Genetic diversity of Mithun population in Bhutan was studied using 14 microsatellite markers. Two sets of two-step polymerase chain reactions were performed with multiplex and individual markers for genotyping 105 hair samples collected from Arong in Samdrupjongkhar (AS, 36) and Wangdigang in Zhemgang (WZ, 69). Fifty-three alleles were detected with average of 3.89 alleles and polymorphism information content of 0.44 ± 0.03 per locus. A low level of genetic variability within population was present with observed heterozygosity at 0.50 ± 0.06 and expected heterozygosity at 0.48 ± 0.06. Analysis of molecular variance attributed 58 percent of total variation to within the individuals. Mean F IS and F IT were −0.056 and 0.005 respectively, indicated low level of population differentiation and limited out-breeding. The normal L-shaped distribution of allelic frequencies without any mode-shift revealed the absence of recent genetic bottleneck in Mithun populations. Therefore to manage inbreeding in the small Mithun population of Bhutan, periodic assessment of inbreeding levels and exchange of animals between farms is recommended to reduce frequency of introduction of animals from India.

Pedigree analysis using genealogical information of 18 315 animals born between 1949 and 2008 was done to quantify genetic variability of the Sahiwal population in Kenya. Generation intervals for sire pathways were longer than dam pathways and increased over year periods, from about 4–16 years. The later was due to use of old bulls for breeding in the last 2 year groups and cessation of progeny testing in the year 2000. Average inbreeding level in last year period studied was 1.2 percent. Genetic variability of the population as assessed based on gene origin statistics decreased over the years. The ratio of effective number of founders to founders of 0.06 showed unequal contribution of founders to the reference population. However, since the founding population, ancestors contributed equally as shown by the ratio of f e/f a of 0.94, which could also be due to lack of effective selection in this population. The ratio of f g/f a of 0.63 indicated genetic loss of genetic variability occurred through genetic drift in the Kenyan Sahiwal population. The small number of ancestors (16) that accounted for 50 percent of the total variation in the reference population suggested overuse of a small number of some animals as parents over generations. The smaller ratio of f g/f e compared with f a/f e also confirms loss of genetic variability in the population by genetic drift than bottlenecks. Therefore the breeding strategy for the Sahiwal population in Kenya should incorporate tools that balance rate of genetic gain and the future rate of inbreeding.

Goats make up the largest group of ruminant livestock in Nigeria and are strategic in bridging animal protein supply gap and improving the economy of rural households. The hypervariable region 1 (HVR1) of the caprine mitochondrial genome was investigated to better understand genetic diversity important for improving selection for animal breeding and conservation programs. We sequenced and analysed the mitochondrial DNA (mtDNA) HVR1 in 291 unrelated indigenous Nigerian goats (West African Dwarf (WAD), Red Sokoto (RSO) and Sahel (SAH)), randomly sampled from around the country, and compared them with the HVR1 sequences of 336 Indian goats and 12 other sequences in five different species in the genus Capra (C. falconeri, C. ibex nubiana, C. aegagrus, C. cylindricornis and C. sibirica). A total of 139 polymorphic sites from 291 individuals were captured in 204 haplotypes. Within and among population variations were 77.25 and 22.74 percent, respectively. Nigerian goats showed high genetic diversity (0.87) and high FST values, and separate from Indian goats and other wild species. Haplogroups in WAD separates it from RSO and SAH concomitant with a different demographic history. Clear genetic structure was found among Nigerian goat breeds with appreciable variation in mtDNA HVR1 region. This study grouped Nigerian goat breeds into two major groups suggesting two different demographic origins for Northern and Southern breeds. High genetic admixing denotes different maternal origins and in contrast to evidence from goats from Levant and Central Asia, where goats were originally domesticated.

