Screening for resistance to four fungal diseases and associated genomic regions in a snap bean diversity panel.

Anthracnose, white mold, powdery mildew, and root rot caused by Colletotrichum lindemuthianum, Scletorinia sclerotiorum, Erysiphe spp., and Pythium ultimum, respectively, are among the most frequent diseases that cause significant production losses worldwide in common bean (Phaseolus vulgaris L.). Reactions against these four fungal diseases were investigated under controlled conditions using a diversity panel of 311 bean lines for snap consumption (Snap bean Panel). The genomic regions involved in these resistance responses were identified based on a genome-wide association study conducted with 16,242 SNP markers. The highest number of resistant lines was observed against the three C. lindemuthianum isolates evaluated: 156 lines were resistant to CL124 isolate, 146 lines resistant to CL18, and 109 lines were resistant to C531 isolate. Two well-known anthracnose resistance clusters were identified, the Co-2 on chromosome Pv11 for isolates CL124 and CL18, and the Co-3 on chromosome Pv04 for isolates CL124 and C531. In addition, other lesser-known regions of anthracnose resistance were identified on chromosomes Pv02, Pv06, Pv08, and Pv10. For the white mold isolate tested, 24 resistant lines were identified and the resistance was localized to three different positions on chromosome Pv08. For the powdery mildew local isolate, only 12 resistant lines were identified, and along with the two previous resistance genes on chromosomes Pv04 and Pv11, a new region on chromosome Pv06 was also identified. For root rot caused by Pythium, 31 resistant lines were identified and two main regions were located on chromosomes Pv04 and Pv05. Relevant information for snap bean breeding programs was provided in this work. A total of 20 lines showed resistant or intermediate responses against four or five isolates, which can be suitable for sustainable farm production and could be used as resistance donors. Potential genes and genomic regions to be considered for targeted improvement were provided, including new or less characterized regions that should be validated in future works. Powdery mildew disease was identified as a potential risk for snap bean production and should be considered a main goal in breeding programs.

Identification of consistent QTL and candidate genes associated with seed traits in common bean by combining GWAS and RNA-Seq.

KEY MESSAGE: Association analysis, colocation study with previously reported QTL, and differential expression analyses allowed the identification of the consistent QTLs and main candidate genes controlling seed traits. Common beans show wide seed variations in shape, size, water uptake, and coat proportion. This study aimed to identify consistent genomic regions and candidate genes involved in the genetic control of seed traits by combining association and differential expression analyses. In total, 298 lines from the Spanish Diversity Panel were genotyped with 4,658 SNP and phenotyped for seven seed traits in three seasons. Thirty-eight significant SNP-trait associations were detected, which were grouped into 23 QTL genomic regions with 1,605 predicted genes. The positions of the five QTL regions associated with seed weight were consistent with previously reported QTL. HCPC analysis using the SNP that tagged these five QTL regions revealed three main clusters with significantly different seed weights. This analysis also separated groups that corresponded well with the two gene pools described: Andean and Mesoamerican. Expression analysis was performed on the seeds of the cultivar 'Xana' in three seed development stages, and 1,992 differentially expressed genes (DEGs) were detected, mainly when comparing the early and late seed development stages (1,934 DEGs). Overall, 91 DEGs related to cell growth, signaling pathways, and transcriptomic factors underlying these 23 QTL were identified. Twenty-two DEGs were located in the five QTL regions associated with seed weight, suggesting that they are the main set of candidate genes controlling this character. The results confirmed that seed weight is the sum of the effects of a complex network of loci, and contributed to the understanding of seed phenotype control.

Genetic control of pod morphological traits and pod edibility in a common bean RIL population.

