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This study investigated the thermophysical and cooking quality properties of both slow-darkening (SD) and regular-darkening (RD) pinto bean varieties, establishing genetic cooking variability in cooking traits and their interrelationships. The equilibrium moisture content (EMC) of the beans at 80, 90 and 100°C were determined. Thermal and physical properties were evaluated for both SD and RD pinto bean varieties at their respective EMC. Cooking quality properties, such as water absorption capacity and cooking time, were also assessed. Principal component and cluster analyses were used to establish interactive effects of the cooking-related traits to the cooking process. Bulk density and cooking time were significantly and negatively correlated (p <.05). The SD beans exhibited better cook characteristics compared to RD beans. Bulk density was the most influential trait during cluster formation. The findings highlight that physical and thermal properties play a critical role in the cooking process. [ABSTRACT FROM AUTHOR]

'ND Rodeo' (PVP no. 202300270; Reg. no. CV‐356, PI 703020) is a new slow‐darkening (SD) pinto bean (Phaseolus vulgaris L.) cultivar developed by the Dry Edible Bean Breeding Program at North Dakota State University and released by the North Dakota Agricultural Experiment Station. Pinto bean is the largest market class grown in the United States, representing over 47% of the total US production for dry beans, and more than 70% is produced in North Dakota. SD pinto beans offer a good alternative to commercial cultivars of regular darkening (RD) pinto beans, which are typically subject to the risk of economic losses due to seed coat darkening. However, reaching seed yields comparable to RD pintos has been challenging. Between 2017 and 2022, ND Rodeo was tested across 25 environments in North Dakota, where seed yield was significantly higher than the SD pinto cultivars 'ND Palomino' and 'Vibrant' (18% and 22%, respectively), and comparable with RD pinto cultivars 'La Paz' and 'Monterrey'. ND Rodeo is resistant to Bean common mosaic virus and has intermediate resistance to common bacterial blight, but similar to the commercial checks, it is susceptible to local races/strains of white mold, anthracnose, and rust pathogens. ND Rodeo has an average height of 56 cm which is significantly higher than the average of ND Palomino, Vibrant, and La Paz, and exhibits a desirable upright architecture to facilitate direct harvest. It has a 100‐seed weight of 36.2 g and matures in 102 days. Canning quality was rated as acceptable. Core Ideas: Pinto bean is the most widely grown dry bean market class in the United States.Slow‐darkening pinto beans retain their light cream background seed coat color after harvest.Achieving seed yields comparable to RD pintos has been challenging.Improvements in slow‐darkening pinto bean productivity, upright plant architecture, disease resistance, and seed quality characteristics have been accomplished. [ABSTRACT FROM AUTHOR]

'ND Redbarn' (PVP. no. 202300271; Reg. no. CV‐357, PI 703021) is a new dark red kidney bean (Phaseolus vulgaris L.) cultivar developed by the Dry Edible Bean Breeding Program at North Dakota State University and released in 2023 by the North Dakota Agricultural Experiment Station. Compared to other market classes, kidney beans usually command higher prices. However, kidney beans are less productive than other market classes. Minnesota is the largest dark red kidney bean producer in the United States, accounting for ∼90% of the total production in 2022. ND Redbarn was released based on its good adaptation to this region, higher seed yield, large seed size, and desirable seed shape characteristics. Between 2012 and 2021, ND Redbarn was tested across 16 environments in Minnesota, where seed yield was significantly higher than commercial checks 'Montcalm', 'Red Hawk', and 'Talon' (14%, 27%, and 9%, respectively) and comparable with 'Dynasty'. ND Redbarn is resistant to Bean common mosaic virus and has intermediate resistance to common bacterial blight. ND Redbarn exhibits higher field tolerance to the root rot fungal complex infection compared to Montcalm, Red Hawk, and Talon, and is similar to Dynasty. ND Redbarn has shown higher levels of tolerance to white mold than Montcalm and Red Hawk. Under Minnesota environments, ND Redbarn shows an average plant height of 51 cm, has a 100‐seed weight of 50.4 g, and matures in approximately 99 days. The canning quality for Redbarn is within acceptable commercial ranges. Core Ideas: Dark red kidney bean is the most predominant market class in Minnesota, which accounts for ∼90% of the total US production.Dark red kidney beans are known to be less productive than other bean market classes, but they respond extremely well to good agronomic management.Strict industry and consumer requirements in terms of visual seed quality for kidney beans hinders genetic progress for this market class.Improvements in dark red kidney bean productivity, disease resistance, and size and shape have been accomplished in the new cultivar ND Redbarn. [ABSTRACT FROM AUTHOR]

