Application of molecular markers in plant genome analysis: a review

Addressing Conservation Needs: Genetic Diversity and Population Ecology of the Endemic Tree Spondias tuberosa Arruda

Spondias tuberosa Arruda (Anacardiaceae), popularly known as umbuzeiro or imbuzeiro, is a fruit tree native to the semiarid region of Brazil. The extractive harvesting of its fruits contributes significantly to the economy, generating an annual revenue of approximately $4,2 million. The present study aimed to assess the spatial pattern, allometric variations, fruit measurements, and genetic diversity of trees within a remaining forest of the Caatinga biome, with a focus on intrapopulation analysis. We used intersimple repeated sequence markers and the second-order function density of neighbours to determine the genetic and spatial structure. The density of neighbours was highest within a 10-meter radius. Biometric analyses revealed average fruit lengths of 31.12 mm (±0.22), diameters of 28.68 mm (±0.25), and fresh masses of 15.56 g (±0.33). Diaspores exhibited an average length, diameter, and thickness of 19.27 mm, 13.95 mm, and 11.14 mm, respectively, with a fresh mass of 2.28 g. Notably, the fresh mass demonstrated the highest coefficient of variation. Ten molecular markers were selected, generating 103 highly polymorphic loci (99.03%) with an average informative content of 0.45. Nei's diversity index (0.37) and Shannon's index (0.55) indicated moderate genetic diversity. Furthermore, Bayesian analysis revealed a population structure with two distinct genetic groups. The Infinite Allele and Mutation Step Models suggested a significant historical decline in population size, indicative of a genetic bottleneck. As a result, proactive in situ conservation strategies, including establishing protected natural areas, become essential, considering the socioeconomic significance of the species. Additionally, it is recommended to establish germplasm banks for ex situ conservation and the development of managed cultivation initiatives to reduce the pressure on native populations of S. tuberosa caused by extraction.

Genome assembly and microsatellite marker development using Illumina and PacBio sequencing in Persicaria maackiana (Polygonaceae) from Korea

BACKGROUND

Persicaria maackiana (Regel) is a potential medicinal plant that exerts anti-diabetic effects. However, the lack of genomic information on P. maackiana hinders research at the molecular level.

OBJECTIVE

Herein, we aimed to construct a draft genome assembly and obtain comprehensive genomic information on P. maackiana using high-throughput sequencing tools PacBio Sequel II and Illumina.

METHODS

Persicaria maackiana samples from three natural populations in Gaecheon, Gichi, and Uiryeong reservoirs in South Korea were used to generate genomic DNA libraries, perform genome de novo assembly, gene ontology analysis, phylogenetic tree analysis, genotyping, and identify microsatellite markers.

RESULTS

The assembled P. maackiana genome yielded 32,179 contigs. Assessment of assembly integrity revealed 1503 (93.12%) complete Benchmarking Universal Single-Copy Orthologs. A total of 64,712 protein-coding genes were predicted and annotated successfully in the protein database. In the Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs, 13,778 genes were annotated into 18 categories. Genes that activated AMPK were identified in the KEGG pathway. A total of 316,992 microsatellite loci were identified, and primers targeting the flanking regions were developed for 292,059 microsatellite loci. Of these, 150 primer sets were randomly selected for amplification, and 30 of these primer sets were identified as polymorphic. These primers amplified 3-9 alleles. The mean observed and expected heterozygosity were 0.189 and 0.593, respectively. Polymorphism information content values of the markers were 0.361-0.754.

CONCLUSION

Collectively, our study provides a valuable resource for future comparative genomics, phylogeny, and population studies of P. maackiana.

