Common bean reaction to angular leaf spot comprises transcriptional modulation of genes in the ALS10.1 QTL

Meta-QTL Analysis for Yield Components in Common Bean (Phaseolus vulgaris L.)

Common bean is one of the most important legumes produced and consumed worldwide because it is a highly valuable food for the human diet. However, its production is mainly carried out by small farmers, who obtain average grain yields below the potential yield of the species. In this sense, numerous mapping studies have been conducted to identify quantitative trait loci (QTL) associated with yield components in common bean. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies. Consequently, the objective of this study was to perform a MQTL analysis to identify the most reliable and stable genomic regions associated with yield-related traits of common bean. A total of 667 QTL associated with yield-related traits reported in 21 different studies were collected. A total of 42 MQTL associated with yield-related traits were identified, in which the average confidence interval (CI) of the MQTL was 3.41 times lower than the CIs of the original QTL. Most of the MQTL (28) identified in this study contain QTL associated with yield and phenological traits; therefore, these MQTL can be useful in common bean breeding programs. Finally, a total of 18 candidate genes were identified and associated with grain yield within these MQTL, with functions related to ubiquitin ligase complex, response to auxin, and translation elongation factor activity.

Characterization of fungal pathogens and germplasm screening for disease resistance in the main production area of the common bean in Argentina

The common bean (Phaseolus vulgaris L.) is the most important grain legume in the human diet, mainly in Africa and Latin America. Argentina is one of the five major producers of the common bean in the world, and the main cultivation areas are concentrated in the northwestern provinces of this country. Crop production of the common bean is often affected by biotic factors like some endemic fungal diseases, which exert a major economic impact on the region. The most important fungal diseases affecting the common bean in Argentina are white mold caused by Sclerotinia sclerotiorum, angular leaf spot caused by Pseudocercospora griseola, web blight and root rot caused by Rhizoctonia solani, which can cause production losses of up to 100% in the region. At the present, the most effective strategy for controlling these diseases is the use of genetic resistance. In this sense, population study and characterization of fungal pathogens are essential for developing cultivars with durable resistance. In this review we report diversity studies carried out on these three fungal pathogens affecting the common bean in northwestern Argentina, analyzing more than 200 isolates by means of molecular, morphological and pathogenic approaches. Also, the screening of physiological resistance in several common bean commercial lines and wild native germplasm is reviewed. This review contributes to the development of sustainable management strategies and cultural practices in bean production aimed to minimize yield losses due to fungal diseases in the common bean.

Angular Leaf Spot Resistance Loci Associated With Different Plant Growth Stages in Common Bean

Angular leaf spot (ALS) is a disease that causes major yield losses in the common bean crop. Studies based on different isolates and populations have already been carried out to elucidate the genetic mechanisms of resistance to ALS. However, understanding of the interaction of this resistance with the reproductive stages of common bean is lacking. The aim of the present study was to identify ALS resistance loci at different plant growth stages (PGS) by association and linkage mapping approaches. An BC₂F₃ inter-gene pool cross population (AND 277 × IAC-Milênio - AM population) profiled with 1,091 SNPs from genotyping by sequencing (GBS) was used for linkage mapping, and a carioca diversity panel (CDP) genotyped by 5,398 SNPs from BeadChip assay technology was used for association mapping. Both populations were evaluated for ALS resistance at the V2 and V3 PGSs (controlled conditions) and R8 PGS (field conditions). Different QTL (quantitative trait loci) were detected for the three PGSs and both populations, showing a different quantitative profile of the disease at different plant growth stages. For the three PGS, multiple interval mapping (MIM) identified seven significant QTL, and the Genome-wide association study (GWAS) identified fourteen associate SNPs. Several loci validated regions of previous studies, and Phg-1, Phg-2, Phg-4, and Phg-5, among the 5 loci of greatest effects reported in the literature, were detected in the CDP. The AND 277 cultivar contained both the Phg-1 and the Phg-5 QTL, which is reported for the first time in the descendant cultivar CAL143 as ALS10.1^UC. The novel QTL named ALS11.1^AM was located at the beginning of chromosome Pv11. Gene annotation revealed several putative resistance genes involved in the ALS response at the three PGSs, and with the markers and loci identified, new specific molecular markers can be developed, representing a powerful tool for common bean crop improvement and for gain in ALS resistance.

