Breeding Farms Research Articles

The first report of triple anthelmintic resistance on a French Thoroughbred stud farm

This study assessed the anthelmintic resistance in strongylid nematodes against commonly used anthelmintic (AH) drugs in a French galloping racehorse stud farm from March to December 2023. Faecal egg count reduction tests (FECRTs) were conducted in three different groups of Thoroughbred yearlings (a group of 6 males, a group of 13 females and a group of 8 females and 3 males) following the new World Association for the Advancement of Veterinary Parasitology (WAAVP) guidelines. The efficacy of fenbendazole was tested in two groups once during the monitoring period (in March), the efficacy of ivermectin in 3 groups twice (in March–April and in November–December) and the efficacy of pyrantel in one group once (in May–June). For each FECRT, the 90% confidence interval of the percentage faecal egg count reduction was calculated using the hybrid Frequentist/Bayesian analysis method. The resistance in strongylids was observed to fenbendazole, pyrantel and ivermectin in all the groups in which these drugs were tested. The number of animals in each group was sufficient to reach ≥80% power for the resistance test. The results highlight the first case of triple AH resistance in strongylids in France. Further studies involving more farms and equids are required to assess the prevalence of AH resistance in France and refine recommendations for owners.

The Use of Interactive Visualizations for Tracking Haplotypic Inheritance in Livestock

Our objective was to harness the power of interactive visualizations by utilizing open-source tools to develop an efficient strategy for visualizing Single Nucleotide Polymorphism data within a livestock population, focusing on tracking the transmission of haplotypes. To achieve this, we simulated a realistic beef cattle population in order to obtain phased haplotypes and generate the necessary inputs for creating our visualizations. The visualization tool was built using Python and the Plotly library, which enables interactivity. We set out to explore three scenarios: trio comparison, visualization of grandparents, and half-sibling evaluation. These scenarios enabled us to trace the inheritance of genetic segments, identify crossover events, and uncover common regions within related and unrelated animals. The potential applications of this approach are significant, particularly for improving genomic selection in smaller breeding programs and farms, and it provides valuable insights for guiding more in-depth genomic region analysis. Beyond its practical applications, we believe this strategy can be a valuable educational tool, helping educators clarify complex concepts like Mendelian sampling and haplotypic diversity. Furthermore, we hope it will encourage livestock producers to adopt advanced technologies like genotyping and genomic selection, thereby contributing to the advancement of livestock genetics.

Acoustic detection of the effects of prolonged fasting on newly hatched broiler chickens

Water and food deprivation during the first few hours of life can act as a significant stressor for birds, as it can negatively affect their physical and immunological development. By providing essential nutrients, new enriched hydrated gels help alleviate the potential risks associated with prolonged fasting periods. Broiler chickens vocalisations are considered reliable indicators of changes in stress, anxiety and well-being. In this study, the results of recorded broiler vocalisations are presented together with a statistical analysis of the acoustic parameterisation. We focused on the hours preceding the transport of chicks from the hatchery to the breeding farm, dividing the animals into a control group that replicated real conditions, and a treatment group with the administration of a hydrated gel. The objectives of this study were to validate the effectiveness of continuous audio recording in monitoring stress level in food-deprived chicks, and to identify the most significant acoustic parameters. The selection of the acoustic parameters was based on a previous study conducted on broiler farms, which showed a strong linear relationship between the number of vocalisations, spectral centroid, and the bandwidth. Significant differences were observed between the first and last three hours. Furthermore, 8 h after gel ingestion, vocalisations indicated reduced stress levels.

Infl uence of feeding carbohydrate feed additives on the productivity of cows and the quality of milk