Assessment of genetic variation among wheat genotypes for drought tolerance utilizing microsatellite markers and morpho-physiological characteristics

Drought is a major abiotic stress that severely limits sustainable wheat (Triticum aestivum L.) productivity via morphological and physio-biochemical alterations of cellular processes. The complex nature and polygenic control of drought tolerance traits make breeding tolerant genotypes quite challenging. However, naturally occurring variabilities among wheat germplasm resources could potentially help combating drought. The present study was conducted to assess the drought tolerance of 18 Bangladeshi hexaploid wheat genotypes, focusing on the identification of potent sources of diversity by combining microsatellite markers, also known as single sequence repeat markers, and morpho-physiological characteristics that might help accelerating wheat crop improvement programs. Initially, the genotypes were evaluated using 25 microsatellite markers followed by an on-field evaluation of 7 morphological traits (plant height, spike number, spike length, grains per spike, 1000-grain weight, grain yield, biological yield) and 6 physiological traits (SPAD value, membrane stability index, leaf relative water content, proline content, canopy temperature depression, and leaf K+ ion content). The field-trial was conducted in a factorial fashion of 18 wheat genotypes and two water regimes (control and drought) following a split-plot randomized complete block design. Regardless of genotype, drought was significantly damaging for all the tested traits; however, substantial variability in drought stress tolerance was evident among the genotypes. Spike length, 1000-grain weight, SPAD value, leaf relative water content, canopy temperature depression, proline content, and potassium (K+) ion content were the most representative of drought-induced growth and yield impairments and also correlated well with the contrasting ability of genotypic tolerance. Microsatellite markers amplified 244 alleles exhibiting 79% genetic diversity. Out of 25 markers, 23 was highly polymorphic showing 77% average polymorphism. Morpho-physiological trait-based hierarchical clustering and microsatellite marker-based neighbor-jointing clustering both revealed three genotypic clusters with 71% co-linearity between them. In both cases, the genotypes Kanchan, BAW-1147, BINA Gom 1, BARI Gom 22, BARI Gom 26, and BARI Gom 33 were found to be comparatively more tolerant than the other tested genotypes, showing potential for cultivation in water-deficit environments. The findings of this study would contribute to the present understanding of drought tolerance in wheat and would provide a basis for future genotype selection for drought-tolerant wheat breeding programs.

Rethinking underutilized cereal crops: pan-omics integration and green system biology

MAIN CONCLUSION

Due to harsh lifestyle changes, in the present era, nutritional security is needed along with food security so it is necessary to include underutilized cereal crops (UCCs) in our daily diet to counteract the rising danger of human metabolic illness. We can attain both the goal of zero hunger and nutritional security by developing improved UCCs using advanced pan-omics (genomics, transcriptomics, proteomics, metabolomics, nutrigenomics, phenomics and ionomics) practices. Plant sciences research progressed profoundly since the last few decades with the introduction of advanced technologies and approaches, addressing issues of food demand of the growing population, nutritional security challenges and climate change. However, throughout the expansion and popularization of commonly consumed major cereal crops such as wheat and rice, other cereal crops such as millet, rye, sorghum, and others were impeded, despite their potential medicinal and nutraceutical qualities. Undoubtedly neglected underutilized cereal crops (UCCs) also have the capability to withstand diverse climate change. To relieve the burden of major crops, it is necessary to introduce the new crops in our diet in the way of UCCs. Introgression of agronomically and nutritionally important traits by pan-omics approaches in UCCs could be a defining moment for the population's well-being on the globe. This review discusses the importance of underutilized cereal crops, as well as the application of contemporary omics techniques and advanced bioinformatics tools that could open up new avenues for future study and be valuable assets in the development and usage of UCCs in the perspective of green system biology. The increased and improved use of UCCs is dependent on number of factors that necessitate a concerted research effort in agricultural sciences. The emergence of functional genomics with molecular genetics might gear toward the reawakening of interest in underutilized cereals crops. The need of this era is to focus on potential UCCs in advanced agriculture and breeding programmes. Hence, targeting the UCCs, might provide a bright future for better health and scientific rationale for its use.

Application of High-Resolution Melting and DNA Barcoding for Discrimination and Taxonomy Definition of Rocket Salad (Diplotaxis spp.) Species

