Traits In Common Bean Research Articles

DTALE approach demonstrates that induction of common bean OVATE Family Protein 7 (PvOFP7) promotes resistance to common bacterial blight

Abstract Common bacterial blight of bean (CBB) is a devastating seed-transmitted disease caused by Xanthomonas phaseoli pv. phaseoli and Xanthomonas citri pv. fuscans on common bean (Phaseolus vulgaris L.). The genes responsible for CBB resistance are largely unknown. Moreover, the lack of a reproducible and universal transformation protocol limits the study of genetic traits in common bean. We produced X. phaseoli pv. phaseoli strains expressing artificially-designed Transcription-Activator Like Effectors (dTALEs) to target 14 candidate genes for resistance to CBB based on previous transcriptomic data. In planta assays in a susceptible common bean genotype showed that induction of PvOFP7, PvAP2-ERF71 or PvExpansinA17 expression by dTALEs resulted in CBB symptom reduction. After PvOFP7 induction, in planta bacterial growth was reduced at early colonisation stages and RNA-Seq analysis revealed up-regulation of cell wall formation and primary metabolism, together with major down-regulation of Heat Shock Proteins. Our results demonstrate that PvOFP7 contributes to CBB resistance, and underline the usefulness of dTALEs for functional validation of genes whose induction impacts Xanthomonas-plant interaction.

Adaptation, Path Coefficient and Correlation Study of Yield and Associated Traits in Common Bean (Phaseolus vulgaris L.) Genotypes

The study evaluated new biofortified, high-yielding and disease-resistant bean varieties for their adaptability in Zimbabwe. The secondary objective was to assess the association between yield and other traits that contribute to grain yield and identify traits that have direct and indirect effects on grain yield. The study was conducted between December 2016 and June 2017 using an augmented design with 24 varieties replicated three times at Chinhoyi University of Technology Research Farm. Data was analysed using analysis of variance in the statistical analysis system (SAS) software. DAB482, DAB494 and DAB539 were identified as high-yielding varieties with desired disease tolerance to common bean blight (CBB), common leaf rust (CLR) and angular leaf spot). Therefore, these improved common bean varieties recommended for further multilocation evaluation with the potential to be released as commercial varieties. Correlation coefficient values and path analysis values (direct and indirect) showed that the weight of 100 randomly selected seeds per variety and the percentage number of plants that germinated per plot could be used for indirect selection for grain yield (kg/ha). A negative correlation indicates an inverse relationship between traits. This study observed significant negative correlations for CBB and CLR relative to grain yield (kg/ha). This suggests that the grain yield (kg/ha) decreases with increased disease incidence and severity, highlighting the importance of disease tolerance in achieving high grain yield. Hence, there is a need for the breeding program to select and advance varieties that are tolerant to diseases to achieve the desired improvement in grain yield performances.

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

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

Assessment of genotypic variability and genome‐wide association analysis of cooking time and canning quality traits in common bean (Phaseolus vulgaris L.)

AbstractDeveloping improved common bean varieties with short cooking time (CT) and good canning quality traits (CQTs) is very key for accelerating bean consumption among the urban and middle‐class population. The objective of this study was to assess the genotypic variability and identify single nucleotide polymorphism (SNP) markers associated with CT and CQTs in common bean. A total of 250 common bean accessions were evaluated under field conditions for two seasons using alpha lattice design with two replications. Three months post‐harvest, the dry bean grains were evaluated for CT and CQTs. Significant variation was observed among the 250 common bean accessions tested for both traits. CT ranged from 51 to 215 min, with 11 genotypes cooking in less than 60 min. The percentage total CQTs' score ranged from 41% to 84% with 31 genotypes scoring 76% and above. Forty‐seven significant GWAS signals were detected for CT on chromosomes Pv01, Pv04, Pv05 and Pv11 and CQTs on Pv01, Pv02, Pv03, Pv04, Pv05, Pv06, Pv07, Pv08, Pv10 and Pv11, respectively. Positional candidate genes including Phvul.005G161200 on chromosome Pv05, Phvul.007G2803001 and Phvul.007G280700 on chromosome Pv07 were associated with seed coat colour retention of the canned beans. Besides their usefulness in breeding research, the identified bean genotypes with shorter CT and good CQTs could enhance bean consumption and processing industries.

