Livestock Genetic Resources Research Articles

Estimation of Heritability and Breeding Value of Weaning Weight Garut Sheep (Case Study at UPTD-BPPTDK Margawat Garut)

Sheep are one type of livestock that has great potential to be developed in Indonesia. One of the sheep raised by Indonesian people is Garut sheep which is a Livestock Genetic Resource (SDGT) of West Java. Researvh on estimating the breeding value of weaning weights of Garut sheep at Technical Implementation Unit of the Margawati Garut Sheep and goat Development Center (UPTD-BPPTDK) has been carried out on January 10-16, 2022. The study aims to estimate the heritability and breeding value of weaning weight of Garut Sheep at UPTD-BPPTDK Margawati Garut. The research objects used were 89 data from 25 males and 75 femaes. The method used is descriptive analytic using analysis of the variety of the half-sib. The fixed effects included in this analysis were sex and birth type as well as additionla parental age correction factors. The results showed that the alleged heritability value of weaning weight 0.84 ± 0.34 was included in the high category. The highest alleged weaning weight breeding values was obtained by sheep with ID No 11181782 of 4.654 foe male sheep and ID No 1810720 of 4.131 for female sheep.

Agroecosystem-based agricultural genetic resources for balanced and diversified food, nutrition, health, business, geographical indication and environment

ABSTRACT Nepal has 15 distinct agroecosystems spread across three major agroecozones: Tarai, Mid Hill, and High Hill. These regions support a rich variety of agrobiodiversity. This paper examines the significance of native agrobiodiversity within each of these agroecosystems for diversified food, nutrition, health, business and environment. The information presented is derived from various literature sources, discussions with key experts, and the authors’ own experiences. Each of these agroecosystems has cultivated and preserved numerous unique species, landraces, and genotypes of agrobiodiversity, including crops, forages, livestock, agro-insects, agro-microorganisms, and aquatic genetic resources. This agrobiodiversity is deeply connected with local cultures, traditional knowledge, and skills. The high diversity of agricultural genetic resources (AGRs) within Nepal’s relatively small area is a crucial factor for ensuring food security, nutrition, health, business opportunities, and environmental sustainability. Many niche products, prized for their purity, quality, taste, health benefits, and nutritional value, are sold at premium prices. However, the focus on production-centric agricultural programs over the years has led to the replacement of many niche-specific varieties by more uniform and limited ones. Introducing new genotypes into a particular agroecosystem may undermine the principles of ecological agriculture. Therefore, it is essential to enhance the competitiveness of native AGRs and associated indigenous technologies within each agroecosystem.

The sustainability of small‐scale sheep and goat farming in a semi‐arid Mediterranean environment

AbstractIntroductionSmall‐scale sheep and goat farming is one of the business models the EU depends on to achieve the objectives of the Green Deal. However, these production systems are characterized by structural weaknesses that risk being aggravated by international events, such as the post‐COVID‐19 crisis and reconstruction, the conflict in the European area and the generalized inflationary wave. Against this scenario, the work aims to expand knowledge of these companies’ sustainability levels to assess their performance, business model, the strategic keys to their resilience and chances of survival in the changed international scenario.Materials & MethodsThe approach chosen is SAFA (Sustainability Assessment of Food and Agriculture Systems), the FAO's holistic framework. The empirical analysis focused on a sample of farms in a semi‐arid Mediterranean area.ResultsThe results demonstrate the sustainability lag in governance, social capital, fertilizer management, landscape heritage and economic terms. This is due to the absence of strategic planning on soil, environmental and livestock management, genetic and human resource management, and farm structure. Regarding economic resilience on performance, the weight of the CAP (common agricultural policy) for these farms and the effect of high production costs are high.ConclusionThe work is helpful for different stakeholders, who are invited both to structure the intervention of eco‐schemes on animal welfare for the 2023/2027 programming period and to support farm development plans to foster the flow of innovation, cooperation and sustainability.

Genome-wide association research on the reproductive traits of Qianhua Mutton Merino sheep.

