Harvey D. Blackburn

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.

Aquaculture genomics, genetics and breeding in the United States: current status, challenges, and priorities for future research

Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries. Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.Advancing the production efficiency and profitability of aquaculture is dependent upon the ability to utilize a diverse array of genetic resources. The ultimate goals of aquaculture genomics, genetics and breeding research are to enhance aquaculture production efficiency, sustainability, product quality, and profitability in support of the commercial sector and for the benefit of consumers. In order to achieve these goals, it is important to understand the genomic structure and organization of aquaculture species, and their genomic and phenomic variations, as well as the genetic basis of traits and their interrelationships. In addition, it is also important to understand the mechanisms of regulation and evolutionary conservation at the levels of genome, transcriptome, proteome, epigenome, and systems biology. With genomic information and information between the genomes and phenomes, technologies for marker/causal mutation-assisted selection, genome selection, and genome editing can be developed for applications in aquaculture. A set of genomic tools and resources must be made available including reference genome sequences and their annotations (including coding and non-coding regulatory elements), genome-wide polymorphic markers, efficient genotyping platforms, high-density and high-resolution linkage maps, and transcriptome resources including non-coding transcripts. Genomic and genetic control of important performance and production traits, such as disease resistance, feed conversion efficiency, growth rate, processing yield, behaviour, reproductive characteristics, and tolerance to environmental stressors like low dissolved oxygen, high or low water temperature and salinity, must be understood. QTL need to be identified, validated across strains, lines and populations, and their mechanisms of control understood. Causal gene(s) need to be identified. Genetic and epigenetic regulation of important aquaculture traits need to be determined, and technologies for marker-assisted selection, causal gene/mutation-assisted selection, genome selection, and genome editing using CRISPR and other technologies must be developed, demonstrated with applicability, and application to aquaculture industries.Major progress has been made in aquaculture genomics for dozens of fish and shellfish species including the development of genetic linkage maps, physical maps, microarrays, single nucleotide polymorphism (SNP) arrays, transcriptome databases and various stages of genome reference sequences. This paper provides a general review of the current status, challenges and future research needs of aquaculture genomics, genetics, and breeding, with a focus on major aquaculture species in the United States: catfish, rainbow trout, Atlantic salmon, tilapia, striped bass, oysters, and shrimp. While the overall research priorities and the practical goals are similar across various aquaculture species, the current status in each species should dictate the next priority areas within the species. This paper is an output of the USDA Workshop for Aquaculture Genomics, Genetics, and Breeding held in late March 2016 in Auburn, Alabama, with participants from all parts of the United States.

The fertility of ram sperm held for 24 h at 5°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.

Implications of the pH and temperature of diluted, cooled boar semen on fresh and frozen-thawed sperm motility characteristics

Boar semen is typically collected, diluted and cooled for AI use over numerous days, or frozen immediately after shipping to capable laboratories. The storage temperature and pH of the diluted, cooled boar semen could influence the fertility of boar sperm. Therefore, the purpose of this study was to determine the effects of pH and storage temperature on fresh and frozen-thawed boar sperm motility end points. Semen samples (n = 199) were collected, diluted, cooled and shipped overnight to the National Animal Germplasm Program laboratory for freezing and analysis from four boar stud facilities. The temperature, pH and motility characteristics, determined using computer automated semen analysis, were measured at arrival. Samples were then cryopreserved and post-thaw motility determined. The commercial stud was a significant source of variation for mean semen temperature and pH, as well as total and progressive motility, and numerous other sperm motility characteristics. Based on multiple regression analysis, pH was not a significant source of variation for fresh or frozen-thawed boar sperm motility end points. However, significant models were derived which demonstrated that storage temperature, boar, and the commercial stud influenced sperm motility end points and the potential success for surviving cryopreservation. We inferred that maintaining cooled boar semen at approximately 16 °C during storage will result in higher fresh and frozen-thawed boar sperm quality, which should result in greater fertility.

Animal genetic resource trade flows: economic assessment.

