Low Heritability Research Articles

Selection of ideal genotypes in peppers with ornamental potential

ABSTRACT Ornamental peppers have a significant economic importance in the national and international markets; however, few cultivars intended for this purpose are grown in Brazil. The objective of this study was to select partially inbred lines (PIL) of peppers with ornamental potential, based on quantitative and qualitative variables with high heritability. The study was conducted over six generations for 4 consecutive years, using the single seed descent method. The last phase (VI) consisted of growing plants of the F5 generation for selection. Qualitative (LD) and quantitative (QD) descriptors were considered and the ideal genotypes were defined. The statistical analyses consisted of estimating variance components and genetic parameters and predicting genetic values, using REML/BLUP for QD, except for cycle to flowering (CF) and cycle to maturation (CM), which were analysed qualitatively. Therefore, CF and CM were analysed through frequency distribution of continuous variables within class intervals. Descriptive statistics were used to evaluate LD. The results showed that residual values exceeded genetic values, resulting in low heritability for QD, and therefore, they were not considered for PIL selection. Regarding LD, genetic variability was found among the population genotypes for all evaluated descriptors. The selection based on ideal genotypes enabled the selection of 82 PIL with LD of high ornamental value, which differ from the materials already available on the market. The selected genotypes will be used for developing future generations until allele fixation, focussed on subsequent selection of candidate lines for new ornamental pepper cultivars.

The timing of reproduction is responding plastically, not genetically, to climate change in yellow-bellied marmots (Marmota flaviventer).

With global climates changing rapidly, animals must adapt to new environmental conditions with altered weather and phenology. The key to adapting to these new conditions is adjusting the timing of reproduction to maximize fitness. Using a long-term dataset on a wild population of yellow-bellied marmots (Marmota flaviventer) at the Rocky Mountain Biological Laboratory (RMBL), we investigated how the timing of reproduction changed with changing spring conditions over the past 50 years. Marmots are hibernators with a 4-month active season. It is thus crucial to reproduce early enough in the season to have time to prepare for hibernation, but not too early, as snow cover prevents access to food. Importantly, climate change in this area has, on average, increased spring temperatures by 5°C and decreased spring snowpack by 50 cm over the past 50 years. We evaluated how female marmots adjust the timing of their reproduction in response to changing conditions and estimated the importance of both microevolution and plasticity in the variation in this timing. We showed that, within a year, the timing of reproduction is not as tightly linked to the date a female emerges from hibernation as previously thought. We reported a positive effect of spring snowpack but not of spring temperature on the timing of reproduction. We found inter-individual variation in the timing of reproduction, including low heritability, but not in its response to changing spring conditions. There was directional selection for earlier reproduction since it increased the number and proportion of pups surviving their first winter. Taken together, the timing of marmot reproduction might evolve via natural selection; however, plastic changes will also be extremely important. Further, future studies on marmots should not operate under the assumption that females reproduce immediately following their emergence.

Protoplasts Isolation from Sardinian Germoplasm of Saffron (Crocus sativus L.)

Genetic studies of saffron indicate low heritability and strong environmental effects for most of the traits examined, suggesting local variability that has been selected over time. In vitro culture can be of support for genetic improvement programs, multiplication, or production of secondary metabolites. This is particularly relevant for saffron due to its triploidy. In the present work, the in vitro culture of Sardinian genotypes of saffron, using protoplasts, is described. Protoplasts were obtained from young leaves using a KAO enzyme mixture and cultured on KM8P substrate. The use of Evans et al. enzymes did not result in the production of protoplasts. The results presented in this work should be considered as the initial phase in the in vitro production of secondary metabolites obtained from local saffron genotypes.

Genetic Variability, Heritability and Genetic Advance Studies in Diverse Genotypes of Tomato (Solanum lycopersicum L.)

The present experiment was conducted utilizing sixteen diverse genotypes of tomato in the autumn-winter season of 2022-23 for assessing the genetic variability, heritability and genetic advance for different growth, reproductive and yield attributes. Analysis of variance revealed significant differences among all the genotypes for all the characters. High degree of genetic variability was observed for all the traits that showed the traits were suitable for selection for further breeding purposes. GCV was higher than PCV for all the characters under study.High PCV accompanied by high GCV was recorded for fruit yield per plant (kg) and fruit yield per plot (kg), number of clusters per plant, plant height (cm), number of primary branches per plant, number of fruits per plant, locule number, average fruit weight (g), number of flower per cluster, however the difference between the PCV and GCV was paltry, which indicating the high contribution of genetic component in phenotypic expression of these characters that provide higher selection efficiency. High heritability along with low genetic advance was observed for, days to first flowering, days to first fruit setting, days to 50% flowering, fruit equatorial diameter (mm), polar diameter (mm), locule number, number of fruits/plantand fruit yield / plant (kg), whereas low heritability with low genetic advance was revealed for pericarp thickness (mm) and no of primary branches/plant which suggests that these traits are highly influenced by the environmental effects and governed by the non-additive gene action, hence selection would not be effects for these particular traits. High heritability coupled with high genetic advance (GA) was recorded for average fruit weight (g) andplant height (cm) which indicates the presence of additive gene action; hence selection could be employed for these traits and provide the opportunity for higher selection response.