Qianhua Mutton Merino sheep is a new breed of meat wool sheep cultivated independently in China. In 2018, it was approved by the state and brought into the national list of livestock and poultry genetic resources. Qianhua Mutton Merino sheep have the common characteristics of typical meat livestock varieties with rapid growth and development in the early stage and high meat production performance. The objective of this research is to investigate the Genome-wide association of the reproductive traits of Qianhua Mutton Merino sheep. Qianhua Mutton Merino sheep from the breeding core group were selected as the research object, genome-wide association analysis was conducted on genes associated with the reproductive traits (singleton or twins, birth weight, age [in days] for sexual maturity, weaning weight, and daily gain from birth to weaning) of Qianhua mutton merino. Our study findings showed that 151 loci of single-nucleotide polymorphisms (SNPs) were detected, among which 3 SNPs related to birth weight and weaning weight occupied a significant portion of the wide genome. The candidate genes preliminarily obtained were SYNE1, SLC12A4, BMP2K, CAMK2D, IMMP2L, DMD, and BCL2. We found 151 SNP loci for five traits related to reproduction (including singleton or twins, birth weight, age [in days] at sexual maturity, weaning weight, and daily weight gain from birth to weaning). The functions of these candidate genes were mainly enriched in nucleotide metabolism, metal ion binding, oxytocin signaling pathway, and neurotrophin signaling pathway.

IMPACT OF COMMUNITY-BASED SHEEP BREEDING PROGRAMME ON FARM’S PROFITABILITY AND LAMB MORTALITY: THE CASE OF THE AKKARAMAN BREED

This study aimed to evaluate the impact of Community-Based Sheep Breeding Program (CBSBP) on gross profit and lamb mortality by comparing participated farms and non-participated farms by focusing on the case of Akkaraman breed in Niğde province of Turkey. The primary data were collected from 108 sheep farms, 54 farms participated and 54 farms those did not participate in the sheep breeding program. According to average treatment effect results derived by utilizing propensity score matching method, if all farms would participate to CBSBP, each farm acquired 6209.13 Turkish Lira (1094.92 USD) more gross profit and would be 3.47% less lamb mortality rate in the farms. The study indicated that CBSBP provided significant economic benefit and welfare of animal. Hence, further supporting and scaling up of community-based small ruminant breeding programs appears to be one of the best solutions for improving livestock genetic resources of rural communities in developing countries. Accordingly, incentive mechanisms for participating in breeding programs should be more focused on small-scale family farms and especially the young people in the rural area. Keywords: sheep farming, propensity score matching, counterfactual impact analysis, genetic improvement, profitability.

Infectious bovine rhinotracheitis: Epidemiology, control, and impacts on livestock production and genetic resources

The present review aims to determine the epidemiology of infectious bovine rhinotracheitis (IBR), control measures, and its impact on livestock production and genetic resources. The literature search was conducted to select and compile peer-reviewed journals, book chapters, and international organization proceedings on the epidemiology, control, and impacts of IBR. IBR is a highly contagious disease of cattle that causes substantial economic losses throughout the world, particularly in the dairy and beef industries. Bovine alphaherpesvirus-1 causes this infectious viral disease, affecting the respiratory, and reproductive systems. IBR causes severe inflammation and dysfunction of the respiratory system. Infection of the reproductive system is responsible for abortion, retained placenta, metritis, and balanoposthitis. The transmission is by inhalation, contact with nasal and genital secretions, and fomites. Epidemiologically, the disease is known for its distinct latency characteristics. The infectious agent establishes a lifelong latent infection in the peripheral nervous system. The introduction of latently infected cattle, high stocking densities, confined pens, concurrent diseases, and low ambient temperatures increase the transmission and severity of the disease. The disease has no specific drug treatments, so control and prevention measures have inevitable roles. IBR is a significant constraint on livestock production globally, particularly in developing countries. It causes poor reproductive performance and productivity, the loss of replacement herds, and the culling of mature, productive animals. The implementation of strict biosecurity measures, immunization, quarantine, herd screening, and proper herd management are the most important control and prevention strategies.

