Search

Bacterial brown spot (BBS) caused by Pseudomonas syringae pv. syringae (Pss), common bacterial blight (CBB) caused by Xanthomonas axonopodis pv. phaseoli (Xap) and Xanthomonas fuscans subsp. fuscans (Xff), and halo bacterial blight (HBB), caused by Pseudomonas syringae pv. phaseolicola (Psph), are major bacterial diseases that severely affect common bean yields and global food security. Andean-origin dry beans, representing large-seeded market classes, are particularly susceptible. Using 140,325 SNPs, a multi-locus GWAS was conducted on subsets of the Andean diversity panel (ADP) phenotyped for BBS in South Africa, CBB in Puerto Rico, South Africa, and Zambia, and HBB in South Africa, through natural infection, artificial inoculation, or both. Twenty-four QTL associated with resistance were identified: nine for BBS, eight for CBB, and seven for HBB. Four QTL intervals on Pv01, Pv03, Pv05, and Pv08 overlapped with BBS and HBB resistance. A genomic interval on Pv01, near the fin gene, which determines growth habit, was linked to resistance to all three pathogens. Different QTLs were detected for BBS and CBB resistance when phenotyped under natural infection versus artificial inoculation. These results underscore the importance of combining phenotyping methods in multi-GWAS to capture the full genetic spectrum. Previously recognized CBB resistance QTL SAP6 and SU91 and HBB resistance QTL HB4.2, and HB5.1, were observed. Other common (MAF >0.25) and rare (MAF <0.05) resistance QTL were also detected. Overall, these findings enhance the understanding and utilization of bacterial resistance present in ADP for the development of common beans with improved resistance. [ABSTRACT FROM AUTHOR]

'Kikatiti' pinto bean (Phaseolus vulgaris L.) (Reg. no. CV‐361, PI 705149) was developed by the dry bean breeding program at the University of Nebraska, Agricultural Research Division, and submitted for release in 2021 by the Sokoine University of Agriculture in Morogoro as an upright indeterminate pinto bean with high yield potential and multiple disease resistance across bean production environments in Tanzania. Kikatiti was officially released in 2024 by the National Seed Committee. Kikatiti is an F7:8 derived line developed using the pedigree breeding method in Nebraska. The exceptional performance of Kikatiti in Tanzania was first identified by evaluation of the Durango Diversity Panel (DDP), which consisted of 200 accessions in on‐station trials conducted in Arusha and Mbeya. Kikatiti was identified as accession DDP‐094 (advanced breeding line NE2‐09‐3). Kikatiti yielded 1584 kg ha−1 across 5 years of trials in Tanzania and matured in 89 days. Kikatiti is resistant to bean rust conferred by the Ur‐3 and Ur‐11 genes, resistant to all strains of Bean common mosaic virus and Bean common mosaic necrosis virus conferred by the I and bc‐3 genes, moderately resistant to common bacterial blight conferred by the SAP6 quantitative trait locus, avoids white mold disease due to its upright architecture, and is moderately susceptible to angular leaf spot disease. Kikatiti has large seed size (35.9 g 100 seeds−1), and in on‐farm trials, farmers ranked Kikatiti above local pinto cultivars for its performance and market potential. Kikatiti has the potential to expand pinto bean production across East Africa. Core Ideas: Kikatiti pinto bean has superior productivity in Tanzania.Kikatiti pinto possesses an effective combination of resistance genes to combat bean rust disease in East Africa.Kikatiti pinto possesses an effective combination of resistance genes to combat Bean common mosaic necrosis virus.Farmers ranked Kikatiti above local pinto cultivars for performance and market potential in on‐farm trials. [ABSTRACT FROM AUTHOR]

Key message: R-BPMV is located within a recently expanded TNL cluster in the Phaseolus genus with suppressed recombination and known for resistance to multiple pathogens including potyviruses controlled by the I gene. Bean pod mottle virus (BPMV) is a comovirus that infects common bean and legumes in general. BPMV is distributed throughout the world and is a major threat on soybean, a closely related species of common bean. In common bean, BAT93 was reported to carry the R-BPMV resistance gene conferring resistance to BPMV and linked with the I resistance gene. To fine map R-BPMV, 182 recombinant inbred lines (RILs) derived from the cross BAT93 × JaloEEP558 were genotyped with polymerase chain reaction (PCR)-based markers developed using genome assemblies from G19833 and BAT93, as well as BAT93 BAC clone sequences. Analysis of RILs carrying key recombination events positioned R-BPMV to a target region containing at least 16 TIR-NB-LRR (TNL) sequences in BAT93. Because the I cluster presents a suppression of recombination and a large number of repeated sequences, none of the 16 TNLs could be excluded as R-BPMV candidate gene. The evolutionary history of the TNLs for the I cluster were reconstructed using microsynteny and phylogenetic analyses within the legume family. A single I TNL was present in Medicago truncatula and lost in soybean, mirroring the absence of complete BPMV resistance in soybean. Amplification of TNLs in the I cluster predates the divergence of the Phaseolus species, in agreement with the emergence of R-BPMV before the separation of the common bean wild centers of diversity. This analysis provides PCR-based markers useful in marker-assisted selection (MAS) and laid the foundation for cloning of R-BPMV resistance gene in order to transfer the resistance into soybean. [ABSTRACT FROM AUTHOR]

The pinto bean (Phaseolus vulgaris L.) cultivar 'USDA Diamondback' (Reg. no. CV‐353, PI 698822) was released by the USDA‐ARS in 2022 as a high‐yielding cultivar with an upright architecture and the slow‐darkening seed coat trait. It was bred for tolerance to multiple abiotic stresses in a "purgatory" plot purposely managed to have compacted soil, low soil fertility, and intermittent drought conditions. Conversely, selection for high yield potential was conducted in non‐stress trials with tillage, irrigations, and fertilizers applied for optimal production. USDA Diamondback exhibits wide adaption to production regions across the United States, as evidenced by an average seed yield of 3808 kg ha−1 across 14 location‐years in the Cooperative Dry Bean Nursery. Virus testing and resistance gene–linked markers indicate USDA Diamondback has a three‐gene combination (bc‐ud, bc‐1, and bc‐3) that confers durable resistance to all known strains of Bean common mosaic virus and Bean common mosaic necrosis virus. A similar combination of pathogen and marker testing indicated that USDA Diamondback possesses the Ur‐3 and Ur‐6 genes for resistance to bean rust. The seed size, appearance, and canning quality characteristics of USDA Diamondback meets the industry standards for packaging and processing. Core Ideas: USDA Diamondback was bred for high yield potential under both favorable and stressful environments.USDA Diamondback has the slow‐darkening trait that maintains seed coat brightness during prolonged storage.USDA Diamondback has above‐average canning quality.USDA Diamondback is resistant to all known strains of Bean common mosaic virus and Bean common mosaic necrosis virus. [ABSTRACT FROM AUTHOR]

Key Message: Quantitative Trait Loci “hotspots” for drought tolerance were identified on chromosomes Pv06, Pv07 and Pv10 of common bean. Drought is a major production constraint of common bean (Phaseolus vulgaris L.) worldwide. The objective of this study was to identify the Quantitative Trait Loci (QTL) for drought tolerance in an Andean population of Recombinant Inbred Lines (RILs). A total of 155 F5:7 RILs derived from a cross between Kijivu (drought tolerant) and Bukoba (drought susceptible) were evaluated for drought tolerance in field and pot experiments. Four field experiments were conducted at three locations in Zambia in 2020 and 2021. All field trials were conducted in the dry season under irrigation. The 155 RILs were genotyped with 11,292 SNPs, and composite interval mapping was conducted to identify QTL for drought tolerance. Seed yield for Kijivu under drought stress was consistently higher than for Bukoba across all four field trials. A total of 60 QTL were identified for morphological, agronomic, and physiological traits under drought stress and non-stress conditions. However, the majority of these QTL were specific to drought stress. QTL “hotspots” for drought tolerance were identified on chromosomes Pv06, Pv07, and Pv10. Extensive co-localizations for agronomic and morpho-physiological traits under drought stress were observed at the three drought-tolerance QTL hotspots. Additionally, these three QTL hotspots overlapped with previously identified QTL for drought tolerance, while several others identified QTL are novel. The three identified QTL hotspots could be used in future marker-assisted selection for drought tolerance in common bean. [ABSTRACT FROM AUTHOR]

