Reliability assessment of new radiographic scales to evaluate radiolucency and bony in-between fin growth of partially cemented all-polyethylene glenoid components.

BACKGROUND: Current methods available for assessment of radiolucency and in-between fin (IBF) growth of a glenoid component have not undergone interobserver reliability testing for an all-polyethylene fluted central peg (FCP) glenoid. The purpose of this study was to evaluate anteroposterior radiographs of an FCP glenoid component at ≥48 months comparing commonly used scales to a new method adapted to the FCP. Our hypothesis was that the new method would result in acceptable intra- and interobserver agreement and a more accurate description of radiographic findings. METHODS: We reviewed ≥48-month follow-up radiographs of patients treated with a primary aTSA using an FCP glenoid. Eighty-three patients were included in the review. Radiographs were evaluated by 5 reviewers using novel IBF radiodensity and radiolucency assessments and the Wirth and Lazarus methods. To assess intraobserver reliability, a subset of 40 images was reviewed. Kappa statistics were calculated to determine intra- and interobserver reliability; correlations were assessed using Pearson correlation. RESULTS: Interobserver agreement (κ score) was as follows: IBF 0.71, radiolucency 0.68, Wirth 0.48, and Lazarus 0.22. Intraobserver agreement ranges were as follows: IBF radiodensity 0.36-0.67, radiolucency 0.55-0.62, Wirth 0.11-0.73, and Lazarus 0.04-0.46. Correlation analysis revealed the following: IBF to Wirth r = 0.93, radiolucency to Lazarus r = 0.92 (P value <.001 for all). CONCLUSION: This study introduces a radiographic assessment method developed specifically for an FCP glenoid component. Results show high interobserver and acceptable intraobserver reliability for the method presented in this study. The new scales provide a more accurate description of radiographic findings, helping to identify glenoid components that may be at risk for loosening.

Combination of meta-analysis of QTL and GWAS to uncover the genetic architecture of seed yield and seed yield components in common bean.

Increasing seed yield in common bean could help to improve food security and reduce malnutrition globally due to the high nutritional quality of this crop. However, the complex genetic architecture and prevalent genotype by environment interactions for seed yield makes increasing genetic gains challenging. The aim of this study was to identify the most consistent genomic regions related with seed yield components and phenology reported in the last 20 years in common bean. A meta-analysis of quantitative trait locus (QTL) for seed yield components and phenology (MQTL-YC) was performed for 394 QTL reported in 21 independent studies under sufficient water and drought conditions. In total, 58 MQTL-YC over different genetic backgrounds and environments were identified, reducing threefold on average the confidence interval (CI) compared with the CI for the initial QTL. Furthermore, 40 MQTL-YC identified were co-located with 210 SNP peak positions reported via genome-wide association (GWAS), guiding the identification of candidate genes. Comparative genomics among these MQTL-YC with MQTL-YC reported in soybean and pea allowed the identification of 14 orthologous MQTL-YC shared across species. The integration of MQTL-YC, GWAS, and comparative genomics used in this study is useful to uncover and refine the most consistent genomic regions related with seed yield components for their use in plant breeding.

Histologic Analysis of Porcine Dermal Graft Augmentation in Treatment of Rotator Cuff Tears.

BACKGROUND: Biologic augmentation via extracellular matrix (ECM) scaffolds has been utilized to address rotator cuff tears with poor-quality tissue. PURPOSE: To evaluate the cellular changes in graft explants taken from patients treated with porcine dermal grafts for rotator cuff tears. STUDY DESIGN: Case series; Level of evidence, 4. METHODS: Four graft biopsy specimens were obtained from patients treated with porcine dermal grafts in an interposition technique for rotator cuff tears and compared with a nonimplanted graft and a normal rotator cuff specimen. Biopsy of the graft site was performed at 18 days, 3 months, 7 months, and 10.5 months after implantation. Hematoxylin and eosin staining was used to evaluate for cellular and vascular changes. Picrosirius red (PSR) stain with 90° polarized light was performed to evaluate collagen fibril size and orientation. All biopsy specimens were analyzed by a pathologist. RESULTS: There was evidence of progressive remodeling of the porcine dermal grafts. The most mature grafts demonstrated vessel infiltration and extensive remodeling without evidence of inflammation, foreign body reaction, or tissue rejection. PSR demonstrated increased organization of collagen domains, resembling normal tendon by 10.5 months postoperatively. CONCLUSION: This series suggests that ECM grafts may serve as an effective scaffold for host cell infiltration, collagen reorganization, and vascularization as a result of histologic changes demonstrated with retrieval of specimens from patients with rotator cuff tears that were augmented with porcine dermal grafts.

