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The anthracnose disease caused by the fungal pathogen Colletotrichum lindemuthianum (Sacc & Magnus) Briosi & Cavara, is a disease that causes significant seed yield losses in common bean (Phaseolus vulgaris L.) worldwide. A germplasm collection of climbing beans from Guatemala was evaluated in the greenhouse for their reaction to race 73 of C. lindemuthianum that occurs in many growing areas worldwide. This germplasm mostly represents the so-called race Guatemala. Approximately 10% of 369 climbing bean accessions showed no symptoms (score of 1 on a 1–9 anthracnose severity visual score scale). Genome wide association study (GWAS) results using 78,754 SNP markers indicated that genomic regions with resistance to race 73 of C. lindemuthianum exist in Pv04 and Pv07, which have been previously reported. We also report four candidate genes located on Pv04 and Pv07 suspected to be responsible for anthracnose resistance, based on their proximity to significantly associated SNP markers.

Linkage and genome-wide association analyses using high-throughput SNP genotyping revealed different loci controlling resistance to different isolates of race 65 of Colletotrichum lindemuthianum in common bean. Development of varieties with durable resistance to anthracnose is a major challenge in common bean breeding programs because of the extensive virulence diversity of Colletotrichum lindemuthianum fungus. We used linkage and genome-wide association analyses to tap the genomic regions associated with resistance to different isolates of race 65. Linkage mapping was done using an F2 population derived from the cross between the Mesoamerican common beans BRS Estilo x Ouro Vermelho, inoculated with two different isolates of race 65. Association genetics relied on a diversity common bean panel containing 189 common bean accessions inoculated with five different isolates of race 65 as an attempt to validate the linkage analysis findings and, eventually, identify other genomic regions associated with resistance to race 65. The F2 population and diversity panel were genotyped with the BARCBean6K_3 Illumina BeadChip containing 5398 SNP markers. Both linkage and genome-wide association analyses identified different loci controlling resistance to different isolates of race 65 on linkage group Pv04. Genome-wide association analysis also detected loci on Pv05, Pv10 and Pv11 associated with resistance to race 65. These findings indicate that resistance to race 65 can be overcome by the virulence diversity among different isolates of the same race and could lead to the loss of resistance after cultivar release. We identified 25 resistant common bean cultivars to all five isolates of race 65 in the diversity panel. The accessions should be useful to develop cultivars combining different resistance genes that favor durable resistance to anthracnose in common bean.

Angular leaf spot (ALS), caused by Pseudocercospora griseola, is one of the most devastating diseases of common bean (Phaseolus vulgaris L.) in tropical and subtropical production areas. Breeding for ALS resistance is difficult due to the extensive virulence diversity of P. griseola and the recurrent appearance of new virulent races. Five major loci, Phg-1 to Phg-5, conferring ALS resistance have been named, and markers tightly linked to these loci have been reported. Quantitative trait loci (QTLs) have also been described, but the validation of some QTLs is still pending. The Phg-1, Phg-4, and Phg-5 loci are from common bean cultivars of the Andean gene pool, whereas Phg-2 and Phg-3 are from beans of the Mesoamerican gene pool. The reference genome of common bean and high-throughput sequencing technologies are enabling the development of molecular markers closely linked to the Phg loci, more accurate mapping of the resistance loci, and the comparison of their genomic positions. The objective of this report is to provide a comprehensive review of ALS resistance in common bean. Furthermore, we are reporting three case studies of ALS resistance breeding in Latin America and Africa. This review will serve as a reference for future resistance mapping studies and as a guide for the selection of resistance loci in breeding programs aiming to develop common bean cultivars with durable ALS resistance., Crop Science, 59 (4), ISSN:0011-183X

Anthracnose, caused by the fungal pathogen Colletotrichum lindemuthianum, is one of the world's most destructive diseases of common bean. The use of resistant cultivars is the most cost-effective strategy to manage this disease; however, durable resistance is difficult to achieve due to the vast virulence diversity of the anthracnose pathogen. Finding new genes with broad-spectrum resistance increases the prospect of designing an effective anthracnose-management strategy. Genetic analysis confirmed the presence of a single, dominant anthracnose-resistance locus in AC, which we provisionally named Co-AC. Bulk segregant analysis and genetic mapping of two F2 populations from the crosses AC × PI207262 and AC × G 2333 were used to determine the position of the Co-AC locus in a 631 Kbp genomic region flanked by the SNP markers SS56 and SS92 on the lower arm of chromosome Pv01. By genotyping 77 F3 plants from the AC × PI207262 cross using nine additional markers, we fine-mapped the Co-AC locus to a significantly smaller genomic region (9.4 Kbp) flanked by the SNP markers SS102 and SS165. This 9.4 Kbp region harbors three predicted genes based on the common bean reference genome, notably including the gene model Phvul.001G244300, which encodes Clathrin heavy chain 1, a protein that supports specific stomatal regulation functions and might play a role in plant defense signaling. Because the Co-AC resistance locus is linked in cis, it can be selected with great efficiency using molecular markers. These results will be very useful for breeding programs aimed at developing bean cultivars with anthracnose resistance using marker-assisted selection. This study revealed the broad-spectrum resistance of AC to C. lindemuthianum and the existence of the Co-AC anthracnose-resistance locus. Fine mapping positioned this locus in a small genomic region on the lower end of chromosome Pv01 that contained three candidate genes for the Co-AC locus.

