Extension of the core map of common bean with EST-SSR, RGA, AFLP, and putative functional markers

Mitotic effects of copper oxide nanoparticle on root development and root tip cells of Phaseolus vulgaris L. seeds

Copper oxide nanoparticle (CuO NP) is used widely in many fields in nanotechnology. For this reason, both production, use, and release to the environment are increasing with each passing day. With the increased use of products that contain nanoparticles (NP) (<100 nm), plants and organisms that constitute the food chain are at risk. In the present study, Phaseolus vulgaris L., a very common food plant, was exposed to metal-based CuO NPs. The anomalies that were caused by CuO NP in germination and mitosis of P. vulgaris were investigated. In the trials, a total of 4 groups (Control, 50, 150, and 300 ppm) were formed and examined in three replications. The determination of the accumulation and elimination rate because of NPs in P. vulgaris that was used in the study was made through X-ray diffraction (XRD), scanning electron microscope (SEM), mapping image, and EDX characteristic spectrum analysis. Also, the mitotic effects on germination, root development, and root tip cells of seeds that were grown by treatment with control, 50, 150, and 300 ppm concentrations were investigated. The study was conducted in three replications in a laboratory setting. All concentrations of CuO NPs caused significant decreases in the mitotic index in the root tip cells of P. vulgaris when compared to the control. The mitotic index reached the lowest level, especially at the highest concentration. Multiple analyzes in the study showed that CuO NPs cause abnormalities in cell division such as C-metaphase, distorted metaphase, distorted anaphase and telophase, chromosome breakage, asynchronous division, advanced chromosomes, micronucleus, and loss of genetic material. These findings also support that the Cytogenetic Test of P. vulgaris can be used to evaluate the genotoxicity of new nanomaterials that are used in many consumer products. In this respect, NPs that are taken up by the organisms in the food chain may pose a danger to higher consumer organisms when they accumulate in the tissue. A control mechanism must be established for the use and contamination of these particles and wider studies must be conducted regarding their effects. HIGHLIGHTS: The effects of CuO nanoparticle, which has a very wide usage area, on root development and mitosis of Phaseolus vulgaris L. plant were investigated in the study. The abnormalities of mitotic division on interphase, prophase, metaphase, anaphase, and telophase were visualized. Evaluation was made considering scanning electron microscopy (SEM) and X-ray diffraction (XRD) results as well.

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.

Marker-Trait Association Analysis of Seed Traits in Accessions of Common Bean (Phaseolus vulgaris L.) in China

Seed weight and seed size are the key agronomic traits that determine yield in common bean. To investigate the genetic architecture of four seed traits (100-seed weight, seed length, seed width, and seed height) of common bean in China, marker-trait association analysis of these seed traits was performed in a nationwide population of 395 common bean accessions using 116 polymorphic SSR markers. The four seed traits were evaluated in six trials across three environments. Seed size varied among the environments. Population structure was evaluated based on SSR markers and phaseolin, which divided the accessions into two main subpopulations representing the two known gene pools. Seed weight and seed size had a strong relationship with population clustering. In addition, in a Genome-wide association studies (GWAS), 21 significantly associated markers were identified for the four seed traits with two models, namely, general linear model (GLM) and mixed linear model (MLM). Some markers had pleiotropic effects, i.e., controlled more than one trait. The significant quantitative trait loci identified in this study could be used in marker-assisted breeding to accelerate the genetic improvement of yield in common bean.

Diversification and genetic structure of the western-to-eastern progression of European Phaseolus vulgaris L. germplasm

BACKGROUND

Common bean (Phaseolus vulgaris L.) is the most important food legume for direct human consumption around the world, as it represents a valuable source of components with nutritional and health benefits.

RESULTS

We conducted a study to define and explain the genetic relatedness and diversification level of common bean (Phaseolus vulgaris L.) germplasm from Portugal to Ukraine, along a western-to-eastern line of southern European countries, including Poland. This was based on the P. vulgaris genetic structure, and was designed to better describe its distribution and domestication pathways in Europe. Using the multi-crop passport descriptors that include geographic origin and different phaseolin types (corresponding to the Mesoamerican and Andean gene pools), 782 accessions were obtained from nine gene banks and 12 geographic origins. We selected 33 genome/ gene-related/ gene-pool-related nuclear simple sequence repeat markers that covered the genetic diversity across the P. vulgaris genome. The overall polymorphic information content was 0.800. Without specifying geographic origin, global structure cluster analysis generated 10 genetic clusters. Among the PvSHP1 markers, the most informative for gene pool assignment of the European P. vulgaris germplasm was PvSHP1-B. Results of AMOVA show that 89% of the molecular variability is shared within the 782 accessions, with 4% molecular variability among the different geographic origins along this western-to-eastern line of southern Europe (including Poland).

CONCLUSIONS

This study shows that the diversification line of the European P. vulgaris germplasm followed from the western areas of southern Europe (Portugal, Spain, Italy, Slovenia) to the more eastern areas of southern Europe. This progression defines three geographically separated subgroups, as the northern (Poland, Ukraine, Romania), southern (Albania, Bulgaria), and central (Bosnia and Herzegovina, Serbia, Hungary) areas of eastern Europe.

