live weight of, but were relatively older by 0.36–0.6 months. According to the milk yield trait, the total yield of milk fat and protein, highly rated fathers in breeding plants were significantly inferior to competitors with low breeding value in milk yield by 688–1136 kg, according to the difference "mother – daughter" in the total yield of milk fat and protein per lactation – by 43.1–97.3 kg. In one of the farms, the "daughter – mother" differences in milk yield in all bull clusters increased by 599–1275 kg of milk; according to mass fat fraction (MFF) — by 0.02–0.20% and for mass protein fraction (MPF) — by 0.19–0.31%; in another farm, the increase in milk yield was by 43.8–1551 kg of milk and 0.05–0.13% according to the MPF. The daughters of the "worst" fathers in terms of MFF and MPF significantly outperformed the group of daughters of the "best" fathers in terms of "daughter–mother" differences by 35.6 and 61.7 kg of total milk protein and fat output over 305 days of lactation. At the same time, there were no significant differences between daughters and peers. The relativity of the official definition of the values of the breeding value of breeding bulls has been proved. It is proposed, regardless of the "commercial" and previously conducted estimates of breeding bulls, to take into account the indices of pedigrees and types of selection when breeding them. Conclusions are drawn about the significant influence of the factor and selection methods on the values of milk production traits; in order to save growing costs, it is proposed to optimize the live weight and age of insemination of heifers in farms.

New okra genotypes for the management of aphids (Hemiptera: Aphididae) in the diverse ecological landscapes of Central Africa.

Various aphid species, including Aphis gossypii Glover (Hemiptera: Aphididae), are considered important pests of okra and other vegetables. Previous studies under 1 environment in Cameroon, Central Africa, had found multiple okra genotypes with resistance to A. gossypii. However, the stability and yield performance of the "resistant" genotypes across different environments were unknown. Ten previously identified aphid-resistant okra genotypes along with 1 commercial variety and a local landrace (specific to a given location) were compared during 2 seasons in replicated trials in 4 agro-ecological zones of Cameroon that also represent large areas of Central Africa. Aphid populations and okra yield parameters were evaluated. Breeding values were predicted using a linear mixed model for all data, and genotypes by location interactions were identified. The area under the infestation pressure curve (AUIPC) was calculated using aphid count data and subjected to resistance analysis. The Local-the most susceptible with the highest breeding value (+2.33)-and VI060794-one of the moderately resistant-genotypes had the highest yield per hectare. The only resistant genotype VI036213 had the lowest breeding value (-2.20). Genotype × location interactions were significant for yield, pod width, and plant height, while location variance was significant for all parameters evaluated. When considering that higher aphid densities could lead to greater pesticide use and, therefore higher production and environmental costs, the high-yielding VI060794-with moderate aphid resistance across multiple environments-presents an alternative or substitute for local landraces across multiple agro-ecologies of Cameroon and (by extension) Central Africa.

30 Effects of using different dietary standardized ileal digestible lysine plans on growth performance and carcass characteristics of grow-finish pigs from high or low breeding value boars

