Population structure and genetic diversity analyses of common bean germplasm collections of East and Southern Africa using morphological traits and high-density SNP markers

Genetic diversity and population structure analyses of tropical maize inbred lines using Single Nucleotide Polymorphism markers

Analyses of the genetic distance and composition of inbred lines are a prerequisite for parental selection and to exploit heterosis in plant breeding programs. The study aimed to assess genetic diversity and population structure of a maize germplasm panel comprising 182 founder lines and 866 derived inbred lines using Single Nucleotide Polymorphism (SNP) markers to identify genetically unique lines for hybrid breeding. The founder lines were genotyped with 1201 SNPs, and the derived lines with 1484 SNPs. Moderate genetic variation, with genetic diversity ranging from 0.004 to 0.44 with a mean of 0.25, was recorded for the founder lines, while corresponding values of 0.004 to 0.34 with a mean of 0.13 were recorded for the derived lines. Heterozygosity values ranging from 0.00 to 0.24 and a mean of 0.08 were recorded for both lines. Of the SNP markers used, 82% of the 1201 markers and 84% of the 1484 markers exhibited polymorphism information content ranging from 0.25 to 0.50. Analysis of molecular variance revealed significant genetic differences (P ≤ 0.001) among and within populations in the founder and derived lines. Most detected variations, i.e., 97% and 88.38%, were attributed to within populations in the founder and derived lines, respectively. Population structure analysis identified three distinct subpopulations among founder lines and two among derived lines. Cluster analysis supported the population structure The following genetically distant founder and derived inbred lines were selected: G15NL337 and G15NL312 (Cluster 1), 15ARG152 and RGS-PL44 (Cluster 2), RGS-PL44 and 15ARG149 (Cluster 2), and RGS-PL33 and RGS-PL44 (Cluster 2), respectively. The selected lines are genetically distinct and recommended for marker-assisted hybrid maize breeding to exploit the frequency of beneficial alleles. This study provides valuable insights for maize breeding programs, enabling the exploitation of beneficial alleles and contributing to improved crop yields and food security through hybrid breeding.

Integrating Morpho-Physiological, Biochemical, and Molecular Genotyping for Selection of Drought-Tolerant Pigeon Pea (Cajanus cajan L.) Genotypes at Seedling Stage

Pigeon pea (Cajanus cajan (L.) Millsp.), a potential legume as an economic source of protein, is commonly cultivated in tropical and subtropical regions of the world. It possesses medicinal properties and acts as a cash crop, benefiting low-income farmers economically. The identification of pigeon peas exhibiting drought tolerance has become crucial in addressing water scarcity issues in the agriculture sector. In addition, exploring the genetic diversity among genotypes is important for conservation, management of genetic resources, and breeding programs. The aim of this study was to evaluate the morpho-physiological and biochemical responses of selected pigeon pea genotypes under pot-induced water stress conditions through different field capacities as well as the genetic diversity using start codon targeted (SCoT) markers. A significant variation was observed for the physiological traits studied. The accumulation of fresh weight (FW) and dry weight (DW) was significantly reduced in moderate and severe drought stress conditions. The lowest % DW decrease was found in LM (35.39%), KAT (39.43%), and SM (46.98%) than other genotypes at severe drought stress. Analyses of physiological responses including the photosynthetic efficiency (Phi2), the chlorophyll content (SPAD), and the relative water content (RWC) revealed positive and negative correlations with various parameters, reflecting the impact of drought stress on the chlorophyll content. The results revealed that biochemical traits including the total phenolic content, soluble sugars, proline, total protein, total amino acids, and free amino acids were variably and significantly increased under water stress. Antioxidant enzyme activity levels, specifically ascorbate peroxidase (APX) and catalase, varied among the genotypes and in response to severe water stress, offering further insights into adaptive responses. The eight genotypes analysed by use of 20 SCoT markers revealed 206 alleles and an average of 10.3 alleles per locus. Genetic similarity ranged from 0.336 to 0.676, clustering the pigeon pea genotypes into two major groups by the unweighted pair group method of arithmetic averages (UPGMA) cluster analysis. Principal coordinate analysis (PCoA) explained 43.11% of genetic variation and based on analysis of molecular variance, a high genetic variation (80%) within populations was observed, emphasizing the potential for genetic improvement. Among the eight genotypes studied, LM and KAT were drought tolerant and genetically diverse and therefore could be used as parents for developing drought tolerance in pigeon pea.