'ND Polar' (Reg. no. CV‐349, PI 700767) is a new navy bean (Phaseolus vulgaris L.) cultivar developed by the Dry Edible Bean Breeding Program at North Dakota State University and released by the North Dakota Agricultural Experiment Station. ND Polar was developed using a modified pedigree method (F1–F5), followed by pure line selection based on agronomic performance, disease resistance, and seed quality characteristics. With ∼16% of the total dry bean production in the United States, navy bean is the third most important market class after pinto and black. Accounting for 35% of the total production, North Dakota is the largest producer of dry bean in the United States. Between 2015 and 2021, ND Polar was tested across 23 environments in North Dakota, where seed yield was significantly higher than 'HMS Medalist', 'Blizzard', and 'Ensign' and similar to 'T9905'. ND Polar is resistant to Bean common mosaic virus and has intermediate resistance to common bacterial blight. ND Polar has desirable upright architecture to facilitate direct harvest. Under North Dakota environments, ND Polar shows an average plant height of 52 cm, has a 100‐seed weight of 18.3 g, and matures in 102 days. Canning quality was rated as acceptable. Similar to the commercial checks, ND Polar is susceptible to local races/strains of the bean rust pathogen, anthracnose, and white mold. Other traits of agronomic and economic importance are within acceptable ranges. Core Ideas: Navy bean is an economically important market class of dry bean in the United States.Improvements in navy bean productivity have been more challenging than other market classes.ND Polar offers improved seed yield thanks to its overall agronomic performance and productivity.ND Polar is resistant to Bean common mosaic virus and has intermediate resistance to common bacterial blight. [ABSTRACT FROM AUTHOR]

Anthracnose, caused by the fungal pathogen Colletotrichum lindemuthianum (Sacc. & Magnus) Lams.-Scrib., is one of the most devastating diseases in dry bean (Phaseolus vulgaris L.) with seed yield losses up to 100%. Most anthracnose resistance genes thus far identified behave in a dominant manner and were identified by seedling screening. The Middle American Diversity Panel (MDP; n=266) was screened with a modified greenhouse screening method to evaluate the response to anthracnose race 73. Thirty MDP genotypes exhibited resistance to the race of which 16 genotypes were not known to contain anthracnose resistance genes to race 73. GWAS with ~93,000 SNP markers identified four genomic regions, two each on Pv01 and Pv10, associated race 73 resistance. A likelihood-ratio-based R2 analysis indicated the peak four SNP markers are responsible for 26% of the observed phenotypic variation, where one SNP, S10_072250, explains 23% of the total variation. SNP S10_072250 is associated with a new region of anthracnose resistance and is in an intron of a ZPR1-like gene. Further greenhouse testing of the 16 resistant lines without previously known resistance to race 73 revealed various levels of resistance under various levels of disease pressure. Disease resistance was further characterized in the field using four representative genotypes. GTS-900 and Remington exhibited field resistance while Merlot and Maverick were susceptible. Field testing with two different fungicide regimes revealed the resistant genotypes had no significant disease differences. The results suggest resistance to anthracnose may differ at various growth stages and that breeders have been selecting for major genes at early seedling stages while ignoring the effect of alternative genes that may be active at later stages. The newly identified resistant lines may be related to Age Related Resistance (ARR) and could be exploited as parental sources of anthracnose resistance in addition to already known major genes. The physical localization of the multiple regions of resistance confirms the presence of two clusters of disease resistance genes on Pv01 and identifies two new regions of anthracnose resistance on Pv10 possibly associated with ARR. Future research should look at the mode of inheritance of this resistance and its effect when combined with other anthracnose resistance loci. [ABSTRACT FROM AUTHOR]

Consumer food choices are often focused on protein intake, but the chosen sources are frequently either animal-based protein that has high fat content or plant-based protein that is low in other nutrients. In either case, these protein sources often lack dietary fiber, which is a nutrient of concern in the 2020-2025 Dietary Guide for Americans. Pulse crops, such as dry edible beans (Phaseolus vulgaris L.), are a rich source of dietary protein and contain approximately equal amounts of dietary fiber per 100 kcal edible portion; yet the consumer's attention has not been directed to this important fact. If product labeling were used to draw attention to the similar ratio of dietary protein to dietary fiber in dry bean and other pulses, measures of carbohydrate quality could also be highlighted. Dietary fiber is categorized into three fractions, namely, soluble (SDF), insoluble (IDF), and oligosaccharides (OLIGO), yet nutrient composition databases, as well as food labels, usually report only crude fiber. The objectives of this research were to measure the content of SDF, IDF, and OLIGO in a large genetically diverse panel of bean cultivars and improved germplasm (n = 275) and determine the impact of growing environment on the content of DF. Dietary fiber was evaluated using the American Association of Analytical Chemist 2011.25 method on bean seed grown at two locations. Dry bean cultivars differed for all DF components (P = 0.05). Insoluble dietary fiber constituted the highest portion of total DF (54.0%), followed by SDF (29.1%) and OLIGO (16.8%). Mean total DF and all components did not differ among genotypes grown in two field environments. These results indicate that value could be added to dry bean by cultivar-specific food labeling for protein and components of dietary fiber. [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]

