Bioclimatic thermal stress indices and their relationships with andrological characteristics in hair rams.

This study evaluated relationships among reproductive parameters and the bioclimatic indices: temperature and humidity index (THI), equivalent temperature index (ETI), black globe temperature and humidity index (BGTHI), and thermal comfort index (TCI), during the first 45 days of spermatogenesis (SP-45) and during the 15 days of sperm transit through the epididymis (STP-15) that preceded the reproductive assessments (ReA). Such information is useful in determining the optimal breeding season in Northeast Brazil. Santa Inês rams (n = 25) underwent two ReA in three periods of the year (D-P = dry; R-P = rainy and RD-P = rainy/dry transition), and the bioclimatic indices were calculated at the corresponding SP-45 and STP-15 timepoints prior to each ReA. Sperm kinetic parameters in D-P were depressed compared to R-P and RD-P (P < 0.05). The index values had an antagonistic relationship with most parameters and regression analysis demonstrated that the BGTHI and the TCI had a negative association with the progressive motility, curvilinear, straight line, and average path velocities, and a positive association with slow sperm in the ejaculate in SP-45 and STP-15 phases (P < 0.01). Semen quality kinetics is affected throughout the year by the environment and it is apparent that it is impaired in D-P and better in R-P and RD-P seasons. The BGTHI and TCI measured in the sperm production phase classified the environment most coherently and presented better association with the behavior of sperm kinetics.

Biobanking animal genetic resources: critical infrastructure and growth opportunities.

National animal gene banks have acquired substantial quantities of germplasm that protect and preserve a wide range of livestock breeds. New challenges and growth opportunities are emerging. A key challenge will be increased gene bank use, but this requires increased characterization of phenotypes and genotypes for populations and collections.

Incorporation of Biotechnologies into Gene Banking Strategies to Facilitate Rapid Reconstitution of Populations.

National animal gene banks that are responsible for conserving livestock, poultry, and aquatic genetic resources need to be capable of utilizing a broad array of cryotechnologies coupled with assisted reproductive technologies to reconstitute either specific animals or populations/breeds as needed. This capability is predicated upon having sufficient genetic diversity (usually encapsulated by number of animals in the collection), units of germplasm or tissues, and the ability to reconstitute animals. While the Food and Agriculture Organization of the United Nations (FAO 2012, 2023) developed a set of guidelines for gene banks on these matters, those guidelines do not consider applications and utilization of newer technologies (e.g., primordial germ cells, cloning from somatic cells, embryo transfer, IVF, sex-sorted semen), which can radically change how gene banks collect, store, and utilize genetic resources. This paper reviews the current status of using newer technologies, explores how gene banks might make such technologies part of their routine operations, and illustrates how combining newer assisted reproductive technologies with older approaches enables populations to be reconstituted more efficiently.

Genetic architecture of a composite beef cattle population.

Composite breeds are widely used in the beef industry. Composites allow producers to combine desirable traits from the progenitor breeds and simplify herd management, without repeated crossbreeding and maintenance of purebreds. In this study, genomic information was used to evaluate the genetic composition and characteristics of a three-breed beef cattle composite. This composite population referred to as Composite Gene Combination (CGC) consisted of 50% Red Angus, 25% Charolais, and 25% Tarentaise. A total of 248 animals were used in this study: CGC (n = 79), Red Angus (n = 61), Charolais (n = 79), and Tarentaise (n = 29). All animals were genotyped with 777k HD panel. Principal component and ADMIXTURE analyses were carried out to evaluate the genetic structure of CGC animals. The ADMIXTURE revealed the proportion of Tarentaise increased to approximately 57%, whereas Charolais decreased to approximately 5% and Red Angus decreased to 38% across generations. To evaluate these changes in the genomic composition across different breeds and in CGC across generations, runs of homozygosity (ROH) were conducted. This analysis showed Red Angus to have the highest total length of ROH segments per animal with a mean of 349.92 Mb and lowest in CGC with a mean of 141.10 Mb. Furthermore, it showed the formation of new haplotypes in CGC around the sixth generation. Selection signatures were evaluated through Fst and HapFlk analyses. Several selection sweeps in CGC were identified especially in chromosomes 5 and 14 which have previously been reported to be associated with coat color and growth traits. The study supports our previous findings that progenitor combinations are not stable over generations and that either direct or natural selection plays a role in modifying the progenitor proportions. Furthermore, the results showed that Tarentaise contributed useful attributes to the composite in a cool semi-arid environment and suggests a re-exploration of this breed's role may be warranted.