Linkage and genome-wide association analyses using high-throughput SNP genotyping revealed different loci controlling resistance to different isolates of race 65 of Colletotrichum lindemuthianum in common bean. Development of varieties with durable resistance to anthracnose is a major challenge in common bean breeding programs because of the extensive virulence diversity of Colletotrichum lindemuthianum fungus. We used linkage and genome-wide association analyses to tap the genomic regions associated with resistance to different isolates of race 65. Linkage mapping was done using an F

Co-segregation analysis and high-throughput genotyping using SNP, SSR, and KASP markers demonstrated genetic linkage between Ur-14 and Co-3 4 /Phg-3 loci conferring resistance to the rust, anthracnose and angular leaf spot diseases of common bean. Rust, anthracnose, and angular leaf spot are major diseases of common bean in the Americas and Africa. The cultivar Ouro Negro has the Ur-14 gene that confers broad spectrum resistance to rust and the gene cluster Co-3 4 /Phg-3 containing two tightly linked genes conferring resistance to anthracnose and angular leaf spot, respectively. We used co-segregation analysis and high-throughput genotyping of 179 F2:3 families from the Ruda (susceptible) × Ouro Negro (resistant) cross-phenotyped separately with races of the rust and anthracnose pathogens. The results confirmed that Ur-14 and Co-3 4 /Phg-3 cluster in Ouro Negro conferred resistance to rust and anthracnose, respectively, and that Ur-14 and the Co-3 4 /Phg-3 cluster were closely linked. Genotyping the F2:3 families, first with 5398 SNPs on the Illumina BeadChip BARCBEAN6K_3 and with 15 SSR, and eight KASP markers, specifically designed for the candidate region containing Ur-14 and Co-3 4 /Phg-3, permitted the creation of a high-resolution genetic linkage map which revealed that Ur-14 was positioned at 2.2 cM from Co-3 4 /Phg-3 on the short arm of chromosome Pv04 of the common bean genome. Five flanking SSR markers were tightly linked at 0.1 and 0.2 cM from Ur-14, and two flanking KASP markers were tightly linked at 0.1 and 0.3 cM from Co-3 4 /Phg-3. Many other SSR, SNP, and KASP markers were also linked to these genes. These markers will be useful for the development of common bean cultivars combining the important Ur-14 and Co-3 4 /Phg-3 genes conferring resistance to three of the most destructive diseases of common bean.

Bean rust is a devastating disease of common bean in the Americas and Africa. The historically important Ur-3 gene confers resistance to many races of the highly variable bean rust pathogen that overcome all known rust resistance genes. Existing molecular markers tagging Ur-3 for use in marker assisted selection produce false results. We described here the fine mapping of Ur-3 for the development of highly accurate markers linked to this gene. An F2 population from Pinto 114 × Aurora was evaluated for its reaction to four different races of the bean rust pathogen. A bulked segregant analysis using the SNP chip BARCBEAN6K_3 positioned the approximate location of the Ur-3 locus to the lower arm of chromosome Pv11. Specific SSR and SNP markers and haplotype analysis of 18 sequenced bean lines led to position the Ur-3 locus to a 46.5 Kb genomic region. We discovered a KASP marker, SS68 that was tightly linked to the Ur-3 locus. Validation of SS68 on a panel of 130 diverse common bean lines and varieties containing all known rust resistance genes revealed that it was highly accurate producing no false results. The SS68 marker will be of great value to pyramid Ur-3 with other rust resistance genes. It will also reduce significantly time and labor associated with the current phenotypic detection of Ur-3. This is the first utilization of fine mapping to discover markers linked to a rust resistance in common bean.

Soybean rust (Phakopsora pachyrhizi) has been reported on common bean (Phaseolus vulgaris) in Asia, South Africa, and the United States. However, there is little information on the interaction of individual isolates of Phakopsora pachyrhizi with common bean germplasm. A set of 16 common bean cultivars with known genes for resistance to Uromyces appendiculatus, the causal agent of common bean rust, three soybean accessions that were sources of the single gene resistance to P. pachyrhizi, and the moderately susceptible soybean ‘Ina’ were evaluated using seedlings inoculated with six isolates of P. pachyrhizi. Among the common bean cultivars, Aurora, Compuesto Negro Chimaltenango, and Pinto 114, were the most resistant to all six P. pachyrhizi isolates, with lower severity, less sporulation, and consistent reddish-brown (RB) lesions associated with resistance in soybean. A differential response was observed among the common bean cultivars, with a cultivar-isolate interaction for both severity and sporulation levels, as well as the presence or absence of the RB lesion type. This differential response was independent of the known genes that condition resistance to U. appendiculatus, suggesting that resistance to P. pachyrhizi was independent of resistance to U. appendiculatus.