Genetic architecture of individual meiotic crossover rate and distribution in Atlantic Salmon

Meiotic recombination through chromosomal crossovers ensures proper segregation of homologous chromosomes during meiosis, while also breaking down linkage disequilibrium and shuffling alleles at loci located on the same chromosome. Rates of recombination can vary between species, but also between and within individuals, sex and chromosomes within species. Indeed, the Atlantic salmon genome is known to have clear sex differences in recombination with female biased heterochiasmy and markedly different landscapes of crossovers between males and females. In male meiosis, crossovers occur strictly in the telomeric regions, whereas in female meiosis crossovers tend to occur closer to the centromeres. However, little is known about the genetic control of these patterns and how this differs at the individual level. Here, we investigate genetic variation in individual measures of recombination in > 5000 large full-sib families of a Norwegian Atlantic salmon breeding population with high-density SNP genotypes. We show that females had 1.6 × higher crossover counts (CC) than males, with autosomal linkage maps spanning a total of 2174 cM in females and 1483 cM in males. However, because of the extreme telomeric bias of male crossovers, female recombination is much more important for generation of new haplotypes with 8 × higher intra-chromosomal genetic shuffling than males. CC was heritable in females (h2 = 0.11) and males (h2 = 0.10), and shuffling was also heritable in both sex but with a lower heritability in females (h2 = 0.06) than in males (h2 = 0.11). Inter-sex genetic correlations for both traits were close to zero, suggesting that rates and distribution of crossovers are genetically distinct traits in males and females, and that there is a potential for independent genetic change in both sexes in the Atlantic Salmon. Together, these findings give novel insights into the genetic architecture of recombination in salmonids and contribute to a better understanding of how rates and distribution of recombination may evolve in eukaryotes more broadly.

Heterosis from eucalypt single and multi-cross hybrids

Hybridizing is one of the most important ways to genetically improve eucalypts; especially to tropical species. Because of the high efficiency of asexual using hybrid heterosis, the current planting eucalypt varieties in most tropical areas in the world are hybrids. It’s well known that crossing different eucalypt species in different ways can create hybrids with different characters. But, it’s unclear what kind of species matings tend to create more heterosis. Here we systematically made and tested hybrids of: pure species by pure species (single cross), pure species by hybrids (three-way cross), hybrids by hybrids (double cross). The tropical eucalypt species we used as parents include: Eucalyptus urophylla, E. grandis, E. pellita, E. tereticornis and hybrids between them. The field testing results found: the overall performance of tree volume was: single cross > three way cross > intraspecies cross > double cross. Their 4-year advantages over intraspecies cross were: 29.9%, 8.0% and -12.5%. The coefficient of variation of the 4 types were: 55.3%, 61.2%, 64.0% and 67.1%. As for the survival rate, 4-year result was: double cross (72.6%) > three way cross (71.6%) > single cross (70.8%) > intraspecies cross (54.0%). This shows that the interspecies hybrids had similar environmental adaption, and they were all significantly higher than that of intraspecies cross. The single and multi-cross hybrids had similar coefficient of variation on survival rate. Combining with the results on family and individual tree level heterosis frequency and magnitude, we found that single-cross has more heterosis on volume growth while muti-cross has more heterosis on adaption. Genetic parameter analysis showed that single-cross hybrids have both high additive and high dominant heritability. But the heritability value on different species combinations can be very different. Three way-cross hybrids had the highest additive heritability, but very low dominant heritability. The double-cross hybrids had high dominant heritability, but very low additive heritability.

Nesting cavity diameter has implications for management of the alfalfa leafcutting bee (Hymenoptera: Megachilidae).

Body size influences performance in many bee species and may be influenced by nesting cavity diameter in cavity-nesting bees. Megachile rotundata (Fabricius) (Hymenoptera: Megachilidae) is a commercially-managed, solitary cavity-nesting bee. In M. rotundata body size has low heritability and is strongly influenced by the size of the larval provision and the diameter of the nesting cavity. Commercial nesting boxes have cavities that are 7 mm in diameter. Our goal was to examine the effects that nesting cavity diameter has on M. rotundata body size and performance by manipulating the size of cavities that are available for nesting. We provided bees with nesting cavities that ranged in size from 4 to 9 millimeters in 1 mm increments. To assess body size we measured mass and intertegular span. To assess performance we measured wing area, wing loading, sex, overwintering survival, pollen ball occurrence, and diapause status in the offspring. We also examined the reproductive output from the different nest cavity diameters. We found that the 8 mm cavities reared bees with the largest mass, and 4 mm cavities reared bees with the smallest mass. We determined that the 7 mm nesting cavity is optimal for offspring yield, the 8 mm nesting cavity is optimal for performance, and the 5 mm nesting cavity may be optimal for conservation efforts of other cavity-nesting bees. Based on the desired outcome of the bee managers, nest sizes differing from the standard may provide an advantage.

