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The African Goat Improvement Network (AGIN) is a collaborative group of scientists focused on genetic improvement of goats in small holder communities across the African continent. The group emerged from a series of workshops focused on enhancing goat productivity and sustainability. Discussions began in 2011 at the inaugural workshop held in Nairobi, Kenya. The goals of this diverse group were to: improve indigenous goat production in Africa; characterize existing goat populations and to facilitate germplasm preservation where appropriate; and to genomic approaches to better understand adaptation. The long-term goal was to develop cost-effective strategies to apply genomics to improve productivity of small holder farmers without sacrificing adaptation. Genome-wide information on genetic variation enabled genetic diversity studies, facilitated improved germplasm preservation decisions, and provided information necessary to initiate large scale genetic improvement programs. These improvements were partially implemented through a series of community-based breeding programs that engaged and empowered local small farmers, especially women, to promote sustainability of the production system. As with many international collaborative efforts, the AGIN work serves as a platform for human capacity development. This paper chronicles the evolution of the collaborative approach leading to the current AGIN organization and describes how it builds capacity for sustained research and development long after the initial program funds are gone. It is unique in its effectiveness for simultaneous, multi-level capacity building for researchers, students, farmers and communities, and local and regional government officials. The positive impact of AGIN capacity building has been felt by participants from developing, as well as developed country partners., Competing Interests: Author TSS was employed by Acceligen Inc. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2023 Van Tassell, Rosen, Woodward-Greene, Silverstein, Huson, Sölkner, Boettcher, Rothschild, Mészáros, Nakimbugwe, Gondwe, Muchadeyi, Nandolo, Mulindwa, Banda, Kaumbata, Getachew, Haile, Soudre, Ouédraogo, Rischkowsky, Mwai, Dzomba, Nash, Abegaz, Masiga, Wurzinger, Sayre, Stella, Tosser-Klopp and Sonstegard.)

In goat breeds, the domestication followed by artificial selection for economically important traits have shaped genetic variation within populations, leading to the fixation of specific alleles for specific traits. This led to the formation and evolution of many different breeds specialised and raised for a particular purpose. However, and despite the intensity of artificial selection, natural selection continues acting, possibly leaving a more diluted contribution over time, whose traces may be more difficult to capture. In order to explore selection footprints as response of environmental adaptation, we analysed a total of 993 goats from four transboundary goats breeds (Angora, Boer, Nubian and Saanen) genotyped with the SNP chip 50 K using outlier detection, runs of homozygosity and haplotype-based detection methods. Our results showed that all methods identified footprints on chromosome 6 (from 30 to 49 Mb) for two specific populations of Nubian goats sampled in Egypt. In Angora and Saanen breeds, we detected two selective sweeps using HapFLK, on chromosome 21 (from 52 to 55 Mb) and chromosome 25 (from 1 to 5 Mb) respectively. The analysis of runs of homozygosity showed some hotspots in all breeds. The overall investigation of the selected regions detected combining the different approaches and the gene ontology exploration revealed both novel and well-known loci related to adaptation, especially for heat stress. Our findings can help to better understand the balance between the two selective pressures in commercial goat breeds providing new insights on the molecular mechanisms of adaptation., (© 2023. The Author(s).)

The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus) based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a ∼400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.

The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50-60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years.

A systems genetics approach combining pathway analysis of quantitative trait loci (QTL) and gene expression information has provided strong evidence for common pathways associated with genetic resistance to internal parasites. Gene data, collected from published QTL regions in sheep, cattle, mice, rats and humans, and microarray data from sheep, were converted to human Entrez Gene IDs and compared to the KEGG pathway database. Selection of pathways from QTL data was based on a selection index that ensured that the selected pathways were in all species and the majority of the projects overall and within species. Pathways with either up- and down-regulated genes, primarily up-regulated genes or primarily down-regulated genes, were selected from gene expression data. After comparing the data sets independently, the pathways from each data set were compared and the common set of pathways and genes was identified. Comparisons within data sets identified 21 pathways from QTL data and 66 pathways from gene expression data. Both selected sets were enriched with pathways involved in immune functions, disease and cell responses to signals. The analysis identified 14 pathways that were common between QTL and gene expression data, and four directly associated with IFNγ or MHCII, with 31 common genes, including three MHCII genes. In conclusion, a systems genetics approach combining data from multiple QTL and gene expression projects led to the discovery of common pathways associated with genetic resistance to internal parasites. This systems genetics approach may prove significant for the discovery of candidate genes for many other multifactorial, economically important traits., (© 2011 The Authors, Animal Genetics © 2011 Stichting International Foundation for Animal Genetics.)

