Adaptive traits of indigenous cattle breeds: The Mediterranean Baladi as a case study

Phenotypic and genetic characterization of unexplored, potential cattle population of Madhya Pradesh

Bawri or Garri, a non-descript cattle population managed under an extensive system in Madhya Pradesh state of India, was identified and characterized both genetically and phenotypically to check whether or not it can be recognised as a breed. The cattle have white and gray colour and are medium sized with 122.5 ± 7.5 cm and 109.45 ± 0.39 cm height at withers in male and female, respectively. Double-digest restriction site associated DNA (ddRAD) sequencing was employed to identify ascertainment bias free SNPs representing the entire genome cost effectively; resulting in calling 1,156,650 high quality SNPs. Observed homozygosity was 0.76, indicating Bawri as a quite unique population. However, the inbreeding coefficient was 0.025, indicating lack of selection. SNPs found here can be used in GWAS and genetic evaluation programs. Considering the uniqueness of Bawri cattle, it can be registered as a breed for its better genetic management.

What Kigali’s open-air markets reveal about achieving food and nutrition security: the role of African indigenous crops

Background

Household dietary diversity in Rwanda remains low and significantly contributes to the double burden of malnutrition. Rwanda has one of the highest under five stunting rates globally, and malnutrition remains one of the most pressing public health issues; therefore, factors that shape food and nutrition security are of utmost concern. Globally, the variety of foods available in open-air markets has been shown to affect dietary diversity. Furthermore, the consumption of indigenous foods can contribute to a diverse diet and improve nutrition status. At present, there are limited data on foods available for purchase in open-air markets in Africa. Therefore, this study was designed to provide data on food availability in the largest open-air markets of Rwanda’s most populated city, Kigali, and to highlight which foods indigenous to Africa can be purchased.

Methods

All consumables were inventoried between October and December of 2020 in three open-air markets of Kigali, the capital city of Rwanda. Consumables were organized by the site of domestication and the nutritional contents of some African indigenous crops were compared to similar non-indigenous items.

Results

A variety of raw and processed consumables was available in the open-air markets inventoried; however, only 25.8% of available species are indigenous to Africa. All Rwanda’s staples, including sweet potatoes, plantains, beans, maize, banana, and cassava, are endemic to other continents. Indigenous plant species, which are often drought-resistant and more nutritious, for example, Africa’s pineapple fruits (Myrianthus holstii), could not be purchased in Kigali’s open-air markets. Pineapple fruits are richer in iron, vitamin C, protein, and vitamin A than banana, which is the most consumed fruit in Rwanda.

Conclusions

Given rapid population growth, limited arable land, and erratic climate patterns, policies to conserve and promote indigenous species, especially those already adapted to harsh environmental conditions, should be enacted in Rwanda. The cultivation of native vegetables and fruits in home gardens, and the conservation of edible wild species, can improve dietary diversity and enhance food and nutrition security across the entire country.

Revisiting Cattle Temperament in Beef Cow-Calf Systems: Insights from Farmers' Perceptions about an Autochthonous Breed

Understanding temperament is an important part of cattle production since undesirable temperament may cause serious problems associated with aggression, maternal care, and human safety. However, little is known about how farmers define or assess temperament, especially in autochthonous cattle breeds. The aim of this study was to explore perceptions of farmers about the temperament of the Pyrenean cattle breed with special attention to beef cow-calf systems in Spain. The methodology used to obtain the information was focus group discussions (FGD). Farmers defined temperament as a behavioural response to challenging situations imposed by human handling. Specific terms used were related to active or passive reactions to fear (e.g., "strong", "aggressive", "nervous", "fearful"). The speed of response to stimuli was also important. Female temperament was thought to become more docile with age while bull temperament was more variable. Maternal aggressiveness was highlighted as a potential human safety problem, but also desirable in an extensively bred animal who may need to defend calves against predators. Anatomical characteristics were seen as unreliable predictors of temperament, while behavioural indicators were more widely used, such as "alertness", which was a general trait of the breed, and "gaze", which, when associated with an alert expression, suggests a potential threat. Sensory acuity, such as sight and smell, were thought to be related with temperament in some FGDs but there was no overall agreement as to whether different behavioural responses were due to differences in sensory acuity. The results from the study could be useful during training programs or in the development of new genetic selection schemes and evaluation protocols involving cattle temperament.

