Traits In Common Bean Research Articles

Marker association study of yield attributing traits in common bean (Phaseolus vulgaris L.).

Common bean is gaining acceptance as one of the most valuable major food consumed worldwide owing to innumerable nutritional and therapeutic benefits. Comparatively less productivity in underdeveloped countries encouraged us to proceed for QTL mining of yield traits in common bean. Heretofore, multiple yield associated markers have been detected all over the world; even so, the present work is looked on as the first report on identification of novel/new potent markers by exploiting the germplasm of Northern India. A panel of one hundred and thirty five genotypes was used for morphological studies and based on preliminary molecular evaluation; a set of ninety six diverse common bean genotypes (core set) was selected for association analysis. Molecular data generated by a total of ninety eight microsatellite markers (53 genomic and 45 genic SSRs) revealed high estimation of polymorphism among the genotypes that were observed to be divided into two major sub-populations and varying levels of admixtures based on population structure analyses. By employing both MLM and GLM analysis approaches, we identified 46 and 16 significant marker-trait associations (p ≤ 0.005) respectively, few of which have already been reported and hence validate our results. PVBR213 marker was found to be strongly associated with days to bud initiation trait when analyzed with both the approaches. Phenotypic variation of identified significant markers ranged from 3.1% to 32.7% where PVBR87, PVBR213, X96999 and X57022 explain more than 30% of phenotypic variation for 100 seed weight, days to bud initiation, pods per plant and pod length traits respectively. These findings introduce highly informative markers to aid marker-assisted selection program in common bean for high yield performance along with good agronomic merit.

Participatory variety selection of common bean (Phaseolus vulgaris L.) genotypes in the major bean producing areas of Ethiopia

This study was conducted to identify suitable parental genotypes for breeding for resistance to bruchid and to identify the farmers’ preferred traits in common bean. For this study, 144 diverse common bean genotypes were planted in an alpha lattice design, with 3 replications at 3 locations. Participatory variety selection was done using 20 farmers at each location. Farmers identified a number of criteria for selecting suitable varieties. Yield and yield-related traits were ranked as the most important selection criteria by all farmers at all locations. However, women ranked culinary traits as the top criteria, while men were more interested in marketable traits. From the 144 genotypes, farmers selected the 10 best genotypes in all the locations. The majority of the genotypes selected at Melkassa and Alemetena were small white-seeded released varieties and breeding lines. However, all the genotypes selected at Arsi Negele were predominantly landraces of small red-seeded beans. Traits such as earliness and resistance to storage insect were important in Melkassa and Alme tena but received less attention in Arsi Negele. The integration of the farmers’ selection preferences with the breeders’ criteria can improve the efficiency of plant breeding by developing crop varieties that better fit the specific needs of the farmers.

Genomic Prediction of Agronomic Traits in Common Bean (Phaseolus vulgaris L.) Under Environmental Stress.

In plant and animal breeding, genomic prediction models are established to select new lines based on genomic data, without the need for laborious phenotyping. Prediction models can be trained on recent or historic phenotypic data and increasingly available genotypic data. This enables the adoption of genomic selection also in under-used legume crops such as common bean. Beans are an important staple food in the tropics and mainly grown by smallholders under limiting environmental conditions such as drought or low soil fertility. Therefore, genotype-by-environment interactions (G × E) are an important consideration when developing new bean varieties. However, G × E are often not considered in genomic prediction models nor are these models implemented in current bean breeding programs. Here we show the prediction abilities of four agronomic traits in common bean under various environmental stresses based on twelve field trials. The dataset includes 481 elite breeding lines characterized by 5,820 SNP markers. Prediction abilities over all twelve trials ranged between 0.6 and 0.8 for yield and days to maturity, respectively, predicting new lines into new seasons. In all four evaluated traits, the prediction abilities reached about 50–80% of the maximum accuracies given by phenotypic correlations and heritability. Predictions under drought and low phosphorus stress were up to 10 and 20% improved when G × E were included in the model, respectively. Our results demonstrate the potential of genomic selection to increase the genetic gain in common bean breeding. Prediction abilities improved when more phenotypic data was available and G × E could be accounted for. Furthermore, the developed models allowed us to predict genotypic performance under different environmental stresses. This will be a key factor in the development of common bean varieties adapted to future challenging conditions.