Abstract The present study aimed to evaluate the impact of using different dietary standardized ileal digestible (SID) lysine (Lys) plans on growth performance and carcass characteristics of grow-finish pigs coming from high or low breeding value boars. A total of 2,080 pigs (PIC 800 × PIC Camborough) were housed in 20 mixed sex pens (26 pigs/pen), blocked by body weight (BW), and randomly allotted in a 2 × 2 factorial arrangement with boar breeding value (high or low) and nutrition Lys plan (current SID Lys curve recommendation for PIC 800 as % of PIC 337 SID Lys curve or alternative SID Lys curve). Pigs were weaned at 21 d of age (6.1 ± 0.05 kg BW) and followed during the wean-to-finish period until reach the market slaughter weight. Pigs were fed either the current recommendation or an alternative SID Lys curve for PIC 800, in a 6 phase feeding program: phase 1 (6-11 kg; 100 vs 100%, respectively); phase 2 (11-23 kg; 97 vs 100%, respectively); phase 3 (23-45 kg; 97 vs 100%, respectively); phase 4 (45-73 kg; 97 vs 95%, respectively); phase 5 (73-102 kg; 97 vs 95%, respectively); and phase 6 (102-132 kg; 97 vs 90%, respectively). Pigs were fed isoenergetic diets. Performance and carcass traits, and removals and mortality were recorded. Data were analyzed using mixed models in R, and considering pen as the experimental unit for performance traits and individual carcasses for carcass traits. There was no evidence of interaction between boar breeding value and nutrition plan factors. Overall, high breeding value pigs had greater average daily gain (ADG; 0.84 ± 0.005 g/d) compared with low breeding value pigs (0.82 ± 0.005 kg/d; P < 0.01), which was driven by increased average daily feed intake (ADFI; 1.92 ± 0.011 and 1.89 ± 0.011 kg/d, respectively; P < 0.05; Table 1). Moreover, high breeding value pigs had greater hot carcass weight (HCW; 97.8 ± 1.09 kg), carcass yield (74.1 ± 0.23%), backfat thickness (16.3 ± 0.29 mm) and lower lean meat % (57.0 ± 0.21%) compared with low breeding value pigs (96.0 ± 1.09 kg; 73.7 ± 0.23 %; 15.4 ± 0.28; 57.5 ± 0.21%, respectively; P < 0.05; Table 1). Regarding nutrition plan, no significant differences were observed for overall performance traits between pigs fed the current or alternative SID Lys curve (P > 0.05; Table 1). Nevertheless, pigs fed the alternative SID Lys curve had heavier HCW (97.3 ± 1.09 kg) compared with pigs fed the current SID Lys curve (96.6±1.09 kg; P < 0.05; Table 1). No significant differences were observed for overall removals and mortality by breeding value or nutrition Lys plan (P > 0.05). In summary, grow finish pigs from high breeding value boars have an improved productive performance. PIC 800 pigs may achieve the same productive performance with lower lysine levels at the end of the grow-finish period.

Genetic Basis of Potato Tuber Defects and Identification of Heat-Tolerant Clones.

Heat stress during the potato growing season reduces tuber marketable yield and quality. Tuber quality deterioration includes external (heat sprouts, chained tubers, knobs) and internal (vascular discoloration, hollow heart, internal heat necrosis) tuber defects, as well as a reduction in their specific gravity and increases in reducing sugars that result in suboptimal (darker) processed products (french fries and chips). Successfully cultivating potatoes under heat-stress conditions requires planting heat-tolerant varieties that can produce high yields of marketable tubers, few external and internal tuber defects, high specific gravity, and low reducing sugars (in the case of processing potatoes). Heat tolerance is a complex trait, and understanding its genetic basis will aid in developing heat-tolerant potato varieties. A panel of 217 diverse potato clones was evaluated for yield and quality attributes in Dalhart (2019 and 2020) and Springlake (2020 and 2021), Texas, and genotyped with the Infinium 22 K V3 Potato Array. A genome-wide association study was performed to identify genomic regions associated with heat-tolerance traits using the GWASpoly package. Quantitative trait loci were identified on chromosomes 1, 3, 4, 6, 8, and 11 for external defects and on chromosomes 1, 2, 3, 10, and 11 for internal defects. Yield-related quantitative trait loci were detected on chromosomes 1, 6, and 10 pertaining to the average tuber weight and tuber number per plant. Genomic-estimated breeding values were calculated using the StageWise package. Clones with low genomic-estimated breeding values for tuber defects were identified as donors of good traits to improve heat tolerance. The identified genomic regions associated with heat-tolerance attributes and the genomic-estimated breeding values will be helpful to develop new potato cultivars with enhanced heat tolerance in potatoes.

Breeding Value of Quality Protein Maize Inbreds

The cultivar with high and positive breeding value can be used as a good parent for breeding of traits in hybridization programs because they can better transfer the desirable characteristics to the progeny in each case. To obtain the breeding value present investigation was carried out in maize with 33 inbreds of maize and seven inbreds of QPM lines to assess the breeding value of maize progenies for the better selection. The progeny values ranged from 62.04 (UMI 48 x CO 1) to 126.26 (CML 145 x CO 1). The breeding value ranged from 0.17 (UMI 48 x CO 1) to 0.39 (CML 145 x CO 1). CML 145 x CO 1 had high breeding value (0.39) with high progeny mean. UMI 48 x CO 1 had low breeding value (-0.17) with low progeny mean (90.80). The parent CML 145 was the superior most both for perse mean (P38=126.26) as well as for its hybrid progeny mean (C2= 168).

Identification of differentially expressed genes and SNPs linked to harvest body weight of genetically improved rohu carp, Labeo rohita.

