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BACKGROUND: Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar. RESULTS: Integration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion. CONCLUSION: Collectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.

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Seed weight and size are important yield components. Thus, selecting for large seeds has been a key objective in crop domestication and breeding. In common bean, seed shape is also important since it influences industrial processing and plays a vital role in determining the choices of consumers and farmers. In this study, we performed genome-wide association studies on a core collection of common bean accessions to dissect the genetic architecture and identify genomic regions associated with seed morphological traits related to weight, size, and shape. Phenotypic data were collected by high-throughput image-based approaches, and utilized to test associations with 10,362 single-nucleotide polymorphism markers using multilocus mixed models. We searched within genome-associated regions for candidate genes putatively involved in seed phenotypic variation. The collection exhibited high variability for the entire set of seed traits, and the Andean gene pool was found to produce larger, heavier seeds than the Mesoamerican gene pool. Strong pairwise correlations were verified for most seed traits. Genome-wide association studies identified marker-trait associations accounting for a considerable amount of phenotypic variation in length, width, projected area, perimeter, and circularity in 4 distinct genomic regions. Promising candidate genes were identified, e.g. those encoding an AT-hook motif nuclear-localized protein 8, type 2C protein phosphatases, and a protein Mei2-like 4 isoform, known to be associated with seed size and weight regulation. Moreover, the genes that were pinpointed are also good candidates for functional analysis to validate their influence on seed shape and size in common bean and other related crops.

Assuntos

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Root-knot nematodes (RKNs), particularly Meloidogyne incognita, are among the most damaging and prevalent agricultural pathogens due to their ability to infect roots of almost all crops. The best strategy for their control is through the use of resistant cultivars. However, laborious phenotyping procedures make it difficult to assess nematode resistance in breeding programs. For common bean, this task is especially challenging because little has been done to discover resistance genes or markers to assist selection. We performed genome-wide association studies and quantitative trait loci mapping to explore the genetic architecture and genomic regions underlying the resistance to M. incognita and to identify candidate resistance genes. Phenotypic data were collected by a high-throughput assay, and the number of egg masses and the root-galling index were evaluated. Complex genetic architecture and independent genomic regions were associated with each trait. Single nucleotide polymorphisms on chromosomes Pv06, Pv07, Pv08, and Pv11 were associated with the number of egg masses, and SNPs on Pv01, Pv02, Pv05, and Pv10 were associated with root-galling. A total of 216 candidate genes were identified, including 14 resistance gene analogs and five differentially expressed in a previous RNA sequencing analysis. Histochemical analysis indicated that reactive oxygen species might play a role in the resistance response. Our findings open new perspectives to improve selection efficiency for RKN resistance, and the candidate genes are valuable targets for functional investigation and gene editing approaches.

Assuntos

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Common bean is a worldwide important crop. The development of varieties with durable resistance to diseases is a major challenge in common bean breeding. The present study aimed at evaluating the phenotypic and molecular selection of anthracnose resistance in a population obtained by assisted backcrossing from IAC Formoso (resistant, donor parent) × BRS Pérola (susceptible, recurrent parent). Nine microsatellites (SSRs) and one Sequence Tagged Sites (STS) markers previously linked to ANT resistance were used to genotype this progeny, and the results showed that the selection of the genotypes closest to the donor parent in the BC1F1 population decreased the number of backcrossing cycles necessary to obtain advanced isogenic lines, potentiating the use of this tool for early selection of resistant cultivars. A total of 31 % of the BC1F1 progeny was selected and backcrossed again. The progeny derived from the second backcross (BC2F3) was selected for the Carioca grain ideotype, and 42 % of the genotypes showed high resistance to anthracnose under controlled conditions of infection for races 65 and 81. Superior resistant plants were selected and evaluated under natural conditions of infection to fusarium wilt and angular leaf spot, allowing the selection of two inbred lines with higher resistance to anthracnose, fusarium wilt, angular leaf spot and postharvest quality traits such as yield, 100 seed weight, L value at seed harvest grain darkening and cooking time. The approach outlined in this paper proved to be effective to simultaneously select for disease resistance without losing technological quality aspects of the bean.