Evidence for Strong Kinship Influence on the Extent of Linkage Disequilibrium in Cultivated Common Beans

Phaseolus vulgaris is an important grain legume for human consumption. Recently, association mapping studies have been performed for the species aiming to identify loci underlying quantitative variation of traits. It is now imperative to know whether the linkage disequilibrium (LD) reflects the true association between a marker and causative loci. The aim of this study was to estimate and analyze LD on a diversity panel of common beans using ordinary r² and r2 extensions which correct bias due to population structure (rS²), kinship (rV²), and both (rVS²). A total of 10,362 single nucleotide polymorphisms (SNPs) were identified by genotyping by sequencing (GBS), and polymorphisms were found to be widely distributed along the 11 chromosomes. In terms of r2, high values of LD (over 0.8) were identified between SNPs located at opposite chromosomal ends. Estimates for rV² were lower than those for rS². Results for rV² and rVS² were similar, suggesting that kinship may also include information on population structure. Over genetic distance, LD decayed to 0.1 at a distance of 1 Mb for rVS². Inter-chromosomal LD was also evidenced. This study showed that LD estimates decay dramatically according to the population structure, and especially the degree of kinship. Importantly, the LD estimates reported herein may influence our ability to perform association mapping studies on P. vulgaris.

Conservation and genetic characterisation of common bean landraces from Cilento region (southern Italy): high differentiation in spite of low genetic diversity

Since its introduction from Central-South America to Italy almost 500 years ago, the common bean (Phaseolus vulgaris L.) was largely cultivated across the peninsula in hundreds of different landraces. However, globalisation and technological modernisation of agricultural practices in the last decades promoted the cultivation of few varieties at the expense of traditional and local agro-ecotypes, which have been confined to local markets or have completely disappeared. The aim of this study was to evaluate the genetic diversity and differentiation in 12 common bean landraces once largely cultivated in the Cilento region (Campania region, southern Italy), and now the object of a recovery program to save them from extinction. The analysis conducted using 13 nuclear microsatellite loci in 140 individuals revealed a high degree of homozygosity within each landrace and a strong genetic differentiation that was reflected in the success in assigning individuals to the source landrace. On the contrary, internal transcribed spacers 1 and 2, analysed in one individual per landrace, were highly similar among common bean landraces but allowed the identification of a cowpea variety (Vigna unguiculata Walp.), a crop largely cultivated in the Old World before the arrival of common bean from Americas. In conclusion, our study highlighted that conservation of landraces is important not only for the cultural and socio-economic value that they have for local communities, but also because the time and conditions in which they have been selected have led to that genetic distinctiveness that is at the basis of many potential agronomical applications and dietary benefits.

Linkage disequilibrium based association mapping of micronutrients in common bean (Phaseolus vulgaris L.): a collection of Jammu & Kashmir, India

Micronutrient deficiencies are of major concern in human health and plant metabolism. Iron (Fe), zinc (Zn), iodine (I), selenium (Se) are regarded as micronutrients having major impact on human health. More than 50% of populations mainly from developing countries are suffering from one or the other micronutrient malnutrition. Ensuring adequate supply of these micronutrients through diet consisting of staple foods, such as common bean (Phaseolus vulgaris L.) is must. Here, we evaluated common bean genotypes that were collected from various regions of Jammu and Kashmir, India for Fe, Zn and protein contents and used SSRs to identify the markers associated with these traits. We found significant variation among genotypes for Fe, Zn and protein contents. Genotype R2 was having 7.22 mg 100 g^-1 of Fe content, genotype K15 with 1.93 mg 100 g^-1 of Zn content and genotype KS6 with 31.6% of protein content. Diversity study was done using both cluster and structure based approach. Further, association mapping analysis using General Linear Method (GLM) approach was done to identify SSRs associated with accumulation of Fe, Zn and protein. 13 SSRs were identified that significantly (p < 0.05) showed association with Fe, Zn and protein contents in common bean. The markers associated with Fe were located on chromosome no. 2, 5, 6, 7, 9 and 10, markers associated with Zn were located on chromosome no. 1, 3, 5, 7 and 10 whereas only one marker located on chromosome no. 4 was found associated with protein content. These findings will provide potential opportunity to improve Fe and Zn concentrations in common bean, through molecular breeding.

Linkage and mapping of quantitative trait loci associated with angular leaf spot and powdery mildew resistance in common beans

Angular leaf spot (ALS) and powdery mildew (PWM) are two important fungi diseases causing significant yield losses in common beans. In this study, a new genetic linkage map was constructed using single sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs), in a segregating population derived from the AND 277 x SEA 5 cross, with 105 recombinant inbred lines. Phenotypic evaluations were performed in the greenhouse to identify quantitative trait loci (QTLs) associated with resistance by means of the composite interval mapping analysis. Four QTLs were identified for ALS resistance. The QTL ALS11^AS, linked on the SNP BAR 5054, mapped on chromosome Pv11, showed the greatest effect (R² = 26.5%) on ALS phenotypic variance. For PWM resistance, two QTLs were detected, PWM2^AS and PWM11^AS, on Pv2 and Pv11, explaining 7% and 66% of the phenotypic variation, respectively. Both QTLs on Pv11 were mapped on the same genomic region, suggesting that it is a pleiotropic region. The present study resulted in the identification of new markers closely linked to ALS and PWM QTLs, which can be used for marker-assisted selection, fine mapping and positional cloning.