Background: Common beans (Phaseolus vulgaris L.) provide important protein and calories globally. Anthracnose (Colletotrichum lindemuthianum (Sacc. & Magnus) Briosi & Cavara, 1889) is a major disease in common bean and causes significant yield losses in bean production areas. Screening for markers linked to known disease resistance genes provides useful information for plant breeders to develop improved common bean varieties. The Kompetitive Allele Specific PCR (KASP) assay is an affordable genetic screening technique that can be used to accelerate breeding programs, but manual DNA extraction and KASP assay preparation are time-consuming. Several KASP markers have been developed for genes involved in resistance to bean anthracnose, which can reduce yield by up to 100%, but their usefulness is hindered by the labor required to screen a significant number of bean lines. Our research objective was to develop publicly available protocols for DNA extraction and KASP assaying using a liquid handling robot (LHR) which would facilitate high-throughput genetic screening with less active human time required. Anthracnose resistance markers were used to compare manual and automated results. Results: The 12 bean anthracnose differential cultivars were screened for four anthracnose KASP markers linked to the resistance genes Co-1, Co-3 and Co-42 both by hand and with the use of an LHR. A protocol was written for DNA extraction and KASP assay thermocycling to implement the LHR. The LHR protocol reduced the active human screening time of 24 samples from 3h44 to 1h23. KASP calls were consistent across replicates but not always accurate for their known linked resistance genes, suggesting more specific markers still need to be developed. Using an LHR, information from KASP assays can be accumulated with little active human time. Conclusion: Results suggest that LHRs can be used to expedite time-consuming and tedious lab work such as DNA extraction or PCR plate filling. Notably, LHRs can be used to prepare KASP assays for large sample sizes, facilitating higher throughput use of genetic marker screening tools. [ABSTRACT FROM AUTHOR]

Whitemold (WM) is a major disease in common bean (Phaseolus vulgaris L.), and its complex quantitative genetic control limits the development of WM resistant cultivars. WM2.2, one of the nine meta-QTL with a major effect on WM tolerance, explains up to 35% of the phenotypic variation andwas previously mapped to a large genomic interval on Pv02. Our objective was to narrow the interval of thisQTL using combined approach of classic QTL mapping and QTL-based bulk segregant analysis (BSA), and confirming those results with Khufu de novo QTL-seq. The phenotypic and genotypic data from two RIL populations, 'Raven'/I9365-31 (R31) and 'AN-37'/PS02-029C-20 (Z0726-9), were used to select resistant and susceptible lines to generate subpopulations for bulk DNA sequencing. The QTL physical interval was determined by considering overlapping interval of the identified QTL or peak region in both populations by three independent QTL mapping analyses. Our findings revealed that meta-QTL WM2.2 consists of three regions, WM2.2a (4.27-5.76 Mb; euchromatic), WM 2.2b (12.19 to 17.61 Mb; heterochromatic), and WM2.2c (23.01-25.74 Mb; heterochromatic) found in both populations. Gene models encoding for gibberellin 2-oxidase 8, pentatricopeptide repeat, and heat-shock proteins are the likely candidate genes associated with WM2.2a resistance. A TIR-NBS-LRR class of disease resistance protein (Phvul.002G09200) and LRR domain containing family proteins are potential candidate genes associated with WM2.2b resistance. Nine gene models encoding disease resistance protein [pathogenesis-related thaumatin superfamily protein and disease resistance-responsive (dirigent-like protein) family protein etc] found within theWM2.2c QTL interval are putative candidate genes. WM2.2a region is most likely associated with avoidance mechanisms while WM2.2b and WM2.2c regions trigger physiological resistance based on putative candidate genes. [ABSTRACT FROM AUTHOR]

Beet curly top virus (BCTV), which is synonymous with curly top virus (CTV), causes significant yield loss in common bean (snap and dry beans) cultivars and several other important crops. Common bean cultivars have been found to be resistant to CTV, but screening for resistance is challenging due to the cyclical nature of epidemics and spotty feeding by the leafhopper that vectors the virus. We used an SNP dataset for the Snap Bean Association Panel (SnAP) agroinoculated with CTV-Logan (CA/Logan) strain to locate the Bct gene region to a 1.7-Mb interval on chromosome Pv07 using genome-wide association study (GWAS) analysis. Recombinant lines from the SnAP were used to further narrow the Bct region to a 58.0-kb interval. A missense SNP (S07_2970381) in candidate gene Phvul.007G036300 Exonuclease V (EXO5) was identified as the most likely causal mutation, and it was the most significant SNP detected by GWAS in a dry bean population (DBP) naturally infected by the CTV-Worland (Wor) strain. Tmshift assay markers developed for SNP S07_2970381 and two linked SNPs, S07_2970276 and S07_2966197, were useful for tracking different origins of the Bct EXO5 candidate gene resistance to CTV in common bean. The three SNPs identified four haplotypes, with haplotype 3-1 (Haplo3-1) of Middle American origin associated with the highest levels of CTV resistance. This SNPhaplotype assay will enable breeders to track resistance sources and to develop cultivars with better CTV resistance. [ABSTRACT FROM AUTHOR]

The pinto bean (Phaseolus vulgaris L.), 'USDA Rattler' (Reg. no. CV‐350, PI 693789), was released by the USDA‐ARS in 2021 as a high‐yielding, upright, full‐season cultivar with abiotic stress tolerance. It was bred for broad adaptation to the different bean production regions across the United States by selection for high yield performance under nonstress and multiple stress trials in Washington state. The multiple stress trials included a "purgatory" plot with low fertility, intermittent drought, and soil compaction, and a separate trial which simulated terminal drought. Conversely, the nonstress trials were well watered and fertilized to optimize yield potential. Yield stability is evidenced by the mean seed yield for the breeding line PT11‐13, from which USDA Rattler was selected, numerically exceeding the trial means for 33 of 38 location‐years. Broad adaptation for USDA Rattler is further evidenced by an average seed yield of 4547 kg ha−1 across 10 location‐years in the Cooperative Dry Bean Nursery. Genetic markers as well as pathogen testing indicate USDA Rattler has I and bc‐3 gene combination for durable resistance to all known strains of Bean common mosaic virus and Bean common mosaic necrosis virus. Greenhouse testing with four races of the rust pathogen indicated USDA Rattler is fixed for the Ur‐3 resistance gene but is heterogenous for presence of the Ur‐11 resistance gene. The seed size, appearance, and canning quality characteristics of USDA Rattler meets the industry standards for packaging and processing. Core Ideas: USDA Rattler was bred for high yield potential under both favorable and stressful environments.USDA Rattler performed well in our "purgatory plot" used to select for drought and low soil fertility tolerance.USDA Rattler is resistant to all known strains of Bean common mosaic virus and Bean common mosaic necrosis virus.USDA Rattler is widely adapted to production regions across the United States. [ABSTRACT FROM AUTHOR]

The classic V (violet, purple) gene of common bean (Phaseolus vulgaris) functions in a complex genetic network that controls seed coat and flower color and flavonoid content. V was cloned to understand its role in the network and the evolution of its orthologs in the Viridiplantae. V mapped genetically to a narrow interval on chromosome Pv06. A candidate gene was selected based on flavonoid analysis and confirmed by recombinational mapping. Protein and domain modeling determined V encodes flavonoid 3′5′ hydroxylase (F3′5′H), a P450 enzyme required for the expression of dihydromyricetin-derived flavonoids in the flavonoid pathway. Eight recessive haplotypes, defined by mutations of key functional domains required for P450 activities, evolved independently in the two bean gene pools from a common ancestral gene. V homologs were identified in Viridiplantae orders by functional domain searches. A phylogenetic analysis determined F3′5′H first appeared in the Streptophyta and is present in only 41% of Angiosperm reference genomes. The evolutionarily related flavonoid pathway gene flavonoid 3′ hydroxylase (F3′H) is found nearly universally in all Angiosperms. F3′H may be conserved because of its role in abiotic stress, while F3′5′H evolved as a major target gene for the evolution of flower and seed coat color in plants. [ABSTRACT FROM AUTHOR]

