Landrace Research Articles

Whole genome sequences of 70 indigenous Ethiopian cattle

Indigenous animal genetic resources play a crucial role in preserving global genetic diversity and supporting the livelihoods of millions of people. In Ethiopia, the majority of the cattle population consists of indigenous breeds. Understanding the genetic architecture of these cattle breeds is essential for effective management and conservation efforts. In this study, we sequenced DNA samples from 70 animals from seven indigenous cattle breeds, generating about two terabytes of pair-end reads with an average coverage of 14X. The sequencing data were pre-processed and mapped to the cattle reference genome (ARS-UCD1.2) with an alignment rate of 99.2%. Finally, the variant calling process produced approximately 35 million high-quality SNPs. These data provide a deeper understanding of the genetic landscape, facilitate the identification of causal mutations, and enable the exploration of evolutionary patterns to assist cattle improvement and sustainable utilization, particularly in the face of unpredictable climate changes.

A Nonsynonymous Substitution of Lhx3 Leads to Changes in Body Size in Dogs and Mice.

Lhx3 is a LIM-homeodomain transcription factor that affects body size in mammals by regulating the secretion of pituitary hormones. Akita, Shiba Inu, and Mame Shiba Inu dogs are Japanese native dog breeds that have different body sizes. To determine whether Lhx3 plays a role in the differing body sizes of these three dog breeds, we sequenced the Lhx3 gene in the three breeds, which led to the identification of an SNP in codon 280 (S280N) associated with body size. The allele frequency at this SNP differed significantly between the large Akita and the two kinds of smaller Shiba dogs. To validate the function of this SNP on body size, we introduced this change into the Lhx3 gene of mice. Homozygous mutant mice (S279N+/+) were found to have significantly increased body lengths and weights compared to heterozygous mutant (S279N+/-) and wild-type (S279N-/-) mice several weeks after weaning. These results demonstrate that a nonsynonymous substitution in Lhx3 plays an important role in regulating body size in mammals.

The status of conservation and management of indigenous sheep breeds in South Africa - A review

Indigenous sheep breeds in South Africa play an important role in local food security and they are adapted to local conditions. Their genetic and cultural values have to be recognised for national importance. The conservation of these breeds is very critical as most of them are already classified as endangered. The South African government has the initiative to attempt the conservation of these animals; however, it comes with several challenges. In addition to funding, breed conservation demands farmers to understand and recognise the role of such breeds in society. This is especially crucial in the rural communal lands where breeds are kept. Farmers that raise indigenous breeds should be taught the necessity of maintaining the purity of these breeds. Indigenous sheep breeds in South Africa are not favored by the commercial farmers and thus they are more vulnerable. This review outlines the nature of sheep farming and the conservation status of four indigenous sheep breeds in South Africa. The effort and challenges that are met in current conservation arrangements are discussed. Moreover, we emphasise on the conservation techniques that are employed in South Africa.

Polymorphism of Cyt-b Gene in Several Indonesian Cattle Using PCR-RFLP Method

The cytochrome b (Cyt-b) gene is one of the genes that is located in the mitochondrial DNA. Variations in the Cyt-b gene can be used to compare different animal species to investigate the origin of certain animal species. This study aimed to assess the genetic diversity of Indonesian local cattle breeds, including Bali cattle as an Indonesian native cattle breed and Banteng as the wild type of Bali cattle, using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). A total of 336 individual DNA samples from Indonesian cattle breeds were analyzed in this study. The RFLP method using three restriction enzymes, i.e., HinfI, HaeIII, or XbaI, was used to identify the variation of the Cyt-b gene. The Cyt-b gene was polymorphic based on the PCR-RFLP method. There were six alleles of the Cyt-b gene found in this study, i.e., A and B allele (HinfI), C and D allele (HaeIII), X and Y allele (XbaI). All alleles can be found in Pasundan, Madura, and PO cattle. Pesisir cattle have the highest allele frequency D. The UPGMA results showed three clusters of Indonesian native cattle in this study. Cluster 1 consists of Pasundan, Banteng, and Bali cattle. Cluster 2 consists of Madura, PO, and SO cattle. Pesisir was separated from other cattle in cluster 3. The X allele could become an indicator to distinguish Banteng and Bali cattle.