Genetic characterisation of non-descript cattle populations in communal areas of South Africa

Context Indigenous cattle breeds represent an important genetic resource for livelihood of communal-area inhabitants. Indigenous breeds have the ability to withstand harsh climatic conditions, can adapt genetically to poor-quality forages and are resistant to parasites and diseases. These unique traits possessed by indigenous breeds are under threat because of unrestrained crossing with exotic commercial breeds, and this can lead to total loss of a breed. Aims The study was conducted to assess the genetic diversity and population structure of South African non-descript communal beef cattle populations by using 25 microsatellite markers. Methods Unrelated and non-descript animals (n = 150) were sampled from communal areas from five (5) provinces of South Africa, namely, Eastern Cape, KwaZulu–Natal, Limpopo, Mpumalanga and the North West, with 30 samples per breed taken. Six (6) known cattle breeds (n = 180) were used as a reference population. This included Angus, Afrikaner, Bonsmara, Brahman, Drakensberger and the Nguni, with 30 samples per breed. Key results High level of genetic diversity was found across the five non-descript populations, with an average heterozygosity of 75%. The Limpopo population was found to be the most diverse population, with the highest average number of alleles (8.5) and heterozygosity (ranging between observed heterozygosity of 70% and expected heterozygosity of 79%). STRUCTURE software assigned populations (2 ≤ K ≤ 20), with the most probable cluster being at K = 7. The Eastern Cape, KwaZulu–Natal and Limpopo populations had genetic material similar to those possessed by the Nguni and Bonsmara reference populations. Conclusions Results from the study showed that most genetic differentiation occurred within populations rather than among populations, and this might be due to the fact that there is no selection for or against any specific production trait expressed in the populations. Implications The obtained information will serve as a baseline for the development and implementation of sound breeding programs that will assist in controlling the gene flow, so as to lower the possible genetic dilution of the currently available genetic material.

An outlook on livestock welfare conditions in African communities - A review

A significant proportion of the African continent is conducive for animal agricultural production, due to its historical experience and available resources to accommodate and nurture various indigenous and exotic animal species and breeds. With food security being a global challenge, animal products can play an important role as nutrient dense food sources in human diets, particularly in Africa. However, this does not seem to reach its full potential in practice, due to numerous reasons that have not been adequately addressed. Animal welfare reservations can be highlighted as one of the major contributing factors to the curbed progress. The consequences have been scientifically proven to affect product quality and market access. However, in the African community, the concept of animal welfare has not been fully embraced. While there are international animal welfare standards in the developed world, there are inherent factors that hinder adoption of such initiatives in most developing regions, particularly among communal farmers. These include cultural norms and practices, social ranking, socio-economic status, available resources, information dissemination and monitoring tools. Therefore, there is need to harmonize what is internationally required and what is feasible to accommodate global variability. The protocols followed to ensure and evaluate farm animal welfare require regular investigation, innovation and a sustainable approach to enhance animal productivity, efficiency and product quality. Additionally, investing in animal wellbeing and health, as well as empowering communities with significant knowledge, has a potential to improve African livelihoods and contribute to food security. This review seeks to highlight the concept of animal welfare in relation to livestock and food production in African conditions.

Livelihood, Food and Nutrition Security in Southern Africa: What Role Do Indigenous Cattle Genetic Resources Play?

