Genetic Merit Research Articles

A breed-of-origin of alleles model that includes crossbred data improves predictive ability for crossbred animals in a multi-breed population

BackgroundRecently, crossbred animals have begun to be used as parents in the next generations of dairy and beef cattle systems, which has increased the interest in predicting the genetic merit of those animals. The primary objective of this study was to investigate three available methods for genomic prediction of crossbred animals. In the first two methods, SNP effects from within-breed evaluations are used by weighting them by the average breed proportions across the genome (BPM method) or by their breed-of-origin (BOM method). The third method differs from the BOM in that it estimates breed-specific SNP effects using purebred and crossbred data, considering the breed-of-origin of alleles (BOA method). For within-breed evaluations, and thus for BPM and BOM, 5948 Charolais, 6771 Limousin and 7552 Others (a combined population of other breeds) were used to estimate SNP effects separately within each breed. For the BOA, the purebreds' data were enhanced with data from ~ 4K, ~ 8K or ~ 18K crossbred animals. For each animal, its predictor of genetic merit (PGM) was estimated by considering the breed-specific SNP effects. Predictive ability and absence of bias were estimated for crossbreds and the Limousin and Charolais animals. Predictive ability was measured as the correlation between PGM and the adjusted phenotype, while the regression of the adjusted phenotype on PGM was estimated as a measure of bias.ResultsWith BPM and BOM, the predictive abilities for crossbreds were 0.468 and 0.472, respectively, and with the BOA method, they ranged from 0.490 to 0.510. The performance of the BOA method improved as the number of crossbred animals in the reference increased and with the use of the correlated approach, in which the correlation of SNP effects across the genome of the different breeds was considered. The slopes of regression for PGM on adjusted phenotypes for crossbreds showed overdispersion of the genetic merits for all methods but this bias tended to be reduced by the use of the BOA method and by increasing the number of crossbred animals.ConclusionsFor the estimation of the genetic merit of crossbred animals, the results from this study suggest that the BOA method that accommodates crossbred data can yield more accurate predictions than the methods that use SNP effects from separate within-breed evaluations.

Exploring the value of genomic predictions to simultaneously improve production potential and resilience of farmed animals.

Sustainable livestock production requires that animals have a high production potential but are also highly resilient to environmental challenges. The first step to simultaneously improve these traits through genetic selection is to accurately predict their genetic merit. In this paper, we used simulations of sheep populations to assess the effect of genomic data, different genetic evaluation models and phenotyping strategies on prediction accuracies and bias for production potential and resilience. In addition, we also assessed the effect of different selection strategies on the improvement of these traits. Results show that estimation of both traits greatly benefits from taking repeated measurements and from using genomic information. However, the prediction accuracy for production potential is compromised, and resilience estimates tends to be upwards biased, when families are clustered in groups even when genomic information is used. The prediction accuracy was also found to be lower for both traits, resilience and production potential, when the environment challenge levels are unknown. Nevertheless, we observe that genetic gain in both traits can be achieved even in the case of unknown environmental challenge, when families are distributed across a large range of environments. Simultaneous genetic improvement in both traits however greatly benefits from the use of genomic evaluation, reaction norm models and phenotyping in a wide range of environments. Using models without the reaction norm in scenarios where there is a trade-off between resilience and production potential, and phenotypes are collected from a narrow range of environments may result in a loss for one trait. The study demonstrates that genomic selection coupled with reaction-norm models offers great opportunities to simultaneously improve productivity and resilience of farmed animals even in the case of a trade-off.

Influence of dairy farmers’ knowledge on their attitudes towards breeding tools and genomic selection