Determination of combining ability and heritability for canning quality traits in common bean

Breeding for common bean (Phaseolus vulgaris L.) genotypes with optimal canning quality holds the potential for increased dry bean consumption among middle-class income urban dwellers in sub-Saharan Africa (SSA). Understanding the genetic control of canning quality traits is central for the improvement of common bean genotypes for desired canning quality. The objective of this study was to determine the combining ability and heritability of canning quality traits (CQTs) in common bean; and to establish entry points for effective breeding for these traits. A population from two contrasting parents for canning quality traits was developed and progressed to F2. The F2:F4 seed was evaluated for CQTs at three months post-harvest. Substantial variation was observed among the canning quality traits tested, including the general appearance of the canned beans, seed coat colour retention namely, clumping, free starch, splitting, and hydration coefficient. Canning quality traits encompassed a spectrum of both additive and non-additive effects. Promising combiners for CQTs were identified among the parents, KK8 and MAC 13, suggesting their potential for utilisation in breeding programmes. Moderate to high Baker’s ratio (BR = 0.41-0.94) values were observed for some CQTs and narrow sense heritability (h2 = 0.47-0.66). Canning quality traits exhibited substantial broad sense heritability (H2) values, ranging from 0.6 to 0.92. These findings provide valuable entry points for breeding programmes focused on improving common bean for canning quality.

Genome-wide association study dissecting drought resistance-associated loci based on physiological traits in common bean

Genetic improvement of drought resistance is one of the main breeding goals for common bean, so molecular markers must be identified to facilitate drought resistance breeding. In this study, we evaluated the proline, trehalose, raffinose, and stachyose contents of 210 common bean accessions under two watering conditions and found large variations in all four. The coefficients of variation ranged from 21.21% for proline content to 78.69% for stachyose content under well-watered conditions, and from 20.11% for proline content to 50.08% for trehalose content under drought stress. According to our genome-wide association analysis, 32 quantitative trait loci were associated with drought resistance, seven of which overlapped with known loci. Four hotspot regions were identified at Pv01, Pv07 and Pv11. A set of candidate genes was identified, including genes encoding MYB, bZIP, bHLH, ERF, and protein kinases. Among these genes, Phvul.001G189400, Phvul.007G273000 and Phvul.008G270500 were annotated as bZIP, ERF and WRKY, respectively. These genes are reportedly involved in drought stress responses in Arabidopsis thaliana and were induced by drought stress in common bean. Significant SNPs in six candidate gene regions formed different haplotypes, and phenotypic analysis revealed significant differences among the haplotypes. These results provide new insight into the genetic basis of drought resistance in common bean and reveal candidate genes and superior natural variations that will be useful for improving common bean.

The Effects of UV Light and Methyl Salicylate on Phytochemical Constituents and Nutritional Traits in Common Bean (Phaseolus vulgaris L.)

Background: Mutagenesis has also been used to improve many desirable traits such as earliness, darkness, resistance or tolerance to biotic and abiotic stress, seed yield and oil quality. There are numerous mutagen agents, both chemical and physical, available to create and obtain valuable mutations in crop plants. Methods: The experiment was done at the laboratory of the Faculty of Applied Sciences, Ton Duc Thang University in Vietnam from September 2021 to December 2022. This study examined the effects of ultraviolet B-light (UV-B) and methyl salicylate (MeSA) treatment on phytochemical constituents (total phenols and flavonoids) and nutritional characteristics (protein and fat content) in a common bean cultivar, GRIS2. Result: The results show that UV irradiation for 3 hours increased the phenolic content in M1 seeds when compared to the control and other treatments. Furthermore, compared to the control and other treatments, UV-B irradiation for up to 5 hours increased the phenolic, protein and lipid content in the pod (in the immature pod, mature pod and seed). Alternatively, treatment with MeSA considerably decreased the levels of these same compounds. Treating the seed with 0.05 mM MeSA did increase the flavonoid content. These findings demonstrate the potential of UV-B treatment for improving bean nutritional quality. On the other hand, the negative general implications of the higher MeSA treatment suggest exogenous treatments should be kept at lower concentrations to ensure the minimization of nutritional losses.