In most of the aquaculture selection programs, harvest body weight has been a preferred performance trait for improvement. Molecular interplay of genes linked to higher body weight is not elucidated in major carp species. The genetically improved rohu carp with 18% average genetic gain per generation with respect to harvest body weight is a promising candidate for studying genes' underlying performance traits. In the present study, muscle transcriptome sequencing of two groups of individuals, with significant difference in breeding value, belonging to the tenth generation of rohu carp was performed using the Illumina HiSeq 2000 platform. A total of 178 million paired-end raw reads were generated to give rise to 173 million reads after quality control and trimming. The genome-guided transcriptome assembly and differential gene expression produced 11,86,119 transcripts and 451 upregulated and 181 downregulated differentially expressed genes (DEGs) between high-breeding value and low-breeding value (HB & LB) groups, respectively. Similarly, 39,158 high-quality coding SNPs were identified with the Ts/Tv ratio of 1.23. Out of a total of 17 qPCR-validated transcripts, eight were associated with cellular growth and proliferation and harbored 13 SNPs. The gene expression pattern was observed to be positively correlated with RNA-seq data for genes such as myogenic factor 6, titin isoform X11, IGF-1 like, acetyl-CoA, and thyroid receptor hormone beta. A total of 26 miRNA target interactions were also identified to be associated with significant DETs (p-value < 0.05). Genes such as Myo6, IGF-1-like, and acetyl-CoA linked to higher harvest body weight may serve as candidate genes in marker-assisted breeding and SNP array construction for genome-wide association studies and genomic selection.

Estimates of genetic parameters and genetic trend for growth traits and Kleiber ratio of Holstein-Friesian calves

Growth traits of calves, which are quantitative characteristics determining cattle business profitability, vary according to genetic and environmental factors. In other words, growth traits depend on the genetics of the individual and vary with farm management. The aim of this study was to investigate the effective environmental factors, genetic parameters, and genetic trends for some growth traits and the Kleiber ratio (KR) in Holstein-Friesian calves. For this purpose, the records of 724 calves, progeny of 566 dams and 29 sires, reared between 2017 and 2019 on a private dairy farm in Türkiye, were used. MTDFREML software was utilized to estimate genetic parameters and genetic trends of growth traits and KR. In this study, regarding weight, the mean of birth weight (BW), 60-day weight (W60), and 90-day weight (W90) were 39.76 ± 6.15 kg, 69.23 ± 10.93 kg, and 95.76 ± 16.48 kg, respectively. Concerning weight gain, 1-60 daily weight gain (DWG1-60), 60-90 daily weight gain (DWG60-90), and 1-90 daily weight gain (DWG1-90) were 0.49 ± 0.16 kg, 0.91 ± 0.34 kg, and 0.63 ± 0.17 kg, respectively. With respect to KR, 1-60 daily KR (KR1-60), 60-90 daily KR (KR60-90), and 1-90 daily KR (KR1-90) were 2.03 ± 0.48, 2.93 ± 0.89, and 2.02 ± 0.34, respectively. As a result of the GLM analysis, only the effect of the birth season on all traits was significant (p < 0.05 or p < 0.01). In addition, it was detected that sex had a significant effect on BW and W60 (p < 0.05 or p < 0.01). For all traits, only the effect of parity on KR1-60 was not significant. In REML analysis, direct heritability differed between 0.26 ± 0.16 and 0.81 ± 0.27 obtained at DWG1-90 and DWG1-60, respectively. Also, the highest repeatability (0.100) was obtained in DWG1-60. It was detected that mass selection could be used in all traits for breeding program. In BLUP analysis, the current population had an increasing trend for BW and W90 and a decreasing trend for W60. However, there was no significant change in other weight gain traits and KR over the years. Calves with high breeding values for BW, W60, W90, DWG1-60, DWG60-90, and DWG1-90 should be chosen for selection programs. But for KR1-60, KR60-90, and KR1-90, calves with low breeding values should be selected for efficiency. Also, KR evaluated would contribute to the literature and other research should be studied regarding KR.

Runs of homozygosity and signatures of selection for number of oocytes and embryos in the Gir Indicine cattle.