Effectiveness of machine learning algorithms as a tool to meat traceability system. A case study to classify Spanish Mediterranean lamb carcasses

Establishing the traceability of meat products has been a major focus of food science in recent decades. In this context, recent advances in food nutritional biomarker identification and improvements in statistical technology have allowed for more accurate identification and classification of food products. Moreover, artificial intelligence has now provided a new opportunity for optimizing existing methods to identify animal products. This study presents a comparative analysis of the effectiveness of different machine learning algorithms based on raw data from analyses of organoleptic, sensory and nutritional meat traits to differentiate categories of commercial lamb from an indigenous Spanish breed (Mallorquina breed) obtained from the following production systems: suckling lambs; light lambs from grazing; and light lambs from grazing supplemented with grain. Six machine learning algorithms were evaluated: Artificial Neural Network (ANN), Decision Tree, K-Nearest Neighbours (KNN), Naive Bayes, Multinomial Logistic Regression, and Support Vector Machine (SVM). For each algorithm, we tested three datasets, namely organoleptic traits and sensorial traits (CIELAB colour, water holding capacity, Warner-Bratzler shear force, volatile compounds and trained tasters), and nutritional traits (proximate composition and fatty acid profile). We also tested a combination of all three datasets. All the data were combined into a dataset with 144 variables resulting from the meat characterization, which included 11,232 event records. The ANN algorithm stood out for its high score with each of the three datasets used. In fact, we obtained an overall accuracy of 0.88, 0.83, and 0.88 for the organoleptic-sensory, nutritional, and combined datasets, respectively. The effectiveness of using the SVM algorithm to assign categories of lambs according to its production system performed better with nutritional traits and the full characterization, with performances equal to those obtained with ANN. The KNN algorithm showed the worst performance, with overall accuracies of 0.54 or lower for each of the datasets used. The results of this study demonstrate that machine learning is a useful tool for classifying commercial lamb carcasses. In fact, the ANN and SVM algorithms could be proposed as tools for differentiating categories of lamb production based on the organoleptic, sensory and nutritional characteristics of Mediterranean light lambs' meat. However, in order to improve the traceability methods of lamb meat production systems as a guarantee for consumers and to improve the learning processes used by these algorithms, more studies along these lines with other lamb breeds are required.

Unveiling the Influence of Copy Number Variations on Genetic Diversity and Adaptive Evolution in China's Native Pig Breeds via Whole-Genome Resequencing.

Copy number variations (CNVs) critically influence individual genetic diversity and phenotypic traits. In this study, we employed whole-genome resequencing technology to conduct an in-depth analysis of 50 pigs from five local swine populations [Rongchang pig (RC), Wuzhishan pig (WZS), Tibetan pig (T), Yorkshire (YL) and Landrace (LR)], aiming to assess their genetic potential and explore their prospects in the field of animal model applications. We identified a total of 96,466 CNVs, which were subsequently integrated into 7112 non-redundant CNVRs, encompassing 1.3% of the swine genome. Functional enrichment analysis of the genes within these CNVRs revealed significant associations with sensory perception, energy metabolism, and neural-related pathways. Further selective scan analyses of the local pig breeds RC, T, WZS, along with YL and LR, uncovered that for the RC variety, the genes PLA2G10 and ABCA8 were found to be closely related to fat metabolism and cardiovascular health. In the T breed, the genes NCF2 and CSGALNACT1 were associated with immune response and connective tissue characteristics. As for the WZS breed, the genes PLIN4 and CPB2 were primarily linked to fat storage and anti-inflammatory responses. In summary, this research underscores the pivotal role of CNVs in fostering the diversity and adaptive evolution of pig breeds while also offering valuable insights for further exploration of the advantageous genetic traits inherent to China's local pig breeds. This facilitates the creation of experimental animal models tailored to the specific characteristics of these breeds, contributing to the advancement of livestock and biomedical research.

Whole-genome selection signature differences between Chaohu and Ji'an red ducks.