Pseudomonas syringae pv. phaseolicola (Psph) Race 6 is a globally prevalent and broadly virulent bacterial pathogen with devastating impact causing halo blight of common bean (Phaseolus vulgaris L.). Common bean lines PI 150414 and CAL 143 are known sources of resistance against this pathogen. We constructed high-resolution linkage maps for three recombinant inbred populations to map resistance to Psph Race 6 derived from the two common bean lines. This was complemented with a genome-wide association study (GWAS) of Race 6 resistance in an Andean Diversity Panel of common bean. Race 6 resistance from PI 150414 maps to a single major-effect quantitative trait locus (QTL; HB4.2) on chromosome Pv04 and confers broad-spectrum resistance to eight other races of the pathogen. Resistance segregating in a Rojo × CAL 143 population maps to five chromosome arms and includes HB4.2. GWAS detected one QTL (HB5.1) on chromosome Pv05 for resistance to Race 6 with significant influence on seed yield. The same HB5.1 QTL, found in both Canadian Wonder × PI 150414 and Rojo × CAL 143 populations, was effective against Race 6 but lacks broad resistance. This study provides evidence for marker-assisted breeding for more durable halo blight control in common bean by combining alleles of race-nonspecific resistance (HB4.2 from PI 150414) and race-specific resistance (HB5.1 from cv. Rojo).

Bean rust, caused by Uromyces appendiculatus, is a devastating disease of common bean (Phaseolus vulgaris) in the Americas and Africa. The historically important Ur-3 gene confers resistance to many races of the highly variable bean rust pathogen that overcome other rust resistance genes. Existing molecular markers tagging Ur-3 for use in marker-assisted selection produce false results. Here, we describe the fine mapping of the Ur-3 locus for the development of highly accurate markers linked to Ur-3. An F2 population from the cross Pinto 114 (susceptible) × Aurora (resistant with Ur-3) was evaluated for its reaction to four different races of U. appendiculatus. A bulked segregant analysis using the SNP chip BARCBEAN6K_3 placed the approximate location of Ur-3 in the lower arm of chromosome Pv11. Specific SSR and SNP markers and haplotype analysis of 18 sequenced bean varieties positioned Ur-3 in a 46.5 kb genomic region from 46.96 to 47.01 Mb on Pv11. We discovered in this region the SS68 KASP marker that was tightly linked to Ur-3. Validation of SS68 on a panel of 130 diverse common bean cultivars containing all known rust resistance genes revealed that SS68 was highly accurate and produced no false results. The SS68 marker will be of great value in pyramiding Ur-3 with other rust resistance genes. It will also significantly reduce time and labor associated with the current phenotypic detection of Ur-3. This is the first utilization of fine mapping to discover markers linked to rust resistance in common bean.

Small-sieve snap beans (Phaseolus vulgaris L.) are an important source of income for smallholder farmers in East Africa. In this region as well as in other tropical and subtropical environments, common bean rust, caused by Uromyces appendiculatus (Pers.:Pers.), and heat stress reduce the yield and quality of snap beans. Small-sieve rust-resistant snap beans and that are heat-tolerant were developed using heat-tolerant snap bean breeding lines that had broad-spectrum rust resistance conditioned by the combination of the Andean Ur-4 and Mesoamerican Ur-11 genes. The Ur-4 and Ur-11 rust gene combination confers resistance to 90 races of the hypervariable pathogen from different parts of the world, including East Africa, that are maintained at Beltsville, MD. Four breeding lines each having the combination of the two rust genes were crossed in a 4 × 5 diallel mating design with five susceptible small-sieve cultivars to give 20 F1 hybrids. The hybrid combinations were advanced through the F2, F3, and F4 generations with selection for heat tolerance, rust resistance, and pod quality to develop lines combining these traits. Twenty F5 breeding lines that had the combination of these traits were selected and evaluated in East Africa at four field sites selected on the basis of differences in altitude, climate, and virulence diversity of the bean rust pathogen and in Puerto Rico at a field site characterized by high temperatures. There was a significant positive correlation between ranks of heat stress influenced yield components (seeds per pod and total yield) at the hot field site and the controlled high-temperature (32/27 °C) greenhouse. Four of the breeding lines developed, L5, L9, L13, and L17, combined heat tolerance and rust resistance in the desired plant type with high yield and good pod quality. These lines are the first known small-sieve snap beans with the combination of traits for heat tolerance and broad-spectrum rust resistance conferred by the Ur-4 and Ur-11 genes. These results demonstrate ability to combine heat tolerance and rust resistance as important traits for adaptation of specific market classes of common bean to tropical and subtropical environments through targeted selection of multiple traits in controlled environments.

