Landrace Research Articles

Deep Ancestral Introgressions between Ovine Species Shape Sheep Genomes via Argali-Mediated Gene Flow.

Previous studies revealed extensive genetic introgression between Ovis species, which affects genetic adaptation and morphological traits. However, the exact evolutionary scenarios underlying the hybridization between sheep and allopatric wild relatives remain unknown. To address this problem, we here integrate the reference genomes of several ovine and caprine species: domestic sheep, argali, bighorn sheep, snow sheep, and domestic goats. Additionally, we use 856 whole genomes representing 169 domestic sheep populations and their six wild relatives: Asiatic mouflon, urial, argali, snow sheep, thinhorn sheep, and bighorn sheep. We implement a comprehensive set of analyses to test introgression among these species. We infer that the argali lineage originated ∼3.08 to 3.35 Mya and hybridized with the ancestor of Pachyceriforms (e.g. bighorn sheep and snow sheep) at ∼1.56 Mya. Previous studies showed apparent introgression from North American Pachyceriforms into the Bashibai sheep, a Chinese native sheep breed, despite of their wide geographic separation. We show here that, in fact, the apparent introgression from the Pachyceriforms into Bashibai can be explained by the old introgression from Pachyceriforms into argali and subsequent recent introgression from argali into Bashibai. Our results illustrate the challenges of estimating complex introgression histories and provide an example of how indirect and direct introgression can be distinguished.

The Morlachs of Dalmatia: A Glimpse on Damages Caused by Morlach Shepherds in Rural Dalmatia during the 15th and 16th Centuries

The Morlachs of Dalmatia, as referred to in Venetian documents from the 15th-century onwards, were a heterogeneous and extremely mobile population of Vlach origin. Even if they were to be found also as merchants, soldiers, thieves, criminals, immigrants, etc., the principal occupation of the late medieval Dalmatian Morlachs remained the traditional sheep breeding. When analysing this latter aspect of Morlach life, we have to keep in mind that the lifestyle of the Morlach shepherds from Dalmatia was strongly connected with that of other Vlachs communities from the Balkans. Together with this, the Morlachs` commercial practices and the ubiquitous presence of Morlach sheep flocks in the agricultural space of the Dalmatian hinterlands in the 15th and 16th-century, contributes equally to the larger topic of the life in border areas. Against this background, this paper exams the crop damages caused by the Morlach shepherds in Dalmatia`s fields and vineyards. These damages reveal information about the legal status of Morlach shepherds in Dalmatian communes, about privileges, concessions, agreements, rental contracts, and also about diplomatic negotiations. Moreover, representative examples of crop damages will be used to study the relation and (partially) cross-cultural interaction of Morlachs shepherds with the great regional powers, particularly Venice’s reaction to the disruptive Morlachs and its consequences at the diplomatic level with the authorities of the Ottoman Empire.

Assessment and characterization of agro-morphological characteristics of rice land races in Nepal

Assessment and characterization of agro-morphological characteristics of rice land races in Nepal

Fecundity Booroola Gene (FecB) Polymorphism in some Indigenous Sheep Breeds in Iraq

Fecundity Booroola Gene (FecB) Polymorphism in some Indigenous Sheep Breeds in Iraq

Mitochondrial Genomes of Korean Native Black Goats Reveal Shared Phylogeographic Patterns and Demographic History.

This study explores the phylogeny of Korean native black goats through analysis of their complete mitochondrial DNA. The National Institute of Animal Science has gathered genetic material on purebred goats from isolated regions such as Tongyeong, Dangjin, and Jangsu, and is actively breeding them on a national level. These populations, however, are small and exhibit high inbreeding rates, highlighting the urgent need to preserve genetic diversity. The haplotype diversity within this native group is 0.659, with 39 haplotypes identified. By contrast, including international breeds in the analysis increases the overall haplotype diversity to 0.925 with 203 haplotypes identified, highlighting the limited genetic diversity among native black goats. For phylogenetic assessment, a neighbor-joining tree and median-joining network were constructed using identified haplogroups (A, B, C, D, G, and F) from prior studies. The results pinpoint the native black goats as closely related to, but distinct from, Haplogroup A with a bootstrap value of 98, establishing them as a separate clade (A'). This supports the notion of a shared ancestry with various global populations. This research provides essential data on the origins and evolutionary history of Korean native black goats, supporting conservation and breeding efforts aimed at enhancing genetic diversity.