Agronomic traits in common bean are influenced by infestation and coexistence with volunteer maize

ABSTRACT Maize seeds lost during harvest may emerge and establish themselves during the cultivation of common bean, becoming a problematic weed in succession crops. This study aimed to evaluate the effect of the infestation level and interference period of volunteer maize on agronomic traits of common bean. The experiment was carried out in a randomized block design, with four replications, in a 2 x 8 factorial scheme consisting of two maize infestation levels (4 plants m-2 and 12 plants m-2) combined with eight coexistence periods between crop and weed (0, 7, 14, 21, 28, 35, 42 and 88 days after the emergence of the common bean). Variables related to the common bean vegetative growth (plant height, stem diameter, number of side branches and shoot dry matter) and to its grain production (number of pods per plant, grain yield and weight of 1,000 grains), as well as the period prior to interference, were assessed. The increase of the coexistence period and volunteer maize infestation level negatively affected the common bean growth and grain yield. The densities with 4 plants m-2 and 12 plants m-2 of volunteer maize reduced the common bean grain yield by 60 % and 84 %, respectively; while the periods prior to interference between crop and weed, for the respective infestation levels, were 15 and 8 days after the common bean emergence. In addition, the volunteer maize reduces the period prior to interference to very low values, indicating the need to anticipate the control of this weed.

Parental effects and provisioning under drought and low phosphorus stress in common bean

AbstractLow soil fertility and drought are primary constraints for crop production and food security in many developing nations. Since smallholder farmers often collect seed for the next year's crop from plants grown with abiotic stress, it is important to understand how progeny from a stressed parental environment perform when they are grown under similar stresses. This study investigates the impact of a low phosphorus (P) or drought parental environment on progeny seed and root traits in common bean (Phaseolus vulgaris), with the intention of distinguishing impacts of reduced parental provisioning from adaptive responses. Greenhouse, field, and seedling experiments were used to evaluate seed, seedling, and mature root phenotypes in progeny from stressed and nonstressed parental conditions. In addition, progeny from different positions within the pod and pod developmental times were evaluated since they are expected to vary in parental provisioning. Seeds from the peduncular position in the pod had less individual seed weight, fewer basal roots, reduced root dry weight, and smaller taproot diameter than those from the stylar position. Progeny of some genotypes from drought‐stressed parents had smaller individual seed weight, fewer basal roots, less total seedling dry weight, shorter seedling basal roots, and smaller basal root diameters. Progeny of some genotypes from a low P parental environment had smaller individual seed P concentration, fewer shoot‐borne roots, and greater basal root whorl number. Progeny from drought‐stressed parents, progeny from a low P parental environment, and seeds from the peduncular position had root phenotypes that were likely to be related to less parental provisioning. Possible adaptive parental effects were found in both parental drought and parental low P studies. Adequate seed provision under stress merits consideration as a selection target in crop breeding for stressful environments.

Single and Multi-trait GWAS Identify Genetic Factors Associated with Production Traits in Common Bean Under Abiotic Stress Environments.

The genetic improvement of economically important production traits of dry bean (Phaseolus vulgaris L.), for geographic regions where production is threatened by drought and high temperature stress, is challenging because of the complex genetic nature of these traits. Large scale SNP data sets for the two major gene pools of bean, Andean and Middle American, were developed by mapping multiple pools of genotype-by-sequencing reads and identifying over 200k SNPs for each gene pool against the most recent assembly of the P. vulgaris genome sequence. Moderately sized Bean Abiotic Stress Evaluation (BASE) panels, consisting of genotypes appropriate for production in Central America and Africa, were assembled. Phylogenetic analyses demonstrated the BASE populations represented broad genetic diversity for the appropriate races within the two gene pools. Joint mixed linear model genome-wide association studies with data from multiple locations discovered genetic factors associated with four production traits in both heat and drought stress environments using the BASE panels. Pleiotropic genetic factors were discovered using a multi-trait mixed model analysis. SNPs within or near candidate genes associated with hormone signaling, epigenetic regulation, and ROS detoxification under stress conditions were identified and can be used as genetic markers in dry bean breeding programs.