The Current Status and Potential Development of Genetic Resources of Indigenous Toraya Spotted Buffalo in Indonesia: A Systematic Review

Buffaloes are integral to the Asiatic market as they are crucial for agricultural work and transportation and provide a significant source of dairy and meat, contributing to various industries, local economies, and cultural practices across the region. Indonesia is a mega biodiversity country abundant in livestock genetic resources, including indigenous, local, and introduced breeds that play a crucial role in agriculture and the livestock industry. These genetic resources offer the potential for selective breeding and improving the quality of livestock populations through well-designed breeding programs, ensuring sustainable livestock production for the future. The current study was performed using the “Publish or Perish” software, and the data obtained was analyzed using the CADIMA web tool. The Toraya buffalo population is the largest in the Tana Toraja and North Toraja regencies and is widely distributed within South Sulawesi Province, Indonesia. The population of Toraya buffalo in this region reached 43674 heads. Toraya buffaloes exhibit diverse body color characteristics, such as black, gray, white, and mixed. Moreover, Toraya buffaloes possess distinct quantitative traits that set them apart from other swamp buffalo breeds. Although there are limited studies on Toraya buffaloes, the potential for broader and more comprehensive studies offers opportunities to uncover new information on the characteristics, genetics, reproduction, health, and management of Toraya buffaloes. The development of Toraya buffalo farms also holds significant economic promise, as it can lead to increased agricultural productivity and improved livelihoods for local communities by enhancing the quality by implementing well-planned breeding programs and leveraging reproductive technology, and genetics-based selection, growth, and productivity can be produced. To increase the population and productivity of Toraya buffaloes, a well-structured breeding program integrating reproductive technology and selection based on quantitative and molecular genetics is essential. The development potential of Toraya buffalo is vast, not only due to its high cultural value but also its superior quantitative traits compared to common swamp buffalo, positioning it as a potential national meat provider. The present review article aimed to discuss the characteristics and development potential of Toraya buffaloes, along with the implementation of reproductive biotechnology and molecular genetics to enhance the population, productivity, and quality of Toraya buffaloes in Indonesia.

Population structure, runs of homozygosity analysis and construction of single nucleotide polymorphism fingerprinting database of Longnan goat population

AbstractThe Longnan goat (LN) is a local breed discovered during the third census of China's livestock and poultry genetic resources. In order to thoroughly comprehend the population traits, this research examined a total of 70 animals from three different goat populations, namely the LN goat, Nanjiang Brown goat (NJ), and Boer goat (Boer). Specific‐Locus Amplified Fragment Sequencing was employed to analyze genetic diversity, population structure, and selective sweep patterns. Additionally, individual DNA fingerprints were generated to provide detailed genetic profiles for each subject. A total of 643,868 single nucleotide polymorphisms (SNPs) were detected, with a majority located in intergenic and intronic regions. Genetic diversity analysis uncovered lower diversity within the LN population compared to the other two populations. The analysis of population structure unveiled significant genetic distance between LN and both NJ and Boer populations, with distinct clustering patterns observed. Moreover, genetic differentiation coefficients (FST) of 0.1019 and 0.0854 were determined between LN and Boer, as well as LN and NJ, respectively, indicating substantial genetic differentiation. Selective sweep analysis, combining FST and π ratio, identified several genes associated with growth and development, reproduction, hair color, and immunity that may serve as valuable candidates for marker‐assisted breeding. Furthermore, identification of 47,541 runs of homozygosity (ROHs) revealed non‐uniform distribution across chromosomes, with the highest frequency on chromosome 1 and the lowest on chromosome 27. Correlations between different inbreeding coefficients varied, with the highest observed between FHOM and FGRM, and the lowest between FROH >1.5Mb and FROH <500kb. A total of 46 candidate genes were annotated within high‐frequency ROH islands, primarily associated with biological processes such as reproduction, growth and development, and immunity. Finally, a DNA fingerprint, consisting of 371 highly polymorphic SNPs, was generated and presented in the form of a two‐dimensional code for convenient access. Based on the population structure analysis, LN goats have been found to have a distant genetic distance and a higher degree of differentiation from both the Boer and NJ populations. Evaluation of genetic diversity parameters and ROH analysis indicates that the LN population exhibits lower genetic diversity and shows signs of inbreeding. Our findings offer theoretical support for the identification of genetic resources within this population.