This study was conducted in three villages of the Trarza region of Mauritania. The purpose of this study was to describe the management of and to characterize the local chicken. In the three surveyed villages, all the breeders were interviewed according to a questionnaire drafted in French and translated orally into hassanya or poular (national languages) as necessary. 56 poultry breeders were surveyed. Measurements were carried out on 260 adult chickens with 191 females and 69 males. The results showed that family poultry rearing is an activity managed by women. In spite of its socioeconomic importance, it is not considered as a main activity among the farmers responding to the survey. Feed resources deficiencies, animal health and the low productivity of the chickens were declared as the main concerns of the breeders. The average age of females when they start to reproduce is 6 months. The average weight of males was 1324 ± 249 g. That of females was 1028 ± 229 g. The average weight for both sexes together was 1107 ± 268 g. The average weight of the egg was 31 ± 4.81 g. The average weight of a chick on any given day was 26 ± 6.03 g. All the considered physical measurements were significantly higher (p < 0.05) in males. The variability of characters observed offers possibilities for genetic improvement (selection or crossbreeding). In the local chicken, the plumage was highly varied and presented several tints.

The objective of this study was to determine the genetic diversity of creole cattle in northwestern Mexico using the BoLA-DRB3.2 locus of the Major Histocompatibility Complex (MHC). A total of 56 creole cattle were sampled from five communities; in the state of Chihuahua (Cerocahui, Guadalupe y Calvo and Cuauhtémoc) and in the state of Baja California Sur (La Paz and Mulegé). The BoLA-DRB3.2 locus was genotyped by PCR-RFLP assay. Thirty-nine alleles were identified, out of which 14 had not been previously reported. The average level of inbreeding in all populations analyzed was FIS = 0.09 (P < 0.0001), but only two populations (Cerocahui and Guadalupe y Calvo) showed an excess of homozygotes (P < 0.05). The breed differentiation in all populations studied was FSC = 0.068 (P < 0.0001). The smallest genetic distance was between La Paz and Mulegé (0.022); but Mulegé presented smaller distances (0.028–0.053) with the populations of La Paz (0.071–0.083) and with Chihuahua. Baja California Sur populations are grouped in a separate branch than Chihuahua populations. We conclude that creole cattle from Baja California Sur and Chihuahua show high genetic diversity in the locus BoLA-DRB3.2.

The chicken major histocompatibility complex B (MHC-B) – a cluster of genes associated with natural disease resistance or susceptibility – has been investigated in experimental and inbred lines by serological typing. However, that method showed some weaknesses for its use on out breeds. This study aims to explore the genetic diversity of the MHC-B of Cameroon indigenous chicken through molecular typing with LEI0258 and MCW0371 microsatellite markers. MHC-B haplotypes of 290 chickens from four agro-ecological zones were identified and compared with published haplotypes. Alleles were analysed for genetic diversity and relationship among Cameroon chicken populations. Hypothetically new LEI0258 alleles and haplotypes were detected. Overall, polymorphism parameters were relatively high in the Cameroon western highlands. The analysis of molecular variance revealed great variability (80.00 percent) between individuals than among and within ecotypes. The inbreeding coefficients of overall populations (FIT), among population (FST) and within population (FIS) were 0.26, 0.04 and 0.22, respectively, and all were highly significant (P < 0.001). A UPGMA tree based on Nei's DA genetic distances showed a clear distinction between Cameroon and out-groups and a structuring of within-country populations into three clusters. There is a great genetic diversity of the MHC-B in Cameroon native chicken and also a need of sequencing of the identified alleles for an accurate identification prior to their assessment for natural disease resistance and responsiveness to vaccination.