Many studies have proven that the genetic potential of animals is realized with proper feeding and this cannot be achieved without the use of biologically active feed additives. The purpose of the research was to use the additives Living Protein and Tanrem Sh with hepatoprotective properties in the rations of lactating cows in the fi rst 100 days of lactation. The scientifi c and farm experiment was carried out at the breeding farm of Razliv LLC in the Kurgan region on 30 mature lactating cows of Black-and-White breed. The experiment was carried out in 2022–2023. New generation additives Living Protein and Tanrem Sh combining nutritional and hepatoprotective properties help increase milk production in the fi rst 100 days of lactation. Feeding the additives to lactating cows at 500 g/head/day contributed to an increase in milk production in the experimental groups compared to the control group. Thus, in the fi rst 100 days of lactation the milk yield of natural fat milk in cows of the 1st experimental group exceeded that of their herdmates in the control group by 310,0 kg or 11,75 % and the milk yield of cows of the 2nd experimental group was higher than the control group by 342,5 kg or 12,98 %. In terms of 4 % milk, the milk yield of cows in the experimental groups receiving the test additives was higher by 375,2 kg and 428,0 kg, which exceeded the milk yield of cows in the control group by 14,38 and 16,40 %, respectively. The inclusion of feed additives in the ration also had a positive eff ect on the fat and protein content in the milk of cows in the experimental groups. Thus, in the 1st experimental group the advantage in the mass fraction of fat compared to the control group was 0,16 abs.%, and protein 0,04 abs.%, and in the 2nd experimental group the superiority was 0,21 and 0,08 abs.%, respectively. Milk indicators for the content of somatic cells and Quantity of Mesophilic Aerobic and Facultative Anaerobic Microorganisms have improved.

The state of horse breeding in the Stavropol Territory

The information on the current state of the horse population in the Russian Federation, its distribution by farm category over the past three years has been provided in the article. Between 2020 and 2022, the number of horses in agricultural organizations in Russia decreased by 21 thousand. On the contrary, in privet households there was an increase in the number of horses by 16 thousand heads, and in peasant (farm) farms by 13 thousand heads. The material on pedigree horse breeding in the Stavropol Territory has been also provided in the work. The founders of horse breeding in the region are the Stavropol and Terek stud farms, which were organized in 1921. On their basis a new promising breed of horses was established as Terek breed, which today is on the verge of extinction. It is bred only by private owners and then in small quantities. Targeted work is needed to preserve the gene pool and restore the population of this horse breed. Information is presented on existing stud farms and multiplication farms, which are located in the Stavropol region. Under the conditions of four stud farms, two multiplication farms located in 5 districts of the region. There the following breeds of horses are bred such as Akhal-Teke, Thoroughbred riding, Arabian and Karachay. The total number of breeding horses in the Stavropol Territory at the beginning of 2023 was 862 heads, including 302 mares and 36 stud stallions. Training and systematic testing of horses take place at the Pyatigorsk Racetrack. Horse racing takes place every Sunday from May to October. In general, the dynamics of the horse population in Russia indicates that horse breeding continues to be an important sector of the economy and can be an attractive area for investors and businessmen.

Evaluating the dynamics and efficacy of a live, attenuated Mycoplasma anserisalpingitidis vaccine candidate under farm conditions

ABSTRACT The aim of the present study was to monitor the dynamics and to measure the safety and efficacy of a live, attenuated, thermosensitive Mycoplasma anserisalpingitidis vaccine candidate, namely MA271, in geese breeder flocks under field conditions. Two rearing flocks were vaccinated with MA271 at 4 weeks of age and boosted at 24 weeks of age by cloaca inoculation (1 ml) and eye-dropping (60 µl). The geese then were transported to multi-aged breeding farms. Two breeding flocks served as controls. Colonization of the cloaca by MA271 showed 75% maximum prevalence between 4 and 6 weeks after the first vaccination. Then the prevalence decreased to 25% until the cooler, humid fall months which coincided with the booster vaccination. Boosting raised cloacal colonization to 100%. No clinical signs were observed in the vaccinated birds. After transportation to five multi-aged breeding farms, the wild-type strain appeared as well as MA271 in three flocks. In one flock, the wild-type strain completely displaced MA271, while in one flock only MA271 was detected. Only wild-type strains were detected in the control flocks; however, due to an HPAI outbreak, both flocks were exterminated before the end of the study. Based on the available data, the median percentage of infertile eggs was 3.7-5.1% in the MA271 vaccinated flocks, and 7.7% in the non-vaccinated flock. In conclusion, MA271 can colonize the cloaca of geese under field conditions. MA271 proved to be safe and presumably protects against M. anserisalpingitidis-induced reproduction losses.

Recent advances in reproductive research in Australia and New Zealand: highlights from the Annual Meeting of the Society for Reproductive Biology, 2022.

In 2022, the Society for Reproductive Biology came together in Christchurch New Zealand (NZ), for its first face-to-face meeting since the global COVID-19 pandemic. The meeting showcased recent advancements in reproductive research across a diverse range of themes relevant to human health and fertility, exotic species conservation, and agricultural breeding practices. Here, we highlight the key advances presented across the main themes of the meeting, including advances in addressing opportunities and challenges in reproductive health related to First Nations people in Australia and NZ; increasing conservation success of exotic species, including ethical management of invasive species; improvements in our understanding of developmental biology, specifically seminal fluid signalling, ovarian development and effects of environmental impacts such as endocrine-disrupting chemicals; and leveraging scientific breakthroughs in reproductive engineering to drive solutions for fertility, including in assisted reproductive technologies in humans and agricultural industries, and for regenerative medicine.