Population Structure Analysis and Selection of Core Set among Common Bean Genotypes from Jammu and Kashmir, India

Understanding the genetic diversity of a crop is useful for its effective utilization in breeding programmes. For better understanding of the genetic variability in common bean, the first and foremost step is to study its genetic diversity. In the present investigation, 138 genotypes of common bean collected from various regions of Jammu and Kashmir, India, representing major common bean growing areas of this region, were evaluated using 23 SSRs. These SSRs were found highly polymorphic and possess high values for various parameters indicating their high discriminatory power. The average PIC value observed was 0.692, with 0.730 as average gene diversity value, and 0.267 as heterozygosity. Twenty-three SSRs produced a total of 251 alleles. The dendrogram generated with un-weighted neighbour joining cluster analysis grouped genotypes into three main clusters with various degrees of sub-clustering within the clusters. The model-based STRUCTURE analysis using 23 SSR markers identified a population with 3 sub-populations which corresponds to distance-based groupings with average F _ST value and expected heterozygosity of 0.1497 and 0.6696, respectively, within the sub-population, as such high level of genetic diversity was observed within the population. Further, Core Hunter II was used to identify a core set of 96 diverse genotypes. This core set of diverse 96 genotypes is a potential resource for association mapping studies and can be used by breeders as a material to make desirable genetic crosses to generate elite varieties for the fulfilling global market needs. These findings have further implications in common bean breeding as well as conservation programs.

Genome-Wide Association Studies of Anthracnose and Angular Leaf Spot Resistance in Common Bean (Phaseolus vulgaris L.)

The common bean (Phaseolus vulgaris L.) is the world’s most important legume for human consumption. Anthracnose (ANT; Colletotrichum lindemuthianum) and angular leaf spot (ALS; Pseudocercospora griseola) are complex diseases that cause major yield losses in common bean. Depending on the cultivar and environmental conditions, anthracnose and angular leaf spot infections can reduce crop yield drastically. This study aimed to estimate linkage disequilibrium levels and identify quantitative resistance loci (QRL) controlling resistance to both ANT and ALS diseases of 180 accessions of common bean using genome-wide association analysis. A randomized complete block design with four replicates was performed for the ANT and ALS experiments, with four plants per genotype in each replicate. Association mapping analyses were performed for ANT and ALS using a mixed linear model approach implemented in TASSEL. A total of 17 and 11 significant statistically associations involving SSRs were detected for ANT and ALS resistance loci, respectively. Using SNPs, 21 and 17 significant statistically associations were obtained for ANT and angular ALS, respectively, providing more associations with this marker. The SSR-IAC167 and PvM95 markers, both located on chromosome Pv03, and the SNP scaffold00021_89379, were associated with both diseases. The other markers were distributed across the entire common bean genome, with chromosomes Pv03 and Pv08 showing the greatest number of loci associated with ANT resistance. The chromosome Pv04 was the most saturated one, with six markers associated with ALS resistance. The telomeric region of this chromosome showed four markers located between approximately 2.5 Mb and 4.4 Mb. Our results demonstrate the great potential of genome-wide association studies to identify QRLs related to ANT and ALS in common bean. The results indicate a quantitative and complex inheritance pattern for both diseases in common bean. Our findings will contribute to more effective screening of elite germplasm to find resistance alleles for marker-assisted selection in breeding programs.

SNP Assay Development for Linkage Map Construction, Anchoring Whole-Genome Sequence, and Other Genetic and Genomic Applications in Common Bean

A total of 992,682 single-nucleotide polymorphisms (SNPs) was identified as ideal for Illumina Infinium II BeadChip design after sequencing a diverse set of 17 common bean (Phaseolus vulgaris L) varieties with the aid of next-generation sequencing technology. From these, two BeadChips each with >5000 SNPs were designed. The BARCBean6K_1 BeadChip was selected for the purpose of optimizing polymorphism among market classes and, when possible, SNPs were targeted to sequence scaffolds in the Phaseolus vulgaris 14× genome assembly with sequence lengths >10 kb. The BARCBean6K_2 BeadChip was designed with the objective of anchoring additional scaffolds and to facilitate orientation of large scaffolds. Analysis of 267 F2 plants from a cross of varieties Stampede × Red Hawk with the two BeadChips resulted in linkage maps with a total of 7040 markers including 7015 SNPs. With the linkage map, a total of 432.3 Mb of sequence from 2766 scaffolds was anchored to create the Phaseolus vulgaris v1.0 assembly, which accounted for approximately 89% of the 487 Mb of available sequence scaffolds of the Phaseolus vulgaris v0.9 assembly. A core set of 6000 SNPs (BARCBean6K_3 BeadChip) with high genotyping quality and polymorphism was selected based on the genotyping of 365 dry bean and 134 snap bean accessions with the BARCBean6K_1 and BARCBean6K_2 BeadChips. The BARCBean6K_3 BeadChip is a useful tool for genetics and genomics research and it is widely used by breeders and geneticists in the United States and abroad.