Background: Anthracnose (Colletotrichum gloeosporioides) is a major limiting factor in the production of yam (Dioscorea spp.) worldwide. Availability of high quality sequence information is necessary for designing molecular markers associated with resistance. However, very limited sequence information pertaining to yam is available at public genome databases. Therefore, this collaborative project was developed for genetic improvement and germplasm characterization of yams using molecular markers. The current investigation is focused on studying gene expression, by large scale generation of ESTs, from one susceptible (TDa 95-0310) and two resistant yam genotypes (TDa 87-01091, TDa 95-0328) challenged with the fungus. Total RNA was isolated from young leaves of resistant and susceptible genotypes and cDNA libraries were sequenced using Roche 454 technology., Results: A total of 44,757 EST sequences were generated from the cDNA libraries of the resistant and susceptible genotypes. Greater than 56% of ESTs were annotated using MapMan Mercator tool and Blast2GO search tools. Gene annotations were used to characterize the transcriptome in yam and also perform a differential gene expression analysis between the resistant and susceptible EST datasets. Mining for SSRs in the ESTs revealed 1702 unique sequences containing SSRs and 1705 SSR markers were designed using those sequences., Conclusion: We have developed a comprehensive annotated transcriptome data set in yam to enrich the EST information in public databases. cDNA libraries were constructed from anthracnose fungus challenged leaf tissues for transcriptome characterization, and differential gene expression analysis. Thus, it helped in identifying unique transcripts in each library for disease resistance. These EST resources provide the basis for future microarray development, marker validation, genetic linkage mapping and QTL analysis in Dioscorea species.

Background: Microsatellites, also called Simple Sequence Repeats (SSRs), repetitions of nucleotide motifs of 1-5 bases, are currently the markers of choice due to their abundant distribution in the genomes, and suitability for high-throughput analysis. A total of five different primer pairs were optimized for polymerase chain reaction (PCR) to amplify microsatellite loci in total genomic DNA of bunchgrass lizards (Sceloporus slevini) collected from three sites in southeastern Arizona; the Sonoita Plain, Chiricahua Mountains and Huachuca Mountains., Findings: The primers used for current investigation were originally designed for the Eastern Fence Lizard (Sceloporus undulatus). Five primer pairs were selected based on annealing temperatures for optimizing the PCR conditions to amplify with bunchgrass lizards. Different concentrations of DNA and annealing temperature were optimized. While keeping other reagents constant, a DNA concentration, 37.5 ng in the final reaction volume and PCR conditions of an initial denaturation of 94°C for five minutes, an annealing temperature of 55°C and final extension of 72°C for four minutes gave the best amplification for all the primer pairs., Conclusions: Modifying the standard protocol for annealing temperatures and final extension time increases the success of cross amplification of specific microsatellite loci in the bunchgrass lizard. A loading volume of 5 ul DNA at a concentration of 10 ng/ul and a 2% agarose for gel electrophoresis were observed the best for cross amplification of selected five primer pairs on bunch grass lizard., Trial Registration: The research was conducted with Arizona Game and Fish Department scientific collecting permits SP565256, SP657407 & SP749119 to Dr. Christian A d'Orgeix.

Salmonella strains and Escherichia coli O157:H7 were detected in 17 and 5 small ruminants in Virginia, respectively, of 287 tested. Background microflora interfered with the fecal analysis. The combination of Salmonella enzyme immunoassay (EIA) detection and xylose-lysine-deoxycholate agar isolation was satisfactory. Modifying enrichment to a 1:100 dilution enabled effective E. coli O157:H7 detection by EIA and isolation by sorbitol-MacConkey agar with cefixime-tellurite.