Assessing the genetic structure of local varieties and understanding their genetic data are crucial for effective management and preservation. However, the genetic differences among local breeds require further explanation. To enhance our understanding of their population structure and genetic diversity, we conducted a genome-wide comparative study of Chaohu and Ji'an Red ducks using genome sequence and restriction site-associated DNA sequencing technology. Our analysis revealed a distinct genetic distinction between the two breeds, leading to divided groups. The phylogenetic tree for Chaohu duck displayed two branches, potentially indicating minimal impact from artificial selection. Additionally, our ROH (runs of homozygosity) analysis revealed that Chaohu ducks had a lower average inbreeding coefficient than Ji'an Red ducks. We identified several genomic regions with high genetic similarity in these indigenous duck breeds. By conducting a selective sweep analysis, we identified 574 candidate genes associated with muscle growth (BMP2, ITGA8, MYLK, and PTCH1), fat deposits (ELOVL1 and HACD2), and pigmentation (ASIP and LOC101797494). These results offer valuable insights for the further enhancement and conservation of Chinese indigenous duck breeds.

Regression Models for In Vivo Discrimination of the Iberian Pig Feeding Regime after Near Infrared Spectroscopy Analysis of Faeces.

The Iberian pig is a native breed of the Iberian Peninsula, which holds an international reputation due to the superior quality and the added value of its products. Different rearing practices and feeding regimes are regulated, resulting in different labelling schemes. However, there is no official analytical methodology that is standardised for certification purposes in the sector. Near Infrared Spectroscopy (NIRS) is a technology that provides information about the physicochemical composition of a sample, with several advantages that have enabled its implementation in different fields. Although it has already been successfully used for the analysis of Iberian pig's final products, samples evaluated with NIRS technology are characterised by a postmortem collection. The goal of this study was to evaluate the potential of NIRS analysis of faeces for in vivo discrimination of the Iberian pig feeding regime, using the spectral information per se for the development of modified partial least squares regressions. Faecal samples were used due to their easy collection, especially in extensive systems where pig handling is difficult. A total of 166 individual samples were collected from 12 farms, where the three different feeding regimes available in the sector were ensured. Although slight differences were detected depending on the chemometric approach, the best models obtained a classification success and a prediction accuracy of over 94% for feeding regime discrimination. The results are considered very satisfactory and suggest NIRS analysis of faeces as a promising approach for the in vivo discrimination of the Iberian pigs' diet, and its implementation during field inspections, a significative achievement for the sector.

Advancements in Genetic Enhancement: CRISPR/Cas-Mediated Genome Editing in Leguminous Crops

Legumes play a crucial role in human nutrition and sustainable agriculture due to their high protein content and health-promoting phytochemicals. To accelerate genetic gain in yield, stress resilience, and nutritional quality, extensive efforts are underway. Recent advancements in genomic resources have paved the way for the application of cutting-edge breeding technologies like genomic selection and genome editing in legume crops. This review focuses on the latest advancements in CRISPR/Cas9-based gene editing technology, specifically tailored for improving traits in legume crops. While successful gene-editing methods have been established for crops like soybean, cowpea, and chickpea, challenges remain, particularly in overcoming the recalcitrance of certain legumes to gene transfer and regeneration in vitro. Strategies to enhance transformation and regeneration rates through modifications in culture methods and DNA delivery are discussed. Despite the potential benefits of gene editing in legume breeding, regulatory barriers pose significant challenges. A comparison of regulatory environments in different regions sheds light on the importance of favourable regulations and public acceptance for realizing CRISPR's potential in enhancing global food security. Additionally, leguminous crops are vital for their nutritional properties, nitrogen-fixing abilities, and contribution to sustainable agriculture. Traditional breeding methods focused on increasing yield, while recent advancements in genome editing techniques, notably CRISPR-Cas technology, have revolutionized the improvement of agronomic traits in legumes. This chapter provides insights into the application of genome editing tools for enhancing traits such as stress tolerance, yield, and seed content in grain legumes. Furthermore, it discusses the challenges and prospects associated with enhancing grain legumes using molecular breeding techniques. Genome editing has been successfully employed in diverse legumes, including model species like Medicago and widely cultivated crops such as soybean and chickpea, offering exciting opportunities for enhancing agronomic characteristics.