Nuclear and cytoplasmic DNA barcoding regions are useful for plant identification, breeding, and phylogenesis. In this study, the genetic diversity of 17 Diplotaxis species, was investigated with 5 barcode markers. The allelic variation was based on the sequences of chloroplast DNA markers including the spacer between trnL and trnF and tRNA-Phe gene (trnL-F), the rubisco (rbcl), the maturase K (matk), as well as the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA. A highly polymorphic marker (HRM500) derived from a comparison of cytoplasmic genome sequences in Brassicaceae, was also included. Subsequently, a real-time PCR method coupled with HRM analysis was implemented to better resolve taxonomic relationships and identify assays suitable for species identification. Integration of the five barcode regions revealed a grouping of the species according to the common chromosomal set number. Clusters including species with n = 11 (D. duveryrieriana or cretacea, D. tenuifolia, D. simplex and D. acris), n = 8 (D. ibicensis, D. brevisiliqua and D. ilorcitana), and n = 9 (D. brachycarpa, D. virgata, D. assurgens, and D. berthautii) chromosomes were identified. Both phylogenetic analysis and the genetic structure of the collection identified D. siifolia as the most distant species. Previous studies emphasized this species' extremely high glucosinolate content, particularly for glucobrassicin. High-resolution melting analysis showed specific curve patterns useful for the discrimination of the species, thus determining ITS1 as the best barcode for fingerprinting. Findings demonstrate that the approach used in this study is effective for taxa investigations and genetic diversity studies.

Drought stress in rice: morpho-physiological and molecular responses and marker-assisted breeding

Rice (Oryza Sativa L.) is an essential constituent of the global food chain. Drought stress significantly diminished its productivity and threatened global food security. This review concisely discussed how drought stress negatively influenced the rice's optimal growth cycle and altered its morpho-physiological, biochemical, and molecular responses. To withstand adverse drought conditions, plants activate their inherent drought resistance mechanism (escape, avoidance, tolerance, and recovery). Drought acclimation response is characterized by many notable responses, including redox homeostasis, osmotic modifications, balanced water relations, and restored metabolic activity. Drought tolerance is a complicated phenomenon, and conventional breeding strategies have only shown limited success. The application of molecular markers is a pragmatic technique to accelerate the ongoing breeding process, known as marker-assisted breeding. This review study compiled information about quantitative trait loci (QTLs) and genes associated with agronomic yield-related traits (grain size, grain yield, harvest index, etc.) under drought stress. It emphasized the significance of modern breeding techniques and marker-assisted selection (MAS) tools for introgressing the known QTLs/genes into elite rice lines to develop drought-tolerant rice varieties. Hence, this study will provide a solid foundation for understanding the complex phenomenon of drought stress and its utilization in future crop development programs. Though modern genetic markers are expensive, future crop development programs combined with conventional and MAS tools will help the breeders produce high-yielding and drought-tolerant rice varieties.

Genome survey sequencing-based SSR marker development and their validation in Dendrocalamus longispathus

Bamboo is an important genetic resource in India, supporting rural livelihood and industries. Unfortunately, most Indian bamboo taxa are devoid of basic genomic or marker information required to comprehend the genetic processes for further conservation and management. In this study, we perform genome survey sequencing for development of de novo genomic SSRs in Dendrocalamus longispathus, a socioeconomically important bamboo species of northeast India. Using Illumina platform, 69.49 million raw reads were generated and assembled into 1,145,321 contig with GC content 43% and N50 1228 bp. In total, 46,984 microsatellite repeats were mined-out wherein di-nucleotide repeats were most abundant (54.71%) followed by mono- (31.91%) and tri-repeats (9.85%). Overall, AT-rich repeats were predominant in the genome, but GC-rich motifs were more frequent in tri-repeats. Afterwards, 21,596 SSR loci were successfully tagged with the primer pairs, and a subset of 50 were validated through polymerase chain reaction amplification. Of these, 36 SSR loci were successfully amplified, and 16 demonstrated polymorphism. Using 13 polymorphic SSRs, a moderate level of gene diversity (He = 0.480; Ar = 3.52) was recorded in the analysed populations of D. longispathus. Despite the high gene flow (Nm = 4.928) and low genetic differentiation (F_ST = 0.119), severe inbreeding (F_IS = 0.407) was detected. Further, genetic clustering and STRUCTURE analysis revealed that the entire genetic variability is captured under two major gene pools. Conclusively, we present a comprehensive set of novel SSR markers in D. longispathus as well as other taxa of tropical woody bamboos.

Transcriptomic Approach for Global Distribution of SNP/Indel and Plant Genotyping

Single Nucleotide Polymorphisms (SNPs) are the most common structural variants found in any genome. They have been used for different genetic studies, from the understanding of genetic structure of populations to the development of breeding selection markers. In this chapter we present the use of transcriptomic data obtained from contrasting phenotypes for a target trait, in searching of SNPs and insertions/deletions (InDels). This approach has the advantage that the identified markers are in or close to differentially expressed genes, and so they have higher chances to tag the genes underlying the phenotypic expression of a particular trait.