Abstract Throughout human history, livestock producers have relied on a vibrant international exchange of genetic resources to achieve improvements in the quality and productivity of their animals. In recent years, however, some observers have argued that changes in the legal, technological, and economic environment now imply that international exchanges of animal genetic resources (AnGR) systematically benefit rich countries at the expense of poor countries. It is argued that international flows of AnGR are displacing the indigenous animal genetic resources of developing countries, and also that the genetic wealth of the developing world is being expropriated by rich countries. In reaction, there have been growing calls for limitations and/or barriers to the exchange of animal genetic resources. These discussions, however, seem to be based on limited information about the magnitude and direction of current trade flows in AnGR. This paper offers an analysis of AnGR trade flows from 1990 to 2005. The paper draws on national-level data from 150 countries that reported information to the United Nations Statistics Division. Three major trade categories were evaluated: live cattle and pigs for breeding, and cattle semen. Over the period studied, Europe and North America were the primary exporters of genetic resources for the species evaluated. OECD countries accounted for 98.7, 92.5, and 95% of cattle semen, live cattle, and swine exports in 2005, respectively. In evaluating the direction of trade between developed (North) and developing (South) countries, North–North trade had the largest magnitude, followed by North–South, South–South, and South–North. The data do not support the notion that Southern genetic resources are being used on a large scale in the North. We believe that importation from South to North is limited by the vast discrepancies in production efficiency and production systems between countries in the North and South. Given the low volume of South–North exchange, it seems doubtful that sufficient revenues could be acquired through a “benefit-sharing mechanism” to have any substantial impact on in situ or ex situ conservation efforts, or to generate benefits for poor livestock keepers in developing countries. We question whether global agreements or restrictions on trade will achieve the desired goal of conserving rare breeds and threatened genetic resources. We also doubt whether these agreements will succeed in improving the well-being of the poor. We suggest that resources instead be urgently employed for conservation and that more direct measures should be taken to aid poor farmers, ranchers, and herders in their efforts to conserve genetic resources.

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.

Opinion: Why we need a National Living Soil Repository

Soils are the keystone of healthy and vibrant ecosystems, providing physical, chemical, and biological substrates and functions necessary to support life. In particular, its the extensive and elaborate matrix of soil microorganisms and other life forms that contributes to soil health and utility. But soils are under constant threat from heavy use, changing climate, and in some cases poor management (1, 2). In view of soil’s key role and threatened status, we believe that there is a need for the scientific community to undertake coordinated research and development efforts that will lead to a unique asset: a National Living Soil Repository (Fig. 1). Fig. 1. A National Living Soil Repository would store agricultural cryogenic and air-dried soil samples, analyze samples for microbial community composition, assess samples for microbial viability, and serve as a potential source of living organisms for various agricultural ecosystem services. Image courtesy of Jennifer Moore-Kucera (USDA Natural Resources Conservation Service) and Daniel Manter (USDA Agricultural Research Service). Already local and national soil archives have been shown to be of great utility for studying, analyzing, and documenting long-term environmental and ecological trends. For example, the historical soil archive at Hubbard Brook helped researchers discover the link between fossil fuels and acidification of rain and snow (3); the Rothamsted Sample Archive in the United Kingdom has shown a steady increase in dioxins during the last century (4). And yet, a soil repository/archive designed to preserve native biological diversity does not currently exist. Such an archive would provide the ability to acquire data on the current biological (e.g., soil health) state of soils around the country across soil types, cropping systems, and ecosystems and over time. Further, by maintaining soil archives and a catalog of their microbial communities, we will gain a better understanding of how soil organisms are distributed … [↵][1]1To whom correspondence should be addressed. Email: Jorge.Delgado{at}ars.usda.gov. [1]: #xref-corresp-1-1

Genetic structure of goat breeds from Brazil and the United States: Implications for conservation and breeding programs.

The objective of this study was to assess genetic diversity among 5 Brazilian (155 animals) and 5 U.S. goat (120 animals) breeds using 23 microsatellite markers. Samples from the United States represented a broad geographic distribution whereas Brazilian samples were from the northeast region. Samples from Boer were common to each countrys breed count. Expected and observed heterozygosity among breeds ranged from 0.55 to 0.72, suggesting ample genetic diversity in the breeds evaluated. United States Angora, U.S. Spanish, and Brazilian Nambi ranked highest for allelic richness, averaging 6.1, 7.1, and 6.5 alleles per locus, respectively. Angora and Spanish also ranked highest in private alleles (7 and 9, respectively). Using STRUCTURE, the U.S. Spanish were also found to share a common cluster assignment with Brazilian Nambi, suggesting that progenitor breeds may have been the same and passed through the Canary Islands or Cape Verde in route to the New World. When non-Boer breeds were pooled by country, the effect of the subpopulation compared with total population () = 0.05, suggesting minor genetic differences exist between countries. The lack of genetic structure among goat breeds when compared with other species (e.g., vs. ) suggests goat breeds may exhibit a plasticity that facilitates productivity across a wide range of countries and environments. Taken a step further, the concept of breed for meat goats may not be as relevant for goat production.