Development of genomic predictions for Angus cattle in Brazil incorporating genotypes from related American sires

Genomic prediction has become the new standard for genetic improvement programs, and currently, there is a desire to implement this technology for the evaluation of Angus cattle in Brazil. Thus, the main objective of this study was to assess the feasibility of evaluating young Brazilian Angus (BA) bulls and heifers for 12 routinely recorded traits using single-step genomic BLUP (ssGBLUP) with and without genotypes from American Angus (AA) sires. The second objective was to obtain estimates of effective population size (Ne) and linkage disequilibrium (LD) in the Brazilian Angus population. The dataset contained phenotypic information for up to 277,661 animals belonging to the Promebo® breeding program, pedigree for 362,900, of which 1,386 were genotyped for 50k, 77k, and 150k SNP panels. After imputation and quality control, 61,666 SNP were available for the analyses. In addition, genotypes from 332 American Angus (AA) sires widely used in Brazil were retrieved from the AA Association database to be used for genomic predictions. Bivariate animal models were used to estimate variance components, traditional EBV, and genomic EBV (GEBV). Validation was carried out with the linear regression method (LR) using young-genotyped animals born between 2013 and 2015 without phenotypes in the reduced dataset and with records in the complete dataset. Validation animals were further split into progeny of BA and AA sires to evaluate if their progenies would benefit by including genotypes from AA sires. The Ne was 254 based on pedigree and 197 based on LD, and the average LD (±SD) and distance between adjacent SNPs across all chromosomes was 0.27 (±0.27) and 40743.68 bp, respectively. Prediction accuracies with ssGBLUP outperformed BLUP for all traits, improving accuracies by, on average, 16% for BA young bulls and heifers. The GEBV prediction accuracies ranged from 0.37 (total maternal for weaning weight and tick count) to 0.54 (yearling precocity) across all traits, and dispersion (LR coefficients) fluctuated between 0.92 and 1.06. Inclusion of genotyped sires from the AA improved GEBV accuracies by 2%, on average, compared to using only the BA reference population. Our study indicated that genomic information could help to improve GEBV accuracies and hence genetic progress in the Brazilian Angus population. The inclusion of genotypes from American Angus sires heavily used in Brazil just marginally increased the GEBV accuracies for selection candidates.

Impact of mother genetic and resource environment on her offspring’s growth features in Munjal sheep

Summary The present study evaluated maternal and additive influences that contribute to phenotypic variation in various growth traits in Munjal sheep. The targeted traits that pertained to 2278 records of 706 lambs were birth weight (BWT), weaning weight (WT3), 6-month body weight (WT6), 12-month body weight (WT12), average daily gain (ADG1: 0–3 months; ADG2: 3–6 months, ADG3: 6–12 months of age) and their corresponding Kleiber ratios designated as KR1, KR2 and KR3. The direct heritability estimates for BWT, WT3, WT6, WT12, ADG1, ADG2, ADG3, KR1, KR2 and KR3 under animal models were 0.20 ± 0.08, 0.28 ± 0.08, 0.17 ± 0.07, 0.47 ± 0.09, 0.33 ± 0.08, 0.09 ± 0.06, 0.36 ± 0.10, 0.33 ± 0.08, 0.09 ± 0.06 and 0.32 ± 0.10, respectively. The estimates of maternal genetic effects contributed significantly and were 8% and 7% for BWT and WT3 traits, respectively, which highlighted the considerable role of maternal effects on early growth traits. Genetic and phenotypic correlations ranged from moderate to high between weaning and post-weaning traits. It was concluded that early selection that considered additive as well as maternal effects at weaning age may be delivered to the desired genetic progress in Munjal sheep.

Genetic Yield Gains and Changes in Morphophysiological-Related Traits of Winter Wheat in Southern Chilean High-Yielding Environments