Selection during plant domestication and improvement often decreases genetic variation, including variation that confers adaptation to local conditions. We report spatial and temporal variation in fitness (seed yield), local adaptation, and segregating genetic variation within three races of common bean (Phaseolus vulgaris L.) with differing domestication histories and genetic diversities. Three‐hundred and twenty‐seven common bean genotypes had seed yield measured at subsets of 70 sites across North America between 1981 and 2015, as part of the Cooperative Dry Bean Nursery (CDBN). We estimated local adaptation using the metric home field advantage (HFA) and segregating genetic variation using heritability. The Durango and Mesoamerican races (Middle American genepool) had higher‐than‐expected (p =.002) HFA, equal to up to 34 yr of average yield gains. Surprisingly, Nueva Granada (Andean genepool) and Durango yields became more heritable across the study period (p <.001), while Mesoamerican heritability decreased (p <.001). Both metrics detected diversity loss corresponding to the timings of major historical gene introgressions. Local adaptation remains an agronomically important phenomenon within some common bean races. Common bean adaptation to new conditions will be most rapid at locations with large local adaptation benefits and high heritability. Core Ideas: Selection history affects genetic variation, which enables adapting crops to new environments and climates.We report spatiotemporal variation in dry bean yield, local adaptation, and segregating genetics.Yields became more heritable in two of three dry bean races across North America over 35 yr.Local adaptation (home field advantage) was worth up to 34 yr of average breeding gains.Sites with high heritability and home field advantage are best for adapting to new environments. [ABSTRACT FROM AUTHOR]

Dry bean (Phaseolus vulgaris L.) is an important worldwide legume crop with low to moderate levels of resistance to common bacterial blight (CBB) caused by Xanthomonas axonopodis pv. phaseoli. A total of 852 genotypes (cultivars, preliminary and advanced breeding lines) from the North Dakota State University dry bean breeding program were tested for their effectiveness as populations for genome-wide association studies (GWAS) to identify genomic regions associated with resistance to CBB, to exploit the associated markers for marker-assisted breeding (MAB), and to identify candidate genes. The genotypes were evaluated in a growth chamber for disease resistance at both the unifoliate and trifoliate stages. At the unifoliate stage, 35% of genotypes were resistant, while 25% of genotypes were resistant at the trifoliate stage. Libraries generated from each genotype were sequenced using the Illumina platform. After filtering for sequence quality, read depth, and minor allele frequency, 41,998 single-nucleotide polymorphisms (SNPs) and 30,285 SNPs were used in GWAS for the Middle American and Andean gene pools, respectively. One region near the distal end of Pv10 near the SAP6 molecular marker from the Andean gene pool explained 26.7–36.4% of the resistance variation. Three to seven regions from the Middle American gene pool contributed to 25.8–27.7% of the resistance, with the most significant peak also near the SAP6 marker. Six of the eight total regions associated with CBB resistance are likely the physical locations of quantitative trait loci identified from previous genetic studies. The two new locations associated with CBB resistance are located at Pv10:22.91–23.36 and Pv11:52.4. A lipoxgenase-1 ortholog on Pv10 emerged as a candidate gene for CBB resistance. The state of one SNP on Pv07 was associated with susceptibility. Its subsequent use in MAB would reduce the current number of lines in preliminary and advanced field yield trial by up to 14% and eliminate only susceptible genotypes. These results provide a foundational SNP data set, improve our understanding of CBB resistance in dry bean, and impact resource allocation within breeding programs as breeding populations may be used for dual purposes: cultivar development as well as genetic studies. [ABSTRACT FROM AUTHOR]

'ND Twilight' (Reg. no. CV‐332, PI 693268; PVP‐202000258) is a new black bean (Phaseolus vulgaris L.) cultivar developed by the Dry Edible Bean Breeding Program at North Dakota State University and released by the North Dakota Agricultural Experiment Station. ND Twilight was developed using a modified pedigree method (F1–F5), followed by pure line selection based on agronomic, disease, and quality traits, along with specific DNA markers. With ∼24% of the total dry bean production in the United States, black bean is the second most important market class after pinto. Accounting for ∼35% of the total production, North Dakota is the largest producer of dry bean in the United States. However, both biotic and abiotic stresses are the main factors responsible for seed yield reductions. Between 2014 and 2019, ND Twilight was tested across more than 21 environments in North Dakota, where seed yield was significantly different from 'Zorro' and similar to 'Eclipse' and 'Loreto'. ND Twilight is resistant to the most common race (20‐3) of the bean rust pathogen and Bean common mosaic virus. It also has intermediate resistance to common bacterial blight and to soybean cyst nematode (HG Type 0). ND Twilight has desirable upright architecture (Type IIa). Under North Dakota conditions, ND Twilight shows an average plant height of 49 cm, has a 100‐seed weight of 19.7 g, and matures in ∼99 d. Canning quality was rated as acceptable. Other traits of agronomic and economic importance are within acceptable commercial ranges. [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]

Common bean (Phaseolus vulgaris L.) production worldwide is hampered by Fusarium root rot (FRR), which is caused by Fusarium solani. Screening for FRR resistance on a large scale is notoriously difficult and often yields inconsistent results due to variability within the environment and pathogen biology. A greenhouse screening assay was developed incorporating multiple isolates of F. solani to improve assay reproducibility. The Andean (ADP; n = 270) and Middle American (MDP; n = 280) Diversity Panels were screened in the greenhouse to identify genetic factors associated with FRR resistance. Forty-seven MDP and 34 ADP lines from multiple market classes were identified as resistant to FRR. Greenhouse phenotyping repeatability was confirmed via five control lines. Genome-wide association mapping using ∼200k SNPs was performed on standard phenotyping score 1–9, as well as binary and polynomial transformation of score data. Sixteen and seven significant genomic regions were identified for ADP and MDP, respectively, using all three classes of phenotypic data. Most candidate genes were associated with plant immune/defense mechanisms. For the ADP population, ortholog of glucan synthase-like enzyme, senescence-associated genes, and NAC domain protein, associated with peak genomic region Pv08:0.04–0.18 Mbp, were the most significant candidate genes. For the MDP population, the peak SNPs Pv07:15.29 Mbp and Pv01:51 Mbp mapped within gene models associated with ethylene response factor 1 and MAC/Perforin domain-containing gene respectively. The research provides a basis for bean improvement through the use of resistant genotypes and genomic regions for more durable root rot resistance. [ABSTRACT FROM AUTHOR]