Genetic differentiation of a southern Africa tepary bean (Phaseolus acutifolius A Gray) germplasm collection using high-density DArTseq SNP markers

Genetic resources of tepary bean (Phaseolus acutifolius A. Gray) germplasm collections are not well characterized due to a lack of dedicated genomic resources. There is a need to assemble genomic resources specific to tepary bean for germplasm characterization, heterotic grouping, and breeding. Therefore, the objectives of this study were to deduce the genetic groups in tepary bean germplasm collection using high-density Diversity Array Technology (DArT) based single nucleotide polymorphism (SNP) markers and select contrasting genotypes for breeding. Seventy-eight tepary bean accessions were genotyped using 10527 SNPs markers, and genetic parameters were estimated. Population structure was delineated using principal component and admixture analyses. A mean polymorphic information content (PIC) of 0.27 was recorded, indicating a relatively low genetic resolution of the developed SNPs markers. Low genetic variation (with a genetic distance [GD] = 0.32) existed in the assessed tepary bean germplasm collection. Population structure analysis identified five sub-populations through sparse non-negative matrix factorization (snmf) with high admixtures. Analysis of molecular variance indicated high genetic differentiation within populations (61.88%) and low between populations (38.12%), indicating high gene exchange. The five sub-populations exhibited variable fixation index (FST). The following genetically distant accessions were selected: Cluster 1:Tars-Tep 112, Tars-Tep 10, Tars-Tep 23, Tars-Tep-86, Tars-Tep-83, and Tars-Tep 85; Cluster 3: G40022, Tars-Tep-93, and Tars-Tep-100; Cluster 5: Zimbabwe landrace, G40017, G40143, and G40150. The distantly related and contrasting accessions are useful to initiate crosses to enhance genetic variation and for the selection of economic traits in tepary bean.

Assessing the effects of 24-epibrassinolide and yeast extract at various levels on cowpea's morphophysiological and biochemical responses under water deficit stress

BACKGROUND

Due to the factor of water deficit, which has placed human food security at risk by causing a 20% annual reduction in agricultural products, addressing this growing peril necessitates the adoption of inventive strategies aimed at enhancing plant tolerance. One such promising approach is employing elicitors such as 24-epibrassinolide (EBR) and yeast extract, which are potent agents capable of triggering robust defense responses in plants. By employing these elicitors, crops can develop enhanced adaptive mechanisms to combat water deficit and improve their ability to withstand drought condition. This study investigates the impact of different levels of EBR (0, 5, 10 µm) and yeast extract (0 and 12 g/l) on enhancing the tolerance of cowpea to water deficit stress over two growing seasons.

RESULTS

The findings of this study demonstrate that, the combined application of EBR (especially 10 µm) and yeast extract (12 g/l) can increase seed yield (18%), 20-pod weight (16%), the number of pods per plant (18%), total chlorophyll content (90%), and decrease malondialdehyde content (45%) in cowpea, compared to plants grown under water deficit stress without these treatments. Upon implementing these treatments, impressive results were obtained, with the highest recorded values observed for the seed yield (1867.55 kg/ha), 20-pod weight (16.29 g), pods number per plant (9), and total chlorophyll content (19.88 mg g-1 FW). The correlation analysis indicated a significant relationship between the seed yield, and total chlorophyll (0.74**), carotenoids (0.82**), weight of 20 seeds (0.67**), and number of pods (0.90**). These traits should be prioritized in cowpea breeding programs focusing on water deficit stress.

