Animal Genetic Resources Research Articles

Caracterización de ovinos Criollos argentinos utilizando índices zoométricos

The rational use of animal genetic resources, involves studying their zootechnical and productive characteristics by objective data. To fulfil this premise in the case of the Argentinean Creole sheep breed, much remains to be done. It is the first sheep breed in the country, is distributed in almost all provinces and occupies the third place of the current sheep stock. The objective of this work was to study the morphology of Creole sheep from four Argentine provinces using zoometric indexes, in order to recognize their ethnic characteristics and functional abilities. We worked with 203 adult sheep according to their dental chronometry: 59 belonging to Buenos Aires province (BA); 40 to Corrientes (CO); 60 to Santiago del Estero (SE) and 44 to Salta (SA). Eight zoometric indexes were calculated: four belonging to the ethnological type: Cephalic index (ICE); Thoracic index (ITO); Corporal index (ICO); Pelvic index (IPE) and four belonging to the functional type: Relative depth index (IPR); Pelvic transversal index (IPT); Pelvic longitudinal index (IPL); Short-sightedness relative index (ICR). Descriptive statistical analyzes were performed, ANOVA and Tukey test to detect differences between regions, linear correlations between indexes and Principal Component Analysis for ethnological and functional indexes separately. The results regarding to the ethnological indexes show that the four regions shared racial characteristics in common, although they present variability within population, the sheep from Salta are more homogeneous and then those from Buenos Aires which present more variability probably because of adaptation of animals to the different environments. The functional indexes indicate that in the four regions, sheep are suitable as meat-wool dual purpose animals. Salta’s sheep resulted to be the most uniform one and to have the best meat conformation.

The Role of Traditional Communities n the Management of Diversity of Sheep Populations in Caras - Severin County

Abstract Modernization of agriculture has led to the erosion of biodiversity of agroecosystems with implications for productivity in the sector. Degradation of genetic resources of plants, animals, insects and soil organisms causing economic losses threatening the food security of the population. This study is based on biodiversity in sheep populations in Caras - Severin and brings attention to traditional practices in the management of animal genetic resources. In the agroecosystem, maintaining the biodiversity is a guarantee for future challenges (growth and diversification of consumer demand, climate change, possible calamities) provided that at the consumer level there is an increased preference to traditional and organic products. From this point of view, it is remarkable the effort of private breeders in Caras - Severin to maintain the rustic varieties of sheep, but we think it requires a more resolute stand of the government and academic organisations for identification, preservation and support of such genetic resources valuable for all species. In Caras-Severin County, diversity of sheep populations is maintained in household or pastoral system in small and medium farms, the animal selection being based on the interest and preferences.

Genomic Regions in Local Endangered Sheep Encode Potentially Favorable Genes

ABSTRACTThe economic evaluation of farm animal genetic resources plays a key role in developing conservation programs. However, to date, the link between diversity as assessed by neutral genetic markers and the functional diversity is not yet understood. Two genome-wide comparisons, using over 44,000 Single Nucleotide Polymorphisms, identified the markers with the highest difference in allele frequency between the Alpago endangered breed and two clusters, composed of four specialized dairy sheep, and four meat breeds respectively. The genes in proximity of these markers were mapped to known pathways of the Gene Ontology to determine which ones were most represented. Our results indicated that the differences of the Alpago breed from the more productive sheep rely upon genes involved in cellular defense and repair mechanisms. A higher number of different markers and genes were detected in the comparison with the specialized dairy sheep. These genes play a role in complex biological processes: metabolic, homeostatic, neurological system, and macromolecular organization; such processes may possibly explain the evolution of gene function as a result of selection to improve milk yield.