Unraveling the efficiency of RAPD and SSR markers in diversity analysis and population structure estimation in common bean

Increase in food production viz-a-viz quality of food is important to feed the growing human population to attain food as well as nutritional security. The availability of diverse germplasm of any crop is an important genetic resource to mine the genes that may assist in attaining food as well as nutritional security. Here we used 15 RAPD and 23 SSR markers to elucidate diversity among 51 common bean genotypes mostly landraces collected from the Himalayan region of Jammu and Kashmir, India. We observed that both the markers are highly polymorphic. The discriminatory power of these markers was determined using various parameters like; percent polymorphism, PIC, resolving power and marker index. 15 RAPDs produced 171 polymorphic bands, while 23 SSRs produced 268 polymorphic bands. SSRs showed a higher PIC value (0.300) compared to RAPDs (0.243). Further the resolving power of SSRs was 5.241 compared to 3.86 for RAPDs. However, RAPDs showed a higher marker index (2.69) compared to SSRs (1.279) that may be attributed to their higher multiplex ratio. The dendrograms generated with hierarchical UPGMA cluster analysis grouped genotypes into two main clusters with various degrees of sub clustering within the cluster. Here we observed that both the marker systems showed comparable accuracy in grouping genotypes of common bean according to their area of cultivation. The model based STRUCTURE analysis using 15 RAPD and 23 SSR markers identified a population with 3 sub-populations which corresponds to distance based groupings. High level of genetic diversity was observed within the population. These findings have further implications in common bean breeding as well as conservation programs.

Analysis of BAC-end sequences in common bean (Phaseolus vulgaris L.) towards the development and characterization of long motifs SSRs

The increasing volume of genomic data on the Phaseolus vulgaris species have contributed to its importance as a model genetic species and positively affected the investigation of other legumes of scientific and economic value. To expand and gain a more in-depth knowledge of the common bean genome, the ends of a number of bacterial artificial chromosome (BAC) were sequenced, annotated and the presence of repetitive sequences was determined. In total, 52,270 BESs (BAC-end sequences), equivalent to 32 Mbp (~6 %) of the genome, were processed. In total, 3,789 BES-SSRs were identified, with a distribution of one SSR (simple sequence repeat) per 8.36 kbp and 2,000 were suitable for the development of SSRs, of which 194 were evaluated in low-resolution screening. From 40 BES-SSRs based on long motifs SSRs (≥ trinucleotides) analyzed in high-resolution genotyping, 34 showed an equally good amplification for the Andean and for the Mesoamerican genepools, exhibiting an average gene diversity (H E) of 0.490 and 5.59 alleles/locus, of which six classified as Class I showed a H E ≥ 0.7. The PCoA and structure analysis allowed to discriminate the gene pools (K = 2, FST = 0.733). From the 52,270 BESs, 2 % corresponded to transcription factors and 3 % to transposable elements. Putative functions for 24,321 BESs were identified and for 19,363 were assigned functional categories (gene ontology). This study identified highly polymorphic BES-SSRs containing tri- to hexanucleotides motifs and bringing together relevant genetic characteristics useful for breeding programs. Additionally, the BESs were incorporated into the international genome-sequencing project for the common bean.

BAC-end microsatellites from intra and inter-genic regions of the common bean genome and their correlation with cytogenetic features

Highly polymorphic markers such as simple sequence repeats (SSRs) or microsatellites are very useful for genetic mapping. In this study novel SSRs were identified in BAC-end sequences (BES) from non-contigged, non-overlapping bacterial artificial clones (BACs) in common bean (Phaseolus vulgaris L.). These so called "singleton" BACs were from the G19833 Andean gene pool physical map and the new BES-SSR markers were used for the saturation of the inter-gene pool, DOR364×G19833 genetic map. A total of 899 SSR loci were found among the singleton BES, but only 346 loci corresponded to the single di- or tri-nucleotide motifs that were likely to be polymorphic (ATT or AG motifs, principally) and useful for primer design and individual marker mapping. When these novel SSR markers were evaluated in the DOR364×G19833 population parents, 136 markers revealed polymorphism and 106 were mapped. Genetic mapping resulted in a map length of 2291 cM with an average distance between markers of 5.2 cM. The new genetic map was compared to the most recent cytogenetic analysis of common bean chromosomes. We found that the new singleton BES-SSR were helpful in filling peri-centromeric spaces on the cytogenetic map. Short genetic distances between some new singleton-derived BES-SSR markers was common showing suppressed recombination in these regions compared to other parts of the genome. The correlation of singleton-derived SSR marker distribution with other cytogenetic features of the bean genome is discussed.

Developing a common bean core collection suitable for association mapping studies

Because of the continuous introduction of germplasm from abroad, some collections have a high number of accessions, making it difficult to explore the genetic variability present in a germplasm bank for conservation and breeding purposes. Therefore, the aim of this study was to quantify and analyze the structure of genetic variability among 500 common bean accessions to construct a core collection. A total of 58 SSRs were used for this purpose. The polymorphism information content (PIC) in the 180 common bean accessions selected to compose the core collection ranged from 0.17 to 0.86, and the discriminatory power (DP) ranged from 0.21 to 0.90. The 500 accessions were clustered into 15 distinct groups and the 180 accessions into four distinct groups in the Structure analysis. According to analysis of molecular variance, the most divergent accessions comprised 97.2% of the observed genetic variability present within the base collection, confirming the efficiency of the selection criterion. The 180 selected accessions will be used for association mapping in future studies and could be potentially used by breeders to direct new crosses and generate elite cultivars that meet current and future global market needs.