Common bean rust disease (caused by Uromyces appendiculatus) and high temperatures (heat stress) limit snap bean (Phaseolus vulgaris) production in many tropical and temperate regions. We have developed snap bean lines combining broad-spectrum rust resistance with heat tolerance for tropical agroecosystems. Eight breeding populations were developed by hybridizing BelJersey-RR-15 and BelFla-RR-1 (each possessing the Ur-4 and Ur-11 rust resistance genes) and the heat-tolerant snap bean breeding lines HT601, HT603, HT608, and HT611. F2–F4 generations of the populations were evaluated under greenhouse conditions and selected for heat tolerance while simultaneously selecting for the rust resistance genes Ur-4 and Ur-11. Three heat-tolerant F5 lines, which were homozygous for Ur-4 and Ur-11 genes, were selected together with a rust-resistant but heat-sensitive control. These and 12 cultivars adapted to different geographical regions were evaluated for their reaction to rust and yield at six contrasting field sites in eastern Africa and their response to high temperature verified in Puerto Rico. Rust incidence and severity was high at three of the trial sites in eastern Africa. Two of the 12 cultivars were resistant to rust at most of these sites, and three of the four breeding lines were resistant at all sites. The Ur-11 gene effectively conferred rust resistance at all sites. Yield in Puerto Rico was strongly correlated (R2 = 0.71, P < 0.001) with that of the hottest site in eastern Africa, highlighting the similarity in genotypic response to high temperatures at the two distinct sites. The newly developed rust-resistant and heat-tolerant breeding lines showed stable yield at the eastern Africa sites with contrasting mean temperatures compared with the cultivars presently grown in the region. Two of these lines, HT1 and HT2, were confirmed to be homozygous for Ur-4 and Ur-11 and with high heat tolerance under both greenhouse and field environments. This research validates the effectiveness of targeted rust resistance gene combinations for tropical environments and the effective selection of high temperature tolerance traits correlating across multiple environments. The breeding lines HT1 and HT2 developed in this research could be used to improve snap beans for the tropics and other environments with similar constraints.

Nine varieties of dry beans representing five market classes were grown in three locations (Maryland, Michigan, and Nebraska), and subsamples were collected for each variety (row composites from each plot). Aqueous methanol extracts of ground beans were analyzed in triplicate by UV spectrophotometry. Analysis of variance-principal component analysis was used to quantify the relative variance arising from location, variety, between rows of plants, and analytical uncertainty and to test the significance of differences in the chemical composition. Statistically significant differences were observed between all three locations, between all nine varieties, and between rows for each variety. PCA score plots placed the nine varieties in four categories that corresponded with known taxonomic groupings: (1) black beans (cv. Jaguar and cv. T-39), (2) pinto beans (cv. Buster and cv. Othello), (3) small red beans (cv. Merlot), and (4) great northern (cv. Matterhorn and cv. Weihing) and navy (cv. Seahawk and cv. Vista) beans. The relative plant-to-plant variance, estimated from the between row variance, was 71-79% for 25-40 plants per row.

Great northern common bean (Phaseolus vulgaris L.) 'Coyne' (Reg. No. CV-287, PI 655574) was developed by the dry bean breeding program at the University of Nebraska Agricultural Research Division and released in 2008. It was bred specifi cally for adaptation to Nebraska growing conditions and for enhanced resistance to common bacterial blight (CBB), a major disease of common bean caused by the seed-borne bacterium Xanthomonas campestris pv. phaseoli (Smith) Dye, and bean common rust Uromyces appendiculatus (Pers.:Pers) Unger. Coyne is a great northern F 7 : 8 line derived from a three-way cross (G95023/Weihing//BelMiNeb-RMR-11). The fi rst cross was made in winter 2003. The F 7:8 was tested in advanced yield trials at Scottsbluff and Mitchell, NE, and in growers' fi elds in Nebraska. Yield of Coyne was only 47 kg ha -1 lower than 'Marquis' in Morrill and Scotts Bluff, NE, counties. Reaction of Coyne to CBB under fi eld conditions was consistent across 3 yr at the West Central Research and Extension Center, North Platte, NE, where fi eld disease ratings of 3.2, 3.5, and 4.4 were recorded in 2005, 2006, and 2007, respectively. Coyne has the Ur-3 and Ur-6 genes for resistance to common bean rust and carries the single dominant hypersensitive I gene that provides resistance to all non-necrotic strains of Bean common mosaic virus. Coyne has bright white seed, blooms 44 d after planting, and is a midseason bean, maturing 91 d after planting.

