Signatures of Environmental Adaptation During Range Expansion of Wild Common Bean (Phaseolus vulgaris)

Abstract Landscape genomics integrates population genetics with landscape ecology, allowing the identification of putative molecular determinants involved in environmental adaptation across the natural geographic and ecological range of populations. Wild Phaseolus vulgaris , the progenitor of common bean ( P. vulgaris ), has a remarkably extended distribution over 10,000 km from northern Mexico to northwestern Argentina. Earlier research has shown that this distribution represents a range expansion from Mesoamerica to the southern Andes through several discrete migration events and that the species colonized areas with different temperature and rainfall compared to its core area of origin. Thus, this species provides an opportunity to examine to what extent adaptation of a species can be broadened or, conversely, ecological or geographical distribution can be limited by inherent adaptedness. In the current study, we applied a landscape genomics approach to a collection of 246 wild common bean accessions representative of its broad geographical and climatic distribution and genotyped for ∼20K SNPs. We applied two different but complementary approaches for identifying loci putatively involved in environmental adaptation: i) an outlier-detection method that identifies loci showing strong differentiation between sub-populations; ii) an association method based on the identification of loci associated with bio-climatic variables. This integrated approach allowed the identification of several genes showing signature of selection across the different natural sub-populations of this species, as well as genes associated with specific bio-climatic variables related to temperature and precipitation. The current study demonstrates the feasibility of landscape genomics approach for a preliminary identification of specific populations and novel candidate genes involved in environmental adaptation in P. vulgaris . As a resource for broadening the genetic diversity of the domesticated gene pool of this species, the genes identified constitute potential molecular markers and introgression targets for the breeding improvement of domesticated common bean. Author Summary The ancestral form of common bean has an unusually large distribution in the Americas, extending over 10,000 km from ∼35° N. Lat. to ∼35° S. Lat. This wide distribution results from discrete long-range dissemination events to the Andes region from the original environments in Mesoamerica. It also suggests adaptation to new environments that are distinct from those encountered in Mesoamerica. In this research, we identified genes that may be involved in adaptation to climate variables in these new environments using two methods. A first method – outlier detection – was used to identify genome regions that differentiated the wild bean groups in the Andes resulting from discrete dissemination events among themselves and the different groups in Mesoamerica. The second method – genome-wide association – was used to identify candidate genome regions correlated with these same variables across the entire distribution from Mesoamerica to the southern Andes. The two methods identified two sets of candidate genes, several of which were related to the water status of plants, and illustrate how the genetic architecture of adaptation following long-range dissemination. This study provides sets of candidate genes as well as candidate wild bean populations that need to be corroborated for their use in increasing the water use efficiency of domesticated beans

Hibridaciones interespecificas para el mejoramiento de Phaseolus vulgaris L.

A study was initiated to determine the barriers that limit the transferences of genes between Phaseolus vulgaris and P. coccineus. The factors that determine the outcome of this crossing are the direction (success is greater when P. vulgaris is used as the mother parent) and the combination of parents. Early generations show reduced viability and fertility. This reduction is more pronounced in progenies P. vulgaris x P. coccineus subspecie coccineus compared with progenies P. vulgaris x P. coccineus subspecie polyanthus. It also depends on the combination of parents. In later generations a progressive restoration of viability and fertility was observed. The combination of parents greatly affects the type of segregation of the characteristics in progeny observed in F2 of P. vulgaris x P. coccineus subspecie coccineus crossing. Moreover, results seem to indicate that in progenies P. vulgaris x P. coccineus subspecie polyanthus there are more possibilities of recombination. Interesting materials were selected for improvement of plant architecture (resistance to lodging, long hypocotyl and epicotyl, small folioles) and disease resistance (tolerance to BGMV). Some suggestions are made on future activities of the project of interspecific crosses: multiplication and evaluation of the P. coccineus collection, studies on segregation, projects on crosses fox specific objectives. (AS-CIAT

Etapas de desarrollo en la planta de frijol

The developmental scale of the bean crop and the general characteristics of plant development are described on the basis of morphological and physiological changes in the plant. The factors influencing the duration of the developmental stages of beans are identified, namely growth habit, earliness, and climate. (CIAT)Se describen las etapas de la escala del desarrollo del cultivo de frijol y las caracteristicas generales del desarrollo de la planta con base en los cambios morfologicos y fisiologicos de la misma. Se identifican los factores que influyen en la duracion de las etapas de desarrollo del frijol: habito de crecimiento, precocidad y clima. (CIAT

Genetic diversity and relationships among 192 public common bean inbred lines assessed by SSR markers.