Elbow hemiarthroplasty for intra-articular distal humerus fractures: results and technique.

Purpose: The purpose of this study was to report results of elbow hemiarthroplasty for comminuted, intra-articular distal humerus fractures in low-demand elderly female patients. Methods: This is a retrospective case series of eight patients who underwent elbow hemiarthroplasty for comminuted, intra-articular distal humerus fractures between 2015 and 2019. Patients were considered for the procedure if the humeral fractures were deemed nonreconstructable by open reduction internal fixation. Patients were excluded if the extensor mechanism was not intact, evidence of significant ulnohumeral osteoarthritis, or a fracture to the proximal radius or ulna. A "triceps-on" approach was used in all cases. Appropriate sizing of the spool and length of the implant were determined by intraoperative fluoroscopy. Both ulnar collateral ligament and the lateral ulnar collateral ligaments were repaired through the central spool after final placement of the implant. Postoperative radiographs, clinical data, and the Mayo Elbow Performance Score were used to assess elbow pain and function. Results: Seven patients were included in final analysis. One patient was excluded from final analysis after sustaining a ground-level elbow dislocation at 13 weeks postoperatively, which subsequently revised to total elbow arthroplasty. The average age at the final follow-up was 72.1 years and duration of follow-up was 29.9 months (range 11.4-58.8 months). Average elbow range of motion was 21° ± 15° extension, 135° ± 9° flexion, 87° ± 5° pronation and 84° ± 8° supination. The average Mayo Elbow Performance Score was 88.3 (range 85-95; or "good" to "excellent") at the final follow-up. Postoperative ulnar neuropathy was reported by one patient at the first postoperative visit. This was followed up clinically and evaluation at 24 months revealed mild residual sensory deficits and adequate strength and motor function. Conclusion: Elbow hemiarthroplasty using the humeral component of the total elbow arthroplasty is an option for treatment of isolated, comminuted distal humerus fractures in select patient populations. The ideal candidates are elderly, low-demand, and able to adhere to postoperative activity and weight-bearing restrictions. Overall patient satisfaction with off-label use of humeral component of commercially available total elbow implants in the United States is promising, yet development of a more anatomic spool is warranted to further optimize outcomes intraoperatively. Some advantages of elbow hemiarthroplasty are a less-demanding operation and avoids complications associated with linked design including polyethylene wear, periprosthetic fracture, or implant loosening. Limitations of this study include small sample size and retrospective nature of the study.

Reliability of the modified Walch classification for advanced glenohumeral osteoarthritis using 3-dimensional computed tomography analysis: a study of the ASES B2 Glenoid Multicenter Research Group.