KEY MESSAGE: QTL mapping, association analysis, and colocation study with previously reported QTL revealed three main regions controlling pod morphological traits and two loci for edible pod characteristics on the common bean chromosomes Pv01 and Pv06. Bean pod phenotype is a complex characteristic defined by the combination of different traits that determine the potential use of a genotype as a snap bean. In this study, the TUM RIL population derived from a cross between 'TU' (dry) and 'Musica' (snap) was used to investigate the genetic control of pod phenotype. The character was dissected into pod morphological traits (PMTs) and edible pod characteristics (EPC). The results revealed 35 QTL for PMTs located on seven chromosomes, suggesting a strong QTL colocation on chromosomes Pv01 and Pv06. Some QTL were colocated with previously reported QTL, leading to the mapping of 15 consensus regions associated with bean PMTs. Analysis of EPC of cooked beans revealed that two major loci with epistatic effect, located on chromosomes Pv01 and Pv06, are involved in the genetic control of this trait. An association study using a subset of the Spanish Diversity Panel (snap vs. non-snap) detected 23 genomic regions, with three regions being mapped at a position similar to those of two loci identified in the TUM population. The results demonstrated the relevant roles of Pv01 and Pv06 in the modulation of bean pod phenotype. Gene ontology enrichment analysis revealed a significant overrepresentation of genes regulating the phenylpropanoid metabolic process and auxin response in regions associated with PMTs and EPC, respectively. Both biological functions converged in the lignin biosynthetic pathway, suggesting the key role of the pathway in the genetic control of bean pod phenotype.

Genetic erosion within the Fabada dry bean market class revealed by high-throughput genotyping.

The Fabada market class within the dry beans has a well-differentiated seed phenotype with very large white seeds. This work investigated the genetic diversity maintained in the seed collections within this market class and possible genetic erosion over the last 30 years. A panel with 100 accessions was maintained in seed collections for 30 years, 57 accessions collected from farmers in 2021, six cultivars developed in SERIDA, and 16 reference cultivars were gathered and genotyped with 108,585 SNPs using the genotyping-by-sequencing method. Filtering based on genotypic and phenotypic data was carried out in a staggered way to investigate the genetic diversity among populations. The dendrogram generated from genotyping revealed 90 lines forming 16 groups with identical SNP profiles (redundant lines) from 159 lines classified as market-class Fabada according to their passport data. Seed phenotyping indicated that 19 lines were mistakenly classified as Fabada (homonymies), which was confirmed in the dendrogram built without redundant lines. Moreover, this study provides evidence of genetic erosion between the population preserved for 30 years and the currently cultivated population. The conserved population contains 54.6% segregation sites and 41 different SNP profiles, whereas the cultivated population has 19.6% segregation sites and 26 SNP profiles. The loss of genetic variability cannot be attributed to the diffusion of modern cultivars, which increase genetic diversity (six new SNP profiles). The results allow for the more efficient preservation of plant genetic resources in genebanks, minimizing redundant accessions and incorporating new variations based on genotypic and phenotypic data.

Selection and adaptive introgression guided the complex evolutionary history of the European common bean.

Domesticated crops have been disseminated by humans over vast geographic areas. Common bean (Phaseolus vulgaris L.) was introduced in Europe after 1492. Here, by combining whole-genome profiling, metabolic fingerprinting and phenotypic characterisation, we show that the first common bean cultigens successfully introduced into Europe were of Andean origin, after Francisco Pizarro's expedition to northern Peru in 1529. We reveal that hybridisation, selection and recombination have shaped the genomic diversity of the European common bean in parallel with political constraints. There is clear evidence of adaptive introgression into the Mesoamerican-derived European genotypes, with 44 Andean introgressed genomic segments shared by more than 90% of European accessions and distributed across all chromosomes except PvChr11. Genomic scans for signatures of selection highlight the role of genes relevant to flowering and environmental adaptation, suggesting that introgression has been crucial for the dissemination of this tropical crop to the temperate regions of Europe.

Genome-wide association study for the extractable phenolic profile and coat color of common bean seeds (Phaseolus vulgaris L.).

BACKGROUND: A large variation in seed coat colors and seed phenolic metabolites is present in common bean (Phaseolus vulgaris L.). The study of the relationships between seed coat color phenotype and the phenolic profile is an important step in the elucidation of the gene network involved in the phenylpropanoid biosynthetic pathway. However, this relationship is still poorly understood in this species. RESULTS: A genome-wide association study (GWAS) was used to investigate the genomic regions associated with the synthesis of 10 flavonoids (5 anthocyanins and 5 flavonols) and with 10 seed coat color traits using a set of 308 common bean lines of the Spanish Diversity Panel (SDP) which have been genotyped with 11,763 SNP markers.. A total of 31 significant SNP-trait associations (QTNs) were identified, grouped in 20 chromosome regions: 6 for phenolic metabolites on chromosomes Pv01, Pv02, Pv04, Pv08, and Pv09, 13 for seed coat color on chromosomes Pv01, Pv02, Pv06, Pv07, and Pv10, and 1 including both types of traits located on chromosome Pv08. In all, 58 candidate genes underlying these regions have been proposed, 31 of them previously described in the phenylpropanoid pathway in common bean, and 27 of them newly proposed in this work based on the association study and their homology with Arabidopsis anthocyanin genes. CONCLUSIONS: Chromosome Pv08 was identified as the main chromosome involved in the phenylpropanoid pathway and in consequence in the common bean seed pigmentation, with three independent chromosome regions identified, Phe/C_Pv08(2.7) (expanding from 2.71 to 4.04 Mbp), C_Pv08(5.8) (5.89-6.59 Mbp), and Phe_Pv08(62.5) (62.58 to 63.28 Mbp). Candidate genes previously proposed by other authors for the color genes V and P were validated in this GWAS. Candidate genes have been tentatively proposed from this study for color genes B and Rk on Pv02, Asp on Pv07, and complex C on Pv08. These results help to clarify the complex network of genes involved in the genetic control of phenolic compounds and seed color in common bean and provide the opportunity for future validation studies.