CONCLUSIONS

The comprehensive exploration of the effects of EBR and yeast extract across various levels on cowpea plants facing water deficit stress presents a pivotal contribution to the agricultural domain. This research illuminates a promising trajectory for future agricultural practices and users seeking sustainable solutions to enhance crops tolerance. Overall, the implications drawn from this study contribute significantly towards advancing our understanding of plant responses to water deficit stress while providing actionable recommendations for optimizing crop production under challenging environmental conditions.

Meta-QTL Analysis for Yield Components in Common Bean (Phaseolus vulgaris L.)

Common bean is one of the most important legumes produced and consumed worldwide because it is a highly valuable food for the human diet. However, its production is mainly carried out by small farmers, who obtain average grain yields below the potential yield of the species. In this sense, numerous mapping studies have been conducted to identify quantitative trait loci (QTL) associated with yield components in common bean. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies. Consequently, the objective of this study was to perform a MQTL analysis to identify the most reliable and stable genomic regions associated with yield-related traits of common bean. A total of 667 QTL associated with yield-related traits reported in 21 different studies were collected. A total of 42 MQTL associated with yield-related traits were identified, in which the average confidence interval (CI) of the MQTL was 3.41 times lower than the CIs of the original QTL. Most of the MQTL (28) identified in this study contain QTL associated with yield and phenological traits; therefore, these MQTL can be useful in common bean breeding programs. Finally, a total of 18 candidate genes were identified and associated with grain yield within these MQTL, with functions related to ubiquitin ligase complex, response to auxin, and translation elongation factor activity.

Analysis of Genetic Diversity and Population Structure of Cowpea (Vigna unguiculata (L.) Walp) Genotypes Using Single Nucleotide Polymorphism Markers

Cowpea (Vigna unguiculata (L.) Walp) is an important legume crop with immense potential for nutritional and food security, income generation, and livestock feed in Sub-Saharan Africa. The crop is highly tolerant to heat and drought stresses which makes it an extremely important crop for improving resilience in crop production in the face of climate change. This study was carried out to assess the genetic diversity and population structure of 90 cowpea accessions using single nucleotide polymorphism (SNP) markers. Out of 11,940 SNPs used, 5864 SNPs were polymorphic and maintained for genome diversity analysis. Polymorphic information content (PIC) values ranged from 0.22 to 0.32 with a mean value of 0.27. The model-based Bayesian STRUCTURE analysis classified 90 cowpea accessions into four subpopulations at K = 4, while the distance-based cluster analysis grouped the accessions into three distinct clusters. The analysis of molecular variance (AMOVA) revealed that 59% and 69% of the total molecular variation was attributed to among individual variation for model-based and distance-based populations, respectively, and 18% was attributed to within individual variations. Furthermore, the low heterozygosity among cowpea accessions and the high inbreeding coefficient observed in this study suggests that the accessions reached an acceptable level of homozygosity. This study would serve as a reference for future selection and breeding programs of cowpea with desirable traits and systematic conservation of these plant genetic resources.

RP, R. L. R. Population structure and genetic diversity characterization of soybean for seed longevity