BACKGROUND: Variations in glenoid morphology affect surgical treatment and outcome of advanced glenohumeral osteoarthritis (OA). The purpose of this study was to assess the inter- and intraobserver reliability of the modified Walch classification using 3-dimensional (3D) computed tomography (CT) imaging in a multicenter research group. METHODS: Deidentified preoperative CTs of patients with primary glenohumeral OA undergoing anatomic or reverse total shoulder arthroplasty (TSA) were reviewed with 3D imaging software by 23 experienced shoulder surgeons across 19 institutions. CTs were separated into 2 groups for review: group 1 (96 cases involving all modified Walch classification categories evaluated by 12 readers) and group 2 (98 cases involving posterior glenoid deformity categories [B2, B3, C1, C2] evaluated by 11 readers other than the first 12). Each case group was reviewed by the same set of readers 4 different times (with and without the glenoid vault model present), blindly and in random order. Inter- and intraobserver reliabilities were calculated to assess agreement (slight, fair, moderate, substantial, almost perfect) within groups and by modified Walch classification categories. RESULTS: Interobserver reliability showed fair to moderate agreement for both groups. Group 1 had a kappa of 0.43 (95% confidence interval [CI]: 0.38, 0.48) with the glenoid vault model absent and 0.41 (95% CI: 0.37, 0.46) with it present. Group 2 had a kappa of 0.38 (95% CI: 0.33, 0.43) with the glenoid vault model absent and 0.37 (95% CI: 0.32, 0.43) with it present. Intraobserver reliability showed substantial agreement for group 1 with (0.63, range 0.47-0.71) and without (0.61, range 0.52-0.69) the glenoid vault model present. For group 2, intraobserver reliability showed moderate agreement with the glenoid vault model absent (0.51, range 0.30-0.72), which improved to substantial agreement with the glenoid vault model present (0.61, range 0.34-0.87). DISCUSSION: Inter- and intraobserver reliability of the modified Walch classification were fair to moderate and moderate to substantial, respectively, using standardized 3D CT imaging analysis in a large multicenter study. The findings potentially suggest that cases with a spectrum of posterior glenoid bone loss and/or dysplasia can be harder to distinguish by modified Walch type because of a lack of defined thresholds, and the glenoid vault model may be beneficial in determining Walch type in certain scenarios. The ability to reproducibly separate patients into groups based on preoperative pathology, including Walch type, is important for future studies to accurately evaluate postoperative outcomes in TSA patient cohorts.

Distal clavicle autograft augmentation for glenoid bone loss in revision shoulder arthroplasty: results and technique.

BACKGROUND: Structural bone graft for reconstruction of glenoid bone stock is often necessary in the setting of revision shoulder arthroplasty. This study introduces a new structural autograft technique using the distal clavicle for treatment of glenoid bone loss in the setting of revision shoulder arthroplasty. METHODS: This is a retrospective, single-surgeon study of patients with significant glenoid bone loss requiring revision shoulder arthroplasty with autologous distal clavicle bone grafting to the glenoid. Twenty patients with failed shoulder arthroplasty who underwent revisions of their glenoid components between 2015 and 2019 were retrospectively identified. Sixteen patients were available with follow-up of greater than 1 year. Patient records and radiographs were reviewed for intraoperative and postoperative complications. Preoperative and postoperative function were evaluated by physical examination and patient-reported outcome surveys. RESULTS: There were no observed intraoperative complications relating to the distal clavicle autograft harvest or placement. There were no iatrogenic nerve injuries or intraoperative instability. One of the 16 patients developed postoperative loosening and subsequent failure of the glenoid baseplate, requiring revision. One additional patient demonstrated increased elevation of the coracoclavicular interval postoperatively, likely related to the distal clavicle autograft harvest. At a mean follow-up of 25 months, 15 of 16 glenoid implants remained well fixed (93.4%), with no evidence of infection, or impingement demonstrated radiographically or clinically. Average patient age was 69 years at the time of surgery. Forward elevation improved from 76° to 123° at final follow-up (P = .0002). The American Shoulder and Elbow Surgeons Standardized Shoulder Assessment Form score improved from an average of 35.8 to 67.8 at mean follow-up (P = .001). The visual analog scale score improved from an average of 5.9 to 2 at mean follow-up, though not statistically significant (P = .068). There was no significant change in external rotation following surgery (P = .319). CONCLUSION: Osteolysis and bone loss of the glenoid poses a challenging problem in revision shoulder arthroplasty. Distal clavicle autograft augmentation is a viable and reproducible technique to manage structural glenoid defects.

QTL mapping of post-processing color retention in two black bean populations.