Disentangling the dynamics of energy allocation to develop a proxy for robustness of fattening pigs

BackgroundThere is a growing need to improve robustness of fattening pigs, but this trait is difficult to phenotype. Our first objective was to develop a proxy for robustness of fattening pigs by modelling the longitudinal energy allocation coefficient to growth, with the resulting environmental variance of this allocation coefficient considered as a proxy for robustness. The second objective was to estimate its genetic parameters and correlations with traits under selection and with phenotypes that are routinely collected. In total, 5848 pigs from a Pietrain NN paternal line were tested at the AXIOM boar testing station (Azay-sur-Indre, France) from 2015 to 2022. This farm is equipped with an automatic feeding system that records individual weight and feed intake at each visit. We used a dynamic linear regression model to characterize the evolution of the allocation coefficient between the available cumulative net energy, which was estimated from feed intake, and cumulative weight gain during the fattening period. Longitudinal energy allocation coefficients were analysed using a two-step approach to estimate both the genetic variance of the coefficients and the genetic variance in their residual variance, which will be referred to as the log-transformed squared residual (LSR).ResultsThe LSR trait, which could be interpreted as an indicator of the response of the animal to perturbations/stress, showed a low heritability (0.05 ± 0.01), a high favourable genetic correlation with average daily growth (− 0.71 ± 0.06), and unfavourable genetic correlations with feed conversion ratio (− 0.76 ± 0.06) and residual feed intake (− 0.83 ± 0.06). Segmentation of the population in four classes using estimated breeding values for LSR showed that animals with the lowest estimated breeding values were those with the worst values for phenotypic proxies of robustness, which were assessed using records routinely collected on farm.ConclusionsResults of this study show that selection for robustness, based on estimated breeding values for environmental variance of the allocation coefficients to growth, can be considered in breeding programs for fattening pigs.

Genetic covariance components for measures of nitrogen utilization in grazing dairy cows

Improved nitrogen utilization of dairy production systems should improve not only the economic output of the systems but also the environmental metrics. One strategy to improve efficiency is through breeding programs. Improving a trait through breeding is conditional on the presence of exploitable genetic variability. Using a database of 1,291 deeply phenotyped grazing dairy cows, the genetic variability for 2 definitions of nitrogen utilization was studied: nitrogen use efficiency (i.e., nitrogen output in milk and meat divided by nitrogen available) and nitrogen balance (i.e., nitrogen available less nitrogen output in milk and meat). Variance components for both variables were estimated using animal repeatability linear mixed models. Genetic variability was detected for both nitrogen utilization metrics, even though their heritability estimates were low (<0.10). Validation of genetic evaluations revealed that animals divergent for nitrogen use efficiency or nitrogen balance indeed differed phenotypically, further demonstrating that breeding for improved nitrogen efficiency should result in a shift in the population mean toward better efficiency. Nitrogen use efficiency and nitrogen balance were not genetically correlated with each other (<|0.28|), and neither metric was correlated with milk urea nitrogen (<|0.12|). Nitrogen balance was unfavorably correlated with milk yield, showing the importance of including the nitrogen utilization metrics in a breeding index to improve nitrogen utilization without negatively impacting milk yield. In conclusion, improvement of nitrogen utilization through breeding is possible, even if more nitrogen utilization phenotypic data need to be collected to improve the selection accuracy considering the low heritability estimates.

PSXII-4 Genomic Improvement of Disease Resistance Using Two Breeding Strategies in a Population of Penaeus Vannamei (Pacific White shrimp): a Simulation Study