Understanding farmers' attitudes towards traits is critical for developing appropriate breeding goals for dairy production. In response to a research gap in regards to the influence of farmers' knowledge of breeding tools, this study aimed to determine the effect of farmers' knowledge on their attitudes towards the use of breeding tools and traits in typical family-owned farms in Slovenia. An online questionnaire was sent to dairy farmers affiliated with Slovenian breeding associations, and 256 dairy farmers responded. The analysis was conducted in three steps. First, the basic response patterns according to the farmers' knowledge level were determined using latent class analysis. Second, farmers' attitudes towards breeding tools were assessed by 15 statements using principal component analysis. Finally, we were interested in the relationship between farmers' attitudes and knowledge about selection. The results showed that farmers had more knowledge about the benefits of genomic selection, followed by general knowledge about breeding values and the definition of genomic selection, and they had the least knowledge about the reference population. Farmers with more knowledge were statistically significantly more likely than farmers with less knowledge to have higher education, be younger, have a larger herd size, have higher milk production per cow, have the intent to increase herd size and milk quantity, and use genomically tested bulls. No significant relationship was found between belonging to a specific knowledge class and the main breed in the herd, the farmer's gender, production system, or farming in less-favoured areas. The results also show that farmers basically agree that they need written recorded performance data about a bull/cow to know exactly how good the animal is, that the genetic merit (breeding value) of bulls/cows adds to the performance of their progeny, that it is very important to maintain the breed characteristics of bulls/cows, that cooperation in being able to compare animals with other farmers is essential for improving herd performance, and that the possibilities of selecting dairy cows with genomic selection and monogenetic traits must be fully exploited, indicating a positive attitude towards genomic selection. The level of knowledge was shown to influence attitudes towards various aspects of breeding. It was found that the higher the level of knowledge, the more positive the attitude towards genetic and genomic selection, and the more negative the attitude towards traditional selection.

A Novel Method of Understanding and Identifying Feeding Management Problems in Dairy Cows

There has been a considerable increase in the number of exotic dairy cows in the country through crossbreeding program. Although the increasing number of exotics cows have brought several benefits, it was envisioned that there is a disparity between feeding management and cows' genetic merit. The discrepancy was evidenced by the low milk production from genetically merit cows wherein it believes that reasons are associated with ignorance and lack of knowledge on managing modern dairy cows. Therefore, a novel approach to identifying dairy cows' problems related to feeding management was introduced for Bhutanese farmers. Under this concept, four noble truths are used to educate farmers on the causes of problems and provide solutions for them. Further, to create awareness of body condition score as a key management tool in feeding dairy cows.

Development of nutrigenomic based precision management model for Hanwoo steers.

Focusing high marble deposition, Hanwoo feedlot system uses high-energy diet over the prolonged fattening period. However, due to the individual genetic variation, around 40% of them are graded into inferior quality grades (QG), despite they utilized the same resources. Therefore, focusing on development of a nutrigenomic based precision management model, this study was to evaluated the response to the divergent selection on genetic merit for marbling score (MS), under different dietary total digestible nutrient (TDN) levels. Total of 111 calves were genotyped and initially grouped according to estimated breeding value (high and low) for marbling score (MS-EBV). Subsequently, managed under two levels of feed TDN%, over the calf period, early, middle, and final fattening periods following 2 × 2 factorial arrangement. Carcasses were evaluated for MS, Back fat thickness (BFT) and Korean beef quality grading standard. As the direct response to the selection was significant, the results confirmed the importance of initial genetic grouping of Hanwoo steers for MS-EBV. However, dietary TDN level did not show an effect (p > 0.05) on the MS. Furthermore, no genetic-by-nutrition interaction for MS (p > 0.05) was also observed. The present results showed no correlation response on BFT (p > 0.05), which indicates that the selection based on MS-EBV can be used to enhance the MS without undesirable effect on BFT. Ultimate turnover of the Hanwoo feedlot operation is primarily determined by the QGs. The present model shows that the initial grouping for MS-EBV increased the proportion of carcasses graded for higher QGs (QG1++ and QG1+) by approximately 20%. Moreover, there appear to be a potential to increase the proportion of QG 1++ animals among the high-genetic group by further increasing the dietary energy content. Overall, this precision management strategy suggests the importance of adopting an MS based initial genetic grouping system for Hanwoo steers with a subsequent divergent management based on dietary energy level.