Three experiments were conducted to examine gene expression during induced luteal regression in the cow; the initial purpose was the identification of potential embryotoxins. In experiment 1, changes in gene expression in the corpus luteum (CL) were identified by differential display reverse transcription-polymerase chain reaction (DD-PCR) during the first 72 h of luteal regression in cows treated with prostaglandin F(2alpha) (PGF(2alpha)) on Days 4-7 after estrus. Expression of insulin-like growth factor-binding protein-1 (IGFBP-1) was up-regulated, with greatest expression at 24 h (P < 0.05) after treatment with PGF(2alpha) began. In experiment. 2, IGFBP-1 and its mRNA were quantified in CL collected 24 or 48 h after treatment with PGF(2alpha) on Day 4 or 10 after estrus. Because local mechanisms for exchange of hormones between the ovary and uterus are known in ruminants, uterine flushings were assayed for IGFBP-1 to seek evidence of local transfer of luteal IGFBP-1 to the uterus. IGFBP-1 mRNA was increased (P < 0.05) in CL 24 h after treatment when PGF(2alpha) that began on Day 10, and by 48 h after treatment that began on Day 4. Concentrations of IGFBP-1 increased (P < 0.05) in a pattern similar to mRNA, by 24 h on Day 10, and by 48 h on Day 4. Concentrations of IGFBP-1 in uterine flushings did not change on either day. Concentrations of progesterone decreased (P < 0.05) by 8 h after treatment with PGF(2alpha) that began on Day 10, but not until 24 h after treatment that began on Day 4. In experiment 3, cows received either saline or PGF(2alpha) and CL were collected 2 or 10 h after a single treatment, or 2 h after a second treatment that was given 8 h after the first. Expression of IGFBP-1 was increased by 2 h after treatment with PGF(2alpha) on both Days 4 and 10 after estrus. In conclusion, secretion of IGFBP-1 is increased during luteolysis, and may inhibit the steroidogenic effects of insulin-like growth factor-I (IGF-I), but no evidence was found to implicate IGFBP-1 in the embryotoxic effect of regressing CL.

Early luteal regression in cattle has an embryotoxic effect that is not overcome by replacement with progesterone, but is prevented by removal of the regressing CL. Two experiments were designed to test the null hypothesis that the luteal component of the embryotoxic effect is delivered by a systemic pathway. Beef heifers and cows (n = 39) received two good quality embryos, one placed into each uterine horn on Day 6 or 7 of the estrous cycle. Treated animals (n = 20) received 15 mg of PGF2alpha three times per day from Day 7 (n = 11; Experiment 1) or 5 (n = 9; Experiment 2) through 8; controls (n = 19) received saline. Progestogen replacement therapy (12 mg flurogestone acetate daily, s.c.) was provided from Day 6 (Experiment 1) or 4 (Experiment 2) until ultrasonographic diagnosis of embryo survival on Day 35 after estrus. The effects of treatment, location of the embryo and location by treatment interaction on embryo survival were tested by Chi square. In Experiment 1, there was no significant difference in embryo survival rate between PGF2alpha-treated and control recipients. In Experiment 2, only 6 of 18 embryos survived to Day 35 when transferred to animals treated with PGF2alpha compared to 12 of 18 in control animals (P< 0.05). The survival of embryos did not differ with location (adjacent or opposite to the regressing CL) or location by treatment interaction. Thus no evidence was obtained to support a local effect of the regressing CL. The embryo mortality associated with luteolytic doses of PGF2alpha in cows receiving replacement therapy with progestogen probably involves compounds that either act systemically or are transported via the uterine lumen to the uterine horn contralateral to the regressing CL.

Based on our previous work, we found that exogenous oxytocin induces uterine tetany and cervical dilation, and permits transcervical access to the uterus. However, the oxytocin does not reduce sustained sperm transport from the uterus to the oviducts. Thus, we hypothesized that exogenous oxytocin may be a useful adjunct to transcervical intrauterine AI procedures for sheep: two experiments were conducted to test our hypothesis. In Experiment 1, purebred ewes (n = 75/group) were artificially inseminated intrauterine with either laparoscopic or oxytocin-transcervical (i.e., 200 USP units of oxytocin 30 min before AI) procedures. At 54 h after progestogenated pessaries were removed, ewes were inseminated with 200 x 10(6) sperm/0.25 ml of fresh, extended semen, which was collected from a purebred ram of the corresponding breed. Pregnancy rate was greater (P < 0.05) after laparoscopic (37.5%) than after transcervical AI (0%). Because of the disappointing results of Experiment 1, Experiment 2 was conducted to determine whether oxytocin or the AI procedure per se reduced ovum fertilization rate. Treatments were designed in a 2 x 2 factorial arrangement. At 60 h after norgestomet implant removal and 10 min before either laparoscopic or transcervical (cervical in a saline group) AI with 100 x 10(6) sperm/0.25 ml, ewes (n = 10/group) received an intravenous injection of either isotonic saline or 200 USP units of oxytocin. Fertilization rate, which was determined 72 h after AI, was greater (P < 0.05) after laparoscopic than after transcervical/cervical AI (92.5 vs 28%), but oxytocin treatment did not affect fertilization rate. The results indicate that exogenous oxytocin did not reduce ovum fertilization rate, but the transcervical AI procedure per se seemed to reduce fertilization rate.