Composite breeds are commonly used in the U.S. beef industry since they provide producers with benefits such as breed complementarity and retained heterosis. However, cattle composite genomes are not well characterized. Therefore, in this study, genomic information was used to evaluate the genetic composition and characteristics of a three-breed composite (50% Red Angus, 25% Charolais, and 25% Tarentaise). The analysis showed an increase in the proportion of Tarentaise to approximately 57%, whereas Charolais decreased to approximately 5% and Red Angus decreased to 38%. Furthermore, new genome segments formed around the sixth generation. These changes show that progenitor breed proportions are not stable over generations and that either direct or natural selection plays a role in modifying the proportions. The increase in Tarentaise proportion suggests useful attributes to the composite in a cool semi-arid environment.

Assessing Population Structure and Genetic Diversity in US Suffolk Sheep to Define a Framework for Genomic Selection.

Long-term sustainability of breeds depends on having sufficient genetic diversity for adaptability to change, whether driven by climatic conditions or by priorities in breeding programs. Genetic diversity in Suffolk sheep in the United States was evaluated in four ways: 1) using genetic relationships from pedigree data [(n = 64 310 animals recorded in the US National Sheep Improvement Program (NSIP)]; 2) using molecular data (n = 304 Suffolk genotyped with the OvineHD BeadChip); 3) comparing Australian (n = 109) and Irish (n = 55) Suffolk sheep to those in the United States using molecular data; and 4) assessing genetic relationships (connectedness) among active Suffolk flocks (n = 18) in NSIP. By characterizing genetic diversity, a goal was to define the structure of a reference population for use for genomic selection strategies in this breed. Pedigree-based mean inbreeding level for the most recent year of available data was 5.5%. Ten animals defined 22.8% of the current gene pool. The effective population size (Ne) ranged from 27.5 to 244.2 based on pedigree and was 79.5 based on molecular data. Expected (HE) and observed (HO) heterozygosity were 0.317 and 0.306, respectively. Model-based population structure included 7 subpopulations. From Principal Component Analysis, countries separated into distinct populations. Within the US population, flocks formed genetically disconnected clusters. A decline in genetic diversity over time was observed from both pedigree and genomic-based derived measures with evidence of population substructure as measured by FST. Using these measures of genetic diversity, a framework for establishing a genomic reference population in US Suffolk sheep engaged in NSIP was proposed.

A Reference Genome Assembly of American Bison, Bison bison bison.

Bison are an icon of the American West and an ecologically, commercially, and culturally important species. Despite numbering in the hundreds of thousands today, conservation concerns remain for the species, including the impact on genetic diversity of a severe bottleneck around the turn of the 20th century and genetic introgression from domestic cattle. Genetic diversity and admixture are best evaluated at genome-wide scale, for which a high-quality reference is necessary. Here, we use trio binning of long reads from a bison-Simmental cattle (Bos taurus taurus) male F1 hybrid to sequence and assemble the genome of the American plains bison (Bison bison bison). The male haplotype genome is chromosome-scale, with a total length of 2.65 Gb across 775 scaffolds (839 contigs) and a scaffold N50 of 87.8 Mb. Our bison genome is ~13× more contiguous overall and ~3400× more contiguous at the contig level than the current bison reference genome. The bison genome sequence presented here (ARS-UCSC_bison1.0) will enable new research into the evolutionary history of this iconic megafauna species and provide a new tool for the management of bison populations in federal and commercial herds.