New Andean source of resistance to anthracnose and angular leaf spot: Fine-mapping of disease-resistance genes in California Dark Red Kidney common bean cultivar

Anthracnose (ANT) and angular leaf spot (ALS) caused by Colletotrichum lindemuthianum and Pseudocercospora griseola, respectively, are devastating diseases of common bean around the world. Therefore, breeders are constantly searching for new genes with broad-spectrum resistance against ANT and ALS. This study aimed to characterize the genetic resistance of California Dark Red Kidney (CDRK) to C. lindemuthianum races 73, 2047, and 3481 and P. griseola race 63-39 through inheritance, allelism testing, and molecular analyses. Genetic analysis of response to ANT and ALS in recombinant inbred lines (RILs) from a CDRK × Yolano cross (CY) showed that the resistance of CDRK cultivar is conferred by a single dominant loci, which we named CoPv01CDRK/PhgPv01CDRK. Allelism tests performed with race 3481showed that the resistance gene in CDRK is independent of the Co-1 and Co-AC. We conducted co-segregation analysis in genotypes of 110 CY RILs and phenotypes of the RILs in response to different races of the ANT and ALS pathogens. The results revealed that CoPv01CDRK and PhgPv01CDRK are coinherited, conferring resistance to all races. Genetic mapping of the CY population placed the CoPv01CDRK/PhgPv01CDRK loci in a 245 Kb genomic region at the end of Pv01. By genotyping 19 RILs from the CY population using three additional markers, we fine-mapped the CoPv01CDRK/PhgPv01CDRK loci to a smaller genomic region of 33 Kb. This 33 Kb region harbors five predicted genes based on the common bean reference genome. These results can be applied in breeding programs to develop bean cultivars with ANT and ALS resistance using marker-assisted selection.

Two tightly linked genes coding for NAD-dependent malic enzyme and dynamin-related protein are associated with resistance to Cercospora leaf spot disease in cowpea (Vigna unguiculata (L.) Walp.)

Cercospora leaf spot (CLS) caused by Cercospora canescens is an important disease of cowpea (Vigna unguiculata). A previous study using an F₂ population [CSR12906 (susceptible) × IT90K-59-120 (resistant)] identified a major QTL qCLS9.1 for resistance to CLS. In this study, we finely mapped and identified candidate genes of qCLS9.1 using an F_3:4 population of 699 individuals derived from two F_2:3 individuals segregating at qCLS9.1 from the original population. Fine mapping narrowed down the qCLS9.1 for the resistance to a 60.6-Kb region on cowpea chromosome 10. There were two annotated genes in the 60.6-Kb region; Vigun10g019300 coding for NAD-dependent malic enzyme 1 (NAD-ME1) and Vigun10g019400 coding for dynamin-related protein 1C (DRP1C). DNA sequence analysis revealed 12 and 2 single nucleotide polymorphisms (SNPs) in the coding sequence (CDS) and the 5' untranslated region and TATA boxes of Vigun10g019300 and Vigun10g019400, respectively. Three SNPs caused amino acid changes in NAD-ME1 in CSR12906, N299S, S488N and S544N. Protein prediction analysis suggested that S488N of CSR12906 may have a deleterious effect on the function of NAD-ME1. Gene expression analysis demonstrated that IT90K-59-120 and CSR12906 challenged with C. canescens showed different expression in both Vigun10g019300 and Vigun10g019400. Taken together, these results indicated that Vigun10g019300 and Vigun10g019400 are the candidate genes for CLS resistance in the cowpea IT90K-59-120. Two derived cleaved amplified polymorphic sequence markers were developed to detect the resistance alleles at Vigun10g019300 and Vigun10g019400 in IT90K-59-120.