Utjecaj sezone parenja i stanja tijela na zootehničke parametre ouled djellal ovaca u polupustinjskim područjima

In this study, a database was created by monitoring 3000 Ouled Djellal ewes, belonging to ten breeding farms and representing two modes of reproduction management. The data collected make it possible to measure the reproductive performance of females and to determine the influence of non-genetic factors on different parameters. The Body Condition Score (BCS) was calculated to compare performance in relation with breeding conditions. The results showed that fertility and prolificacy accounted for 91.1±0.1% and 116.4±0.2% in the reproduction mode respectively based on one lambing/year with exclusive spring control, and of 53.5±0.2% and 101.2±0.1% respectively in the traditional lambing system spread overthe year (with the ram permanently present in the flock) (P<0.05). The BCS varied according to mating season and feeding system. Indeed, as the BCS at mating increased, fertility, prolificacy and productivity improved. Ewes whose BCS at mating was equal to or greater than 3 obtained the best performance, while those with a lower BCS were less fertile, less prolific, and less productive. The average productivity of Ouled Djellal sheep was 107.0±0.1%, and 54.8±0.3%, respectively, in the first and second mode of reproduction management (P<0.05). This study highlights the main sources of variations and their interactions.

Machine Learning Offers Insights into the Impact of In Vitro Drought Stress on Strawberry Cultivars

This study aimed to assess the susceptibility of three strawberry cultivars (“Festival”, “Fortuna”, and “Rubygem”) to drought stress induced by varying polyethylene glycol (PEG) concentrations in the culture medium. Plantlets were cultivated on a solid medium supplemented with 1 mg/L BAP, and PEG concentrations (0, 2, 4, and 6 mg/L) were introduced to simulate drought stress. Morphological changes were observed, and morphometric analysis was conducted. Additionally, artificial neural network (ANN) analysis and machine learning approaches were integrated into this study. The results showed significant effects of PEG concentrations on plant height and multiplication coefficients, highlighting genotype-specific responses. This study employed various machine learning models, with random forest consistently demonstrating superior performance. Our findings revealed the random forest model outperformed others with a remarkable global diagnostic accuracy of 91.164%, indicating its superior capability in detecting and predicting water stress effects in strawberries. Specifically, the RF model excelled in predicting root length and the number of roots for “Festival” and “Fortuna” cultivars, demonstrating its reliability across different genetic backgrounds. Meanwhile, for the “Rubygem” cultivar, the multi-layer perceptron (MLP) and Gaussian process (GP) models showed particular strengths in predicting proliferation and plant height, respectively. These findings highlight the potential of ML models, particularly RF, to enhance agricultural breeding and cultivation strategies through accurate phenotypic predictions, suggesting a promising direction for future research to improve these predictions further. This research contributes to understanding strawberry responses to drought stress and emphasizes the potential of machine learning in predicting plant characteristics.

DGS1 improves rice disease resistance by elevating pathogen-associated molecular pattern-triggered immunity.

The online version contains supplementary material available at 10.1007/s42994-024-00137-9.

Experience of breeding char (genus Salvelinus) under industrial fish harvedy farming conditions

Of undoubted interest is the introduction into the aquaculture of the region of such a species native to the basins of the Kara and Laptev seas as the Arctic char Salvelinus alpinus (L.). A number of biological features of this species give special relevance to the prospects of the char as an object of aquaculture. The purpose of the work is experimental research and experience in breeding Arctic char using the example of the freshwater form of char on the Taimyr Peninsula. Information provided. Objectives: to study the conditions of keeping, feeding and growth characteristics of freshwater char when kept in cages on the Yenisei River. The object of the study was the freshwater form of char of the Taimyr Peninsula of generations 2021–2022. The study was carried out at two sites of Maltat LLC (Balahtinsky district of the Krasnoyarsk Territory, fish breeding farm in the city of Divnogorsk near the dam of the Krasnoyarsk hydroelectric power station) and at the Department of Breeding, Genetics, Biology and Aquatic Bioresources of the Federal State Budgetary Educational Institution of Higher Education Krasnoyarsk State Agrarian University. Environmental conditions, growth characteristics, growth rate and waste (mortality) were determined. When growing, granulated feed produced by Coppens were used. It has been shown that the weight of fish during cage rearing is higher than that of loaches from their native range. The growth rate of fish is minimal in January (about 2%), maximum in June-July. Freshwater char during cage cultivation on artificial feeds in the lower reaches of the Krasnoyarsk hydroelectric power station shows high weight growth characteristics exceeding those of fish from native habitats. Thus, research has confirmed the feasibility of factory reproduction of freshwater char from reservoirs of the Taimyr Peninsula in cages on the Yenisei River.