A Reference Genome Assembly of Simmental Cattle, Bos taurus taurus.

Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison-cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS_Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.

Mixed ancestry from wild and domestic lineages contributes to the rapid expansion of invasive feral swine.

Invasive alien species are a significant threat to both economic and ecological systems. Identifying the processes that give rise to invasive populations is essential for implementing effective control strategies. We conducted an ancestry analysis of invasive feral swine (Sus scrofa, Linnaeus, 1758), a highly destructive ungulate that is widely distributed throughout the contiguous United States, to describe introduction pathways, sources of newly emergent populations and processes contributing to an ongoing invasion. Comparisons of high-density single nucleotide polymorphism genotypes for 6,566 invasive feral swine to a comprehensive reference set of S. scrofa revealed that the vast majority of feral swine were of mixed ancestry, with dominant genetic associations to Western heritage breeds of domestic pig and European populations of wild boar. Further, the rapid expansion of invasive feral swine over the past 30 years was attributable to secondary introductions from established populations of admixed ancestry as opposed to direct introductions of domestic breeds or wild boar. Spatially widespread genetic associations of invasive feral swine to European wild boar deviated strongly from historical S. scrofa introduction pressure, which was largely restricted to domestic pigs with infrequent, localized wild boar releases. The deviation between historical introduction pressure and contemporary genetic ancestry suggests wild boar-hybridization may contribute to differential fitness in the environment and heightened invasive potential for individuals of admixed domestic pig-wild boar ancestry.

Random regression of Hereford percentage intramuscular fat on geographical coordinates.

Accounting for genotype-environment interactions may improve genetic prediction and parameter estimation. The objective was to use random regression analyses to estimate variances and thereby heritability for intramuscular fat (IMF) across longitude and latitude coordinates within the continental United States. Records from the American Hereford Association (n = 169,440) were used. Analyses were first conducted using the continental United States in its entirety, and then as subdivided into two or four regions. Data were analyzed with an animal model, and linear and quadratic random regressions of additive genetic merit on longitude or latitude as covariate (separately). Subdivided data were analyzed with linear random regressions unique to regions. Regions were North and South separated at 40°N latitude, or West and East separated at 99°W longitude using longitude or latitude as covariate, respectively. Further subdivision to four regions included additional boundaries of 44.46° and 36.46°N latitude and 104.55° and 92.22°W longitude. The estimated heritability of IMF from the traditional model was 0.19 ± 0.004. Without regional subdivision of data, quadratic random regression had the best fit for the data based on likelihood ratio tests using longitude or latitude as covariate (P < 0.01). Estimates of heritability from quadratic random regression on latitude ranged from 0.12 in the South to a high of 0.27 at the extreme Northern latitude. Estimates of heritability from quadratic random regression on longitude ranged from 0.17 in the middle of the parameter space (corresponding to the central United States) to 0.37; higher estimates were noted at the extremes, that is, the far West and East longitudes. Random regression analyses of data divided into regions were conducted with a linear coefficient, as increasing to a quadratic polynomial was never accomplished. Results from random regression on latitude in the East region were similar to results from analyses without regions (h2 ranged from 0.09 to 0.32); however, estimates of heritability in the West region had a lower range from South to North (0.14 to 0.27). Estimates of heritability from random regression on longitude with data divided into two regions were similar to those from analyses that did not include region. Estimates in the South region were somewhat lower and had a lower range (0.15 to 0.31) than those from the North region (0.19 to 0.47). When data were further subdivided, estimation of only a subset of covariances among random regression coefficients was possible, that is, within-region covariances of intercept and linear terms (latitude); those and covariances between all linear random regression coefficients were estimated when longitude was the covariate. Results from random regression analyses of data with four regions modeled produced very high estimates of heritability in low latitudes in the furthest West and high latitudes in the furthest East region, with approximate difference of 0.3 and 0.2 between estimates in the two West regions and the two East regions, respectively. Results from random regression on longitude indicated higher estimates of heritability in North region, especially at the furthest East longitudes of the most Northern region. There appeared to be substantial additive genetic variance differences, as well as estimates of heritability, that correspond to different geographical environments as modeled by random regressions on within-region latitude or longitude coordinates.