Genomics, genetics and breeding of common bean in Africa: A review of tropical legume project

Common bean (Phaseolus vulgaris L.) is an important legume crop worldwide. The International Centre for Tropical Agriculture (CIAT) and its national partners in Africa aim to overcome production constraints of common bean and address the food, nutrition needs and market demands through development of multitrait bean varieties. Breeding is guided by principles of market-driven approaches to develop client-demanded varieties. Germplasm accessions from especially two sister species, P. coccineus and P. acutifolius, have been utilized as sources of resistance to major production constraints and interspecific lines deployed. Elucidation of plant mechanisms governing pest and disease resistance, abiotic stress tolerance and grain nutritional quality guides the selection methods used by the breeders. Molecular markers are used to select for resistance to key diseases and insect pests. Efforts have been made to utilize modern genomic tools to increase scale, efficiency, accuracy and speed of breeding. Through gender-responsive participatory variety selection, market-demanded varieties have been released in several African countries. These new bean varieties are a key component of sustainable food systems in the tropics.

A Review of Angular Leaf Spot Resistance in Common Bean

Angular leaf spot (ALS), caused by Pseudocercospora griseola, is one of the most devastating diseases of common bean (Phaseolus vulgaris L.) in tropical and subtropical production areas. Breeding for ALS resistance is difficult due to the extensive virulence diversity of P. griseola and the recurrent appearance of new virulent races. Five major loci, Phg-1 to Phg-5, conferring ALS resistance have been named, and markers tightly linked to these loci have been reported. Quantitative trait loci (QTLs) have also been described, but the validation of some QTLs is still pending. The Phg-1, Phg-4, and Phg-5 loci are from common bean cultivars of the Andean gene pool, whereas Phg-2 and Phg-3 are from beans of the Mesoamerican gene pool. The reference genome of common bean and high-throughput sequencing technologies are enabling the development of molecular markers closely linked to the Phg loci, more accurate mapping of the resistance loci, and the comparison of their genomic positions. The objective of this report is to provide a comprehensive review of ALS resistance in common bean. Furthermore, we are reporting three case studies of ALS resistance breeding in Latin America and Africa. This review will serve as a reference for future resistance mapping studies and as a guide for the selection of resistance loci in breeding programs aiming to develop common bean cultivars with durable ALS resistance.

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.

Fine Mapping of Ur-3, a Historically Important Rust Resistance Locus in Common Bean

Bean rust, caused by Uromyces appendiculatus, is a devastating disease of common bean (Phaseolus vulgaris) in the Americas and Africa. The historically important Ur-3 gene confers resistance to many races of the highly variable bean rust pathogen that overcome other rust resistance genes. Existing molecular markers tagging Ur-3 for use in marker-assisted selection produce false results. Here, we describe the fine mapping of the Ur-3 locus for the development of highly accurate markers linked to Ur-3 An F2 population from the cross Pinto 114 (susceptible) × Aurora (resistant with Ur-3) was evaluated for its reaction to four different races of U. appendiculatus A bulked segregant analysis using the SNP chip BARCBEAN6K_3 placed the approximate location of Ur-3 in the lower arm of chromosome Pv11. Specific SSR and SNP markers and haplotype analysis of 18 sequenced bean varieties positioned Ur-3 in a 46.5 kb genomic region from 46.96 to 47.01 Mb on Pv11. We discovered in this region the SS68 KASP marker that was tightly linked to Ur-3 Validation of SS68 on a panel of 130 diverse common bean cultivars containing all known rust resistance genes revealed that SS68 was highly accurate and produced no false results. The SS68 marker will be of great value in pyramiding Ur-3 with other rust resistance genes. It will also significantly reduce time and labor associated with the current phenotypic detection of Ur-3 This is the first utilization of fine mapping to discover markers linked to rust resistance in common bean.

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.