Antonio M. De Ron

Genetic diversity of Argentinean common bean and its evolution during domestication

Wild populations of common bean pertainingto the Andean gene pool are distributedfrom southern Peru to northern Argentina.The objectives of this study were todetermine the genetic structure of Andeanlandraces from northern Argentina, as oneof the potential domestication sites of theAndean domesticated gene pool, and toestablish a correspondence between Andeanprimitive landraces and wild populationsthat might have served as the source ofdomesticated bean. Forty-four landraces and21 wild populations representing thediversity of common bean in northernArgentina were included in this study. Results indicated that Andean gene pool inArgentina has a large genetic base on thebasis of morphological and adaptivevariability and biochemical analysis. Theexistence of introgressed populations withsympatric wild forms was evidenced.

Uncovering the genetic architecture of Colletotrichum lindemuthianum resistance through QTL mapping and epistatic interaction analysis in common bean

Colletotrichum lindemuthianum is a hemibiotrophic fungal pathogen that causes anthracnose disease in common bean. Despite the genetics of anthracnose resistance has been studied for a long time, few quantitative trait loci (QTLs) studies have been conducted on this species. The present work examines the genetic basis of quantitative resistance to races 23 and 1545 of C. lindemuthianum in different organs (stem, leaf and petiole). A population of 185 recombinant inbred lines (RIL) derived from the cross PMB0225 × PHA1037 was evaluated for anthracnose resistance under natural and artificial photoperiod growth conditions. Using multi-environment QTL mapping approach, 10 and 16 main effect QTLs were identified for resistance to anthracnose races 23 and 1545, respectively. The homologous genomic regions corresponding to 17 of the 26 main effect QTLs detected were positive for the presence of resistance-associated gene cluster encoding nucleotide-binding and leucine-rich repeat (NL) proteins. Among them, it is worth noting that the main effect QTLs detected on linkage group 05 for resistance to race 1545 in stem, petiole and leaf were located within a 1.2 Mb region. The NL gene Phvul.005G117900 is located in this region, which can be considered an important candidate gene for the non-organ-specific QTL identified here. Furthermore, a total of 39 epistatic QTL (E-QTLs) (21 for resistance to race 23 and 18 for resistance to race 1545) involved in 20 epistatic interactions (eleven and nine interactions for resistance to races 23 and 1545, respectively) were identified. None of the main and epistatic QTLs detected displayed significant environment interaction effects. The present research provides essential information not only for the better understanding of the plant-pathogen interaction but also for the application of genomic assisted breeding for anthracnose resistance improvement in common bean through application of marker-assisted selection (MAS).

Assessment of runner bean ( Phaseolus coccineus L.) germplasm for tolerance to low temperature during early seedling growth

The runner bean requires moderately high temperatures for optimum germination and growth. Low temperature at sowing delays both germination and plant emergence, and can reduce establishment of beans planted early in the growing season. The objective of this work was to identify potential runner bean germplasm with tolerance to low temperature and to assess the role of this germplasm for production and breeding. Seeds of 33 runner bean accessions were germinated in a climate-controlled chamber at optimal (17°C-day/15°C-night) and at sub-optimal (14°C-day/8°C-night) temperature. The low temperature tolerance was evaluated on the basis of germination, earliness, ability to grow and vigor. Differences in agronomical characters were significant at low temperatures for germination, earliness, ability to grow and early vigor except for emergence score. The commercial cultivars Painted Lady Bi-color, Scarlet Emperor, the Rwanda cultivar NI-15c, and the Spanish cultivars PHA-0013, PHA-0133, PHA-0311, PHA-0664, and PHA-1025 had the best performance under cold conditions.

Marker-based linkage map of Andean common bean (Phaseolus vulgaris L.) and mapping of QTLs underlying popping ability traits

BackgroundNuña bean is a type of ancient common bean (Phaseolus vulgaris L.) native to the Andean region of South America, whose seeds possess the unusual property of popping. The nutritional features of popped seeds make them a healthy low fat and high protein snack. However, flowering of nuña bean only takes place under short-day photoperiod conditions, which means a difficulty to extend production to areas where such conditions do not prevail. Therefore, breeding programs of adaptation traits will facilitate the diversification of the bean crops and the development of new varieties with enhanced healthy properties. Although the popping trait has been profusely studied in maize (popcorn), little is known about the biology and genetic basis of the popping ability in common bean. To obtain insights into the genetics of popping ability related traits of nuña bean, a comprehensive quantitative trait loci (QTL) analysis was performed to detect single-locus and epistatic QTLs responsible for the phenotypic variance observed in these traits.ResultsA mapping population of 185 recombinant inbred lines (RILs) derived from a cross between two Andean common bean genotypes was evaluated for three popping related traits, popping dimension index (PDI), expansion coefficient (EC), and percentage of unpopped seeds (PUS), in five different environmental conditions. The genetic map constructed included 193 loci across 12 linkage groups (LGs), covering a genetic distance of 822.1 cM, with an average of 4.3 cM per marker. Individual and multi-environment QTL analyses detected a total of nineteen single-locus QTLs, highlighting among them the co-localized QTLs for the three popping ability traits placed on LGs 3, 5, 6, and 7, which together explained 24.9, 14.5, and 25.3% of the phenotypic variance for PDI, EC, and PUS, respectively. Interestingly, epistatic interactions among QTLs have been detected, which could have a key role in the genetic control of popping.ConclusionsThe QTLs here reported constitute useful tools for marker assisted selection breeding programs aimed at improving nuña bean cultivars, as well as for extending our knowledge of the genetic determinants and genotype x environment interaction involved in the popping ability traits of this bean crop.