The study investigated the genetic make-up of different ecotypes of indigenous chickens (ICs) in Kenya based on major histocompatibility complex (MHC)-linked and non-MHC microsatellite markers. Blood samples were collected from eight regions (48 birds per region) of Kenya: Kakamega (KK), Siaya (BN), West Pokot (WP), Turkana (TK), Bomet (BM), Narok (NR), Lamu (LM) and Taita-Taveta (TT) and genotyped using two MHC-linked and ten non-MHC markers. All MHC-linked and non-MHC markers were polymorphic with a total of 140 alleles, of which 56 were identified in MHC-linked markers. Mean number of alleles (Na and Ne), private alleles, heterozygosity and genetic distances were higher for MHC-linked markers compared with non-MHC markers. The ad hoc statistic ΔK detected the true numbers of clusters to be three for MHC-linked markers and two in non-MHC markers. In conclusion, Kenyan ICs belong into two to three genetically distinct groups. Different markers systems have different clustering system. MHC-linked markers divided ICs into three mixed clusters, composing of individuals from the different ecotypes whereas non-MHC markers grouped ICs into two groups. These IC ecotypes host many and highly diverse MHC-linked alleles. Higher allelic diversity indicated a huge amount of genetic variation in the MHC region of ICs and supported their reputation of being hardy and resistant to diseases.

As part of the global sheep Hapmap project, 24 individuals from each of seven indigenous Swiss sheep breeds (Bundner Oberländer sheep (BOS), Engadine Red sheep (ERS), Swiss Black-Brown Mountain sheep (SBS), Swiss Mirror sheep (SMS), Swiss White Alpine (SWA) sheep, Valais Blacknose sheep (VBS) and Valais Red sheep (VRS)), were genotyped using Illumina's Ovine SNP50 BeadChip. In total, 167 animals were subjected to a detailed analysis for genetic diversity using 45 193 informative single nucleotide polymorphisms. The results of the phylogenetic analyses supported the known proximity between populations such as VBS and VRS or SMS and SWA. Average genomic relatedness within a breed was found to be 12 percent (BOS), 5 percent (ERS), 9 percent (SBS), 10 percent (SMS), 9 percent (SWA), 12 percent (VBS) and 20 percent (VRS). Furthermore, genomic relationships between breeds were found for single individuals from SWA and SMS, VRS and VBS as well as VRS and BOS. In addition, seven out of 40 indicated parent–offspring pairs could not be confirmed. These results were further supported by results from the genome-wide population cluster analysis. This study provides a better understanding of fine-scale population structures within and between Swiss sheep breeds. This relevant information will help to increase the conservation activities of the local Swiss sheep breeds.

The genetic structure and diversity of nine ganadarias (the Portuguese word for bull farmer) of the Portuguese “Brava de Lide” (Bullfighting) breed were assessed with 30 microsatellites. Allelic richness per locus was low, with an overall average of 2 547. The mean number of alleles corrected for the size of the smaller sample ranged between 2,4 in ganadaria Jorge Mendes and 1,9 in ganadaria Vaz Monteiro. The mean expected and observed heterozygosities ranged between 0.627 in ganadaria Palha and 0.461 in ganadaria Vaz Monteiro and between 0.617 in ganadaria Cabral D'Ascension and 0.4485 in ganadaria Vaz Monteiro, respectively. The ganadaria Vaz Monteiro was the one that systematically showed the lowest values of genetic diversity. To analyse the substructure among the 51 animals studied, a factorial correspondence analysis and a Bayesian approach were performed using the Genetix and STRUCTURE programs, respectively. The outcome of the factorial correspondence analysis resulted in the formation of four well-defined clusters. On the other hand, the analysis with the STRUCTURE program has allowed us to obtain six well-defined clusters. One well-defined cluster corresponded to the oldest Portuguese ganadaria, the Vaz Monteiro. This ganadaria was established, at its inception in 1843, with bulls and cows of pure Portuguese caste and has been kept in the same family owing to its formation without the introduction of any other blood, constituting a unique caste that must be preserved, which is the true offspring of the Portuguese cattle breed “Brava de Lide”. In turn, the other clusters formed corresponded to the ganadarias Mario Vinhas, Murteira Grave, Nuno Casquinha, Palha and Jorge Carvalho.