Assuntos

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ABSTRACT: Common bean is a worldwide important crop. The development of varieties with durable resistance to diseases is a major challenge in common bean breeding. The present study aimed at evaluating the phenotypic and molecular selection of anthracnose resistance in a population obtained by assisted backcrossing from IAC Formoso (resistant, donor parent) × BRS Pérola (susceptible, recurrent parent). Nine microsatellites (SSRs) and one Sequence Tagged Sites (STS) markers previously linked to ANT resistance were used to genotype this progeny, and the results showed that the selection of the genotypes closest to the donor parent in the BC1F1 population decreased the number of backcrossing cycles necessary to obtain advanced isogenic lines, potentiating the use of this tool for early selection of resistant cultivars. A total of 31 % of the BC1F1 progeny was selected and backcrossed again. The progeny derived from the second backcross (BC2F3) was selected for the Carioca grain ideotype, and 42 % of the genotypes showed high resistance to anthracnose under controlled conditions of infection for races 65 and 81. Superior resistant plants were selected and evaluated under natural conditions of infection to fusarium wilt and angular leaf spot, allowing the selection of two inbred lines with higher resistance to anthracnose, fusarium wilt, angular leaf spot and postharvest quality traits such as yield, 100 seed weight, L value at seed harvest grain darkening and cooking time. The approach outlined in this paper proved to be effective to simultaneously select for disease resistance without losing technological quality aspects of the bean.

RESUMO

Common bean is a worldwide important crop. The development of varieties with durable resistance to diseases is a major challenge in common bean breeding. The present study aimed at evaluating the phenotypic and molecular selection of anthracnose resistance in a population obtained by assisted backcrossing from IAC Formoso (resistant, donor parent) × BRS Pérola (susceptible, recurrent parent). Nine microsatellites (SSRs) and one Sequence Tagged Sites (STS) markers previously linked to ANT resistance were used to genotype this progeny, and the results showed that the selection of the genotypes closest to the donor parent in the BC1F1 population decreased the number of backcrossing cycles necessary to obtain advanced isogenic lines, potentiating the use of this tool for early selection of resistant cultivars. A total of 31 % of the BC1F1 progeny was selected and backcrossed again. The progeny derived from the second backcross (BC2F3) was selected for the Carioca grain ideotype, and 42 % of the genotypes showed high resistance to anthracnose under controlled conditions of infection for races 65 and 81. Superior resistant plants were selected and evaluated under natural conditions of infection to fusarium wilt and angular leaf spot, allowing the selection of two inbred lines with higher resistance to anthracnose, fusarium wilt, angular leaf spot and postharvest quality traits such as yield, 100 seed weight, L value at seed harvest grain darkening and cooking time. The approach outlined in this paper proved to be effective to simultaneously select for disease resistance without losing technological quality aspects of the bean.

Assuntos

RESUMO

Water deficit can alter the morphological, agronomic, physiological, and technological traits of the common bean plant, affecting bean grain yield. In addition to yield aspects, the grain post-harvest quality is a decisive factor for the adoption of a new cultivar. Thus, this study evaluated the effect of water deficit on the physiological, morphoagronomic, and technological traits of common bean. The experiment was carried out at in a greenhouse in a randomized block design with a 30 × 2 factorial arrangement, consisting of 30 carioca common bean genotypes and two water regimes (with and without water stress), with three replications. The water deficit affected most morphological, agronomic, and physiological traits; however, it was not significant on the darkening of the seed coat. Cultivars IAC 1849 Polaco, ANFc 5, ANFc 9, BRSMG Madrepérola, IAC Carioca Aruã, TAA Dama, and Branquinho exhibited high yield potential under water stress treatment as well as slow seed coat darkening during nine months of storage. The selection of bean genotypes with slow seed coat darkening could be performed at 30 days of storage.