Start codon targeted (SCoT) polymorphism marker in plant genome analysis: current status and prospects

The present review illustrates a comprehensive overview of the start codon targeted (SCoT) polymorphism marker and their utilization in various applications related to genetic and genomic studies. Start codon targeted (SCoT) polymorphism marker, a targeted fingerprinting marker technique, has gained considerable importance in plant genetics, genomics, and molecular breeding due to its many desirable features. SCoT marker targets the region flanking the start codon, a highly conserved region in plant genes. Therefore, it can distinguish genetic variations in a specific gene that link to a specific trait. It is a simple, novel, cost-effective, highly polymorphic, and reproducible molecular marker for which there is no need for prior sequence information. In the recent past, SCoT markers have been employed in many commercially important and underutilized plant species for a variety of applications, including genetic diversity analysis, interspecific/generic genetic relationships, cultivar/hybrid/species identification, sex determination, construction of linkage map, association mapping/analysis, differential gene expression, and genetic fidelity analysis of tissue culture-raised plants. The main aim of this review is to provide up-to-date information on SCoT markers and their application in many commercially important and underutilized plant species, mainly progress made in the last 8-10 years.

Miracle Tree Moringa oleifera: Status of the Genetic Diversity, Breeding, In Vitro Propagation, and a Cogent Source of Commercial Functional Food and Non-Food Products

Moringa oleifera Lam. (MO) is a fast-growing drought-resistant tree belonging to the family Moringaceae and native to the Indian subcontinent and cultivated and/or naturalized worldwide with a semi-arid climate. MO is also popularly known as a miracle tree for its repertoire of nutraceutical, pharmacological, and phytochemical properties. The MO germplasm is collected, conserved, and maintained by various institutions across the globe. Various morphological, biochemical, and molecular markers are used for determining the genetic diversity in MO accessions. A higher yield of leaves and pods is often desirable for making various products with commercial viability and amenable for trade in the international market. Therefore, breeding elite varieties adapted to local agroclimatic conditions and in vitro propagation are viable and sustainable approaches. Here, we provide a comprehensive overview of MO germplasm conservation and various markers that are employed for assessing the genetic diversity among them. Further, breeding and in vitro propagation of MO for various desirable agronomic traits are discussed. Finally, trade and commerce of various functional and biofortified foods and non-food products are enumerated albeit with a need for a rigorous and stringent toxicity evaluation.

Cis-element amplified polymorphism (CEAP), a novel promoter- and gene-targeted molecular marker of plants

In this study, we selected eight cis-elements: AAAG, ACGTG, CCGA, ACTCAT, GGTCA, TATCC, TGAC and GATAA, which are closely related to plant growth and development, signal transduction and stress response. The CEAP primers were 18 nucleotides long and consisted of a central cis-element nucleotide core flanked by a filler sequence at the 5' end and di- or tri-nucleotides at the 3' end. A total of two hundred and twenty-four primers were developed, and the PCR procedure consisted of 5 cycles of low-temperature annealing and 35 subsequent cycles of annealing at 50°C. The PCR products are electrophoretically separated by 1.8-2.3% agarose. The polymorphism of the CEAP marker was amplified in eight mango (Mangifera indica L.) species. The results showed that the CEAP primers could amplify clear, repeatable bands in mango and combine at least four cis-elements from which a large number of bands were amplified and six highly polymorphic primers for each cis-element can reach an accurate clustering result. The results of CEAP marker assays compared with ISSR, CBDP and iPBS marker assays showed that CEAP marker was better than the other three markers in the number of fragment bands, H and I indexes. In addition, we also tested the CEAP markers in rice, tomato, potato, wax gourd, citrus and longan and the results showed that the CEAP marker assay could amplify clear polymorphic bands in different species. Our results indicate that the CEAP markers could be universally used in different species for genetic diversity analysis, relationship analysis, and marker-assisted selection for breeding.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-022-01212-5.