Study of Pollen Traits, Production, and Artificial Pollination Methods in Zea mays L.

The optimization of artificial pollination is crucial in breeding programs for allogamous plants. In maize, achieving a balance between the labor-intensive nature of controlled pollinations and the need for large-scale production of hybrid seeds, along with considerations of germinability and pollen production, determines the success of genetic improvement programs. Breeding programs in maize have resulted in a reduction in the number of tassel branches to increase light interception and plant density in production fields. However, despite this genetic improvement, the decreased pollen production per plant has raised critical concerns regarding pollination and subsequent ear filling, especially under adverse environmental conditions. The aim of this work was the analysis of factors that can contribute to increasing the efficiency of controlled pollination in maize. The data obtained showed that pollen diameter, flavonoid, and phenolic acid content do not influence the percentage of germination and therefore the efficiency of pollination. The quantity of pollen is a central factor in ensuring the efficiency of controlled pollinations, and the data obtained by comparing traditional varieties with modern hybrids of maize showed that an increase in pollen production is determined by the increase in branching of the male inflorescence. Furthermore, we propose the use of a “smart” pollination method to make this step in maize breeding programs easier and faster.

Susceptibility of olive cultivars and selections to Colletotrichum species causing anthracnose in Spain.

Anthracnose, the most critical fruit disease affecting olive crops, necessitates the evaluation of the susceptibility of traditional and new varieties. In Spain and Portugal, Anthracnose is caused by several Colletotrichum species, with C. godetiae and C. nymphaeae being dominant and C. acutatum and C. fioriniae being secondary. This study explores the susceptibility of fruits from an F1 progeny resulting from a cross between 'Picual' (resistant) and 'Arbequina' (moderately susceptible) cultivars to C. godetiae. While most genotypes showed resistance levels comparable to their parents, seven showed a 50% reduction in disease severity compared to 'Picual.' The normal distribution of genotypes' response to the pathogen suggests a complex resistance mechanism. Furthermore, we assessed the susceptibility of four traditional cultivars, two new cultivars ('Sikitita-2' and 'Martina'), and five advanced selections (pre-commercial genotypes) to C. godetiae and C. nymphaeae. Despite the significant interaction between the olive genotype and Colletotrichum species in this experiment, the new cultivars and advanced selections were classified as susceptible or moderately susceptible against both species. A subsequent analysis of the interaction between 'Picual' (resistant) and 'Hojiblanca' (susceptible) fruits with the four mentioned Colletotrichum species revealed significant differences among cultivars but no interaction between genotype and pathogen species. Colletotrichum species were categorized as follows: i) C. godetiae and C. nymphaeae as highly virulent, ii) C. acutatum as moderately virulent, and iii) C. fioriniae as weakly virulent. Finally, C. nymphaeae exhibited an enhanced ability to infect and develop acervuli in olive leaves, potentially serving as an inoculum source for this species. The absence of a correlation between leaf and fruit susceptibilities to the pathogen suggests differences in resistance mechanisms. In conclusion, this study provides valuable insights into the complex interactions between olive genotype and Colletotrichum species, essential for cultivar selection and understanding the disease cycle.

Guadeloupe and Haiti's coffee genetic resources reflect the crop's regional and global history