Runs of homozygosity (ROH) and signatures of selection are the results of selection processes in livestock species that have been shown to affect several traits in cattle. The aim of the current work was to verify the profile of ROH and inbreeding depression in the number of total (TO) and viable oocytes (VO) and the number of embryos (EMBR) in Gir Indicine cattle. In addition, we aim to identify signatures of selection, genes, and enriched regions between Gir subpopulations sorted by breeding value for these traits. The genotype file contained 2093 animals and 420,718 SNP markers. Breeding values used to sort Gir animals were previously obtained. ROH and signature of selection analyses were performed using PLINK software, followed by ROH-based (FROH) and pedigree-based inbreeding (Fped) and a search for genes and their functions. An average of 50 ± 8.59 ROHs were found per animal. ROHs were separated into classes according to size, ranging from 1 to 2Mb (ROH1-2Mb: 58.17%), representing ancient inbreeding, ROH2-4Mb (22.74%), ROH4-8Mb (11.34%), ROH8-16Mb (5.51%), and ROH>16Mb (2.24%). Combining our results, we conclude that the increase in general FROH and Fped significantly decreases TO and VO; however, in different chromosomes traits can increase or decrease with FROH. In the analysis for signatures of selection, we identified 15 genes from 47 significant genomic regions, indicating differences in populations with high and low breeding value for the three traits.

Comparative evaluation of the breeding value of Holstein bulls-producers

Modern dairy cattle breeding efficiency is largely determined by the strategy of choosing a producer for herd reproduction, which determines the growth rate of herd productivity for the next 3 to 5 years. According to the results of 2022, there are 20 organisations in the Sverdlovsk region with milk production per feed cow of more than 9 thousand kg, including 10 farms with milk production of more than 10 thousand kg. The best farm in the region, APC “Kilachevsky”, produced an average of 12829 kg of milk for each of 3000 cows. Two record-breaking cows were milked there, each of which yielded more than 21 tonnes of milk for a standard lactation. Thirty-four breeding bulls were included in the study. As a result of their evaluation, it was found that in bulls whose genomic breeding value for milk yield exceeded 1000 kg of milk 80.0% of producers were actual improvers for this trait, and in bulls with low genomic breeding value for milk yield (0-99 kg) only 25.0% of producers were actual improvers. Bulls with a negative breeding value for milk production in 66.6 percent of cases turned out to be actual improvers. In terms of protein content in milk, the dependence is similar, the higher the genomic value of the sire according to MDB, the more bulls actually have a positive effect on the protein-milk content of daughters (Tables 3,4). However, the number of sires that confirmed genomic breeding value for protein-milk yield is much less than for milk yield. For milk yield, 17 sires out of 34 (50.0%) received confirmation of breeding value, and for protein-milk yield only 11 (32.0%).

Growth Performance, Carcass and Pork Quality Traits of Growing-Finishing Pigs with High and Low Breeding Values for Residual Feed Intake Fed Diets with Macauba (Acrocomia aculeata) Pulp as Alternative Raw Material

This study evaluated the effects of dietary macauba pulp on the growth performance, carcass, and pork traits of growing-finishing pigs; and whether differences in residual feed intake breeding values could influence the pigs’ growth responses to macauba pulp inclusion in the diet. A total of 282 (34.8 ± 4.40 kg) pigs (barrows and females), progeny of sires with high (HRFI) or low (LRFI) breeding value for residual feed intake, were pair-housed on the basis of sex, breeding value, and initial BW. Diets with (macauba) or without (control) of 50 g/kg of macauba pulp inclusion were randomly assigned to the experimental pens. There were eight treatment groups: HRFI barrows were fed the control diet; HRFI barrows were fed the macauba diet; LRFI barrows were fed the control diet; LRFI barrows were fed the macauba diet; HRFI female pigs were fed the control diet; HRFI female pigs were fed the macauba diet; LRFI female pigs were fed the control diet; and LRFI female pigs were fed the macauba diet. The trial lasted 90 days and was divided into four phases: growing phase 1 (G1) and 2 (G2); and finishing phases 1 (F1) and 2 (F2). There was no interaction between sex, breeding value, and diet for performance, carcass, and pork traits. Barrows had higher feed intake (ADFI), daily gain (ADG), feed conversion rate (FCR), and final body weight than female pigs. The breeding value had no effect on performance measurements. The inclusion of macauba pulp in the pigs’ diets did not affect any growth parameter during G1, G2 and F1 phases. However, reduced ADFI and improved FCR were observed in F2. Female pigs had lower backfat thickness (BF) and higher loin eye area (LEA) than barrows. HRFI pigs had higher hot carcass weight and LEA, and lower BF than LRFI pigs. There was no effect of macauba pulp inclusion on carcass traits. Pork from barrows presented lower Warner–Bratzler shear force and higher fat content than pork from the females. There was no effect of breeding value on pork traits. Pork from pigs fed the macauba diet showed lower moisture content and water-holding capacity. In conclusion, macauba pulp can partially replace corn without reducing the performance of pigs. Regardless of sex and breeding value for RFI, pigs responded similarly to macauba pulp inclusion in diets.