Correlation and Path Coefficient Analysis for Seed Yield and some of its Traits in ‎Common Bean (Phaseolus vulgaris L.)‎

Common bean (Phaseolus vulgaris L.) is one of the most important vegetable crops grown in Egypt. This study was conducted to determine the phenotypic, genotypic, and environmental correlations between seed yield and some of its traits, and to perform path analysis to assessthe direct and indirect effects between seed yield per plant as dependent variable and the other traits as explanatory variables.Twenty-seven accessions of common bean were evaluated at El-Dalgamon village, El-Gharbia Governorate, Egypt during the two successive summer seasons of 2016 and 2017 using a randomized complete block designwith three replications.The results revealed the importance of genotypic correlations coefficients compared to the corresponding values of phenotypic ones. The genotypic correlations were positive ranging from 0.60 to 0.99 for the correlation between seed yield per plant and each of plant height, number of leaves per plant, number of days to flowering, number of racemes per plant, number of days to maturity, number of pods per plant,and number of seeds per pod. Genotypic path analysis indicated the importance of positive direct effects of plant height, number of pods per plant,number of days to maturity, andnumber of seeds per pod,suggesting thedirect selection of these traits to improve seed yield. Whereas, number of leaves per plant,number of days to flowering,ornumber of racemes per plant should be selected simultaneously with plant height ornumber of pods per plant since they had high positive indirect effects on seed yield through these two traits.

Quantile regression for genome-wide association study of flowering time-related traits in common bean.

Flowering is an important agronomic trait. Quantile regression (QR) can be used to fit models for all portions of a probability distribution. In Genome-wide association studies (GWAS), QR can estimate SNP (Single Nucleotide Polymorphism) effects on each quantile of interest. The objectives of this study were to estimate genetic parameters and to use QR to identify genomic regions for phenological traits (Days to first flower—DFF; Days for flowering—DTF; Days to end of flowering—DEF) in common bean. A total of 80 genotypes of common beans, with 3 replicates were raised at 4 locations and seasons. Plants were genotyped for 384 SNPs. Traditional single-SNP and 9 QR models, ranging from equally spaced quantiles (τ) 0.1 to 0.9, were used to associate SNPs to phenotype. Heritabilities were moderate high, ranging from 0.32 to 0.58. Genetic and phenotypic correlations were all high, averaging 0.66 and 0.98, respectively. Traditional single-SNP GWAS model was not able to find any SNP-trait association. On the other hand, when using QR methodology considering one extreme quantile (τ = 0.1) we found, respectively 1 and 7, significant SNPs associated for DFF and DTF. Significant SNPs were found on Pv01, Pv02, Pv03, Pv07, Pv10 and Pv11 chromosomes. We investigated potential candidate genes in the region around these significant SNPs. Three genes involved in the flowering pathways were identified, including Phvul.001G214500, Phvul.007G229300 and Phvul.010G142900.1 on Pv01, Pv07 and Pv10, respectively. These results indicate that GWAS-based QR was able to enhance the understanding on genetic architecture of phenological traits (DFF and DTF) in common bean.

Agronomic and qualitative traits of common bean as a function of the straw and nitrogen fertilization1

ABSTRACT The no-tillage system can change the nitrogen dynamics in the soil, being necessary to adjust the nitrogen fertilization in order to provide this nutrient during critical phases of the common bean growth. This study aimed at evaluating the agronomic and qualitative traits of common bean grown under different straw types, as a function of the topdressing nitrogen fertilization splitting. A randomized block experimental design, in a split-plot arrangement, with four replications, was used. The plots consisted of three straw types (maize, maize intercropped with brachiaria and brachiaria), while the subplots comprised the combination of these straw materials with 8 topdressing nitrogen fertilization splitting arrangements. The common bean on brachiaria straw shows higher grain yields and crude protein contents. The nitrogen fertilization splitting, as topdressing, interacts with the straw types, increasing the number of pods per plant. The common bean plants growing on plots with single-maize straw had a shorter time for maximum hydration. The topdressing nitrogen fertilization splitting has no effect on the common bean qualitative traits.

Effect of genotypes-Rhizobium-environment interaction on nodulation and productivity of common bean (Phaseolus vulgaris L.) in eastern Ethiopia