KEY MESSAGE: Several QTL governing color retention in processed black beans were identified by traditional and novel phenotyping methods applied to two black bean mapping populations. When black beans are hydrothermally processed prior to consumption, water-soluble anthocyanins are released from the seed coat, resulting in an undesirable faded brown color in the cooked product. The aim of this research was to develop mapping populations with different genetic sources of color retention in order to identify regions of the bean genome associated with canning quality traits. Two half-sibling black bean recombinant inbred line (RIL) populations segregating for post-processing color retention were developed. These RIL populations were phenotyped for canning quality traits over two years and genotyped using the BARCBean6k_3 BeadChip. In addition to traditional phenotyping by trained panelists, cooked beans were also phenotyped using a novel digital image analysis pipeline. Measurements of post-processing seed coat color from both phenotyping methods were compared, and the digital image analysis was shown to outperform the trained panelists. Quantitative trait loci (QTL) for post-processing color retention were detected on six chromosomes, with QTL on Pv08 and Pv11 consistently detected across phenotyping methods, populations, and years. Color retention QTL on Pv08 explained up to 32% of phenotypic variation but were significant over a large physical interval due to low SNP marker coverage. However, color retention QTL on Pv11 also explained a substantial amount of phenotypic variation (r2 ≈ 25%) and mapped to a small genomic region near 52.5 Mbp. The QTL and methods described in this study will be useful for dry bean breeders and food scientists to produce high quality black beans that meet consumer needs.

Induction of competent cells for Agrobacterium tumefaciens-mediated stable transformation of common bean (Phaseolus vulgaris L.).

Stable transformation of common bean (Phaseolus vulgaris L.) has been successful, to date, only using biolistic-mediated transformation and shoot regeneration from meristem-containing embryo axes. In this study, using precultured embryo axes, and optimal co-cultivation conditions resulted in a successful transformation of the common bean cultivar Olathe using Agrobacterium tumefaciens strain EHA105. Plant regeneration through somatic embryogenesis was attained through the preculture of embryo axes for 12 weeks using induced competent cells for A. tumefaciens-mediated gene delivery. Using A. tumefaciens at a low optical density (OD) of 0.1 at a wavelength of 600 nm for infection and 4-day co-cultivation, compared to OD600 of 0.5, increased the survival rate of the inoculated explants from 23% to 45%. Selection using 0.5 mg L-1 glufosinate (GS) was effective to identify transformed cells when the bialaphos resistance (bar) gene under the constitutive 35S promoter was used as a selectable marker. After an 18-week selection period, 1.5% -2.5% inoculated explants, in three experiments with a total of 600 explants, produced GS-resistant plants through somatic embryogenesis. The expression of bar was confirmed in first- and second-generation seedlings of the two lines through reverse polymerase chain reaction. Presence of the bar gene was verified through genome sequencing of two selected transgenic lines. The induction of regenerable, competent cells is key for the successful transformation, and the protocols described may be useful for future transformation of additional Phaseolus germplasm.

On-farm multi-location evaluation of genotype by environment interactions for seed yield and cooking time in common bean.

Common bean variety choice by farmers in Uganda is driven by seed yield plus end-use quality traits like market class and cooking time. Limited genotype by environment information is available for traits valued by consumers. This research evaluated yield, seed size, hydration properties, and cooking time of 15 common bean genotypes within market classes recognized by consumers along with three farmers' checks at nine on-farm locations in Uganda for two seasons. Yield ranged from 71 to 3,216 kg ha-1 and was largely controlled by location (21.5% of Total Sums of Squares [TSS]), plus the interaction between location and season (48.6% of TSS). Cooking time varied from 19 to 271 minutes with the genotypes Cebo Cela and Ervilha consistently cooking fastest in 24 and 27 minutes respectively. Comparatively, the local checks (NABE-4, NABE-15, and Masindi yellow) took 35 to 45 minutes to cook. Cooking time was largely controlled by genotype (40.6% of TSS). A GGE biplot analysis uncovered the presence of two mega-environments for yield and one mega-environment for cooking time. Identification of mega-environments for these traits will help expedite common bean breeding, evaluation, and variety selection through reduction of number of test environments needed for phenotype evaluations. The high yielding and fast cooking genotypes from this study can be targeted as parental materials to improve existing common bean germplasm for these important traits.