Populations of Tuvan Shot-Fat-Tailed Sheep in the Structure of the Gene Pool of Sheep Breeds of the Russian Federation

Using 11 microsatellite markers (ОarCP49, INRA063, HSC, OarAE129, MAF214, OarFCB11, INRA005, SPS113, INRA23, MAF65, McM527), data were obtained on the levels of variability and degree of differentiation of 24 populations (1140 samples) of the Tuvan coarse-haired short-fat-tailed sheep of different regions of the Republic of Tyva and 24 breeds of sheep (721 samples) of various origins, covering the main sheep-breeding regions of the Russian Federation. During the analysis, a high level of genetic isolation and variability of Tuvan sheep was found, and in the general structure of Russian sheep breeds, a pronounced genetic divergence was revealed into two large groups, one of which unites fine-fleeced and semi-fine-fleeced sheep, and the other indigenous coarse-wooled breeds of North Caucasian and Asian origin

Integrating Multiple Database Resources to Elucidate the Gene Flow in Southeast Asian Pig Populations.

The domestic pig (Sus scrofa) and its subfamilies have experienced long-term and extensive gene flow, particularly in Southeast Asia. Here, we analyzed 236 pigs, focusing on Yunnan indigenous, European commercial, East Asian, and Southeast Asian breeds, using the Pig Genomics Reference Panel (PGRP v1) of Pig Genotype-Tissue Expression (PigGTEx) to investigate gene flow and associated complex traits by integrating multiple database resources. In this study, we discovered evidence of admixtures from European pigs into the genome of Yunnan indigenous pigs. Additionally, we hypothesized that a potential conceptual gene flow route that may have contributed to the genetic composition of the Diannan small-ear pig is a gene exchange from the Vietnamese pig. Based on the most stringent gene introgression scan using the fd statistic, we identified three specific loci on chromosome 8, ranging from 51.65 to 52.45 Mb, which exhibited strong signatures of selection and harbored the NAF1, NPY1R, and NPY5R genes. These genes are associated with complex traits, such as fat mass, immunity, and litter weight, in pigs, as supported by multiple bio-functionalization databases. We utilized multiple databases to explore the potential dynamics of genetic exchange in Southeast Asian pig populations and elucidated specific gene functionalities.

Genetic Characterization of Criolla and European Grapevines Recently Found in Chile: A Key Step for Their Rescue and Conservation

Genetic erosion of grapevine is becoming a serious worldwide problem and preserving its germplasm is an urgent task. Chile is not an exception to this scenario, where diverse factors led by the replacement of traditional varieties by renown cultivars have reduced the vineyard diversity. Therefore, discovering and characterizing minor varieties were the main objectives of this study. In addition to the official catalogue of around 100 grapevine varieties used to produce wine, we present here 89 genotypes not previously described as present in Chile, widely dispersed in the main wine valleys, which were retrieved from vineyards, small collections, and city gardens. Strikingly, we found 49 grapevines with allele patterns not described before. Ten of these may be old European varieties; the other 39 have allele patterns similar to Criolla varieties (e.g., descendants from the crossing of European varieties born in America). A parentage analysis performed with 15 SSR markers in these 39 N.N. samples revealed that most of them are descendants of the so-called foundational varieties Listán Prieto and Muscat of Alexandria, plus others in lower proportion such as Mollar Cano and Muscat à petit grains blancs, as well as known Criollas varieties such as Italiona and Moscatel Rosado. The 89 genotypes not described in Chile structured in three distinguishable groups: Criolla varieties, Central European varieties, and a third group enriched in Iberic varieties. The prevalence of each Criolla accession was quite variable, some corresponding to a single or a few vines found at a single place, while others were spread in several vineyards, even in different valleys, suggesting they were positively selected and propagated at some time. All the new Criolla varieties were different than the recently described Criollas found in Argentina. The discovery, rescue, and documentation of this rich heritage of Vitis vinifera L. genotypes found in Chile is the first step of a long-term work that should be continued with the evaluation of their enological characteristics, yield, and optimal management systems, aiming for the diversification of the local wine industry.