Bean common mosaic virus (BCMV) is a major disease in common bean (Phaseolus vulgaris L.). Host plant resistance is the most effective strategy to minimize crop damage against BCMV and the related Bean common mosaic necrosis virus (BCMNV). To facilitate breeding for resistance, we sought to identify candidate genes and develop markers for the bc-2 gene and the unknown gene with which it interacts. Genome-wide association study (GWAS) of the Durango Diversity Panel (DDP) identified a peak region for bc-2 on chromosome Pv11. Haplotype mapping narrowed the bc-2 genomic interval and identified Phvul.011G092700, a vacuolar protein-sorting 4 (Vps4) AAA+ ATPase endosomal sorting complexes required for transport (ESCRT) protein, as the bc-2 candidate gene. The race Durango Phvul.011G092700 gene model, bc-2 [UI111], contains a 10-kb deletion, while the race Mesoamerican bc-2 [Robust] consists of a single nucleotide polymorphism (SNP) deletion. Each mutation introduces a premature stop codon, and they exhibit the same interaction with the pathogroups (PGs) tested. Phvul.005G125100, another Vps4 AAA+ ATPase ESCRT protein, was identified as the candidate gene for the new recessive bc-4 gene, and the recessive allele is likely an amino acid substitution in the microtubule interacting and transport (MIT) domain. The two Vps4 AAA+ ATPase ESCRT proteins exhibit high similarity to the Zym Cucsa.385040 candidate gene associated with recessive resistance to Zucchini yellow mosaic virus in cucumber. bc-2 alone has no resistance effect but, when combined with bc-4 , provides resistance to BCMV (except PG-V) but not BCMNV, and, when combined with bc-u d, provides resistance to BCMV (except BCMV PG-VII) and BCMNV. So instead of different resistance alleles (i.e., bc-2 and bc-2 2), there is only bc-2 with a differential reaction based on whether it is combined with bc-4 or bc-u d , which are tightly linked in repulsion. The new tools and enhanced understanding of this host-virus pathogen interaction will facilitate breeding common beans for resistance to BCMV and BCMNV. [ABSTRACT FROM AUTHOR]

Bean common mosaic necrosis virus (BCMNV) is a major disease in common bean (Phaseolus vulgaris L.). Host plant resistance is the primary disease control. We sought to identify candidate genes to better understand the host-pathogen interaction and develop tools for marker-assisted selection (MAS). A genome-wide association study (GWAS) approach using 182 lines from a race Durango Diversity Panel (DDP) challenged by BCMNV isolates NL-8 [Pathogroup (PG)-III] and NL-3 (PG-VI), and genotyped with 1.26 million single-nucleotide polymorphisms (SNPs), revealed significant peak regions on chromosomes Pv03 and Pv05, which correspond to bc-1 and bc-u resistance gene loci, respectively. Three candidate genes were identified for NL-3 and NL-8 resistance. Side-by-side receptor-like protein kinases (RLKs), Phvul.003G038700 and Phvul.003G038800 were candidate genes for bc-1. These RLKs were orthologous to linked RLKs associated with virus resistance in soybean (Glycine max). A basic Leucine Zipper (bZIP) transcription factor protein is the candidate gene for bc-u. bZIP protein gene Phvul.005G124100 carries a unique non-synonymous mutation at codon 14 in the first exon (Pv05: 36,114,516 bases), resulting in a premature termination codon that causes a nonfunctional protein. SNP markers for bc-1 and bc-u and new markers for I and bc-3 genes were used to genotype the resistance genes underpinning BCMNV phenotypes in the DDP, host group (HG) differentials, and segregating F3 families. Results revealed major adjustments to the current host-pathogen interaction model: (i) there is only one resistance allele bc-1 for the Bc-1 locus, and differential expression of the allele is based on presence vs. absence of bc-u ; (ii) bc-1 exhibits dominance and incomplete dominance; (iii) bc-1 alone confers resistance to NL-8; (iv) bc-u was absent from HGs 2, 4, 5, and 7 necessitating a new gene symbol bc-u d to reflect this change; (v) bc-u d alone delays susceptible symptoms, and when combined with bc-1 enhanced resistance to NL-3; and (vi) bc-u d is on Pv05, not Pv03 as previously thought. These candidate genes, markers, and adjustments to the host-pathogen interaction will facilitate breeding for resistance to BCMNV and related Bean common mosaic virus (BCMV) in common bean. [ABSTRACT FROM AUTHOR]

Identifying the molecular basis of resistance to pathogens is critical to promote a chemical-free cropping system. In plants, nucleotide-binding leucine-rich repeat constitute the largest family of disease resistance (R) genes, but this resistance can be rapidly overcome by the pathogen, prompting research into alternative sources of resistance. Anthracnose, caused by the fungus Colletotrichum lindemuthianum , is one of the most important diseases of common bean. This study aimed to identify the molecular basis of Co-x , an anthracnose R gene conferring total resistance to the extremely virulent C. lindemuthianum strain 100. To that end, we sequenced the Co-x 58 kb target region in the resistant JaloEEP558 (Co-x) common bean and identified KTR2/3 , an additional gene encoding a truncated and chimeric CRINKLY4 kinase, located within a CRINKLY4 kinase cluster. The presence of KTR2/3 is strictly correlated with resistance to strain 100 in a diversity panel of common beans. Furthermore, KTR2/3 expression is up-regulated 24 hours post-inoculation and its transient expression in a susceptible genotype increases resistance to strain 100. Our results provide evidence that Co-x encodes a truncated and chimeric CRINKLY4 kinase probably resulting from an unequal recombination event that occurred recently in the Andean domesticated gene pool. This atypical R gene may act as a decoy involved in indirect recognition of a fungal effector. [ABSTRACT FROM AUTHOR]

Genetic resistance is the primary means for control of Bean golden yellow mosaic virus (BGYMV) in common bean (Phaseolus vulgaris L.). Breeding for resistance is difficult because of sporadic and uneven infection across field nurseries. We sought to facilitate breeding for BGYMV resistance by improving marker-assisted selection (MAS) for the recessive bgm-1 gene and identifying and developing MAS for quantitative trait loci (QTL) conditioning resistance. Genetic linkage mapping in two recombinant inbred line populations and genome-wide association study (GWAS) in a large breeding population and two diversity panels revealed a candidate gene for bgm-1 and three QTL BGY4.1, BGY7.1, and BGY8.1 on independent chromosomes. A mutation (5 bp deletion) in a NAC (No Apical Meristem) domain transcriptional regulator superfamily protein gene Phvul.003G027100 on chromosome Pv03 corresponded with the recessive bgm-1 resistance allele. The five bp deletion in exon 2 starting at 20 bp (Pv03: 2,601,582) is expected to cause a stop codon at codon 23 (Pv03: 2,601,625), disrupting further translation of the gene. A T m -shift assay marker named PvNAC1 was developed to track bgm-1. PvNAC1 corresponded with bgm-1 across ∼1,000 lines which trace bgm-1 back to a single landrace "Garrapato" from Mexico. BGY8.1 has no effect on its own but exhibited a major effect when combined with bgm-1. BGY4.1 and BGY7.1 acted additively, and they enhanced the level of resistance when combined with bgm-1. T m -shift assay markers were generated for MAS of the QTL, but their effectiveness requires further validation. [ABSTRACT FROM AUTHOR]