Subscapularis Function After Total Shoulder Arthroplasty Using Lesser Tuberosity Osteotomy or Tenotomy.

INTRODUCTION: Subscapularis dysfunction is a recognized complication after total shoulder arthroplasty (TSA). However, optimal subscapularis management during TSA is controversial. Subscapularis tenotomy (ST) has been used, whereas lesser tuberosity osteotomy (LTO) has gained popularity. This study compares the clinical outcomes in patients undergoing TSA with either ST or LTO, focusing on subscapularis strength and overall function. METHODS: Records were reviewed for TSA performed from 2010 to 2016 by a single surgeon at one institution. Patient age, sex, hand dominance, and the time of follow-up were recorded. Radiographs were obtained and interpreted. Range of motion was measured and the American Shoulder and Elbow Surgeons scores obtained. A graded belly-press test was used to determine the overall subscapularis function. Subscapularis strength was measured during a resisted belly-press maneuver. Statistical analysis was performed using a paired Student t-test or Fisher exact test, with P < 0.05 determining statistical significance. RESULTS: Overall, 28 shoulders constituted the LTO group with 37 in the ST group. No difference was found regarding age, whether their surgical site was their dominant extremity, or the time to follow-up. Radiographically, all osteotomies went on to union, with one malunion noted. Range of motion was equivalent. No statistical difference was noted in subscapularis strength or in the American Shoulder and Elbow Surgeons scores. The overall subscapularis function also failed to show any notable difference. DISCUSSION: In conclusion, either LTO or ST can be used during TSA to achieve successful clinical outcomes. The method of subscapularis management did not affect the subscapularis strength or overall function.

Baking performance of 25 edible dry bean powders: Correlation between cookie quality and rapid test indices.

This study was designed to evaluate the baking performances of 25 edible dry bean (Phaseolus vulgaris L.) varieties and to investigate correlations among cookie features and rapid test indices (i.e., water and lactic acid retention capacities, oil binding capacity and Rapid Visco Analyzer indices). Two bean powder particle sizes (≤0.5 mm, ≤1.0 mm) were investigated. Cookies were evaluated in terms of nutritional, geometrical and textural properties. Bean powders doubled the amount of cookie protein and increased cookie resistant starch content. Baking potential varied according to bean genotype and powder particle size: coarse powders resulted in larger (+26%) and thinner (-19%) cookies characterized by easier breaking texture (fracture strengths of 41-157 vs. 48-226 kPa for fine powders). Water retention and oil binding capacities and pasting properties significantly (p < 0.05) correlated with cookie features. In conclusion, these accumulated findings can be used in designing value-added traditional and gluten-free cookies.

Identification of quantitative trait loci for symbiotic nitrogen fixation in common bean.

KEY MESSAGE: QTL were identified for symbiotic nitrogen fixation in common bean. These QTL were detected in both greenhouse and field studies, and many overlapped with previously reported QTL in diverse mapping populations. Common bean (Phaseolus vulgaris L.) productivity can be improved through the genetic enhancement of its symbiotic nitrogen fixation (SNF) capacity. This study was aimed at understanding the genetic architecture of SNF through QTL analysis of a recombinant inbred line (RIL) population contrasting for SNF potential. The mapping population consisted of 188 F4:5 RILs derived from a cross of Solwezi and AO-1012-29-3-3A that were evaluated for SNF in the greenhouse and field in Zambia. The population was genotyped with 5398 single-nucleotide polymorphism (SNP) markers. QTL for shoot biomass, nitrogen percentage in shoot biomass, nitrogen percentage in seed, total nitrogen derived from atmosphere (Ndfa) and percentage of nitrogen derived from the atmosphere (%Ndfa) were identified. Three QTL for %Ndfa were identified on chromosomes Pv01, Pv04 and Pv09. Five QTL for Ndfa were identified on Pv04, Pv06, Pv07, Pv09 and Pv11. The QTL Ndfa9.1SA identified in the current study overlapped with a previously reported QTL for SNF. A major QTL Ndfa7.1DB, SA (R2 = 14.9%) was consistently identified in two greenhouse studies and overlapped with previously reported QTL. The QTL Ndfa4.2SA identified from the greenhouse experiment is novel and overlapped with the QTL %NB4.3SA, %NS4.2SA and %Ndfa4.2SA from the field experiment. These QTL identified in both greenhouse and field experiments, which overlap with previously reported QTL, could potentially be deployed by marker-assisted breeding to accelerate development of bean cultivars with enhanced SNF.