A REVIEW ON EFFICIENCY OF ARTIFICIAL INSEMINATION IN CATTLE BREEDING IN ETHIOPIA

Ethiopia has large cattle population in Africa. The output of decades of crossbreeding programme in Ethiopia through AI service was quite insignificant because the exotic breeds and their crossbreds of the country accounted for about 1.44%. The objective of this review is to present the efficiency of Artificial Insemination (AI) service in cattle breeding in Ethiopia. The optimum recommended mean number of services per conception (NSC) for profitable dairy cow is about 1.4. However, conventional cattle AI breeding indicated that the mean NSC of different studies ranged from 1.14 in local cows up to 2.47 in different genotypes of cows kept under different management systems and conception rate at first insemination (CR1) ranged from 7.14% to 75.5% in different genotypes of dairy cows kept under extensive and intensive management systems. Estrus synchronization followed AI breeding indicated that CR1 ranged from 24.69% to 70.6% in Zebu cows kept under semi-intensive management system. Calving rate (CR) is the most appropriate measure of fertility of dairy cows which is defined as the number of calves born per 100 services. The poor efficiency of the country cattle AI service is a huge biological economic loss in cattle production and managerial monetary losses. Strategic interventions on cattle AI service efficiency improvement options should be identified and practiced considering breed type, production system and agro-ecology.

Phenotypic characteristics of Sakub sheep as local livestock genetic resources

Abstract. Nurasih AD, Sumaryadi MY, Hidayah CN, Nugroho AP, Setyaningrum A, Haryoko I, Yuwono P, Sodiq A. 2023. Phenotypic characteristics of Sakub sheep as local livestock genetic resources. Biodiversitas 24: 5671-5675. Sakub sheep is an indigenous sheep with a giant body in the Brebes Regency. Phenotypic characterization is important to increase the population and productivity of Sakub sheep. By combining quantitative and qualitative data, this study will provide a comprehensive insight into the phenotypic profile of Sakub sheep. This study determined the quantitative and qualitative phenotypic characteristics of Sakub sheep. The Sakub sheep used were owned by smallholder farmers using the survey method with interview techniques, observation, and direct measurement of livestock. Samples were taken using purposive sampling in Pandansari and Wanareja villages, which have the largest sheep populations and are easily accessible. The sheep used were rams and ewes sheep in the age group of 1-1.5 years (P0), 1.5-2 years (P1), 2-2.5 years (P2), 2.5-3 years (P3). Phenotypic characteristics observed included quantitative characteristics of body size and qualitative characteristics of body morphology. Body size was measured using measuring tape and hanging scales, including Body Weight (BW), Body Length (BL), Whither Height (WH), Chest Girth (CG), Ear Length (EL), And Tail Length (TL). Body morphology includes head color, body color, face profile, and tail shape. Quantitative characters were analyzed using descriptive statistics, and qualitative characters were analyzed descriptively using relative frequency. The results showed quantitative phenotypic characteristics of Sakub sheep at the age of 1-1.5 years; 1.5-2 years; 2-2.5 years, and 2.5-3 years, such as body weight, body length, chest circumference, whither height, ear length, and tail length increased with age. The qualitative phenotypic characteristics of Sakub sheep are having a head and body with a combination of colors but dominant white, a convex head profile, no horns, and a thin and fat tail.