Societal Impact StatementDespite strong historical declines, Guadeloupe and Haiti's coffee sectors remain important to rural communities' livelihood and resilience. Coffee also holds value as part of the islands' historical legacy and cultural identities. Furthermore, it is often grown in agroforestry systems providing important ecosystem services, which will become more important as these vulnerable islands work to adapt to a changing climate. Current efforts to revitalize coffee farms and target strategically important specialty markets would benefit from understanding existing genetic resources and the historical factors that shaped them. Our study reveals the rich history reflected in current coffee stands on the islands.Summary The West Indies, particularly former French colonies like Haiti and Guadeloupe, were central to the spread of coffee in the Americas. The histories of these Islands are shared until the 19th century, where they diverged significantly. Still, both Islands experienced a strong decline in their coffee sector. Characterizing the genetic and varietal diversity of their coffee resources and understanding historical factors shaping them can help support revitalization efforts. To that end, we performed Kompetitve Allele‐Specific PCR (KASP) genotyping of 80 informative single nucleotide polymorphism (SNP) markers on field samples from across main coffee‐growing region of Guadeloupe, and two historically important ones in Haiti, as well as 146 reference accessions from international collections. We also compared bioclimatic variables from sampled geographic areas and searched for historical determinants of present coffee resources. At least five Coffea arabica varietal groups were found in Haiti, versus two in Guadeloupe, with admixed individuals in both. The traditional Typica variety is still present in both islands, growing across a variety of climatic environments. We also found Coffea canephora on both islands, with multiple likely origins, and identified C. liberica var. liberica in Guadeloupe. These differences are explained by the Islands' respective histories. Overall, Guadeloupe experienced fewer, but older introductions of non‐Typica coffee. By contrast, several recent introductions have taken place in Haiti, driven by local and global factors and reflecting the history of Arabica varietal development and spread. Diversity on these islands is dynamic, and our results reveal opportunities and limits to the future of Guadeloupean and Haitian coffee.

Estimation of genetic components and assessing heterosis association with molecular markers in half diallel derived rice hybrids developed with landraces of NE India

Combining ability and heterosis were estimated in 45 rice hybrids generated by mating 10 parents, comprising both land races and advance breeding lines, in half diallel fashion. Hayman’s graphical analysis showed that all the twelve morphological traits studied had significant positive dominance variance. Narrow sense heritability was high for Days to fifty percentage flowering, Plant height, Panicle length and Test weight (> 30 %), and low for Grain yield per plant. According to the VrWr graph, traits like GYPP, PL, PH, TN and plot yield showed partial dominance, whereas traits like Blast disease index showed overdominance. A significant improvement over check was observed for heterosis and the crosses Mynri x CAUS103, Joha x CAUS107, CAUS 126 x CAUS107 and CAUS103 x CP, exhibited significantly positive standard heterosis for GYPP (>80 %) and PY (>100 %). Genetic distance based on fourteen markers revealed significant positive association with mid parent and better parent heterosis for Spikelet’s per plant, Filled grains per plant, Harvest index, Grain yield per plant, Panicle number and Plot yield. Therefore, it is evident that crosses with larger genetic distance between the parents gave hybrids with higher heterosis. Keywords: Landraces, Hayman’s graphical analysis, Heterosis, Genetic distance

Comparative histological and ultrastructural studies of thymus of indigenous and cross-bred broiler breeds of poultry of India

The present study was aimed to compare structure of thymus between the two poultry breeds, namely, Kadaknath and Narmada Nidhi. The aim was to understand the anatomical differences which could provide insights into how different breeds respond to diseases. The study involved histomorphological analysis of thymus tissue samples from 72 chicks (36 from each breed) that were divided into 6 groups with 6 birds in each group. The study results revealed that both poultry breeds exhibited similarities in the histology and ultrastructure of the thymus. This similarity is likely due to the Narmada Nidhi breed having a 25% genetic contribution from the Kadaknath breed.

Analysis of genetic diversity and genetic structure of indigenous chicken populations in Guizhou province based on genome-wide single nucleotide polymorphism markers

Guizhou province in China is rich in indigenous chicken breeds, playing an essential role in the genetic improvement of modern chickens. Genetic diversity has decreased in recent decades due to accelerated breeding processes and changing conservation priorities. To determine the genetic diversity and population structure of Guizhou indigenous chicken breeds, we used 55K genotyping arrays to conduct population genetic analysis on 233 individuals from 8 Guizhou indigenous breeds and 263 individuals from 9 Guizhou indigenous chicken populations. We evaluated the genetic diversity parameter (heterozygosity, proportion of polymorphic markers, and nucleotide diversity), linkage disequilibrium (LD), population structure, and genetic differentiation (FST and genetics distance). Genetic diversity results indicated that the genetic diversity of chicken breeds in Guizhou province is relatively affluent. Among Guizhou breeds, Baiyi black-bone and Guizhou yellow chicken displayed the lowest genetic diversity, as the 2 breeds exhibit lower PN and heterozygosity, the extent of linkage disequilibrium is higher. According to the LD pattern, Guizhou indigenous breeds can be divided into 3 categories. Population structure analysis showed a certain degree of genetic differentiation among local chickens in Guizhou. We argue that Chishui black-bone and Puan black-bone chickens are 2 different geographical regional groups of the same breed. In principal component analysis, individuals from the 2 groups clustered together, and the phylogenetic tree results showed that the 2 groups clustered together to form a branch independent of other breeds, and they displayed an identical pattern of ancestral lineage composition. The research results will provide a reference for protecting local chicken genetic resources in Guizhou Province and promote the protection and utilization of genetic resources.