Abstract This study aimed to investigate the impact of SNP density chip and genotyping strategies on the accuracy of genomic estimated breeding values (EBV) in a simulated population mimicking a commercial Pacific white shrimp (Penaeus vannamei) breeding program. The chromosome number and length mimicked the P. vannamei genome. To create an initial linkage disequilibrium (LD), a historical population of 5,000 animals was randomly bred for 1,000 generations and included a bottleneck on generation 750. In the last generation of the historical population, animals were randomly selected to create a breeding population with an effective population size (Ne) of 40. From the breeding population, a total of 40,000 animals were simulated over 20 generations. Phenotypes for a trait with a heritability of 0.1 was simulated, and genetic variance was 100% explained by 1,000 QTLs. Phenotypes and genotypes were saved for all animals in the last 10 generations, while pedigree from all 20 generations was used. To mimic the selection of young animals, a forward-in-time prediction was implemented by masking the phenotypes from the 20th generation in the data analysis. The accuracy of prediction was the correlation between the simulated true breeding value and the EBV in the last generation. Genomic information consisted of SNP chips with 6K, 11K, 22K, 45K, and 90K markers evenly spaced across the genome. The two breeding strategies considered in this study were 1) 25 families with 40 animals each, and 2) 50 families with 20 animals each. Additionally, the number of generations with phenotypes varied from nine to one. This was done to identify the minimum number of generations to collect data, as phenotyping individuals may be challenging in aquaculture. In all scenarios, genomic selection outperformed family selection. Results indicated that genotyping more individuals within families, instead of more families with fewer individuals, improved the accuracy of predictions. Furthermore, the maximum accuracy was achieved with 45K and 90K SNPs in both scenarios, showing that SNP density will reach a plateau. Finally, maximum accuracy plateaued at five generations. Finally, having one generation with phenotypes and genotypes yielded greater accuracies than nine generations with only phenotypes. Overall, the results from the present study suggest that genomic selection using the single-step genomic best linear unbiased prediction (ssGBLUP) methodology is a feasible tool to improve P. vannamei commercial populations, even for traits with low heritability. Moreover, it is recommended to collect data on more individuals per family than increasing the number of families, and data collection should be continued for at least four generations. Tests with real data will provide further insights into the ideal number of animals and SNP density necessary for maximum accuracy.

PSVII-9 Heterosis Effects on Reproductive Traits in a Multibreed Beef Cattle Herd in Panama

Abstract The aim of this study was to estimate the influence of heterosis and breed percentage on calving interval (CI) and gestation length (GL), and the correlation between age at first calving (AFC) and CI, in beef cows. Data included 1,291 repeated observations of CI and GL from 502 cows with 2,840 individuals in the pedigree, including 3 generations from the multi-breed herd of the livestock experimental station of the Panama Agricultural Innovation Institute (IDIAP) in Gualaca, Panama. The herd was composed of the following genetic groups based on their breed percentage: tropically adapted Brahman (BR), Nellore (Ne), Undefined Bos indicus (BI), Guaymi Creole (CR), Senepol (SP) and Romosinuano (RS); Bos taurus (BT), Simmental (SM), Angus (A), Red Angus (AR), Limousin (LM), Charolais (CH), Wagyu (Wa), and Others (Oth); crossbreeds (cx), Beefmaster (BF), Three CX (F1 x different BT), R1(Backcross BR), R2 (Backcross BT), Composite (combination of at least 4 different breeds with less than 25% of Zebu), Upgrade (87.5% BR 12.5% BT), B1 (62.5% Zebu + 37.5% BT), and B2 (62.5% BT + 37.5% Zebu). The Zebu influenced breed group represents 50.03% of this population, followed by the F1, the three CX, composites, and R1, representing 22%, 13.89%, 6.11%, and 5.34%, respectively. The other breed groups represented less than 2.5% of the population. A repeated records animal model was used to estimate variance components for both CI and GL. A bivariate animal model was used to estimate the genetic correlation between CI and age at first calving (AFC). Fixed effects for all models consisted of contemporary group, age of dam, calf sex, degree of outcross, and breed percentage. Contemporary group was defined by calving year and season of birth. The average CI was 572.6 ± 140 d, with a range of 315 d to 910 d; and the average GL was 284.2 ± 6.3 d. The estimated regression coefficient for CI on heterosis was -0.114 ± 0.10 d/heterosis % (P = 0.266), and for GL was -0.01 ± 0.052 d/heterosis %. A shorter CI was observed for the F1, and three CX, with 558.7 days and 567.2 days, representing a 2.3% and 1.3% reduction in CI, respectively, when compared with the Zebu group. A larger CI was observed for the Nellore and Romosinuano breeds % with 0.17 ± 1.23 d, (P = 0.373) and 0.64± 0.13 d (P = 0.406), respectively. A low heritability (0.037 ± 0.026) for CI was estimated, with a positive genetic trend over the duration of the study. The analysis between CI and AFC revealed a moderate genetic correlation (0.49 ± 0.36) that allows the establishment of a selection program to improve AFC and CI, which would improve the fertility of this multi-breed herd in Panama.

