High-density DArTSeq SNP markers revealed wide genetic diversity and structured population in common bean (Phaseolus vulgaris L.) germplasm in Ethiopia

INTRODUCTION

Common bean is one of the widely consumed food security crop in Africa, Asia, and South America. Understanding genetic diversity and population structure is crucial for designing breeding strategies.

MATERIALS

Two hundred and eighty-nine germplasm were recently collected from different regions of Ethiopia and introduced from CIAT to estimate genetic diversity and population structure using 11,480 DArTSeq SNP markers.

RESULTS

The overall mean genetic diversity and polymorphic information content (PIC) were 0.38 and 0.30, respectively, suggested the presence of adequate genetic diversity among the genotypes. Among the geographical regions, landraces collected from Oromia showed the highest diversity (0.39) and PIC (0.30). The highest genetic distance was observed between genotypes collected from SNNPR and CIAT (0.49). In addition, genotypes from CIAT were genetically more related to improved varieties than the landraces which could be due to sharing of parents in the improvement process. The analysis of molecular variance revealed that the largest proportion of variation was due to within the population both in geographical region (63.67%) and breeding status (61.3%) based classification. Model-based structure analysis delineated the 289 common bean genotypes into six hypothetical ancestoral populations.

CONCLUSIONS

The genotypes were not clustered based on geographical regions and they were not the main drivers for the differentiation. This indicated that selection of the parental lines should be based on systematic assessment of the diversity rather than geographical distance. This article provides new insights into the genetic diversity and population structure of common bean for association studies, designing effective collection and conservation for efficient utilization for the improvement of the crop.

Genome wide association analysis for grain micronutrients and anti-nutritional traits in mungbean [Vigna radiata (L.) R. Wilczek] using SNP markers

Mungbean is an important food grain legume for human nutrition and nutritional food due to its nutrient-dense seed, liked palatability, and high digestibility. However, anti-nutritional factors pose a significant risk to improving nutritional quality for bio-fortification. In the present study, genetic architecture of grain micronutrients (grain iron and zinc concentration) and anti-nutritional factors (grain phytic acid and tannin content) in association mapping panel of 145 diverse mungbean were evaluated. Based on all four parameters genotypes PUSA 1333 and IPM 02-19 were observed as desired genotypes as they had high grain iron and zinc concentration but low grain phytic acid and tannin content. The next generation sequencing (NGS)-based genotyping by sequencing (GBS) identified 14,447 genome-wide SNPs in a diverse selected panel of 127 mungbean genotypes. Population admixture analysis revealed the presence of four different ancestries among the genotypes and LD decay of ∼57.6 kb kb physical distance was noted in mungbean chromosomes. Association mapping analysis revealed that a total of 20 significant SNPs were shared by both GLM and Blink models associated with grain micronutrient and anti-nutritional factor traits, with Blink model identifying 35 putative SNPs. Further, this study identified the 185 putative candidate genes. Including potential candidate genes Vradi07g30190, Vradi01g09630, and Vradi09g05450 were found to be associated with grain iron concentration, Vradi10g04830 with grain zinc concentration, Vradi08g09870 and Vradi01g11110 with grain phytic acid content and Vradi04g11580 and Vradi06g15090 with grain tannin content. Moreover, two genes Vradi07g15310 and Vradi09g05480 showed significant variation in protein structure between native and mutated versions. The identified SNPs and candidate genes are potential powerful tools to provide the essential information for genetic studies and marker-assisted breeding program for nutritional improvement in mungbean.

Genetic Diversity and Population Structure of Common Bean (Phaseolus vulgaris L.) Landraces in the Lazio Region of Italy

Common bean cultivation has historically been a typical component of rural economies in Italy, particularly in mountainous and hilly zones along the Apennine ridge of the central and southern regions, where the production is focused on local landraces cultivated by small-scale farmers using low-input production systems. Such landraces are at risk of genetic erosion because of the recent socioeconomic changes in rural communities. One hundred fourteen accessions belonging to 66 landraces still being grown in the Lazio region were characterized using a multidisciplinary approach. This approach included morphological (seed traits), biochemical (phaseolin and phytohemagglutinin patterns), and molecular (microsatellite loci) analyses to investigate their genetic variation, structure, and distinctiveness, which will be essential for the implementation of adequate ex situ and in situ conservation strategies. Another objective of this study was to determine the original gene pool (Andean and Mesoamerican) of the investigated landraces and to evaluate the cross-hybridization events between the two ancestral gene pools in the P. vulgaris germplasm in the Lazio region. Molecular analyses on 456 samples (four for each of the 114 accessions) revealed that the P. vulgaris germplasm in the Lazio region exhibited a high level of genetic diversity (He = 0.622) and that the Mesoamerican and Andean gene pools were clearly differentiated, with the Andean gene pool prevailing (77%) and 12% of landraces representing putative hybrids between the two gene pools. A model-based cluster analysis based on the molecular markers highlighted three main groups in agreement with the phaseolin patterns and growth habit of landraces. The combined utilisation of morphological, biochemical, and molecular data allowed for the differentiation of all landraces and the resolution of certain instances of homonymy and synonymy. Furthermore, although a high level of homozygosity was found across all landraces, 32 of the 66 examined (49%) exhibited genetic variability, indicating that the analysis based on a single or few plants per landrace, as usually carried out, may provide incomplete information.

