Applications of Omics Technology for Livestock Selection and Improvement

Deciphering the molecular drivers for cashmere/pashmina fiber production in goats: a comprehensive review

Cashmere, also known as pashmina, is derived from the secondary hair follicles of Cashmere/Changthangi goats. Renowned as the world's most luxurious natural fiber, it holds significant economic value in the textile industry. This comprehensive review enhances our understanding of the complex biological processes governing cashmere/pashmina fiber development and quality, enabling advancements in selective breeding and fiber enhancement strategies. The review specifically examines the molecular determinants influencing fiber development, with an emphasis on keratins (KRTs) and keratin-associated proteins (KRTAPs). It also explores the roles of key molecular pathways, including Wnt, Notch, BMP, NF-kappa B, VEGF, cAMP, PI3K-Akt, ECM, cell adhesion, Hedgehog, MAPK, Ras, JAK-STAT, TGF-β, mTOR, melanogenesis, FoxO, Hippo, and Rap1 signaling. Understanding these intricate molecular cascades provides valuable insights into the mechanisms orchestrating hair follicle growth, further advancing the biology of this coveted natural fiber. Expanding multi-omics approaches will enhance breeding precision and deepen our understanding of molecular pathways influencing cashmere production. Future research should address critical gaps, such as the impact of environmental factors, epigenetic modifications, and functional studies of genetic variants. Collaboration among breeders, researchers, and policymakers is essential for translating genomic advancements into practical applications. Such efforts can promote sustainable practices, conserve biodiversity, and ensure the long-term viability of high-quality cashmere production. Aligning genetic insights with conservation strategies will support the sustainable growth of the cashmere industry while preserving its economic and ecological value.

Advancing genetic improvement in the omics era: status and priorities for United States aquaculture

BACKGROUND

The innovations of the "Omics Era" have ushered in significant advancements in genetic improvement of agriculturally important animal species through transforming genetics, genomics and breeding strategies. These advancements were often coordinated, in part, by support provided over 30 years through the 1993-2023 National Research Support Project 8 (NRSP8, National Animal Genome Research Program, NAGRP) and affiliate projects focused on enabling genomic discoveries in livestock, poultry, and aquaculture species. These significant and parallel advances demand strategic planning of future research priorities. This paper, as an output from the May 2023 Aquaculture Genomics, Genetics, and Breeding Workshop, provides an updated status of genomic resources for United States aquaculture species, highlighting major achievements and emerging priorities.

MAIN TEXT

Finfish and shellfish genome and omics resources enhance our understanding of genetic architecture and heritability of performance and production traits. The 2023 Workshop identified present aims for aquaculture genomics/omics research to build on this progress: (1) advancing reference genome assembly quality; (2) integrating multi-omics data to enhance analysis of production and performance traits; (3) developing resources for the collection and integration of phenomics data; (4) creating pathways for applying and integrating genomics information across animal industries; and (5) providing training, extension, and outreach to support the application of genome to phenome. Research focuses should emphasize phenomics data collection, artificial intelligence, identifying causative relationships between genotypes and phenotypes, establishing pathways to apply genomic information and tools across aquaculture industries, and an expansion of training programs for the next-generation workforce to facilitate integration of genomic sciences into aquaculture operations to enhance productivity, competitiveness, and sustainability.

CONCLUSION

This collective vision of applying genomics to aquaculture breeding with focus on the highlighted priorities is intended to facilitate the continued advancement of the United States aquaculture genomics, genetics and breeding research community and industries. Critical challenges ahead include the practical application of genomic tools and analytical frameworks beyond academic and research communities that require collaborative partnerships between academia, government, and industry. The scope of this review encompasses the use of omics tools and applications in the study of aquatic animals cultivated for human consumption in aquaculture settings throughout their life-cycle.