Novel sources of resistance are continuously needed to combat anthracnose disease in common bean (Phaseolus vulgaris L.) caused by the hypervariable pathogen Colletotrichum lindemuthianum (Sacc. and Magnus) Briosi and Cavara. We sought to characterize the novel anthracnose resistance in Andean common bean landrace ‘Jalo Listras Pretas’ (JLP). Jalo Listras Pretas is resistant to races 9, 64, 65, and 73 of the anthracnose pathogen used in this study. To examine inheritance of anthracnose resistance in JLP, F 2 populations JLP/Mexico 222 and JLP/Cornell 49242 were inoculated with discriminating races of the pathogen. Segregation for resistance in both F 2 populations fi t a 3:1 resistant/susceptible ratio suggesting that the anthracnose resistance in JLP is controlled by a single dominant gene. To establish independence of the resistance gene in JLP from other published resistance genes, allelism tests were conducted with 14 F 2 populations derived from crossing JLP with Andean cultivars carrying anthracnose resistance genes Co-1, Co-1 2 , Co-1 3 , Co-1 5 , and Co-12, and with Middle American cultivars with Co-2, Co-3, Co-4 3 , Co-5, Co-6, Co-7, Co-9, Co-10, and Co-11. Results revealed the resistance gene in JLP was independent of the Andean loci Co-1 and Co-12, and the nine Middle American anthracnose resistance genes. The symbol Co-13 was assigned to this newly discovered anthracnose resistance gene in Brazilian Andean common bean landrace JLP.

Drought stress reduces dry bean (Phaseolus vulgaris L.) yield in more than 60% of the production regions worldwide. Pinto bean germplasm line C046348 (Reg. No. GP-275, PI 651500) was developed by the Colorado Agricultural Experiment Station in cooperation with the University of Idaho and USDA-ARS and released 1 Apr. 2007. C046348 is a drought-tolerant pinto bean germplasm with a 95 to 98 d growing season, high yield potential, excellent pinto seed quality, and resistance to rust caused by Uromyces appendiculatus. The complete pedigree of C046348 is unknown; however, it was derived from a single cross made in 1989 with the pinto cultivar Othello as the female parent. Othello is a short-season pinto cultivar released in 1987 that combines excellent pinto seed color and resistance to some strains of bean common mosaic caused by Bean common mosaic virus (a potyvirus).

Based on the phenolic profiles obtained by high performance liquid chromatography-electrospray ionization mass spectrometry (HPLC-DAD-ESI/MS), 24 common bean samples, representing 17 varieties and 7 generic off-the-shelf items, belonging to ten US commercial market classes can be organized into six different groups. All of them contained the same hydroxycinnaminic acids, but the flavonoid components showed distinct differences. Black beans contained primarily the 3-O-glucosides of delphinidin, petunidin and malvidin, while pinto beans contained kaempferol and its 3-O-glycosides. Light red kidney bean contained traces of quercetin 3-O-glucoside and its malonates, but pink and dark red kidney beans contained the diglycosides of quercetin and kaempferol. Small red beans contained kaempferol 3-O-glucoside and pelargonidin 3-O-glucoside, while no flavonoids were detected in alubia, cranberry, great northern, and navy beans. This is the first report of the tentative identification of quercetin 3-O-pentosylhexoside and flavonoid glucoside malonates, and the first detailed detection of hydroxycinnamates, in common beans.

Common bean (Phaseolus vulgaris L.) is an important legume, useful for its high protein and dietary fiber. The fungal pathogen Uromyces appendiculatus (Pers.) Unger can cause major loss in susceptible varieties of the common bean. The Ur-3 locus provides race specific resistance to virulent strains or races of the bean rust pathogen along with Crg, (Complements resistance gene), which is required for Ur-3-mediated rust resistance. In this study, we inoculated two common bean genotypes (resistant “Sierra” and susceptible crg) with rust race 53 of U. appendiculatus, isolated leaf RNA at specific time points, and sequenced their transcriptomes. First, molecular markers were used to locate and identify a 250 kb deletion on chromosome 10 in mutant crg (which carries a deletion at the Crg locus). Next, we identified differential expression of several disease resistance genes between Mock Inoculated (MI) and Inoculated (I) samples of “Sierra” leaf RNA within the 250 kb delineated region. Both marker assisted molecular profiling and RNA-seq were used to identify possible transcriptomic locations of interest regarding the resistance in the common bean to race 53. Identification of differential expression among samples in disease resistance clusters in the bean genome may elucidate significant genes underlying rust resistance. Along with preserving favorable traits in the crop, the current research may also aid in global sustainability of food stocks necessary for many populations.

We investigated the occurrence of two plant endornaviruses, Phaseolus vulgaris endornavirus 1 and Phaseolus vulgaris endornavirus 2, in breeding lines, cultivars, landraces, and wild genotypes of common bean (Phaseolus vulgaris) collected from the two centers of common bean domestication: Mesoamerica and the Andes. The two endornaviruses were detected in many genotypes of Mesoamerican origin but rarely in genotypes of Andean origin. The results suggest that these two endornaviruses were introduced into the Mesoamerican modern genotypes during common bean domestication and provide more evidence for the existence of two divergent gene pools of common bean.