Ghumusar is an inadequately studied goat population of western region of Ganjam district of Orissa state. Sporadic information is available on its morphological traits but no information is found on its genetic variability. Therefore, an attempt was made to measure the genetic diversity in Ghumusar goat population using 25 microsatellite markers. Genomic DNA isolated from blood samples drawn at random from 50 individuals were utilized for this study. The average number of observed allele was 9.80 and the effective average number of allele was 4.28. The polymorphic information contents ranged from 0.53 to 0.91. The average observed and expected heterozygosity was 0.73 and 0.71, respectively. The values of Nei's gene diversity in Ghumusar goat population ranged from 0.11 to 0.87 with a mean of 0.69. The overall Fis value was observed to be 0.002, which is not significantly different from zero; hence indicating no global deficit of heterozygotes. Under sign test, expected number of loci with heterozygosity excess (Hee) was 14.88, 14.79 and 14.74 for the infinite allele model (IAM), stepwise mutation model (SMM) and two-phased model (TPM) of mutation, respectively. The observed number of loci with heterozygotic excess (He) was 14, 8 and 2 under these three models, respectively. Under all the three models, He was less than Hee and this deviation was significant under SMM and TPM models. There was no serious genetic reduction in effective population size as indicated by L-shaped curve in Ghumusar goat population.

The American Shire horse breed is currently listed in “critical condition”, the most serious threat category assigned by the American Livestock Breeds Conservancy. Despite concern for the breed's future, however, a thorough genetic analysis of the breed has not been conducted to date. Pedigree data from 85 671 Shire horses born between 1806 and 2011 were used to determine current and historical genetic variability in the Shire horse since the first imported animals arrived from the United Kingdom to the United States. From this larger dataset, a reference population of 1 152 animals representing the most current generation was defined. Effective population size was 330.5, with 832 total founders and high pedigree completeness (98.2 percent) to five generations. Effective number of founders, ancestors and genomes were 104.5, 28.6 and 13.9, respectively. Average inbreeding coefficient was 2.4 percent from complete pedigree data and 1.3 percent when the most recent five generations were considered. Demographic analysis also revealed a population bottleneck in the 1950s. The ten most influential male and female ancestors contributed 48.5 percent and 11.6 percent, respectively, to the reference population, and only three foundation sires are responsible for 95.6 percent of all sire lines in the current generation. Although current assessment of genetic variability indicates a relatively healthy population, the small number of breeding animals, low birth rates and steady rise in inbreeding coefficients mark the American Shire as an at-risk breed for which conservation strategies should be considered.

This study aimed at characterising the genetic diversity of two Fipa cattle populations (Sumbawanga and Nkasi) of South-Western Tanzania, and establishing their genetic relationships with the other indigenous cattle strains (Tarime, Iringa red and Ankole) and Friesian cattle found in the area. The genetic diversity was analysed using 30 microsatellite markers. All the markers used were highly polymorphic. The Nkasi Fipa cattle exhibited the highest mean number of alleles (7.31) and mean genetic diversity (0.732) per locus, followed by Sumbawanga Fipa cattle with 7.10 mean number of alleles and 0.725 mean genetic diversity per locus, with the latter population having a very low mean inbreeding coefficient (FIS = 0.027). Three percent of the genetic diversity was due to differences among indigenous strains while the rest was due to differences among individuals within the strains. Small genetic distances (DA) were observed between Sumbawanga Fipa and Nkasi Fipa (0.032), Tarime (0.073), Iringa red (0.076) and Ankole cattle (0.086). As expected, the largest genetic distances were observed between the Friesian and all indigenous strains since this breed has a quite distinct genetic origin. In the assignment test, the proportion of animals from each group correctly assigned to their source population ranged from 55.3 percent (for Nkasi Fipa) to 100 percent (for Friesian). Despite the low genetic differentiation and genetic indistinctiveness of the Sumbawanga Fipa population from the other indigenous strains, its high genetic diversity, very low inbreeding coefficient and a threat emanating from population admixture with other indigenous strains underscore the importance of establishing appropriate conservation and management strategies for it.