Slow‐darkening (SD) pinto beans (Phaseolus vulgaris L.) possess a desirable new trait, conditioned by the recessive sd gene, that slows seed coat darkening under delayed harvest and under storage. The effect sd may have on performance needs investigation. We examined agronomic performance and cooking quality of SD pinto beans. There were 30 (15 SD and 15 regular darkening [RD]) recombinant inbred lines (RILs) from each of two biparental inbred populations. The 60 RILs were tested across three locations in North Dakota and Washington. In addition, advanced SD and RD pinto breeding lines were tested in trials from 2010 to 2012 and in 2018. Across 2010–2012 trials, the "early generation bred" SD pintos, as a group, had significantly lower emergence, increased lodging, less seed yield, and smaller seed size than the RD group. Conversely, in the 2018 trial, "recently bred" SD pinto breeding lines had competitive agronomic performance to RD lines for seed yield, reduced lodging, and increased emergence. Further research on cooking time is warranted given that SD RILs cooked 20% faster than the RD RILs in one population. Overall, SD pintos exhibited slightly better canning quality than RD pintos. Whether raw or cooked, SD pintos were much lighter in color than RD pintos, emphasizing the need to keep them separated as distinct market classes. Breeders should continue to focus on improving agronomic performance for emergence, lodging, seed yield, seed size, and canning quality of SD pinto beans. [ABSTRACT FROM AUTHOR]

Site-specific crop management is a promising approach to maximize crop yield with optimal use of rapidly depleting natural resources. Availability of high resolution crop data at critical growth stages is a key for real-time data-driven decisions during the production season. The goal of this study was to evaluate the possibility of using small unmanned aerial system (UAS)-based remote sensing technologies to monitor the crop stress of irrigated pinto beans (Phaseolus vulgaris L.) with varied irrigation and tillage treatments. A small UAS with onboard multispectral and infrared thermal imaging sensors was used to collect data from bean field plots on three growth stages in 2015 and 2016, respectively. Indicators including green normalized vegetation index (GNDVI), canopy cover (CC, ratio of ground covered by crop canopy to the total plot area) and canopy temperature (CT, °C) of crops were extracted from imaging data and correlated with ground-reference crop yield and leaf area index (LAI) estimated with a handheld ceptometer. Results show that GNDVI, CC and CT were able to differentiate crops with full and deficit irrigation treatments at each of the three growth stages in both years. Developed indicators were strongly correlated with to the crop yield with Pearson correlation coefficients (r) of approximate 0.71 and 0.72 for GNDVI and CC, respectively, in the early growth stage (54 days after planting) in both years. Canopy temperature showed even stronger correlation (r > 0.8) with yield at early growth stage. Performance of small UAS-based imagery-based indicators in crop stress monitoring and crop yield estimation was better than or comparable to that of the ground-based LAI estimates, indicating the potential of such remote sensing tool in rapid crop stress monitoring and management. [ABSTRACT FROM AUTHOR]

Dry bean (Phaseolus vulgaris L.) seeds are a major protein, carbohydrate and mineral source in the human diet of peoples in multiple regions of the world. Seed mineral biofortification is an ongoing objective to improve this important food source. The objective of this research was to assess the seed mineral concentration of five macroelements and eight microelements in a large panel (n = 277) of modern race Durango and race Mesoamerica genotypes to determine if variability existed that could be exploited for targeted seed biofortification. Varieties that derive from these races are found in many diets throughout the world. The panel was grown in replicated trials under typical production conditions in the major bean growing regions of the United States and a subset of the panel was also grown in replicated trials at three locations under control and terminal drought conditions. Except for K, seed mineral concentrations were higher for race Mesoamerica genotypes. Significantly higher seed concentrations for the majority of the minerals were observed for white-seeded genotypes and race Durango genotypes with the now preferred indeterminate, upright growth habit. Modern genotypes (since 1997) had equal or increased mineral concentrations compared with older genotypes. Drought affected mineral content differentially, having no effect on the microelement content but increased Co, Fe and Ni concentrations. The correlation of Ca and Mn concentrations suggests that these elements may share seed deposition mechanisms. The high heritability for seed mineral concentration implies that breeding progress can be achieved by parental selection from this panel. [ABSTRACT FROM AUTHOR]

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 x 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 x PI 150414 and Rojo x 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). [ABSTRACT FROM AUTHOR]

Common bacterial blight (CBB) disease limits dry bean (Phaseolus vulgaris L.) production worldwide. Resistance quantitative trait loci (QTL) from tepary bean (Phaseolus acutifolius A. Gray) have been used to develop dry bean lines with high levels of CBB resistance. This study examines the effects that two QTL from tepary bean BC420 (B) on chromosome Pv06 and SU91 (S) on Pv08 have on agronomic (seed yield and seed weight) and canning quality traits (water uptake, percentage washed drained weight [PWDWT], texture, and visual appearance). Sixteen small white dry bean near-isogenic lines, representing four homozygous genotypes for the BC420 and SU91 QTL BBSS, bbSS, BBss, and bbss, the donor resistant parent Teebus-BC5 (BBSS), and the recurrent susceptible parent 'Teebus' (bbss) were tested in replicated, inoculated and non-inoculated field plots across five environments in South Africa. Plots were inoculated with a mixture of Xanthomonas axonopodis pv. phaseoli and X. fuscans sbsp. fuscans isolates. The BC420 and SU91 QTL did not cause a yield penalty in non-inoculated plots in environments with low to no disease. SU91 provided yield protection under severe disease pressure, and both QTL in combination reduced disease severity score under moderate to high disease pressure. Seed weight was maintained in lines with the QTL under severe to moderate pressure and was unaffected by the QTL in low- to no-disease environments. Water uptake was significantly reduced in genotypes with BC420 (BBSS, BBss) and likely influenced traits measured subsequently: lower PWDWT, firmer texture, and less attractive visual appearance, which contributed to a reduced canning quality overall. Deployment of BC420 and SU91 QTL can be safely recommended for control of CBB, as no agronomic penalty was observed in CBB-free conditions, but canning quality should be closely monitored in lines with BC420 QTL. [ABSTRACT FROM AUTHOR]

White mold, caused by the fungus Sclerotinia sclerotiorum (Lib.) de Bary, is a major disease that limits common bean production and quality worldwide. The host-pathogen interaction is complex, with partial resistance in the host inherited as a quantitative trait with low to moderate heritability. Our objective was to identify meta-QTL conditioning partial resistance to white mold from individual QTL identified across multiple populations and environments. The physical positions for 37 individual QTL were identified across 14 recombinant inbred bi-parental populations (six new, three re-genotyped, and five from the literature). A meta-QTL analysis of the 37 QTL was conducted using the genetic linkage map of Stampede x Red Hawk population as the reference. The 37 QTL condensed into 17 named loci (12 previously named and five new) of which nine were defined as meta-QTL WM1.1, WM2.2, WM3.1, WM5.4, WM6.2, WM7.1, WM7.4, WM7.5, and WM8.3. The nine meta-QTL had confidence intervals ranging from 0.65 to 9.41 Mb. Candidate genes shown to express under S. sclerotiorum infection in other studies, including cell wall receptor kinase, COI1, ethylene responsive transcription factor, peroxidase, and MYB transcription factor, were found within the confidence interval for five of the meta-QTL. The nine meta-QTL are recommended as potential targets for MAS for partial resistance to white mold in common bean. [ABSTRACT FROM AUTHOR]

An ideotype breeding strategy to improve an economically important trait is achievable if subcomponent phenotypes most associated with the trait are targeted for selection. The success of this strategy in modern breeding history can be highlighted in dry bean (Phaseolus vulgaris L.), where an enhancement in dry bean production was facilitated in the last 25 yr by replacing Type III prostrate growth habit with Type II upright growth habit. This growth habit leads to disease avoidance and enables cost-effective management practices. To better understand the ideotype breeding trajectory in dry bean, and guarantee further improvements, we characterized 16 traits at three locations using a panel consisting of 122 genotypes with different growth habits. Among the growth habit types, significant differences were detected for seven architectural traits, three seed yield (SY) traits, and one phenological trait. Genetic variance was greater in the Type II genotypes than the Type III genotypes for five of the significant traits, including canopy height (CNH) and SY. Furthermore, in Type II genotypes, moderate narrow-sense heritability was detected for CNH, lodging (LDG), plant length (PL), and stem diameter (STD), suggesting positive gain can be made for growth habit from crosses between Type II genotypes. A network analysis of Type II genotypes revealed these four traits are highly correlated, and suggests possible genetic relatedness among the traits. Breeders often use CNH as a selection criterion, and the positive correlation between this trait and STD suggests a possible anatomical mechanism responsible for the more upright plant types. [ABSTRACT FROM AUTHOR]