Climate Resilience in Farm Animals: Transcriptomics-Based Alterations in Differentially Expressed Genes and Stress Pathways

The livestock sector, essential for maintaining food supply and security, encounters numerous obstacles as a result of climate change. Rising global populations exacerbate competition for natural resources, affecting feed quality and availability, heightening livestock disease risks, increasing heat stress, and contributing to biodiversity loss. Although various management and dietary interventions exist to alleviate these impacts, they often offer only short-lived solutions. We must take a more comprehensive approach to understanding how animals adapt to and endure their environments. One such approach is quantifying transcriptomes under different environments, which can uncover underlying pathways essential for livestock adaptation. This review explores the progress and techniques in studies that apply gene expression analysis to livestock production systems, focusing on their adaptation to climate change. We also attempt to identify various biomarkers and transcriptomic differences between species and pure/crossbred animals. Looking ahead, integrating emerging technologies such as spatialomics could further accelerate genetic improvements, enabling more thermoresilient and productive livestock in response to future climate fluctuations. Ultimately, insights from these studies will help optimize livestock production systems by identifying thermoresilient/desired animals for use in precise breeding programs to counter climate change.

Proteomic identification of potential biomarkers for heat tolerance in Caracu beef cattle using high and low thermotolerant groups

BACKGROUND

Heat stress has deleterious effects on physiological and performance traits in livestock. Within this context, using tropically adapted cattle breeds in pure herds or terminal crossbreeding schemes to explore heterosis is attractive for increasing animal production in warmer climate regions. This study aimed to identify biological processes, pathways, and potential biomarkers related to thermotolerance in Caracu, a tropically adapted beef cattle breed, by proteomic analysis of blood plasma. To achieve this goal, 61 bulls had their thermotolerance evaluated through a heat tolerance index. A subset of 14 extreme animals, including the seven most thermotolerant (HIGH group) and the seven least thermotolerant (LOW group), had their blood plasma samples used for proteomic analysis by liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). The differentially regulated proteins detected between HIGH and LOW groups were used to perform functional enrichment analysis and a protein-protein interaction network analysis.

RESULTS

A total of 217 proteins were detected only in the HIGH thermotolerant group and 51 only in the LOW thermotolerant group. In addition, 81 and 87 proteins had significantly higher and lower abundancies in the HIGH group, respectively. Regarding proteins with the highest absolute log-fold change values, we highlighted those encoded by DUSP5, IGFALS, ROCK2, RTN4, IRAG1, and NNT genes based on their functions. The functional enrichment analysis detected several biological processes, molecular functions, and pathways related to cellular responses to stress, immune system, complement system, and hemostasis in both HIGH and LOW groups, in addition to terms and pathways related to lipids and calcium only in the HIGH group. Protein-protein interaction (PPI) network revealed as important nodes many proteins with roles in response to stress, hemostasis, immune system, inflammation, and homeostasis. Additionally, proteins with high absolute log-fold change values and proteins detected as essential nodes by PPI analysis highlighted herein are potential biomarkers for thermotolerance, such as ADRA1A, APOA1, APOB, APOC3, C4BPA, CAT, CFB, CFH, CLU, CXADR, DNAJB1, DNAJC13, DUSP5, FGA, FGB, FGG, HBA, HBB, HP, HSPD1, IGFALS, IRAG1, KNG1, NNT, OSGIN1, PROC, PROS1, ROCK2, RTN4, RYR1, TGFB2, VLDLR, VTN, and VWF.

CONCLUSIONS

Identifying potential biomarkers, molecular mechanisms and pathways that act in response to heat stress in tropically adapted beef cattle contributes to developing strategies to improve performance and welfare traits in livestock under tropical climates.

Evaluation of sperm quality and male fertility: The use of molecular markers in boar sperm and seminal plasma

In pig production, the optimization of artificial insemination (AI) efficiency significantly relies on the accurate assessment of semen quality and fertility of boars. Traditional methods such as conventional seminogram techniques, although long-standing, exhibit limited sensitivity in predicting boar fertility, warranting the exploration of novel molecular markers. This review synthesizes the current knowledge on the utilization of molecular markers for semen quality evaluation and male fertility prediction in boars, providing an in-depth examination of molecular markers in this context. Specifically, the present work delves into the potential of OMICs technologies, encompassing genetic and genomic approaches, transcriptomics, proteomics, and metabolomics. A diverse array of molecular markers, including genomic regions associated with sperm quality and male fertility, chromatin integrity, mitochondrial DNA content, mRNA and non-coding RNA signatures, as well as proteins and metabolites in sperm and seminal plasma, are identified as promising molecular markers for fertility prediction in boars. Furthermore, the need of validating biomarkers and their practical implementation in AI centres is here emphasized. Addressing these considerations and integrating molecular markers within the swine breeding field holds the potential to enhance reproductive management practices and optimize productivity in boar breeding programs. This integration can significantly improve overall efficiency within the pig breeding industry.