Differentially expressed genes against Colletotrichum lindemuthiamum in a bean genotype carrying the Co-2 gene revealed by RNA-sequencing analysis.

Anthracnose is responsible for large yield losses in common bean crops. RNA-sequencing was used to investigate the differentially expressed genes (DEGs) in response to race 38 of Colletotrichum lindemuthianum in two near-isogenic lines (A25 and A4804) that differ in the presence of a resistance gene located in the cluster Co-2. Their responses were analyzed at different hours after inoculation (0, 24, and 48) and within and between genotypes. In all, 2,850 DEGs were detected, with 2,373 assigned to at least one functional GO term. Enriched GO terms in the resistant genotype were mainly related to functions as a response to stimulus, hormone signaling, cellular component organization, phosphorylation activities, and transcriptional regulation. The region containing the Co-2 cluster was delimited at the end of chromosome Pv11 (46.65-48.65 Mb) through a comparison with the SNP genotypes, obtained using 'Genotyping by Sequencing,' among seven resistant lines harboring the Co-2 gene and the susceptible line A25. The delimited region contained 23 DEGs, including 8 typical R genes, that showed higher expression levels in the resistant genotype and non-changes in the susceptible genotype after inoculation. Six R genes encoding protein kinases and an LRR domain formed a cluster in a core region between 46.98 and 47.04 Mb. The alignment of the raw transcriptome reads in the core region revealed structural changes that were used to design four potential breeder-friendly DNA markers, and it revealed some alignments with the intergenic regions, suggesting the presence of genes in addition to those annotated in the reference genome.

A Core Set of Snap Bean Genotypes Established by Phenotyping a Large Panel Collected in Europe.

Snap beans are a group of bean cultivars grown for their edible immature pods. The objective of this work was to characterize the diversity of pod phenotypes in a snap bean panel (SBP), comprising 311 lines collected in Europe, and establish a core set (Core-SBP) with the maximum diversity of pod phenotypes. Phenotyping of the SBP was carried out over two seasons based on 14 quantitative pod dimension traits along with three qualitative traits: pod color, seed coat color, and growth habit. Phenotypes were grouped into 54 classes using a hierarchical method, and a Core-SBP with one line per phenotype class was established. A further field-based evaluation of the Core-SBP revealed higher diversity index values than those obtained for the SBP. The Core-SBP was also genotyped using 24 breeder-friendly DNA markers tagging 21 genomic regions previously associated with pod trait control. Significant marker-trait associations were found for 11 of the 21 analyzed regions as well as the locus fin. The established Core-SBP was a first attempt to classify snap bean cultivars based on pod morphology and constituted a valuable source of characteristics for future breeding programs and genetic analysis.

Variation of Morphological, Agronomic and Chemical Composition Traits of Local Hazelnuts Collected in Northern Spain.