Knowledge of germplasm diversity and of relationships among elite breeding materials has a significant impact on the improvement of crop plants and on the development of strategies for genetic resources management and exploration. The present study was conducted to determine the level of genetic variation and relatedness among some selected common bean varieties by using microsatellite markers. In this investigation, we used 61 SSRs to fingerprint 192 common bean inbred public lines released over the last 50 years in the U.S.A. All the lines are commercial seed type classes that are grown in the USA and include both dry bean classes and snap beans for the fresh and processing markets.The 344 alleles identified were used as raw data for estimating the amount of diversity and to describe the genetic structure of the commercial bean gene pool. A model-based clustering analysis placed the varieties in six clusters that correspond to major breeding groups plus a set of lines showing evidence of mixed origins. Neighbor-joining tree was constructed to further assess the genetic structure of common bean lines, showing good agreement with the pedigree information and the cluster analysis. A significant fixation index FST, also revealed genetic substructure within the U.S. common bean gene pool with Kidney and Pinto-Great Northern beans being the most different from the other varietal groups.The results of this study - based on a much larger number of SSRs -confirm a previous observation indicating a relatively low level of genetic variation and a molecular variability that parallels phenotypic characters distinguishing different commercial groups. Our results indicate also a strong subpopulation structure and provide additional tools for breeding and breeder’s rights implementation

Morphological and Agronomic Characterization of Spanish Landraces of Phaseolus vulgaris L