Proximate composition, micronutrient and dietary fiber analysis of ten traditional rice varieties of Wayanad District

Proximate composition, micronutrient and dietary fiber analysis of ten traditional rice varieties of Wayanad District

Local Management in the Varietal Diversity of Rainfed Rice (Oryza glaberrima) from Goh-Djiboua and Mountains Districts in Côte d’Ivoire

The awareness of farming practices regarding the varietal diversity management of cultivated crops is essential for setting up an in-situ preservation strategy. The objective of the current work was to probe the varietal diversity status of the rainfed rice and its management design in farming conditions. The study was implemented from Goh-Djiboua and Mountain Districts as significant locations for rainfed rice production in Côte d’Ivoire, through descriptive investigation at field led from 450 local farmers of traditional rainfed rice varieties. Data on the anthropological, production, and post-harvest preservation of the traditional rice varieties were collected. The investigation evidenced the rice production as a gender activity accounting 58.5% men against 41.5% women. The most produced traditional rice varieties are spelled Danané (20.22%) and Danané fowl (17.80%). The rice seeds mainly result from self-production by the farmers investigated (91.3%), especially deriving from traditional varieties (96.6%). The cultivated lands are below 1 ha acreage for most farmers (63.1%) and are worked for auto-consumption needs (99.8%). Besides the survey exhibited four storage structures, most significant of which are the granaries (79.4%). Further attempts focusing nutritional and technological advantages of the traditional rice varieties could enhance their spreading in local culture of rainfed rice.

Gene-deficient mouse model established by CRISPR/Cas9 system reveals 15 reproductive organ-enriched genes dispensable for male fertility.

Since the advent of gene-targeting technology in embryonic stem cells, mice have become a primary model organism for investigating human gene function due to the striking genomic similarities between the two species. With the introduction of the CRISPR/Cas9 system for genome editing in mice, the pace of loss-of-function analysis has accelerated significantly. This has led to the identification of numerous genes that play crucial roles in male reproductive processes, including meiosis, chromatin condensation, flagellum formation in the testis, sperm maturation in the epididymis, and fertilization in the oviduct. Despite the advancements, the functions of many genes, particularly those enriched in male reproductive tissues, remain largely unknown. In our study, we focused on 15 genes and generated 13 gene-deficient mice [4933411K16Rik, Adam triple (Adam20, Adam25, and Adam39), BC048671, Cfap68, Gm4846, Gm4984, Gm13570, Nt5c1b, Ppp1r42, Saxo4, Sh3d21, Spz1, and Tektl1] to elucidate their roles in male fertility. Surprisingly, all 13 gene-deficient mice exhibited normal fertility in natural breeding experiments, indicating that these genes are not essential for male fertility. These findings have important implications as they may help prevent other research laboratories from duplicating efforts to generate knockout mice for genes that do not demonstrate an apparent phenotype related to male fertility. By shedding light on the dispensability of these genes, our study contributes to a more efficient allocation of research resources in the exploration of male reproductive biology.

Validation of the Indigenous Technical Knowledge of Cattle Pastoralists of Andhra Pradesh and Telangana, India

Indigenous technical knowledge (ITK) of livestock breeding is often tacit and not necessarily expressed in conventional forms of scientific research and documentation. Indigenous livestock breeding systems rely mostly on qualitative traits than pure quantitative qualities. Qualitative traits are difficult to measure and most of the indigenous knowledge systems are in forms of qualitative traits. The lack of documentation and predominant qualitative nature makes it difficult to validate the ITK related to livestock breeding. In this context a study was conducted to examine the traditional breeding practices associated with two heritage cattle breeds of the Deccan Plateau region of India. The study examines the criteria used for selection of the breeding bulls of the indigenous Poda Thurpu and Nallmala-Pasa/Kamma, cattle breeds native to the study area. Results of the study identifies fourteen traits specific to breeding bulls and four traits that are generic to the breeding stock/cows. These traits/characteristics are ‘deemed desirable’ by the local cattle breeders for the ‘heritage breeds’, believed to have been bred and managed by them for generations. Observations of the present study supports the notion that traditional breeders of heritage breeds lay more emphasis on qualitative traits (ability to warding-off predators, fending off-springs, coat colour and texture, gait of the animal, temperament, and response and obedience to instructions of the master) than quantitative traits. It was found that local breeders give significant importance to the fertility of bovine bulls than cows. Breeding bulls are meticulously chosen with extreme caution and care, following a very long and meticulous selection process that could last for four years. Traditionally local cattle breeders of the study follow open nucleus breeding system for breeding and are strictly against promotion of inbreeding among their cattle herds. Only men are involved in cattle breeding in the study area and women usually stay away.