Abiotic stress tolerance in dry bean (Phaseolus vulgaris L.) is complex. Increased population sizes are contributing to finding QTL conditioning stress response but phenotyping has not kept pace with high throughput genotyping for such studies. Our objectives were to determine effectiveness of 20 most tolerant and 20 most susceptible lines representing phenotypic extremes from a RIL population ('Buster' × 'Roza' [BR]) to facilitate examination of 19 traits for relevance to stress response and to validate existing QTL conditioning stress response. Using phenotypic extremes tested across multiple trials, eight of the 19 traits were clearly associated with drought stress. Pod wall ratio (PW), plant biomass by weight or a visual rating, and greenness index (NDVI) were most associated with seed yield (SY) under stress followed by phenology traits. The phenotypic extreme lines were also useful for validating QTL previously identified in the whole RIL population conditioning SY, seed weight (SW) and days to flower (DF), harvest maturity (HM), and seed fill (DSF). New QTL were identified for biomass, PW, and NDVI which co-segregated with major QTL for seed yield SY1.1BR and SY2.1BR. The preliminary finding of NDVI 1.1BR supports aerial imaging in larger genetic populations geared toward QTL analysis of stress response. In summary, phenotypic extremes helped sort through traits relevant to stress response in the Buster × Roza RIL population and verified the effect of two major QTL in response to terminal drought. [ABSTRACT FROM AUTHOR]

Dry beans (Phaseolus vulgaris L.) of the Andean gene pool, including red mottled, kidney, cranberry, and yellow seed types are important in Africa and the Americas. Andean dry bean breeding gains have lagged behind those of Mesoamerican beans. This difference may result from a narrower genetic base in the Andean gene pool and reduced breeding efforts. The objective of this research was to establish, genotype, and phenotype a panel of bean germplasm to be used for Andean dry bean breeding. An Andean diversity panel (ADP) was assembled, consisting of 396 accessions and including important cultivars, breeding lines, and landraces that originate mostly from Africa, the Caribbean, and North and South America. The panel was genotyped using the Illumina BARCBean6K_3 SNP BeadChip. The population contained two subgroups: Andean and Mesoamerican bean germplasm. The ADP was comprised of 349 Andean, 21 Mesoamerican, and 26 Andean-Mesoamerican admixed accessions. Most admixed lines came from Africa (12 accessions) and the Caribbean (five accessions). Association mapping was conducted for determinacy. Significant single-nucleotide polymorphism (SNP) trait associations were found on chromosome Pv01, with the most significant SNP marker being 3.1 kb from the Terminal Flower 1 PvTFL1y gene. The ADP was evaluated for numerous traits in field trials in the United States and Africa. Variability was found for resistance to rust, angular leaf spot and common bacterial blight diseases; tolerance to low soil fertility; cooking time; and other traits that can be used to improve Andean bean germplasm for Africa and the Americas. [ABSTRACT FROM AUTHOR]

Terminal and intermittent drought limits dry bean (Phaseolus vulgaris L.) production worldwide. Tolerance to drought exists but is difficult to breed for because of inconsistent expression across environments. Our objective was to identify quantitative trait loci (QTL) conditioning yield in a recombinant inbred line (RIL) population with consistent expression across multiple drought-stress environments. We tested 140 RILs from 'Buster' pinto (susceptible)/'Roza' pink (tolerant) for yield under multiple stresses (intermittent drought, compaction, and low fertility) across 3 yr and terminal drought across four location-years. A genetic linkage map (953 cM) was generated using single nucleotide polymorphism (SNP) markers. Two majoreffect QTL were detected on Pv01 and Pv02. The Pv01 QTL, defined by the closest marker SNP50809 (47.7 Mb), explained up to 37% of the phenotypic variance for seed yield under multiple stress (including intermittent drought) and was consistently expressed each year. The Pv02 QTL, nearest SNP40055 (11.8 Mb), was detected under drought stress (R2 = 33%) in addition to multiple stress (R2 = 17-23%). Phenological traits cosegregated with the yield QTL and affirmed the importance of phenological plasticity in adaptation to drought stress. Late maturity contributed to increased yield under multiple and nonstress and early maturity to increased yield under terminal drought. Given major and consistent effect, further investigation of the potential for the Pv01 and Pv02 QTL in breeding for multiple abiotic stress and drought tolerance in dry bean is warranted. [ABSTRACT FROM AUTHOR]

Common blight [caused by Xanthomonas campestris pv. phaseoli Smith (Dye)] is a major bacterial disease causing >40% seed yield and quality losses in common bean (Phaseolus vulgaris L.) worldwide. Use of resistant cultivars is crucial for its effective, economical, and environment friendly integrated management and control. Common blight resistant germplasm are found in the primary, secondary, and tertiary gene pools of the common bean. Substantial progress has been made in understanding the pathogenic variation, germplasm screening methods, identification of resistant germplasm, genetics of resistance, identifying and mapping molecular markers linked with resistance quantitative trait loci (QTL), introgressing resistance from the secondary and tertiary gene pools, transferring resistance from the Middle American common bean landraces to Andean cultivars and germplasm lines, and pyramiding or combining resistance from diverse germplasm sources into common bean. Backcross, pedigree, gamete, and recurrent selection methods or their modifications singularly or in combination have been used to introgress and pyramid resistance. Also, molecular markers with or without direct disease screening have been used for breeding for resistance. However, Andean and Middle American common bean cultivars with high levels of combined resistance to less-aggressive and aggressive bacterial strains in all aerial plant parts are not available. We will review progress achieved in breeding for resistance, briefly describe problems faced, and discuss strategies for integrated genetic improvement for common blight resistance for cultivar development. [ABSTRACT FROM AUTHOR]

Halo bacterial blight caused by Pseudomonas syringae pv. phaseolicola (Psp) is a serious seed-borne disease of common bean (Phaseolus vulgaris L.). The disease can be controlled by major resistance (R) genes effective against specific races of the pathogen. Our objective was to characterize the R gene(s) conferring resistance to Psp Races 1, 5, 7, and 9 in the great northern dry bean germplasm release BelNeb-RR-1. A recombinant inbred population consisting of 76 F9-derived lines (RILs) from the cross BelNeb-RR-1/A55 was inoculated with Races 1, 5, 7, and 9 and genotyped with 5398 single nucleotide polymorphism markers. Resistance to Races 1, 5, 7, and 9 cosegregated with each other and mapped to the proximal end of Pv04 in a known region of R genes that condition resistance to bean anthracnose and bean rust. Location on Pv04, combined with F2 allelism tests, confirmed the presence of a new gene, Pse-6, for halo blight resistance. We mapped other unnamed R genes to proximal end of Pv04 that were segregating in Minuette/ OSU5630 and Raven/I9365-31 RIL populations and that conditioned resistance to Psp Race 7 and Race 1, respectively. A second R gene, Pse-4, conditioning resistance solely to Race 5, was detected in BelNeb-RR-1 and tentatively positioned on chromosome Pv10. A sequencecharacterized amplified region marker SB10.550 tightly linked (1.4 cM) with Pse-6 was generated for potential use in marker-assisted selection for resistance to halo bacterial blight. [ABSTRACT FROM AUTHOR]