[EN] Beans (Phaseolus vulgaris L.) originated on the American continent, specifically in the Mesoamerican zone, and their domestication took place independently in the Mesoamerican area and the Andean zone, giving rise to two well-dierentiated genetic pools. It was also noted that the Andean wild populations originated from only a few thousand individuals from the Mesoamerican wild populations, which produced a great bottleneck in the formation of the Andean population. During centuries of cultivation in the Iberian Peninsula after its ntroduction in the 16th century, beans adapted to new environments, evolving numerous local landraces. Twenty-four local landraces of P. vulgaris from Spain were analyzed in the greenhouse during two onsecutive seasons. From each genotype, five plants were grown and characterized for 17 quantitative and 15 qualitative traits using the International Board for Plant Genetic Resources (IBPGR) descriptors. Data were analyzed statistically by analysis of variance (ANOVA), principal component analysis (PCA), and cluster analysis. The results obtained indicate a high variability for most traits, especially those related to the yield and its components. The PCA and cluster analysis separated the landraces according to the color of the seed, the yield, and the pod and seed traits related to yield. Numerous traits exhibited interactions between the genotype and the environment. Most accessions reached higher yields in spring, in which solar radiation favors photosynthesis and, consequently, photoassimilation. The dierent response to the changing environment of the set of accessions studied in the present work is of great interest, and it can be exploited in breeding cultivars adapted to a broader range of environmental conditionsThis research was funded by the Spanish "Ministerio de Economia, Industria y Competitividad", grant number RFP2015-00013-00-00.Arteaga-Castillo, SM.; Yabor, L.; Torres Aliaga, J.; Solbes García, EM.; Muñoz Fernández, E.; Díez-Niclós, MJTDJ.; Vicente, O.... (2019). Morphological and Agronomic Characterization of Spanish Landraces of Phaseolus vulgaris L. Agriculture. 9(7):1-16. https://doi.org/10.3390/agriculture9070149S11697FAOSTAT http://faostat3.fao.org/browse/Q/QC/SGepts, P. (1990). Biochemical evidence bearing on the domestication ofPhaseolus (Fabaceae) beans. Economic Botany, 44(S3), 28-38. doi:10.1007/bf02860473Koenig, R., & Gepts, P. (1989). Allozyme diversity in wild Phaseolus vulgaris: further evidence for two major centers of genetic diversity. Theoretical and Applied Genetics, 78(6), 809-817. doi:10.1007/bf00266663Tohme, J., Gonzalez, D. O., Beebe, S., & Duque, M. C. (1996). AFLP Analysis of Gene Pools of a Wild Bean Core Collection. Crop Science, 36(5), 1375-1384. doi:10.2135/cropsci1996.0011183x003600050048xBeebe, S., Skroch, P. W., Tohme, J., Duque, M. C., Pedraza, F., & Nienhuis, J. (2000). Structure of Genetic Diversity among Common Bean Landraces of Middle American Origin Based on Correspondence Analysis of RAPD. Crop Science, 40(1), 264-273. doi:10.2135/cropsci2000.401264xDurán, L. A., Blair, M. W., Giraldo, M. C., Macchiavelli, R., Prophete, E., Nin, J. C., & Beaver, J. S. (2005). Morphological and Molecular Characterization of Common Bean Landraces and Cultivars from the Caribbean. Crop Science, 45(4), 1320-1328. doi:10.2135/cropsci2004.0501Singh, S. P., Gepts, P., & Debouck, D. G. (1991). Races of common bean (Phaseolus vulgaris, Fabaceae). Economic Botany, 45(3), 379-396. doi:10.1007/bf02887079Bitocchi, E., Nanni, L., Bellucci, E., Rossi, M., Giardini, A., Zeuli, P. S., … Papa, R. (2012). Mesoamerican origin of the common bean (Phaseolus vulgaris L.) is revealed by sequence data. Proceedings of the National Academy of Sciences, 109(14), E788-E796. doi:10.1073/pnas.1108973109Berglund-Brücher, O., & Brücher, H. (1976). The south American wild bean (Phaseolus aborigineus Burk.) as ancestor of the common bean. Economic Botany, 30(3), 257-272. doi:10.1007/bf02909734Santalla, M., Rodiño, A., & De Ron, A. (2002). Allozyme evidence supporting southwestern Europe as a secondary center of genetic diversity for the common bean. Theoretical and Applied Genetics, 104(6), 934-944. doi:10.1007/s00122-001-0844-6Boyer, J. S. (1982). Plant Productivity and Environment. Science, 218(4571), 443-448. doi:10.1126/science.218.4571.443Cramer, W., Guiot, J., Fader, M., Garrabou, J., Gattuso, J.