Increasing the density of markers around a major QTL controlling resistance to angular leaf spot in common bean

Angular leaf spot (ALS) causes major yield losses in the common bean (Phaseolus vulgaris L.), an important protein source in the human diet. This study describes the saturation around a major quantitative trait locus (QTL) region, ALS10.1, controlling resistance to ALS located on linkage group Pv10 and explores the genomic context of this region using available data from the P. vulgaris genome sequence. DArT-derived markers (STS-DArT) selected by bulk segregant analysis and SCAR and SSR markers were used to increase the resolution of the QTL, reducing the confidence interval of ALS10.1 from 13.4 to 3.0 cM. The position of the SSR ATA220 coincided with the maximum LOD score of the QTL. Moreover, a new QTL (ALS10.2(UC)) was identified at the end of the same linkage group. Sequence analysis using the P. vulgaris genome located ten SSRs and seven STS-DArT on chromosome 10 (Pv10). Coincident linkage and genome positions of five markers enabled the definition of a core region for ALS10.1 spanning 5.3 Mb. These markers are linked to putative genes related to disease resistance such as glycosyl transferase, ankyrin repeat-containing, phospholipase, and squamosa-promoter binding protein. Synteny analysis between ALS10.1 markers and the genome of soybean suggested a dynamic evolution of this locus in the common bean. The present study resulted in the identification of new candidate genes and markers closely linked to a major ALS disease resistance QTL, which can be used in marker-assisted selection, fine mapping and positional QTL cloning.

Genetic mapping of two genes conferring resistance to powdery mildew in common bean (Phaseolus vulgaris L.)

Powdery mildew (PM) is a serious disease in many legume species, including the common bean (Phaseolus vulgaris L.). This study investigated the genetic control behind resistance reaction to PM in the bean genotype, Cornell 49242. The results revealed evidence supporting a qualitative mode of inheritance for resistance and the involvement of two independent genes in the resistance reaction. The location of these resistance genes was investigated in a linkage genetic map developed for the XC RIL population. Contingency tests revealed significant associations for 28 loci out of a total of 329 mapped loci. Fifteen were isolated or formed groups with less than two loci. The thirteen remaining loci were located at three regions in linkage groups Pv04, Pv09, and Pv11. The involvement of Pv09 was discarded due to the observed segregation in the subpopulation obtained from the Xana genotype for the loci located in this region. In contrast, the two subpopulations obtained from the Xana genotype for the BM161 locus, linked to the Co-3/9 anthracnose resistance gene (Pv04), and from the Xana genotype for the SCAReoli locus, linked to the Co-2 anthracnose resistance gene (Pv11), exhibited monogenic segregations, suggesting that both regions were involved in the genetic control of resistance. A genetic dissection was carried out to verify the involvement of both regions in the reaction to PM. Two resistant recombinant lines were selected, according to their genotypes, for the block of loci included in the Co-2 and Co-3/9 regions, and they were crossed with the susceptible parent, Xana. Linkage analysis in the respective F2 populations supported the hypothesis that a dominant gene (Pm1) was located in the linkage group Pv11 and another gene (Pm2) was located in the linkage group Pv04. This is the first report showing the localization of resistance genes against powdery mildew in Phaseolus vulgaris and the results offer the opportunity to increase the efficiency of breeding programs by means of marker-assisted selection.

Isolation and characterization of nucleotide-binding site resistance gene homologues in common bean (Phaseolus vulgaris)

Common bean production is constrained by many fungal, viral, and bacterial pathogens. Thus, the identification of resistance (R) genes is an important focal point of common bean research. The main goal of our study was to identify resistance gene homologues (RGH) in the crop, using degenerate primers designed from conserved sequences in the nucleotide-binding site (NBS) domains of R-genes from the model legume Medicago truncatula. Total DNA of the Andean common bean genotype G19833 was used for amplification of over 500 primer combinations. Sequencing of amplicons showed that 403 cloned fragments had uninterrupted open reading frames and were considered representative of functional RGH genes. The sequences were grouped at two levels of nucleotide identity (90 and 80%) and representative sequences of each group were used for phylogenetic analyses. The RGH sequence diversity of common bean was divided into TIR and non-TIR families, each with different clusters. The TIR sequences grouped into 14 clades while non-TIR sequences grouped into seven clades. Pairwise comparisons showed purifying selection, although some sequences may have been the result of diversifying selection. Knowledge about RGH genes in common bean can allow the design of molecular markers for pyramiding of resistance genes against various pathogens.

