Ana María González

Flowering time is a critical trait in common bean (Phaseolus vulgaris), influencing yield stability and geographical adaptation. While PvCOL2 and PvPHYA3 are known regulators under long-day (LD) conditions, we identified a third major locus through fine-mapping of the QTL DTF9.4/DTF9.5. Within this region, PvE1 (Phvul.009G204600) emerged as a strong candidate, sharing sequence homology with the soybean E1 gene and acting as a transcriptional repressor of flowering. A naturally occurring 34-bp deletion in its 3′ UTR (e1-del) was associated with early flowering and reduced photoperiod sensitivity. Expression analysis revealed that PvE1 displays a circadian rhythm under LD conditions, with a bimodal pattern peaking in the morning and early evening, resembling that reported for soybean E1. Phenotypic analyses of near-isogenic lines (NILs) confirmed that PvE1 delays flowering specifically under LD and also influences plant architecture, as e1 genotypes exhibited reduced plant height and node number. Functional dissection revealed that PvE1 and PvCOL2 act in partially redundant pathways to repress PvFT gene expression, with evidence of functional interaction. This regulatory module resembles that in soybean but shows species-specific divergence likely shaped by separate evolutionary paths. Genetic diversity analysis identified two rare PvE1 alleles, e1-del and e1-fs, both associated with earlier flowering when combined with col2 mutations, indicating additive effects and reduced photoperiod sensitivity. Although functional validation by transformation was not performed, the use of NILs provides robust genetic evidence of PvE1 activity. Together, these findings establish PvE1 as a conserved legume-specific floral repressor in common bean, with novel allelic variants that can be exploited to develop early-flowering, photoperiod-insensitive cultivars adapted to temperate and high-latitude regions.

Root-knot nematodes (RKNs, Meloidogyne spp.) have become the major yield-limiting biological factor in common bean production in many warmer-climate regions such as the south of Europe. Broadening the genetic base of resistance in elite common bean cultivars is the most effective and environmentally friendly method for managing this disease. Toward this goal, F₁, F₂, and F₃ populations from crosses between susceptible snap beans (Helda and Perona) and the resistant Ouro Negro cultivar were phenotyped for M. incognita and M. javanica-induced root-galling (GI) and egg mass production (EM) in controlled growth chamber infection assays. F₁ progenies showed a susceptible response to both RKN isolates, with high GI and EM values, indicating a recessive inheritance of nematode resistance. The estimates for broad-sense heritability for GI and EM in the F₂ Helda × Ouro Negro population infected with M. incognita were 0.62 and 0.54, respectively. RKN resistance in Ouro Negro is largely controlled by partial to overdominant genetic effects and that susceptibility factor leads recessive resistance. The minimum number of genes involved in nematode resistance was estimated to be about two or three. In agreement, genetic analysis of F₂ segregating populations supported duplicate recessive epistasis as the inheritance pattern involved in the resistance provided by the Ouro Negro cultivar. Ouro Negro is an important resource for broadening RKN resistance in elite common bean cultivars.

The common bean has received attention as a model plant for legume studies, but little information is available about the morphology of its pods and the relation of this morphology to the loss of seed dispersal and/or the pod string, which are key agronomic traits of legume domestication. Dehiscence is related to the pod morphology and anatomy of pod tissues because of the weakening of the dorsal and ventral dehiscence zones and the tensions of the pod walls. These tensions are produced by the differential mechanical properties of lignified and non-lignified tissues and changes in turgor associated with fruit maturation. In this research, we histologically studied the dehiscence zone of the ventral and dorsal sutures of the pod in two contrasting genotypes for the dehiscence and string, by comparing different histochemical methods with autofluorescence. We found that the secondary cell wall modifications of the ventral suture of the pod were clearly different between the dehiscence-susceptible and stringy PHA1037 and the dehiscence-resistant and stringless PHA0595 genotypes. The susceptible genotype had cells of bundle caps arranged in a more easily breakable bowtie knot shape. The resistant genotype had a larger vascular bundle area and larger fibre cap cells (FCCs), and due to their thickness, the external valve margin cells were significantly stronger than those from PHA1037. Our findings suggest that the FCC area, and the cell arrangement in the bundle cap, might be partial structures involved in the pod dehiscence of the common bean. The autofluorescence pattern at the ventral suture allowed us to quickly identify the dehiscent phenotype and gain a better understanding of cell wall tissue modifications that took place along the bean’s evolution, which had an impact on crop improvement. We report a simple autofluorescence protocol to reliably identify secondary cell wall organization and its relationship to the dehiscence and string in the common bean.