103 Does ewe genetic merit influence phenotypic performance for reproductive traits?

103 Does ewe genetic merit influence phenotypic performance for reproductive traits?

Surgical repair of ruptured omphalocele in a high genetic merit neonatal Holstein bull calf

AbstractA neonatal Holstein bull calf presented emergently for abdominal evisceration. Calving was unassisted. Ninety minutes postpartum, farm staff noted the defect and brought the patient to the hospital. On presentation, the calf was recumbent, dull, and in hypovolemic shock with uncompensated hyperlactatemic metabolic acidosis. Multiple organs were identified through a 4–5 cm defect in the caudoventral midline. Differentials included a ruptured omphalocele, gastroschisis, trauma and schistosomus reflexus. This presentation was consistent with a ruptured omphalocele. Following triage and haemodynamic stabilisation, the eviscerated abdominal contents were lavaged, surgically replaced and an umbilical resection with partial cystectomy performed to remove a patent urachus. Postoperatively, the patient was hospitalised with aggressive nursing care. Pharmacotherapy included prophylactic antibiotics, gastroprotectants and anti‐inflammatory medication. The calf developed mild postoperative pneumonia, but was discharged after 6 days. This report details management of omphalocele evisceration in a calf and the pathology of congenital midline anomalies in neonatal ruminants.

We have Some Calves left! Socially Accepted Alternatives to the Current Handling of Male Calves from Dairy Production

Consumers’ actual knowledge about modern food production is limited, and their judgment is often guided by assumptions or associations that are not necessarily in line with reality. Consumers’ rather unrealistic idea of livestock farming is driven by beautiful and romanticized pictures in advertising. If confronted with the reality of modern livestock farming, consumers’ responses are mainly negative. So far, dairy farming still has a more positive image and thus is less affected by public criticism. However, if made public, some of the current production practices in dairy farming have the potential to reduce consumer acceptance which in turn can have a tremendous effect on farmers. A particularly urgent topic is the handling of male dairy calves. Such calves are often treated as surplus animals due to their low genetic merits for meat, with the risk of resulting in the deprivation of animal welfare. To maintain consumer acceptance of dairy products and find socially accepted alternatives for the handling of male calves, insights into consumer perception of current and future production practices in dairy farming are needed. Thus, the aim of this study is to analyze how consumers evaluate the current situation of male dairy calves and alternatives in male calf management. A quantitative online survey, representative for the German population in terms of gender, age, education, region, and income, was carried out with 1 194 participants in February 2022. Overall, 60% of participants were not aware of the fact that male dairy calves are less appropriate for fattening purposes. Respondents saw a clear need for alternative methods for handling male calves from dairy production. More, our results show that the use of sexed semen encounters consumer resistance, while other alternatives that were evaluated as more natural were more accepted. A cluster analysis identified 3 distinct consumer segments labelled “sexed semen opponents” (31.6%), “undecided” (30.4%), and “proponents of all alternatives” (38.0%) that differed in their acceptance of alternative handling practices of male dairy calves. The results emphasize the gap between consumers’ expectations and reality on farms and the importance of considering consumer preferences when developing future pathways for dairy farming.

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.

Dynamics of inflammatory cytokine expression in bovine endometrial cells exposed to cow blood plasma small extracellular vesicles (sEV) may reflect high fertility

Aberrant inflammation in the endometrium impairs reproduction and leads to poor fertility. Small extracellular vesicles (sEV) are nanoparticles 30–200 nm in-size and contain transferable bioactive molecules that reflect the parent cell. Holstein–Friesian dairy cows with divergent genetic merit, high- (n = 10) and low-fertile (n = 10), were identified based on fertility breeding value (FBV), cow ovulation synchronization and postpartum anovulatory intervals (PPAI). In this study, we evaluated the effects of sEVs enriched from plasma of high-fertile (HF-EXO) and low-fertile (LF-EXO) dairy cows on inflammatory mediator expression by bovine endometrial epithelial (bEEL) and stromal (bCSC) cells. Exposure to HF-EXO in bCSC and bEEL cells yielded lower expression of PTGS1 and PTGS2 compared to the control. In bCSC cells exposed to HF-EXO, pro-inflammatory cytokine IL1-α was downregulated compared to the untreated control, IL-12α and IL-8 were downregulated compared to the LF-EXO treatment. Our findings demonstrate that sEVs interact with both endometrial epithelial and stromal cells to initiate differential gene expression, specifically genes relate to inflammation. Therefore, even subtle changes on the inflammatory gene cascade in the endometrium via sEV may affect reproductive performance and/or outcomes. Further, sEV from high-fertile animals acts in a unique direction to deactivate prostaglandin synthases in both bCSC and bEEL cells and deactivate pro-inflammatory cytokines in the endometrial stroma. The results suggest that circulating sEV may serve as a potential biomarker of fertility.