New world goat populations are a genetically diverse reservoir for future use.

Western hemisphere goats have European, African and Central Asian origins, and some local or rare breeds are reported to be adapted to their environments and economically important. By-in-large these genetic resources have not been quantified. Using 50 K SNP genotypes of 244 animals from 12 goat populations in United States, Costa Rica, Brazil and Argentina, we evaluated the genetic diversity, population structure and selective sweeps documenting goat migration to the "New World". Our findings suggest the concept of breed, particularly among "locally adapted" breeds, is not a meaningful way to characterize goat populations. The USA Spanish goats were found to be an important genetic reservoir, sharing genomic composition with the wild ancestor and with specialized breeds (e.g. Angora, Lamancha and Saanen). Results suggest goats in the Americas have substantial genetic diversity to use in selection and promote environmental adaptation or product driven specialization. These findings highlight the importance of maintaining goat conservation programs and suggest an awaiting reservoir of genetic diversity for breeding and research while simultaneously discarding concerns about breed designations.

Genetic variation and differentiation of bison (Bison bison) subspecies and cattle (Bos taurus) breeds and subspecies.

The genetic relationship of American plains bison (Bison bison bison) and wood bison (Bison bison athabascae) was quantified and compared with that among breeds and subspecies of cattle. Plains bison from 9 herds (N = 136), wood bison from 3 herds (N = 65), taurine cattle (Bos taurus taurus) from 14 breeds (N = 244), and indicine cattle (Bos taurus indicus) from 2 breeds (N = 53) were genotyped for 29 polymorphic microsatellite loci. Bayesian cluster analyses indicate 3 groups, 2 of which are plains bison and 1 of which is wood bison with some admixture, and genetic distances do not show plains bison and wood bison as distinct groups. Differentiation of wood bison and plains bison is also significantly less than that of cattle breeds and subspecies. These and other genetic data and historical interbreeding of bison do not support recognition of extant plains bison and wood bison as phylogenetically distinct subspecies.

Combining US and Brazilian microsatellite data for a meta-analysis of sheep (Ovis aries) breed diversity: facilitating the FAO Global Plan of Action for Conserving Animal Genetic Resources.

Microsatellites are commonly used to understand genetic diversity among livestock populations. Nevertheless, most studies have involved the processing of samples in one laboratory or with common standards across laboratories. Our objective was to identify an approach to facilitate the merger of microsatellite data for cross-country comparison of genetic resources when samples were not evaluated in a single laboratory. Eleven microsatellites were included in the analysis of 13 US and 9 Brazilian sheep breeds (N = 706). A Bayesian approach was selected and evaluated with and without a shared set of samples analyzed by each country. All markers had a posterior probability of greater than 0.5, which was higher than predicted as reasonable by the software used. Sensitivity analysis indicated no difference between results with or without shared samples. Cluster analysis showed breeds to be partitioned by functional groups of hair, meat, or wool types (K = 7 and 12 of STRUCTURE). Cross-country comparison of hair breeds indicated substantial genetic distances and within breed variability. The selected approach can facilitate the merger and analysis of microsatellite data for cross-country comparison and extend the utility of previously collected molecular markers. In addition, the result of this type of analysis can be used in new and existing conservation programs.

Effect of number of motile, frozen-thawed boar sperm and number of fixed-time inseminations on fertility in estrous-synchronized gilts.