Great northern common bean (Phaseolus vulgaris L.) germplasm line ABC-Weihing (Reg. No. GP-246, PI 647964) was developed by the University of Nebraska Agricultural Research Division in cooperation with USDA-ARS and released in 2006. This line, tested as NE1-05-4, was bred specifi cally for enhanced resistance to common bacterial blight (CBB), a major seed borne disease of common bean caused by the bacterium Xanthomonas campestris pv. phaseoli (Smith) Dye (Xcp). ABC-Weihing is a great northern BC 5 F 3:6 line obtained from fi ve backcrosses ('Weihing'*5//'Chase'/XAN 159). The fi rst cross was made in spring 1997. Only BC n F 1 plants resistant to Xcp isolates Dominican Republic DR-7 and Nebraska SC4A, as determined by multiple needle leaf inoculation tests in the greenhouse, were used for successive backcrossing. In addition to phenotypic selection for CBB resistance, marker-assisted selection for the resistant QTL- linked marker SU91 was conducted in the BC 1 F 1 , BC 2 F 1 , and ABC-Weihing. When inoculated with Nebraska Xcp strains in the fi eld, ABC-Weihing exhibited resistance in both 2005 and 2006. ABC-Weihing has Ur-3 and Ur-6 genes for resistance to common bean rust and carries the single dominant hypersensitive I gene that provides resistance to all non-necrotic strains of the Bean common mosaic virus (BCMV). ABC-Weihing has bright white seed, blooms 45 d after planting, and is a midseason bean maturing 92 d after planting.

Growing cultivars that possess multiple disease-and-pest resistance minimizes crop losses, reduces the need for pesticides, and lowers production costs. Our objective was to use gamete selection (i.e., selection based on F 1 -derived families that come from crosses that are multiple-parent, heterogeneous, and heterogametic) to develop upright carioca-type beans (Phaseolus vulgaris L.) with resistance to angular leaf spot (ALS), anthracnose (ANT), bean common mosaic (BCM), bean golden mosaic (BGM), common bacterial blight (CBB), and leafhopper (LHP). Two multiple-parent, interracial crosses (BZ 9780 and GX 9792) were made, using plant-to-plant pollinations, in 1990-1991. The F 1 -derived F 2 (F 1.2 ) families were evaluated for ALS and CBB, and F 1.3 families for ANT and LHP. In F 4 , carioca-type seeds from promising families were saved. The F 1.4 families were then evaluated for BGM. All 127 F 1.2 families from BZ 9780 were discarded by F 4 because none segregated for six resistances and possessed carioca-type seeds. Of the GX 9792 population, 260 Fs-derived F 9 (F 5.9 ) lines, originating from only 12 of 460 F 1.2 families, were evaluated for ALS, ANT, BCM, BGM, CBB, and LHP. Six parents, eight checks, and 86 F 5.9 lines resistant to at least ANT, BCM, and CBB were tested for yield in seven environments in 1995-1996, using a partially balanced lattice design with three replicates. Only eight lines, originating from four of the 460 F 1.2 families, possessed resistance to all five diseases and LHP. Of these lines, one outyielded the check cultivar Carioca, and that line with one other outyielded the two carioca-type parents (A 769 and EMP 250) used in the GX 9792 populations. Thus, the use of gamete selection and early generation testing was effective in developing high- yielding upright lines with resistance to multiple biotic stresses.

If we are to breed common bean (Phaseolus vulgaris L.) for durable resistance to diseases, we must understand pathogenic variation and find sources of resistance. Our first objective was to determine the patterns of pathogenic variation found among isolates of Phaeoisariopsis griseola (PG), the fungus that causes angular leaf spot (ALS) in common bean. We characterized 433 PG isolates from 11 Latin American and 10 African countries, using differential cultivars, isozymes, and/or random amplified polymorphic DNA (RAPD) markers. We also systematically screened, for ALS resistance, common bean accessions from the world collection held at CIAT, and assessed the progress so far made in breeding for resistance to ALS. Despite their great diversity within and between countries on both continents, the PG isolates were classified into two major groups: Andean, and Middle American. Although each group had internal differences for virulence, and biochemical and molecular characteristics, the ‘Andean’ PG isolates were more virulent on common beans of Andean origin, than on those of Middle American origin, thus, suggesting a host-pathogen co-evolution. The ‘Middle American’ PG isolates, although more virulent on common beans from Middle America, also attacked Andean beans, thus, exhibiting a much broader virulence spectrum. To find sources of resistance, we tested 22,832 common bean accessions against naturally occurring PG isolates in the field at CIAT's Experiment Station, Quilichao, Colombia, between 1985 and 1992. The resulting 123 intermediate (scores of 4 to 6) and resistant (scores of 1 to 3) accessions were then tested in the greenhouse against selected 14 PG isolates of diverse origins. Nineteen accessions were intermediate or resistant to at least 13 of 14 PG isolates. Similarly, of 13,219 bred lines tested in the field between 1978 and 1996, 89 were intermediate or resistant. Of these, 33 bred lines proved intermediate or resistant to at least eight of nine PG isolates to which they were challenged in the greenhouse. We suggest that, to breed for durable resistance to ALS, common bean populations should be developed from crosses between Andean and Middle American gene pools. The populations should then be systematically evaluated and selected against the broadest range of the most virulent PG isolates of diverse evolutionary origins.