Common bacterial blight is a severe disease of common bean (Phaseolus vulgaris L.) worldwide. Use of resistant cultivars is crucial for its control. The objectives were to (i) assess the progress made in breeding large-seeded Andean bean developed between 1974 and 2010 and (ii) determine their resistance-linked sequence characterized amplified region (SCAR) marker composition. Ten Andean and four Middle American common bacterial blight resistant beans including checks were evaluated in the greenhouse in 2011. Bacterial strains ARX8AC and Xcp25 were used to inoculate primary and trifoliolate leaves. The mean disease score of the trifoliolate was 5.0 and of the primary leaf was 2.8. Strain Xcp25 had a mean score of 3.8 in primary and 5.9 in trifoliolate leaves. The respective scores for ARX8AC were 1.9 and 4.2. Andean 'Montcalm', with the SAP6 quantitative trait loci (QTL) and USDK-CBB-15, and USWK-CBB-17, with the SAP6 and SU91 QTL, showed an intermediate response to ARX8AC and a susceptible response to Xcp25. Middle American VAX 1 with SAP6, Andeans 08SH-840 and CXR 1 with SAP6 and SU91, and RCS52-2, RCS53-3, and RCS63-5B with SU91 and BC420 were resistant or intermediate to both strains. Middle American VAX 3 and VAX 6, with SAP6 and SU91, had the highest levels of resistance to ARX8AC, but their responses to Xcp25 were similar to the latter Andean group. Thus, significant improvement has been achieved, but breeding for yet higher levels of resistance, recovery of commercial seed types, and improving yield and other agronomic traits should be emphasized. [ABSTRACT FROM AUTHOR]

Common bacterial blight (CBB) is a severe disease in common bean (Phaseolus vulgaris L.). New resistance quantitative trait loci (QTL) should facilitate development of cultivars with high levels of resistance. Our objectives were to (i) identify new resistance QTL in VAX 1 and verify its presence in VAX 3, (ii) determine the interaction between QTL with existing SAP6 and SU91 QTL, and (iii) examine the interaction between QTL with less aggressive ARX8AC and aggressive Xcp25 bacterial strains. Sixty-one F6:7 recombinant inbred lines (RIL) from 'Othello'/VAX 1 and 100 RIL from Othello/VAX 3 were screened in the greenhouse. Disease severity of inoculated primary leaves, first and second trifoliolate leaves, and pods, was scored from 1 = no symptoms to 9 = completely diseased. Genotyping was performed using 5398 single nucleotide polymorphism (SNP) BeadChip and CBB resistance QTL-linked sequence characterized amplified region (SCAR) markers, SAP6 and SU91. A novel resistance QTL with major effect was detected on Pv11 linkage group in Othello/ VAX 1 and verified in Othello/VAX 3. This Pv11 QTL, defined by the closest marker SNP47467 (45,059,806 bp), explained 23% of the phenotypic variance for resistance in primary and 18% in trifoliolate leaves in Othello/VAX 1, and 13% and 22%, respectively, in Othello/VAX 3 to ARX8AC. The Pv11 QTL, named Xa11.4OV1,OV3, had greater influence against Xcp25, with respective values for variance for resistance explained in primary and trifoliolate leaves of 45% and 51% in Othello/ VAX 1 and 26% and 37% in Othello/VAX 3. Conversely, SAP6 was only effective against ARX8AC in both populations, and surprisingly, SU91 was only effective against Xcp25 in Othello/VAX 3. SAP6 was the only QTL to condition resistance in pods. QTL interactions and differential reactions to strains indicate that the new Xa11.4OV1,OV3 QTL is critical in breeding for stable and higher levels of foliage resistance to CBB in common bean. [ABSTRACT FROM AUTHOR]

Background: Common bean was one of the first crops that benefited from the development and utilization of molecular marker-assisted selection (MAS) for major disease resistance genes. Efficiency of MAS for breeding common bean is still hampered, however, due to the dominance, linkage phase, and loose linkage of previously developed markers. Here we applied in silico bulked segregant analysis (BSA) to the BeanCAP diversity panel, composed of over 500 lines and genotyped with the BARCBEAN_3 6K SNP BeadChip, to develop codominant and tightly linked markers to the I gene controlling resistance to Bean common mosaic virus (BCMV). Results: We physically mapped the genomic region underlying the I gene. This locus, in the distal arm of chromosome Pv02, contains seven putative NBS-LRR-type disease resistance genes. Two contrasting bulks, containing BCMV host differentials and ten BeanCAP lines with known disease reaction to BCMV, were subjected to in silico BSA for targeting the I gene and flanking sequences. Two distinct haplotypes, containing a cluster of six single nucleotide polymorphisms (SNP), were associated with resistance or susceptibility to BCMV. One-hundred and twenty-two lines, including 115 of the BeanCAP panel, were screened for BCMV resistance in the greenhouse, and all of the resistant or susceptible plants displayed distinct SNP haplotypes as those found in the two bulks. The resistant/susceptible haplotypes were validated in 98 recombinant inbred lines segregating for BCMV resistance. The closest SNP (~25-32 kb) to the distal NBS-LRR gene model for the I gene locus was targeted for conversion to codominant KASP (Kompetitive Allele Specific PCR) and CAPS (Cleaved Amplified Polymorphic Sequence) markers. Both marker systems accurately predicted the disease reaction to BCMV conferred by the I gene in all screened lines of this study. Conclusions: We demonstrated the utility of the in silico BSA approach using genetically diverse germplasm, genotyped with a high-density SNP chip array, to discover SNP variation at a specific targeted genomic region. In common bean, many disease resistance genes are mapped and their physical genomic position can now be determined, thus the application of this approach will facilitate further development of codominant and tightly linked markers for use in MAS. [ABSTRACT FROM AUTHOR]

Seed coat darkening in pinto bean (Phaseolus vulgaris L) primarily occurs during prolonged storage and can result in significant loss in value based on it being a consumer perceived product flaw. Several slow darkening (SD) pintos, conditioned by the presence of the recessive sd gene, exist but are poorly adapted. Breeding for improved SD pintos is complicated by the recessive inheritance and expression of the trait in maternal tissue. We sought to develop capacity for marker-assisted selection (MAS) for the SD trait. Three F2 populations (159 individuals) derived from crosses between SD parents, representing two different sources (1533-15 and SDIP-1) for the trait, and commercial regular darkening (RD) pintos were used to screen for single nucleotide polymorphisms (SNPs) linked with the sd locus. Separate DNA pools from SD and from RD F2 individuals genotyped for the sd locus were used to detect putative sd-linked SNPs using the bulked-segregant analysis strategy. Two of 1536 SNPs differentiated between the SD and RD DNA bulks for all three populations. The whole genome sequence scaffold possessing the two SNPs was canvassed for simple sequence repeats (SSRs). Three of 12 SSRs from the SNP region distinguished between the SD and RD lines. The three SSRs, Pvsd-1157, Pvsd-1158, and Pvsd- 0028, were observed to be tightly linked with the sei locus at 0.9, 0.4, and 3.1 cM, respectively, across the F2 populations. The SSRs assayed across a recombinant inbred line mapping population (CDC Pintium × 1533-15) placed the sd gene on bean linkage group 7 between framework SSR markers BM210 and PvBR35. A survey of SD and RD advanced lines and cultivars revealed the SSRs will have utility for MAS of the SD trait in pinto bean and perhaps in other dry bean market classes as well. [ABSTRACT FROM AUTHOR]

Pseudomonas syringae pv. phaseolicola (Burkholder) Young et al. (Psp) causes halo blight, which is a serious bacterial disease of common bean (Phaseolus vulgaris L.). Several resistance (R) genes have been discovered in host differéntial cultivar ZAA 12. Our objectives were to further characterize and enable marker-assisted selection (MAS) of the Pse-2 gene in ZAA 12 purported to have broad effect against multiple Psp races. A recombinant inbred population, ZAA 12 x 'Canadian Wonder', was challenged by the halo blight pathogen differential set consisting bf nine Psp races. The resistance conferred by Pse-2 to races 2, 3, 4, 5, 7, 8, and 9 expanded the effect known for this gene from three to seven races. Segregation in F2 populations confirmed dominant inheritance for Pse-2 against all races except Race 8. Resistance to Race 8 was recessively inherited and most closely fit a V resistant to 9 susceptible segregation ratio in the F2 generation. Perhaps other genes are segregating that modify the effect of Pse-2 against Race 8. A sequence characterized amplified region (SCAR) marker tightly linked with Pse-2 was generated. The marker was used to inte~rate Pse-2 to chromosome 10. A survey of lines and cultivars revealed the SCAR will have broad utility for MAS of Pse-2. [ABSTRACT FROM AUTHOR]