Integrating metabolomics into reproduction: Sperm metabolism and fertility enhancement in pigs

The last decades of research have revealed that many other factors besides gamete genomes are able to determine the reproductive outcomes. Indeed, paternal factors have been observed to be capable of modulating multiple crucial features of the reproductive process, such as sperm physiology, the maternal environment and, even, the offspring health. These recent advances have been encompassed with the emergence of OMICS technologies, as they comprehensively characterise the molecular composition of biological systems. The present narrative review aimed to take a closer look at the potential of these technologies in the field of reproductive biology. This literature revision shows that most studies up to date have followed a non-targeted approach to screen mammalian seminal plasma (SP) and sperm metabolite composition through different metabolome platforms. These studies have proposed metabolites of multiple natures as potential in vivo fertility biomarkers. Yet, targeted approaches can be used to answer specific biological question, and their power is exemplified herein. For instance, metabolomic studies have uncovered not only that glycolysis is the main ATP energy source of pig sperm, but also that sperm metabolism can trigger DNA damage, hence compromise embryo development. In conclusion, this review shows the potential of both non-targeted and targeted metabolomics for the discovery of cell pathways that govern the reproductive process. Understanding these systems could help make progress in different areas, including livestock efficient breeding, the improvement of artificial reproductive technologies, and the development of biomarkers for infertility detection.

Genome-Wide Association Study for Weight Loss at the End of Dry-Curing of Hams Produced from Purebred Heavy Pigs

Dissecting the genetics of production traits in livestock is of outmost importance, both to understand biological mechanisms underlying those traits and to facilitate the design of selection programs incorporating that information. For the pig industry, traits related to curing are key for protected designation of origin productions. In particular, appropriate ham weight loss after dry-curing ensures high quality of the final product and avoids economic losses. In this study, we analyzed data (N = 410) of ham weight loss after approximately 20 months of dry-curing. The animals used for ham production were purebred pigs belonging to a commercial line. A genome-wide association study (GWAS) of 29,844 SNP markers revealed the polygenic nature of the trait: 221 loci explaining a small percentage of the variance (0.3-1.65%) were identified on almost all Sus scrofa chromosomes. Post-GWAS analyses revealed 32 windows located within regulatory regions and 94 windows located in intronic regions of specific genes. In total, 30 candidate genes encoding receptors and enzymes associated with ham weight loss (MTHFD1L, DUSP8), proteolysis (SPARCL1, MYH8), drip loss (TNNI2), growth (CDCA3, LSP1, CSMD1, AP2A2, TSPAN4), and fat metabolism (AGPAT4, IGF2R, PTDSS2, HRAS, TALDO1, BRSK2, TNNI2, SYT8, GTF2I, GTF2IRD1, LPCAT3, ATN1, GNB3, CMIP, SORCS2, CCSER1, SPP1) were detected.

A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle

Intramuscular fat (IMF) deposition profoundly influences meat quality and economic value in beef cattle production. Meanwhile, contemporary developments in epigenetics have opened new outlooks for understanding the molecular basics of IMF regulation, and it has become a key area of research for world scholars. Therefore, the aim of this paper was to provide insight and synthesis into the intricate relationship between epigenetic mechanisms and IMF deposition in beef cattle. The methodology involves a thorough analysis of existing literature, including pertinent books, academic journals, and online resources, to provide a comprehensive overview of the role of epigenetic studies in IMF deposition in beef cattle. This review summarizes the contemporary studies in epigenetic mechanisms in IMF regulation, high-resolution epigenomic mapping, single-cell epigenomics, multi-omics integration, epigenome editing approaches, longitudinal studies in cattle growth, environmental epigenetics, machine learning in epigenetics, ethical and regulatory considerations, and translation to industry practices from perspectives of IMF deposition in beef cattle. Moreover, this paper highlights DNA methylation, histone modifications, acetylation, phosphorylation, ubiquitylation, non-coding RNAs, DNA hydroxymethylation, epigenetic readers, writers, and erasers, chromatin immunoprecipitation followed by sequencing, whole genome bisulfite sequencing, epigenome-wide association studies, and their profound impact on the expression of crucial genes governing adipogenesis and lipid metabolism. Nutrition and stress also have significant influences on epigenetic modifications and IMF deposition. The key findings underscore the pivotal role of epigenetic studies in understanding and enhancing IMF deposition in beef cattle, with implications for precision livestock farming and ethical livestock management. In conclusion, this review highlights the crucial significance of epigenetic pathways and environmental factors in affecting IMF deposition in beef cattle, providing insightful information for improving the economics and meat quality of cattle production.