Seed longevity is an important trait in the context of germplasm conservation and economics of seed production. The identification of populations with high level of genetic variability for seed longevity and associated traits will become a valuable resource for superior alleles for seed longevity. In this study, Genotyping-by-sequencing (GBS)-single nucleotide polymorphism (SNP) approach, simple sequence repeats (SSR) markers and agro-morphological traits have been explored to investigate the diversity and population structure of assembled 96 genotypes. The GBS technique performed on 96 genotypes of soybean (Glycine max (L.) Merrill) resulted in 37,897 SNPs on sequences aligned to the reference genome sequence. The average genome coverage was 6.81X with a mapping rate of 99.56% covering the entire genome. Totally, 29,955 high quality SNPs were identified after stringent filtering and most of them were detected in non-coding regions. The 96 genotypes were phenotyped for eight quantitative and ten qualitative traits by growing in field by following augmented design. The STRUCTURE (Bayesian-model based algorithm), UPGMA (Un-weighed Pair Group Method with Arithmetic mean) and principal component analysis (PCA) approaches using SSR, SNP as well as quantitative and qualitative traits revealed population structure and diversity in assembled population. The Bayesian-model based STRUCTURE using SNP markers could effectively identify clusters with higher seed longevity associated with seed coat colour and size which were subsequently validated by UPGMA and PCA based on SSR and agro-morphological traits. The results of STRUCTURE, PCA and UPGMA cluster analysis showed high degree of similarity and provided complementary data that helped to identify genotypes with higher longevity. Six black colour genotypes, viz., Local black soybean, Kalitur, ACC Nos. 39, 109, 101 and 37 showed higher seed longevity during accelerated ageing. Higher coefficient of variability observed for plant height, number of pods per plant, seed yield per plant, 100 seed weight and seed longevity confirms the diversity in assembled population and its suitability for quantitative trait loci (QTL) mapping.

Genetic diversity and grouping of pigeonpea [Cajanus cajan Millspaugh] Germplasm using SNP markers and agronomic traits

Knowledge of genetic interrelationships and grouping among pigeonpea germplasm collections is fundamental to selecting breeding parents with unique genetic constitutions. The objectives of this study were to assess the genetic diversity and genetic grouping present among 81 pigeonpea genotypes collected from Malawi, Tanzania and Kenya using 4122 single nucleotide polymorphism (SNP) markers and complementary morphological traits. The SNP markers and phenotypic traits revealed significant genetic variation among the assessed genotypes. The test genotypes were resolved into three distinct clusters based on both marker systems. The mean gene diversity and the polymorphic information content (PIC) were 0.14 and 0.11, suggesting moderate genetic differentiation among the genotypes. The analysis of molecular variance revealed that differences among populations accounted for only 2.7% of the variation, while within the population (among individuals) accounted for 97.3% of the variation. The results based on the DArT SNP genotyping complemented the phenotypic data and led to the selection of unique pigeonpea genotypes for effective breeding programs in Malawi and related agroecologies. This suggested that unique breeding populations could be created by identifying and selecting divergent individuals as parental lines. There is a need to create a new genetic variation or introgress genes from genetically unrelated parents to increase the genetic base of the current pigeonpea breeding populations.

A Multi-Level Approach as a Powerful Tool to Identify and Characterize Some Italian Autochthonous Common Bean (Phaseolus vulgaris L.) Landraces under a Changing Environment

A prime role in matters of agrobiodiversity is held by landraces, which serve as a repository gene pool able to meet sustainable development goals and to face the ongoing challenges of climate change. However, many landraces are currently endangered due to environmental and socio-economic changes. Thus, effective characterization activities and conservation strategies should be undertaken to prevent their genetic and cultural erosion. In the current study, the morphological, genetic, and biochemical analyses were integrated with stress response-related studies to characterize the diversity of seven Italian autochthonous common bean landraces. The results showed that the morphological descriptors and the neutral molecular markers represent powerful tools to identify and distinguish diversity among landrace populations, but they cannot correlate with the stress tolerance pattern of genetically similar populations. The study also supported the use of proline as a biochemical marker to screen the most salt-sensitive bean landraces. Thus, to fully elucidate the future dynamics of agrobiodiversity and to establish the basis for safeguarding them while promoting their utilization, a multi-level approach should always be included in any local and national program for the characterization/conservation/use of genetic resources. This study should represent the basis for further joint research that effectively contributes to set/achieve Italian priorities towards sustainability in the framework of emerging environmental, societal, and economic challenges.