43 Induced Pluripotent/Totipotent Stem Cells: Inexhaustible Genetic Stocks for Regeneration and Development of Regionally Adapted Climate-Resilient Livestock

Abstract Escalating impacts of climate change present a credible threat to livestock-based food production. Increasing environmental challenges directly affect animal fitness, production performance, and reproductive efficiency with accumulative morbidities and mortality. Albeit extant livestock breeds are adapted to different climate extremes, the steep trajectory of decline in genetic diversity poses a serious threat to the sustenance of livestock farming. After pluripotent stem cells (PSCs) were derived for mice more than 30 years ago, scientists were quick to recognize PSCs as an approach to accelerate livestock biotechnology and assisted reproduction. We posited that core PSC characteristics such as indefinite self-renewal make them ideal for setting up an inexhaustible diploid livestock genetic resource bank. Nevertheless, it has been difficult to derive and sustain naïve PSCs from ruminants. Even reports of generating induced-PSCs (iPSCs) via reprogramming somatic cells that circumvents the embryo and factors such as sex, age or reproductive status, has been crippled with reproducibility issues precluding any livestock applications. In recent systematic studies, we documented two roadblocks: First, that signaling pathways necessary to sustain self-renewal of PSCs from cattle remained unknown. Second, bovine somatic cells have a stable epigenome that is resistant to complete reprogramming to pluripotency. Through systems biology examination of signal homeostasis in the bovine blastocyst inner cell mass (ICM), we uncovered that transforming growth factor (TGF) β effects are actively perturbed in the bovine ICM. This led to the discovery that inhibition of downstream ALK 4/5/7 together with GSK3β and MEK1/2 signaling, supported robust in vitro self-renewal of naïve bovine iPSCs. Simultaneously, we uncovered that epigenetic regulation by the SV40 large T antigen together with the reprogramming genes (OCT4, SOX2, KLF4 and MYC) could result in not only complete reprogramming, but also cells that are set to a stable ground state of pluripotency akin to totipotent stem cells (TPSCs) seen in 16-cell-stage bovine embryos. Cloning performed using the induced TPSCs (iTPSCs) showed significantly greater efficiency of blastocyst formation. Surprisingly, applying identical methods to murine somatic cells also resulted in iTPSCs that can contribute to placenta formation in vivo indicating that the mechanistic basis for sustaining the ground state of developmental plasticity was conserved across species. These findings have now defined a high-fidelity platform for achieving iPSC-based biotechnologies (gene editing and cloning) and for exploring different ruminant livestock applications that have not been previously practicable. Of central importance, these findings also open a path to establishing a live regenerative repository of inexhaustible diploid livestock that can secure the evolving genetic needs for sustaining animal production into the future. Permanent assets of genetic diversity preserved as iTPSCs would ensure rapid resilience in production, health and fertility through propagating heterosis and enabling genetic fixes for regional climate-resilient livestock phenotypes that better tolerate environmental extremes.

Incorporation of Biotechnologies into Gene Banking Strategies to Facilitate Rapid Reconstitution of Populations.

National animal gene banks that are responsible for conserving livestock, poultry, and aquatic genetic resources need to be capable of utilizing a broad array of cryotechnologies coupled with assisted reproductive technologies to reconstitute either specific animals or populations/breeds as needed. This capability is predicated upon having sufficient genetic diversity (usually encapsulated by number of animals in the collection), units of germplasm or tissues, and the ability to reconstitute animals. While the Food and Agriculture Organization of the United Nations (FAO 2012, 2023) developed a set of guidelines for gene banks on these matters, those guidelines do not consider applications and utilization of newer technologies (e.g., primordial germ cells, cloning from somatic cells, embryo transfer, IVF, sex-sorted semen), which can radically change how gene banks collect, store, and utilize genetic resources. This paper reviews the current status of using newer technologies, explores how gene banks might make such technologies part of their routine operations, and illustrates how combining newer assisted reproductive technologies with older approaches enables populations to be reconstituted more efficiently.

Origin, Selection and Current Status of the Utrerana Chicken Breed: A Review.