First use of microsatellite markers in a large collection of cultivated and wild accessions of tepary bean (Phaseolus acutifolius A. Gray)

Tepary bean (Phaseolus acutifolius A. Gray) is a dry-land crop species that originated in the deserts of Mexico and the south-western United States and therefore is proposed as a source of drought and salt tolerance for related species and for production in marginal rainfall areas. Few genetic tools have been developed or tested for tepary bean but microsatellites from common bean are an obvious choice for diversity analysis in the crop. The first goal of this study was to validate a set of gene-derived and non-gene simple sequence repeat or microsatellite markers from common bean in tepary bean cultivars and wild relative accessions. The second and more extensive objective of this study was to evaluate the genetic diversity and population structure of the tepary bean accessions to determine if leaf-morphology variants are valid as separate sub-groups of wild tepary beans; if P. parvifolius exist as a separate variants or species; and if cultivated tepary beans originated from one domestication event or several events. Our analysis of 140 tepary bean genotypes showed that a single domestication was likely as the cultivars were most closely related to accessions from Sinaloa and northern Mexico and that diversity was much higher in the wild genotypes compared to the cultivated ones. Other results were that P. parvifolius was classified as a separate species by population structure analysis while the variants P. acutifolius var. acutifolius and var. tenuifolius were admixed and inter-crossed. P. latifolius is not a valid species or variant of P. acutifolius but represents a group of cultivars within tepary bean. This is the first analysis of microsatellite diversity in tepary beans and has implications for breeding and conservation of this crop and its wild relatives.

Dissecting Phaseolus vulgaris innate immune system against Colletotrichum lindemuthianum infection

Background

The genus Colletotrichum is one of the most economically important plant pathogens, causing anthracnose on a wide range of crops including common beans (Phaseolus vulgaris L.). Crop yield can be dramatically decreased depending on the plant cultivar used and the environmental conditions. This study aimed to identify potential genetic components of the bean immune system to provide environmentally friendly control measures against this fungus.

Methodology and Principal Findings

As the common bean is not amenable to reverse genetics to explore functionality and its genome is not fully curated, we used putative Arabidopsis orthologs of bean expressed sequence tag (EST) to perform bioinformatic analysis and experimental validation of gene expression to identify common bean genes regulated during the incompatible interaction with C. lindemuthianum. Similar to model pathosystems, Gene Ontology (GO) analysis indicated that hormone biosynthesis and signaling in common beans seem to be modulated by fungus infection. For instance, cytokinin and ethylene responses were up-regulated and jasmonic acid, gibberellin, and abscisic acid responses were down-regulated, indicating that these hormones may play a central role in this pathosystem. Importantly, we have identified putative bean gene orthologs of Arabidopsis genes involved in the plant immune system. Based on experimental validation of gene expression, we propose that hypersensitive reaction as part of effector-triggered immunity may operate, at least in part, by down-regulating genes, such as FLS2-like and MKK5-like, putative orthologs of the Arabidopsis genes involved in pathogen perception and downstream signaling.

Conclusions/Significance

We have identified specific bean genes and uncovered metabolic processes and pathways that may be involved in the immune response against pathogens. Our transcriptome database is a rich resource for mining novel defense-related genes, which enabled us to develop a model of the molecular components of the bean innate immune system regulated upon pathogen attack.

Marker-based linkage map of Andean common bean (Phaseolus vulgaris L.) and mapping of QTLs underlying popping ability traits

BACKGROUND

Nuña bean is a type of ancient common bean (Phaseolus vulgaris L.) native to the Andean region of South America, whose seeds possess the unusual property of popping. The nutritional features of popped seeds make them a healthy low fat and high protein snack. However, flowering of nuña bean only takes place under short-day photoperiod conditions, which means a difficulty to extend production to areas where such conditions do not prevail. Therefore, breeding programs of adaptation traits will facilitate the diversification of the bean crops and the development of new varieties with enhanced healthy properties. Although the popping trait has been profusely studied in maize (popcorn), little is known about the biology and genetic basis of the popping ability in common bean. To obtain insights into the genetics of popping ability related traits of nuña bean, a comprehensive quantitative trait loci (QTL) analysis was performed to detect single-locus and epistatic QTLs responsible for the phenotypic variance observed in these traits.

RESULTS

A mapping population of 185 recombinant inbred lines (RILs) derived from a cross between two Andean common bean genotypes was evaluated for three popping related traits, popping dimension index (PDI), expansion coefficient (EC), and percentage of unpopped seeds (PUS), in five different environmental conditions. The genetic map constructed included 193 loci across 12 linkage groups (LGs), covering a genetic distance of 822.1 cM, with an average of 4.3 cM per marker. Individual and multi-environment QTL analyses detected a total of nineteen single-locus QTLs, highlighting among them the co-localized QTLs for the three popping ability traits placed on LGs 3, 5, 6, and 7, which together explained 24.9, 14.5, and 25.3% of the phenotypic variance for PDI, EC, and PUS, respectively. Interestingly, epistatic interactions among QTLs have been detected, which could have a key role in the genetic control of popping.

CONCLUSIONS

The QTLs here reported constitute useful tools for marker assisted selection breeding programs aimed at improving nuña bean cultivars, as well as for extending our knowledge of the genetic determinants and genotype x environment interaction involved in the popping ability traits of this bean crop.

New gene-derived simple sequence repeat markers for common bean (Phaseolus vulgaris L.)