112 Definition and Genetic Parameters Estimation for Climatic Resilience Indicators Derived from Longitudinal Vaginal Temperature Records in Lactating Sows Under Heat Stress Conditions

Abstract Climatic resilience (CR) can be defined as the ability of an animal to maintain euthermia under thermally stressful conditions. However, CR based on longitudinal physiological variables has not been included in current swine genetic selection schemes. This is the first study deriving novel CR indicators using automatically recorded vaginal temperatures (TV) and estimating genetic parameters for them. Therefore, the study objectives were to: 1) derive novel indicators of CR based on automatically recorded vaginal temperature (TV); and 2) estimate (co)variance components and genetic parameters for these indicators. TV of 1,381 lactating sows (parities 2 to 7; Landrace × Large White) were measured automatically every 10 minutes from June 5th, 2021 to July 30th, 2021 using a vaginally implanted thermochron data recorder. A total of 1,639 F1 (Landrace x Large White) sows within the studied population were genotyped using the PorcineSNP50K Bead Chip. A total of 18 HS indicators derived from Tv, their definitions, heritability estimates, and mean genomic estimated breeding value (GEBV) accuracies are shown in Table 1. Multi-trait animal models were fitted for estimating the (co)variance components, considering the effects of week of data collection, parity, and location (barn and room within barn) as fixed. Heritability estimates for these resilience traits ranged from 0.0004 ± 7.16E-6 (SlopeDe) to 0.291 ± 0.047 (HSAB). Most traits derived directly from vaginal temperature (e.g., Duration: 0.201 ± 0.033, MaxTv: 0.203 ± 0.032) are moderately heritable with substantial additive genetic variance. Besides, LnVar(Med) that is derived from the deviation between the real and predicted value had moderate heritability (0.196 ± 0.041) and high mean GEBV accuracy (0.616 ± 0.042). The indicators defined based on the slope of Tv and time had low heritability estimates, which are close to zero, and low mean GEBV accuracy (0.106 ± 0.050 – 0.337 ± 0.065). Among all the CR indicators, Duration, MaxTv, Nor_medvar, Nor_avevar, HSAA, and HSAB outperformed the other indicators with moderate heritability estimates and high average GEBV accuracies. Genetic correlations were estimated among the six indicators with moderate heritability and high mean GEBV accuracy. Moderate to high positive genetic correlations (0.508 ± 0.034 to 0.992 ± 0.025) were estimated among Duration, MaxTv, Nor_medvar, HSAB, and HSAA. LnVar(Med) showed low negative genetic correlations (-0.218 ± 0.028 to -0.039 ± 0.018) with the traits Duration, MaxTv, HSAA, and HSAB, except with Nor_medvar, which was positive (0.156 ± 0.022). Thus, Duration, LnVar(Med), MaxTv, Nor_medvar, HSAB, and HSAA might be promising CR indicator and contribute toward improving lactating sows’ resilience to thermal stress through genetic selection. New studies about the relationship between these new indicators and other economic important traits in pigs are required before including them in selection indexes.

PSVI-17 Application of Stride Length to Assess Leg Soundness for Growing Gilt

Abstract The durability of sows would be affected by their leg soundness. Problems of leg or lameness is the second reason for culling especially in the first three parities. Observing the leg structure during the growth period of pigs is necessary in selection programs because traits related to leg structure have intermediate to low heritability. However, long-term tracking of changes in feet and leg structure of pigs using quantitative measuring methods has not been conducted. Such measuring methods have not yet been applied on farms so far. Thus, this study aimed to use stride length data from pressure mat to evaluate leg soundness in growing gilts. A pressure mat system was used in this study to collect stride length (SL) data and ground reaction force (GRF) data of 23 purebred gilts at 4.5, 6.0, and 7.5 months of age. The SL data obtained in each pig was used to calculate the symmetry index with the SL records of the left and right legs for both front and rear. Similarly, the GRF data enabled the calculation of GRF symmetry index of the left and right leg of a pig for both front and rear. The confusion matrix was applied to compute the accuracy, sensitivity, and specificity by comparing visual inspection of gilt culling or the SL symmetry index to the GRF symmetry index as the standard. The accuracy, sensitivity, and specificity of visual inspection of gilt culling versus GRF symmetry index at 7.5 months of age were 80%, 31%, and 100%, respectively. Meanwhile, the accuracy, sensitivity, and specificity of the SL symmetry index versus GRF symmetry index at 7.5 months of age were 96%, 85%, and 100%, respectively. At 6.0 months of age, such accuracy, sensitivity, and specificity of the SL were 89%, 67%, and 97%, respectively. But, at 4.5 months of age, such accuracy, sensitivity, and specificity of the SL were 87%, 50%, and 97%, respectively. These findings suggest that visual inspection for leg soundness of gilt has limited capability to identify pigs with an asymmetry gait which might cause current and future leg problems. But the SL symmetric index shows better potential for that purpose that it will be a suitable objective measure to replace visual inspection for leg soundness in pigs.