Variation for nodulation and plant yield of common bean genotypes and environmental effects on the genotype expression

Common bean symbiotic nitrogen fixation provides an ecological and economical alternative to increase bean production but it depends on soil fertility and climate conditions. The objectives of this work were to characterize common bean genotypes for their ability to establish symbiosis under controlled conditions and to study the effect of the environment on the expression of those genotypes. The experiment under controlled conditions was conducted in a greenhouse with 158 genotypes that represented the major dry bean market classes. The field experiment was carried out in six environments with 64 genotypes that were previously selected for their contrasting nodulation ability and/or root development under the controlled conditions experiment. Nodulation, plant, and grain yield data of the bean genotypes were measured in both experiments. There was a significant high variability in plant development responses among the studied genotypes associated with the rhizobial strain inoculated under controlled conditions. Two nodulation phenotypes were observed among the genotypes tested: the big-nodules phenotype (BNO) associated with almost 63% fewer nodules and 58% higher proportion of nodule biomass in the below-ground compartment than the small-nodules phenotype (SNO) with less developed aerial parts. Genotype plus genotype × environment (GGE) biplot model analysis enabled identification of the highest-yielding genotypes for the different environments. The soil chemical factors of these environments were associated with the nodule number or the biomass of the common bean genotypes. Genotypes with a BNO phenotype showed a good plant response, indicating that this phenotype may be more beneficial for plant growth and seed yield in environmental conditions that may limit nodule development. The amplitude of the genotypic variability found in this work confirms the potential for rhizobial symbiosis of adapted bean genotypes, which could constitute a preferential material for initial breeding of symbiotically active lines. The data also indicate the potential of bean breeding to identify environments containing effective strains of rhizobia essential for sustainable agriculture, improving productivity, and maintaining environmental quality.

Variation in primitive landraces of common bean (Phaseolus vulgaris L.) from Argentina

The phenotypic variation found in four common bean (Phaseolus vulgaris L.) complex primitive landraces, among a group of accessions collected in Northwestern Argentina in several missions is described, with particular attention to the wide diversity found in some small areas. It is presented a hypothesis about the maintenance of such diversity in bean mixtures or complex primitive landraces that grow close to their wild relative. Wide diversity regarding to seed type and plant characteristics was displayed by the landraces MCM-SV (composed of 11 lines), MCM-292 (14 lines), MCM-298 (5 lines) and VAV-3716 (14 lines). Food uses of dry seed and fresh pod seemed to be more relevant than the aesthetic use although all of them were presumably considered by humans for centuries resulting in the current phenotypes of these complex primitive landraces. Additionally, some weedy types (intermediate between wild and domesticated types) were detected in the landracesMCM-292 and MCM-298. The four complex landraces described consisted of highly diverse mixtures and they could play a role in breeding to enlarge the genetic basis of domesticated bean varieties belonging to the Andean gene pool.

Genetic variation underlying pod size and color traits of common bean depends on quantitative trait loci with epistatic effects

Common bean is an important vegetable legume in many regions of the world. Size and color of fresh pods are the key factors for deciding the commercial acceptance of bean as a fresh vegetable. The genetic basis of important horticultural traits of common bean is still poorly understood, which hinders DNA marker-assisted breeding in this crop. Here we report the identification of single-locus and epistatic quantitative trait loci (QTLs), as well as their environment interaction effects for six pod traits, namely width, thickness, length, size index, beak length and color, using an Andean intra-gene pool recombinant inbred line population from a cross between a cultivated common bean and an exotic nuña bean. The QTL analyses performed detected a total of 23 QTLs (single-locus QTLs and epistatic QTLs): five with only individual additive effects and six with only epistatic effects, while the remaining twelve showed both effects. These QTLs were distributed across linkage groups (LGs) 1, 2, 4, 6, 7, 8, 9, 10 and 11; particularly noteworthy are the QTLs for pod size co-located on LGs 1 and 4, indicative of tight linkage or genes with pleiotropic effects governing these traits. Overall, the results obtained showed that additive and epistatic effects are the major genetic basis of pod size and color traits. The mapping of QTLs including epistatic loci for the six pod traits evaluated provides support for implementing marker-assisted selection toward genetic improvement of common bean.