Height to first pod: A review of genetic and breeding approaches to improve combine harvesting in legume crops

Height from soil at the base of plant to the first pod (HFP) is an important trait for mechanical harvesting of legume crops. To minimise the loss of pods, the HFP must be higher than that of the blades of most combine harvesters. Here, we review the genetic control, morphology, and variability of HFP in legumes and attempt to unravel the diverse terminology for this trait in the literature. HFP is directly related to node number and internode length but through different mechanisms. The phenotypic diversity and heritability of HFP and their correlations with plant height are very high among studied legumes. Only a few publications describe a QTL analysis where candidate genes for HFP with confirmed gene expression have been mapped. They include major QTLs with eight candidate genes for HFP, which are involved in auxin transport and signal transduction in soybean [Glycine max (L.) Merr.] as well as MADS box gene SOC1 in Medicago trancatula, and BEBT or WD40 genes located nearby in the mapped QTL in common bean (Phaseolus vulgaris L.). There is no information available about simple and efficient markers associated with HFP, which can be used for marker-assisted selection for this trait in practical breeding, which is still required in the nearest future. To our best knowledge, this is the first review to focus on this significant challenge in legume-based cropping systems.

Morphological and molecular characterization of variation in common bean (Phaseolus vulgaris L.) germplasm from Azad Jammu and Kashmir, Pakistan

Phaseolus vulgaris, an essential food and source of protein, is cultivated across the world. This study was carried out to investigate the diversity and population structure of 34 P. vulgaris landrace accessions collected from the Azad Jammu and Kashmir (AJ&K) regions of Pakistan. The samples were analyzed both morphologically and using genetic variation identified through RNA sequencing. Our results indicated that most genetic variation occurs among local accessions, with little genetic variation occurring between geographical regions. In addition, the accessions fell into two major genetic groups. Morphological analysis revealed that these two genetic groups differ in a number of quantitative traits, including seed length, seed width, and seed weight. One accession, DUD-11, appears to be a mixture of the two major groups genetically as well as morphologically. Among the other accessions, DUD-8, RWK-2, and NGD-1 depicted particularly high seed weight along with higher seed length, seed width, and seed yield per plant. We suggest focusing on these accessions in future breeding programs. More generally, our results provide baseline data that will be useful for crop improvement and effective cultivation practices in Pakistan.

Identification of QTLs/ Candidate Genes for Seed Mineral Contents in Common Bean (Phaseolus vulgaris L.) Through Genotyping-by-Sequencing

Throughout the ages, the common bean has been consumed by humanity as an important food staple crop and source of nutrition on a global scale. Since its domestication, a wide spectrum of phenotypic and genotypic investigations have been carried out to unravel the potential of this crop and to understand the process of nutrient accumulation along with other desirable characteristics. The common bean is one of the essential legume crops due to its high protein and micronutrient content. The balance in micronutrients is critical for the growth and development of plants as well as humans. Iron (Fe), Zinc (Zn), Copper (Cu), Manganese (Mn), Magnesium (Mg), Calcium (Ca), and Molybdenum (Mo) are some of the important micronutrients present in legumes. Thus, we aimed to investigate the quantitative trait loci’s (QTLs)/single nucleotide polymorphisms (SNPs) to identify the candidate genes associated with micronutrients through genotyping by sequencing (GBS). In our investigation, through GBS we identified SNPs linked with traits and assessed seven micronutrients in 96 selected common bean genotypes for screening nutritionally rich genotypes. Among 96399 SNPs total identified through GBS, 113 SNPs showed significant phenotypic variance, ranging from 13.50 to 21.74%. SNPs associated with most of the seed micronutrients (Mg, Mn, Fe, Ca, Cu) were found on chr3 & chr11 (Mg, Mn, Mo, Ca, Zn). The findings from this study could be used for haplotype-based selection of nutritionally rich genotypes and for marker-assisted genetic enhancement of the common bean. Further, the identified SNPs for candidate genes/transporters associated with micronutrient content may pave the way for the enrichment of seeds by employing genomics-assisted breeding programs.