Runs of Homozygosity Decipher Genetic Diversity in Cattle Breed Dwelling in the Colder Regions of the World

Background: Our study focuses on Yakutian cattle, a Siberian native breed, examining its inbreeding and diversity through genome-wide analysis of runs of homozygosity (ROHs). Yakutian cattle are adapted to Siberia’s harsh sub-arctic conditions, enduring temperatures below −70°C. However, the population genetics studies on this breed are scanty, to document the genetic uniqueness in these cattle. Results: We analyzed 40 Yakutian cattle with strict quality control for ROH detection yielding 683 homozygous segments, averaging 17 per individual with an average length of 9 Mb. ROH regions were found to be involved in important pathways pertaining to cold adaptation. Autozygosity ranged from 1% to 12% of the genome, with a relatively low average inbreeding coefficient (FROH) of 0.057, as compared to other breeds. Also, the different diversity indicators, namely, principal component analysis, heterozygosity, and effective population size analysis, revealed the prevalence of genetic diversity within the breed. Conclusion: Our findings on ROH are the first of its kind in Yakutian cattle that support their adaptability to colder environments, as evidenced by low inbreeding and high genetic diversity.

Sex-Specific Perching: Monitoring of Artificial Plants Reveals Dynamic Female-Biased Perching Behavior in the Black Soldier Fly, Hermetia illucens (Diptera: Stratiomyidae).

Artificial perches are implemented by many companies that mass-rear the black soldier fly (BSF), to emulate a natural breeding environment or provide additional surface area for flies to rest; however, basic information about perching behavior is lacking. This experiment tested the effect of adding 0.00, 0.04, 0.26, or 0.34 m2 of surface area to 0.93 m3 cages, each supplied with 90 male and 90 female adults. Female thoraxes marked with acrylic paint, and the number of perching flies of each sex were recorded over 6 d. A time-series analysis revealed the following: (a) females utilized perches 1.42 times more often than males across two trials; (b) especially in the morning where the difference could be as high as 2.56 times as great; (c) this decreased to 0.20-1.57 times more females than males by 1600 h; and (d) this cyclical pattern repeated each day throughout the week with a decreasing female-bias, starting from 2.41-times more females on day 1, which fell to 0.88-1.98-times more females than males on day 6. These dynamics are likely due to the presence of male flies engaging in aerial contests near ultraviolet lamps required for mating, especially during the early hours and early adulthood, aligning with and expanding prior knowledge of black soldier fly mating behavior.

Ovum Pick-Up and Ovaries Characterization of Black Bengal Goat from Slaughterhouse

Black Bengal goat is the only indigenous breed in Bangladesh. These are small-sized goats renowned for their high-quality meat, skin, and adaptability to adverse environmental conditions. To conserve the originality of this species, it is mandatory to develop an effective methodology for their germ cells to be harvested after death. Therefore, the study was conducted to assess the ovarian status and evaluate the most suitable method of ovum pick-up as well as the characterization of ovum from slaughterhouse specimens. A total of 182 ovaries were collected from local slaughterhouses from June 2022 to July 2023 and grossly examined to assess their status. Two methods were used to retrieve oocytes from the ovaries: aspiration and slicing. The grading of the ovum was done based on the germ layer present surrounding the oocytes. From 182 ovaries, the rates of corpus luteum (CL), tumor, and cyst were found to be 14.29%, 6.59%, and 27.47%, respectively. In the aspiration method, the significantly highest percentage of recovery rate (38.89%) and grade A oocytes (51.06%) were found within 1–3 hours of slaughtering. In the slicing method, the significantly highest percentage of recovery rate (19.57%) and grade A (60.61%) oocytes were found within 1–3 hours of slaughtering. The recovery rate was significantly higher (34.1%) in the aspiration method than in the slicing method (17.1%). There was no significant relationship in oocyte quality between the two methods. The recovery rate was not significantly dependent on the presence of CL. In conclusion, the findings from this study may be useful for assessing the quality of oocytes to preserve the germ cells and utilize them for in vitro fertilization for conserving Black Bengal goat.