Of the 345 million people in the Southern African Development Community (SADC), 30.6% are severely food insecure, 8% malnourished and 50% live with less than US $1 per day, respectively. Livelihood, food and nutrition security have, therefore, become key priorities for the SADC region in response to these complex challenges. Given that 70% of the SADC population directly rely on agriculture for food, nutrition and income, sustained agricultural productivity may play an important role in achieving livelihood, food and nutrition security in the region. Being an important part of the agri-food system of marginalised communities in the region, cattle have great potential to contribute to the goal of reducing food and nutrition insecurity. The region has a population size of about 64 million cattle of which 75% of the population is kept under the smallholder farming systems, and primarily composed of indigenous tropical breeds. Most indigenous cattle breeds are, however, either undergoing rapid genetic dilution or at risk of extinction. At the same time, their environments, production and marketing systems are experiencing high rates of change in time and space. More importantly, indigenous cattle breeds in the region are undervalued. This makes it uncertain that future systems will have the adapted cattle breeds required for optimal livelihoods, food and nutrition security. To this end, the promotion of sustainable use of indigenous cattle for livelihood, food and nutrition security in the SADC region is strongly recommended.

Strategies for Sustainable Use of Indigenous Cattle Genetic Resources in Southern Africa

Indigenous cattle breeds are the most important livestock species in the Southern African Development Community (SADC) region owing to their role in human food, nutrition, income, and social security. Despite the role of these breeds in the household and national economies, they are currently underutilised, their productivity remains low, and populations are faced with extinction. In addition, there are insufficient measures taken to secure their present and future value. The current review highlights strategies for sustainable use of indigenous cattle genetic resources in the region, including the use of novel production and marketing practices, women and youth empowerment, and development of the appropriate capacity building, legislative, and policy structures. At present, the lack of coordination among the different stakeholders still poses a challenge to the implementation of these strategies. To this end, partnerships, collaboration, and stakeholders’ participation are recommended to effectively implement strategies for sustainable use of indigenous cattle breeds.

Genome Analysis Reveals Genetic Admixture and Signature of Selection for Productivity and Environmental Traits in Iraqi Cattle

The Near East cattle are adapted to different agro-ecological zones including desert areas, mountains habitats, and humid regions along the Tigris and Euphrates rivers system. The region was one of the earliest and most significant areas of cattle husbandry. Currently, four main breeds of Iraqi cattle are recognized. Among these, the Jenoubi is found in the southern more humid part of Iraq, while the Rustaqi is found in the middle and drier region of the country. Despite their importance, Iraqi cattle have up to now been poorly characterized at the genome level. Here, we report at a genome-wide level the diversity and signature of positive selection in these two breeds. Thirty-five unrelated Jenoubi cattle, sampled in the Maysan and Basra regions, and 60 Rustaqi cattle, from around Baghdad and Babylon, were genotyped using the Illumina Bovine HD BeadChip (700K). Genetic population structure and diversity level were studied using principal component analysis (PCA), expected heterozygosity (He), observed heterozygosity (Ho), and admixture. Signatures of selection were studied using extended haplotype homozygosity (EHH) (iHS and Rsb) and inter-population Wright's Fst. The results of PCA and admixture analysis, including European taurine, Asian indicine, African indicine, and taurine indicate that the two breeds are crossbreed zebu × taurine, with more zebu background in Jenoubi cattle compared with Rustaqi. The Rustaqi has the greatest mean heterozygosity (He = 0.37) among all breeds. iHS and Rsb signatures of selection analyses identify 68 candidate genes under positive selection in the two Iraqi breeds, while Fst analysis identifies 220 candidate genes including genes related to the innate and acquired immunity responses, different environmental selection pressures (e.g., tick resistance and heat stress), and genes of commercial interest (e.g., marbling score).