Genome‐wide association study for bacterial leaf streak resistance in maize

AbstractMaize (Zea mays L.), one of the most important crops worldwide, is affected by foliar diseases that limit its global production. Bacterial diseases have increased in Argentina during the last years. The aim of this work was to explore a maize panel provided by the International Maize and Wheat Improvement Center (CIMMYT) to identify alleles associated with resistance to bacterial leaf streak (BLS) of maize, a disease caused by Xanthomonas vasicola pv. vasculorum, in central Argentina. A diverse panel of 200 maize lines was evaluated for resistance to bacterial diseases in four environments of central Argentina in 2020 and 2021. The predictor of the genetic merit does not include environmental effects and 46,990 single‐nucleotide polymorphisms obtained by genotyping‐by‐sequencing were used in the genome‐wide association study (GWAS). The 10 lines with the lowest severity across environments belonged to different environmental adaptation programs defined by CIMMYT. The GWAS allowed us to identify 11 genomic regions associated with BLS, located in chromosomes 1, 2, 5, 7, 8, and 9. Five of those regions, located in bins 1.04, 2.01, 5.03, 8.06, and 9.03, were associated with plant defense candidate genes such as strictosidine synthase‐like 11, protein‐serine/threonine phosphatase, and a putative Leucine‐Rich repeats receptor‐like serine/threonine‐protein kinase gene. Our study provides potential resistance alleles to BLS that can be incorporated to improve maize breeding programs.

Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection

Key messageR/StageWise enables fully efficient, two-stage analysis of multi-environment, multi-trait datasets for genomic selection, including support for dominance heterosis and polyploidy.Plant breeders interested in genomic selection often face challenges to fully utilizing multi-trait, multi-environment datasets. R package StageWise was developed to go beyond the capabilities of most specialized software for genomic prediction, without requiring the programming skills needed for more general-purpose software for mixed models. As the name suggests, one of the core features is a fully efficient, two-stage analysis for multiple environments, in which the full variance–covariance matrix of the Stage 1 genotype means is used in Stage 2. Another feature is directional dominance, including for polyploids, to account for inbreeding depression in outbred crops. StageWise enables selection with multi-trait indices, including restricted indices with one or more traits constrained to have zero response. For a potato dataset with 943 genotypes evaluated over 6 years, including the Stage 1 errors in Stage 2 reduced the Akaike Information Criterion (AIC) by 29, 67, and 104 for maturity, yield, and fry color, respectively. The proportion of variation explained by heterosis was largest for yield but still only 0.03, likely because of limited variation for the genomic inbreeding coefficient. Due to the large additive genetic correlation (0.57) between yield and maturity, naïve selection on an index combining yield and fry color led to an undesirable response for later maturity. The restricted index coefficients to maximize genetic merit without delaying maturity were identified. The software and three vignettes are available at https://github.com/jendelman/StageWise.

Increasing genomic prediction accuracy for unphenotyped full-sib families by modeling additive and dominance effects with large datasets in white spruce.

Genomic selection is becoming a standard technique in plant breeding and is now being introduced into forest tree breeding. Despite promising results to predict the genetic merit of superior material based on their additive breeding values, many studies and operational programs still neglect non-additive effects and their potential for enhancing genetic gains. Using two large comprehensive datasets totaling 4,066 trees from 146 full-sib families of white spruce (Picea glauca (Moench) Voss), we evaluated the effect of the inclusion of dominance on the precision of genetic parameter estimates and on the accuracy of conventional pedigree-based (ABLUP-AD) and genomic-based (GBLUP-AD) models. While wood quality traits were mostly additively inherited, considerable non-additive effects and lower heritabilities were detected for growth traits. For growth, GBLUP-AD better partitioned the additive and dominance effects into roughly equal variances, while ABLUP-AD strongly overestimated dominance. The predictive abilities of breeding and total genetic value estimates were similar between ABLUP-AD and GBLUP-AD when predicting individuals from the same families as those included in the training dataset. However, GBLUP-AD outperformed ABLUP-AD when predicting for new unphenotyped families that were not represented in the training dataset, with, on average, 22% and 53% higher predictive ability of breeding and genetic values, respectively. Resampling simulations showed that GBLUP-AD required smaller sample sizes than ABLUP-AD to produce precise estimates of genetic variances and accurate predictions of genetic values. Still, regardless of the method used, large training datasets were needed to estimate additive and non-additive genetic variances precisely. This study highlights the different quantitative genetic architectures between growth and wood traits. Furthermore, the usefulness of genomic additive-dominance models for predicting new families should allow practicing mating allocation to maximize the total genetic values for the propagation of elite material.