Combining ability of common bean (Phaseolus vulgaris) genotypes for root traits across diverse environments

AbstractRoot system architecture is important for common bean (Phaseolus vulgaris) adaptability to diverse environments. Beans employ complex adaptive root mechanisms for coping with multiple stresses in production environments. Understanding genetic control of root traits is central to improvement of common bean for adaptation to marginal environments. The objectives of this study were to (i) determine combining ability of root and agronomic traits and (ii) estimate the heritability and genetic correlation of root and agronomic traits in common bean. Four bean lines with superior root traits were crossed with four locally adapted varieties in a North Carolina II mating scheme to generate 16 crosses. The 16 F1s were selfed and advanced to F2 generation. Eight parents and their F2 progenies were evaluated in an alpha‐Lattice design with two replications. General and specific combing ability mean squares were significant (p ≤ .05) for all traits measured. General predictability ratios ranged from .47 to .68 across locations suggesting that both additive and non‐additive gene action modulate root traits and seed yield. Positive and significant (p ≤ .05) phenotypic and genetic correlations revealed significant association between root traits and yield. Moderate to high heritability estimates of between .43 and .67 were realized. Such estimates point to possible deployment of a successful selection programme. Genotype AFR398 displayed significant positive GCA effects among its crosses for both root and agronomic traits hence a potential candidate genotype for inclusion in a bean genetic improvement programme for marginal environments.

Novel candidate loci for morpho-agronomic and seed quality traits detected by targeted genotyping-by-sequencing in common bean.

Phaseolus vulgaris L., known as common bean, is one of the most important grain legumes cultivated around the world for its immature pods and dry seeds, which are rich in protein and micronutrients. Common bean offers a cheap food and protein sources to ameliorate food shortage and malnutrition around the world. However, the genetic basis of most important traits in common bean remains unknown. This study aimed at identifying QTL and candidate gene models underlying twenty-six agronomically important traits in common bean. For this, we assembled and phenotyped a diversity panel of 200P. vulgaris genotypes in the greenhouse, comprising determinate bushy, determinate climbing and indeterminate climbing beans. The panel included dry beans and snap beans from different breeding programmes, elite lines and landraces from around the world with a major focus on accessions of African, European and South American origin. The panel was genotyped using a cost-conscious targeted genotyping-by-sequencing (GBS) platform to take advantage of highly polymorphic SNPs detected in previous studies and in diverse germplasm. The detected single nucleotide polymorphisms (SNPs) were applied in marker-trait analysis and revealed sixty-two quantitative trait loci (QTL) significantly associated with sixteen traits. Gene model identification via a similarity-based approach implicated major candidate gene models underlying the QTL associated with ten traits including, flowering, yield, seed quality, pod and seed characteristics. Our study revealed six QTL for pod shattering including three new QTL potentially useful for breeding. However, the panel was evaluated in a single greenhouse environment and the findings should be corroborated by evaluations across different field environments. Some of the detected QTL and a number of candidate gene models only elucidate the understanding of the genetic nature of these traits and provide the basis for further studies. Finally, the study showed the possibility of using a limited number of SNPs in performing marker-trait association in common bean by applying a highly scalable targeted GBS approach. This targeted GBS approach is a cost-efficient strategy for assessment of the genetic basis of complex traits and can enable geneticists and breeders to identify novel loci and targets for marker-assisted breeding more efficiently.