Analysis of GH1, GHR and PRL gene polymorphisms for estimation of the genetic diversity of Buryat and Altai cattle breeds

Small and unique Buryat and Altai cattle breeds of TuranoMongolian origin are well adapted to harsh conditions of the continental climate to be their habitat. However, the population-genetic structure of the breeds has been poorly studied. This paper presents the results of analysis of polymorphisms GH1 (AC_000176.1: BTA 19, exon 5, rs41923484, g.2141C>G, L127V), GHR (AC_000177.1: BTA 20, exon 10, rs109300983, g.257A>G, S555G) and PRL (AC_000180.1: BTA 23, exon 3, g.35108342A>G) in the samples of Buryat cattle breed of Russia, China and Mongolia, and indigenous Altai cattle breed (Russia) that belong to TuranoMongolian cattle. The Russian sample of Buryat breed was differentiated from the Mongolian sample based on pairwise G-test and FST values for the PRL-RsaI polymorphism and from the Chinese sample – based on pairwise G-test values for the GH1-AluI polymorphism. All the three samples of Buryat breed clearly differed from the sample of Altai breed based on pairwise G-test and FST values for the GHR-AluI polymorphism as well as on the base of FST values for the joint polymorphism of the three genes. Nei’s genetic distances calculated from the three gene polymorphisms also confirmed the difference between the two breeds. The results of AMOVA demonstrated that GHR gene variability (16 %) gave the largest contribution to the differentiation that was confirmed by FST values (0.12–0.27). The STRUCTURE software enabled us to reveal four clusters, with a specific ratio for each sample, in the Chinese and Mongolian samples of Buryat breed, and in the sample of Altai breed, while the Russian sample of Buryat breed had only three clusters. The differences within the breed level were determined based on the GH1-AluI and PRL-RsaI polymorphisms, while at the inter-breed level – based on the GHR-AluI polymorphism. Linkage disequilibrium analysis demonstrated significant linkage of the following pairs of genes in the Buryat breed: GH1-GHR, GH1-PRL, GHR-PRL.

Landscape genomic approach to detect selection signatures in locally adapted Brazilian swine genetic groups

Samples of 191 animals from 18 different Brazilian locally adapted swine genetic groups were genotyped using Illumina Porcine SNP60 BeadChip in order to identify selection signatures related to the monthly variation of Brazilian environmental variables. Using BayeScan software, 71 SNP markers were identified as FST outliers and 60 genotypes (58 markers) were found by Samβada software in 371 logistic models correlated with 112 environmental variables. Five markers were identified in both methods, with a Kappa value of 0.073 (95% CI: 0.011-0.134). The frequency of these markers indicated a clear north-south country division that reflects Brazilian environmental differences in temperature, solar radiation, and precipitation. Global spatial territory correlation for environmental variables corroborates this finding (average Moran's I = 0.89, range from 0.55 to 0.97). The distribution of alleles over the territory was not strongly correlated with the breed/genetic groups. These results are congruent with previous mtDNA studies and should be used to direct germplasm collection for the National gene bank.

Conservation of indigenous cattle genetic resources in Southern Africa's smallholder areas: turning threats into opportunities - A review

The current review focuses on characterization and conservation efforts vital for the development of breeding programmes for indigenous beef cattle genetic resources in Southern Africa. Indigenous African cattle breeds were identified and characterized using information from refereed journals, conference papers and research reports. Results of this current review reviewed that smallholder beef cattle production in Southern Africa is extensive and dominated by indigenous beef cattle strains adaptable to the local environment. The breeds include Nguni, Mashona, Tuli, Malawi Zebu, Bovino de Tete, Angoni, Landim, Barotse, Twsana and Ankole. These breeds have important functions ranging from provision of food and income to socio-economic, cultural and ecological roles. They also have adaptive traits ranging from drought tolerant, resistance to ticks and tick borne diseases, heat tolerance and resistance to trypanosomosis. Stakeholders in the conservation of beef cattle were also identified and they included farmers, national government, research institutes and universities as well as breeding companies and societies in Southern Africa. Research efforts made to evaluate threats and opportunities of indigenous beef cattle production systems, assess the contribution of indigenous cattle to household food security and income, genetically and phenotypically characterize and conserve indigenous breeds, and develop breeding programs for smallholder beef production are highlighted. Although smallholder beef cattle production in the smallholder farming systems contributes substantially to household food security and income, their productivity is hindered by several constraints that include high prevalence of diseases and parasites, limited feed availability and poor marketing. The majority of the African cattle populations remain largely uncharacterized although most of the indigenous cattle breeds have been identified.