Community-Based Livestock Breeding: Coordinated Action or Relational Process?

Over the past decade, community-based breeding programs (CBBPs) have been promoted as a viable approach to improving smallholder livelihoods through a systematic livestock breeding. CBBPs aim to initiate systematic breeding at the community level, including an organized animal identification and recording of performance and pedigree data. To ensure the breeding programs' continuity, building capacities, and ownership among participants are essential to the approach. This study's purpose was to understand how CBBPs have evolved in specific institutional settings and which dynamics occur in the course of implementation. We addressed these questions in reflective conversations with six coordinators of a diverse sample of CBBPs: goats (Malawi, Uganda, and Mexico), sheep (Ethiopia), alpaca (Peru), and cattle (Burkina Faso). The interviews and analysis were guided by categories of the multi-level perspective. The respondents considered lack of funding and weak institutionalization as the main constraints on the CBBPs. While the idea of participation and localized ownership was at the center of the programs, linear paradigms of knowledge transfer prevailed. In all cases, the impulse to start a CBBP came from individual researchers, who relied on intermediaries, such as extension agents, for implementation. Personal relations and trust were seen as both a factor in the success and a positive outcome of CBBPs. We conclude that these findings have different implications depending on how rural development is conceptualized: proponents of the innovation systems perspective would call for stakeholders to further align their interests and coordinate their actions. Proponents of process-relational concepts, in contrast, would not consider the CBBP a product but a starting-point for initiators and participants to continuously discover new ways of collaboration and engagement.

Development of a 76k Alpaca (Vicugna pacos) Single Nucleotide Polymorphisms (SNPs) Microarray.

Small farm producers' sustenance depends on their alpaca herds and the production of fiber. Genetic improvement of fiber characteristics would increase their economic benefits and quality of life. The incorporation of molecular marker technology could overcome current limitations for the implementation of genetic improvement programs. Hence, the aim of this project was the generation of an alpaca single nucleotide polymorphism (SNP) microarray. A sample of 150 Huacaya alpacas from four farms, two each in Puno and Cerro de Pasco were used for SNP discovery by genotyping by sequencing (GBS). Reduced representation libraries, two per animal, were produced after DNA digestion with ApeK1 and double digestion with Pst1-Msp1. Ten alpaca genomes, sequenced at depths between 12× to 30×, and the VicPac3.1 reference genome were used for read alignments. Bioinformatics analysis discovered 76,508 SNPs included in the microarray. Candidate genes SNPs (302) for fiber quality and color are also included. The microarray SNPs cover 90.5% of the genome length with a density of about 39 ± 2.51 SNPs/Mb of DNA at an average interval of 26.45 ± 18.57 kbp. The performance was evaluated by genotyping 30 family trios and comparing them to their pedigrees, as well as comparing microarray to GBS genotypes. Concordance values of 0.93 and 0.94 for ApeK1 and Pst1-Msp1 generated SNPs were observed. Similarly, 290 fiber quality and color candidate gene SNPs were validated. Availability of this microarray will facilitate genome-wide association studies, marker-assisted selection and, in time, genomic selection.

Cytogenetic Mapping of 35 New Markers in the Alpaca (Vicugna pacos).

Alpaca is a camelid species of broad economic, biological and biomedical interest, and an essential part of the cultural and historical heritage of Peru. Recently, efforts have been made to improve knowledge of the alpaca genome, and its genetics and cytogenetics, to develop molecular tools for selection and breeding. Here, we report cytogenetic mapping of 35 new markers to 19 alpaca autosomes and the X chromosome. Twenty-eight markers represent alpaca SNPs, of which 17 are located inside or near protein-coding genes, two are in ncRNA genes and nine are intergenic. The remaining seven markers correspond to candidate genes for fiber characteristics (BMP4, COL1A2, GLI1, SFRP4), coat color (TYR) and development (CHD7, PAX7). The results take the tally of cytogenetically mapped markers in alpaca to 281, covering all 36 autosomes and the sex chromosomes. The new map assignments overall agree with human-camelid conserved synteny data, except for mapping BMP4 to VPA3, suggesting a hitherto unknown homology with HSA14. The findings validate, refine and correct the current alpaca assembly VicPac3.1 by anchoring unassigned sequence scaffolds, and ordering and orienting assigned scaffolds. The study contributes to the improvement in the alpaca reference genome and advances camelid molecular cytogenetics.

Genetic Diversity and Population Structure of Llamas (Lama glama) from the Camelid Germplasm Bank-Quimsachata.