Common bean is an important and diverse crop legume with several wild relatives that are all part of the Phaseoleae tribe of tropical crop legumes. Sequence databases have been a good source of sequences to mine for simple sequence repeats (SSRs). The objective of this research was to evaluate 14 sequence collections from common bean for SSRs and to evaluate the diversity of the polymorphic microsatellites derived from these collections. SSRs were found in 10 of the GenBank sequence collections with an average of 11.3% of sequences containing microsatellite motifs. The most common motifs were based on tri- and dinucleotides. In a marker development programme, primers were designed for 125 microsatellites which were tested on a panel of 18 common bean genotypes. The markers were named as part of the bean microsatellite-database (BMd) series, and the average polymorphism information content was 0.404 for polymorphic markers and predicted well the genepool structure of common beans and the status of the wild and cultivated accessions that were included in the study. Therefore, the BMd series of microsatellites is useful for multiple studies of genetic relatedness and as anchor markers in future mapping of wide crosses in the species.

A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers

BACKGROUND

The development of sugarcane as a sustainable crop has unlimited applications. The crop is one of the most economically viable for renewable energy production, and CO2 balance. Linkage maps are valuable tools for understanding genetic and genomic organization, particularly in sugarcane due to its complex polyploid genome of multispecific origins. The overall objective of our study was to construct a novel sugarcane linkage map, compiling AFLP and EST-SSR markers, and to generate data on the distribution of markers anchored to sequences of scIvana_1, a complete sugarcane transposable element, and member of the Copia superfamily.

RESULTS

The mapping population parents ('IAC66-6' and 'TUC71-7') contributed equally to polymorphisms, independent of marker type, and generated markers that were distributed into nearly the same number of co-segregation groups (or CGs). Bi-parentally inherited alleles provided the integration of 19 CGs. The marker number per CG ranged from two to 39. The total map length was 4,843.19 cM, with a marker density of 8.87 cM. Markers were assembled into 92 CGs that ranged in length from 1.14 to 404.72 cM, with an estimated average length of 52.64 cM. The greatest distance between two adjacent markers was 48.25 cM. The scIvana_1-based markers (56) were positioned on 21 CGs, but were not regularly distributed. Interestingly, the distance between adjacent scIvana_1-based markers was less than 5 cM, and was observed on five CGs, suggesting a clustered organization.

CONCLUSIONS

Results indicated the use of a NBS-profiling technique was efficient to develop retrotransposon-based markers in sugarcane. The simultaneous maximum-likelihood estimates of linkage and linkage phase based strategies confirmed the suitability of its approach to estimate linkage, and construct the linkage map. Interestingly, using our genetic data it was possible to calculate the number of retrotransposon scIvana_1 (~60) copies in the sugarcane genome, confirming previously reported molecular results. In addition, this research possibly will have indirect implications in crop economics e.g., productivity enhancement via QTL studies, as the mapping population parents differ in response to an important fungal disease.

Saturation of an intra-gene pool linkage map: towards a unified consensus linkage map for fine mapping and synteny analysis in common bean

Map-based cloning and fine mapping to find genes of interest and marker assisted selection (MAS) requires good genetic maps with reproducible markers. In this study, we saturated the linkage map of the intra-gene pool population of common bean DOR364 × BAT477 (DB) by evaluating 2,706 molecular markers including SSR, SNP, and gene-based markers. On average the polymorphism rate was 7.7% due to the narrow genetic base between the parents. The DB linkage map consisted of 291 markers with a total map length of 1,788 cM. A consensus map was built using the core mapping populations derived from inter-gene pool crosses: DOR364 × G19833 (DG) and BAT93 × JALO EEP558 (BJ). The consensus map consisted of a total of 1,010 markers mapped, with a total map length of 2,041 cM across 11 linkage groups. On average, each linkage group on the consensus map contained 91 markers of which 83% were single copy markers. Finally, a synteny analysis was carried out using our highly saturated consensus maps compared with the soybean pseudo-chromosome assembly. A total of 772 marker sequences were compared with the soybean genome. A total of 44 syntenic blocks were identified. The linkage group Pv6 presented the most diverse pattern of synteny with seven syntenic blocks, and Pv9 showed the most consistent relations with soybean with just two syntenic blocks. Additionally, a co-linear analysis using common bean transcript map information against soybean coding sequences (CDS) revealed the relationship with 787 soybean genes. The common bean consensus map has allowed us to map a larger number of markers, to obtain a more complete coverage of the common bean genome. Our results, combined with synteny relationships provide tools to increase marker density in selected genomic regions to identify closely linked polymorphic markers for indirect selection, fine mapping or for positional cloning.

The characterization of a new set of EST-derived simple sequence repeat (SSR) markers as a resource for the genetic analysis of Phaseolus vulgaris

Background

Over recent years, a growing effort has been made to develop microsatellite markers for the genomic analysis of the common bean (Phaseolus vulgaris) to broaden the knowledge of the molecular genetic basis of this species. The availability of large sets of expressed sequence tags (ESTs) in public databases has given rise to an expedient approach for the identification of SSRs (Simple Sequence Repeats), specifically EST-derived SSRs. In the present work, a battery of new microsatellite markers was obtained from a search of the Phaseolus vulgaris EST database. The diversity, degree of transferability and polymorphism of these markers were tested.