Sweet Cherry Diversity and Relationships in Modern and Local Varieties Based on SNP Markers

The sweet cherry is an important fruit species that is widespread globally. In addition to the well-known traditional and modern varieties, a myriad of landraces is present in Europe, as well as in southern Italy. This study aims to evaluate the population structure, genetic relationships, and cases of duplicate samples in a collection of 143 accessions using GBS-derived SNP markers. The genetic material under investigation includes modern commercial varieties, ancient European and American varieties, landraces, and individuals retrieved from small orchards. Some of the known varieties were genetically analyzed here for the first time. In addition, several genotypes were collected from the Basilicata region (southern Italy), an area largely unexplored for sweet cherry genetic resources. The relationships among genotypes were assessed using four different methods: allele frequency and ancestry estimation, principal component analysis, Neighbor-Joining tree, and identity-by-state estimation. The analyses returned quite congruent results and highlighted the presence of four main genetic groups, namely: (i) American varieties, (ii) the 'Germersdorfer-Ferrovia' cluster, (iii) the 'Burlat' group, and (iv) the group of Italian landraces. The main drivers of clustering were ancestry, geographical distribution, and some important traits such as self-compatibility. The sweet cherries from Basilicata, herewith examined for the first time, were mostly distributed within the group of Italian landraces, being particularly linked to the autochthonous varieties of the Campania region. However, some genotypes were outside this group, thus suggesting the introduction of genetic material from other Italian regions or from European countries. The considerable amount of American and European modern varieties analyzed are genetically very closely related, suggesting a reduced genetic basis. In addition, we highlighted the discriminating ability of SNP markers to distinguish between an original variety and its mutant. Overall, our results may be useful in defining conservation strategies for sweet cherry germplasm and developing future breeding programs to enlarge the genetic basis of commercial varieties.

Novel candidate loci for morpho-agronomic and seed quality traits detected by targeted genotyping-by-sequencing in common bean

Phaseolus vulgaris L., known as common bean, is one of the most important grain legumes cultivated around the world for its immature pods and dry seeds, which are rich in protein and micronutrients. Common bean offers a cheap food and protein sources to ameliorate food shortage and malnutrition around the world. However, the genetic basis of most important traits in common bean remains unknown. This study aimed at identifying QTL and candidate gene models underlying twenty-six agronomically important traits in common bean. For this, we assembled and phenotyped a diversity panel of 200 P. vulgaris genotypes in the greenhouse, comprising determinate bushy, determinate climbing and indeterminate climbing beans. The panel included dry beans and snap beans from different breeding programmes, elite lines and landraces from around the world with a major focus on accessions of African, European and South American origin. The panel was genotyped using a cost-conscious targeted genotyping-by-sequencing (GBS) platform to take advantage of highly polymorphic SNPs detected in previous studies and in diverse germplasm. The detected single nucleotide polymorphisms (SNPs) were applied in marker-trait analysis and revealed sixty-two quantitative trait loci (QTL) significantly associated with sixteen traits. Gene model identification via a similarity-based approach implicated major candidate gene models underlying the QTL associated with ten traits including, flowering, yield, seed quality, pod and seed characteristics. Our study revealed six QTL for pod shattering including three new QTL potentially useful for breeding. However, the panel was evaluated in a single greenhouse environment and the findings should be corroborated by evaluations across different field environments. Some of the detected QTL and a number of candidate gene models only elucidate the understanding of the genetic nature of these traits and provide the basis for further studies. Finally, the study showed the possibility of using a limited number of SNPs in performing marker-trait association in common bean by applying a highly scalable targeted GBS approach. This targeted GBS approach is a cost-efficient strategy for assessment of the genetic basis of complex traits and can enable geneticists and breeders to identify novel loci and targets for marker-assisted breeding more efficiently.

Genetic structure and geneflow of Malus across the Korean Peninsula using genotyping-by-sequencing

This study was to understand the genetic structure and diversity of the Korean Malus species. We used genotyping-by-sequencing (GBS) technology to analyze samples of 112 individuals belonging to 18 populations of wild Malus spp. Using GBS, we identified thousands of single nucleotide polymorphisms in the species analyzed. M. baccata and M. toringo, two dominant mainland species of the Korean Peninsula, were distinguishable based on their genetic structure. However, M. toringo collected from Jeju Island exhibited a different genetic profile than that from the mainland. We identified M. cf. micromalus as a hybrid resulting from the Jeju Island M. toringo (pollen donor) and the mainland M. baccata, (pollen recipient). Putative M. mandshurica distributed on the Korean Peninsula showed a high structural and genetic similarity with M. baccata, indicating that it might be an ecotype. Overall, this study contributes to the understanding of the population history and genetic structure of Malus in the Korean Peninsula.