Success of different therapies for bacterial endometritis in stud farm practice

Bacterial endometritis is a major problem in equine reproduction usually treated with antibiotics, however reports of success rates are scarce. This study collected data from mares diagnosed with intrauterine bacterial growth and compared the outcome of different therapies for bacterial endometritis in German stud farm practice. Data on mares with positive uterine culture results were collected retrospectively in veterinary practices (n = 5; 2018-2022). Information relating to 30 factors (mare, diagnostics, therapy, pregnancy rate) of bacterial endometritis cases (n = 772) were recorded and analyzed. Possible effects on treatment success (positive pregnancy result in the first cycle after treatment) were tested by binomial logistic regression. In most cases β-hemolytic streptococci were detected (n = 707). Treatments for the endometritis included trimethoprim-sulfonamides (n = 409), procaine-penicillin (n = 227), marbofloxacin (n = 53) or no antibiotics (n = 59) and most antibiotics were administered systemically (n = 711) rather than locally (n = 23). Uterine lavage was reported in 49 % of mares. Uterotonic drugs were administered in 42.2 % of mares. Breeding programs included artificial insemination (AI) with chilled semen (n = 667), AI with frozen semen (n = 169), transfer of fresh (n = 112) or cryopreserved (n = 27) embryos and natural cover (n = 27). In the first cycle after treatment, the pregnancy rate was 47 % and it rose to 69 % by end of the season. Treatment success was affected by duration of antibiotic treatment, veterinary practice, and presence of clinical signs. In conclusion, reported treatment practices in German stud farm practice resulted in acceptable pregnancy results and the multiple binomial logistic regression approach identified factors affecting the pregnancy outcome in this dataset.

State and prospects of external economic activity in Russian horse breeding in 2015–2023

The article examines the dynamics of export and import indicators of horse breeding products (in the category of goods “Live horses”) from 2015 to 2022, both in absolute and monetary terms, including taking into account the categories of breeding and use animals. For the first time, the foreign trade balance of the horse breeding industry in 2019–2022 has been analyzed, and the prospects for domestic and foreign markets for the products of Russian horse breeding farms have been assessed. It has been established that the export flows of the eastern regions of the country, and primarily the Trans-Baikal Territory, the Republic of Tyva, the Altai Territory and the Altai Republic, are focused primarily on the Republic of Kazakhstan, which makes commercial farms for the production of horses for meat production in the Siberian Federal District dependent on the political situation in Central Asia and the general state of veterinary well-being of the region. The ban on the export of horses classified as luxury goods from the European Union, introduced as part of a package of anti-Russian sanctions, affected the import of breeding and use animals, significantly limiting the opportunities for domestic consumers focused on trained horses. The state program for the development of horse breeding in the Republic of Uzbekistan may influence the increase in demand for products from enterprises involved in breeding riding horses.

Plant science in the age of simulation intelligence.

Historically, plant and crop sciences have been quantitative fields that intensively use measurements and modeling. Traditionally, researchers choose between two dominant modeling approaches: mechanistic plant growth models or data-driven, statistical methodologies. At the intersection of both paradigms, a novel approach referred to as "simulation intelligence", has emerged as a powerful tool for comprehending and controlling complex systems, including plants and crops. This work explores the transformative potential for the plant science community of the nine simulation intelligence motifs, from understanding molecular plant processes to optimizing greenhouse control. Many of these concepts, such as surrogate models and agent-based modeling, have gained prominence in plant and crop sciences. In contrast, some motifs, such as open-ended optimization or program synthesis, still need to be explored further. The motifs of simulation intelligence can potentially revolutionize breeding and precision farming towards more sustainable food production.