'ND Whitetail' (Reg. no. CV‐327, PI 690447; PVP‐201900175) is a new white kidney bean cultivar developed by the dry bean breeding program at North Dakota State University and released by the North Dakota Agricultural Experiment Station. Within the Andean gene pool, kidney beans are the most economically important market classes worldwide, with dark‐red kidney bean being the most commonly grown class, followed by light‐red and white kidneys. There is an increased interest in white kidney bean in the United States, mostly stimulated by novel research claiming additional health benefits related to its consumption. However, biotic and abiotic stresses still limit the full seed yield potential of kidney bean cultivars. Averaged across environments, the seed yield of ND Whitetail was significantly higher by 650, 976, and 459 kg ha−1 than 'Beluga', 'Silver Cloud', and 'Snowdon', respectively. ND Whitetail has an average plant height of 52 cm and matures in approximately 101 d. Results from canning tests showed that ND Whitetail received a canning score of 5.1. ND Whitetail has high levels of resistance to white mold and Bean common mosaic virus (BCMV) along with intermediate resistance to bacterial diseases. Given the superior seed yield quality and agronomic performance, useful agronomic traits such as seed size, BCMV resistance, white mold and halo blight resistance, and superior canning quality, ND Whitetail could become an important white kidney cultivar in the United States. [ABSTRACT FROM AUTHOR]

'ND Pegasus' great northern bean (PVP‐201900176, Reg. no. CV‐328, PI 690448) is a new cultivar developed by the dry bean breeding program at North Dakota State University and released by the North Dakota Agricultural Experiment Station. Great northern bean is a market class of significant economic importance in the United States. In North Dakota especially, biotic and abiotic stresses are the main factors for seed yield reductions. Between 2013 and 2018, ND Pegasus, along with great northern cultivars commonly grown in the region, was tested across more than 35 environments in North Dakota and other states. Seed yield of ND Pegasus was significantly higher by 560, 414, and 571 kg ha‐1 compared with 'Matterhorn', 'Aries', and 'Powderhorn', respectively. However, seed yield of ND Pegasus and 'Taurus' were similar. ND Pegasus has an excellent upright architecture that improves the efficiency of direct harvest. Based on greenhouse and DNA marker data, ND Pegasus is resistant to Bean common mosaic virus and has improved resistance to white mold. ND Pegasus has excellent seed quality (color, shape, and size) and is larger than most commercial cultivars commonly grown in the region. ND Pegasus has acceptable canning quality based on some pilot testing. The average plant height of ND Pegasus is 71 cm, and 100‐seed weight 36.8 g. It matures in approximately 103 d. Other agronomic traits of economic importance are within commercial acceptable ranges. [ABSTRACT FROM AUTHOR]

'ND Falcon' pinto bean (PVP‐201900174, Reg. no. CV‐326, PI 690446) is a new cultivar developed by the Dry Edible Bean Breeding Program at North Dakota State University and released by the North Dakota Agricultural Experiment Station. Pinto bean is the most important dry bean market class in the United States. North Dakota is the largest producer of dry bean in the country, where ∼50% of production is pinto bean. Both biotic and abiotic stresses are the main factors responsible for seed yield reductions. Between 2013 and 2018, ND Falcon was tested across more than 22 environments in North Dakota. Averaged across environments, seed yield of ND Falcon was not significantly different from commonly grown pinto bean cultivars in the region. Nonetheless, ND Falcon is resistant to the most common race (20‐3) of the bean rust pathogen and to soybean cyst nematode (HG Type 0). Therefore, a seed yield advantage under disease pressure would be expected for ND Falcon compared with other pinto bean cultivars while eliminating or reducing the need for fungicide and/or nematicide applications. ND Falcon has desirable upright architecture (type IIa) with short vines. Under North Dakota conditions, ND Falcon shows an average plant height of 53 cm, has a 100‐seed weight of 37.0 g, and matures in approximately 103 d. Other traits of agronomic or economic importance are within acceptable commercial ranges for pinto bean. [ABSTRACT FROM AUTHOR]

Inoculation of dry bean (Phaseolus vulgaris L.) might have potential to increase symbiotic nitrogen fixation (SNF) and to reduce dependency on chemical fertilizers. Peat based inoculant can cause clogging of air seeder and therefore, the potential of liquid inoculant was compared to peat based- and without inoculant during 2016 and 2017 growing seasons in the Red River Valley of ND and MN. Seed yield and SNF, using 15N isotope enrichment, response to inoculation were studied for four pinto and four kidney bean cultivars. Inoculation did not increase seed yield; moreover, both liquid and peat inoculation reduced kidney cultivars' seed yield by 47% and 62% over control (without inoculation) treatment, respectively in 2016. In 2017, percent N derived from the atmosphere (%Ndfa) was significantly reduced by peat inoculation (61.2%) over control (76.7%). On average, pinto cultivars fixed 90.5 and 73.7 kg N ha−1 and kidney cultivars fixed 73.8 and 65.1 kg N ha−1, respectively in 2016 and 2017. The interaction between inoculation and cultivar influenced the quantity of SNF, specifically for kidney cultivars in 2017. Rather than inoculation, selection of cultivars had a more pronounced effect on seed yield and SNF. [ABSTRACT FROM AUTHOR]