Hazelnut is a traditional crop in northern Spain, where it grows wild as well as being cultivated. A field collection of 41 local and 17 non-local accessions, including 15 well-known cultivars, was established at SERIDA in Villaviciosa, Spain. Here, phenotypic variation was documented for phenological and morphological traits and chemical composition. A large degree of variation for most morphological and phenological traits, except nut maturity date, was revealed. Estimates of broad-sense heritability were high (>0.75) for most of the assessed characters, except for the first male bloom date (0.65), male and female flowering periods (0.40, 0.31), kernel weight (0.69), and kernel percentage (0.33). Local accessions produced smaller nuts and kernels than well-known cultivars but with higher kernel percentage. Limited overlapping between the male and female flowering periods (dychogamy) was observed, except for 'Forcinas 1', 'Forcinas 2', and 'Morell'. The local accessions generally exhibited significantly later male and female flowering compared with the reference cultivars. The local materials showed similar nutritional values to those reported previously for hazelnut. Moreover, the local accessions presented average values similar to the non-local accessions for total fat, ash and carbohydrate contents, as well as energy value, but their protein contents were lower. Their oils were rich in functional compounds, such as unsaturated fatty acids (average: 90.1%), tocopherols (514 mg/kg) and squalene (294.3 mg/kg). A hierarchical clustering on principal components analysis grouped the accessions and differentiated eight local accessions from the rest, including the landrace 'Casina'. This finding provides potential new cultivars, as well as sources of desirable traits, for European hazelnut breeding programs.

Dissecting the genetic control of seed coat color in a RIL population of common bean (Phaseolus vulgaris L.).

KEY MESSAGE: Three genes associated with the seed coat color in a TU/Musica RIL population were located on a genetic map, and two candidate genes proposed to control black seed coat in the TU genotype were characterized. Seed coat color is an important characteristic of common bean (Phaseolus vulgaris L.) associated with the marketability of dry bean cultivars, quality and nutritional characteristics of seed, as well as response to pathogens. In this study, the genetic control of seed coat color in a recombinant inbred line population (175 lines) obtained from the cross 'TU' × 'Musica' was investigated. Phenotypic segregation fitted 1:1 for white vs. nonwhite, and 3:1 for brown versus black, indicating the involvement of three independent genes, one controlling white color and two (with epistatic interaction) controlling black color. Using a genetic map built with 842 SNPs, the gene responsible for the white seed coat was mapped on the linkage group Pv07, in the position previously described for the P gene. For the black seed coat phenotype, two genes were mapped to the beginning of chromosomes Pv06 and Pv08, in the positions estimated for the V gene and the complex C locus, respectively, by classical studies. The involvement of these two genomic regions was verified through two crosses between three selected RILs exhibiting complementary and dominant inheritance, in which the TU alleles for both genes resulted in a black phenotype. Two genes involved in the anthocyanin biosynthesis pathway were proposed as candidate genes: Phvul.006G018800 encoding a flavonoid 3'5'hydroxylase and Phvul.008G038400 encoding MYB113 transcription factor. These findings add knowledge to the complex network of genes controlling seed coat color in common bean as well as providing genetic markers to be used in future genetic analysis or plant breeding.

GWAS of pod morphological and color characters in common bean.

BACKGROUND: Common bean (Phaseolus vulgaris L.) is an important legume species which can be consumed as immature pods and dry seeds after re-hydration and cooking. Many genes and QTL, and epistatic interactions among them, condition pod morphological traits. However, not all them have been mapped or validated nor candidate genes proposed. We sought to investigate the genomic regions conditioning pod morphological and color characters through GWAS. RESULTS: Single and multi-locus genome wide association analysis was used to investigate pod traits for a set of 301 bean lines of the Spanish Diversity Panel (SDP). The SDP was genotyped with 32,812 SNPs obtained from Genotyping by Sequencing. The panel was grown in two seasons and phenotypic data were recorded for 17 fresh pods traits grouped in four pod characters: pod length, pod cross-section, pod color, and number of seeds per pod. In all, 23 QTL for pod length, 6 for cross-section, 18 for pod color, 6 for number of seeds per pod and 9 associated to two or more pod characters were detected. Most QTL were located in the telomeric region of chromosomes Pv01, Pv02, Pv04, Pv08, Pv09 and Pv10. Eighteen detected QTL co-localized with 28 previously reported QTL. Twenty-one potential candidate genes involving developmental processes were detected underlying 11 QTL for pod morphological characters, four of them homologous to A. thaliana genes FIS2, SPL10, TTG2 and AML4 affecting silique size. Eight potential candidate genes involved in pigment synthesis, were found underlying five QTL for pod color. CONCLUSIONS: GWAS for pod morphological and color characters in the bean Spanish Diversity Panel revealed 62 QTL, 18 co-localized with previously reported QTL, and 16 QTL were underlain by 25 candidate genes. Overall 44 new QTL identified and 18 existing QTL contribute to a better understanding of the complex inheritance of pod size and color traits in common bean and open the opportunity for future validation works.