Genetic Variability Analysis and Association of Traits in Common Bean (Phaseolus vulgaris L.) Landraces Collected from Ethiopia at Jimma

This study was conducted on one hundred common bean landraces at the Jimma Agricultural Research Center, Melko, with the objective of assessing genetic variability and association of traits in common bean landraces collected from different parts of Ethiopia. The experiment was laid out in a simple lattice design with two replications. Analysis of variance showed significant differences among genotypes for all traits. This highly significant difference indicates the existence of large variability among genotypes. High phenotypic coefficients of variation and genotypic coefficients of variation were obtained for plant height (19.43, 11.73), pod length (11.27, 10.69), and 100-seed weight (15.42, 12.74). High heritability in the broad sense was found for days to 50% flowering (66.98), days to 90% maturity (87.43), pod length (90.03), pod width (78.23), harvest index (98.67), and 100-seed weight (68.31). High genetic advance as a percentage of mean with high heritability was obtained for pod length, pod width, harvest index, and hundred seed weight. Grain yield had a positive and significant association with pod length (rp = 0.153 ∗ , rg = 0.282 ∗ ∗ ) and 100-seed weight (rp = 0.294 ∗ ∗ , rg = 0.492 ∗ ∗ ). Hundred seed weight exerted the highest positive direct effect (0.294) on grain yield at genotypic level. The D2 classified landraces into 7 clusters and one solitary, which makes them moderately divergent. The highest inter-cluster distance was observed between clusters VII and IV. The first five principal components with eigenvalues greater than one altogether explained about 79.56% of the total variation. In conclusion, the top high-yielding landraces, namely, P#1247, P#1092, P#1077, P#861, P#990, P#763, P#58, and P#857, should be included in the next breeding program. 100-seed weight had the highest direct effect and a positive significant association with grain yield. Thus, it should be considered as the selection criteria for further common bean yield improvement. However, the current result is merely indicative and cannot be used to draw definite conclusions. Therefore, the experiment should be replicated in different locations and seasons for greater consistency.

Number of experiments that should be considered in the cluster analysis of common bean genotypes for plant architecture and grain yield traits

The number of experiments that allows the choice of parents to be used in controlled crossings in a more assertive way in cluster analysis is unknown for plant architecture and grain yield traits in common bean. Therefore, the objective of this work was to determine the number of experiments that should be considered in Tocher's and the unweighted pair group method with arithmetic mean (UPGMA) cluster analyses to identify promising common bean parents for several plant architecture and grain yield traits. Four experiments were carried out in different years and growing seasons, in the same site. The randomized block design was used and 17 common bean genotypes with carioca (beige seed coat with brown streaks) and black grains were evaluated in relation to 12 traits related to plant architecture and five traits related to grain yield. Statistical analyses were performed with data obtained from individual and combined experiments. Significant genotype × experiment interaction was observed for most of the evaluated traits. When Tocher's and UPGMA cluster analyses was performed from data obtained in individual experiments different groups were formed. The use from data obtained in two, three or four experiments allowed greather reliability in the formation of groups. Three and two experiments are sufficient in the Tocher's and the UPGMA cluster analyses, respectively, to identify promising carioca and black common bean parents for several plant architecture and grain yield traits in a more assertive way.