Rhizoctonia solani Kühn (teleomorph Thanatephorus cucumeris) is an important root rot pathogen of common bean (Phaseolus vulgaris L.). To uncover genetic factors associated with resistance to the pathogen, the Andean (ADP; n = 273) and Middle American (MDP; n = 279) diversity panels, which represent much of the genetic diversity known in cultivated common bean, were screened in the greenhouse using R. solani anastomosis group 2-2. Repeatability of the assay was confirmed by the response of five control genotypes. The phenotypic data for both panels were normally distributed. The resistance responses of ∼10% of the ADP (n = 28) and ∼6% of the MDP (n = 18) genotypes were similar or higher than that of the resistant control line VAX 3. A genome-wide association study (GWAS) was performed using ∼200k single nucleotide polymorphisms to discover genomic regions associated with resistance in each panel, For GWAS, the raw phenotypic score, and polynomial and binary transformation of the scores, were individually used as the input data. A major QTL peak was observed on Pv02 in the ADP, while a major QTL was observed on Pv01 with the MDP. These regions were associated with clusters of TIR-NB_ARC-LRR (TNL) gene models encoding proteins similar to known disease resistance genes. Other QTL, unique to each panel, were mapped within or adjacent to a gene model or cluster of related genes associated with disease resistance. This is a first case study that provides evidence for major as well as minor genes involved in resistance to R. solani in common bean. This information will be useful to integrate more durable root rot resistance in common bean breeding programs and to study the genetic mechanisms associated with root diseases in this important societal legume. [ABSTRACT FROM AUTHOR]

Common bean (Phaseolus vulgaris L.) is an important high protein crop grown worldwide. North Dakota and Minnesota are the largest producers of common beans in the USA, but crop production is threatened by soybean cyst nematode (SCN; Heterodera glycines Ichinohe) because most current cultivars are susceptible. Greenhouse screening data using SCN HG type 0 from 317 plant introductions (PI’s) from the USDA core collection was used to conduct a genome wide association study (GWAS). These lines were divided into two subpopulations based on principal component analysis (Middle American vs. Andean). Phenotypic results based on the female index showed that accessions could be classified as highly resistant (21% and 27%), moderately resistant (51% and 48%), moderately susceptible (27% and 22%) and highly susceptible (1% and 3%) for Middle American and Andean gene pools, respectively. Mixed models with two principal components (PCs) and kinship matrix for Middle American genotypes and Andean genotypes were used in the GWAS analysis using 3,985 and 4,811 single nucleotide polymorphic (SNP) markers, respectively which were evenly distributed across all 11 chromosomes. Significant peaks on Pv07, and Pv11 in Middle American and on Pv07, Pv08, Pv09 and Pv11 in Andean group were found to be associated with SCN resistance. Homologs of soybean rhg1, a locus which confers resistance to SCN in soybean, were identified on chromosomes Pv01 and Pv08 in the Middle American and Andean gene pools, respectively. These genomic regions may be the key to develop SCN-resistant common bean cultivars. [ABSTRACT FROM AUTHOR]

Climate change models predict temporal and spatial shifts in precipitation resulting in more frequent incidents of flooding, particularly in regions with poor soil drainage. In these flooding conditions, crop losses are inevitable due to exposure of plants to hypoxia and the spread of root rot diseases. Improving the tolerance of bean cultivars to flooding is crucial to minimize crop losses. In this experiment, we evaluated the phenotypic responses of 277 genotypes from the Andean Diversity Panel to flooding at germination and seedling stages. A randomized complete block design, with a split plot arrangement, was employed for phenotyping germination rate, total weight, shoot weight, root weight, hypocotyl length, SPAD index, adventitious root rate, and survival score. A subset of genotypes (n = 20) were further evaluated under field conditions to assess correlations between field and greenhouse data and to identify the most tolerant genotypes. A genome-wide association study (GWAS) was performed using ~203 K SNP markers to understand the genetic architecture of flooding tolerance in this panel. Survival scores between field and greenhouse data were significantly correlated (r = 0.55, P = 0.01). Subsequently, a subset of the most tolerant and susceptible genotypes were evaluated under pathogenic Pythium spp. pressure. This experiment revealed a potential link between flooding tolerance and Pythium spp. resistance. Several tolerant genotypes were identified that could be used as donor parents in breeding pipelines, especially ADP-429 and ADP-604. Based on the population structure analysis, a subpopulation consisting of 20 genotypes from the Middle American gene pool was detected that also possessed the highest root weight, hypocotyl length, and adventitious root development under flooding conditions. Genomic regions associated with flooding tolerance were identified including a region on Pv08/3.2Mb, which is associated with germination rate and resides in vicinity of SnRK1.1, a central gene involved in response of plants to hypoxia. Furthermore, a QTL at Pv07/4.7Mb was detected that controls survival score of seedlings under flooding conditions. The association of these QTL with the survivability traits including germination rate and survival score, indicates that these loci can be used in marker-assisted selection breeding to improve flooding tolerance in the Andean germplasm. [ABSTRACT FROM AUTHOR]