New cycle, same old mistakes? Overlapping vs. discrete generations in long-term recurrent selection

BackgroundRecurrent selection is a foundational breeding method for quantitative trait improvement. It typically features rapid breeding cycles that can lead to high rates of genetic gain. Usually, generations are discrete in recurrent selection, which means that breeding candidates are evaluated and considered for selection for only one cycle. Alternately, generations can overlap, with breeding candidates considered for selection as parents for multiple cycles. With recurrent genomic selection but not phenotypic selection, candidates can be re-evaluated by using genomic estimated breeding values without additional phenotyping of the candidates themselves. Therefore, it may be that candidates with true high breeding values discarded in one cycle due to underestimation of breeding value could be identified and selected in subsequent cycles. The consequences of allowing generations to overlap in recurrent selection are unknown. We assessed whether maintaining overlapping and discrete generations led to differences in genetic gain for phenotypic, genomic truncation, and genomic optimum contribution recurrent selection by stochastic simulation.ResultsWith phenotypic selection, overlapping generations led to decreased genetic gain compared to discrete generations due to increased selection error bias. Selected individuals, which were in the upper tail of the distribution of phenotypic values, tended to also have high absolute error relative to their true breeding value compared to the overall population. Without repeated phenotyping, these individuals erroneously believed to have high value were repeatedly selected across cycles, leading to decreased genetic gain. With genomic truncation selection, overlapping and discrete generations performed similarly as updating breeding values precluded repeatedly selecting individuals with inaccurately high estimates of breeding values in subsequent cycles. Overlapping generations did not outperform discrete generations in the presence of a positive genetic trend with genomic truncation selection, as individuals from previous breeding cycles typically had truly lower breeding values than candidates from the current generation. With genomic optimum contribution selection, overlapping and discrete generations performed similarly, but overlapping generations slightly outperformed discrete generations in the long term if the targeted inbreeding rate was extremely low.ConclusionMaintaining discrete generations in recurrent phenotypic selection leads to increased genetic gain, especially at low heritabilities, by preventing selection error bias. With genomic truncation selection and genomic optimum contribution selection, genetic gain does not differ between discrete and overlapping generations assuming non-genetic effects are not present. Overlapping generations may increase genetic gain in the long term with very low targeted rates of inbreeding in genomic optimum contribution selection.

Importance of humidity and temperature in breech strike of Merino sheep

Context Breech strike is a serious disease particularly in wool sheep. Skin wrinkle and dags are known predisposing factors for breech strike, although a large part of the variation between sheep is unexplained. Aims We used sensor buttons to determine whether there were differences in humidity and temperature in the breech area of Merino sheep exposed to blowflies without traditional preventive measures being used in the flock. Methods Sixty-two Merino rams and 62 Merino ewes that had high or low breeding values for breech strike were each fitted with a sensor button to record hourly temperature and humidity in the breech over 49 days. The sensors were fitted before the onset of the blowfly season. The sensor was tied to a wool staple close to the skin in the breech and was removed when a sheep was struck. All remaining buttons were removed prior to shearing. Breech wrinkle, neck wrinkle, breech cover and faecal soiling (dags) were recorded on all the sheep. A total of 98 213 hourly temperature and humidity records were analysed with cubic smoothing splines to assess how humidity and temperature differed between struck and unstruck sheep, and whether the breech indicator traits affect temperature and humidity in the breech. Results Time of day and day-to-day variation prior to being struck explained most of the variation of temperature and humidity in the breech of the sheep. Humidity and temperature increased with an increase in breech cover. The humidity in the breech area was, on average, 2% higher in struck sheep prior to being struck. There was a sharp increase in humidity in struck sheep in the 8 days leading up to detection of breech strike relative to unstruck animals, most probably due to exudate from the wound. Conclusions Sheep prone to be struck have higher humidity in the breech than sheep less prone to be struck. Implications Temperature in the breech does not qualify as a potential indicator trait for breech strike in wool sheep, whereas humidity needs further research to determine its effectiveness as a potential indicator trait.