Isolates of Pseudomonas syringae pv. phaseolicola from Africa and other bean growing areas were categorized into nine races on the basis of their reactions to eight differential cultivars following artificial inoculation. Eight hundred and ninety-three isolates representing 303 disease occurrences were initially identified as P.s. pv. phaseolicola by their pathogenicity to bean, cultural and serological characteristics and phage sensitivity. These tests also served to distinguish P.s. pv. phaseolicola from the closely related pathovars P.s. pv. glycinea and P.s. pv. syringae. Detailed race determinations were carried out on 175 selected isolates of p.s. pv. phaseolicola representative of the different geographical regions and hosts in which the pathogen was found and nine races were identified. A number of races (1,2,5,6 and 7) were distributed worldwide with race 6 predominant. Other races were found mainly in Africa; races 3 and 4 in East/Central Africa and races 8 and 9 in Southern Africa. Most isolates were obtained from the major host, Phaseolus vulgaris. Alternative natural hosts included 10 legume species representative of seven different genera (Cajanus cajan, Desmodium sp., Lablab purpureus, Macroptilium atropurpureum, Neonotonia wightii, Phaseolus acutifolius, P. coccineus, P. lunatus, Vigna angularis and V. radiata). Of these, Desmodium sp. constitutes a new host record.

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 × Ruda and AND 277 × Ouro Negro crosses and F(2:3) families from the AND 277 × Ouro Negro cross. Ruda 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.

Two double-cross populations were used to evaluate the efficiency of independent, alternate, and simultaneous selection practiced from the F2 to F8 for resistance to anthracnose and angular leaf spot of common bean (Phaseolus vulgaris L.). Seven resistant and high-yielding lines were selected from each of the four environments used during this study. These lines and the seven parents involved in two populations were evaluated in an 8 × 8 lattice design with three replications in two cropping seasons. Pathogen inoculum was used to create the three test environments: anthracnose alone, angular leaf spot alone, and anthracnose and angular leaf spot together. All entries were also evaluated in a fourth, disease-free environment. Selection for resistance to anthracnose and angular leaf spot was effective in both populations. Mean disease scores of all selected lines for anthracnose were lower than that of angular leaf spot irrespective of selection environment. Among the three stress environments, yields were higher in the anthracnose environment. However, lines selected alternately for anthracnose and angular leaf spot were usually higher yielding, and the highest yielding line in both populations originated from this selection environment. The mean yield of selected lines was higher and the highest yielding line originated from the population involving a parent (G 1805) belonging to the Mexican highland race ‘Jalisco’. Positive association existed between seed yield of protected and pathogen-inoculated environments. No association was found between resistance to anthracnose and angular leaf spot.

Plants appear to have two types of active defenses, a broad-spectrum basal system and a system controlled by R-genes providing stronger resistance to some pathogens that break the basal defense. However, it is unknown if the systems are separate entities. Therefore, we analyzed proteins from leaves of the dry bean crop plant Phaseolus vulgaris using a high-throughput liquid chromatography tandem mass spectrometry method. By statistically comparing the amounts of proteins detected in a single plant variety that is susceptible or resistant to infection, depending on the strains of a rust fungus introduced, we defined basal and R-gene-mediated plant defenses at the proteomic level. The data reveal that some basal defense proteins are potential regulators of a strong defense weakened by the fungus and that the R-gene modulates proteins similar to those in the basal system. The results satisfy a new model whereby R-genes are part of the basal system and repair disabled defenses to reinstate strong resistance.

Based on the phenolic profiles obtained by high performance liquid chromatography-electrospray ionization mass spectrometry (HPLC-DAD-ESI/MS), 24 common bean samples, representing 17 varieties and 7 generic off-the-shelf items, belonging to ten US commercial market classes can be organized into six different groups. All of them contained the same hydroxycinnaminic acids, but the flavonoid components showed distinct differences. Black beans contained primarily the 3-O-glucosides of delphinidin, petunidin and malvidin, while pinto beans contained kaempferol and its 3-O-glycosides. Light red kidney bean contained traces of quercetin 3-O-glucoside and its malonates, but pink and dark red kidney beans contained the diglycosides of quercetin and kaempferol. Small red beans contained kaempferol 3-O-glucoside and pelargonidin 3-O-glucoside, while no flavonoids were detected in alubia, cranberry, great northern, and navy beans. This is the first report of the tentative identification of quercetin 3-O-pentosylhexoside and flavonoid glucoside malonates, and the first detailed detection of hydroxycinnamates, in common beans.