The conservation of threatened local livestock genetic resources involves characterising them to implement conservation strategies. The Utrerana is a Mediterranean-type chicken breed, included in the Official Catalogue of Livestock Breeds of Spain and in the Domestic Animal Diversity Information System (DAD-IS) of the Food and Agriculture Organization (FAO), native to south Spain created in 1926 by a farmer from Utrera (Seville province). It was selected for laying performance and with four plumage varieties (White, Black, Black-barred and Partridge), reaching average yields of 180 eggs per hen per year. It was widely used in commercial farming in the second quarter of the 20th century, being subsequently displaced in the second half of the 20th century by the spreading of the improved foreign breeds and lines. The Utrerana breed was reared from then on for its aesthetic values and in backyard systems, being endangered with a vulnerable local risk status (1822 birds in 2022 with an increasing trend) and having worsened its laying performance as selection for productivity ceased. The breed has received little attention from the research community. Therefore, this work aims to review the literature on the origin, selection, genetic and productive characterisation and status of the populations of the breed, as well as the conservation strategies. The Utrerana chicken is a polymorphic breed showing high genetic diversity, sexual dimorphism and morpho-functional differences among varieties. Currently, Utrerana hens start laying at 6 months of age, and a hen lays 94-121 high quality eggs (59-64 g) per year, showing seasonality. It is a slow-growing breed with mature weights of 2.4-2.6 kg for roosters and 1.9-2.0 g for hens. The Utrerana chicken breed is rustic and adapted to alternative farming systems. This review has identified research gaps to be filled, such as characterising the carcass and meat quality of the Utrerana chicken, and evidences the need to make efforts to promote the breed and expand its populations.

THE IMPACT OF THE FREQUENCY OF DIFFERENT FORAGE MIXED WITH GINGER POWDER ON THE PRODUCTIVITY OF KAUR CATTLE

Kaur cattle, Bengkulu's local livestock genetic resources (SDG-T), must be preserved and utilized to increase livestock production. The purpose of this study was to determine the productivity of Kaur cattle through observing the results of feed consumption, daily body weight gain, and feed conversion. For the purpose of this study, twelve Kaur bulls aged 1.5 to two years, weighing between 160 and 180 kilograms were used. Green feed is given by adding ginger flour 1% of body weight and is regulated in the number of times it is given. Cattle feed consists of dry matter as much as 3% of body weight. For this study, the main feed was concentrate and elephant grass (70%: 30%). There were three treatment groups, each with four repetitions. P1 is given once every day at 08.00 am; P2 is administered twice daily at 08.00 am and 12.00 pm; and P3 is given three times every day at 08.00 am, 12.00 noon, and 16.00 pm. Data is evaluated by ANOVA and unidirectional pattern. The results showed that the average daily feed consumption from highest to lowest was P3=9.44±9.50; P2=9.33±9.39; P1=8.87±8.90 kg/head/day. The average daily body weight gain from highest to lowest was P3=1.45±1.49; P2=1.32±1.36; P1=1.12±1.17 kg/head/day. The results show that there is no significant difference between the two. P3=9.19±9.23; P2=9.05±9.10; and P1=8.71±8.79. There was no significant difference in feed conversion from highest to lowest. Consumption of forage and ginger flour at different times did not affect the productivity of Kaur cattle.

Haplotype and phylogenetic diversity using mitochondrial 12S rRNA gene marker in Bali cattle

Bali cattle is one of Indonesia's original livestock genetic resources. The 12S rRNA can be used as a marker of genetic diversity, and until now, there has been no report on Bali cattle. The study was aimed to analyze the gene of mtDNA 12S rRNA to determine haplotype diversity and phylogenetics in Bali cattle populations of the eastern region of Indonesia. A total of 95 blood samples used consisted of three different populations which were Bali cattle, Ongole crossbred (PO) and Madura cattle as a comparison. This research was analyzed using PCR and sequencing methods. The data were analyzed using the cluster W method for estimating genetic distances, calculating diversity, and reconstructing phylogenetic trees using the MEGAX, DNAsP and Network. The genetic distance values ranged from 0.00200 to 0.01508, and the Haplotype diversity values ranged from 0.66000 to 0.91111. The nucleo-tide diversity values ranged from 0.00174 to 0.01673. There were 16 haplotypes found. The values of Gst, Nst and Fst were 0.00803, 0.07550, 0.07622; respectively. Based on the analysis, there were dif-ferences between Bali cattle from various populations, there were specific haplotypes. The 12S rRNA gene can be used as a genetic marker for diversity studies in Bali cattle and other cattle breeds although the diversity is low.