Characterization of semen type prevalence and allocation in Holstein and Jersey females in the United States

Our objective was to characterize semen type prevalence and allocation to inseminate US Holstein and Jersey females by year, parity, service number, and herd size. A secondary objective was to identify the prevalence of beef breed sires selected to create beef × Holstein and beef × Jersey crossbred calves. The final data set included 8,244,653 total inseminations of 4,880,752 Holstein females across 9,155 herds, and 435,267 total inseminations of 266,058 Jersey females across 2,759 herds from October 2019 to July 2021. This data set represents approximately 42 and 27% of the total dairy cows and heifers, respectively, across approximately 40% of the total licensed dairy herds in the continental United States. Holstein and Jersey females were inseminated with 1 of 4 semen types: (1) beef, (2) conventional, (3) sexed, or (4) other dairy. The top 4 beef breeds used to produce beef × Holstein and beef × Jersey crossbred calves, respectively, were Angus (55.1 and 39.1%), Limousin (13.9, and 23.5%), Simmental (11.7 and 20.5%), and Crossbreed Beef (11.3 and 4.8%). From 2019 to 2021, the use of sexed semen to inseminate Holstein and Jersey females increased from 11.0 and 24.5% to 17.7 and 32.1%, respectively, and the use of beef semen to inseminate Holstein and Jersey females increased from 18.2 and 11.4% to 26.1 and 21.2%, respectively. The use of beef semen to inseminate Holstein and Jersey females increased with increasing parity and service number, whereas the use of sexed semen decreased with increasing parity and service number supporting that farmers used sexed semen more aggressively in higher fertility and younger females with greater genetic merit. Overall, the increase in sexed and beef semen inseminations was driven primarily by larger herds. In conclusion, sexed and beef semen inseminations in US Holstein and Jersey females increased from 2019 to 2021 and was allocated differentially based on parity and service number. This increase was driven primarily by larger dairy herds possibly due to differences in reproductive performance and economies of scale.

Evaluation of the Crossbreeding Scheme and Farmers’ Perception of Awassi and Dorper Crossbred Sheep

The objectives of this study were to characterize the performance of crossbred sheep and crossbreeding scheme and to solicit farmers’ opinions about crossbred sheep. A total of 238 respondents were selected from five districts and data were collected through a personal interview, focus group discussion, measurement of animals, and field observation. Continuous type of data were analyzed using different procedures of SAS, while the estimated breeding value (EBV) for distributed rams was estimated by the WOMBAT software fitting animal model. The findings showed that sheep were the most significant species and that they were primarily raised for meat consumption and income generation. The proportions of crossbred sheep were 79.6% in Angot, 61.3% in Dessie zuria, 64.2% in Gazo, 80.6% in Legambo, and 27.5% in the Kobo area. The sheep crossbreeding program was constrained by feed shortage, lack of improved genotype, and diseases. The ongoing sheep crossbreeding program lacks a proper recording scheme, rams were not selected based on genetic merit, not exchanged in time, lack periodic importation of genetically unrelated rams, and lacks fixing the maximum exotic gene level suitable for the production system. The EBVs of Dorper crossbred rams for birth weight and weaning weight were 0.007 kg and 0.273 kg, respectively. Tikur sheep had an earlier age at first lambing (AFL) than Awassi x Tikur sheep. Likewise, the indigenous Wollo sheep had earlier AFL, short lambing interval, and produced a large number of lambs per lifetime than their Awassi crossbreds. Dorper crossbreds were preferred (9.30 - 72.2 times greater and P &lt; 0.001 ) for their growth rate, physical appearance, preference in the market or price, and milk production of ewes compared with indigenous Tumele sheep. The Awassi crossbred sheep were preferred (odds ratio = 12.7– 90.0 and P &lt; 0.001 ) due to their good physical appearance, fast growth rate, wool yield, milk yield, and better preference in the market compared with Tikur and Wollo sheep breeds. The implementation of the crossbreeding program needs some sort of revision, monitoring, and periodic evaluation. Besides, it must be accompanied by improved management to exploit the expected benefits from the crossbreeding program in the low-input production system.