One and two-year clinical outcomes for a polyethylene glenoid with a fluted peg: one thousand two hundred seventy individual patients from eleven centers.

PURPOSE: Clinical shoulder science lacks a benchmark against which the early clinical value of new glenoid components can be compared; such a benchmark may be derived from a multicenter study of patients receiving an established, internationally used design of glenoid component. METHODS: We obtained data from 11 centers on 1270 patients having total shoulder arthroplasty using an all-polyethylene component with a fluted central peg. We analyzed individual patient outcomes at 1 and 2 years after surgery. We compared the improvement for each patient to the minimal clinically important difference (MCID) and calculated each patient's improvement as a percent of maximal possible improvement (MPI). RESULTS: The preoperative scores improved from SST 3 ± 2, ASES 37 ± 15, Constant score 36 ± 16, and Penn score 30 ± 19 to SST 10 ± 2, ASES 90 ± 12, Constant 76 ± 13, and Penn 80 ± 24 (p < 0.001 for each). A high percentage of patients improved by more than the MCID (SST 96%, ASES 98%, Constant 94%, Penn 93%) and obtained improvement of at least 30% of the MPI (SST 95%, ASES 98%, Constant 91%, Penn 87%). The clinical outcomes realized with this glenoid design were not worse for the 41% of shoulders with preoperative type B glenoids or for the 30% of shoulders with more than 15 degrees of glenoid retroversion. CONCLUSIONS: Individual patients from 11 international practices having total shoulder arthroplasty using a basic glenoid component design obtained highly significant clinical outcomes, providing a benchmark against which the early outcomes of new designs can be compared to determine whether they provide increased clinical value.

Seed characteristics and physicochemical properties of powders of 25 edible dry bean varieties.

Information on the physicochemical variability in dry bean seeds from different varieties grown over distinct crop years is lacking. This study was designed to investigate the relationship between the environment and the seed characteristics of 25 edible dry bean varieties and to expand the knowledge on their proximate composition, starch digestibility, solvent retention capacity, and pasting and thermal properties. The impact of bean genotype (25 varieties), growing environment (two crop years), and powder particle size (≤0.5 mm, ≤1.0 mm) was investigated. Statistical differences (P > 0.05) in seed characteristics and in starch, amylose and protein contents were found among the 25 varieties. Unique pasting and thermal properties were observed, and genotype and particle size greatly affected these properties. The accumulated information can be used in breeding programs to select bean lines possessing unique properties for food ingredients while increasing the market value of the crop and enhancing human health.

Prediction of canned black bean texture (Phaseolus vulgaris L.) from intact dry seeds using visible/near infrared spectroscopy and hyperspectral imaging data.