Multivariate genomic analysis and optimal contributions selection predicts high genetic gains in cooking time, iron, zinc, and grain yield in common beans in East Africa

Common bean (Phaseolus vulgaris L.) is important in African diets for protein, iron (Fe), and zinc (Zn), but traditional cultivars have long cooking time (CKT), which increases the time, energy, and health costs of cooking. Genomic selection was used to predict genomic estimated breeding values (GEBV) for grain yield (GY), CKT, Fe, and Zn in an African bean panel of 358 genotypes in a two-stage analysis. In Stage 1, best linear unbiased estimates (BLUE) for each trait were obtained from 898 genotypes across 33 field trials in East Africa. In Stage 2, BLUE in a training population of 141 genotypes were used in a multivariate genomic analysis with genome-wide single nucleotide polymorphism data from the African bean panel. Moderate to high genomic heritability was found for GY (0.45 ± 0.10), CKT (0.50 ± 0.15), Fe (0.57 ± 0.12), and Zn (0.61 ± 0.13). There were significant favorable genetic correlations between Fe and Zn (0.91 ± 0.06), GY and Fe (0.66 ± 0.17), GY and Zn (0.44 ± 0.19), CKT and Fe (-0.57 ± 0.21), and CKT and Zn (-0.67 ± 0.20). Optimal contributions selection (OCS), based on economic index of weighted GEBV for each trait, was used to design crossing within four market groups relevant to East Africa. Progeny were predicted by OCS to increase in mean GY by 12.4%, decrease in mean CKT by 9.3%, and increase in mean Fe and Zn content by 6.9 and 4.6%, respectively, with low achieved coancestry of 0.032. Genomic selection with OCS will accelerate breeding of high-yielding, biofortified, and rapid cooking African common bean cultivars.

Productivity of Newly Released Common Bean (Phaseolus vulgaris L.) Varieties Under Sole Cropping and Intercropping With Maize (Zea mays L.)

Intercropping maize (Zea mays L.) with common bean (Phaseolus vulgaris L.) is one of the predominant farming practices in eastern and southern Africa (ESA) for effective use of resources and continuous household food supply. The productivity of sole or intercropped crops is subject to variety, location, year, and their interaction. Therefore, the objective of this study was to determine the productivity of newly released common bean varieties NUA45 and SER83 under sole cropping and intercropping with a maize hybrid variety SC672 as a guide to large-scale production. Experiments were conducted at Chitedze Agricultural Research Station (13.85°S; 33.38°E) and Linthipe Extension Planning Area (12.06°S; 33.25°E) in 2019 and 2020 in Malawi using a factorial arrangement laid out in a randomized complete block design (RCBD) with four replications. The numbers of pods per plant (NPP) and seeds per pod (NSP), grain yield (GYD), and 100-seed weight were collected for common bean included, while GYD was recorded for maize. The main effects for genotype, location, year, and intercropping system were significant (p < 0.05) for GYD in common bean. The effects of the year and cropping system and location by intercropping system interaction were significant for maize GYD. The maize yield did not vary between sole cropped and intercropped systems. The total land equivalent ratios (LERs) for NUA45 and SER83 were 1.59 and 1.77, respectively. The LER-values showed a significant difference (p < 0.034), suggesting a considerably higher benefit of maize and common bean intercropping. Overall, intercropping maize with common bean rendered higher yields in the SER83/SC672 intercropping system than the sole crop in the study areas. Therefore, intra-row intercropping of the newly released common bean variety SER83 with a maize hybrid variety SC672 is recommended in the study area and other similar agro-ecologies for stable and sustainable production of both crops.

Genetic and phenotypic diversity of selected Kenyan mung bean (Vigna radiata L. Wilckzek) genotypes

BACKGROUND

Mung bean is a pulse crop principally grown in the tropic and subtropic parts of the world for its nutrient-rich seeds. Seven mung beans accessions from Eastern Kenya were evaluated using thirteen phenotypic traits. In addition, 10 SSR markers were used to determine their genetic diversity and population structure. This aimed at enhancing germplasm utilization for subsequent mung bean breeding programs.