Common bean has received attention as a model plant for legume studies, but little information is available about the morphology of its pods and the relation of this morphology to loss of seed dispersal and/or the pod string, which are key agronomic traits of legume domestication. Dehiscence is related to pod morphology and the anatomy of pod tissues because of the weakening of the dorsal and ventral dehiscence zones and the tensions of the pod walls. These tensions are produced by the differential mechanical properties of lignified and non-lignified tissues and changes in turgor associated with fruit maturation. In this research, we histologically studied the dehiscence zone of the ventral and dorsal sutures of the pod in two contrasting genotypes for dehiscence and string, by comparing different histochemical methods with autofluorescence. We found that the secondary cell wall modifications of the ventral suture of the pod were clearly different between the dehiscence-susceptible and stringy PHA1037 and the dehiscence-resistant and stringless PHA0595 genotypes. The susceptible genotype had cells of bundle caps arranged in a more easily breakable bowtie knot shape. The resistant genotype had a larger vascular bundle area and fibre cap cells (FCCs), and due to their thickness, the external valve margin cells were significantly stronger than those from PHA1037. Our findings suggest that the FCC area, and the cell arrangement in the bundle cap, might be a partial structure involved in the pod dehiscence of common bean. The autofluorescence pattern at the ventral suture allowed us to quickly identify the dehiscent phenotype and gain a better understanding of cell wall tissue modifications that took place along the bean's evolution, which had an impact on crop improvement. We report a simple autofluorescence protocol to reliably identify secondary cell wall organization and its relationship to dehiscence and string in common bean.

Legumes have an important role in European agriculture. They assimilate N₂ to sustainably support maximum crop growth, in turn providing high-protein food for human consumption and livestock feed. However, the extent of the area for legume cultivation in Europe has declined due to the lower economic competitiveness of legumes in relation to other crops, particularly of cereals and oilseed. To increase yields, there is a need to increase the genetic diversity of legumes in terms of adaptation to environmental stresses. We attempted to address this by conducting field and controlled experiments under drought vs. nondrought and different photoperiod conditions. The current study identified the physiological and agronomic traits correlated with productivity and quality performance in five economically important grain legume species (Pisum sativum, Phaseolus vulgaris, Cicer arietinum, Lupinus spp., and Vicia faba). In all species, the days to flowering and seed yield were affected by temperature and photoperiod. For cool-season legume species, long-day photoperiods were favorable and days to flowering was negatively correlated with the average air temperature. For the warm-season legumes, short-day photoperiods and warm temperatures were favorable. Under drought stress, the C/N balance, leaf nutrient (Ca, Fe, and K) concentrations, and yield were significantly reduced, contrary to Zn accumulation, and this information may contribute to improving our understanding and ability to develop sustainable growth. Based on our results, we conclude that the drought-tolerant and photoperiod-insensitive legume genotypes identified in this study constitute valuable starting materials for future programs aimed at improvement of legume productivity at a global/regional scale, which helps to strengthen the competitiveness and economic growth of legumes for European farmers.

The tropical common bean (Phaseolus vulgaris L.) is an obligatory short-day plant that requires relaxation of the photoperiod to induce flowering. Similar to other crops, photoperiod-induced floral initiation depends on the differentiation and maintenance of meristems. In this study, the global changes in transcript expression profiles were analyzed in two meristematic tissues corresponding to the vegetative and inflorescence meristems of two genotypes with different sensitivities to photoperiods. A total of 3396 differentially expressed genes (DEGs) were identified, and 1271 and 1533 were found to be up-regulated and down-regulated, respectively, whereas 592 genes showed discordant expression patterns between both genotypes. Arabidopsis homologues of DEGs were identified, and most of them were not previously involved in Arabidopsis floral transition, suggesting an evolutionary divergence of the transcriptional regulatory networks of the flowering process of both species. However, some genes belonging to the photoperiod and flower development pathways with evolutionarily conserved transcriptional profiles have been found. In addition, the flower meristem identity genes APETALA1 and LEAFY, as well as CONSTANS-LIKE 5, were identified as markers to distinguish between the vegetative and reproductive stages. Our data also indicated that the down-regulation of the photoperiodic genes seems to be directly associated with promoting floral transition under inductive short-day lengths. These findings provide valuable insight into the molecular factors that underlie meristematic development and contribute to understanding the photoperiod adaptation in the common bean.