BACKGROUND: Texture is a major quality parameter for the acceptability of canned whole beans. Prior knowledge of this quality trait before processing would be useful to guide variety development by bean breeders and optimize handling protocols by processors. The objective of this study was to evaluate and compare the predictive power of visible and near infrared reflectance spectroscopy (visible/NIRS, 400-2498 nm) and hyperspectral imaging (HYPERS, 400-1000 nm) techniques for predicting texture of canned black beans from intact dry seeds. Black beans were grown in Michigan (USA) over three field seasons. The samples exhibited phenotypic variability for canned bean texture due to genetic variability and processing practice. Spectral preprocessing methods (i.e. smoothing, first and second derivatives, continuous wavelet transform, and two-band ratios), coupled with a feature selection method, were tested for optimizing the prediction accuracy in both techniques based on partial least squares regression (PLSR) models. RESULTS: Visible/NIRS and HYPERS were effective in predicting texture of canned beans using intact dry seeds, as indicated by their correlation coefficients for prediction (Rpred ) and standard errors of prediction (SEP). Visible/NIRS was superior (Rpred = 0.546-0.923, SEP = 7.5-1.9 kg 100 g-1 ) to HYPERS (Rpred = 0.401-0.883, SEP = 7.6-2.4 kg 100 g-1 ), which is likely due to the wider wavelength range collected in visible/NIRS. However, a significant improvement was reached in both techniques when the two-band ratios preprocessing method was applied to the data, reducing SEP by at least 10.4% and 16.2% for visible/NIRS and HYPERS, respectively. Moreover, results from using the combination of the three-season data sets based on the two-band ratios showed that visible/NIRS (Rpred = 0.886, SEP = 4.0 kg 100 g-1 ) and HYPERS (Rpred = 0.844, SEP = 4.6 kg 100 g-1 ) models were consistently successful in predicting texture over a wide range of measurements. CONCLUSION: Visible/NIRS and HYPERS have great potential for predicting the texture of canned beans; the robustness of the models is impacted by genotypic diversity, planting year and phenotypic variability for canned bean texture used for model building, and hence, robust models can be built based on data sets with high phenotypic diversity in textural properties, and periodically maintained and updated with new data. © 2017 Society of Chemical Industry.

Genome-wide Association Analysis for Drought Tolerance and Associated Traits in Common Bean.

A genome-wide association study explored the genetic basis of variation for drought tolerance and related traits in a Middle American diversity panel comprising 96 common bean ( L.) genotypes. The panel was grown under irrigated and rainfed conditions and single nucleotide polymorphism (SNP) data were used to explore the genetic diversity and ancestry of the panel. Varying levels of admixtures and distinctly divergent individuals were observed. Estimations of genome-wide heterozygosity revealed that, on average, greater diversity is present in individuals with Mesoamerica (3.8%) ancestry, followed by admixed individuals (2.3%). The race Durango had the lowest level of heterozygosity (1.4%). We report 27 significant marker-trait associations based on best linear unbiased predictors. These associations include seven markers for shoot biomass at harvest under irrigation and five markers under rainfed conditions on () chromosome 11, two markers for shoot biomass at flowering under irrigation on 02 and 08, two markers for seed size under irrigated and rainfed conditions on 09, seven markers for lodging score under irrigation on 02 and 07, one marker for leaf elongation rate on 03 and one for wilting score on 11. Positional candidate genes, including on 11, associated with wilting, were identified. The SNP ss715639327 marker was located in the exon region of the gene, which codes for an aquaporin associated with water movement in beans. Significant quantitative trait loci identified in this study could be used in marker-assisted breeding to accelerate genetic improvement of drought tolerance in common bean.

Transcriptome analysis of two recombinant inbred lines of common bean contrasting for symbiotic nitrogen fixation.

Common bean (Phaseolus vulgaris L.) fixes atmospheric nitrogen (N2) through symbiotic nitrogen fixation (SNF) at levels lower than other grain legume crops. An understanding of the genes and molecular mechanisms underlying SNF will enable more effective strategies for the genetic improvement of SNF traits in common bean. In this study, transcriptome profiling was used to identify genes and molecular mechanisms underlying SNF differences between two common bean recombinant inbred lines that differed in their N-fixing abilities. Differential gene expression and functional enrichment analyses were performed on leaves, nodules and roots of the two lines when grown under N-fixing and non-fixing conditions. Receptor kinases, transmembrane transporters, and transcription factors were among the differentially expressed genes identified under N-fixing conditions, but not under non-fixing conditions. Genes up-regulated in the stronger nitrogen fixer, SA36, included those involved in molecular functions such as purine nucleoside binding, oxidoreductase and transmembrane receptor activities in nodules, and transport activity in roots. Transcription factors identified in this study are candidates for future work aimed at understanding the functional role of these genes in SNF. Information generated in this study will support the development of gene-based markers to accelerate genetic improvement of SNF in common bean.