Pod indehiscence in common bean is associated with the fine regulation of PvMYB26.

In legumes, pod shattering occurs when mature pods dehisce along the sutures, and detachment of the valves promotes seed dispersal. In Phaseolus vulgaris (L)., the major locus qPD5.1-Pv for pod indehiscence was identified recently. We developed a BC4/F4 introgression line population and narrowed the major locus down to a 22.5 kb region. Here, gene expression and a parallel histological analysis of dehiscent and indehiscent pods identified an AtMYB26 orthologue as the best candidate for loss of pod shattering, on a genomic region ~11 kb downstream of the highest associated peak. Based on mapping and expression data, we propose early and fine up-regulation of PvMYB26 in dehiscent pods. Detailed histological analysis establishes that pod indehiscence is associated with the lack of a functional abscission layer in the ventral sheath, and that the key anatomical modifications associated with pod shattering in common bean occur early during pod development. We finally propose that loss of pod shattering in legumes resulted from histological convergent evolution and that it is the result of selection at orthologous loci.

Genome-Wide Association Study (GWAS) for Resistance to Sclerotinia sclerotiorum in Common Bean.

White mold (WM) is a devastating fungal disease affecting common bean (Phaseolus vulgaris L.). In this research, a genome-wide association study (GWAS) for WM resistance was conducted using 294 lines of the Spanish diversity panel. One single-locus method and six multi-locus methods were used in the GWAS. Response to this fungus showed a continuous distribution, and 28 lines were identified as potential resistance sources, including lines of Andean and Mesoamerican origin, as well as intermediate lines between the two gene pools. Twenty-two significant associations were identified, which were organized into 15 quantitative trait intervals (QTIs) located on chromosomes Pv01, Pv02, Pv03, Pv04, Pv08, and Pv09. Seven of these QTIs were identified for the first time, whereas eight corresponded to chromosome regions previously identified in the WM resistance. In all, 468 genes were annotated in these regions, 61 of which were proposed potential candidate genes for WM resistance, based on their function related to the three main defense stages on the host: recognition (22), signal transduction (8), and defense response (31). Results obtained from this work will contribute to a better understanding of the complex quantitative resistance to WM in common bean and reveal information of significance for future breeding programs.

Integrating genetic and physical positions of the anthracnose resistance genes described in bean chromosomes Pv01 and Pv04.

A complex landscape of anthracnose resistance genes (Co-) located at the telomeric regions of the bean chromosomes Pv01 and Pv04 has been reported. The aim of this work was to investigate the genetic and physical positions of genes conferring resistance to races 6, 38, 39, 357, 65, and 73 as well as the relationships among the resistance genes identified herein and the previously described Co- genes in these telomeric regions. The linkage analysis using a genetic map of 497 SNPs from the recombinant inbred line population Xana/BAT93 revealed that the gene conferring resistance to race 65 in cultivar Xana (Co-165-X) was located in the Co-1 cluster, at the distal end of chromosome Pv01. The fine mapping of Co-165-X indicated that it was positioned between the physical positions 49,512,545 and 49,658,821 bp. This delimited physical position agrees with the positions of the previously mapped genes Co- 14, Co-x, Co-14, Co-1HY, and Co-Pa. Responses to races 6, 38, 39, and 357 in BAT93 exhibited co-segregation suggesting that the same gene, or very closely linked genes, were involved in the control. The linkage analysis showed that the resistance gene to race 38 in the genotype BAT93 (Co-338-B) was located at the beginning of chromosome Pv04, in the genetic position of the Co-3 cluster, and was flanked by markers with physical positions between 1,286,490 and 2,047,754 bp. Thus, the genes Co-3, Co-9, Co-10, Co-16, and Co-338-B, found in this work, form part of the same anthracnose resistance cluster at the beginning of chromosome Pv04, which is consistent with the discontinuous distribution of typical R genes annotated in the underlying genomic region. Resistance loci involved in the response to race 73 in the genotypes Xana (R) and BAT93 (R) were mapped to the same positions on clusters Co-1 and Co-3, respectively. The positioning of the resistance genes in the bean genome based on fine linkage mapping should play an important role in the characterization and differentiation of the anthracnose resistance genes. The assignment of Co- genes to clusters of race specific genes can help simplify the current scenario of anthracnose resistance.

Genetic diversity assessed by genotyping by sequencing (GBS) and for phenological traits in blueberry cultivars.