Climbing bean breeding for disease resistance and grain quality traits

AbstractCommon bean (Phaseolus vulgaris) is grown in two growth types, bush and climbing beans. The latter are preferred in several regions in East and Southern African as well as in Latin America (dominant in Rwanda and Colombia), due to higher yields and resilience compared with bush type. Common bean productivity is reduced by several pests and diseases between them. Bean common mosaic virus (BCMV), which is the most common and destructive poty‐virus affecting bean production worldwide, and anthracnose, caused by the fungus Colletotrichum lindemuthianum, can cause yield losses as high as 95% in susceptible cultivars. Further important traits in common bean are high micro mineral contents to alleviate malnutrition and grain quality traits such as the canning quality of bean varieties, which is important for farmers to access the processing market. In this study, new climbing bean populations were generated (coded ENF/CGA) to combine high seed iron (SdFe) and multiple diseases resistance. Double and triple crosses between parents with virus and anthracnose resistance, high SdFe, and good agronomic traits were employed. In trials in Darien and Popayan, lines were identified that combine BCMNV/BCMV and anthracnose resistance with seed yields above 4000 kg/ha. Phenotypic evaluations validated the usefulness of SNP markers tagging the genes bc‐3 and I for BCMN and Co‐3 for anthracnose as a selection tool for field resistance. These results show the genetic potential of the lines that are now being tested in target regions to be delivered to smallholder farmers.

English

Common beans are an important nutritious food crop to many people in developing countries. Inadequate soil-P is one of the major constraints to high bean seed yield productivity. Information about genetic effects that control inheritance of root traits in common bean grown under low soil-P conditions is scarce, and that is a challenge for genetic enhancement. This study was therefore implemented to determine inheritance and gene action of root traits in common bean for tolerance to low soil-P. The six generations were evaluated in a completely randomised design with two replicates under low soil-P in a pot experiment. Generation mean analysis revealed that both allelic and non-allelic genetic interactions controlled inheritance of root traits studied. Cumulative main gene effect was higher than epistasis effects. Additive genetic effects were more predominant than dominance effects. Additive and additive × dominance epistatic gene effects were more important in controlling inheritance of root traits under low soil-P. Broad-sense heritability for hypocotyl root number was the highest (93.98 %) while the narrow-sense heritability was moderate (51.13 %). To develop improved genotypes tolerant to low soil-P, recombination crossing should be followed by screening and selection in later generations for high seed yield, root and other preferred traits. Key words: Common bean, inheritance, genotype, gene effect, heritability, low soil-P.

Genome‐wide association analysis of drought adaptive traits in common bean

AbstractGenome‐wide association study (GWAS) was conducted to determine the genetic architecture of yield component and photosynthetic (PS) traits in 256 common bean (Phaseolus vulgaris L.) genotypes from the Andean gene pool. The panel was evaluated under drought stress (DS) and non‐stress (NS) conditions at two locations for two seasons in Uganda and genotyped with 260K single nucleotide polymorphism (SNP) markers. Significant association signals were detected for yield component and PS traits on chromosomes Pv02, Pv03, Pv04, Pv06, Pv09, Pv10, and Pv11. Colocalized GWAS signals were detected for pod weight per plant (PW) and seed yield per plant (SY) on Pv06 with ten significant markers and for PhiNPQ, LEF, Phi2, and PhiNO on Pv11 under DS. Positional candidate genes were identified within the 1.76 Mb common region for PW and SY under DS on Pv06 including Phvul.006G117500, Phvul.006G119800, and Phvul.006G130500 annotated as plant invertase/pectin methylesterase inhibitor (INH/PMEI) superfamily protein, involved in sucrose metabolism and signaling. Phvul.006G121200, 14.9Kb upstream of marker S06_23021418 (23.02Mb) on Pv06, encodes Protein phosphatase 2C family protein involved in ABA signaling pathway. Positional candidate genes for PS traits PhiNPQ, LEF, Phi2, and PhiNO on Pv11 under DS were identified including Phvul.011G178200, Phvul.011G178250, Phvul.011G178300, and Phvul.011G178500 between 48.94–49.96 Mb annotated as “RING/U‐BOX SUPERFAMILY PROTEIN”, ubiquitin ligase (E3) involved in ABA‐mediated responses. Significant markers associated with colocalized GWAS signal for SY and PW on Pv06 identified in this study can be validated for marker assisted breeding to improve drought tolerance in large‐seeded Andean beans.

Genome-wide association analysis of bean fly resistance and agro-morphological traits in common bean.