Polymorphism of serum blood proteins of herd horses (<i>Equus ferus caballus</i>) of the transbaikal breed

The results of a study of the genetic diversity of the Transbaikal horse breed based on the polymorphism of whey proteins TF, Es, and ALB in four herds of the Transbaikal region are presented. The Transbaikal horse belongs to the ancient aboriginal breeds and is most adapted to the local climatic conditions of dry, hot summers and frosty winters with little snow. It is unpretentious, hardy, and has a strong constitution. Research is aimed at preserving the breed’s genetic diversity by studying polymorphic variants of whey proteins, which are reliable genetic markers due to their codominant inheritance and comprehensive polymorphism. In the albumin locus, two alleles and three genotypes were identified. In the esterase locus, there are six alleles and 13 genotypes. In the transferrin locus - 7 alleles and 18 genotypes occur with different frequencies in the studied herds, which makes it possible to characterise their genotypic characteristics. Rarely encountered genotypes of the transferrin locus (less than 10 %) include eight genotypes: TFDD, TFDH, TFDI, TFDR, TFFI, TFFM, TFOR, TFR; esterase locus – 6 genotypes: EsGI, EsHH, EsHI, EsHO, EsII, EsGI. Based on the frequency of genotypes and alleles, homozygosity was calculated for each whey protein system and for the entire sample from the herd, the level of which ranges from 7.87 to 12.25 %. The overall homozygosity rate varies from 34.35 to 43.36 %, and the number of effective alleles (Na) in all herds is almost the same (2.30–2.91). Genetic variability ranges from 56.96–63.74 %. The index of gene similarity between herds is at the level of 0.8439–0.9058. The analysed herds form two subclusters: the first includes horses from the APC (Agricultural Production Cooperative) Livestock Breeding Farm named after. Kalinin and SPK “Rassvet”. In the second - animals from APC (Agricultural Production Cooperative) “Livestock Breeding Farm “Rodina” and AC (Agricultural Cooperative) “Taptanay”.

Genetic markers in sheep breeding

The priority direction in developing domestic sheep breeding is the creation of new and improved breeding forms that combine high meat and wool productivity rates with good adaptive qualities to breeding conditions. In Russia, 404.2 thousand heads of coarse-wool sheep breeds and 21.2 thousand heads of semi-coarse-wool sheep are concentrated on breeding farms. Compared to 2000, the number of breeding animals increased by 5.0 times, while the yield of lambs for slaughter per 100 breeding queens increased by 5.7 times. One way to increase the selection and breeding work with breeds is to search and use genetic markers of productivity and vitality. The work aimed to summarise and analyse information about the genetic polymorphism of genes associated with traits of productivity and disease resistance in different breeds of sheep. The results of studies of polymorphic variants of genes related to the growth energy of young animals, wool quality and meat productivity in sheep are presented. The calpastatin (CAST) gene is described, which is associated with meat productivity and tenderness of meat the KRT (keratins) gene - with wool productivity and wool quality, the growth hormone gene GH and the differential growth factor gene GDF9 - with the regulation of growth and development, reproductive qualities and meat production, sheep productivity. In most studies, the predominant genotype in all breeds is CASTMM. The frequency of genotypes for the KRT and GH genes in breeds of different directions of productivity varies significantly. The relationship of genotypes CAST, GН, and GDF9 with economically valuable traits is described, making it possible to consider their genetic markers.

Assessment of the selection structure of the kazakh white-headed cattle herd

In the breeding farm Kolos LLC in the Altai Territory, which is engaged in the breeding and selecting Kazakh white-headed cattle, bulls were assessed by their productivity, sires by the quality of their offspring, lines, breeding and production groups. It has been established that, regardless of which trait is taken as the base one, the bulls of the selection group exhibit highly productive qualities. Analysis of correlation coefficients allows us to note a strong connection between live weight and average daily gain, feed costs, assessment of meat qualities, relative gain, and the “A” index. A comparative evaluation of stud bulls based on the quality of their offspring indicates that the sons of Zaur 70099, Pankrat 6809, and Simons 6633 are improvers. When assessing the genealogical structure, the best indicators are shown by bulls belonging to the line of Castle 3335. When comparatively evaluating the strength of the influence of the line and the sire bull on the variability of traits, it was established that the stability of the impact of the sire bull is, as a rule, higher than the influence of the line and for the most critical traits it is more than two times. The highest power of the sire’s influence is noted for such characteristics as live weight, average daily gain, assessment of meat qualities, and complex index “A”. The population of the Kazakh white-headed breed has a high selection potential in assessing animal gene pool and phenol. Also, it has an optimal level of genetic variability of traits, expressed through the strength of the sire’s influence on the variability of traits.