Flooding is a devastating abiotic stress that endangers crop production in the twenty-first century. Because of the severe susceptibility of common bean (Phaseolus vulgaris L.) to flooding, an understanding of the genetic architecture and physiological responses of this crop will set the stage for further improvement. However, challenging phenotyping methods hinder a large-scale genetic study of flooding tolerance in common bean and other economically important crops. A greenhouse phenotyping protocol was developed to evaluate the flooding conditions at early stages. The Middle-American diversity panel (n = 272) of common bean was developed to capture most of the diversity exits in North American germplasm. This panel was evaluated for seven traits under both flooded and non-flooded conditions at two early developmental stages. A subset of contrasting genotypes was further evaluated in the field to assess the relationship between greenhouse and field data under flooding condition. A genome-wide association study using ~150 K SNPs was performed to discover genomic regions associated with multiple physiological responses. The results indicate a significant strong correlation (r > 0.77) between greenhouse and field data, highlighting the reliability of greenhouse phenotyping method. Black and small red beans were the least affected by excess water at germination stage. At the seedling stage, pinto and great northern genotypes were the most tolerant. Root weight reduction due to flooding was greatest in pink and small red cultivars. Flooding reduced the chlorophyll content to the greatest extent in the navy bean cultivars compared with other market classes. Races of Durango/Jalisco and Mesoamerica were separated by both genotypic and phenotypic data indicating the potential effect of eco-geographical variations. Furthermore, several loci were identified that potentially represent the antagonistic pleiotropy. The GWAS analysis revealed peaks at Pv08/1.6 Mb and Pv02/41 Mb that are associated with root weight and germination rate, respectively. These regions are syntenic with two QTL reported in soybean (Glycine max L.) that contribute to flooding tolerance, suggesting a conserved evolutionary pathway involved in flooding tolerance for these related legumes. [ABSTRACT FROM AUTHOR]

The article focuses on a research to analyze RNA sequencing of common bean scientifically known as Phaseolus vulgaris which is double-infected with Phaseolus vulgaris endornavirus 1 and Phaseolus endornavirus 2.

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]

Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) reproduces on the roots of common bean (Phaseolus vulgaris L.) and can cause reductions in plant growth and seed yield. The molecular changes in common bean roots caused by SCN infection are unknown. Identification of genetic factors associated with SCN resistance could help in development of improved bean varieties with high SCN resistance. Gene expression profiling was conducted on common bean roots infected by SCN HG type 0 using next generation RNA sequencing technology. Two pinto bean genotypes, PI533561 and GTS-900, resistant and susceptible to SCN infection, respectively, were used as RNA sources eight days post inoculation. Total reads generated ranged between ~ 3.2 and 5.7 million per library and were mapped to the common bean reference genome. Approximately 70–90% of filtered RNA-seq reads uniquely mapped to the reference genome. In the inoculated roots of resistant genotype PI533561, a total of 353 genes were differentially expressed with 154 up-regulated genes and 199 down-regulated genes when compared to the transcriptome of non- inoculated roots. On the other hand, 990 genes were differentially expressed in SCN-inoculated roots of susceptible genotype GTS-900 with 406 up-regulated and 584 down-regulated genes when compared to non-inoculated roots. Genes encoding nucleotide-binding site leucine-rich repeat resistance (NLR) proteins, WRKY transcription factors, pathogenesis-related (PR) proteins and heat shock proteins involved in diverse biological processes were differentially expressed in both resistant and susceptible genotypes. Overall, suppression of the photosystem was observed in both the responses. Furthermore, RNA-seq results were validated through quantitative real time PCR. This is the first report describing genes/transcripts involved in SCN-common bean interaction and the results will have important implications for further characterization of SCN resistance genes in common bean. [ABSTRACT FROM AUTHOR]

Next generation sequence data provides valuable information and tools for genetic and genomic research and offers new insights useful for marker development. This data is useful for the design of accurate and user-friendly molecular tools. Common bean (Phaseolus vulgaris L.) is a diverse crop in which separate domestication events happened in each gene pool followed by race and market class diversification that has resulted in different morphological characteristics in each commercial market class. This has led to essentially independent breeding programs within each market class which in turn has resulted in limited within market class sequence variation. Sequence data from selected genotypes of five bean market classes (pinto, black, navy, and light and dark red kidney) were used to develop InDel-based markers specific to each market class. Design of the InDel markers was conducted through a combination of assembly, alignment and primer design software using 1.6x to 5.1x coverage of Illumina GAII sequence data for each of the selected genotypes. The procedure we developed for primer design is fast, accurate, less error prone, and higher throughput than when they are designed manually. All InDel markers are easy to run and score with no need for PCR optimization. A total of 2687 InDel markers distributed across the genome were developed. To highlight their usefulness, they were employed to construct a phylogenetic tree and a genetic map, showing that InDel markers are reliable, simple, and accurate. [ABSTRACT FROM AUTHOR]