The bean fly (Ophiomyia spp) is a key insect pest causing significant crop damage and yield loss in common bean (Phaseolus vulgaris L., 2n = 2x = 22). Development and deployment of agronomic superior and bean fly resistant common bean varieties aredependent on genetic variation and the identification of genes and genomic regions controlling economic traits. This study’s objective was to determine the population structure of a diverse panel of common bean genotypes and deduce associations between bean fly resistance and agronomic traits based on single nucleotide polymorphism (SNP) markers. Ninety-nine common bean genotypes were phenotyped in two seasons at two locations and genotyped with 16 565 SNP markers. The genotypes exhibited significant variation for bean fly damage severity (BDS), plant mortality rate (PMR), and pupa count (PC). Likewise, the genotypes showed significant variation for agro-morphological traits such as days to flowering (DTF), days to maturity (DTM), number of pods per plant (NPP), number of seeds per pod (NSP), and grain yield (GYD). The genotypes were delineated into two populations, which were based on the Andean and Mesoamerican gene pools. The genotypes exhibited a minimum membership coefficient of 0.60 to their respective populations. Eighty-three significant (P<0.01) markers were identified with an average linkage disequilibrium of 0.20 at 12Mb across the 11 chromosomes. Three markers were identified, each having pleiotropic effects on two traits: M100049197 (BDS and NPP), M3379537 (DTF and PC), and M13122571 (NPP and GYD). The identified markers are useful for marker-assisted selection in the breeding program to develop common bean genotypes with resistance to bean fly damage.

GWAS of pod morphological and color characters in common bean

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

Genome-Wide Association Studies of Mineral Content in Common Bean.

Micronutrient malnutrition is one of the main public health problems in many parts of the world. This problem raises the attention of all valuable sources of micronutrients for the human diet, such as common bean (Phaseolus vulgaris L.). In this research, a panel of 174 accessions representing Croatian common bean landraces was phenotyped for seed content of eight nutrients (N, P, K, Ca, Mg, Fe, Zn, and Mn), and genotyped using 6,311 high-quality DArTseq-derived SNP markers. A genome-wide association study (GWAS) was then performed to identify new genetic sources for improving seed mineral content. Twenty-two quantitative trait nucleotides (QTN) associated with seed nitrogen content were discovered on chromosomes Pv01, Pv02, Pv03, Pv05, Pv07, Pv08, and Pv10. Five QTNs were associated with seed phosphorus content, four on chromosome Pv07, and one on Pv08. A single significant QTN was found for seed calcium content on chromosome Pv09 and for seed magnesium content on Pv08. Finally, two QTNs associated with seed zinc content were identified on Pv06 while no QTNs were found to be associated with seed potassium, iron, or manganese content. Our results demonstrate the utility of GWAS for understanding the genetic architecture of seed nutritional traits in common bean and have utility for future enrichment of seed with macro– and micronutrients through genomics-assisted breeding.

Allelic Diversity, Structural Analysis, and Genome-Wide Association Study (GWAS) for Yield and Related Traits Using Unexplored Common Bean (Phaseolus vulgaris L.) Germplasm From Western Himalayas.

The north-western Indian Himalayas possesses vast diversity in common bean germplasm due to several years of natural adaptation and farmer’s selection. Systematic efforts have been made for the first time for the characterization and use of this huge diversity for the identification of genes/quantitative trait loci (QTLs) for yield and yield-contributing traits in common bean in India. A core set of 96 diverse common bean genotypes was characterized using 91 genome-wide genomic and genic simple sequence repeat (SSR) markers. The study of genetic diversity led to the identification of 691 alleles ranging from 2 to 21 with an average of 7.59 alleles/locus. The gene diversity (expected heterozygosity, He) varied from 0.31 to 0.93 with an average of 0.73. As expected, the genic SSR markers detected less allelic diversity than the random genomic SSR markers. The traditional clustering and Bayesian clustering (structural analysis) analyses led to a clear cut separation of a core set of 96 genotypes into two distinct groups based on their gene pools (Mesoamerican and Andean genotypes). Genome-wide association mapping for pods/plant, seeds/pod, seed weight, and yield/plant led to the identification of 39 significant marker–trait associations (MTAs) including 15 major, 15 stable, and 13 both major and stable MTAs. Out of 39 MTAs detected, 29 were new MTAs reported for the first time, whereas the remaining 10 MTAs were already identified in earlier studies and therefore declared as validation of earlier results. A set of seven markers was such, which were found to be associated with multiple (two to four) different traits. The important MTAs will be used for common bean molecular breeding programs worldwide for enhancing common bean yield.