White mold caused by the necrotrophic fungus Sclerotinia sclerotiorum (Lib.) de Bary limits common bean (Phaseolus vulgaris L.) production in temperate climates. Disease resistance has been identified, but breeding is hampered by a paucity of resistance sources and complex inheritance, as numerous quantitative trait loci (QTL) conditioning partial resistance have been found. Our objectives were to characterize the partial white mold resistance found in breeding lines 19365-31 and VA19 and to construct a comparative linkage map for all the white mold resistance QTL identified to date. Recombinant inbred line (RIL) populations `Benton'/VA19 (BV) and `Raven'/l9365-31 (R31) consisting of 79 F5 and 105 F5 RILs, respectively, were evaluated for white mold (WM) reaction in multiple green-house and field tests. Two QTL were found in By, WM2.2 expressed in the greenhouse (R² = 33%) and the field (13%) and WM8.3 expressed in field (11%) only, and seven were found in R31 (WM2.2, WM4.2, WM5.3, WM5.4, WM6.1, WM7.3, WM8.4), three expressed in greenhouse tests and four in the field, ranging in phenotypic variance from 5 to 52%. These QTL were compared with 26 previously identified QTL, resulting in a comparative linkage map of 35 QTL, which coalesced into 21 distinct regions across nine linkage groups. Four QTL found in R31 were novel. Sequence characterized amplified region markers associated with WM2.2, WM8.3, and WM7.3 QTL were generated. The comparative linkage map provides a framework for integrating and interpreting future QTL studies concerning white mold resistance in common bean. [ABSTRACT FROM AUTHOR]

The color of the seed coats of 'Dorado' ( Phaseolus vulgaris L.) is garnet brown (dark red kidney bean color) and differs from most other dry bean varieties in the Honduran red bean market class. A genetic investigation of the color of 'Dorado' (same as DOR364) and G19833 (Liborino market class) seed coats was conducted. Crosses with genetic tester stocks demonstrated that the gene for garnet brown (GB) in 'Dorado' was not allelic with the R gene for dominant red (oxblood) seed coat. An allelism test between the 'Dorado' gene for GB seed coat and the rk gene for recessive expression of GB demonstrated allelism. We propose the gene symbol for Rk for the 'Dorado' GB seed coat color gene. Rk expresses partial dominance over Rk, where Rk/ Rk expresses a paler and highly variable intermediate red color. The interactions of Rk, rk, and c are discussed. Segregation analysis in the mapping population made up of DOR364 (same as 'Dorado') × G19833 recombinant inbred lines showed that the Rk gene mapped to linkage group 1. The new allele at Rk was located at a distance of 17 cM from the RFLP marker Bng130 with a LOD > 3.0. [ABSTRACT FROM AUTHOR]

Halo blight [caused by Pseudomonas syringae pv. phaseolicola (Burkh.) Young et al. (Psp)] is a serious seed-borne bacterial disease of common bean (Phaseolus vulgaris L.). A few resistance (R) genes and quantitative trait loci provide control to one or more races of the pathogen. To better understand monogenic resistance and improve breeding efficiency, we sought to tag and map a gene (Pse-1) in host differential cultivar Ul-3 (previously named 'Red Mexican Ul-3') that provides resistance to races 1, 5, 7, and 9 of Psp. Cosegregation for resistance to races 1, 5, 7, and 9, in a recombinant inbred population, 'Canadian Wonder'/Ul-3 (CU), confirmed the effect of Pse-1 against multiple races of the pathogen. Bulked-segregant analysis in the CU population identified six random amplified polymorphic DNA (RAPD) markers tightly linked (0-3.3 cM) to Pse-1. Three of the RAPD5 completely linked with Pse-1 in the CU population were converted to sequence characterized amplified region (SCAR) markers SH11.800, SR13.1150, and ST8.1350. The linked markers were used to integrate Pse-1 to link- age group Bl0 of the core map. Allelism tests (F2) confirmed relationships of Pse-1 and Pse-4 derived from Ul-3 with R genes in the other host differential cultivars. A survey of advanced lines and cultivars revealed that the SCAR markers generated in this study will have utility for marker-assisted selection of Pse-1 in germplasm from the Andean gene pool (e.g., kidney, calima) and from race Mesoamerican within the Middle American gene pool (black, carioca). [ABSTRACT FROM AUTHOR]

White mold caused by Scierotinia sclerotiorum (Lib.) de Bary is a major disease limiting dry bean (Phaseolus vulgaris L.) production. Genetic resistance provides some control but is difficult to breed for because of low heritability. We sought to determine if marker-assisted selection for quantitative trait loci (QTL) conferring partial resistance could facilitate breeding for resistance to white mold in dry bean. The Phs marker linked with a QTL derived from landrace G122 on linkage group B7 was backcrossed into ‘Winchester’ pinto, forming two BC3F4:6 inbred line populations. The AW9.1200 and SS18.1 650 markers linked with a QTL from snap bean breeding line NY6020-4 on B8 were backcrossed into ‘Maverick’ pinto and ‘Matterhorn’ great northern, forming BC2F4:6 inbred line populations. The B7 QTL in the BC3F4:6 populations on average explained 52% of the phenotypic variation for disease reaction in the greenhouse test and 10% across four field tests. The B8 QTL explained 30% in the greenhouse and 10% in the field. Averaged across tests and populations the B7 and B8 QTL conditioned 15 and 17% reduction in disease severity score, respectively. Linkage drag from selection of the B7 QTL was observed for yield. MAS for the B7 and 88 QTL was an effective breeding tool for introgressing partial resistance to white mold into susceptible pinto and great northern dry bean market classes, but further selection for agronomic performance may be required to obtain lines worthy of commercial production. [ABSTRACT FROM AUTHOR]

Breeding for genetic resistance to white mold [Sclerotinia sclerotiorum (Lib.) de Bary] in dry bean (Phaseolus vulgaris L.) is difficult because of low heritability. To facilitate breeding, researchers have sought to identify QTL underpinning genetic resistance to white mold. We identified two QTL conditioning ICA Bunsi-derived resistance to white mold in a pinto x navy bean (Aztec/ND88-106-04) recombinant inbred line (85 RILs) population. ND88-106-04 is a navy breeding line with resistance to white mold derived from ICA Bunsi navy. Aztec pinto is susceptible. The QTL were located to linkage groups B2 and B3 of the core map. The B2 QTL expressed in three of four field environments explaining 24.7, 9.0, and 8.7% of the phenotypic variation for disease severity score. The B3 QTL expressed in two of four environments, explaining 15.7 and 5.3% of the phenotypic variation. The B2 QTL was identified previously in ICA Bunsi x navy and ICA Bunsi x black bean RIL populations. The resistance conferred by the B2 QTL has a physiological basis due to association with stay green stem trait and lack of association with disease avoidance traits. The B3 QTL, undetected in previous studies, was associated with disease avoidance traits (canopy porosity, plant height), stay green stem trait, and maturity. The B2 QTL with stable expression in multiple environments and across genetic backgrounds will be most amenable to manipulation by breeders. [ABSTRACT FROM AUTHOR]

Genetic resistance is an important component of integrated strategies used to control problematic diseases in common bean (Phaseolus vulgaris L.). Molecular linkage maps have been used to identify, tag, and map disease resistance genes and QTL in common bean, leading to improved breeding strategies and implementation of marker-assisted selection. Most widely used marker types, random amplified polymorphic DNA (RAPD) and amplified fragment length polymorphisms (AFLP), for linkage mapping in bean are located randomly throughout the genuine and associate with particular traits by chance. We sought to determine the potential application of a new marker system, TRAP, which uses expressed sequence information and a bioinformatics approach to generate polymorphic markers around targeted candidate gene sequences. TRAP markers were amplified by fixed primers designed against sequenced expressed sequence tag (EST) associated with disease resistance in the Compositae Genomics database or against sequenced resistance gene analog (RGA) from common bean. Seventeen of 85 TRAP markers located in the BAT 93/Jalo EEP558 core mapping population mapped in the vicinity of R genes. Six of 21 TRAP markers generated in the Dorado/XAN 176 mapping population were linked with newly identified QTL, two conditioning resistance to ashy stem blight (14% and 16% of the phenotypic variation explained, R²), and one each conferring resistance to Bean golden yellow mosaic virus (BGYMV) (15%) and common bacterial blight (30%). The TRAP marker system has potential for mapping regions of the common bean genome linked with disease resistance. [ABSTRACT FROM AUTHOR]