Genetic variation for response of flowering time to photoperiod plays an important role in adaptation to environments with different photoperiods, and as consequence is an important contributor to plant productivity and yield. To elucidate the genetic control of flowering time [days to flowering (DTF); growing degree days (GDD)] in common bean, a facultative short-day plant, a quantitative trait loci (QTL) analysis was performed in a recombinant inbred mapping population derived from a cultivated accession and a photoperiod sensitive landrace, grown in different long-day (LD) and short-day (SD) environments by using a multiple-environment QTL model approach. A total of 37 QTL across 17 chromosome regions and 36 QTL-by-QTL interactions were identified for six traits associated with time to flowering and response to photoperiod. The DTF QTL accounted for 28 and 11% on average of the phenotypic variation in the population across LD and SD environments, respectively. Of these, a genomic region on chromosome 4 harboring the major DTF QTL was associated with both flowering time in LD and photoperiod response traits, controlling more than 60% of phenotypic variance, whereas a major QTL on chromosome 9 explained up to 32% of flowering time phenotypic variation in SD. Different epistatic interactions were found in LD and SD environments, and the presence of significant QTL × environment (QE) and epistasis × environment interactions implies that flowering time control may rely on different genes and genetic pathways under inductive and non-inductive conditions. Here, we report the identification of a novel major locus controlling photoperiod sensitivity on chromosome 4, which might interact with other loci for controlling common bean flowering time and photoperiod response. Our results have also demonstrated the importance of these interactions for flowering time control in common bean, and point to the likely complexity of flowering time pathways. This knowledge will help to identify and develop opportunities for adaptation and breeding of this legume crop.

Pod maturation of common bean relies upon complex gene expression changes, which in turn are crucial for seed formation and dispersal. Hence, dissecting the transcriptional regulation of pod maturation would be of great significance for breeding programs. In this study, a comprehensive characterization of expression changes has been performed in two common bean cultivars (ancient and modern) by analyzing the transcriptomes of five developmental pod stages, from fruit setting to maturation. RNA-seq analysis allowed for the identification of key genes shared by both accessions, which in turn were homologous to known Arabidopsis maturation genes and furthermore showed a similar expression pattern along the maturation process. Gene- expression changes suggested a role in promoting an accelerated breakdown of photosynthetic and ribosomal machinery associated with chlorophyll degradation and early activation of alpha-linolenic acid metabolism. A further study of transcription factors and their DNA binding sites revealed three candidate genes whose functions may play a dominant role in regulating pod maturation. Altogether, this research identifies the first maturation gene set reported in common bean so far and contributes to a better understanding of the dynamic mechanisms of pod maturation, providing potentially useful information for genomic-assisted breeding of common bean yield and pod quality attributes.

Common bean (Phaseolus vulgaris L.) is an important grain legume domesticated independently in Mexico and Andean South America approximately 8000 years ago. Wild forms are obligate short-day plants, and relaxation of photoperiod sensitivity was important for expansion to higher latitudes and subsequent global spread. To better understand the nature and origin of this key adaptation, we examined its genetic control in progeny of a wide cross between a wild accession and a photoperiod-insensitive cultivar. We found that photoperiod sensitivity is under oligogenic control, and confirm a major effect of the Ppd locus on chromosome 1. The red/far-red photoreceptor gene PHYTOCHROME A3 (PHYA3) was identified as a strong positional candidate for Ppd, and sequencing revealed distinct deleterious PHYA3 mutations in photoperiod-insensitive Andean and Mesoamerican accessions. These results reveal the independent origins of photoperiod insensitivity within the two major common bean gene pools and demonstrate the conserved importance of PHYA genes in photoperiod adaptation of short-day legume species.