Reproductive characteristics of ethiopian indigenous sheep breeds in different production and management settings as inputs for selective breeding schemes: a review

Reproductive characteristics of ethiopian indigenous sheep breeds in different production and management settings as inputs for selective breeding schemes: a review

Identification of Differentially Expressed Genes and microRNAs in the Gray and White Feather Follicles of Shitou Geese.

The Shitou goose, a highly recognized indigenous breed with gray plumage originating from Chaozhou Raoping in Guangdong Province, China, is renowned for being the largest goose species in the country. Notably, during the pure breeding process of Shitou geese, approximately 2% of the offspring in each generation unexpectedly exhibited white plumage. To better understand the mechanisms underlying white plumage color formation in Shitou geese, we conducted a comparative transcriptome analysis between white and gray feather follicles, aiming to identify key genes and microRNAs that potentially regulate white plumage coloration in this unique goose breed. Our results revealed a number of pigmentation genes, encompassing TYR, TYRP1, EDNRB2, MLANA, SOX10, SLC45A2, GPR143, TRPM1, OCA2, ASIP, KIT, and SLC24A5, which were significantly down-regulated in the white feather follicles of Shitou geese. Among these genes, EDNRB2 and KIT emerged as the most promising candidate genes for white plumage coloration in Shitou geese. Additionally, our analysis also uncovered 46 differentially expressed miRNAs. Of these, miR-144-y may play crucial roles in the regulation of feather pigmentation. Furthermore, the expression of novel-m0086-5p, miR-489-y, miR-223-x, miR-7565-z, and miR-3535-z exhibits a significant negative correlation with the expression of pigmentation genes including TYRP1, EDNRB2, MLANA, SOX10, TRPM1, and KIT, suggesting these miRNAs may indirectly regulate the expression of these genes, thereby influencing feather color. Our findings provide valuable insights into the genetic mechanisms underlying white plumage coloration in Shitou geese and contribute to the broader understanding of avian genetics and coloration research.

Recent Advances in Understanding and Controlling Fusarium Diseases of Alliums

Allium species are known for their culinary, medicinal, and ornamental purposes. Fusarium basal rot is one of the most damaging soilborne fungal diseases of Allium species and poses a significant threat to yield, quality, and storage life worldwide. Various species of Fusarium have been identified as causal agents for Fusarium basal rot, depending on the Allium species involved. Diverse disease management practices have been implemented to mitigate the impact of Fusarium basal rot. This review article provides a comprehensive overview of the recent progress in detecting different species of Fusarium involved in Fusarium basal rot and strategies to control them in affected Allium species involving chemical, biological, and cultural methods. It covers the latest advancements in host plant resistance research from traditional breeding to modern molecular techniques and studying secondary metabolites involved in defense mechanisms against Fusarium basal rot.

Weak purifying selection in allelic diversity of the ADSL gene in indigenous and local chicken breeds and red junglefowl in Thailand

High levels of purine and uric acid, which are associated with health issues such as gout and cardiovascular disease, are found in the meat of fast-growing broiler chickens, which raises concerns about the quality of chicken meat and the health of the consumers who consume it. High genetic homogeneity and uniformity, particularly in genes involved in the synthesis of inosine monophosphate (IMP) and subsequent process of purine synthesis, which are associated with the meat quality, are exhibited in commercial broiler chickens owing to intensive inbreeding programs. Adenosine succinate lyase (ADSL) is a key enzyme involved in de novo purine biosynthetic pathway and its genetic polymorphisms affect IMP metabolism and purine content. In this study, we investigated the polymorphism of the ADSL gene in indigenous and local chicken breeds and red junglefowl in Thailand, using metabarcoding and genetic diversity analyses. Five alleles with 73 single nucleotide polymorphisms in exon 2, including missense and silent mutations, which may act on the synthesis efficiency of IMP and purine. Their protein structures revealed changes in amino acid composition that may affect ADSL enzyme activity. Weak purifying selection in these ADSL alleles was observed in the chicken population studied, implying that the variants have minor fitness impacts and a greater probability of fixation of beneficial mutations than strong purifying selection. A potential selective sweep was observed in Mae Hong Son chickens, whose purine content was lower than that in other breeds. This suggests a potential correlation between variations of the ADSL gene and reduced purine content and an impact of ADSL expression on the quality of chicken meat. However, further studies are required to validate its potential availability as a genetic marker for selecting useful traits that are beneficial to human health and well-being.