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In a common bean plant exhibiting determinate growth, the terminal shoot meristem switches from a vegetative to reproductive state, resulting in a terminal inflorescence. Contrary to this, indeterminate growth habit results in a terminal meristem that remains vegetative where it further regulates the production of lateral vegetative and reproductive growth. In the last century, breeders have selected determinate growth habit, in combination with photoperiod insensitivity, to obtain varieties with a shorter flowering period, earlier maturation and ease of mechanized harvest. Previous work has identified TFL1 as a gene controlling determinate growth habit in Arabidopsis thaliana. In this work, we have validated that the Phaseolus vulgaris candidate gene, PvTFL1y, is the functional homolog of TFL1 using three independent lines of evidence. First, in a population of ~1,500 plants, PvTFL1y was found to co-segregate with the phenotypic locus for determinate growth habit ( fin ) on chromosome 01. Second, using quantitative PCR, we found that two unique haplotypes associated with determinacy at the PvTFL1y locus, a 4.1-kb retrotransposon and a splice-site mutation, cause mRNA abundance to decrease 20–133 fold, consistent with the recessive nature of fin . Finally, using a functional complementation approach, through Agrobacterium -mediated transformation of determinate Arabidopsis , we rescued tfl1 - 1 mutants with the wild-type PvTFL1y gene. Together, these three lines of evidence lead to the conclusion that PvTFL1y is the functional homolog of the Arabidopsis gene, TFL1 , and is the gene responsible for naturally occurring variation for determinacy in common bean. Further work exploring the different haplotypes at the PvTFL1y locus may lead to improved plant architecture and phenology of common bean cultivars.

Several claims have been made about genetic engineering (GE) in comparison with crop domestication and classical plant breeding, including the similarity of genetic changes between those taking place during domestication and by GE, the increased speed and accuracy of GE over classical plant breeding, and the higher level of knowledge about the actual genes being transferred by GE compared with classical breeding. In reviewing evidence pertaining to these claims, I suggest that (i) it is unlikely that changes introduced by GE will make crops weedier, although exceptions have been noted, (ii) changes brought about by GE currently often involve gain‐of‐function mutations, whereas changes selected during domestication generally involve loss‐of‐function mutations, (iii) adoption of GE cultivars has been much faster than any previous introduction and spread of agriculture that occurred earlier but has occurred at about the same rate as the spread of cultivars obtained by plant breeding, (iv) introduction of agriculture reduced the health of agriculturists compared with that of hunter–gatherers, suggesting that introduction of innovations do not automatically improve well being, (v) although GE is not a substitute for plant breeding, it can significantly contribute to plant breeding by generating additional genetic diversity, (vi) uncertainties associated with the site of insertion of transgenes in the genome and the expression of transgenes following insertion, makes GE less rapid and precise than originally claimed, and (vii) a potential advantage of GE over classical breeding is the knowledge of the actual gene(s) being inserted, although few cases of unwanted gene introductions through classical plant breeding have been documented. Further advances in GE will increase the precision of the technique, its relevance to consumers, and its environmental friendliness. What is most needed are even‐handed, case‐by‐case assessments of the benefits and potential pitfalls of GE in comparison with other crop improvement techniques. Classical plant breeding may, in the end, also be regulated in the same way as GE.

Wild crop relatives have been potentially subjected to stresses on an evolutionary time scale prior to domestication. Among these stresses, drought is one of the main factors limiting crop productivity and its impact is likely to increase under current scenarios of global climate change. We sought to determine to what extent wild common bean (Phaseolus vulgaris) exhibited adaptation to drought stress, whether this potential adaptation is dependent on the climatic conditions of the location of origin of individual populations, and to what extent domesticated common bean reflects potential drought adaptation. An extensive and diverse set of wild beans from across Mesoamerica, along with a set of reference Mesoamerican domesticated cultivars, were evaluated for root and shoot traits related to drought adaptation. A water deficit experiment was conducted by growing each genotype in a long transparent tube in greenhouse conditions so that root growth, in addition to shoot growth, could be monitored. Phenotypic and landscape genomic analyses, based on single-nucleotide polymorphisms, suggested that beans originating from central and north-west Mexico and Oaxaca, in the driest parts of their distribution, produced more biomass and were deeper-rooted. Nevertheless, deeper rooting was correlated with less root biomass production relative to total biomass. Compared with wild types, domesticated types showed a stronger reduction and delay in growth and development in response to drought stress. Specific genomic regions were associated with root depth, biomass productivity and drought response, some of which showed signals of selection and were previously related to productivity and drought tolerance. The drought tolerance of wild beans consists in its stronger ability, compared with domesticated types, to continue growth in spite of water-limited conditions. This study is the first to relate bean response to drought to environment of origin for a diverse selection of wild beans. It provides information that needs to be corroborated in crosses between wild and domesticated beans to make it applicable to breeding programmes.