RESULTS

Analysis of variance for most of the phenology traits showed significant variation, with the yield traits recording the highest. The first three principal components (PC) explained 83.4% of the overall phenotypic variation, with the highest (PC1) being due to variation of majority of the traits studied such as pod length, plant height, and seeds per pod. The dendogram revealed that the improved genotypes had common ancestry with the local landraces. The seven mung beans were also genotyped using 10 microsatellite markers, eight of which showed clear and consistent amplification profiles with scorable polymorphisms in all the studied genotypes. Genetic diversity, allele number, and polymorphic information content (PIC) were determined using powermarker (version 3.25) and phylogenetic tree constructed using DARWIN version 6.0.12. Analysis of molecular variance (AMOVA) was calculated using GenALEx version 6.5. A total of 23 alleles were detected from the seven genotypes on all the chromosomes studied with an average of 2.875 across the loci. The PIC values ranged from 0.1224 (CEDG056) to 0.5918 (CEDG092) with a mean of 0.3724. Among the markers, CEDG092 was highly informative while the rest were reasonably informative except CEDG056, which was less informative. Gene diversity ranged from 0.1836 (CEDG050) to 0.5102 (CDED088) with an average of 0.3534. The Jaccards dissimilarity matrix indicated that genotypes VC614850 and N26 had the highest level of dissimilarity while VC637245 and N26 had lowest dissimilarity index. The phylogenetic tree grouped the genotypes into three clusters as revealed by population structure analysis (K = 3), with cluster III having one unique genotype (VC6137B) only. AMOVA indicated that the highest variation (99%) was between individual genotype. In addition, marker traits association analysis revealed 18 significant associations (P < 0.05).

CONCLUSION

These findings indicate sufficient variation among the studied genotypes that can be considered for germplasm breeding programs.

Assessment of the Origin and Diversity of Croatian Common Bean Germplasm Using Phaseolin Type, SSR and SNP Markers and Morphological Traits

Landraces represent valuable genetic resources for breeding programmes to produce high-yielding varieties adapted to stressful environmental conditions. Although the common bean (Phaseolus vulgaris L.) is an economically important food legume for direct human consumption worldwide, common bean production in Croatia is based almost exclusively on landraces and there is no common bean breeding program. Information on phaseolin type and results of population structure and genetic diversity obtained by analysis of SSR and SNP markers, in combination with the morphological characterization of 174 accessions of 10 common bean landraces (morphotypes), enabled thorough classification of accessions. The accessions were classified into phaseolin type H1 (“S”) of Mesoamerican origin and phaseolin types H2 (“H” or “C”) and H3 (“T”) of Andean origin. By applying distance- and model-based clustering methods to SSR markers, the accessions were classified into two clusters at K = 2 separating the accessions according to the centres of origin, while at K = 3, the accessions of Andean origin were further classified into two clusters of accessions that differed in phaseolin type (H2 and H3). Using SNP markers, model-based analysis of population structure was performed, the results of which were consistent with those of SSR markers. In addition, 122 accessions were assigned to 14 newly formed true-type morphogenetic groups derived from three different domestication events: (1) Mesoamerican (H1A) (“Biser”, “Kukuruzar”, “Tetovac”, “Trešnjevac”), (2) Andean—indeterminate type (H2B1) (“Dan noć”, “Sivi”, “Puter”, ”Sivi prošarani”, “Trešnjevac”) and (3) Andean—determinate type (H3B2) (“Bijeli”, “Dan noć”, “Puter”, “Trešnjevac”, “Zelenčec”). The rest of the accessions could represent putative hybrids between morphogenetic groups. The differences between the true-type groups of accessions were further analysed based on nine quantitative traits, and the subsets of traits that best distinguish among centres of origin (A: Mesoamerican, B: Andean) and genetic groups (H1A, H2B1, H3B2) were proposed.