Next generation sequence data provides valuable information and tools for genetic and genomic research and offers new insights useful for marker development. This data is useful for the design of accurate and user-friendly molecular tools. Common bean (Phaseolus vulgaris L.) is a diverse crop in which separate domestication events happened in each gene pool followed by race and market class diversification that has resulted in different morphological characteristics in each commercial market class. This has led to essentially independent breeding programs within each market class which in turn has resulted in limited within market class sequence variation. Sequence data from selected genotypes of five bean market classes (pinto, black, navy, and light and dark red kidney) were used to develop InDel-based markers specific to each market class. Design of the InDel markers was conducted through a combination of assembly, alignment and primer design software using 1.6x to 5.1x coverage of Illumina GAII sequence data for each of the selected genotypes. The procedure we developed for primer design is fast, accurate, less error prone, and higher throughput than when they are designed manually. All InDel markers are easy to run and score with no need for PCR optimization. A total of 2,687 InDel markers distributed across the genome were developed. To highlight their usefulness, they were employed to construct a phylogenetic tree and a genetic map, showing that InDel markers are reliable, simple, and accurate. [ABSTRACT FROM AUTHOR]

[Display omitted] • Microstructures of beans were affected by thermal processing. • The cell walls impact the functionality and digestibility of bean flour. • Four bean classes resulted in different functionality and digestibility. • Dry-heated bean flours presented a toasted and caramel flavor profile. • Moist-heat treatment improved macronutrients digestibility. The utilization of beans (Phaseolus vulgaris L.) is hindered by unpleasant flavors, low macronutrients digestibility, and long cooking time. The pre-thermally treated beans can overcome these limitations. Therefore, the effect of thermal methods (moist–heat and dry-heat) and bean market classes (black, navy, kidney, and pinto) on functional properties and digestibility of bean flours were compared to raw counterparts. Within bean class, moist-heated samples showed increased water-holding capacities of 2.54–2.87 g H 2 O/g sample and starch/protein digestibility whereas dry-heated samples showed enhanced flavor profile and increased oil-holding capacities of 1.04–1.14 g oil/g sample. Among bean classes, moist-heated kidney bean flour showed the highest water-holding capacity of 2.87 g H 2 O/g sample and starch/protein digestibility while dry-heated pinto bean flour had the highest oil-holding capacity of 1.14 g oil/g sample. The current result may provide a basis for the development of pre-thermally treated legume flours and facilitate their applications. [ABSTRACT FROM AUTHOR]

Next generation sequence data provides valuable information and tools for genetic and genomic research and offers new insights useful for marker development. This data is useful for the design of accurate and user-friendly molecular tools. Common bean (Phaseolus vulgaris L.) is a diverse crop in which separate domestication events happened in each gene pool followed by race and market class diversification that has resulted in different morphological characteristics in each commercial market class. This has led to essentially independent breeding programs within each market class which in turn has resulted in limited within market class sequence variation. Sequence data from selected genotypes of five bean market classes (pinto, black, navy, and light and dark red kidney) were used to develop InDel-based markers specific to each market class. Design of the InDel markers was conducted through a combination of assembly, alignment and primer design software using 1.6× to 5.1× coverage of Illumina GAII sequence data for each of the selected genotypes. The procedure we developed for primer design is fast, accurate, less error prone, and higher throughput than when they are designed manually. All InDel markers are easy to run and score with no need for PCR optimization. A total of 2687 InDel markers distributed across the genome were developed. To highlight their usefulness, they were employed to construct a phylogenetic tree and a genetic map, showing that InDel markers are reliable, simple, and accurate. [ABSTRACT FROM AUTHOR]

Increasing soil-N in a dry bean (Phaseolus vulgaris L.) crop may increase seed yield. However, excessive N can inhibit nodule formation, delay maturity, and promote vegetative growth. In the same way, the effect of row spacing on yield and other traits appears to be different for variable levels of available N. With releases of new upright pinto bean cultivars, it is unknown how factors such as row spacing and soil-N level may affect seed yield and seed losses under direct harvest operations. Experiments were conducted in North Dakota to evaluate the effect of row spacing and soil-N level on agronomic traits of pinto bean cultivars under direct harvest. The experimental design was a randomized complete block design in a split-plot arrangement, where whole plots were three row spacings (30, 46, and 76cm), and subplots were a factorial with three pinto cukivars (Lariat, Stampede, and Maverick) and two soil-N levels (56 and 112 kg N ha-1). Cultivar and row spacing were the most important factors determining seed yield and seed loss. Lariat produced the greatest seed yield (2045 kg ha-1) and had the lowest harvest loss (11.6%). The intermediate row spacing (46 cm) had the highest seed yield with no significant changes in the amount of seed loss when compared with the wide rows (76 cm). The N level did not influence seed yield or yield potential. Therefore, to maximize productivity with upright pinto cukivars, growers should plant at intermediate row spacing and reduce the amount of N applied. [ABSTRACT FROM AUTHOR]