-P., Iglesias, A., … Xoplaki, E. (2018). Climate change and interconnected risks to sustainable development in the Mediterranean. Nature Climate Change, 8(11), 972-980. doi:10.1038/s41558-018-0299-2Fita, A., Rodríguez-Burruezo, A., Boscaiu, M., Prohens, J., & Vicente, O. (2015). Breeding and Domesticating Crops Adapted to Drought and Salinity: A New Paradigm for Increasing Food Production. Frontiers in Plant Science, 6. doi:10.3389/fpls.2015.00978Santos, M. G., Ribeiro, R. V., Machado, E. C., & Pimentel, C. (2009). Photosynthetic parameters and leaf water potential of five common bean genotypes under mild water deficit. Biologia plantarum, 53(2), 229-236. doi:10.1007/s10535-009-0044-9Rosales, M. A., Ocampo, E., Rodríguez-Valentín, R., Olvera-Carrillo, Y., Acosta-Gallegos, J., & Covarrubias, A. A. (2012). Physiological analysis of common bean (Phaseolus vulgaris L.) cultivars uncovers characteristics related to terminal drought resistance. Plant Physiology and Biochemistry, 56, 24-34. doi:10.1016/j.plaphy.2012.04.007Beebe, S. E., Rao, I. M., Blair, M. W., & Acosta-Gallegos, J. A. (2013). Phenotyping common beans for adaptation to drought. Frontiers in Physiology, 4. doi:10.3389/fphys.2013.00035Al Hassan, M., Morosan, M., López-Gresa, M., Prohens, J., Vicente, O., & Boscaiu, M. (2016). Salinity-Induced Variation in Biochemical Markers Provides Insight into the Mechanisms of Salt Tolerance in Common (Phaseolus vulgaris) and Runner (P. coccineus) Beans. International Journal of Molecular Sciences, 17(9), 1582. doi:10.3390/ijms17091582Morosan, M., Hassan, M. A., Naranjo, M. A., López-Gresa, M. P., Boscaiu, M., & Vicente, O. (2017). Comparative analysis of drought responses in Phaseolus vulgaris (common bean) and P. coccineus (runner bean) cultivars. The EuroBiotech Journal, 1(3), 247-252. doi:10.24190/issn2564-615x/2017/03.09Arteaga, S., Al Hassan, M., Chaminda Bandara, W., Yabor, L., Llinares, J., Boscaiu, M., & Vicente, O. (2018). Screening for Salt Tolerance in Four Local Varieties of Phaseolus lunatus from Spain. Agriculture, 8(12), 201. doi:10.3390/agriculture8120201Mohammadi, S. A., & Prasanna, B. M. (2003). Analysis of Genetic Diversity in Crop Plants—Salient Statistical Tools and Considerations. Crop Science, 43(4), 1235-1248. doi:10.2135/cropsci2003.1235Gil, J., & Ron, A. D. (1992). Variation in Phaseolus vulgaris in the Northwest of the Iberian Peninsula. Plant Breeding, 109(4), 313-319. doi:10.1111/j.1439-0523.1992.tb00190.xRodiño, A. P. (2003). Euphytica, 131(2), 165-175. doi:10.1023/a:1023973309788Pérez-Vega, E., Campa, A., De la Rosa, L., Giraldez, R., & Ferreira, J. J. (2009). Genetic Diversity in a Core Collection Established from the Main Bean Genebank in Spain. Crop Science, 49(4), 1377-1386. doi:10.2135/cropsci2008.07.0409Escribano, M. R., De Ron, A. M., & Amurrio, J. M. (1994). Diversity in agronomical traits in common bean populations from Northwestern Spain. Euphytica, 76(1-2), 1-6. doi:10.1007/bf00024014Nienhuis, J., & Singh, S. P. (1986). Combining Ability Analyses and Relationships Among Yield, Yield Components, and Architectural Traits in Dry Bean 1. Crop Science, 26(1), 21-27. doi:10.2135/cropsci1986.0011183x002600010005xSills, G. R., & Nienhuis, J. (1993). Field Plot Technique Affects Snap Bean Yield Evaluation. Journal of the American Society for Horticultural Science, 118(5), 672-674. doi:10.21273/jashs.118.5.672Escribano, M. R., Santalla, M., Casquero, P. A., & de Ron, A. M. (1998). Patterns of genetic diversity in landraces of common bean (Phaseolus vulgarisL.) from Galicia. Plant Breeding, 117(1), 49-56. doi:10.1111/j.1439-0523.1998.tb01447.