Co-evolution and Migration of Bean and Rhizobia in Europe

The legumes crop, as common bean, is one of the most important crops for the human nutrition, to be the protein basis from developing countries. This crop presents many limitations as are the deficiencies or toxicities of minerals in soils. These limitations in common bean production regions occur throughout the world. To overcome mineral deficiencies and toxicities, common bean growers must use corrective soil amendments. Symbiotic nitrogen fixation (SNF) is important as a source of N for agriculture, because the use of nitrogenous fertilizers has resulted in unacceptable levels of water and atmosphere pollution and by nitrate and N2O emissions, contributing to the increase of greenhouse effect. The common bean grown in Europe, and other continents, is the result of a process of domestication and evolution, from wild forms found exclusively in the Americas, and it is possible to distinguish two major domestication centers, Andean and Mesoamerican centers. Most of the European germplasm is from Andean locations since the type T phaseolin pattern is found in their seeds. It is thought that Mesoamerican lines were less popular because of their lower adaptability to winter cold and to short duration summers. Subsequently, new cultivars may have evolved within and between the two gene pools in Spain and Portugal making the Southern Europe a secondary center of diversity for the common bean. The microorganisms associated with the common bean plant for its SNF may exhibit a similar arrangement of genetic diversity in Mesoamerica and Andean gene pools. R. etli bv. phaseoli is the dominant microsymbiont in both the Mesoamerican and Andean centers of origin. Many other species have been found in bean nodules in region where they have been introduced. In Europe, rhizobia strains that nodulate common bean have a narrow genetic diversity that was correlative to beans being an introduced crop. In this respect, the large number of rhizobia species capable of nodulating bean supports the premise that bean is a promiscuous host and a diversity of bean–rhizobia interactions exists. Since there seems to be a large variation in the capacity of bean genotypes to nodulate with a large range of host or non-host-specific strains, this knowledge could be used to enhance the symbiosis and possibly to enhance nitrogen fixation.

Protein markers and seed size variation in common bean segregating populations.

Selection and random genetic drift are the two main forces affecting allele frequencies in common bean breeding programs. Therefore, knowledge on allele frequency changes attributable to these forces is of fundamental importance for breeders. The changes in frequencies of alleles of biochemical markers were examined in F2 to F7 populations derived from crosses between cultivated Mesoamerican and Andean common bean accessions (Phaseolus vulgaris L.). Biochemical markers included the seed proteins phaseolin, lectin and other seed polypeptides, and six isozymes. The Schaffer’s test detected a high significant linear trend of the 63% of the polymorphic loci studied, meaning that directional selection was acting on those loci. Associations between seed size traits, phaseolin seed-storage protein and isozyme markers were detected based on the comparisons of the progeny genotypic means. In the interracial populations the intermediate form PhaH/T, b6, and Rbcs98 alleles had a positive effect on seed size. In the inter-gene pool populations, a higher transmission of Mesoamerican alleles in all loci was showed, although the Andean alleles PhaT, Skdh100, Rbcs98, and Diap100 showed positive effects on seed weight. Our results suggest that phaseolin and other seed proteins markers are linked to loci affecting seed size. These markers have good potential for improving the results of the selection and should be considered as a strategy for germplasm enhancement and to avoid the reduced performance of the inter-gene pool populations.

Major Contribution of Flowering Time and Vegetative Growth to Plant Production in Common Bean As Deduced from a Comparative Genetic Mapping

Determinacy growth habit and accelerated flowering traits were selected during or after domestication in common bean. Both processes affect several presumed adaptive traits such as the rate of plant production. There is a close association between flowering initiation and vegetative growth; however, interactions among these two crucial developmental processes and their genetic bases remain unexplored. In this study, with the aim to establish the genetic relationships between these complex processes, a multi-environment quantitative trait locus (QTL) mapping approach was performed in two recombinant inbred line populations derived from inter-gene pool crosses between determinate and indeterminate genotypes. Additive and epistatic QTLs were found to regulate flowering time, vegetative growth, and rate of plant production. Moreover, the pleiotropic patterns of the identified QTLs evidenced that regions controlling time to flowering traits, directly or indirectly, are also involved in the regulation of plant production traits. Further QTL analysis highlighted one QTL, on the lower arm of the linkage group Pv01, harboring the Phvul.001G189200 gene, homologous to the Arabidopsis thaliana TERMINAL FLOWER1 (TFL1) gene, which explained up to 32% of phenotypic variation for time to flowering, 66% for vegetative growth, and 19% for rate of plant production. This finding was consistent with previous results, which have also suggested Phvul.001G189200 (PvTFL1y) as a candidate gene for determinacy locus. The information here reported can also be applied in breeding programs seeking to optimize key agronomic traits, such as time to flowering, plant height and an improved reproductive biomass, pods, and seed size, as well as yield.