Em. andgreatnorthernMontanaNo.5(Miklasetal.,2003)sourcesMarchal) develops more slowly on P961341 than on suscepti- of common bacterial blight resistance. Combined resistanceble wheat lines; P961341 is typically scored at 2 to 4 (0–9, 0 wasconfirmedbythepresenceofpreviouslydevelopedSCARno lesions to 9 severe disease) compared to scores of 6 to markers SU91 (Pedraza et al., 1997) and SAP6 (Miklas et al.,8 for cultivar Patterson in the same tests in Indiana. P961341 2003) tightly linked with quantitative trait loci (QTL) fromis resistant to

Background Next generation sequencing has significantly increased the speed at which single nucleotide polymorphisms (SNPs) can be discovered and subsequently used as molecular markers for research. Unfortunately, for species such as common bean (Phaseolus vulgaris L.) which do not have a whole genome sequence available, the use of next generation sequencing for SNP discovery is much more difficult and costly. To this end we developed a method which couples sequences obtained from the Roche 454-FLX system (454) with the Illumina Genome Analyzer (GA) for high-throughput SNP discovery. Results Using a multi-tier reduced representation library we discovered a total of 3,487 SNPs of which 2,795 contained sufficient flanking genomic sequence for SNP assay development. Using Sanger sequencing to determine the validation rate of these SNPs, we found that 86% are likely to be true SNPs. Furthermore, we designed a GoldenGate assay which contained 1,050 of the 3,487 predicted SNPs. A total of 827 of the 1,050 SNPs produced a working GoldenGate assay (79%). Conclusions Through combining two next generation sequencing techniques we have developed a method that allows high-throughput SNP discovery in any diploid organism without the need of a whole genome sequence or the creation of normalized cDNA libraries. The need to only perform one 454 run and one GA sequencer run allows high-throughput SNP discovery with sufficient sequence for assay development to be performed in organisms, such as common bean, which have limited genomic resources.

During 2003, a new disease, dry bean phyllody (DBPh), was observed in the Columbia Basin of Washington in dry bean (Phaseolus vulgaris L.) cultivars of Andean origin grown in Mattawa and Paterson, WA that caused great reduction in dry bean production. Symptoms of DBPh became apparent during mid-to-late pod development and were characterized by leafy petals (phyllody) and aborted seed pods resembling thin, twisted, and corrugated leaf-like structures. Deformed sterile pods that were small, sickle-shaped, upright, and leathery were also observed. The infected plants generally exhibited chlorosis, stunting, or bud proliferation from leaf axils. Symptoms of DBPh were indicative of possible infection by phytoplasmas. Restriction fragment length polymorphism (RFLP) and phylogenetic analyses of amplified 16S rDNA sequences were used for phytoplasma identification. Four symptomatic bean plants were analyzed and tested positive for phytoplasma infection on the basis of results of initial polymerase chain reaction (PCR) and subsequent nested-PCR amplifications (2). RFLP analyses of 16S rDNA sequences with restriction enzymes, MseI, AluI, HhaI, RsaI, and HpaII indicated that the phytoplasma strains associated with DBPh belonged to the clover proliferation group (16SrVI) subgroup A (16SrVI-A) (2). This subgroup currently consists of three members, clover proliferation (CP; GenBank Accession No. AY500130), potato witches'-broom (PWB; GenBank Accession No. AY500818), and vinca virescence (VR; GenBank Accession No. AY500817), a strain of beet leafhopper-transmitted virescence agent (BLTVA) phytoplasmas (1,2). The taxonomic affiliations of the DBPh phytoplasma strains were confirmed by phylogenetic analysis of cloned 16S rRNA gene sequences (GenBank Accession Nos. DBPh2, AY496002; DBPh3, AY496003). Among the existing members of subgroup 16SrVI-A, the four DBPh strains were closely related to the VR strain with 99.7% 16S rDNA sequence homology and to the CP strain with 99.2% sequence homology. To gain further evidence on the role of 16SrVI-A phytoplasma strains in DBPh disease, a modified test of Koch's postulates was conducted. Infected tissue from one phytoplasma-positive dry bean sample was grafted onto three Pinto UI-114 bean seedlings in the greenhouse. Within 60 days, the bean seedlings exhibited corrugated leaf-like structures from aborted seedpods, a lack of flower formation, general chlorosis, and stunting similar to the original diseased plants. The lower leaves of the inoculated bean plants became epinastic and leathery. The transmitted phytoplasma was detected in each of the grafted symptomatic seedlings, and the RFLP patterns of its 16S rRNA gene sequences were identical to those of the phytoplasmas in the scions. A high correlation between the presence of disease symptoms and the presence of subgroup 16SrVI-A phytoplasmas in the bean plants suggests that these phytoplasmas play an etiological role in DBPh disease. To our knowledge, these findings provide the first confirmed case of phytoplasma-associated DBPh in the United States. References: (1) D. A. Golino et al. Plant Dis. 73:850, 1989. (2) I.-M. Lee et al. Int. J. Syst. Bacteriol. 48:1153, 1998.