Results

From 9,583 valid ESTs, 4,764 had microsatellite motifs, from which 377 were used to design primers, and 302 (80.11%) showed good amplification quality. To analyze transferability, a group of 167 SSRs were tested, and the results showed that they were 82% transferable across at least one species. The highest amplification rates were observed between the species from the Phaseolus (63.7%), Vigna (25.9%), Glycine (19.8%), Medicago (10.2%), Dipterix (6%) and Arachis (1.8%) genera. The average PIC (Polymorphism Information Content) varied from 0.53 for genomic SSRs to 0.47 for EST-SSRs, and the average number of alleles per locus was 4 and 3, respectively. Among the 315 newly tested SSRs in the BJ (BAT93 X Jalo EEP558) population, 24% (76) were polymorphic. The integration of these segregant loci into a framework map composed of 123 previously obtained SSR markers yielded a total of 199 segregant loci, of which 182 (91.5%) were mapped to 14 linkage groups, resulting in a map length of 1,157 cM.

Conclusions

A total of 302 newly developed EST-SSR markers, showing good amplification quality, are available for the genetic analysis of Phaseolus vulgaris. These markers showed satisfactory rates of transferability, especially between species that have great economic and genomic values. Their diversity was comparable to genomic SSRs, and they were incorporated in the common bean reference genetic map, which constitutes an important contribution to and advance in Phaseolus vulgaris genomic research.

Gene-based SSR markers for common bean (Phaseolus vulgaris L.) derived from root and leaf tissue ESTs: an integration of the BMc series

BACKGROUND

Sequencing of cDNA libraries for the development of expressed sequence tags (ESTs) as well as for the discovery of simple sequence repeats (SSRs) has been a common method of developing microsatellites or SSR-based markers. In this research, our objective was to further sequence and develop common bean microsatellites from leaf and root cDNA libraries derived from the Andean gene pool accession G19833 and the Mesoamerican gene pool accession DOR364, mapping parents of a commonly used reference map. The root libraries were made from high and low phosphorus treated plants.

RESULTS

A total of 3,123 EST sequences from leaf and root cDNA libraries were screened and used for direct simple sequence repeat discovery. From these EST sequences we found 184 microsatellites; the majority containing tri-nucleotide motifs, many of which were GC rich (ACC, AGC and AGG in particular). Di-nucleotide motif microsatellites were about half as common as the tri-nucleotide motif microsatellites but most of these were AGn microsatellites with a moderate number of ATn microsatellites in root ESTs followed by few ACn and no GCn microsatellites. Out of the 184 new SSR loci, 120 new microsatellite markers were developed in the BMc (Bean Microsatellites from cDNAs) series and these were evaluated for their capacity to distinguish bean diversity in a germplasm panel of 18 genotypes. We developed a database with images of the microsatellites and their polymorphism information content (PIC), which averaged 0.310 for polymorphic markers.

CONCLUSIONS

The present study produced information about microsatellite frequency in root and leaf tissues of two important genotypes for common bean genomics: namely G19833, the Andean genotype selected for whole genome shotgun sequencing from race Peru, and DOR364 a race Mesoamerica subgroup 2 genotype that is a small-red seeded, released variety in Central America. Both race Peru and Mesoamerica subgroup 2 (small red beans) have been understudied in comparison to race Nueva Granada and Mesoamerica subgroup 1 (black beans) both with regards to gene expression and as sources of markers. However, we found few differences between SSR type and frequency between the G19833 leaf and DOR364 root tissue-derived ESTs. Overall, our work adds to the analysis of microsatellite frequency evaluation for common bean and provides a new set of 120 BMc markers which combined with the 248 previously developed BMc markers brings the total in this series to 368 markers. Once we include BMd markers, which are derived from GenBank sequences, the current total of gene-based markers from our laboratory surpasses 500 markers. These markers are basic for studies of the transcriptome of common bean and can form anchor points for genetic mapping studies in the future.

Genetic analysis and molecular mapping of quantitative trait loci in common bean against Pythium ultimum

Pythium ultimum is a soil pathogen that can cause seed decay and damage to roots in common bean. In this study, the response of a set of 40 common bean genotypes to P. ultimum and inheritance of the resistance in the 92 F₇ recombinant inbred lines (RIL) developed from a cross between Xana and Cornell 49242 was investigated by using emergence rate and seedling vigor. Emergence of the 40 genotypes showed a significant association between white seed coat and response to this pathogen. Among these, 11 common bean genotypes, all with colored seeds, exhibited a high percentage of emergence and seedling vigor not significantly different (P > 0.05) to noninoculated plants. Response of the RIL population revealed both qualitative and quantitative modes of inheritance. A major gene (Py-1) controlling the emergence rate was mapped in the region of the gene P, a basic color gene involved in control of seed coat color, located on LG 7. Using the RIL subpopulation with colored seeds, a significant quantitative trait loci (QTL) associated with the emergence rate (ER3(XC)) and another with seedling vigor (SV6(XC)) were identified on the LG 3 and 6, respectively. QTL SV6(XC) was mapped in the region of the gene V, another gene involved the genetic control of color. QTLs associated with seed traits were mapped in the same relative position as regions involved in responses to P. ultimum suggesting the possible implication of avoidance mechanisms in the response to this pathogen.