Transcriptome Profiling of the Phaseolus vulgaris - Colletotrichum lindemuthianum Pathosystem.

Bean (Phaseolus vulgaris) anthracnose caused by the hemi-biotrophic pathogen Colletotrichum lindemuthianum is a major factor limiting production worldwide. Although sources of resistance have been identified and characterized, the early molecular events in the host-pathogen interface have not been investigated. In the current study, we conducted a comprehensive transcriptome analysis using Illumina sequencing of two near isogenic lines (NILs) differing for the presence of the Co-1 gene on chromosome Pv01 during a time course following infection with race 73 of C. lindemuthianum. From this, we identified 3,250 significantly differentially expressed genes (DEGs) within and between the NILs over the time course of infection. During the biotrophic phase the majority of DEGs were up regulated in the susceptible NIL, whereas more DEGs were up-regulated in the resistant NIL during the necrotrophic phase. Various defense related genes, such as those encoding PR proteins, peroxidases, lipoxygenases were up regulated in the resistant NIL. Conversely, genes encoding sugar transporters were up-regulated in the susceptible NIL during the later stages of infection. Additionally, numerous transcription factors (TFs) and candidate genes within the vicinity of the Co-1 locus were differentially expressed, suggesting a global reprogramming of gene expression in and around the Co-1 locus. Through this analysis, we reduced the previous number of candidate genes reported at the Co-1 locus from eight to three. These results suggest the dynamic nature of P. vulgaris-C. lindemuthianum interaction at the transcriptomic level and reflect the role of both pathogen and effector triggered immunity on changes in plant gene expression.

Effects of extrusion cooking on the chemical composition and functional properties of dry common bean powders.

The impact of extrusion cooking on the chemical composition and functional properties of bean powders from four common bean varieties was investigated. The raw bean powders were extruded under eight different conditions, and the extrudates were then dried and ground (particle size⩽0.5mm). Compared with corresponding non-extruded (raw) bean powders (particle size⩽0.5mm), the extrusion treatments did not substantially change the protein and starch contents of the bean powders and showed inconsistent effects on the sucrose, raffinose and stachyose contents. The extrusion cooking did cause complete starch gelatinization and protein denaturation of the bean powders and thus changed their pasting properties and solvent-retention capacities. The starch digestibilities of the cooked non-extruded and cooked extruded bean powders were comparable. The extruded bean powders displayed functional properties similar to those of two commercial bean powders.

Genome-Wide Association Study of Anthracnose Resistance in Andean Beans (Phaseolus vulgaris).

Anthracnose is a seed-borne disease of common bean (Phaseolus vulgaris L.) caused by the fungus Colletotrichum lindemuthianum, and the pathogen is cosmopolitan in distribution. The objectives of this study were to identify new sources of anthracnose resistance in a diverse panel of 230 Andean beans comprised of multiple seed types and market classes from the Americas, Africa, and Europe, and explore the genetic basis of this resistance using genome-wide association mapping analysis (GWAS). Twenty-eight of the 230 lines tested were resistant to six out of the eight races screened, but only one cultivar Uyole98 was resistant to all eight races (7, 39, 55, 65, 73, 109, 2047, and 3481) included in the study. Outputs from the GWAS indicated major quantitative trait loci (QTL) for resistance on chromosomes, Pv01, Pv02, and Pv04 and two minor QTL on Pv10 and Pv11. Candidate genes associated with the significant SNPs were detected on all five chromosomes. An independent QTL study was conducted to confirm the physical location of the Co-1 locus identified on Pv01 in an F4:6 recombinant inbred line (RIL) population. Resistance was determined to be conditioned by the single dominant gene Co-1 that mapped between 50.16 and 50.30 Mb on Pv01, and an InDel marker (NDSU_IND_1_50.2219) tightly linked to the gene was developed. The information reported will provide breeders with new and diverse sources of resistance and genomic regions to target in the development of anthracnose resistance in Andean beans.