North Dakota is the leading producer of dry beans (Phaseolus vulgaris L.) in the United States. In order to remain competitive, growers need to find ways to optimize yields and minimize input costs. Direct harvest may decrease equipment investment, harvest time, and operational costs when compared with conventional methods. However, direct harvest is often associated with reduced seed yield and quality. Experiments were conducted at four environments in North Dakota to evaluate the harvest efficiency of nine dry bean cultivars representing three market classes. Seed yield, seed loss, and other agronomic/morphological traits were measured using a split plot design. Harvest method and cultivar were consistently the most important factors contributing to seed yield and seed loss. Seed yield was significantly greater (830 kg ha-1) with the conventional method and seed loss was significantly greater (23.2%) under direct harvest. For conventional harvest, there was no difference in seed yield among cultivars within a market class. However, under direct harvest, one pinto (Lariat) and two black bean (T-39 and Eclipse) cultivars showed the highest yield. There were no differences among the navy cultivars for seed yield. Lariat was the most efficient cultivar across and within both harvest methods, with the best combination of highest yield (2232 kg ha-1) and lowest seed loss (11.1%). None of the morphological traits measured had a strong association with seed yield or seed loss. Results indicate that for optimal yields, growers need to select a cultivar with the best harvest efficiency possible, in addition to other factors. [ABSTRACT FROM AUTHOR]

Flavonoids are secondary metabolites associated with plant seed coat and flower color. These compounds provide health benefits to humans as anti-inflammatory and antioxidant compounds. The expression of the late biosynthetic genes in the flavonoid pathway is controlled by a ternary MBW protein complex consisting of interfacing M YB, b eta-helix–loop–helix (bHLH), and WD 40 R epeat (WDR) proteins. P , the master regulator gene of the flavonoid expression in common bean (Phaseolus vulgaris L.), was recently determined to encode a bHLH protein. The T and Z genes control the distribution of color in bean seeds and flowers and have historically been considered regulators of the flavonoid gene expression. T and Z candidates were identified using reverse genetics based on genetic mapping, phylogenetic analysis, and mutant analysis. Domain and AlphaFold2 structure analyses determined that T encodes a seven-bladed β-propeller WDR protein, while Z encodes a R2R3 MYB protein. Deletions and SNPs in T and Z mutants, respectively, altered the 3D structure of these proteins. Modeling of the Z MYB/P bHLH/T WDR MBW complex identified interfacing sequence domains and motifs in all three genes that are conserved in dicots. One Z MYB motif is a possible beta-molecular recognition feature (β-MoRF) that only appears in a structured state when Z MYB is modeled as a component of a MBW complex. Complexes containing mutant T and Z proteins changed the interaction of members of the complex in ways that would alter their role in regulating the expression of genes in the flavonoid pathway. [ABSTRACT FROM AUTHOR]

Multienvironment trials (METs) are widely used to assess the performance of promising crop germplasm. Though seldom designed to elucidate genetic mechanisms, MET data sets are often much larger than could be duplicated for genetic research and, given proper interpretation, may offer valuable insights into the genetics of adaptation across time and space. The Cooperative Dry Bean Nursery (CDBN) is a MET for common bean (Phaseolus vulgaris) grown for . 70 years in the United States and Canada, consisting of 20-50 entries each year at 10-20 locations. The CDBN provides a rich source of phenotypic data across entries, years, and locations that is amenable to genetic analysis. To study stable genetic effects segregating in this MET, we conducted genome-wide association studies (GWAS) using best linear unbiased predictions derived across years and locations for 21 CDBN phenotypes and genotypic data (1.2 million SNPs) for 327 CDBN genotypes. The value of this approach was confirmed by the discovery of three candidate genes and genomic regions previously identified in balanced GWAS. Multivariate adaptive shrinkage (mash) analysis, which increased our power to detect significant correlated effects, found significant effects for all phenotypes. Mash found two large genomic regions with effects on multiple phenotypes, supporting a hypothesis of pleiotropic or linked effects that were likely selected on in pursuit of a crop ideotype. Overall, our results demonstrate that statistical genomics approaches can be used on MET phenotypic data to discover significant genetic effects and to define genomic regions associated with crop improvement. [ABSTRACT FROM AUTHOR]

The common bean is a tropical facultative short-day legume that is now grown in tropical and temperate zones. This observation underscores how domestication and modern breeding can change the adaptive phenology of a species. A key adaptive trait is the optimal timing of the transition from the vegetative to the reproductive stage. This trait is responsive to genetically controlled signal transduction pathways and local climatic cues. A comprehensive characterization of this trait can be started by assessing the quantitative contribution of the genetic and environmental factors, and their interactions. This study aimed to locate significant QTL (G) and environmental (E) factors controlling time-to-flower in the common bean, and to identify and measure G x E interactions. Phenotypic data were collected from a biparental [Andean x Mesoamerican] recombinant inbred population (F11:14, 188 genotypes) grown at five environmentally distinct sites. QTL analysis using a dense linkage map revealed 12 QTL, five of which showed significant interactions with the environment. Dissection of G x E interactions using a linear mixed-effect model revealed that temperature, solar radiation, and photoperiod play major roles in controlling common bean flowering time directly, and indirectly by modifying the effect of certain QTL. The model predicts flowering time across five sites with an adjusted r-square of 0.89 and root-mean square error of 2.52 d. The model provides the means to disentangle the environmental dependencies of complex traits, and presents an opportunity to identify in silico QTL allele combinations that could yield desired phenotypes under different climatic conditions. [ABSTRACT FROM AUTHOR]