Development and application of microsatellite markers in Hippophae rhamnoides subsp. sinensis Rousi (Hippophae rhamnoides L.) based on transcriptome sequencing

Hippophae rhamnoides subsp. sinensis Rousi is a cold- and drought-tolerant pioneer species with significant economic and ecological value. Evaluating its genetic diversity and population structure is of great importance for guiding the development and utilization of resources. In this study, a total of 41,804 SSRs were generated by transcriptome sequencing of Hippophae rhamnoides subsp. sinensis Rousi. Among the different SSR motif types, mononucleotide repeats (26,972) were the most abundant, followed by trinucleotides, tetranucleotides, and pentanucleotides. 200 pairs of SSR primers were selected to detect polymorphisms, of which 15 pairs primers were selected as validated polymorphic SSRs used for genetic diversity and population structure analysis. A total of 63 alleles were identified with 15 pairs primers, with Nei's genetic diversity index ranged from 0.27 to 0.83 (average: 0.54), and the expected heterozygosity ranged from 0.16 to 0.73 (average: 0.46). The polymorphism information content ranged from 0.23 to 0.81 (average: 0.48). Genetic structure analyses showed that the 10 populations could be broadly categorized into two groups. AMOVA denoted that genetic variations primarily originated from within the populations, with minimal differences observed between the groups, accounting for only 7% of the total genetic variation. This implies that mutation in H. rhamnoides subsp. sinensis Rousi mainly occurred within the populations. The results showed that the 10 populations of H. rhamnoides subsp. sinensis Rousi are rich in genetic diversity, with low levels of population differentiation and a high degree of gene exchange, which should be taken into consideration for the future work of germplasm resource preservation and seedling breeding.

A veterinary cerumenomic assay for bovine laminitis identification

Bovine laminitis disorder results in animal welfare and economic concerns in dairy and beef farms worldwide. However, the affected metabolic pathways, pathophysiologic characteristics, and inflammatory mechanisms remain unclear, hampering the development of new diagnostics. Using cerumen (earwax) as a source of volatile metabolites (cerumenomic) that carry valuable biological information has interesting implications for veterinary medicine. Nonetheless, up to now, no applications of veterinary cerumenomic assays have been made to identify bovine laminitis. This work aims to develop a veterinary cerumenomic assay for bovine laminitis identification that is non-invasive, robust, accurate, and sensitive to detecting the metabolic disturbances in bovine volatile metabolome. Twenty earwax samples (10 from healthy/control calves and 10 from laminitis calves) were collected from Nellore cattle, followed by Headspace/Gas Chromatography-Mass Spectrometry (HS/GC-MS) analysis and biomarker selection in two multivariate approaches: semiquantitative (intensity data) and semiqualitative (binary data). Following the analysis, cerumen volatile metabolites were indicated as candidate biomarkers for identifying bovine laminitis by monitoring their intensity or occurrence. In the semiquantitative strategy, the p-cresol presented the highest diagnostic figures of merit (area under the curve: 0.845, sensitivity: 0.700, and specificity: 0.900). Regarding the binary approach, a panel combining eight variables/volatiles, with formamide being the most prominent one, showed an area under the curve, sensitivity, and specificity of 0.97, 0.81, and 0.90, respectively. In summary, this work describes the first veterinary cerumenomic assay for bovine laminitis that indicates new metabolites altered during the inflammatory condition, paving the way for developing laminitis early diagnosis by monitoring the cerumen metabolites.