Embryo Production and Development from Superovulated Donors in Double-Muscled Cattle and Their Crosses

Belgian Blue was introduced in Indonesia to increase the biodiversity of livestock genetic resources.  Belgian Blue was crossed with Ongole grade to increase the productivity of local cattle. Therefore, this study evaluates reproduction traits, especially the response to superovulation, embryonic development, and quality of Belgian Blue, Ongole grade, and their crosses. Estrous was synchronized with intravaginal progesterone Cue-Mate before artificial insemination (AI). Superovulation was performed with Follicle Stimulating Hormone (FSH) intramuscularly with non-surgical embryo flushing.  In addition, embryo quality was assessed microscopically according to the International Embryo Transfer Society (IETS) criteria. The study was performed in a quasi-experimental design, and data were analyzed with an analysis of variance. After superovulation, oocytes/embryos were obtained from all donor breeds. Oocyte and embryo production from Ongole grade and Belgian Blue differed at 11.83±1.91 and 4.86±1.33, respectively, P0.05 (mean±SEM). In addition, there are differences in recovery rate (89.63% vs. 75.35%) and fertilization rate (77.35% vs. 68.22%) between Ongole grade and Belgian Blue, respectively (P0.05). There is no difference in embryo development quality and proportion of transferable embryos between Ongole grade, Belgian Blue, and their crosses. This study concluded that the cross-bred Belgian Blue x Ongole donor had identical oocyte and embryo production, recovery rate, fertilization rate, and degenerative embryos compared to its purebred.

Genetic diversity analysis of Indonesian indigenous goat breeds based on microsatellite markers

Goats are important livestock in Indonesia as a source of animal protein and income. Indonesia has several indigenous goat breeds with distinct characteristics. 379 unrelated goats were randomly selected from seven indigenous Indonesian goat breeds and collected from individual farmers in various Indonesian provinces. Microsatellite characterization of indigenous Indonesian goats was carried out using 12 specific microsatellite markers. The total number of alleles obtained from the 12 microsatellite loci was 97, with an average score of 8.08, and the number of effective alleles ranged from 1.413 (ILSTS005) to 4168 (INRA23), with an average value of 2.608. A total of 11 private alleles was found in some goat breeds, but the frequencies were very low, 0.71 – 8.86%. The average of polymorphic information content ranged from 0.239 (ETH10) to 0.726 (INRA23). The mean rate of inbreeding value between populations (Fis) was 0.050, and within the population (Fit) was 0.151. The mean expected heterozygosity was 0.54, and the mean observed heterozygosity was 0.52. Except for the Gembrong goat (GEM), the observed number of alleles, polymorphic information content, and expected heterozygosity were all moderate. This study will support the management of livestock genetic resources and conserving endangered Indonesian goat breeds, such as the Gembrong goat.

Quantifying morphometric and adaptive characteristics of indigenous cattle genetic resources in northwest Ethiopia.

Ethiopia is the gateway of livestock genetic resources to Africa and has a wide range of altitude. It is endowed with huge diverse cattle genetic resources. The aim of this research was to determine the morphometric and potentioally adaptive characteristics of cattle populations. Multi-stage purposive and random sampling methods were employed to select the study areas, households and animals. A total of 1200 adult cattle were sampled and characterized for 14 qualitative and eight morphometric variables. The comparison of marginal means, chi-square tests, canonical discriminant analysis, and clustering analysis were employed using SAS and SPSS statistical software. The sex of the animal, location and agro-ecology were fitted as fixed effects in the model and had highly significant (p<0.001) effects for most body measurements. The chi-square test values of all categorical variables were significantly different (p<0.001) and potentioally adaptive characteristics such as coat colour type, navel flap, and tail length had higher association (> 0.45) values. White with red, light red, black and dark red were the most predominant coat colour types of cattle. The maximum hit rates were recorded in Enebsie and Sinan cattle. From five extracted canonical variate, (can1 and can2) accounted 75.4% and 78.8% in the female and male cattle populations, respectively. The canonical class has separated cattle populations of Sinan from Banja at can1 and Mecha from Sinan populations at can2. The square Mahalanobis distances between sites were significant (p<0.001) and the largest distance was found between Banja and Sinan locations. Cluster analysis result classified the study populations into four major cattle groups. The cumulative analysis results showed that the cattle populations of the study area can be categorized into four breed types as Jawi Sanga, Gojjam Zenga, Banja cattle, and Sinan cattle. However, this morphology based grouping need to be confirmed by molecular data.