Blueberry is a small fruit crop which includes a complex group of different Vaccinium species of various ploidy levels. Commercial blueberries have been grown in Europe most recently, so there is not much information available about their adaptation into new regions. In this work we investigated adaptation to the environmental conditions of northern Spain, in terms of flowering and ripening seasons, of a set of 70 blueberry cultivars including several of the most important cultivated American species (V. corymbosum, V. virgatum, V. macrocarpon and V. uliginosum) in order to identify which types are best-suited in this geographical area of Europe. Most materials showed high chilling requirements for flowering under local conditions, while materials with low-chilling requirements showed problems in the maturation process of the flowers. Most cultivars were early or mid-season while a relative lack of late-season cultivars was observed. GBS was used for the analysis of genetic diversity in this sample of 70 cultivars. A total of 5255 SNP markers were obtained and a cluster analysis revealed three main groups associated with the ploidy level of the species. A Principal Component Analysis revealed a grouping of the V. corymbosum cultivars according to their chilling requirements. A total of 29 SNPs were identified as being highly informative for diversity analysis and potentially useful for cultivar identification and for breeding purposes. The results obtained from this research should contribute to the expansion of this crop, as well as providing data about genetic diversity useful for the preservation of genetic resources or for future breeding programs.

Genetic Diversity, Population Structure, and Linkage Disequilibrium in a Spanish Common Bean Diversity Panel Revealed through Genotyping-by-Sequencing.

A common bean (Phaseolus vulgaris) diversity panel of 308 lines was established from local Spanish germplasm, as well as old and elite cultivars mainly used for snap consumption. Most of the landraces included derived from the Spanish common bean core collection, so this panel can be considered to be representative of the Spanish diversity for this species. The panel was characterized by 3099 single-nucleotide polymorphism markers obtained through genotyping-by-sequencing, which revealed a wide genetic diversity and a low level of redundant material within the panel. Structure, cluster, and principal component analyses revealed the presence of two main subpopulations corresponding to the two main gene pools identified in common bean, the Andean and Mesoamerican pools, although most lines (70%) were associated with the Andean gene pool. Lines showing recombination between the two gene pools were also observed, most of them showing useful for snap bean consumption, which suggests that both gene pools were probably used in the breeding of snap bean cultivars. The usefulness of this panel for genome-wide association studies was tested by conducting association mapping for determinacy. Significant marker⁻trait associations were found on chromosome Pv01, involving the gene Phvul.001G189200, which was identified as a candidate gene for determinacy in the common bean.

Identification of Clusters that Condition Resistance to Anthracnose in the Common Bean Differential Cultivars AB136 and MDRK.

The correct identification of the anthracnose resistance systems present in the common bean cultivars AB136 and MDRK is important because both are included in the set of 12 differential cultivars proposed for use in classifying the races of the anthracnose causal agent, Colletrotrichum lindemuthianum. In this work, the responses against seven C. lindemuthianum races were analyzed in a recombinant inbred line population derived from the cross AB136 × MDRK. A genetic linkage map of 100 molecular markers distributed across the 11 bean chromosomes was developed in this population to locate the gene or genes conferring resistance against each race, based on linkage analyses and χ2 tests of independence. The identified anthracnose resistance genes were organized in clusters. Two clusters were found in AB136: one located on linkage group Pv07, which corresponds to the anthracnose resistance cluster Co-5, and the other located at the end of linkage group Pv11, which corresponds to the Co-2 cluster. The presence of resistance genes at the Co-5 cluster in AB136 was validated through an allelism test conducted in the F2 population TU × AB136. The presence of resistance genes at the Co-2 cluster in AB136 was validated through genetic dissection using the F2:3 population ABM3 × MDRK, in which it was directly mapped to a genomic position between 46.01 and 47.77 Mb of chromosome Pv11. In MDRK, two independent clusters were identified: one located on linkage group Pv01, corresponding to the Co-1 cluster, and the second located on LG Pv04, corresponding to the Co-3 cluster. This report enhances the understanding of the race-specific Phaseolus vulgaris-C. lindemuthianum interactions and will be useful in breeding programs.

Introgressed Genomic Regions in a Set of Near-Isogenic Lines of Common Bean Revealed by Genotyping-by-Sequencing.