The exact mechanisms controlling uterine secretion of PGF2 alpha are not known. An animal model in which progestogen concentrations are kept high and corpora lutea are allowed to regress should be useful for studying the effects of progestogen and estrogens on uterine secretion of PGF2 alpha. Thus, the primary objectives of this study with ovarian-intact ewes were to determine 1) the effect of 6 alpha-methyl-17 alpha-hydroxyprogesterone acetate (MPA) on luteal life span and changes in jugular and vena caval concentrations of PGF2 alpha, 13,14-dihydro-15-keto-PGF2 alpha (PGFM), progesterone, and estrogens around the time of luteolysis, and 2) the relationships among changes in those compounds. The results indicate that MPA 1) reduced (P < .05) vena caval and jugular PGF2 alpha and PGFM concentrations, 2) did not affect luteal life span or progesterone concentrations, 3) increased (P < .05) jugular concentrations of estrogens, and 4) prolonged (P < .05) the interestrous interval by 7 d. Stepwise regression procedures indicated that MPA disrupted a number of the relationships among PGF2 alpha, PGFM, progesterone, and estrogens in vena caval and jugular plasma. Ovarian-intact, MPA-treated ewes may be useful for determining the mechanisms involved in controlling uterine secretion of PGF2 alpha.

Two experiments were conducted to determine if early ovine embryos produce prostaglandins and if prostaglandins may have a role in the shedding of the zona pellucida, i.e., embryo hatching. For Experiment 1, embryos were collected on day (d) 4, 8, 10, 12 or 14 of pregnancy and incubated with 1 microCi of [14C] arachidonic acid (AA) for 24 h. Based upon high-performance liquid chromatography, embryos from all days converted AA to a number of compounds; the amounts produced differed with day. Primarily, embryos produced an unidentified polar compound, 6-keto-PGF1 alpha, PGF2 alpha, PGE2, 13,14-dihydro-15-keto-PGF2 alpha and PGB2. For Experiment 2, embryos collected on d 7 of pregnancy were incubated for a maximum of 6 d in 500 microL of medium containing either ethanol (control; 20 microL), indomethacin (INDO; 10(-4) M), PGE2 (2 ng) or INDO (10(-4) M) + PGE2 (2 ng). Embryos were evaluated daily for hatching from the zona pellucida. The hatching rates (percentage) for control, INDO, PGE2 and INDO + PGE2 were 46.4, 34.5, 60.0, and 30.0, respectively. There was a main effect (P < .09) of treatment, and the hatching rate for embryos treated with PGE2 alone was greater (P < .05) than that for embryos in any group with INDO. The results indicate that early ovine embryos can convert AA to various compounds in vitro, and prostaglandins may have a role in the hatching of sheep embryos from the zona pellucida.

Cervical anatomy in ewes usually prevents nonsurgical, intrauterine AI and transcervical embryo transfer (ET), which limits their commercial use in sheep. This study was conducted to determine whether oxytocin would dilate the cervix in ewes and permit passage of a stainless steel rod into the uterus. In Exp. 1, at 44 and 52 h after removal of progestogenated pessaries, ewes were injected i.v. with 0 (saline), 200, 400, or 600 USP units of oxytocin. Immediately before and after treatments, stainless steel rods were used to evaluate cervical dilation and determine whether the uterus could be entered. A rod could not be passed through the cervix and into the uterus in any of the saline-treated ewes. All doses of oxytocin given at 44 and 52 h after pessary removal dilated the cervix and permitted easy passage of a rod into the uterus. At both 44 and 52 h, a stainless steel rod was passed into the uterus in 33 of 43 (77%) of the oxytocin-treated ewes. In 93% (40/43) of these ewes, a rod could be passed into the uterus during either the 44-h or during the 52-h attempt. In Exp. 2, on d 9 after pessary removal, ewes were injected i.v. with oxytocin (400 USP units) at 6 or 12 h after i.v. estradiol-17 beta (0, 100, or 200 micrograms). Cervical dilation was evaluated as in Exp. 1. Dose of estradiol x time of oxytocin affected (P less than .01) the proportion of ewes in which a rod could be passed transcervically into the uterus.(ABSTRACT TRUNCATED AT 250 WORDS)