Common bean is an important legume crop having high quality protein, micronutrients, vitamins and antioxidants, which makes it a “grain of hope” for poor communities. Hence, a good number of breedi...

Common bean as a potential crop for future food security: an overview of past, current and future contributions in genomics, transcriptomics, transgenics and proteomics

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-Milenio - 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 ALS10.1UC. The novel QTL named ALS11.1AM 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.

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

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.

https://www.mdpi.com/2073-4425/12/5/765/pdf

Genome-Wide Association Study Reveals Genomic Regions Associated with Fusarium Wilt Resistance in Common Bean.

Common bean (Phaseolus vulgaris) is considered a staple food in a number of developing countries. Several diseases attack the crop leading to substantial economic losses around the globe. However, the crop has rarely been investigated for multiple disease resistance traits using Meta-analysis approach.In this study, in order to identify the most reliable and stable quantitative trait loci (QTL) conveying disease resistance in common bean, we carried out a meta-QTL (MQTL) analysis using 152 QTLs belonging to 44 populations reported in 33 publications within the past 20 years. These QTLs were decreased into nine MQTLs and the average of confidence interval (CI) was reduced by 2.64 folds with an average of 5.12 cM in MQTLs. Uneven distribution of MQTLs across common bean genome was noted where sub-telomeric regions carry most of the corresponding genes and MQTLs. One MQTL was identified to be specifically associated with resistance to halo blight disease caused by the bacterial pathogen Pseudomonas savastanoi pv. phaseolicola, while three and one MQTLs were specifically associated with resistance to white mold and anthracnose caused by the fungal pathogens Sclerotinia sclerotiorum and Colletotrichum lindemuthianum, respectively. Furthermore, two MQTLs were detected governing resistance to halo blight and anthracnose, while two MQTLs were detected for resistance against anthracnose and white mold, suggesting putative genes governing resistance against these diseases at a shared locus. Comparative genomics and synteny analyses provide a valuable strategy to identify a number of well‑known functionally described genes as well as numerous putative novels candidate genes in common bean, Arabidopsis and soybean genomes. 

/pdf/genome-wide-meta-qtl-analyses-provide-novel-insight-into-28k8u8r9.pdf

Genome-wide meta-QTL analyses provide novel insight into disease resistance repertoires in common bean

Anthracnose is a severe disease of common bean that, under favorable conditions, can cause a 100% yield loss. For effective resistance breeding, the virulence and genetic variability of the causal pathogen, Colletotrichum lindemuthianum, must be understood and the emergence of new races monitored to ensure the development of broad-spectrum, durable resistance. In the present study, 28 isolates of C. lindemuthianum collected in Pernambuco, Brazil, were characterized: i) for their pathogenicity on a differential common bean cultivar set, ii) for their genetic variability, based on the Internally Transcribed Spacer (ITS) region sequences, and iii) for their ability to cause anthracnose on a selection of 20 common bean accessions. The 12 differential cultivars were inoculated with the 28 isolates, identifying 16 races of C. lindemuthianum: 2, 3, 8, 9, 10, 64, 65, 72, 73, 75, 81, 85, 89, 117, 139, and 331. Except for race 81, all were reported for the first time in Pernambuco; this was the first report of race 139 in Brazil and of race 331 in the world. The ITS region sequence of 17 isolates revealed the presence of 27 SNPs, four SNPs in the ITS 1 region, and 23 SNPs in the ITS 2 region. Of the 20 common bean accessions screened for resistance with the 16 isolates of C. lindemuthianum, the Andean accessions ‘Praia’ and ‘Africano 4’ were the most resistant. The broad resistance detected in some common bean accessions indicates their utility as potential sources of resistance to C. lindemuthianum, particularly in areas where Mesoamerican beans and Mesoamerican races of the pathogen are predominant.

Virulence and genetic diversity of Colletotrichum lindemuthianum and resistance of local common bean germplasm to anthracnose in Pernambuco State, Brazil

Genome-wide association study of resistance to anthracnose and angular leaf spot in Brazilian Mesoamerican and Andean common bean cultivars

Anthracnose (ANT) is among the common bean fungal diseases responsible for significant yield and grain quality losses. Durable genetic resistance is the primary ANT control method due to the pathogen's high variability. Genetic studies showed that the common bean chromosome Pv01 contains multiple disease resistance genes, including the ANT resistance loci Co-1 (Co-12, Co-13, Co-14, Co-15, Co-1HY, and Co-1x), Co-AC, Co-14, Co-Pa, Co-Perla, Co-w, Co-x, and CoPv01CDRK. This work aimed to: (i) perform the genetic fine-mapping of the Co-14 allele present in the cultivar AND 277, using recombinant inbred lines derived from the cross between Rudá × AND 277; and (ii) identify candidate resistance genes in the Co-14 allele based on the common bean reference genome. Initially, the Co-14 allele was mapped between the single-nucleotide polymorphism markers ss715645251 and ss715645250 at a distance of 2.0 and 19.6 cM, respectively. Fine-mapping localized Co-14 between the markers ss715645251 and BARCPVSSR01356, spanning a 40.51 kb region at the end of Pv01. Two genes are described within the Co-14 region in the reference genome, Phvul.001G243800 and Phvul.001G243900. The linkage between the Co-14 allele and the markers ss715645251 and BARCPVSSR01356 will be essential for plant breeding programs during the resistance gene transfer to elite cultivars via marker-assisted selection (MAS). Identifying and functionally analyzing candidate resistance genes in this region will allow more efficient MAS by developing accurate markers for ANT resistance. 

Laíze Raphaelle Lemos Lima

Papers

Genome-wide association study of resistance to anthracnose and angular leaf spot in Brazilian Mesoamerican and Andean common bean cultivars

Genetic present in the Andean common bean cultivar AND 277