Unravelling genetic variability for moisture stress tolerance in Indian mustard and identification of high breeding value donor lines

Aim: Identification of high breeding value donor lines harbouring tolerance to moisture stress from diversity stock of 443 genotypes of Brassica juncea. Methodology: Germplasm stock of 443 Indian mustard (Brassica juncea L.) genotypes, comprising introgression lines, land races, old cultivars and advance breeding lines, were evaluated under two environments viz., irrigated and rainfed conditions to check the variability for yield and related traits. Statistical software META-Rver 6.0 (Multi Environment Trial Analysis using R) was used for computation of Best Linear Unbiased Predictions, Analysis of Variance (ANOVA), Genetic Correlations and Heritability. Drought susceptibility index and per cent seed yield reduction under rainfed conditions were used as indicators to determine moisture stress tolerance in genotypes. Results: The variability for moisture stress tolerance has been unravelled in a diverse genetic stock of Brassica juncea under two environments: irrigated and rainfed. For high prediction accuracy, the ranking of genotypes was done based on Best Linear Unbiased Predictions for seed yield and its component traits. PBR-378, RGN-329, RB-73, RB-50 and PBR-422 and Giriraj were identified as moisture stress tolerant genotypes. One land race Sahib 36 and three introgression lines viz., MCP 12-211, PTJ-3-69 and MSC-3 have also been identified as potential genetic resources for moisture stress tolerance. Principal component analysis based on biplots depicted specific distribution of variables for each environment. Interpretation: This study led to the identification of potential donors for moisture stress tolerance with high predictive accuracy. Low drought susceptibility index and high breeding value in a land race and three introgression lines derived from Erucastrum cardaminoides, B. tournefortii and B. carinata emphasized their utilization as potential genetic resources to breed for moisture stress tolerance in B. juncea.

A variance component estimation approach to infer associations between Mendelian polledness and quantitative production and female fertility traits in German Simmental cattle

BackgroundManaging beneficial Mendelian characteristics in dairy cattle breeding programs implies that the correlated genetic effects are considered to avoid possible adverse effects in selection processes. The Mendelian trait polledness in cattle is traditionally associated with the belief that the polled locus has unfavorable effects on breeding goal traits. This may be due to the inferior breeding values of former polled bulls and cows in cattle breeds, such as German Simmental, or to pleiotropic or linkage effects of the polled locus.MethodsWe focused on a variance component estimation approach that uses a marker-based numerator relationship matrix reflecting gametic relationships at the polled locus to test for direct pleiotropic or linked quantitative trait loci (QTL) effects of the polled locus on relevant traits. We applied the approach to performance, health, and female fertility traits in German Simmental cattle.ResultsOur results showed no evidence for any pleiotropic QTL effects of the polled locus on test-day production traits milk yield and fat percentage, on the mastitis indicator ‘somatic cell score’, and on several female fertility traits, i.e. 56 days non return rate, days open and days to first service. We detected a significant and unfavorable QTL effect accounting for 6.6% of the genetic variance for protein percentage only.ConclusionsPleiotropy does not explain the lower breeding values and phenotypic inferiority of polled German Simmental sires and cows relative to the horned population in the breed. Thus, intensified selection in the polled population will contribute to increased selection response in breeding goal traits and genetic merit and will narrow the deficit in breeding values for production traits.

Exploring genetic resistance to infectious salmon anaemia virus in Atlantic salmon by genome-wide association and RNA sequencing