118 Variance Components for Age at First Calving and Yearling Weight When Accounting for Age Differences at Fixed Breeding Dates in a Contemporary Group

Abstract The ability of a heifer to calve earlier in a breeding season has implications on the economic success of heifers in a production system. Heifers that calve earlier in a calving season have increased calf performance, improved subsequent fertility, and a longer productive life in the herd. Production systems typically breed heifers during fixed breeding dates, with heifers of variable ages in the same contemporary group. The objective of this study was to determine if heifer yearling weight (YW) or age differences going into a fixed breeding period influenced the additive genetic variance of age at first calving (AFC) explained in a multi-breed population. Heifer fertility data were obtained from International Genetic Solutions. Females with exposure and calf production records were used to identify individuals calving between 630 and 810 days of age. Females with embryo transfer, multiple birth progeny, and an age differential (DIFF) greater than 100 days were excluded. Age differential was defined as the difference in days between an individual’s birth date and the earliest birth date of an animal in a defined contemporary group. Contemporary group was defined as; breeder, herd, year born, birth and yearling group. After data filtering, there were 149,350 calving records. A 3-generation pedigree file was used containing 365,637 animals, with 37,420 unique sires and 219,533 unique dams. Two bivariate multi-trait animal models for AFC and YW with random additive genetic and residual effects and fixed effects of contemporary group, breed proportion, and % retained hybrid vigor were used. The first model consisted of the aforementioned effects while the second model included DIFF as an additional fixed effect. Analyses were performed using ASReml 3.0. When DIFF was not included as a fixed effect, the additive, residual and phenotypic variances for AFC were 126.1, 456.8, and 582.9 d2, respectively, and the genetic correlation between AFC and YW was 0.36 ± 0.02. When DIFF was included as a fixed effect, the additive, residual, and phenotypic variances for AFC were 10.0, 326.0, and 336.0 d2, respectively. The genetic correlation between AFC and YW was 0.19 ± 0.04. In the absence of DIFF, the heritability estimates for AFC and YW were 0.22 ± 0.01 and 0.44 ± 0.01, respectively but were 0.03 ± 0.003 and 0.44 ± 0.01 respectively, when DIFF was included. Age differential was a significant effect on AFC at –0.86 (P &amp;lt; 0.0001). The low additive variance of AFC when accounting for DIFF suggests that the influence of a female's age going into a fixed breeding date explains much of the variation in AFC. The low heritability estimate for AFC and genetic correlation with YW suggests that selection for improved AFC will be difficult using this method and that producers should instead focus on improved management practices to ensure females calve earlier in a calving season.

142 Genotype-By-Environment Interactions in Dairy Cattle Raised in California and New England

Abstract Genotype-by-environmental interactions (G x E) have been reported to cause sire reranking in dairy populations. However, the effects of such interactions are not included in the current US national dairy genetic evaluation. Phenotypes collected from animals across the country are considered the same trait, disregarding interactions between genetic effects and region or other environmental factors. Variations in production systems may interact with the genotypes of the animals, leading to distinct phenotypes. Separating data into regions could change decision-making on bull selection, which is the most important step of a breeding program. The goal of this study is to evaluate the extent of genotype-by-environment interaction between the state of California and the region of New England in the US Holstein Population. Data from Holstein cows in the aforementioned regions collected from 2010 to 2020 were provided by the Council on Dairy Cattle Breeding. The genetic evaluation models used for the national evaluation were modified to account for New England and California phenotypes as separated yet correlated traits. The mixed model accounted for additive genetic, sire-by-herd interaction, and permanent environmental effects as random, and for the management group, age of parity, birth year, and parity as fixed effects. In some scenarios, sire-by-herd interaction and permanent environment were removed due to convergence problems. Variance components were estimated using AIREML under the Method R procedure. Such a method allows computing variance components for large databases by splitting the data into several random groups. Ten random samples of data containing 100,000 records were used for each analysis. The scenarios included single trait for each state, single trait with both states, and two-trait with separated states. Breeding values from the top 100 bulls in each region were compared with evaluate potential sire reranking. Heritabilities varied across regions for all three traits (Table 1). California presented lower heritability than New England across methods. The genetic correlations on the two-trait analysis averaged at 0.96, 0.92, and 0.95 for yield, fat, and protein, respectively. The Spearman correlation coefficient between breeding values of the bulls with more than 200 daughters was 0.87 for milk yield, suggesting that the reranking is unimportant. The genetic correlations suggested that GxE between the two regions is small and that the traits should not be split in the current genetic evaluation. In conclusion, no critical effect of genotype-by-environment interaction was observed, even though top bulls may differ across regions. The next step of this project is to evaluate GxE for somatic cell score and to include genomic information in the evaluations. Finally, a genome-wide association study across the two regions will be performed to investigate changes in genomic regions associated with the phenotypes.