Both the temperate-humid zone and the southern part of the Mediterranean climate region of Chile are characterized by high wheat productivity. Study objectives were to analyze the yield potential, yield progress, and genetic progress of the winter bread wheat (Triticum aestivum L.) cultivars and changes in agronomic and morphophysiological traits during the past 60 years. Thus, two field experiments: (a) yield potential and (b) yield genetic progress trials were conducted in high-yielding environments of central-southern Chile during the 2018/2019 and 2019/2020 seasons. In addition, yield progress was analyzed using yield historical data of a high-yielding environment from 1957 to 2017. Potential yield trials showed that, at the most favorable sites, grain yield reached ∼20.46 Mg ha–1. The prolonged growing and grain filling period, mild temperatures in December-January, ample water availability, and favorable soil conditions explain this high-potential yield. Yield progress analysis indicated that average grain yield increased from 2.70 Mg ha–1 in 1959 to 12.90 Mg ha–1 in 2017, with a 128.8 kg ha–1 per-year increase due to favorable soil and climatic conditions. For genetic progress trials, genetic gain in grain yield from 1965 to 2019 was 70.20 kg ha–1 (0.49%) per year, representing around 55% of the yield progress. Results revealed that the genetic gains in grain yield were related to increases in biomass partitioning toward reproductive organs, without significant increases in Shoot DW production. In addition, reducing trends in the NDVI, the fraction of intercepted PAR, the intercepted PAR (form emergence to heading), and the RGB-derived vegetation indices with the year of cultivar release were detected. These decreases could be due to the erectophile leaf habit, which enhanced photosynthetic activity, and thus grain yield increased. Also, senescence of bottom canopy leaves (starting from booting) could be involved by decreasing the ability of spectral and RGB-derived vegetation indices to capture the characteristics of green biomass after the booting stage. Contrary, a positive correlation was detected for intercepted PAR from heading to maturity, which could be due to a stay-green mechanism, supported by the trend of positive correlations of Chlorophyll content with the year of cultivar release.

Estimation of Genetic Parameters of Biomass Production and Composition Traits in Miscanthus Sinensis Using a Staggered-start Design

Traits for biomass production and composition make Miscanthus a promising bioenergy crop for different bioconversion routes. They need to be considered in miscanthus breeding programs as they are subjected to genetic and genetic x environment factors. The objective was to estimate the genetic parameters of an M. sinensis population grown during four years in two French locations. In each location, the experiment was established according to a staggered-start design in order to decompose the year effect into age and climate effects. Linear Mixed Models were used to estimate genetic variance, genotype x age, genotype x climate interaction variances and residual variances. Individual plant broad-sense heritability means ranged from 0.42 to 0.62 for biomass production traits, and were more heritable than biomass composition traits with means ranging from 0.26 to 0.47. Heritability increased through time for most of the biomass production and composition traits. Low genetic variance along with large genotype x age and genotype x climate interaction variances tended to decrease the heritability of biomass production traits for young plant ages. Most of the production traits showed large interaction variances for age and climate in both locations, while biomass composition traits highlighted large interaction variances due to climate in Orléans. The genetic and phenotypic correlations between biomass production and composition traits were moderate and positive, while hemicelluloses were negatively correlated with all traits. Efficient genetic progress is achievable for miscanthus breeding when plants get older. The joint improvement of biomass production and composition traits would help provide a better response of miscanthus to selection.

PROGRESSO GENÉTICO E SELEÇÃO PRECOCE EM GENÓTIPOS DE PINHÃO-MANSO EM FASE JUVENIL

O pinhão manso (Jatropha curcas L.) é uma euforbiácea utilizada na produção de biodiesel. A espécie possui base genética estreita o que dificulta o processo de lançamento de cultivares. Caracterizar precocemente os genótipos constitui etapa importante no melhoramento da cultura. Objetivou-se com este estudo realizar uma seleção precoce em caracteres morfoagronômicos, predizer o progresso genético de tais caracteres e indicar genitores potenciais para obtenção de progênies. O delineamento experimental utilizado foi o de blocos casualizados com 26 tratamentos e três repetições. As variáveis morfoagronômicas foram analisadas via modelos mistos e o progresso genético obtido pela seleção direta, indireta e índices de seleção. A dissimilaridade genética foi determinada pela distância de Mahalanobis, com agrupamento hierárquico UPGMA e coeficiente de correlação cofenética adquirido de 1.000 permutações. As estimativas demonstraram variabilidade genética, com identificação de genótipos juvenis promissores. Os genótipos JCCE034, JCCE014 e JCCE103 apresentam melhores progressos genéticos e os genótipos JCCE036 e JCCE86 apresentam maiores divergências genéticas, formando clusters individuais. Os genótipos de pinhão-manso são promissores na seleção precoce e possuem satisfatórios ganhos com a seleção para os caracteres avaliados. Os genótipos apresentam boa capacidade para compor grupos de genitores em cruzamentos direcionados, constituindo populações-base no melhoramento de J. curcas. Palavras-chave: Jatropha curcas; diversidade genética; ganhos com a seleção; índices de seleção. Genetic progress and early selection of juvenile physic nut genotypes ABSTRACT: Physic nut (Jatropha curcas L.) is a euphorbia used in the production of biodiesel. The species has a narrow genetic base which the process of launching cultivars is difficult. Early characterization of the genotypes is an important step in crop breending. The aims of this study were to perform an early selection in morpho-agronomic traits, to predict the genetic progress of such traits and to indicate potential parents for progeny development. The experimental design used for the randomized blocks with 26 treatments and three replications. The morpho-agronomic traits were analyzed via mix models and the genetic progress added by direct, indirect selection and selection indexes. The genetic dissimilarity was provided by the Mahalanobis distance, with UPGMA hierarchical grouping and co-phenetic correlation coefficient acquired from 1,000 permutations. The indicators demonstrated genetic variability, with the identification of promising juvenile genotypes. The genotypes JCCE034, JCCE014 and JCCE103 show better genetic progress and the genotypes JCCE036 and JCCE86 show greater genetic divergences, forming individual clusters. J. curcas genotypes are promising in early selection and have satisfactory genetics gains for the traits. The genotypes have a good ability to compose groups of parents in targeted crosses, constituting base populations in the improvement of J. curcas. Keywords: Jatropha curcas; genetic diversity; selection gains; selection indexes.