Establishment of Tibetan-Sheep-Specific SNP Genetic Markers

Tibetan sheep are one of the three major coarse sheep breeds in China, and they possess a long history of formation. However, few studies have been conducted on the identification of Tibetan sheep breeds at the molecular level. In this study, a total of 448 individuals from 24 Tibetan sheep populations in the 5 regions of Tibet, Qinghai, Gansu, Yunnan, and Sichuan were analyzed using the Affymetrix Ovine SNP 600K high-density chip to construct specific single-nucleoside polymorphism (SNP) genetic marker sets of Tibetan sheep breeds. Firstly, the genetic structure analysis showed that Yunnan–Tibetan sheep (NL, Ninglang; JC, Jianchuan), Zuogong (ZG), Heizang (HZ), Gongga (GG,) and Tao sheep (TS) can be clearly distinguished from other Tibetan sheep populations. Next, based on the population differentiation index FST, the PCA and NJ tree results showed that only 60 specific SNPs can successfully separate Tibetan sheep in the Yunnan region from Tibetan sheep in other regions, and the distinguishing effect on Yunnan–Tibetan sheep reached 100%. Using the same method, we found that 4 Tibetan sheep breeds, including Zuogong (ZG, 20 SNPs), Heizang (HZ, 60 SNPs), Gongga (GG, 60 SNPs), and Tao sheep (TS, 30 SNPs), can also be distinguished from other Tibetan sheep populations with only a few SNP loci (20–60), and the distinguishing effect reached 100%. Overall, we successfully obtained a Yunnan region-specific (60 SNPs) genetic marker set and 4 breed-specific SNP genetic marker sets (20–60 SNPs) for the first time for the identification of Tibetan sheep breeds at the molecular level. These made up for the lack of genetic marker sets for the identification of Tibetan sheep breeds, and provided a genomic basis for the scientific classification and accurate identification of livestock and poultry genetic resources on the Qinghai–Tibet Plateau.

Analysis of genetic diversity and selection characteristics using the whole genome sequencing data of five buffaloes, including Xilin buffalo, in Guangxi, China.

Buffalo is an economically important livestock that renders useful services to manhood in terms of meat, milk, leather, and draught. The Xilin buffalo is among the native buffalo breeds of China. In the present study, the genetic architecture and selection signature signals of Xilin buffalo have been explored. Correlation analysis of the population structure of Xilin buffalo was conducted by constructing NJ tree, PCA, ADMIXTURE and other methods. A total of twenty-five (n = 25) Xilin buffalo whole genome data and data of forty-six (n = 46) buffaloes published data were used. The population structure analysis showed that the Xilin buffalo belong to the Middle-Lower Yangtze. The genome diversity of Xilin buffalo was relatively high. The CLR, π ratio, F ST, and XP-EHH were used to detect the candidate genes characteristics of positive selection in Xilin buffalo. Among the identified genes, most of the enriched signal pathways were related to the nervous system and metabolism. The mainly reported genes were related to the nervous system (GRM5, GRIK2, GRIA4), reproductive genes (CSNK1G2, KCNIP4), and lactation (TP63). The results of this study are of great significance for understanding the molecular basis of phenotypic variation of related traits of Xilin buffalo. We provide a comprehensive overview of sequence variations in Xilin buffalo genomes. Selection signatures were detected in genomic regions that are possibly related to economically important traits in Xilin buffalo and help in future breeding and conservation programs of this important livestock genetic resource.