130 Genetic Analysis of Count-Based Horn Fly Abundance Phenotypes in Beef Cattle

Abstract Horn flies are a major irritant to livestock. In cattle, horn flies can cause increased heart and respiratory rates, decreased feed efficiency, decreased weaning weights, and reduced milk production, resulting in substantial economic losses. In the United States, horn flies are estimated to cause more than $1 billion in economic losses on pastured cattle, annually. Reliance on management and insecticides has proven inadequate. Additionally, intensive use of insecticides has led to increased resistance in horn fly populations. Thus, there is an increasing need for a long-term solution to the horn fly problem in cattle. Assessing horn fly abundance related phenotypes under commercial conditions is costly and logistically complex. Consequently, the genetic basis of these traits remains largely unknown due to the lack of sufficient phenotypic data. Although several studies reported clear differences in fly abundance within and across breeds, only a few heritability estimates are available based on small-scale studies. This study was conducted during the summers of 2019 and 2022 (two data collections per year) on two University of Georgia associated farms, Northwest Georgia Research and Education center and Eatonton Beef Research Unit. A total of 1,047 cows and heifers were assessed by trained evaluators and several digital images were taken for each animal. Each animal was scored at least twice with some cows scored both years for a total of 4 times during the study period. During each scoring period, the best image for each animal was used to assess fly abundance using direct and sampling-based counting approaches. After edits, the data consisted of 2,197 records collected on 936 cows and heifers. The pedigree consisted of 1,226 animals. A mixed linear model that included year, farm-pen, month, and age (in years) as fixed effects and the random additive and permanent effects was used to jointly analyze three fly abundance related phenotypes. Estimates of heritability of horn fly abundance was between 0.15 and 0.21 for subjective and image-based phenotypes. Genetic correlation was high (0.83) between the image-based phenotypes and moderate between the image-based phenotypes and the subjective assessment (0.61 to 0.65). Repeatability ranged between 0.28 and 0.35 across the three traits. The lower heritability for the subjective assessment points towards added variability due to variation between evaluators. Although the results of this study support the potential to improve horn fly resistance using genetic tools, alternative phenotypes to assess fly abundance are needed. Non-count-based phenotypes could provide an attractive alternative for selecting against horn fly abundance.

Genotype-by-Environment Interaction Analysis for Quantity and Quality Traits in Faba Beans Using AMMI, GGE Models, and Stability Indices.

Faba beans are considered one of the most important crops for animal feed. The genotype × environment interaction (GEI) has a considerable effect on faba bean seed production. The objectives of this study included assessing multiple locations and genotypes to understand how various ecosystems and faba bean genotypes relate to one another, and suggesting the ideal climatic conditions, crop management system, and genotypes so that they are carefully chosen for their stability. A 2-year experiment was conducted in order to define the stability across four environments based on stability indices for certain characteristics: moisture (%), ash content (%), crude protein content (%), crude fat (%), total starch (%), and crude fiber content (%). Statistically significant differences indicated that GEIs were present. The heritability was generally high for qualitative traits in comparison with quantitative traits. The crude protein content, plant height, and thousand-seed weight were all positively correlated with the seed yield; however, the other qualitative variables were adversely correlated. The crude protein content of the cultivar Tanagra displayed a high stability index, followed by Ste1. Under conventional management, Tanagra demonstrated high values for the seed yield in Giannitsa and Florina. Ste1 and Ste2 are particularly promising genetic materials that showed high values under low-input conditions. The best genotypes to use and the most favorable environments/types of cultivation were the Tanagra cultivar, followed by the Ste2 genotype, according to the additive main effects and multiplicative interaction (AMMI) and genotype plus genotype-by-environment (GGE) biplot models. Earliness showed significant heritability values and very high stability indices, again indicating qualitative behavior according to genetic parameters. With the exception of the number of pods per plant, which demonstrated low heritability while having excellent index values, traits like seed yield showed relatively low-stability-based heritability values. Global efforts aimed at improving the genetics of faba beans might benefit from genotypes that exhibit consistent yields in various conditions.

Genetic parameters for calf feeding traits derived from automated milk feeding machines and number of bovine respiratory disease treatments in North American Holstein calves