Genetic Diversity and Population Structure of Myanmar Rice (Oryza sativa L.) Varieties Using DArTseq-Based SNP and SilicoDArT Markers

Myanmar is well known as a primary center of plant genetic resources for rice. A considerable number of genetic diversity studies have been conducted in Myanmar using various DNA markers. However, this is the first report using DArTseq technology for exploring the genetic diversity of Myanmar rice. In our study, two ultra-high-throughput diversity array technology markers were employed to investigate the genetic diversity and population structure of local rice varieties in the Ayeyarwady delta, the major region of rice cultivation. The study was performed using 117 rice genotypes with 7643 SNP and 4064 silicoDArT markers derived from the DArT platform. Genetic variance among the genotypes ranged from 0 to 0.753 in SNPs, and from 0.001 to 0.954 in silicoDArT. Two distinct population groups were identified from SNP data analysis. Cluster analysis with both markers clearly separated traditional Pawsan varieties and modern high-yielding varieties. A significant divergence was found between populations according to the Fst values (0.737) obtained from the analysis of molecular variance, which revealed 74% genetic variation at the population level. These findings support rice researchers in identifying useful DNA polymorphisms in genes and pinpointing specific genes conferring desirable phenotypic traits for further genome-wide association studies and parental selection for recombination breeding to enhance rice varietal development and release.

Genome-wide development and application of miRNA-SSR markers in Melilotus genus

Genetic diversity of plants is the brace of biodiversity and diversity within species, between species, and of ecosystems. SSR markers are the most preferable molecular marker tool that has been successfully used to study the genetic diversity of plant species. Development of miRNA-SSR markers has been deed in animals but is still limited in plants. In this study, 365 precursors miRNA were extracted from Melilotus albus (Ma) genome and used to design Ma miRNA-SSR primers. 137 Ma primer pairs (79 from known and 58 from novel pre-miRNAs) were obtained. 66 pairs of Ma miRNA-SSR primers were selected with polymorphisms and expected fragment size. The polymorphisms of primers were evaluated in 60 individuals of 15 Ma accessions. A total of 66 primer pairs showed high polymorphism, with average polymorphic information content of 0.49 among 15 Ma accessions and 0.63 among 18 Melilotus species, indicating that these primers have high polymorphisms. The number of alleles produced per primer ranged from 2 to 6 with an average of 3.6 alleles per locus in Ma accessions, and 2 to 10 numbers of alleles with a mean of 5.24 alleles per locus in Melilotus spp. For further studies, the genetic relationship was examined and the cluster analysis showed that 15 Ma accessions were grouped in three groups, on the other hand, 18 Melilotus species clustered into two groups. The analysis of molecular variance (AMOVA) revealed that 64.82% of the variation was found within the species and 35.18% between the species. The population structure analysis showed similar results with PCA analysis in that 18 species were grouped in two groups. In addition, 16,450 miRNA target genes were identified and used for GO and KEGG analysis. This is the first study to develop miRNA-SSR molecular markers in Melilotus spp., which has a great potential for marker-assisted, genetic improvement, genotyping applications, QTL analysis, and molecular-assisted selection studies for plant breeders and other researchers.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01086-z.

Pumpkin (Cucurbita spp.): A Crop to Mitigate Food and Nutritional Challenges

The world’s food and agricultural programs have gradually declined into an unsustainable situation due to challenges such as increase in world population, varied agro-climatic regions, increase temperature, extreme sole-culture growing techniques, and water shortage. A considerable emphasis has been put on few staple food crops coupled with repeated dieting, food scarcity, and essential mineral deficits, frequently inducing dietary disorders. Because relying on staple crops may lead to serious food shortages in the future, we must adjust our dietary habits to include a diverse range of non-staple foods and maximize their use in order to achieve food security and reduce the nutritional gap. To assure healthy meals around the world, an authentic and reasonable strategy is presented to draw additional awareness towards variations in agricultural production techniques and dietary preferences. The EAT-Lancet declaration highlighted the importance of increasing agri-based foods to achieve sustainable health. Expanding overlooked crops with abundant genetic stocks and possibly beneficial characteristics is an approach that might meet food and nutritional security challenges. Although undervalued, pumpkin is a valuable vegetable herbaceous plant that contributes to global food and nutritional security. This crop has already been identified as a revolutionary age crop, balanced food, and more adapted to low soil and atmospheric circumstances than other major crops. This review paper focuses on the potential uses of pumpkin as an underutilized crop; diversification and development of hybrids, particularly hybridization breeding through diallel mating design; and how implementation of this “modern” technology would contribute to the breeding of the neglected pumpkin vegetable and stimulate productivity and nourish the world’s largest malnourished, deprived, and starved populations.

Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing

Forest tree breeding efforts have focused mainly on improving traits of economic importance, selecting trees suited to new environments or generating trees that are more resilient to biotic and abiotic stressors. This review describes various methods of forest tree selection assisted by genomics and the main technological challenges and achievements in research at the genomic level. Due to the long rotation time of a forest plantation and the resulting long generation times necessary to complete a breeding cycle, the use of advanced techniques with traditional breeding have been necessary, allowing the use of more precise methods for determining the genetic architecture of traits of interest, such as genome-wide association studies (GWASs) and genomic selection (GS). In this sense, main factors that determine the accuracy of genomic prediction models are also addressed. In turn, the introduction of genome editing opens the door to new possibilities in forest trees and especially clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9). It is a highly efficient and effective genome editing technique that has been used to effectively implement targetable changes at specific places in the genome of a forest tree. In this sense, forest trees still lack a transformation method and an inefficient number of genotypes for CRISPR/Cas9. This challenge could be addressed with the use of the newly developing technique GRF-GIF with speed breeding.

Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants

Simple sequence repeats (SSRs) are one of the most important genetic markers and widely exist in most species. Here, we identified 249,822 SSRs from 3,951,919 genes in 112 plants. Then, we conducted a comprehensive analysis of these SSRs and constructed a plant SSR database (PSSRD). Interestingly, more SSRs were found in lower plants than in higher plants, showing that lower plants needed to adapt to early extreme environments. Four specific enriched functional terms in the lower plant Chlamydomonas reinhardtii were detected when it was compared with seven other higher plants. In addition, Guanylate_cyc existed in more genes of lower plants than of higher plants. In our PSSRD, we constructed an interactive plotting function in the chart interface, and users can easily view the detailed information of SSRs. All SSR information, including sequences, primers, and annotations, can be downloaded from our database. Moreover, we developed Web SSR Finder and Batch SSR Finder tools, which can be easily used for identifying SSRs. Our database was developed using PHP, HTML, JavaScript, and MySQL, which are freely available at http://www.pssrd.info/ . We conducted an analysis of the Myb gene families and flowering genes as two applications of the PSSRD. Further analysis indicated that whole-genome duplication and whole-genome triplication played a major role in the expansion of the Myb gene families. These SSR markers in our database will greatly facilitate comparative genomics and functional genomics studies in the future.

Assessment of genetic diversity of pumpkins (Cucurbita spp.) from western Kenya using SSR molecular markers

Pumpkins (Cucurbita spp.) are among most neglected and underutilized crops cultivated for food and medicine. The major constraint to pumpkin production is lack of genetically improved seeds. The current study was aimed at evaluating the genetic diversity of pumpkins from eight counties in western Kenya using five SSR markers. Seeds were extracted from pumpkin fruits, dried and planted on plastic trays for 4 weeks. DNA was isolated from young leaves using CTAB method and amplified. The samples were genotyped using an ABI 3730 genetic analyzer and the allelic data analyzed using Power Marker V 3.25, DARwin V 6.0.12 and GenAIEx V 6.41software. The five SSR loci were polymorphic with a total of 33 alleles and a mean PIC value of 0.534. The gene diversity and observed heterozygosity was 0.796-0.329 and 0.967-0.164, respectively. Most of genetic variations were found within and among individual samples rather than among counties, with samples of some counties having private alleles. Based on the inbreeding coefficient (F), there was outbreeding in pumpkins from Kakamega county (F = - 0.282) and inbreeding in pumpkins from Kisii, Bungoma and Nyamira counties (F = 0.500, 0.409 and 0.286 respectively). The findings of this study suggest that genetic variation and distribution of pumpkins in western Kenya was due to monocropping and intercropping farming systems, trading of pumpkins in markets and exchange of seeds among local farmers rather than geographical and climatic differences.