Pod indehiscence is a domestication and aridity resilience trait in common bean.

Plant domestication has strongly modified crop morphology and development. Nevertheless, many crops continue to display atavistic characteristics that were advantageous to their wild ancestors but are deleterious under cultivation, such as pod dehiscence (PD). Here, we provide the first comprehensive assessment of the inheritance of PD in the common bean (Phaseolus vulgaris), a major domesticated grain legume. Using three methods to evaluate the PD phenotype, we identified multiple, unlinked genetic regions controlling PD in a biparental population and two diversity panels. Subsequently, we assessed patterns of orthology among these loci and those controlling the trait in other species. Our results show that different genes were selected in each domestication and ecogeographic race. A chromosome Pv03 dirigent-like gene, involved in lignin biosynthesis, showed a base-pair substitution that is associated with decreased PD. This haplotype may underlie the expansion of Mesoamerican domesticates into northern Mexico, where arid conditions promote PD. The rise in frequency of the decreased-PD haplotype may be a consequence of the markedly different fitness landscape imposed by domestication. Environmental dependency and genetic redundancy can explain the maintenance of atavistic traits under domestication

Identification and characterization in common bean of a putative homologue to the Arabidopsis Indehiscent gene.

Pod shattering represents a key component of the domestication syndrome in common bean, because it makes this species dependent upon the farmer for seed dispersal. Attempts to elucidate the genetic control of this process have led to the identification of a major gene(St) linked to the presence of pod suture fibers involved in pod shattering. Although St has been placed on the common bean genetic map, the sequence and the specific functions of this gene remain unknown. The purpose of the current study was to identify a candidate gene for St. Arabidopsis thaliana INDEHISCENT gene (IND) is the primary factory required for silique shattering. A sequence homologous to IND was successfully amplified in Phaseolus vulgaris and mapped on the common bean map using two recombinant inbred population (BAT93 x Jalo EEP558; Midas x G12873). Although PvIND maps near the St locus, the lack of complete co-segregation between PvIND and St and the lack of polymorphisms at the PvIND locus correlating with the dehiscent/indehiscent phenotype suggests that PvIND may be not directly involved in pod shattering and may not be the gene underlying the St locus. Alternatively, a more precise phenotyping method needs to be developed to more accurately map the St locus

Beans ( Phaseolus spp.) - model food legumes

Globally, 800 million people are malnourished. Heavily subsidised farmers in rich countries produce sufficient surplus food to feed the hungry, but not at a price the poor can afford. Even donating the rich world's surplus to the poor would not solve the problem. Most poor people earn their living from agriculture, so a deluge of free food would destroy their livelihoods. Thus, the only answer to world hunger is to safeguard and improve the productivity of farmers in poor countries. Diets of subsistence level farmers in Africa and Latin America often contain sufficient carbohydrates (through cassava, corn/maize, rice, wheat, etc.), but are poor in proteins. Dietary proteins can take the form of scarce animal products (eggs, milk, meat, etc.), but are usually derived from legumes (plants of the bean and pea family). Legumes are vital in agriculture as they form associations with bacteria that 'sfix-nitrogen' from the air. Effectively this amounts to internal fertilisation and is the main reason that legumes are richer in proteins than all other plants. Thousands of legume species exist but more common beans (Phaseolus vulgaris L.) are eaten than any other. In some countries such as Mexico and Brazil, beans are the primary source of protein in human diets. As half the grain legumes consumed worldwide are common beans, they represent the species of choice for the study of grain legume nutrition. Unfortunately, the yields of common beans are low even by the standards of legumes, and the quality of their seed proteins is sub-optimal. Most probably this results from millennia of selection for stable rather than high yield, and as such, is a problem that can be redressed by modern genetic techniques. We have formed an international consortium called Phaseomics' to establish the necessary framework of knowledge and materials that will result in disease-resistant, stress-tolerant, high-quality protein and high-yielding beans. Phaseomics will be instrumental in improving living conditions in deprived regions of Africa and the Americas. It will contribute to social equity and sustainable development and enhance inter- and intra-cultural understanding, knowledge and relationships. A major goal of Phaseomics is to generate new common bean varieties that are not only suitable for but also desired by the local farmer and consumer communities. Therefore, the socio-economic dimension of improved bean production and the analysis of factors influencing the acceptance of novel varieties will be an integral part of the proposed research (see Figure 1). Here, we give an overview of the economic and nutritional importance of common beans as a food crop. Priorities and targets of current breeding programmes are outlined, along with ongoing efforts in genomics. Recommendations for an international coordinated effort to join knowledge, facilities and expertise in a variety of scientific undertakings that will contribute to the overall goal of better beans are given. To be rapid and effective, plant breeding programmes (i.e., those that involve crossing two different 'sparents') rely heavily on molecular 'smarkers'. These genetic landmarks are used to positio

Dispersal of transgenes through maize seed systems in Mexico.

ObjectivesCurrent models of transgene dispersal focus on gene flow via pollen while neglecting seed, a vital vehicle for gene flow in centers of crop origin and diversity. We analyze the dispersal of maize transgenes via seeds in Mexico, the crop's cradle.MethodsWe use immunoassays (ELISA) to screen for the activity of recombinant proteins in a nationwide sample of farmer seed stocks. We estimate critical parameters of seed population dynamics using household survey data and combine these estimates with analytical results to examine presumed sources and mechanisms of dispersal.ResultsRecombinant proteins Cry1Ab/Ac and CP4/EPSPS were found in 3.1% and 1.8% of samples, respectively. They are most abundant in southeast Mexico but also present in the west-central region. Diffusion of seed and grain imported from the United States might explain the frequency and distribution of transgenes in west-central Mexico but not in the southeast.ConclusionsUnderstanding the potential for transgene survival and dispersal should help design methods to regulate the diffusion of germplasm into local seed stocks. Further research is needed on the interactions between formal and informal seed systems and grain markets in centers of crop origin and diversification