Genotyping-by-sequencing (GBS) was used to investigate and identify the introgressed genomic regions that corresponded to resistance alleles for anthracnose ( and ), (BCMV), and (BCMNV, and ) in a set of bean near-isogenic lines (NIL). The GBS analysis provided 12,697 single nucleotide polymorphisms (SNPs) although the densities along the chromosomes were not uniform, and some chromosomal regions, such as centromeric or pericentromeric regions, were less tagged. The backcrossing method resulted in the introgression of genomic regions into specific chromosomes. The number of introgressed region-tagging SNPs varied between 1 and 13, representing between 0.33 and 6.88% of the bean genome. The changes detected among the recurrent parent and NIL in chromosomal regions are candidate regions that may contain the introgressed genes. By comparing the NIL derived from the same resistance source, it was possible to delimit in chromosomes Pv02, Pv04, Pv06, and Pv11 the genomic regions containing the resistance genes , , , and . Results allowed verification of the physical positions of the resistance genes and a clearer physical position of the anthracnose resistance genes and . Two nonoverlapping regions were delimited in chromosome Pv11 from common regions in NIL with resistance loci mapped to the Co-2 cluster. Alleles of the loci included within these genomic regions show strong linkage disequilibrium. This knowledge can be used in selection programs involving these regions rich in resistance genes.

Gene coding for an elongation factor is involved in resistance against powdery mildew in common bean.

KEY MESSAGE: Genetic control of the resistance response against powdery mildew in common bean was studied combining genetic, genomic and transcriptomic analyses. A candidate resistance gene in cultivar Porrillo Sintetico was proposed. The species causing the fungal disease powdery mildew (PM) in the local common bean crop was identified as Erysiphe polygoni through the molecular analysis of the internal transcribed spacer region. A genetic analysis of the resistance in cultivar Porrillo Sintetico was conducted using different F2:3 populations, and a dominant gene conferring total resistance against a local PM isolate was physically located between 84,188 and 218,664 bp of chromosome Pv04. An in silico analysis of this region, based on the common bean reference sequence, revealed four genes candidate to be involved in the resistance reaction. Relative expression levels of these genes after PM infection showed a significant over-expression of the candidate gene Phvul.004G001500 in the resistant genotype Porrillo Sintetico. This gene was re-sequenced in the parental genotypes X2776 and Porrillo Sintetico to explain their different phenotypic responses against PM. Several substitutions where identified in exon regions, all of them synonymous, so differences in the produced amino acid sequence were not expected. However, a total of 37 mutations were identified in non-coding regions of the gene sequence, suggesting that intron variation could be responsible for the different gene expression levels after PM infection. No evidence of other regulatory mechanisms, such as alternative splicing or methylation, was identified. Candidate resistance gene Phvul.004G001500 codes for an elongation factor that is not a typical gene related to recognition of specific pathogens in plants, suggesting its involvement in the resistance through plant immune system.

Identification of a New Chromosomal Region Involved in the Genetic Control of Resistance to Anthracnose in Common Bean.

Anthracnose caused by Colletotrichum lindemuthianum (Sacc. & Magnus) Lams.-Scrib. is a major disease affecting common bean (Phaseolus vulgaris L.) crops worldwide. Response to five C. lindemuthianum isolates, classified as races 3, 6, 7, 38, and 73, were analyzed in 156 F2:3 families derived from the cross between line SEL1308 and cultivar Michigan Dark Red Kidney (MDRK). SEL1308 was resistant to all five races, while MDRK was susceptible to all except for race 73. Segregation ratio for response to races 3 and 7 indicated that single dominant genes were responsible for the resistance reaction to each race. Recombination between both race-specific genes was observed and no linkage was found with any of the molecular markers tagging Co-genes or clusters previously described. Linkage analyses allowed the location of both genes at the beginning of linkage group (LG) Pv03, a region tentatively named as Co-17. Segregation ratio for response to races 6 and 38 indicated that two dominant and independent genes conferred resistance to these races. Contingency tests and subpopulation analyses suggested the implication of one region on LG Pv08, corresponding to the Co-4 cluster, and the Co-17 region. For reaction to race 73, the most likely scenario was that two dominant and independent genes conferred resistance: Co-1 in MDRK and Co-42 in SEL1308. Results indicated that, in addition to Co-42 , SEL1308 carries resistance genes located at the beginning of LG Pv03, in which no anthracnose resistance genes were previously mapped. In silico analysis revealed the presence of seven genes codifying typical resistance proteins (R-proteins) in the underlying physical position of the Co-17 region.