Assessment of degree of endangerment of livestock breeds in India

Complete national inventories, supported by periodic monitoring of trends and associated risks, are basic requirements for the effective management of farm animal genetic resources. Government of India conducted breed survey in 2013 to estimate breed-wise data for livestock belonging to different categories, breeds, age and sex groups. FAO has developed criteria for assessment of risk to the livestock breeds, which were used to assess the risk status of all the breeds of livestock species. Breed-wise populations of breeding males and females, overall population size, effective population size and rate of inbreeding were estimated. Cattle, sheep and pigs species were classified as indigenous purebreds, graded to indigenous breeds, indigenous non-descript, exotic purebreds and crossbreds to exotic breeds; while buffalo and goat species were classified under first three categories only. Proportion of indigenous purebreds of cattle, buffalo, sheep, goat and pig were found as 9.4, 17, 36.6, 27 and 3%, respectively of the total population of the species; whereas corresponding figures of graded to indigenous breeds and non-descript animals were estimated to be 10.5, 39.6, 18.9, 11.8 and 0% and 59.3, 43.4, 38.7, 61.2 and 73.1%, respectively. Large non-descript proportion of all the livestock species should be screened for identification, characterization and registration of new breeds. Exotic breeds and crossbreds to exotic breeds in cattle, sheep and pig were obtained as 0.7 and 20.1%; 0.7 and 5.1% and 2.3 and 21.6%, respectively of total population. The rate of inbreeding estimated for most of the breeds were well below 0.5% except for Mewati (1.193%), Pullikulam (0.72%) and Vechur (17.893%) cattle breeds and Chilika (0.731%) buffalo breed. Using the FAO criteria, Bargur and Siri cattle breeds and Attapadi goat breeds were categorized under vulnerable status of risk; Krishna Valley, Mewati, Pullikulam and Punganur cattle breeds, Chilika and Toda buffalo breeds and Karnah and Poonchi sheep breeds under endangered status of under risk and Vechur cattle under critical status of risk. All these breeds need immediate steps for rescue by using suitable conservation methodology. Breed-wise census should be continued in future so that trends in breed populations may also be estimated for fine tuning of risk assessment of breeds.

The Domestic Livestock Resources of Turkey: Silkworm (Bombyx Mori, L. 1758) (Lepidoptera: Bombycidae) Lines and their Conservation

This paper reviews the current status of Turkish silkworm genetic resources and activities being undertaken for their conservation. Silk production and the trade in silk have been important activities in Turkey, which lies on the ancient Silk Road, for many hundreds of years. Current production of silk is on the rise after a period of very low production. Turkey has a well-established programme of conservation and development of all of its domestic animal genetic resources, of which silkworm is considered a constituent part. Three distinct lines of native silkworm have been registered with the national standards body, the Turkish Standards Institute. Distribution of silkworm germplasm is regulated by the Ministry of Food, Agriculture and Livestock through Cooperative Unions which have more than 10,000 members. Renewed and increased international demand for natural and biological products is favourable to Turkey’s silkworm industry. The prognosis for the future development of silk production is strongly positive.

Genetic diversity of common carp (Cyprinus carpio L.) strains breed in Poland based on microsatellite, AFLP, and mtDNA genotype data

The common carp (Cyprinus carpio L.) has a long-standing history in Polish pond aquaculture, which has given rise to a great number of local breeds, strains and hatchery populations. They are well adapted to their local conditions, play an important role for fisherman's livelihoods and embody valuable genetics for future breeding programs. Proper maintenance of animal genetic resources (AnGR) requires an appropriate strategy based upon the precise knowledge of their genetic structure. This study genetically characterizes 20 common carp strains breed in Poland alongside with wild carp from Onuma Lake in Japan. We study three different types of genetic markers including the 963 AFLP markers, a set of 11 microsatellite loci (STR) and DNA sequences of the mitochondrial control region (D-loop). Bayesian clustering analysis of microsatellite loci divided the studied strains into 17 distinct clusters. Using population assignment test 92.4% of carp individuals were correctly assigned to their strain of origin. Microsatellite and AFLP marker analysis have shown the moderate but significant level of genetic variation between strains (AMOVA 23% and 18.2% respectively). AFLP and STR analysis of genetic distances gave equivalent values and were positively correlated with high values of the Mantel test (r=0.553, n=20, p=0.001). Only two mtDNA haplotypes (H5 and H2) were detected in all studied carp strains with H2 being the most prevalent.This is the first comprehensive genetic research of common carp strains breed in Poland which provided crucial data for the national conservation strategy. This study means that this resource can now be placed within the context of similar studies worldwide allowing the further improvement and breeding work.