Precision livestock farming technologies, such as automatic milk feeding machines, have increased the availability of on-farm data collected from dairy operations. We analyzed feeding records from automatic milk feeding machines to evaluate the genetic background of milk feeding traits and bovine respiratory disease (BRD) in North American Holstein calves. Data from 10,076 preweaning female Holstein calves were collected daily over a period of 6 yr (3 yr included per-visit data), and daily milk consumption (DMC), per-visit milk consumption (PVMC), daily sum of drinking duration (DSDD), drinking duration per-visit, daily number of rewarded visits (DNRV), and total number of visits per day were recorded over a 60-d preweaning period. Additional traits were derived from these variables, including total consumption and duration variance (TCV and TDV), feeding interval, drinking speed (DS), and preweaning stayability. A single BRD-related trait was evaluated, which was the number of times a calf was treated for BRD (NTT). The NTT was determined by counting the number of BRD incidences before 60 d of age. All traits were analyzed using single-step genomic BLUP mixed-model equations and fitting either repeatability or random regression models in the BLUPF90+ suite of programs. A total of 10,076 calves with phenotypic records and genotypic information for 57,019 SNP after the quality control were included in the analyses. Feeding traits had low heritability estimates based on repeatability models (0.006 ± 0.0009 to 0.08 ± 0.004). However, total variance traits using an animal model had greater heritabilities of 0.21 ± 0.023 and 0.23 ± 0.024, for TCV and TDV, respectively. The heritability estimates increased with the repeatability model when using only the first 32 d preweaning (e.g., PVMC = 0.040 ± 0.003, DMC = 0.090 ± 0.009, DSDD = 0.100 ± 0.005, DS = 0.150 ± 0.007, DNRV = 0.020 ± 0.002). When fitting random regression models (RRM) using the full dataset (60-d period), greater heritability estimates were obtained (e.g., PVMC = 0.070 [range: 0.020, 0.110], DMC = 0.460 [range: 0.050, 0.680], DSDD = 0.180 [range: 0.010, 0.340], DS = 0.19 [range: 0.070, 0.430], DNRV = 0.120 [range: 0.030, 0.450]) for the majority of the traits, suggesting that RRM capture more genetic variability than the repeatability model with better fit being found for RRM. Moderate negative genetic correlations of -0.59 between DMC and NTT were observed, suggesting that automatic milk feeding machines records have the potential to be used for genetically improving disease resilience in Holstein calves. The results from this study provide key insights of the genetic background of early in-life traits in dairy cattle, which can be used for selecting animals with improved health outcomes and performance.

Loss of plasticity in maturation timing after ten years of captive spawning in a delta smelt conservation hatchery.

Adaptation to captivity in spawning programs can lead to unintentional consequences, such as domestication that results in reduced fitness in the wild. The timing of sexual maturation has been shown to be a trait under domestication selection in fish hatcheries, which affects a fish's access to mating opportunities and aligning their offspring's development with favorable environmental conditions. Earlier maturing fish may be favored in hatchery settings where managers provide artificially optimal growing conditions, but early maturation may reduce fitness in the wild if, for example, there is a mismatch between timing of reproduction and availability of resources that support recruitment. We investigated patterns of maturation timing in a delta smelt (Hypomesus transpacificus) conservation hatchery by quantifying changes to the median age at maturity since the captive spawning program was initiated in 2008. Over the span of a decade, we observed a small, but significant increase in age at maturity among broodstock by 2.2 weeks. This trait had low heritability and was largely controlled by phenotypic plasticity that was dependent on the time of year fish were born. Fish that were born later in the year matured faster, potentially a carryover from selection favoring synchronous spawning in the wild. However, higher DI (domestication index) fish showed a loss of plasticity, we argue, as a result of hatchery practices that breed individuals past peak periods of female ripeness. Our findings suggest that the hatchery setting has relaxed selection pressures for fish to mature quickly at the end of the year and, consequently, has led to a loss of plasticity in age at maturity. Hatchery fish that are re-introduced in the wild may not be able to align maturation with population peaks if their maturation rates are too slow with reduced plasticity, potentially resulting in lower fitness.

Estimation of Genetic Parameters for Selected Quantitative Traits in Introduced African Yam Bean (Sphenosylis stenocarpa Hochst. ex. A. Rich Harms) Genotypes

A solid understanding of the genetic control of traits within breeding populations is essential for selecting superior genotypes and parent plants for African yam bean (AYB) cultivation. In this study, we explored the phenotypic breeding values and genetic parameter estimates for various traits in 10 introduced AYB varieties. These traits included seed emergence speed (SES), seedling vigor index (SVI), final germination percentage (FGP), seed yield, days to first flower bud initiation (DAYSFBI), days to first flowering (DAYSF), and days to first pod initiation (DAYSPI). We conducted the trial using a randomized complete block (RCB) design with the following varieties: TSs2, TSs60, TSs11, TSs33, TSs282, TSs450, TSs10, TSs432, TSs424, and TSs151B. Traits showing high and medium genotypic coefficient of variation (GCV) were seed yield (20.7), SVI (12.1), and seed emergence speed (10.8), respectively. Traits with high phenotypic coefficient of variation (PCV) included seed yield (36.8), SVI (22.8), and SES (37.5). The presence of variability in all studied traits was evident from both GCV and PCV values. However, PCV values were slightly higher than GCV, suggesting the influence of environmental factors on these traits. Seed yield exhibited high genetic advance (23.9) and intermediate heritability (31.5%), while SES showed low heritability (8.4%) and low genetic advance (6.5), and FGP displayed low heritability (8.3%) and low genetic advance (2.1). High heritability and genetic advance in certain traits indicate the presence of additive gene action, suggesting that these traits can be improved through direct selection. These findings suggest the presence of valuable variations that can be harnessed for AYB genetic enhancement and selection purposes. Our study results offer valuable insights for the genetic improvement, conservation, management, multi-location evaluations, short-term recommendations, and potential release of new AYB genotypes.