Using amplified fragment length polymorphisms (AFLPs), we analyzed the genetic structure of wild and domesticated common bean (Phaseolus vulgaris L.) from Mesoamerica at different geographical levels to test the hypothesis of asymmetric gene flow and investigate the origin of weedy populations. We showed both by phenetic and admixture population analyses that gene flow is about three- to four-fold higher from domesticated to wild populations than in the reverse direction. This result, combined with other work, points to a displacement of genetic diversity in wild populations due to gene flow from the domesticated populations. The weedy populations appear to be genetically intermediate between domesticated and wild populations, suggesting that they originated by hybridization between wild and domesticated types rather than by escape from cultivation. In addition, the domesticated bean races were genetically similar confirming a single domestication event for the Mesoamerican gene pool. Finally, the genetic diversity of the domesticated bean population showed a lower level of geographic structure in comparison to that of the wild populations.

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 'fix-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 'parents') rely heavily on molecular 'markers'. These genetic landmarks are used to position important genes (e.g. for resistance to particular pests, for yield, etc.) on a chromosome and ensure that they can be 'crossed in' to another plant. There are several ways of obtaining molecular markers but the project will establish partial sequences of messenger RNA's extracted from tissues of interest (e.g. developing pods). These so-called expressed sequence-tags (ESTs), can be used like milestones on a chromosome, to position these and other genes. These efforts will complement current studies on other legumes such as Lotus japonicus and Medicago truncatula as well as the EST projects in soybean by providing a framework for comparative genomics between legumes. Complete sequencing and molecular analysis of the bean genome will follow. Individual laboratories will be encouraged to internally finance or find additional funding for the construction of cDNA libraries and the sequencing of thousands ESTs. Funds donated to the consortium will be used primarily for sequencing the genome and to co-ordinate the consortium's activities. As sequence and expression data become available it will provide an elaborate framework for plant geneticists to 'design' new, improved common bean lines. Amongst these lines will be higher-yielding varieties, cultivars that are resistant to drought, pests and so on. It will also be possible to enhance the content of essential amino acids, minerals and vitamins in the seeds and so improve the nutrition and health of countless people who consume beans. By considering the socio-economic implications of common bean improvement from the outset, this project should lead to sustainable development, to increased social equity, and to greater use of beans in international trade. The added value in this innovative approach to common beans as model food legumes lies in the combination of existing and novel genetic approaches with socio-economic criteria that will efficiently target the end users.

A total of 150 microsatellite markers developed for common bean ( Phaseolus vulgaris L.) were tested for parental polymorphism and used to determine the positions of 100 genetic loci on an integrated genetic map of the species. The value of these single-copy markers was evident in their ability to link two existing RFLP-based genetic maps with a base map developed for the Mesoamerican x Andean population, DOR364 x G19833. Two types of microsatellites were mapped, based respectively on gene-coding and anonymous genomic-sequences. Gene-based microsatellites proved to be less polymorphic (46.3%) than anonymous genomic microsatellites (64.3%) between the parents of two inter-genepool crosses. The majority of the microsatellites produced single bands and detected single loci, however four of the gene-based and three of the genomic microsatellites produced consistent double or multiple banding patterns and detected more than one locus. Microsatellite loci were found on each of the 11 chromosomes of common bean, the number per chromosome ranging from 5 to 17 with an average of ten microsatellites each. Total map length for the base map was 1,720 cM and the average chromosome length was 156.4 cM, with an average distance between microsatellite loci of 19.5 cM. The development of new microsatellites from sequences in the Genbank database and the implication of these results for genetic mapping, quantitative trait locus analysis and marker-assisted selection in common bean are described.