Assessing the impact of meta-genomic tools on current cutting-edge genome engineering and technology

Metagenomics is defined as the study of the genome of the total microbiota found in nature and is often referred to as microbial environmental genomics because it entails the examination of a group of genetic components (genomes) from a diverse community of organisms in a particular setting. It is a sub-branch of omics technology that encompasses Deoxyribonucleic Acid (DNA), Ribonucleic acid (DNA), proteins, and various components associated with comprehensive analysis of all aspects of biological molecules in a system-wide manner. Clustered regularly interspaced palindromic repeats and its endonuclease, CRISPR-associated protein which forms a complex called CRISPR-cas9 technology, though it is a different technique used to make precise changes to the genome of an organism, it can be used in conjunction with metagenomic approaches to give a better, rapid, and more accurate description of genomes and sequence reads. There have been ongoing improvements in sequencing that have deepened our understanding of microbial genomes forever. From the time when only a small amount of gene could be sequenced using traditional methods (e.g., "the plus and minus" method developed by Allan and Sanger and the "chemical cleavage" method that is known for its use in the sequencing the phiX174 bacteriophage genome via radio-labeled DNA polymerase-primer in a polymerization reaction aided by polyacrylamide gel) to the era of total genomes sequencing which includes "sequencing-by-ligation" and the "sequencing-by-synthesis" that detects hydrogen ions when new DNA is synthesized (Second Generation) and then Next Generation Sequencing technologies (NGS). With these technologies, the Human Genome Project (HGP) was made possible. The study looks at recent advancements in metagenomics in plants and animals by examining findings from randomly selected research papers. All selected case studies examined the functional and taxonomical analysis of different microbial communities using high-throughput sequencing to generate different sequence reads. In animals, five studies indicated how Zebrafish, Livestock, Poultry, cattle, niches, and the human microbiome were exploited using environmental samples, such as soil and water, to identify microbial communities and their functions. It has also been used to study the microbiome of humans and other organisms, including gut microbiomes. Recent studies demonstrated how these technologies have allowed for faster and more accurate identification of pathogens, leading to improved disease diagnostics. They have also enabled the development of personalized medicine by allowing for the identification of genetic variations that can impact drug efficacy and toxicity. Continued advancements in sequencing techniques and the refinement of CRISPR-Cas9 tools offer even greater potential for transformative breakthroughs in scientific research and applications. On the other hand, metagenomic data are always large and uneasy to handle. The complexity of taxonomical profiling, functional annotation, and mechanisms of complex interaction still needs better bioinformatics tools. Current review focuses on better (e.g., AI-driven algorithms) tools that can predict metabolic pathways and interactions, and manipulate complex data to address potential bias for accurate interpretation.

Microsatellite markers reveal genetic diversity and population structure of Portunus trituberculatus in the Bohai Sea, China

The swimming crab, Portunus trituberculatus, is one of the main aquaculture species in Chinese coastal regions due to its palatability and high economic value. To obtain a better understanding of the genetic diversity of P. trituberculatus in the Bohai Sea, the present study used 40 SSR loci to investigate the genetic diversity and population structure of 420 P. trituberculatus individuals collected from seven populations in the Bohai Sea. Genetic parameters revealed a low level of genetic diversity in the cultured population (SI = 1.374, He = 0.687, and PIC = 0.643) in comparison with wild populations (SI ≥ 1.399, He ≥ 0.692, and PIC ≥ 0.651). The genetic differentiation index (Fst) and gene flow (Nm) ranged from 0.001 to 0.060 (mean: 0.022) and 3.917 to 249.750 (mean: 31.289) respectively, showing a low differentiation among the seven populations of P. trituberculatus. Population structure analysis, phylogenetic tree, and principal component analysis (PCA) demonstrated that the seven groups of P. trituberculatus were divided into four subpopulations (K = 4), but the correlation between genetic structure and geographical distribution was not obvious. These results are expected to provide useful information for the fishery management of wild swimming crabs.

Candidate Genes and Gene Networks Change with Age in Japanese Black Cattle by Blood Transcriptome Analysis

Age is an important physiological factor that affects the metabolism and immune function of beef cattle. While there have been many studies using the blood transcriptome to study the effects of age on gene expression, few have been reported on beef cattle. To this end, we used the blood transcriptomes of Japanese black cattle at different ages as the study subjects and screened 1055, 345, and 1058 differential expressed genes (DEGs) in the calf vs. adult, adult vs. old, and calf vs. old comparison groups, respectively. The weighted co-expression network consisted of 1731 genes. Finally, blue, brown, and yellow age-specific modules were obtained, in which genes were enriched in signaling pathways related to growth and development and immune metabolic dysfunction, respectively. Protein-protein interaction (PPI) analysis showed gene interactions in each specific module, and 20 of the highest connectivity genes were chosen as potential hub genes. Finally, we identified 495, 244, and 1007 genes by exon-wide selection signature (EWSS) analysis of different comparison groups. Combining the results of hub genes, we found that VWF, PARVB, PRKCA, and TGFB1I1 could be used as candidate genes for growth and development stages of beef cattle. CORO2B and SDK1 could be used as candidate marker genes associated with aging. In conclusion, by comparing the blood transcriptome of calves, adult cattle, and old cattle, the candidate genes related to immunity and metabolism affected by age were identified, and the gene co-expression network of different age stages was constructed. It provides a data basis for exploring the growth, development, and aging of beef cattle.