Stakeholder involvement and the management of animal genetic resources across the world

The sustainability of activities related to animal genetic resources (AnGR) management depends largely on the participation of a range of stakeholders, both public and private. In this study, we investigated factors explaining differences in stakeholder involvement in AnGR management across countries, based on an historical perspective and an analysis of the 128 official country reports provided during preparation of The Second Report on the State of the World's Animal Genetic Resources for Food and Agriculture. Results of principal component analyses indicated that countries differed in the involvement of stakeholders in AnGR management, generally with greater involvement of livestock breeders and their organizations in developed countries. Developing countries tended to be divided into two groups, those with little involvement by stakeholders and those with high involvement by government/research organizations. Depending on the country, the involvement of government/research organizations versus breeders/livestock keepers organizations and commercial companies also differed, which could be linked to some extent to their historical background. The level of involvement of breeders ‘associations or cooperatives was positively correlated (r=0.68) to the general extent of AnGR activities within the country. Our results underline the importance of involving breeders and livestock keepers in the development of management activities, while public support is required as well, especially in the early stages of capacity development. In developing countries, development policies relative to AnGR management should therefore seek to promote coordination among livestock keepers through creation and empowerment of cooperatives, associations or community-based approaches.

Origin and phylogenetic status of the local Ashanti Dwarf pig (ADP) of Ghana based on genetic analysis

BackgroundThe Ashanti Dwarf Pig (ADP) of Ghana is an endangered pig breed with hardy and disease resistant traits. Characterisation of animal genetic resources provides relevant data for their conservation and sustainable use for food security and economic development. We investigated the origin and phylogenetic status of the local ADP of Ghana and their crosses with modern commercial breeds based on mtDNA, MC1R, Y-chromosome sequence polymorphisms, and genome-wide SNP genotyping.ResultsThe study involved 164 local pigs sampled from the three agro-ecological zones of Ghana. Analyses of the mitochondrial D-loop region and Y-chromosome sequences revealed both European and Asian genetic signatures, with differences between the geographical zones. Black coat colour is the most predominant within the breed, with black MC1R alleles of both Asian and European origin. European alleles for spotting are present at a low frequency in the sample set, and may account for the occurrence of spotted piglets in some APD litters. PCA analysis of SNP data revealed a strong location and breed effect on clustering of local Ghanaian pigs. On a global level, Ghanaian local pigs cluster closely with European pigs of commercial origin, but we identified intervals via FST analyses that may elucidate loci for ADP specific traits.ConclusionsThe presence of both European and Asian contributions, with differences between geographical zones probably reflects trading and colonial influences. Understanding the effects of admixture on important adaptive and economic traits of the ADP and other local breeds in Africa is critical for developing sustainable conservation programmes to prevent the decline of these genetic resources.

Detection of deltamethrin resistance in eggs and larva of Rhipicephalus (Boophilus) microplus

Rhipicephalus (Boophilus) microplus is the most common tick species in India infesting cattle and buffaloes and cause significant economic losses to dairy and leather industries by adversely affecting the milk production and quality of hides. Egg hatch assay and larval packet test were used to evaluate the comparative acaricidal efficacy of the market formulations of deltamethrin, cypermethrin and amitraz on eggs and larval stages of R. (B.) microplus. The regression graphs of probit hatchability, % inhibition of hatching (IH) of eggs and probit mortality were plotted against log concentrations of various acaricides. The results revealed that cypermethrin and amitraz were effective and produced complete inhibition of hatching. LC95 values of cypermethrin and amitraz calculated by larval packet test were estimated to be 244.91 ppm and 369.83 ppm, respectively. On the other hand, deltamethrin failed to completely inhibit the hatching. LC95 values by egg hatch assay and larval packet test were estimated to be 42.27 ppm and 39.36 ppm, respectively. The data on field status of acaricide resistance from the area with diversified animal genetic resources will be helpful to adopt suitable strategy to overcome the process of development of resistance in ticks.