Assuntos

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Brazil is among the largest producers and consumers of common bean (Phaseolus vulgaris L.) and can be considered a secondary center of diversity for the species. The aim of this study was to estimate the genetic diversity, population structure, and relationships among 288 common bean accessions in an American Diversity Panel (ADP) genotyped with 4,042 high-quality single nucleotide polymorphisms (SNPs). The results showed inter-gene pool hybridization (hybrids) between the two main gene pools (i.e., Mesoamerican and Andean), based on principal component analysis (PCA), discriminant analysis of principal components (DAPC), and STRUCTURE analysis. The genetic diversity parameters showed that the Mesoamerican group has higher values of diversity and allelic richness in comparison with the Andean group. Considering the optimal clusters (K), clustering was performed according to the type of grain (i.e., market group), the institution of origin, the period of release, and agronomic traits. A new subset was selected and named the Mesoamerican Diversity Panel (MDP), with 205 Mesoamerican accessions. Analysis of molecular variance (AMOVA) showed low genetic variance between the two panels (i.e., ADP and MDP) with the highest percentage of the limited variance among accessions in each group. The ADP showed occurrence of high genetic differentiation between populations (i.e., Mesoamerican and Andean) and introgression between gene pools in hybrids based on a set of diagnostic SNPs. The MDP showed better linkage disequilibrium (LD) decay. The availability of genetic variation from inter-gene pool hybridizations presents a potential opportunity for breeders towards the development of superior common bean cultivars.

Assuntos

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BACKGROUND: Common bean (Phaseolus vulgaris L.) is a legume whose grain can be stored for months, a common practice among Brazilian growers. Over time, seed coats become darker and harder to cook, traits that are undesirable to consumers, who associate darker-colored beans with greater age. Like commercial pinto and cranberry bean varieties, carioca beans that have darker seeds at harvest time and after storage are subject to decreased market values. RESULTS: The goal of our study was to identify the genetic control associated with lightness of seed coat color at harvest (HL) and with tolerance to post-harvest seed coat darkening (PHD) by a genome-wide association study. For that purpose, a carioca diversity panel previously validated for association mapping studies was used with 138 genotypes and 1,516 high-quality SNPs. The panel was evaluated in two environments using a colorimeter and the CIELAB scale. Shelf storage for 30 days had the most expressive results and the L* (luminosity) parameter led to the greatest discrimination of genotypes. Three QTL were identified for HL, two on chromosome Pv04 and one on Pv10. Regarding PHD, results showed that genetic control differs for L* after 30 days and for the ΔL* (final L*-initial L*); only ΔL* was able to properly express the PHD trait. Four phenotypic classes were proposed, and five QTL were identified through six significant SNPs. CONCLUSIONS: Lightness of seed coat color at harvest showed an oligogenic inheritance corroborated by moderate broad-sense heritability and high genotypic correlation among the experiments. Only three QTL were significant for this trait - two were mapped on Pv04 and one on Pv10. Considering the ΔL, six QTL were mapped on four different chromosomes for PHD. The same HL QTL at the beginning of Pv10 was also associated with ΔL* and could be used as a tool in marker-assisted selection. Several candidate genes were identified and may be useful to accelerate the genetic breeding process.

Assuntos

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Fusarium wilt (Fusarium oxysporum f. sp. phaseoli, Fop) is one of the main fungal soil diseases in common bean. The aim of the present study was to identify genomic regions associated with Fop resistance through genome-wide association studies (GWAS) in a Mesoamerican Diversity Panel (MDP) and to identify potential common bean sources of Fop's resistance. The MDP was genotyped with BARCBean6K_3BeadChip and evaluated for Fop resistance with two different monosporic strains using the root-dip method. Disease severity rating (DSR) and the area under the disease progress curve (AUDPC), at 21 days after inoculation (DAI), were used for GWAS performed with FarmCPU model. The p-value of each SNP was determined by resampling method and Bonferroni test. For UFV01 strain, two significant single nucleotide polymorphisms (SNPs) were mapped on the Pv05 and Pv11 for AUDPC, and the same SNP (ss715648096) on Pv11 was associated with AUDPC and DSR. Another SNP, mapped on Pv03, showed significance for DSR. Regarding IAC18001 strain, significant SNPs on Pv03, Pv04, Pv05, Pv07 and on Pv01, Pv05, and Pv10 were observed. Putative candidate genes related to nucleotide-binding sites and carboxy-terminal leucine-rich repeats were identified. The markers may be important future tools for genomic selection to Fop disease resistance in beans.

Assuntos