Antibiotic action and resistance: updated review of mechanisms, spread, influencing factors, and alternative approaches for combating resistance.

Antibiotics represent a frequently employed therapeutic modality for the management of bacterial infections across diverse domains, including human health, agriculture, livestock breeding, and fish farming. The efficacy of antibiotics relies on four distinct mechanisms of action, which are discussed in detail in this review, along with accompanying diagrammatic illustrations. Despite their effectiveness, antibiotic resistance has emerged as a significant challenge to treating bacterial infections. Bacteria have developed defense mechanisms against antibiotics, rendering them ineffective. This review delves into the specific mechanisms that bacteria have developed to resist antibiotics, with the help of diagrammatic illustrations. Antibiotic resistance can spread among bacteria through various routes, resulting in previously susceptible bacteria becoming antibiotic-resistant. Multiple factors contribute to the worsening crisis of antibiotic resistance, including human misuse of antibiotics. This review also emphasizes alternative solutions proposed to mitigate the exacerbation of antibiotic resistance.

Environmental impact of Italian pig herds as affected by farm management factors

This study aimed at evaluating the environmental impact (EI) of herds representative of the Italian heavy pig production system to investigate the EI variation associated with farm management (FM), diet formulation (DF) and animal response (AR) variables. Data originated from 8 breeding farms, which included the sows and preweaning piglets (Site1) and the post-weaned piglets (7.5–30 kg body weight – BW, Site2) and 10 growing–fattening farms, dealing with 30–170 kg BW pigs (Site3). A cradle-to-farm gate Life Cycle Assessment was used, with 1 kg BW gain (BWG) as functional unit. Impact categories were global warming (GWP), acidification (AP) and eutrophication (EP) potentials and land occupation (LO). Whole-production cycle EI (Site123, 0–170 kg BW) was obtained summing up EIs of 0–30 and 30–170 kg BW animals. Impacts were analysed with one- or two-way PERMANOVA to test the effect of FM, DF and AR variables. The Site123-related EI averaged nearly 3.1 kg CO2-eq (GWP), 50 g SO2-eq (AP), 22 g PO4-eq (EP) and 4.9 m2/y (LO) per kg BWG. Site3 contributed nearly 80% of the whole impact. Regarding Site1, GWP resulted mitigated by increasing sow productivity. Site2 EI resulted mitigated by decreasing feed conversion ratio and increasing average daily gain, whereas Site3 EI by increasing feed self-sufficiency and decreasing dietary crude protein and mortality. In perspective, given the relevance of Site3 on the whole-pig system EI, a deeper integration between the farm agronomical management and the growing–finishing pigs’ diets formulation would support the environmental sustainability of heavy pig operations.

Natural and artificial selection of multiple alleles revealed through genomic analyses.

Genome-to-phenome research in agriculture aims to improve crops through in silico predictions. Genome-wide association study (GWAS) is potent in identifying genomic loci that underlie important traits. As a statistical method, increasing the sample quantity, data quality, or diversity of the GWAS dataset positively impacts GWAS power. For more precise breeding, concrete candidate genes with exact functional variants must be discovered. Many post-GWAS methods have been developed to narrow down the associated genomic regions and, ideally, to predict candidate genes and causative mutations (CMs). Historical natural selection and breeding-related artificial selection both act to change the frequencies of different alleles of genes that control phenotypes. With higher diversity and more extensive GWAS datasets, there is an increased chance of multiple alleles with independent CMs in a single causal gene. This can be caused by the presence of samples from geographically isolated regions that arose during natural or artificial selection. This simple fact is a complicating factor in GWAS-driven discoveries. Currently, none of the existing association methods address this issue and need to identify multiple alleles and, more specifically, the actual CMs. Therefore, we developed a tool that computes a score for a combination of variant positions in a single candidate gene and, based on the highest score, identifies the best number and combination of CMs. The tool is publicly available as a Python package on GitHub, and we further created a web-based Multiple Alleles discovery (MADis) tool that supports soybean and is hosted in SoyKB (https://soykb.org/SoybeanMADisTool/). We tested and validated the algorithm and presented the utilization of MADis in a pod pigmentation L1 gene case study with multiple CMs from natural or artificial selection. Finally, we identified a candidate gene for the pod color L2 locus and predicted the existence of multiple alleles that potentially cause loss of pod pigmentation. In this work, we show how a genomic analysis can be employed to explore the natural and artificial selection of multiple alleles and, thus, improve and accelerate crop breeding in agriculture.