Biochemical profiling of metabolomics in heavy metal-intoxicated impaired metabolism and its amelioration using plant-based bioactive compound

Exposure to Pb is widely spreading and has far-reaching negative effects on living systems. This study aimed to investigate the toxic effects of Pb, through biochemical profiling and the ameliorative effects of quercetin against Pb-toxicity. Twenty-five male Wistar albino mice were divided into the following five groups. The CON-group received normal saline; the Pb-group received PbAc; the Pb + Q-CRN group received lead acetate followed by quercetin; the Q-CRN group received quercetin; and the CRN group received corn oil. After 4 weeks, the mice were euthanized. It was speculated that Pb significantly increased the levels of serine, threonine, and asparagine and decreased the levels of valine, lysine, and glutamic acid in the plasma of Pb-group, thus impairing amino acid metabolism. However, in the Pb + Q-CRN group, the level of these six amino acids was restored significantly due to the ameliorative effect of quercetin. The presence of lipid metabolites (L-carnitine, sphinganine, phytosphingosine, and lysophosphatidylcholine) in mice serum was confirmed by ESI/MS. The GPx, SOD, GSH, and CAT levels were significantly decreased, and the MDA level was significantly increased, thus confirming the oxidative stress and lipid peroxidation in the Pb group. The antioxidant effect of quercetin was elucidated in the Pb + Q-CRN group. Expression of CPT-I, CPT-II, LCAT, CROT, CACT, and MTR genes was significantly upregulated in the liver of Pb goup mice. Hence, the findings of this study proved that Pb exposure induced oxidative stress, upregulated gene expression, and impaired the lipid and amino acid metabolism in mice.

Development of Microsatellite Markers Based on Transcriptome Sequencing and Evaluation of Genetic Diversity in Swimming Crab (Portunus trituberculatus)

P. trituberculatus is an economically important mariculture species in China. Evaluating its genetic diversity and population structure can contribute to the exploration of germplasm resources and promote sustainable aquaculture production. In this study, a total of 246,243 SSRs were generated by transcriptome sequencing of P. trituberculatus. Among the examined 254,746 unigenes, 66,331 had more than one SSR. Among the different SSR motif types, dinucleotide repeats (110,758, 44.98%) were the most abundant. In 173 different base repeats, A/T (96.86%), AC/GT (51.46%), and ACC/GGT (26.20%) were dominant in mono-, di-, and trinucleotide, respectively. GO annotations showed 87,079 unigenes in 57 GO terms. Cellular process, cell, and binding were the most abundant terms in biological process, cellular component, and molecular function categories separately. A total of 34,406 annotated unigenes were classified into 26 functional categories according to the functional annotation analysis of KOG, of which “general function prediction only” was the biggest category (6,028 unigenes, 17.52%). KEGG pathway annotations revealed the clustering of 34,715 unigenes into 32 different pathways. Nineteen SSRs were identified as polymorphic and, thus, used to assess the genetic diversity and structure of 240 P. trituberculatus individuals from four populations in the Bohai Sea. Genetic parameter analysis showed a similar level of genetic diversity within wild populations, and the cultured population indicated a reduction in genetic diversity compared with wild populations. The pairwise F_ST values were between 0.001 and 0.04 with an average of 0.0205 (p < 0.05), suggesting a low but significant level of genetic differentiation among the four populations. Structure analysis demonstrated that the four populations were classified into two groups including the cultured group and other populations. The phylogenetic tree and PCA revealed that a vast number of samples were clustered together and that cultivated individuals were distributed more centrally than wild individuals. The findings contribute to the further assessment of germplasm resources and assist to provide valuable SSRs for marker-assisted breeding of P. trituberculatus in the future.