BackgroundEffectiveness of Rhizobium inoculation is determined by common bean genotypes. Environmental factors also affect common bean genotypes-Rhizobium-symbiosis. The effect of common bean genotypes-Rhizobium strains-environment interaction on nodulation and common bean production is not well studied. Three genotypes (Dursitu, Gofta, and Kufanzik) and eight selected isolates of common bean nodulating-rhizobia with N-fertilized and control check were used for field experiments at four locations (Babile, Fedis, Haramaya, and Hirna) to evaluate the effect of genotypes-Rhizobium strains-environment interaction on the nodulation, yield and yield traits of common bean. The treatments were laid out in a randomized complete block design with three replications.ResultsThis study revealed that Rhizobium inoculation, the genotypes, environment and their interaction significantly (P ≤ 0.05) affected all investigated traits of common bean. Common bean genotypes Rhizobium inoculation and experimental locations significantly affected nodule number (NN) and nodule dry weight (NDW). The highest NN and NDW as compared to the uninoculated control across locations were recorded with the genotype Dursitu in all inoculation treatments. However, the result revealed the lowest mean total biomass (TBY) and grain yield (GY) over locations with the same genotype Dursitu. The highest mean grain yields of 3358.89, 3257.82, 1499.25 and 2204.82 kg ha−1 across the treatments were recorded at Haramaya, Hirna, Babile and Fedis sites, respectively, with the genotype Gofta, thereby implying that there was none specificity between common bean genotypes × locations in the study locations of eastern Ethiopia with tested common bean genotypes. None of the tested isolates produced statistically better NN, NDW, TBY, GY and total plant N accumulation consistently in all locations with all tested common bean genotypes, indicating the presence of Rhizobium strains × location specificity.ConclusionTherefore, the result showed the need for a specific strain of Rhizobium development for common bean production in different locations.

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.

Genome-Wide Association Study Identifies Candidate Loci Underlying Agronomic Traits in a Middle American Diversity Panel of Common Bean.

Common bean ( L.) breeding programs aim to improve both agronomic and seed characteristics traits. However, the genetic architecture of the many traits that affect common bean production are not completely understood. Genome-wide association studies (GWAS) provide an experimental approach to identify genomic regions where important candidate genes are located. A panel of 280 modern bean genotypes from race Mesoamerica, referred to as the Middle American Diversity Panel (MDP), were grown in four US locations, and a GWAS using >150,000 single-nucleotide polymorphisms (SNPs) (minor allele frequency [MAF] ≥ 5%) was conducted for six agronomic traits. The degree of inter- and intrachromosomal linkage disequilibrium (LD) was estimated after accounting for population structure and relatedness. The LD varied between chromosomes for the entire MDP and among race Mesoamerica and Durango-Jalisco genotypes within the panel. The LD patterns reflected the breeding history of common bean. Genome-wide association studies led to the discovery of new and known genomic regions affecting the agronomic traits at the entire population, race, and location levels. We observed strong colocalized signals in a narrow genomic interval for three interrelated traits: growth habit, lodging, and canopy height. Overall, this study detected ∼30 candidate genes based on a priori and candidate gene search strategies centered on the 100-kb region surrounding a significant SNP. These results provide a framework from which further research can begin to understand the actual genes controlling important agronomic production traits in common bean.

Inorganic nitrogen application improves the yield and yield traits of common bean (Phaseolus vulgaris L.) irrespective of the indigenous rhizobial population

The effect of number and efficiency of indigenous rhizobia on the need for external inorganic nitrogen (N) application to boost common bean production is unknown. Hence, field experiments were conducted at four locations with soil populations of <100, 100–1 000 and >1 000 rhizobia to evaluate the effect of the indigenous rhizobial population on N requirement of common bean in eastern Ethiopia. The treatments comprised six levels of N application arranged in a randomised complete block design with three replications. The results showed decreases in nodule number (NN) and nodule dry weight (NDW) with increasing rate of inorganic N application in all soil types. Application of 20 kg N ha−1 resulted in a significant increase in the NN and NDW in soil with a low and moderate rhizobial population but not in soils with a high rhizobial population. The highest yield and yield traits in soil containing a high and low rhizobial population was recorded with <40 and >60 kg N ha−1 application, respectively. The association between grain yield and N application was negative in soils with a high and moderate rhizobial population, and positive in soil containing a low rhizobial population. In general, the results revealed that the number of indigenous rhizobia could affect the quantity of N applied.

Natural Variation for Seed Physical, Biochemical and Culinary traits in Common bean (Phaseolus vulgaris L.)