BackgroundInfectious Salmonid Anaemia Virus (ISAV) causes a notifiable disease that poses a large threat for Atlantic salmon (Salmo salar) aquaculture worldwide. There is no fully effective treatment or vaccine, and therefore selective breeding to increase resistance to ISAV is a promising avenue for disease prevention. Genomic selection and potentially genome editing can be applied to enhance host resistance, and these approaches benefit from improved knowledge of the genetic and functional basis of the target trait. The aim of this study was to characterise the genetic architecture of resistance to ISAV in a commercial Atlantic salmon population and study its underlying functional genomic basis using RNA Sequencing.ResultsA total of 2833 Atlantic salmon parr belonging to 194 families were exposed to ISAV in a cohabitation challenge in which cumulative mortality reached 63% over 55 days. A total of 1353 animals were genotyped using a 55 K SNP array, and the estimate of heritability for the trait of binary survival was 0.13–0.33 (pedigree-genomic). A genome-wide association analysis confirmed that resistance to ISAV was a polygenic trait, albeit a genomic region in chromosome Ssa13 was significantly associated with resistance and explained 3% of the genetic variance. RNA sequencing of the heart of 16 infected (7 and 14 days post infection) and 8 control fish highlighted 4927 and 2437 differentially expressed genes at 7 and 14 days post infection respectively. The complement and coagulation pathway was down-regulated in infected fish, while several metabolic pathways were up-regulated. The interferon pathway showed little evidence of up-regulation at 7 days post infection but was mildly activated at 14 days, suggesting a potential crosstalk between host and virus. Comparison of the transcriptomic response of fish with high and low breeding values for resistance highlighted TRIM25 as being up-regulated in resistant fish.ConclusionsISAV resistance shows moderate heritability with a polygenic architecture, but a significant QTL was detected on chromosome 13. A mild up-regulation of the interferon pathway characterises the response to the virus in heart samples from this population of Atlantic salmon, and candidate genes showing differential expression between samples with high and low breeding values for resistance were identified.

Investigating mechanisms underlying genetic resistance to Salmon Rickettsial Syndrome in Atlantic salmon using RNA sequencing

BackgroundSalmon Rickettsial Syndrome (SRS), caused by Piscirickettsia salmonis, is one of the primary causes of morbidity and mortality in Atlantic salmon aquaculture, particularly in Chile. Host resistance is a heritable trait, and functional genomic studies have highlighted genes and pathways important in the response of salmon to the bacteria. However, the functional mechanisms underpinning genetic resistance are not yet well understood. In the current study, a large population of salmon pre-smolts were challenged with P. salmonis, with mortality levels recorded and samples taken for genotyping. In parallel, head kidney and liver samples were taken from animals of the same population with high and low genomic breeding values for resistance, and used for RNA-Sequencing to compare their transcriptome profile both pre and post infection.ResultsA significant and moderate heritability (h2 = 0.43) was shown for the trait of binary survival. Genome-wide association analyses using 38 K imputed SNP genotypes across 2265 animals highlighted that resistance is a polygenic trait. Several thousand genes were identified as differentially expressed between controls and infected samples, and enriched pathways related to the host immune response were highlighted. In addition, several networks with significant correlation with SRS resistance breeding values were identified, suggesting their involvement in mediating genetic resistance. These included apoptosis, cytoskeletal organisation, and the inflammasome.ConclusionsWhile resistance to SRS is a polygenic trait, this study has highlighted several relevant networks and genes that are likely to play a role in mediating genetic resistance. These genes may be future targets for functional studies, including genome editing, to further elucidate their role underpinning genetic variation in host resistance.

Spatial and competition models increase the progeny testing efficiency of Japanese larch

The main purpose of this study was to examine spatial and competition effects on estimates of genetic parameters, as well as on selection options for growth traits, including height (H), diameter at breast height (DBH), and volume (V), in a progeny test of Japanese larch (Larix kaempferi (Lam.) Carrière) at age 20 years. We compared performances among the individual-tree additive genetic base model (B) with design factors only, the spatial effect model (AR1), the competition model (C), and the combined competition and spatial model (CS). We found that spatial heterogeneity had significant effects on growth traits and that plot variance decreased by more than 80% in the AR1 model relative to the B model. Competition had significant effects on DBH and V but a smaller effect on H. In the C model, direct additive genetic variances ([Formula: see text]) for DBH and V increased by 205% and 93%, respectively, whereas residual variances ([Formula: see text]) decreased by 8% and 6%, respectively. In the CS model, the correlations between direct and competitive genetic effects were 0.83, −0.97, and −0.98 for H, DBH, and V, respectively. Competition significantly affected the forward selection. The proportions of selected elite trees were only 39% and 25% common between the B and CS models for DBH and V, respectively, when selection intensity was 5%. For breeding selection, depending on thinning regimes planned, trees of high additive breeding values but low competitive breeding values are preferable for plantation.