Genotyping-by-Sequencing in Vigna unguiculata Landraces and Its Utility for Assessing Taxonomic Relationships

Genotyping by sequencing (GBS) was used to analyze relationships among cowpea and asparagus bean landraces from southern Italy and to assess the utility of this technology to study taxonomy in a wider panel, including V. unguiculata cultigroups, subspecies, and other Vigna species. The analysis of SNPs derived from GBS highlighted that, among the cowpea landraces, the African samples were separated from the other material, while, for the Italian landraces, a certain clustering depending on seed color/pattern was observed in the dendrogram. When examining the V. unguiculata species complex, a clear separation between the two groups of wild subspecies, i.e., the allogamous wild perennials and the perennial out/inbreds, could be observed, the former representing the more ancestral wild progenitors of V. unguiculata. The species V. vexillata appeared more closely related to V. unguiculata than to the other Vigna species analyzed.

Population structure, genetic diversity and genomic selection signatures among a Brazilian common bean germplasm

Brazil is the world's largest producer of common bean. Knowledge of the genetic diversity and relatedness of accessions adapted to Brazilian conditions is of great importance for the conservation of germplasm and for directing breeding programs aimed at the development of new cultivars. In this context, the objective of this study was to analyze the genetic diversity, population structure, and linkage disequilibrium (LD) of a diversity panel consisting of 219 common bean accessions, most of which belonging to the Mesoamerican gene pool. Genotyping by sequencing (GBS) of these accessions allowed the identification of 49,817 SNPs with minor allele frequency > 0.05. Of these, 17,149 and 12,876 were exclusive to the Mesoamerican and Andean pools, respectively, and 11,805 SNPs could differentiate the two gene pools. Further the separation according to the gene pool, bayesian analysis of the population structure showed a subdivision of the Mesoamerican accessions based on the origin and color of the seed tegument. LD analysis revealed the occurrence of long linkage blocks and low LD decay with physical distance between SNPs (LD half decay in 249 kb, corrected for population structure and relatedness). The GBS technique could effectively characterize the Brazilian common bean germplasms, and the diversity panel used in this study may be of great use in future genome-wide association studies.

The Beneficial Health Effects of Vegetables and Wild Edible Greens: The Case of the Mediterranean Diet and Its Sustainability

The Mediterranean diet (MD) concept as currently known describes the dietary patterns that were followed in specific regions of the area in the 1950s and 1960s. The broad recognition of its positive effects on the longevity of Mediterranean populations also led to the adoption of this diet in other regions of the world, and scientific interest focused on revealing its health effects. MD is not only linked with eating specific nutritional food products but also with social, religious, environmental, and cultural aspects, thus representing a healthy lifestyle in general. However, modern lifestyles adhere to less healthy diets, alienating people from their heritage. Therefore, considering the increasing evidence of the beneficial health effects of adherence to the MD and the ongoing transitions in consumers’ behavior, the present review focuses on updating the scientific knowledge regarding this diet and its relevance to agrobiodiversity. In addition, it also considers a sustainable approach for new marketing opportunities and consumer trends of the MD.

Genetic Diversity, Nitrogen Fixation, and Water Use Efficiency in a Panel of Honduran Common Bean (Phaseolus vulgaris L.) Landraces and Modern Genotypes

Common bean (Phaseolus vulgaris L.) provides critical nutrition and a livelihood for millions of smallholder farmers worldwide. Beans engage in symbiotic nitrogen fixation (SNF) with Rhizobia. Honduran hillside farmers farm marginal land and utilize few production inputs; therefore, bean varieties with high SNF capacity and environmental resiliency would be of benefit to them. We explored the diversity for SNF, agronomic traits, and water use efficiency (WUE) among 70 Honduran landrace, participatory bred (PPB), and conventionally bred bean varieties (HON panel) and 6 North American check varieties in 3 low-N field trials in Ontario, Canada and Honduras. Genetic diversity was measured with a 6K single nucleotide polymorphism (SNP) array, and phenotyping for agronomic, SNF, and WUE traits was carried out. STRUCTURE analysis revealed two subpopulations with admixture between the subpopulations. Nucleotide diversity was greater in the landraces than the PPB varieties across the genome, and multiple genomic regions were identified where population genetic differentiation between the landraces and PPB varieties was evident. Significant differences were found between varieties and breeding categories for agronomic traits, SNF, and WUE. Landraces had above average SNF capacity, conventional varieties showed higher yields, and PPB varieties performed well for WUE. Varieties with the best SNF capacity could be used in further participatory breeding efforts.