There are advantages for use of frozen-thawed boar sperm (FTS) as a tool for preservation and transfer of valuable genetic material, despite its practical limitations. It was hypothesized that increasing the number of motile FTS and number of fixed-time artificial inseminations (AI) would improve pregnancy rate and litter size. Semen from six boars was frozen in 0.5mL straws at 500x10(6)cells/mL. Gilts approximately 170 days of age, were induced into estrus with PG600 and synchronized using MATRIX (synthetic progestagen). Following last feeding of MATRIX (LFM), gilts were checked twice daily for estrus. At onset of estrus, gilts were randomly assigned in a 3x2 factorial treatment design to receive 1x10(9) motile FTS (n=19), 2x10(9) motile FTS (n=19), 4x10(9) motile FTS (n=19) in a single AI at 32h after onset of estrus, or 1x10(9) motile FTS (n=18), 2x10(9) motile FTS (n=17), or 4x10(9) motile FTS (n=19) in each of the two AI at 24 and 32h following onset of estrus. Ultrasonography was performed at 12h intervals after estrus to estimate time of ovulation. Reproductive tracts were collected 28-34 days following AI. Estrus occurred at 139+/-2h (mean+/-SE) after LFM and ovulation at 33+/-1h following onset of estrus. Dose and number of inseminations did not interact or individually influence pregnancy rate at slaughter (73+/-4.2%) or numbers of normal fetuses (10.8+/-0.5). However, number of fetuses tended (P=0.14) to increase with double AI but not with dose. Boar did not affect pregnancy rate but did affect number of normal fetuses and embryonic survival (P<0.01). Longer intervals from insemination to ovulation reduced pregnancy rate (P<0.05), number of normal fetuses (P<0.001), and embryonic survival (P<0.01). Ovarian abnormalities at slaughter were associated with reduced pregnancy rate (P<0.001). The results of this experiment indicate that a double insemination using 2x10(9) motile sperm would produce the greatest number of piglets with fewest numbers of frozen sperm used, while double AI with 1x10(9) motile sperm would be most practical for pig production with limited genetic resources. Fertility was also influenced by boar, interval from insemination to ovulation, and gilt ovarian abnormalities.

The fertility of ram sperm held for 24h at 5 degrees C prior to cryopreservation.

Diluted ram sperm can be held for 24h at 5 degrees C prior to cryopreservation without impacting cryosurvival rates, however, the effects this storage has on subsequent fertility are unknown. These studies were conducted to evaluate the fertility of semen held for 24h (to mimic shipping semen to a cryopreservation center), prior to freezing. Semen from Suffolk rams (n=3 in experiment 1 and n=6 in experiment 2) with initial motility of greater than 70%, were diluted to 200 x 10(6)sperm/mL, in one step, with a Tris-egg yolk-glycerol diluent. In experiment 1, diluted samples were cooled to 5 degrees C over 2h, and then divided. Sperm in one fraction were loaded into 0.5mL straws, frozen (T0) and stored in liquid nitrogen until thawing. Sperm in the second fraction were held at 5 degrees C for 24h (T24) before being frozen. In experiment 2 ejaculates were collected and divided into two fractions. Sperm in one fraction were treated with cholesterol-loaded cyclodextrin (CLC) and sperm in the other served as control. Both fractions were diluted, cooled, and cryopreserved as described in experiment 1. Stage of the estrous cycle was synchronized in ewes (n=196) using controlled internal drug releasing devices (CIDR) for 12d and at CIDR removal each ewe was administered PMSG (500IU in experiment 1 and 350IU in experiment 2) immediately before insemination. Ewes were stratified by age and randomly assigned to one of the semen treatments; experiment 1: Fresh (F), T0, or T24; experiment 2: F, T24, or CLC, and inseminated laparoscopically 56h after CIDR removal. Differences in fertility were detected between experiments, but not for treatments within experiments. Differences in fertility were also observed due to ewe age, with the 3-year-old ewes having the greatest fertility (50.7%) and 6-year-old ewes having the least fertility (9.6%; P<0.05). Differences in the prolificacy rates due to semen treatment were also observed but differences due to ewe age were not detected. Therefore, sperm can be held at 5 degrees C for 24h prior to cryopreservation without altering sperm fertility.