Response of the Salmon Heart Transcriptome to Pancreas Disease: Differences Between High- and Low-Ranking Families for Resistance

Pancreas disease caused by salmonid alphaviruses leads to severe losses in Atlantic salmon aquaculture. The aim of our study was to gain a better understanding of the biological differences between salmon with high and low genomic breeding values (H-gEBV and L-gEBV respectively) for pancreas disease resistance. Fish from H- and L-gEBV families were challenged by intraperitoneal injection of salmonid alphavirus or co-habitation with infected fish. Mortality was higher with co-habitation than injection, and for L- than H-gEBV. Heart for RNA-seq and histopathology was collected before challenge and at four- and ten-weeks post-challenge. Heart damage was less severe in injection-challenged H- than L-gEBV fish at week 4. Viral load was lower in H- than L-gEBV salmon after co-habitant challenge. Gene expression differences between H- and L-gEBV manifested before challenge, peaked at week 4, and moderated by week 10. At week 4, H-gEBV salmon showed lower expression of innate antiviral defence genes, stimulation of B- and T-cell immune function, and weaker stress responses. Retarded resolution of the disease explains the higher expression of immune genes in L-gEBV at week 10. Results suggest earlier mobilization of acquired immunity better protects H-gEBV salmon by accelerating clearance of the virus and resolution of the disease.

Temporal changes in circulatory blood cell parameters of sheep genetically different for faecal worm egg count and diarrhoea from late summer to spring in a Mediterranean environment

Differences in haematology traits were investigated in worm-resistant and worm-susceptible Merino sheep that were genetically prone or less prone to developing diarrhoea in a winter rainfall region. The experiment was a 2 × 2 × 2 × 5 design. Male and female sheep aged 8–9 months old identified as having high (H) or low (L) breeding values for dags (breech soiling) and for worm egg counts (WEC) were allocated to one of four genetic groups: HH, HL, LH and LL (the first letter refers to dags and the second to WEC). The animals were sampled five times from autumn through winter to spring, in March, May, June (ewes only), July (rams only), August and in September after exposure to a natural paddock infection dominated by Trichostrongylus, Teladorsagia, Chabertia and Oesophagostomum. Measurements were packed cell volume, haemoglobin, red blood cell count, differential white cell counts, WEC and faecal consistency score. At all sampling times, there were large (P &amp;lt; 0.01) differences between groups within sex for both the faecal consistency score and WEC. The genetic effect for WEC was large (P &amp;lt; 0.01), as worm-susceptible sheep shed 10- (ewes) and 6-fold (rams) as many worm eggs at their WEC peak as the worm-resistant sheep at the end of the experiment. In the high-dag groups, the faecal consistency score was ~0.5 units higher for rams and 0.4 units higher for ewes, throughout the experiment. The optimum time to measure dags and WEC in this environment appears to be 6–8 weeks after the start of the winter rain. No differences were found among any of the treatment groups for any haematology trait. The haematogram changed significantly throughout the experiment, but genetic selection for low-dag score (reduced diarrhoea) or low WEC did not provide an acceptable discriminator in circulatory haematology traits between these genetically distinct groups of Merino sheep. It was concluded that circulatory haematology traits do not offer opportunities to select against diarrhoea or increased worm resistance in sheep.

Genomic Divergence in Swedish Warmblood Horses Selected for Equestrian Disciplines.

The equestrian sport horse Swedish Warmblood (SWB) originates from versatile cavalry horses. Most modern SWB breeders have specialized their breeding either towards show jumping or dressage disciplines. The aim of this study was to explore the genomic structure of SWB horses to evaluate the presence of genomic subpopulations, and to search for signatures of selection in subgroups of SWB with high or low breeding values (EBVs) for show jumping. We analyzed high density genotype information from 380 SWB horses born in the period 2010–2011, and used Principal Coordinates Analysis and Discriminant Analysis of Principal Components to detect population stratification. Fixation index and Cross Population Extended Haplotype Homozygosity scores were used to scan the genome for potential signatures of selection. In accordance with current breeding practice, this study highlights the development of two separate breed subpopulations with putative signatures of selection in eleven chromosomes. These regions involve genes with known function in, e.g., mentality, endogenous reward system, development of connective tissues and muscles, motor control, body growth and development. This study shows genetic divergence, due to specialization towards different disciplines in SWB horses. This latter evidence can be of interest for SWB and other horse studbooks encountering specialized breeding.