RESTRICTED SELECTION INDEX FOR GROWTH TRAITS OF SHAMI KIDS

A Restricted Selection Index was constructed to genetically evaluate animals using a dataset composed of body weights of Shami kids at the ages of birth, weaning, and 6-month. The variance-covariance matrix (VCV) was generated and used to estimate genetic parameters for the index construction after adjusting the fixed effects; year, birth month, kid sex, type (single, twin or triplet) of birth, doe age, weights at kidding (KW), birth (BWT) and weaning (WWT) as covariates. General Linear Model and Restricted Maximum Likelihood methods were used to estimate BLUE for fixed effects and variance components for random effects, respectively. BW was 3.6 ± 0.017, WW 16.8 ± 0.10, and weight at 6 months (MWT) was 26.7 ± 0.21 Kg. With the exception of buck origin and doe age, all tested factors significantly affected growth traits. Heritability for BWT, WWT, and MWT was 0.70 ± 0.10, 0.32 ± 0.075, and 0.41 ± 0.12, and repeatability was 0.78, 0.35, and 0.47, respectively. Genetic and phenotypic correlations were positive and significant between BWT and WWT, and between WWT and MWT. The restricted selection index constructed for increasing weights at MWT and WWT with restriction on BWT yielded a strong correlation coefficient (rIA) between the genetic merit and the index at 0.54 (p&lt;0.01).

Genomic selection models substantially improve the accuracy of genetic merit predictions for fillet yield and body weight in rainbow trout using a multi-trait model and multi-generation progeny testing

BackgroundIn aquaculture, the proportion of edible meat (FY = fillet yield) is of major economic importance, and breeding animals of superior genetic merit for this trait can improve efficiency and profitability. Achieving genetic gains for fillet yield is possible using a pedigree-based best linear unbiased prediction (PBLUP) model with direct and indirect selection. To investigate the feasibility of using genomic selection (GS) to improve FY and body weight (BW) in rainbow trout, the prediction accuracy of GS models was compared to that of PBLUP. In addition, a genome-wide association study (GWAS) was conducted to identify quantitative trait loci (QTL) for the traits. All analyses were performed using a two-trait model with FY and BW, and variance components, heritability, and genetic correlations were estimated without genomic information. The data used included 14,165 fish in the pedigree, of which 2742 and 12,890 had FY and BW phenotypic records, respectively, and 2484 had genotypes from the 57K single nucleotide polymorphism (SNP) array.ResultsThe heritabilities were moderate, at 0.41 and 0.33 for FY and BW, respectively. Both traits were lowly but positively correlated (genetic correlation; r = 0.24), which suggests potential favourable correlated genetic gains. GS models increased prediction accuracy compared to PBLUP by up to 50% for FY and 44% for BW. Evaluations were found to be biased when validation was performed on future performances but not when it was performed on future genomic estimated breeding values.ConclusionsThe low but positive genetic correlation between fillet yield and body weight indicates that some improvement in fillet yield may be achieved through indirect selection for body weight. Genomic information increases the prediction accuracy of breeding values and is an important tool to accelerate genetic progress for fillet yield and growth in the current rainbow trout population. No significant QTL were found for either trait, indicating that both traits are polygenic, and that marker-assisted selection will not be helpful to improve these traits in this population.

Variability and genetic merits of white Guinea yam landraces in Nigeria.

