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.

Genotype-by-environment interaction on canning and cooking quality of advanced large-seeded common bean genotypes.

Developing beans for high canning and cooking quality has been a major concern of plant breeders as the demand of consumers for beans in terms of quality is increasing. This study determined the effect of genotype-by-environment (GEI) on canning and cooking quality of common beans. Twenty three newly developed large-seeded bean genotypes and two standard checks collected from five growing sites of Ethiopia were tested using randomized completed block design with three replicates. Additive main effect and multiplicative Interaction (AMMI) and genotype plus genotype-by-environment interaction (GGE) biplot models were used in the data analysis. Genotypes were genetically different (P ≤ 0.01) for all of the quality traits varied from 42.3 to 57.4 minutes for cooking time and 260.4-278.6g for washed drained weight. Percent washed drained weight of all the tested genotypes was >60%, as required by processors. However, hydration coefficient (HC) was below the desired optimum level of 1.8, which could be improved through prolonged soaking period. From moderate to no clumping, and from moderately clear to clear brine were observed for canned beans. Generally, the newly developed genotypes had better canning and cooking quality except for HC. However, GEI exerted considerable effect on the quality traits especially cooking time. The interaction effect (34.25%) shared nearly three times greater effect than genotype (13.31%) and environment (11.44%); hence highly determined the cooking time. Both AMMI2 and GGE polygon view biplots captured 69.05 and 74.10% of the GEI variation, respectively, using the first and the second principal component axes (PCAs). In conclusion, plant breeders should think of GEI when testing beans for canning and cooking quality at substantial environments.

Identification of putative CLE peptide receptors involved in determinate nodulation on soybean.

CLAVATA3/EMBRYO SURROUNDING REGION (CLE) peptides tightly control the balance between stem cell proliferation and differentiation in several plant developmental processes. Transmission of the CLE peptide signal has been shown to be rather complex. Despite their recent identification, little is known about the receptors by which nodulation-specific CLE peptides, which were identified in soybean, are perceived. Genetic analysis has indicated that the leucine-rich repeat receptor-like kinase NARK of soybean (Glycine max) and its orthologs in other legumes are possible candidates. However, more receptors need to be identified because CLE peptides are often detected by heteromultimeric complexes. Here, we identified two additional putative CLE peptide receptor pairs in the soybean genome with a nodulation-related expression pattern, GmRLK1-GmRLK2 and GmRLK3-GmRLK4, and discuss their role in CLE peptide perception during nodulation.

Search for nodulation-related CLE genes in the genome of Glycine max.

CLE peptides are potentially involved in nodule organ development and in the autoregulation of nodulation (AON), a systemic process that restricts nodule number. A genome-wide survey of CLE peptide genes in the soybean glycine max genome resulted in the identification of 39 GmCLE genes, the majority of which have not yet been annotated. qRT-PCR analysis indicated two different nodulation-related CLE expression patterns, one linked with nodule primordium development and a new one linked with nodule maturation. Moreover, two GmCLE gene pairs, encoding group-III CLE peptides that were previously shown to be involved in AON, had a transient expression pattern during nodule development, were induced by the essential nodulation hormone cytokinin, and one pair was also slightly induced by the addition of nitrate. Hence, our data support the hypothesis that group-III CLE peptides produced in the nodules are involved in primordium homeostasis and intertwined in activating AON, but not in sustaining it.