This study investigated the prevalence of scab caused by Elsinoë phaseoli causing yield losses on beans in Kenya. The research focused on common practices and challenges faced by subsistence farmers with the aim of providing insights into scab prevalence, impact, and potential management challenges. A structured questionnaire was employed in a survey conducted in 2022 and 2023, covering major bean‐growing regions using a three‐stage sampling design. Data from 128 bean farmers included information on farm size, seed sources, cropping systems, awareness of challenges, and pest/disease management practices. Scab prevalence was determined by scouting for symptoms, with a total of 84 farms surveyed in 2021. The incidence of bean scab was confirmed in all surveyed clusters, indicating its widespread occurrence across various agro‐ecological zones. Farmers exhibited common practices such as preference for uniform bean seeds (61%), use of uncertified seeds (83%), intercropping (80%), and limited crop rotation. Challenges included disease and pest infestations, with limited diversity in management options. Confirmation of the presence of bean scab in diverse agro‐ecological zones emphasizes its importance and the need for further research on its impact and epidemiology. Challenges with crop rotation were evident due to small farm sizes and subsistence‐focused farming. The study recommends further research for a comprehensive understanding of the link between increased scab importance and current bean farming practices such as short rotation periods and the use of susceptible varieties. Training programs are also vital to improve farmers' knowledge on safe agro‐chemical use, ensuring sustainable constraint management in common bean cultivation in Kenya.

Evolutionary studies in plant and animal breeding are aimed at understanding the structure and organization of genetic variations of species. We have identified and characterized a genomic sequence in Phaseolus vulgaris of 1,200 bp ( PvSHP1) that is homologous to SHATTERPROOF-1 ( SHP1 ), a gene involved in control of fruit shattering in Arabidopsis thaliana. The PvSHP1 fragment was mapped to chromosome Pv06 in P. vulgaris and is linked to the flower and seed color gene V . Amplification of the PvSHP1 sequence from the most agronomically important legume species showed a high degree of interspecies diversity in the introns within the Phaseoleae, while the coding region was conserved across distant taxa. Sequencing of the PvSHP1 sequence in a sample of 91 wild and domesticated genotypes that span the geographic distribution of this species in the centers of origin showed that PvSHP1 is highly polymorphic and, therefore, particularly useful to further investigate the origin and domestication history of P. vulgaris . Our data confirm the gene pool structure seen in P. vulgaris along with independent domestication processes in the Andes and Mesoamerica; they provide additional evidence for a single domestication event in Mesoamerica. Moreover, our results support the Mesoamerican origin of this species. Finally, we have developed three indel-spanning markers that will be very useful for bean germplasm characterization, and particularly to trace the distribution of the domesticated Andean and Mesoamerican gene pools.

The Andean common bean AND 277 has the Co-1(4) and the Phg-1 alleles that confer resistance to 21 and eight races, respectively, of the anthracnose (ANT) and angular leaf spot (ALS) pathogens. Because of its broad resistance spectrum, Co-1(4) is one of the main genes used in ANT resistance breeding. Additionally, Phg-1 is used for resistance to ALS. In this study, we elucidate the inheritance of the resistance of AND 277 to both pathogens using F(2) populations from the AND 277 × Rudá and AND 277 × Ouro Negro crosses and F(2:3) families from the AND 277 × Ouro Negro cross. Rudá and Ouro Negro are susceptible to all of the above races of both pathogens. Co-segregation analysis revealed that a single dominant gene in AND 277 confers resistance to races 65, 73, and 2047 of the ANT and to race 63-23 of the ALS pathogens. Co-1(4) and Phg-1 are tightly linked (0.0 cM) on linkage group Pv01. Through synteny mapping between common bean and soybean we also identified two new molecular markers, CV542014(450) and TGA1.1(570), tagging the Co-1(4) and Phg-1 loci. These markers are linked at 0.7 and 1.3 cM, respectively, from the Co-1(4) /Phg-1 locus in coupling phase. The analysis of allele segregation in the BAT 93/Jalo EEP558 and California Dark Red Kidney/Yolano recombinant populations revealed that CV542014(450) and TGA1.1(570) segregated in the expected 1:1 ratio. Due to the physical linkage in cis configuration, Co-1(4) and Phg-1 are inherited together and can be monitored indirectly with the CV542014(450) and TGA1.1(570) markers. These results illustrate the rapid discovery of new markers through synteny mapping. These markers will reduce the time and costs associated with the pyramiding of these two disease resistance genes.