Effectiveness of breeding selection for grain quality in common bean

AbstractThe aims of this study were to investigate the genetic variability and the genotype × environment interaction for quality and yield traits in common bean (Phaseolus vulgaris L.), to evaluate the degree of informativeness of the evaluations of grain quality in only one environment, to estimate genetic parameters for grain quality traits, and to select lines with superior grain quality. We evaluated 81 carioca common bean lines in preliminary line trials in several environments for nutritional, technological, and commercial quality and selected the 20 superior lines, which were evaluated in validation trials in nine environments. Individual and combined ANOVAs were performed for all the traits. Correlations were estimated between Fe and Zn concentrations and yield; adaptability and phenotypic stability were analyzed; and superior genotypes were selected based on the Mulamba &amp; Mock index. It is possible to increase the Fe, Zn, and crude protein concentrations and reduce cooking time; however, increasing crude fiber is a challenge. Preliminary evaluation of the quality traits in only one environment was effective and sufficient for selection of genotypes superior in Fe concentration, crude fiber, crude protein, and cooking time; and genetic gains can be obtained from selection for these traits. Genetic and phenotypic correlations were observed between Fe and Zn concentrations. The lines CNFC 16627, CNFC 16518, CNFC 16602, CNFC 16615, and CNFC 16520 are superior based on the selection index and are recommended for breeding for grain quality in carioca common bean.

Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress.

Drought stress is an important abiotic factor limiting common bean yield, with great impact on the production worldwide. Understanding the genetic basis regulating beans’ yield and seed weight (SW) is a fundamental prerequisite for the development of superior cultivars. The main objectives of this work were to conduct genome-wide marker discovery by genotyping a Mesoamerican panel of common bean germplasm, containing cultivated and landrace accessions of broad origin, followed by the identification of genomic regions associated with productivity under two water regimes using different genome-wide association study (GWAS) approaches. A total of 11,870 markers were genotyped for the 339 genotypes, of which 3,213 were SilicoDArT and 8,657 SNPs derived from DArT and CaptureSeq. The estimated linkage disequilibrium extension, corrected for structure and relatedness (r2sv), was 98.63 and 124.18 kb for landraces and breeding lines, respectively. Germplasm was structured into landraces and lines/cultivars. We carried out GWASs for 100-SW and yield in field environments with and without water stress for 3 consecutive years, using single-, segment-, and gene-based models. Higher number of associations at high stringency was identified for the SW trait under irrigation, totaling ∼185 QTLs for both single- and segment-based, whereas gene-based GWASs showed ∼220 genomic regions containing ∼650 genes. For SW under drought, 18 QTLs were identified for single- and segment-based and 35 genes by gene-based GWASs. For yield, under irrigation, 25 associations were identified, whereas under drought the total was 10 using both approaches. In addition to the consistent associations detected across experiments, these GWAS approaches provided important complementary QTL information (∼221 QTLs; 650 genes; r2 from 0.01% to 32%). Several QTLs were mined within or near candidate genes playing significant role in productivity, providing better understanding of the genetic mechanisms underlying these traits and making available molecular tools to be used in marker-assisted breeding. The findings also allowed the identification of genetic material (germplasm) with better yield performance under drought, promising to a common bean breeding program. Finally, the availability of this highly diverse Mesoamerican panel is of great scientific value for the analysis of any relevant traits in common bean.