Strategy to Fulfill the Requirements for Concession and Release of New Animal Breed or Strain

Law of the Republic of Indonesia Number 5 of 1994 on Ratification of the United Nations Convention on Biological Diversity and Regulation of the Minister of Agriculture of the Republic of Indonesia Number: 117/Permentan/SR.120/10/2014 regarding the concession and release of animal breed or strain in Indonesia should be followed up. This paper aims to improve the understanding of concession and release of animal breed or strain. Requirements of breed or strain concession has to declare (a) Its origin; (b) Original geographic distribution where the breed or strain formed; (c) Characteristics; (d) Genetic information; (e) The animal number and structure of their population; and (f) Animal picture. Requirements for the release of breed or strain should have (1) The method to obtain animal breed or strain; (2) Characteristics; (3) Genetic information; (4) New invention, unique, uniform and stable (NUUS); (5) The current number of animal; (6) Animal picture; (7) A guarantee certificate of quality standard; and (8) At the time of receipt of the request release, breed or strain has never been traded/distributed in Indonesia or already traded less than five years. Therefore, the government operational policy is necessary to regulate the preservation and improvement of animal genetic resources either breed or strain beneficial for future generations.

Market organization and animal genetic resource management: a revealed preference analysis of sheep pricing

Farm animal genetic resources are threatened worldwide. Participation in markets, while representing a crucial way out of poverty for many smallholders, affects genetic management choices with associated sustainability concerns. This paper proposes a contextualized study of the interactions between markets and animal genetic resources management, in the case of sheep markets in Ouagadougou, Burkina Faso. It focusses on the organization of marketing chains and the valuation of genetic characteristics by value chain actors. Marketing chain characterization was tackled through semi-structured interviews with 25 exporters and 15 butchers, both specialized in sheep. Moreover, revealed preference methods were applied to analyse the impact of animals’ attributes on market pricing. Data were collected from 338 transactions during three different periods: Eid al-Adha, Christmas and New Year period, and a neutral period. The neutral period is understood as a period not close to any event likely to influence the demand for sheep. The results show that physical characteristics such as live weight, height at withers and coat colour have a strong influence on the animals’ prices. Live weight has also had an increasing marginal impact on price. The different markets (local butcher, feasts, export market, sacrifices) represent distinct demands for genetic characteristics, entailing interesting consequences for animal genetic resource management. Any breeding programme should therefore take this diversity into account to allow this sector to contribute better to a sustainable development of the country.

Phenotype and ultrastructure of stem cells derived from amniotic fluid of Nitra rabbit

The isolation of amniotic fluid-derived mesenchymal stem cells (AF-MSCs) has been already shown in human and several other species including rabbit. However, prior to the preclinical research on various animal models it is desirable to define AF-MSCs by a panel of surface protein markers. Therefore, the aim of this preliminary study was to detect the expression of several protein markers on the surface of AF-MSCs isolated from local breed of Nitra rabbit. Amniotic fluid was collected from humanely sacrificed rabbits (n = 3) and AF-MSCs were cultured to a third passage. Flow cytometry was used to detect surface protein marker expression and for viability testing. Rabbit AF-MSCs (rAF-MSCs) were also analyzed by transmission electron microscopy to define the ultrastructure. rAF-MSCs showed both sufficient viability (more than 80%) and low apoptosis rates at third passage and highly expressed CD29 (88.17 ± 7.17%) and CD44 (80.00 ± 2.28%). However, a dim expression of CD90 (17.24 ± 1.31%) and negative expression of CD73 (1.21 ± 0.56% and 4.41 ± 1.46%), CD105 (1.67 ± 0.37%) and CD166 (0.96 ± 2.26%) was observed. Additionally, ultrastructure analysis revealed eccentrically located nucleoli, an abundance of thin pseudopodia on cells’ surfaces and proved the presence of typical mesenchymal stem cell features. In conclusion, this set of data contributes to more detailed information on rAF-MSCs, which were previously proposed feasible for preclinical stem cell research and as a suitable source for the cryopreservation of animal genetic resources in gene bank.