Resistance (R) genes containing nucleotide-binding site (NBS)-leucine rich repeats (LRR) are the most prevalent types of R gene in plants. The objective of this study was to develop PCR-based R-gene analog polymorphism (RGAP) markers for common bean ( Phaseolus vulgaris L). Twenty degenerate primers were designed from the conserved kinase-1a (GVGKTT) and hydrophobic domains (GLPLAL) of known NBS-LRR type R-genes and from EST databases. Sixty-six of the 100 primer combinations tested yielded polymorphism. Thirty-two RGAP markers were mapped in the BAT 93/Jalo EEP558 core mapping population for common bean. The markers mapped to 10 of 11 linkage groups with a strong tendency for clustering. In addition, the RGAP markers co-located, on six linkage groups, with 15 resistance gene analogs (RGAs) that were previously mapped in other populations of common bean. The distance between the priming sites in NBS-LRR type R-genes is around 500 bp. Of the 32 RGAP markers, 19 had sizes larger and 13 less than 500 bp. RGAP markers mapped close to known R-genes on B11, and to QTLs for resistance on B1, B2, B6, B7, B8, B10, and B11. RGAP appears to provide a useful marker technique for tagging and mapping R-genes in segregating common bean populations, discovery of candidate genes underlying resistance QTL, and future cloning of R-genes in common bean. [ABSTRACT FROM AUTHOR]

Breeding for resistance to biotic and abiotic stresses of global importance in common bean is reviewed with emphasis on development and application of marker-assisted selection (MAS). The implementation and adoption of MAS in breeding for disease resistance is advanced compared to the implementation of MAS for insect and abiotic stress resistance. Highlighted examples of breeding in common bean using molecular markers reveal the role and success of MAS in gene pyramiding, rapidly deploying resistance genes via marker-assisted backcrossing, enabling simpler detection and selection of resistance genes in absence of the pathogen, and contributing to simplified breeding of complex traits by detection and indirect selection of quantitative trait loci (QTL) with major effects. The current status of MAS in breeding for resistance to angular leaf spot, anthracnose, Bean common mosaic and Bean common mosaic necrosis viruses, Beet curly top virus, Bean golden yellow mosaic virus, common bacterial blight, halo bacterial blight, rust, root rots, and white mold is reviewed in detail. Cumulative mapping of disease resistance traits has revealed new resistance gene clusters while adding to others, and reinforces the co-location of QTL conditioning resistance with specific resistance genes and defense-related genes. Breeding for resistance to insect pests is updated for bean pod weevil (Apion), bruchid seed weevils, leafhopper, thrips, bean fly, and whitefly, including the use of arcelin proteins as selectable markers for resistance to bruchid seed weevils. Breeding for resistance to abiotic stresses concentrates on drought, low soil phosphorus, and improved symbiotic nitrogen fixation. The combination of root growth and morphology traits, phosphorus uptake mechanisms, root acid exudation, and other traits in alleviating phosphorus deficiency, and identification of numerous QTL of relatively minor effect associated with each trait, reveals the complexity to be addressed in breeding for abiotic stress resistance in common bean. [ABSTRACT FROM AUTHOR]

Pinto beans (Phaseolus vulgaris L.) of cool subtropical and temperate origins are extremely susceptible to white mold disease caused by Sclerotinia sclerotiorum (Lib.) de Bary. Breeding pinto beans with resistance to white mold is difficult because of the paucity of resistant germplasm in a closely related background. White mold resistant 'ICA Bunsi', a small white navy bean, is from the same Middle American gene pool, but it is of warm tropical origin and needs to be exploited in pinto bean improvement. Our objectives were to determine inheritance of ICA Bunsi-derived resistance in a cross with pinto bean, determine association of the resistance with disease avoidance, and identify white mold resistant pinto beans. White mold reactions of 85 F5:8 recombinant inbred lines (RIL) from the cross 'Aztec'/ND88- 106-04 were characterized in the field in North Dakota and Washington in 2001 and 2002. Aztec pinto is susceptible to white mold, and ND88-106-04 navy bean has partial resistance derived from ICA Bunsi. Disease severity score (1 = no disease to 9 = completely susceptible), yield, and disease avoidance traits were measured. Disease severity for Aztec and ND88-106-04 across environments was 6.9 and 2.5, respectively, compared with 4.6 for WA Bunsi. Reduced lodging and late maturity enhanced disease avoidance. The RILs with stay-green stem at harvest, similar to ND88-106-04, also exhibited less disease. Normal distribution and moderate heritability (Hns = 56 and 36% for WA and ND environments, respectively) for disease score indicated resistance was influenced by environment and likely conditioned by genes with small effects. Nonetheless, white mold resistance was present in a few RILs with high yield potential and pinto seed type. [ABSTRACT FROM AUTHOR]

Copyright of Genome is the property of Canadian Science Publishing and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Knowledge of the evolutionary origin and sources of pest resistance genes will facilitate gene deployment and development of crop cultivars with durable resistance. Our objective was to determine the source of common bacterial blight (CBB) resistance in the common bean Great Northern Nebraska #1 (GN#1) and GN#1 Selection 27 (GN#1 Sel 27). Several great northern cultivars including GN#1, GN#1 Sel 27, and Montana No.5 (the female parent of the common x tepary bean interspecific population from which GN #1 and GN # 1 Sel 27 were derived) and known susceptible checks were evaluated for CBB reaction in field and greenhouse environments. These genotypes and CBB resistant and susceptible tepary bean including Tepary #4, the male parent and presumed contributor of CBB resistance to GN#1 and GN#1 Sel 27, were assayed for presence or absence of three SCAR markers tightly linked with independent QTLs conditioning CBB resistance. The parents and F2 of Montana No. 5/GN #1 Sel 27 and Montana No.5/Othello (CBB susceptible) were screened for CBB reaction and SCAR markers. CBB resistance in Montana No.5 was comparable to that of GN#1 and GN#1 Sel 27. The SAP6 SCAR marker present in GN#1 and GN#1 Sel 27 was also present in Montana No.5, and it co-segregated (R2 =35%) with the CBB resistance in the Montana No.5/Othello F2 population. Although a few CBB resistant and susceptible transgressive segregants were found in the F2 of Montana No.5/GN #1 Sel 27 and later confirmed by F3 progeny tests, SAP6 SCAR marker was present in all progenies. None of the tepary bean specific CBB resistance-linked SCAR markers were present in GN#1, GN#1 Sel 27, or Montana No.5. A cluster analysis of 169 polymorphic PCR-based markers across three common bean and Tepary #4 indicated that GN#1, GN#1 Sel 27, and Montana No.5 were closely related, and not related at all with Tepary #4. Thus, these results clearly indicate Montana No.5, not Tepary #4, as the source of CBB resistance in GN#1 and GN#1 Sel 27. [ABSTRACT FROM AUTHOR]

Evaluates heritability of physiological resistance to white mold in dry bean landrace cultivar g 122 by the greenhouse straw test. Identification of quantitative trait locus conditioning resistance on linkage group B1; Heritability estimates for physiological and field resistance to white mold; Agronomic traits associated with disease avoidance.

Screens a subsample of the core collection of Phaseous vulgris L. accessions representing the active United States Department of Agriculture National Plant Germplasm System collection of 1698 accessions for reaction to white mold using a greenhouse straw test. Identification of new sources of resistance to white mold in the common bean.

Studies the ashy stem blight disease of the common bean (Phaseolus vulgaris L.), studying the inheritance of field resistance to ashy stem blight using the recombinant inbred lines (RILs). What the inbred population consisted of; Investigation of the phenotypic variation across a subgroup of 79 RILs; Detection of five quantitative trait loci (QTL) in 1993; Details on the study; Results of the study.