&lt;p&gt;Twenty genotypes of common bean including 17 breeding lines were evaluated for various seed physical, nutritional and culinary traits viz., seed colour, seed shape, seed brilliance, seed coat pattern, seed length, seed breadth and seed weight, traits protein content, phytic acid, raffinose, water absorption percentage, coat percentage, swelling and hydration coefficient as well as cooking score. Most of the genotypes were kidney shaped with plain seed coat and medium seed brilliance. Among biochemical traits, highest protein content was recorded for Arka Anoop (22.15 %) followed by WB-341 (21.45 %), WB-216 (21.16 %) and WB-249 (20.99). Low phytic acid was recorded in WB-970 (0.440 %), WB-258 (0.968 %) and WB-102 (1.068 %). Low values for raffinose was recorded for WB-102 (3.800 mg/g) followed by WB-482 (3.833 mg/g). Highest water absorption percentage was recorded for WB-249 (136.363), Arka Anoop (131.818) and SFB-1 (126.923). The swelling coefficient was highest in case of WB-642 (300.000), WB-249 (266.667) and WB-335 (250.000) whereas lowest values for swelling coefficient were recorded in case of WB-341 (114.285), WB-216 (145.454) and WB-1006 (124.554). Among correlations between various seed physical, biochemical and culinary traits, raffinose was positively and significantly correlated with phytic acid. Phytic acid was also significantly and positively correlated with protein, coat proportion and 100-seed weight. Coat proportion was negatively correlated water absorption percentage, swelling coefficient, hydration coefficient as well as cooking time score. Cooking time score was positively correlated with hydration and swelling coefficients as well as seed weight but negatively correlated with coat proportion. &lt;/p&gt;

Genome-Wide Association Study of Agronomic Traits in Common Bean.

A genome-wide association study (GWAS) using a global Andean diversity panel (ADP) of 237 genotypes of common bean (Phaseolus vulgaris L.) was conducted to gain insight into the genetic architecture of phenology, biomass, yield components, and seed yield traits. The panel was evaluated for 2 yr in field trials in Michigan and genotyped with 5398 single nucleotide polymorphism (SNP) markers. After correcting for population structure and cryptic relatedness, significant SNP markers associated with several agronomic traits were identified. Positional candidate genes, including Phvul.001G221100 on P. vulgaris (Pv) chromosome 01, associated with days to flowering and maturity were identified. Significant SNPs for seed yield were identified on Pv03 and Pv09 and colocalized with quantitative trait loci (QTL) for yield from previous studies conducted in several environments and contrasting genetic backgrounds. The majority of germplasm carrying the alleles with positive effects on seed yield was of African origin and largely underutilized in US breeding programs. The study provided insights into the genetic architecture of agronomic traits in Andean beans.

Quantitative analysis of race-specific resistance to Colletotrichum lindemuthianum in common bean

Molecular genetic maps continue to play a major role in breeding of crop species. The common bean genetic map of the recombinant inbred line population IAC-UNA × CAL 143 (UC) has been used to detect loci controlling important agronomic traits in common bean. In the current study, new microsatellite markers were added to the UC map and the linkage analysis was refined using current genomic resources of common bean, in order to identify quantitative resistance loci (QRL) associated with different races of the anthracnose pathogen. A single race inoculation was conducted in greenhouse using four plants per plot. Both race-specific and joint-adjusted disease severity means, obtained from linear-mixed model, were used to perform multiple interval mapping (MIM) and multi-trait MIM (MTMIM). In total, 13 and 11 QRL were identified by MIM and MTMIM analyses, respectively; with nine being observed in both analyses. ANT02.1UC and ANT07.1UC showed major effects on resistance both for MIM and MTMIM. Common major QRL for resistance to the three anthracnose races were expected, since high genetic pairwise-correlation was observed between the race-specific and joint-adjusted disease severity means. Therewith, both ANT02.1 and ANT07.1 can be regarded as valuable targets for marker-assisted selection; and so, putative genes potentially involved in the resistance response were identified in these QRL regions. Minor effect QRL were also observed, showing differential affects either on race-specific or multi-trait analyses and may play a role on durable horizontal resistance. These results contribute to a better understanding of the host-pathogen interaction and to breeding for enhancing resistance to Colletotrichum lindemuthianum in common bean.

An RNA-Seq based gene expression atlas of the common bean.