Predicting Livestock Farmers’ Attitudes towards Improved Sheep Breeds in Ahar City through Data Mining Methods

Sheep breeding is one of the most important economic activities in Ahar City, Iran. However, due to traditional production techniques, livestock farmers face the problem of low productivity. To address this issue, traditional breeds can be replaced with improved and high-yielding ones; in the first stage, this requires the acceptance of these new sheep breeds by the region’s ranchers. This research aimed to evaluate the attitudes of the livestock breeders of Ahar City towards the improved breeds of sheep and the influential factors. We collected data through in-person interviews using a simple random sampling method, surveying 100 sheep breeders in Ahar. The breeders were categorized into three groups based on their attitudes towards improved breeds: negative, indifferent, and positive. Next, we employed data mining-based methods, including multilayer perceptron neural networks, random forest, and random tree algorithms. These helped identify essential variables affecting ranchers’ attitudes. The results showed that several factors contribute to the ranchers’ philosophy, with the number of sheep sold in the past year and the total sheep ownership being the most significant ones. Comparing statistical evaluation criteria, we found that the random tree algorithm outperformed other methods in predicting and classifying livestock farmers, achieving a prediction accuracy rate of 86% for a sample of 100 farmers. Based on our findings, promoting training courses and raising awareness about the benefits of breeding new sheep breeds, along with providing facilities and credits based on economic conditions, can foster a positive attitude among herders. Increasing the number of sheep owned and improving marketing strategies can further enhance this positive outlook.

Influence of age at slaughter and sex on carcass characteristics, meat quality, fatty acids, and ribonucleotides in white-tailed yellow native chickens.

This study investigated the effects of age and sex on carcass and meat characteristics of one of Thailand's major indigenous chicken breeds, the white-tailed yellow native chicken (NC). A total of 120 one-day-old NC (60 males and 60 females) were raised, and harvested at either 16, 20 or 24 weeks. The results showed that body, carcass, breast and fillet weights did not differ (P > 0.05) between 16- and 20-week-old NC, but were lower (P < 0.05) than those of 24-week-old NC. Male NC had higher (P < 0.05) body, carcass, wing, back and thigh weights than female NC. Neither sex nor age affected muscle pH, sarcomere length, redness and yellowness, guanosine monophosphate, and hypoxanthine. The interaction between age and sex was significant (P < 0.05) for %dressing, %leg, L*, C14:1, C18:1n9 and C20:4n6. Shear force was lower in 16-week-old NC (P < 0.05). The 24-week-old NC had lower (P < 0.05) C13:0, C16:0, C18:0, C18:2n6t, C20:4n6, C22:6n-3, intramuscular fat and inosine 5'-monophosphate levels and higher (P < 0.05) C18:2n6c, C18:3n-3 and C20:3n-6 levels than the 16- and 20-week-old NC. Male NC had higher (P < 0.05) C13:0-, C14:0-, C18:2n6t-, C20:3n-6- and lower inosine levels than female NC. In conclusion, these data highlight age- and sex-specific differences in carcass and meat quality of NC and provide relevant information to support consumer-oriented decisions on the production, processing and nutritional value of NC.

Chromosome-level genome assembly of Huai pig (Sus scrofa)

Although advances in long-read sequencing technology and genome assembly techniques have facilitated the study of genomes, little is known about the genomes of unique Chinese indigenous breeds, including the Huai pig. Huai pig is an ancient domestic pig breed and is well-documented for its redder meat color and high forage tolerance compared to European domestic pigs. In the present study, we sequenced and assembled the Huai pig genome using PacBio, Hi-C, and Illumina sequencing technologies. The final highly contiguous chromosome-level Huai pig genome spans 2.53 Gb with a scaffold N50 of 138.92 Mb. The Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness score for the assembled genome was 95.33%. Remarkably, 23,389 protein-coding genes were annotated in the Huai-pig genome, along with 45.87% repetitive sequences. Overall, this study provided new foundational resources for future genetic research on Chinese domestic pigs.