Indigenous livestock resources are strategic in the socio-economics of rural agricultural systems to ensure food security in resource-poor countries. Therefore, better understanding of genetic variation holds the key to future utilization through conservation. We report the first analysis of genetic diversity of Nigerian sheep based on the D-loop region of the Ovis aries mitochondrial genome using 1 179 bases between sites 15 437 and 16 616 base pairs. A sample of 290 animals made up of Balami, West African Dwarf (WAD), Uda and Yankasa breeds were randomly collected from across Nigeria. Ninety-six haplotypes were observed with a high mean haplotype diversity of 0.899 ± 0.148. Gene diversity was highest in Uda (0.921 ± 0.021) and lowest in WAD (0.852 ± 0.061). Population specific FST indices varied from 0.00133 in Uda to 0.00335 in WAD. Yankasa had the highest number of polymorphic sites (201), while the least was in Uda (96). Analysis of molecular variance revealed that 0.23 percent of the variation is found among populations compared with 99.77 percent variation found within populations. The phylogenetic tree indicates that the mitochondrial lineages of these sheep breeds originated from a common source consistent with first divergence of Yankasa followed by WAD, while Balami and Uda remain more closely related. These results suggest that evolutionary divergence of Nigerian sheep breeds based on mitochondrial DNA D-loop sequence may be coincident with geographical distribution in Nigeria and suggest significant interbreeding. This could have implications for managing improvement and conservation strategies and long-term conservation of Nigerian indigenous sheep.

To better understand natural genetic variation in indigenous livestock resources, as well as formulate conservation policies, better genetic characterization is required to balance the competing needs of genetic improvement and conservation of native germplasm, primarily in rural agricultural systems in developing countries. Genetic diversity of goats in southern Nigeria was assessed using 295 indigenous goats with ten microsatellite DNA markers. The breeds are West African Dwarf (WAD), Red Sokoto (RS) and Sahel (SA) sampled from farms, market places and rural homesteads. The mean expected heterozygosity (HE) ranged from 0.608 to 0.784 in two sub-populations of WAD goats. Deviations from Hardy–Weinberg equilibrium (HWE) were statistically significant (p < 0.05) indicating that these populations are under various forces stemming from the management choices of rural dwellers. Polymorphic information content of these markers averaged 0.803 and mean GST index was 0.176. The measure of genetic distance between pairs of breeds indicated that the lowest distance was between WAD and RS (0.268) and the highest distance was between WAD and SA (0.662) goats, respectively. The estimated dendogram clustered these Nigerian goats into nine sub-populations and two major genetic groups. The study suggests that indigenous goat populations in southern Nigeria may be collapsed from three breeds into two distinct genetic groups, possibly due to extensive cross-breeding and gene flow between them, which are symptomatic of uncontrolled crossing across much of the country.

Pedigrees of a reference population of 1 659 North American Norwegian Fjord horses were traced to founders and analysed for coefficients of inbreeding and genetic variability. Effective population size was 207.8 and there were 641 total founders. Pedigree completeness was close to 100 percent for 6 generations, with 9.8 average complete generation equivalents. The average inbreeding coefficient was 3.2 percent for the entire pedigree and 1.6 percent for pedigrees traced back five generations. Average inbreeding coefficients by year of birth increased until 1983, before decreasing and then stabilizing through 2009. Effective number of founders, ancestors and genomes were 96, 30.0 and 12.7, respectively. Low effective number of founders and ancestors indicate that genetic diversity has been lost in the development of the breed in North America. However, registry-enforced breeding strategies have contributed to lower inbreeding coefficients in the current generation.