BackgroundCommon bean (Phaseolus vulgaris) is grown throughout the world and comprises roughly 50% of the grain legumes consumed worldwide. Despite this, genetic resources for common beans have been lacking. Next generation sequencing, has facilitated our investigation of the gene expression profiles associated with biologically important traits in common bean. An increased understanding of gene expression in common bean will improve our understanding of gene expression patterns in other legume species.ResultsCombining recently developed genomic resources for Phaseolus vulgaris, including predicted gene calls, with RNA-Seq technology, we measured the gene expression patterns from 24 samples collected from seven tissues at developmentally important stages and from three nitrogen treatments. Gene expression patterns throughout the plant were analyzed to better understand changes due to nodulation, seed development, and nitrogen utilization. We have identified 11,010 genes differentially expressed with a fold change ≥ 2 and a P-value < 0.05 between different tissues at the same time point, 15,752 genes differentially expressed within a tissue due to changes in development, and 2,315 genes expressed only in a single tissue. These analyses identified 2,970 genes with expression patterns that appear to be directly dependent on the source of available nitrogen. Finally, we have assembled this data in a publicly available database, The Phaseolus vulgaris Gene Expression Atlas (Pv GEA), http://plantgrn.noble.org/PvGEA/ . Using the website, researchers can query gene expression profiles of their gene of interest, search for genes expressed in different tissues, or download the dataset in a tabular form.ConclusionsThese data provide the basis for a gene expression atlas, which will facilitate functional genomic studies in common bean. Analysis of this dataset has identified genes important in regulating seed composition and has increased our understanding of nodulation and impact of the nitrogen source on assimilation and distribution throughout the plant.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-866) contains supplementary material, which is available to authorized users.

Comparison among direct, indirect and index selections on agronomic traits and nutritional quality traits in common bean

Selection indices are linear combinations that allow the selection of several characters simultaneously. The objective of this study was to verify the efficiency of direct selection, indirect selection and selection indices in the identification of higher inbred common bean lines for grain yield, morphological, phenological and nutritional traits. There is genetic variability for grain yield, lodging, general adaptation note, cycle, insertion of the first pod, calcium and iron concentrations in the seeds. Moderate phenotypic correlation coefficients were observed between grain yield and general adaptation note (r = -0.57) and cycle (r = -0.57). When direct selection was performed for grain yield, the insertion of the first pod, calcium and iron concentrations showed negative indirect selection gains. The classic index showed that the distribution of gains has become more balanced: grain yield (39.05%), calcium (8.29%) and iron concentration (1.64%). Direct selection and indirect selection are not efficient in the simultaneous selection of agronomic traits and nutritional quality in common bean. The classical, base and multiplicative indexes provide responses of gain balanced among traits and superior genetic progress in the selection of inbred common bean lines, and have a high coincidence between the lines selected.

Identifying quantitative trait loci for symbiotic nitrogen fixation capacity and related traits in common bean

Symbiotic nitrogen fixation (SNF) through association with root-nodulating rhizobia effectively contributes to improved nitrogen nutrition of leguminous plants and is an ecologically sound and low-cost strategy for improving pulse productivity. One of the main factors determining the efficiency of SNF is the plant genotype, but little is known about the plants’ genetic contribution to SNF in the case of common bean. Therefore, quantitative trait loci (QTL) analysis for SNF and related growth traits was performed in a common bean recombinant inbred line (RIL) population under both greenhouse and field conditions. The RIL population was generated from the cross G2333 × G19839. Additionally, the existing genetic map of the population was improved through the mapping of 42 markers out of a set of 108 nodulation gene-based markers. All greenhouse and field experiments showed significant differences between RIL genotypes for most SNF and related growth traits. In the first greenhouse experiment, two QTL for percent nitrogen (N%) fixed were identified on linkage groups b01 and b04, explaining 21 and 20 % of the observed phenotypic variance, respectively. The QTL on linkage group b01 overlapped with a QTL detected for total N content at harvest in the field experiment (R2 = 14 %). In the second greenhouse experiment, two QTL for total plant N fixed were identified on linkage groups b04 and b10 (R2 = 18 and 17 %, respectively). The field experiment also yielded one QTL for the N% fixed at harvest on linkage group b04 and another for the total N fixed in the shoot at late pod-filling stage on linkage group b01. The latter two QTL identified in the field explained 19 and 21 %, respectively, of the observed phenotypic variance. DNA sequence comparison of markers closely linked to QTL identified some potential candidate genes underlying the QTL. One of these genes encodes for an auxin-responsive transcription factor which could explain differences in growth and possibly yield and N accumulation between climbing beans and bush beans. Another putative gene was identified for an AP2/ERF-domain-containing transcription factor underlying the QTL for the total amount of symbiotic nitrogen fixed in the field.