Llamas (Lama glama) are invaluable resources of Peru. Despite their importance, their population is decreasing. The Camelid Germplasm Bank-Quimsachata was created as a guardian of this South American camelid (SAC) species and established a bank of llamas from their two types, Ch'aku and Q'ara. However, these populations need to present high genetic diversity to be considered suitable conservation stocks. Thus, in the present study, 13 microsatellites specific for the SAC were used to assess the current genetic variability and differentiation of the llama population from the Bank. The global population showed high genetic diversity with a total of 157 different alleles, with an average of 12.08 alleles per microsatellite, an expected and observed heterozygosity of 0.758 and 0.707, respectively, and an average polymorphic information content (PIC) of 0.723. Although considered as two different breeds and managed separately, the genetic differentiation between Ch'aku and Q'ara was low (FST = 0.01). Accordingly, the gene flow value was high (Nm = 30.5). Overall, our results indicate the existence of high genetic variation among individuals, and thus, this llama population could be considered a suitable genetic stock for their conservation and for sustainability programs. Additionally, the 13 microsatellites can be used to study other Peruvian llama populations and monitor the genetic variability of llamas from the Camelid Germplasm Bank-Quimsachata.

Genomics and animal production / Genómica y producción animal

Abstract Developing countries have the challenge of achieving food security in a world context that is affected by climate change and global population growth. Molecular Genetics and genomics are proposed as technologies that will help to achieve sustainable food security. Technologies that have been developed in the last decade such as the development of genetic markers, genetic maps, genomic selection, next-generation sequencing, and DNA editing systems are discussed. Examples of some discoveries and achievements are provided.

Resumen Los países en vías de desarrollo tienen el reto de alcanzar seguridad alimentaria en un contexto mundial afectado por el cambio climático y crecimiento poblacional global. La genética molecular y la genómica son propuestas como tecnologías que ayudarán a alzanzar una seguridad alimentaria sostenible. Tecnologías que han sido desarrolladas en la última década como el desarrollo de marcadores moleculares, mapeo genético, selección genómica, secuenciamiento de próxima generación y sistemas de edición de ADN son discutidos. Se proveen ejemplos de algunos descubrimientos y logros.

Comparative FISH-Mapping of MC1R, ASIP, and TYRP1 in New and Old World Camelids and Association Analysis With Coat Color Phenotypes in the Dromedary (Camelus dromedarius).

Melanocortin 1 receptor (MC1R), the agouti signaling protein (ASIP), and tyrosinase related protein 1 (TYRP1) are among the major regulators of pigmentation in mammals. Recently, MC1R and ASIP sequence variants were associated with white and black/dark brown coat colors, respectively, in the dromedary. Here we confirmed this association by independent sequencing and mutation discovery of MC1R and ASIP coding regions and by TaqMan genotyping in 188 dromedaries from Saudi Arabia and United States, including 38 black, 53 white, and 97 beige/brown/red animals. We showed that heterozygosity for a missense mutation c.901C > T in MC1R is sufficient for the white coat color suggesting a possible dominant negative effect. Likewise, we confirmed that the majority of black dromedaries were homozygous for a frameshift mutation in ASIP exon 2, except for 4 animals, which were heterozygous. In search for additional mutations underlying the black color, we identified another frameshift mutation in ASIP exon 4 and 6 new variants in MC1R including a significantly associated SNP in 3'UTR. In pursuit of sequence variants that may modify dromedary wild-type color from dark-reddish brown to light beige, we identified 4 SNPs and one insertion in TYRP1 non-coding regions. However, none of these were associated with variations in wild-type colors. Finally, the three genes were cytogenetically mapped in New World (alpaca) and Old World (dromedary and Bactrian camel) camelids. The MC1R was assigned to chr21, ASIP to chr19 and TYRP1 to chr4 in all 3 species confirming extensive conservation of camelid karyotypes. Notably, while the locations of ASIP and TYRP1 were in agreement with human-camelid comparative map, mapping MC1R identified a new evolutionary conserved synteny segment between camelid chromosome 21 and HSA16. The findings contribute to coat color genomics and the development of molecular tests in camelids and toward the chromosome level reference assemblies of camelid genomes.

New World simian foamy virus infections in vivo and in vitro.

Foamy viruses (FV) are complex retroviruses that naturally infect all nonhuman primates (NHP) studied to date. Zoonotic transmission of Old World NHP simian foamy viruses (SFV) has been documented, leading to nonpathogenic persistent infections. To date, there have been no reports concerning zoonotic transmission of New World monkey (NWM) SFV to humans and resulting infection. In this study, we developed a Western blot assay to detect antibodies to NWM SFV, a nested PCR assay to detect NWM SFV DNA, and a ß-galactosidase-containing indicator cell line to assay replication of NWM SFV. Using these tools, we analyzed the plasma and blood of 116 primatologists, of whom 69 had reported exposures to NWM. While 8 of the primatologists tested were seropositive for SFV from a NWM, the spider monkey, none had detectable levels of viral DNA in their blood. We found that SFV isolated from three different species of NWM replicated in some, but not all, human cell lines. From our data, we conclude that while humans exposed to NWM SFV produce antibodies, there is no evidence for long-term viral persistence.