Genetic and non-genetic effects associated with ewe productivity in Harnali sheep

Summary The objective of the current study was to estimate the genetic parameters for ewe productivity traits of Harnali sheep by examining non-genetic effects. The data records of 440 animals born to 85 sires and 259 dams were collected with respect to various traits such as litter size at birth (LSB), litter weight at birth (LWB), litter size at weaning (LSW), litter weight at weaning (LWW) and age at first lambing (AFL) for the period of 2001 to 2020. Genetic parameters were estimated by fitting a series of animal models using an average information restricted maximum likelihood (REML) algorithm in WOMBAT software. Least-squares analysis revealed significant (P < 0.05) influences of period of lambing, age and weight of ewe at lambing on the studied traits. These results indicated that heavier ewes had significantly higher (P < 0.05) values of litter weight traits than their counterparts. On the basis of likelihood ratio test, the estimates of direct heritability under best model for AFL, LSB, LWB, LSW and LWW were 0.06, 0.18, 0.09, 0.07 and 0.16, respectively. Maternal permanent environment effect made a significant contribution to the LSB trait (0.20). The genetic correlation between litter size and LWW was negative, while the remaining correlations were positive. The present results suggest that selection based on ewe productivity traits will result in low genetic progress and therefore the management role is more important for better gains.

Definition of Environmental Variables and Critical Periods to Evaluate Heat Tolerance in Large White Pigs Based on Single-Step Genomic Reaction Norms

Properly quantifying environmental heat stress (HS) is still a major challenge in livestock breeding programs, especially as adverse climatic events become more common. The definition of critical periods and climatic variables to be used as the environmental gradient is a key step for genetically evaluating heat tolerance (HTol). Therefore, the main objectives of this study were to define the best critical periods and environmental variables (ENV) to evaluate HT and estimate variance components for HT in Large White pigs. The traits included in this study were ultrasound backfat thickness (BFT), ultrasound muscle depth (MDP), piglet weaning weight (WW), off-test weight (OTW), interval between farrowing (IBF), total number of piglets born (TNB), number of piglets born alive (NBA), number of piglets born dead (NBD), number of piglets weaned (WN), and weaning to estrus interval (IWE). Seven climatic variables based on public weather station data were compared based on three criteria, including the following: (1) strongest G×E estimate as measured by the slope term, (2) ENV yielding the highest theoretical accuracy of the genomic estimated breeding values (GEBV), and (3) variable yielding the highest distribution of GEBV per ENV. Relative humidity (for BFT, MDP, NBD, WN, and WW) and maximum temperature (for OTW, TNB, NBA, IBF, and IWE) are the recommended ENV based on the analyzed criteria. The acute HS (average of 30 days before the measurement date) is the critical period recommended for OTW, BFT, and MDP in the studied population. For WN, WW, IBF, and IWE, a period ranging from 34 days prior to farrowing up to weaning is recommended. For TNB, NBA, and NBD, the critical period from 20 days prior to breeding up to 30 days into gestation is recommended. The genetic correlation values indicate that the traits were largely (WN, WW, IBF, and IWE), moderately (OTW, TNB, and NBA), or weakly (MDP, BFT, and NBD) affected by G×E interactions. This study provides relevant recommendations of critical periods and climatic gradients for several traits in order to evaluate HS in Large White pigs. These observations demonstrate that HT in Large White pigs is heritable, and genetic progress can be achieved through genetic and genomic selection.