Quality and Processability of Meat in Polish Native Pigs – A Review

Abstract The primary aim of pig breeding efforts is to produce animals characterized by outstanding performance, including also fattening and slaughter performance traits. However, improved carcass leanness and reduced carcass fatness, especially intramuscular fat content, have led to a deterioration of pork quality and processability. Due to the growing frequency of meat defects and the limited potential use of such meat in the production of premium products this constitutes a considerable problem for the meat industry. The breeds superior in terms of meat quality are native pig breeds, such as those kept in Poland, i.e. Pulawska (Pul), Zlotnicka Spotted (ZS) and Zlotnicka White (ZW) pigs. The aim of this paper is to present a review of research results concerning quality and processability of meat produced by the Polish native pig breeds. The presented results indicate that pigs of local breeds exhibit a low level of performance traits (daily gain, carcass leanness, backfat thickness) while maintaining very good parameters of meat quality and processability (muscle composition and physical properties, fatty acids profile, sensory traits). Thus, they are used as a source material for premium products. In view of the small size of local populations and higher production costs in Poland it is a niche production. Therefore, the current aim of breeding indigenous breeds is both to maintain a safe population size and genetic diversity and to increase popularity of their meat and processed meat products among consumers. This objective is attained, among other things, thanks to efforts to reduce cost of their production through optimization of environmental conditions and wider use of less expensive traditional feed formulations, which make it possible to fully utilize the potential of local pork resources.

A Preliminary Study on Perception of Non – Vegetarian Consumers about Backyard Poultry Farming

The present study was conducted in District Ludhiana of Punjab state to know about perception of non-vegetarian consumers about backyard poultry farming. The study was conducted by personally interviewing randomly selected Urban (Group A, n=50) and Rural (Group B, n=50) non vegetarian consumers. None of the respondent was above 60 years. Most of the non vegetarian consumers were having education level of graduation. Majority of the respondents were consuming non vegetarian food 1-2 times per week. Most of the Group A consumers were purchasing non vegetarian products from local market, while Group B consumers were purchasing it from farmers. Most of the Group A consumers has no knowledge about breeds of backyard poultry. A large chunk of consumers belonging to both Group A and Group B did not know about differences between exotic and indigenous breed. The present study highlighted the importance of strengthening of extension activities related with backyard poultry and strengthening of marketing linkages of backyard poultry farmers to the urban consumers. Fast-tracking the supply of a backyard poultry farmer’s produce to a city dweller’s doorstep ensures fresher, higher-quality food by reducing transit time, which helps to minimize spoilage and waste. It also expands market access for farmers, increases convenience for consumers, supports local economies, and can lower environmental impact by reducing transportation distances. Overall, it enhances food security and fosters a more efficient food system.

Influence of Management Systems on Severity of Heat Stress and Reproductive Performance of Rams in the Tropics – A Review

Abstract Sheep are an important source of protein for humans, and recent decades have seen a significant increase in the production of sheep-based products, thus indicating an increase in demand for this commodity. At a time when this sector is growing, sheep are exposed to various challenges. These include climate change, which can cause heat stress in sheep, including rams, which later negatively affects their growth and reproductive performance. Exposure to heat stress results in physiological and reproductive behaviour responses in rams, which could also be used to visually identify the effect of heat stress as it will affect the productivity of livestock. In addition, the year-round hot and humid climate of the tropics is expected to contribute to a higher probability of heat stress occurrences in rams reared in developing countries around the equator. Nevertheless, the adaptability of rams to heat stress varies according to their origin, whereby native breeds tend to adapt better. Despite that, native breeds still can be affected by adverse environmental conditions and rely on thermoregulation mechanisms to mitigate heat stress. This results in numerous negative physiological changes, such as sweating and increased heart rate. This review highlights the effects of heat stress on the physiology, reproductive behaviour and reproductive performance of male sheep. The review also discusses the impact of management systems on heat stress in rams, which affects sheep productivity.