Advances in genomic strategies to improve growth and meat production traits in sheep: An overview

Growth and meat production traits (body weight at birth, 3-months and 6-months, eye muscle area, fat thickness, pre-weaning and post-weaning gains, average daily weight gain, chest girth, height at withers and shin circumference) are reviewed to know the relationship with the loci which are controlled by specific genes that are associated with these traits. Quantitative trait loci (QTL) for different body and carcass weight traits are identified. Chromosomes 1, 2, 3, 4, 5, 6, 16, 18 and 20 are considered as candidate genomic regions for body weight and some major gene effects like transferrin gene on chromosome 1, Belgium Texel double muscling and myostatin (MSTN) gene on chromosome 2, growth effect around insulin-like growth factor 1 (IGF-1) on chromosome 3, calpastatin gene on chromosome 5, leptin gene on chromosome 4, Booroola fecundity gene on chromosome 6, growth hormone receptor (GHR) gene in chromosome 16, callipyge effect and carawell muscle hypertrophy on chromosome 18 and MHC complex on chromosome 20 have been identified. High-throughput genotyping and next-generation sequencing technologies are the advanced techniques for the creation of the high-density SNP array as a tool for the genomic analysis of domestic animals. Genome-wide association studies (GWAS) and genomic selection are the ultimate use of SNP array for the improvement of economically important traits. Hence, genome-wide sequencing is an advanced tool which may help in better selection of animal genetic resources. It may be used for applying molecular breeding strategies in genetic improvement programmes oflivestock.

Importance of native animal genetic resources

While population growth rate and economic pressure force the changes in traditional agricultural systems, biodiversity has been reducing rapidly.

A deterministic evaluation of heat stress mitigation and feed cost under climate change within the smallholder dairy sector

In the global South, dairying is often promoted as a means of poverty alleviation. Yet, under conditions of climate warming, little is known regarding the ability of small-scale dairy producers to maintain production and/or the robustness of possible adaptation options in meeting the challenges presented, particularly heat stress. The authors created a simple, deterministic model to explore the influence of breed and heat stress relief options on smallholder dairy farmers in Odisha, India. Breeds included indigenous Indian (non-descript), low-grade Jersey crossbreed and high-grade Jersey crossbreed. Relief strategies included providing shade, fanning and bathing. The impact of predicted critical global climate parameters, a 2°C and 4°C temperature rise were explored. A feed price scenario was modelled to illustrate the importance of feed in impact estimation. Feed costs were increased by 10% to 30%. Across the simulations, high-grade Jersey crossbreeds maintained higher milk yields, despite being the most sensitive to the negative effects of temperature. Low-capital relief strategies were the most effective at reducing heat stress impacts on household income. However, as feed costs increased the lower-grade Jersey crossbreed became the most profitable breed. The high-grade Jersey crossbreed was only marginally (4.64%) more profitable than the indigenous breed. The results demonstrate the importance of understanding the factors and practical trade-offs that underpin adaptation. The model also highlights the need for hot-climate dairying projects and programmes to consider animal genetic resources alongside environmentally sustainable adaptation measures for greatest poverty impact.

Nucleotide sequence variability analysis of Major Histocompatibility Complex Class II DQA1 gene in Nigerian goats

Major Histocompatibility Complex (MHC) molecules loaded with peptides derived from invading pathogens are recognised by the immune system to produce a highly effective and specific response against foreign pathogens. A 310-bp fragment of exon 2 of the MHC Class II DQA1 gene was amplified in 27 animals made up of three major Nigerian goat breeds [West African Dwarf (WAD), Red Sokoto (RS) and Sahel (SH)]. Twenty amino acid polymorphic sites were found in Nigerian goats. Comparison of predicted amino acid residues of DQA1 exon 2 alleles of Nigerian goats with similar alleles from other caprine species revealed considerable congruence in amino acid substitution pattern. A significant positive selection signature was detected at the DQA1 locus of Nigerian goats in that non-synonymous substitutions occurred at a faster rate compared to synonymous substitutions (dN:dS ratio = 1.28 ; Z-Statistics= 1.634; P<0.05). The evolutionary tree constructed using UPGMA, revealed that the southern WAD goat appeared to be more related to the northern RS than SH goat at the DQA1 locus. It will be interesting therefore, for future studies to investigate the association of the genetic variants in DQA1 gene of Nigerian goats with resistance/susceptiblity to diseases in order to conserve these precious animal genetic resources.