Pigs are the most important livestock species in Papua New Guinea (PNG) from economic as well as cultural perspectives. Most of the estimated population of 1.8 million pigs are maintained by smallholder farmers. The genetic attributes, differentiation and production capacities of indigenous pigs are largely unknown. But the rich socio-cultural diversity of rural communities living in geographically isolated pristine environments, with long and strong attachments with indigenous pigs implies that indigenous pigs may harbour unique genetic diversity. This study reports preliminary survey of indigenous pigs sampled from major pig farming areas of the country as part of a South Asia-wide regional indigenous pig genetic diversity study. It assesses farmers’ perceptions about the origin, population trend and utility value of indigenous pigs, as well as their trait preferences. Average herd sizes and external physical forms and appearances of pigs are described. About 19 percent of the sampled indigenous pigs were identified through pedigree checks to have an admixtured genotype with some distant indigenous or exotic parentage. The importance of indigenous pig genetic resources in PNG requires a policy and legislative framework to support sustainable utilization. As a first step in informing such development, a comprehensive molecular genetic study is required to elucidate the genetic attributes of this unique genetic resource.

The need to provide policy-makers with succinct, yet informative, messages is widespread in biodiversity management, and has led to the development of various “indicators” that can serve this purpose. While global data on the status of animal genetic resources for food and agriculture (AnGR) have been made available in a number of publications, the issue of developing a global indicator for AnGR has come to prominence only relatively recently. This paper describes the policy background to these developments and reviews initiatives in AnGR indicator development at national and regional levels. It also outlines some of the issues raised at an expert meeting on indicators organized by Food and Agriculture Organization of the United Nations (FAO) in January 2010. To date, AnGR indicator development has largely been restricted to Europe. Globally, options are restricted by the limited availability of data. The expert meeting favoured an indicator set that describes both the relative abundance of native versus non-native breeds and summarizes breed risk status. The former will require a new breed classification system that is acceptable to countries and applicable globally. The risk-status categories of approximately 64 percent of reported breeds are available in the Domestic Animal Diversity Information System, but a lack of regular updates of countries' breed population data means that trends cannot be described adequately at present.

The Australasian Merino population has declined significantly over the last 15 years in response to a decline in the price of apparel wool, both in absolute terms and relative to the price of sheep meat. Over the same period, a national genetic evaluation system based on BLUP methods has been introduced, that is achieving steady growth in adoption by breeders. Genetic parameter estimates for the population provide evidence for considerable genetic diversity for all recorded traits, providing ample opportunity for genetic improvement. More recently, there is considerable evidence for increasingly rapid progress, both in fleece traits and a range of meat production and adaptation traits. The Merino population is evolving towards two broad types – one focused on high quality apparel wools finer than 19 µm and used in enterprises with a wool/meat income ratio of about 3:1, and the other a more dual-purpose animal producing 19–21 µm wool and an enterprise wool/meat income ratio between 1.5:1 and 1:1. Underlying these trends is a growing focus on adaptation traits including worm resistance; reduced need for veterinary interventions; and increased early growth, fertility and mothering ability. Together these trends point to increasingly ‘easy-care’ sheep and exploitation of the available genetic diversity to rapidly increase profitability.

A study of the genetic diversity of Sardinian sheep identified a small population of Pecora Nera di Arbus sheep. This population is composed of about 1000 ewes located in the southwest of Sardinia (Medio-Campidano district), mainly in the area surrounding the village of Arbus. The main features of this breed are black fleece, small size, small or absent auricles and a high frequency of horns in both sexes. These ancestral traits suggest that the population escaped the selection process, that was mainly oriented toward milk yield and the white colour of the fleece, for which the predominant white strain of Sardinian sheep was established. Currently, a programme of promoting this new breed is ongoing. It is mainly based on the production of natural black wool for apparel without chemical dyes.

Species diversity of animals and plants is relevant to pest management in very different ways. Plant diversity provides sources of biologically active natural products and of genes for plant resistance. Animal diversity is involved in both harmful and beneficial interactions between crops and weeds or uncultivated land and in provision of potential biological control agents. The pest management implications of changes in biological diversity therefore need to be considered at a smaller scale in the management of cropping systems and on a larger scale in development programmes and national land use planning.