Landraces represent a significant gene pool of African cultivated white Guinea yam diversity. They could, therefore, serve as a potential donor of important traits such as resilience to stresses as well as food quality attributes that may be useful in modern yam breeding. This study assessed the pattern of genetic variability, quantitative trait loci (QTLs), alleles, and genetic merits of landraces, which could be exploited in breeding for more sustainable yam production in Africa. A total of 86 white Guinea yam landraces representing the popular landraces in Nigeria alongside 16 elite clones were used for this study. The yam landraces were genotyped using 4,819 DArTseq SNP markers and profiled using key productivity and food quality traits. Genetic population structure through admixture and hierarchical clustering methods revealed the presence of three major genetic groups. Genome-wide association scan identified thirteen SNP markers associated with five key traits, suggesting that landraces constitute a source of valuable genes for productivity and food quality traits. Further dissection of their genetic merits in yam breeding using the Genomic Prediction of Cross Performance (GPCP) allowed identifying several landraces with high crossing merit for multiple traits. Thirteen landraces were identified as potential genitors to develop segregating progenies to improve multiple traits simultaneously for desired gains in yam breeding. Results of this study provide valuable insights into the patterns and the merits of local genetic diversity which can be utilized for identifying desirable genes and alleles of interest in yam breeding for Africa.

Performance Based on Measurements from Individual-Tree Progeny Tests Strongly Predicts Early Stand Yield in Loblolly Pine

Abstract To facilitate the utility of genetic improvement in loblolly pine, individual-tree volume (productivity) scores estimated from single-tree plot or row-plot progeny test designs were compared with stand-level volume per unit area from block plots. A large number of families representing a wide range of progeny test scores for volume were established in growth and yield trials to generalize the results to families created by the breeding program. Individual-tree volume scores from progeny tests strongly corresponded with stand-level volume from block plots, especially after accounting for site quality and the risk of fusiform rust disease. A ten-point increase in the volume score from progeny test data was estimated to increase stand-level volume by 3.9 m3 ha-1 at age 6 years. A prediction model is presented that includes a new statistic, rust risk index, which is the expected rust incidence for a family at a new site when the hazard of rust for a checklot can be estimated from historical data. The study results through age 6 years corroborate the Performance Rating System as effective in guiding family deployment decisions. The models presented are based on pre-crown closure data at 6 years and will be updated with older measurements as the study matures. Study Implications: The Performance Rating System (PRS™) has been a successful tool for presenting genetic merit of improved loblolly pine families for landowners and forest managers in a more coherent and standardized manner. This system can be easily applied in other forest tree improvement programs, because it makes genetic improvement user-friendly for silviculturists and forest managers. Landowners can use this system to make decisions for selecting improved families suited to their specific forest management objectives. Seed orchard and nursery managers also depend on the PRS to choose the families to produce and as a third-party verification to market their genetic merit to customers. This study demonstrates that higher stand-level volume per unit area can be achieved when forest managers plant fast growing families with low fusiform rust disease risk on productive sites. The combined effect of genetic improvement for productivity and fusiform rust disease resistance is significant on stand-level volume per unit area.

A refined culture system of oocytes from early antral follicles promotes oocyte maturation and embryo development in cattle.

The proposed culture system improves the current state of in vitro culture of growing oocytes in the bovine species and allows access to the untapped gamete reserve, thus improving reproductive efficiency. The present study aimed to improve the in vitro culture of bovine oocytes collected from early antral follicles (EAFs) to support the progressive acquisition of meiotic and developmental competence. The rationale that drove the development of such a culture system was to maintain as much as possible the physiological conditions that support the oocyte growth and differentiation in vivo. To this extent, oocytes were cultured for 5 days, which parallels the transition from early to medium antral follicles (MAFs) in the bovine, and supports promoting a 3D-like structure were provided. Additionally, the main hormones (follicle-stimulating hormone, estradiol, progesterone, and testosterone) were added in concentrations similar to the ones previously observed in bovine EAFs. The meiotic arrest was imposed using cilostamide. The cultured cumulus-oocyte complexes (COCs) reached a mean diameter of 113.4 ± 0.75 µm and showed a progressive condensation of the chromatin enclosed in the germinal vesicle (GV), together with a gradual decrease in the global transcriptional activity, measured by 5-ethynyl uridine incorporation. The described morpho-functional changes were accompanied by an increased ability to mature and develop to the blastocyst stage in vitro, although not matching the rates obtained by MAF-retrieved oocytes. The described system improves the current state of in vitro culture of growing oocytes in the bovine species, and it can be used to increase the number of gametes usable for in vitro embryo production in animals of high genetic merit or with specific desirable traits.