Regional conference on conservation of animal genetic resources

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Phenotypic characterization and documentation of animal genetic resources in India: A review

Phenotypic characterization is essential for planning and managing the animal genetic resources at local, national, regional and global levels. Large proportion of non-descript animals of different livestock species indicated that the characterization and inventorization of animal genetic resources of India is still incomplete. After establishment of National Bureau of Animal Genetic Resources (NBAGR) at Karnal by Indian Council of Agricultural Research (ICAR), phenotypic characterization of domestic animal diversity of India, accelerated. A large number of recognized livestock and poultry breeds and populations were systematically studied and documented in last three decades. A system of registration of livestock and poultry breeds was initiated by ICAR in India in 2008 with the registration of 129 livestock and poultry breeds. Thirty one new breeds were registered from 2010 to 2016. With the introduction these newly registered breeds, total number of indigenous breeds in the country now stands at 160, which include 40 breeds of cattle, 13 buffalo, 26 goat, 42 sheep, 6 horse and pony, 9 camel, 6 pig, 1 donkey and 17 of chicken. After registration of breeds, the breed descriptors were published in The Indian Journal of Animal Sciences. A large number of breed monographs were also published by different agencies. This review provides information of the breeds or population of livestock and poultry undertaken for phenotypic characterization and documentation in India.

Cytogenetical techniques for improvement of cattle

The animal genetic resources of India are represented by a broad spectrum of livestock. The genetic characterization of synthetic crossbred cattle is a major prerequisite in its conservation as well as improvement programmes. It helps in confirmation of the species of origin.

Interspecies somatic cell nuclear transfer in Asiatic cheetah using nuclei derived from post-mortem frozen tissue in absence of cryo-protectant and in vitro matured domestic cat oocytes

Recent accomplishments in the field of somatic cell nuclear transfer (SCNT) hold tremendous promise to prevent rapid loss of animal genetic resources using ex situ conservation technology. Most of SCNT studies use viable cells for nuclear transfer into recipient oocytes. However, preparation of live cells in extreme circumstances, in which post-mortem material of endangered/rare animals is improperly retained frozen, is difficult, if not impossible. This study investigated the possibility of interspecies-SCNT (iSCNT) in Asiatic cheetah (Acinonyx jubatus venaticus), a critically endangered subspecies, using nuclei derived from frozen tissue in absence of cryo-protectant at −20 °C and in vitro matured domestic cat oocytes. No cells growth was detected in primary culture of skin and tendon pieces or following culture of singled cells prepared by enzymatic digestion. Furthermore, no live cells were detected following differential viable staining and almost all cells had ruptured membrane. Therefore, direct injection of donor nuclei into enucleated cat oocytes matured in vitro was carried out for SCNT experiments. Early signs of nuclear remodeling were observed as early as 2 h post-iSCNT and significantly increased at 4 h post-iSCNT. The percentages of iSCNT reconstructs that cleaved and developed to 4–16 cell and morula stages were 32.3 ± 7.3, 18.2 ± 9.8 and 5.9 ± 4.3%, respectively. However, none of the iSCNT reconstructs developed to the blastocyst stage. When domestic cat somatic and oocytes were used for control SCNT and parthenogenetic activation, the respective percentages of oocytes that cleaved (51.3 ± 13.9 and 77.3 ± 4.0%) and further developed to the blastocyst stage (11.3 ± 3.3 and 16.8 ± 3.8%) were comparable. In summary, this study demonstrated that enucleated cat oocytes can partially remodel and reactivate non-viable nuclei of Asiatic cheetah and support its reprogramming back to the embryonic stage. To our knowledge, this is the first report of iSCNT in cheetah using non-viable frozen cells.