Amélioration génétique bovine par voie de croisement et de sélection en Afrique Tropicale : Expériences du Cameroun

Ce travail passe en revue les résultats des travaux de recherches sur l’amélioration génétique des zébus locaux (Goudali, White et Red Fulani) par voie de sélection et de croisement avec les races exotiques (Holstein, Montbéliarde, Brahman américain, Jersiais, Tarentaise, Limousine et Charolaise). Ces travaux ont été conduits depuis 1952 dans les Centres de Recherches Zootechniques de Wakwa et Bambui par l’Institut de Recherches Zootechniques (IRZ, aujourd’hui connue sous le nom de l’Institut de Recherche Agricole pour le Développement) du Cameroun, en système d’élevage semi-intensif dans les zones des hautes savanes guinéennes et des hauts plateaux de l’Ouest Cameroun. Les données proviennent des rapports d’activité et de consultations, des publications scientifiques et des entrevues. L’objectif est de ressortir les résultats saillants utiles pour les décideurs politiques, les chercheurs et les éleveurs. Les principaux résultats montrent que le potentiel laitier des croisés est généralement supérieur (>4 litres) à celui des races locales (>3,5 litres). Les génotypes ayant moins de 75% de sang exotique sont les plus performants en lait et viande. Les causes de mortalité par ordre d’importance sont nutritionnelles (36,8%), accidentelles (29,6%), pathologiques (21,1%), parasitaires (7,7%) et reproductives (4,8%). Par rapport aux autres produits de croisement, les croisés Holsteins ont été plus lourds à la naissance (34,75 kg) avec une vitesse de croissance plus élevée (0,46 kg), une production laitière plus élevée (5,47 ± 0,17 litres), plus précoces (40,87 mois) et moins susceptibles au stress Nuenvironnemental. Pour la filière bovin-à-viande, les performances de viande de la race synthétique Wakwa sont légèrement supérieures à celles des zébus Goudali sélectionnés dans le cheptel local. Cependant, le taux de susceptibilité à la dermatophilose est estimé à 71,0%, 34,4% et 5,0% chez le pur, ½ et ¼ sang Brahman, respectivement. La sélection massale du zébu Goudali (variété Ngaoundéré) et la race synthétique Wakwa a permis d’obtenir des progrès génétiques significatifs, soient, respectivement, 8,60 kg et 20,40 kg. Cependant, les corrélations génétiques négatives entre les effets directs et maternels montrent que le progrès génétique serait davantage plus important si la sélection était concentrée sur les performances directes et maternelles. Les expériences d’insémination artificielle menées à la SODEPA et à « Tadu Dairy Cooperative Society»montrent que l’industrie laitière est une entreprise rentable avec un rapport bénéfice-coût de 4,21. This work reviews the results of research on the genetic improvement of local zebus (Gudali, White and Red Fulani) through selection and crossbreeding with exotic cattle breeds (Holstein, Montbeliard, American Brahman, Jersey, Tarentaise, Limousine and Charolais). This work was started since 1952 by Institute of Animal Research (IRZ, now known as the Institute of Agricultural Research for Development) at the Wakwa and Bambui Research Centers, under semi-intensive management conditions in the high Guinea savannah areas of the Adamawa Plateau and the highlands of West Cameroon. Data were obtained from activity and consultation reports, scientific publications and interviews. The objective is to highlight salient findings that are useful for policy makers, researchers and livestock producers. The main results show that the milk potential of crosses is generally higher (>4 liters) than that of local breeds (>3.5 liters). Genotypes with less than 75% exotic blood had the best milk and meat production performance. The reported causes of mortality in order of importance are nutritional (36.8%), accidental (29.6%), pathological (21.1%), parasitic (7.7%) and reproductive (4.8%). Compared to the others crosses, Holstein crosses were found to be relatively heavier at birth (34.75 kg) with a higher growth rate (0.46 kg), higher daily milk production (5.47 ± 0.17 liters), earlier maturing (40.87 months), but more adapted to the breeding conditions and less susceptible to environmental stress. For the beef industry, the meat performance of the synthetic Wakwa breed is slightly better than that of the Gudali zebus selected from the local herd. However, the susceptibility rate to dermatophilosis was estimated at 71.0%, 34.4% and 5.0% in pure, ½ and ¼ blood Brahman, respectively. Individual selection of the Gudali zebu (Ngaoundéré subtype) and the synthetic Wakwa breed has resulted in significant genetic progress, 8.60 kg and 20.40 kg, respectively. However, the negative genetic correlations between direct and maternal effects showed that genetic progress would be more important if selection was concentrated on direct and maternal performance. Artificial insemination experiments conducted at SODEPA and Tadu Dairy Cooperative Society showed that the dairy industry is a profitable enterprise with a benefit-cost ratio of 4.21.