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

Abstract

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 ALS10.1UC. 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.

Genome-wide association mapping reveals race-specific SNP markers associated with anthracnose resistance in carioca common beans

“…These vary from the first cultivar carioca released by the Instituto Agronômico—IAC (Campinas, SP, Brazil) in 1971 (i.e., Carioquinha or Carioca comum) to more recent cultivars, such as IPR-Sábia and IAC-1850, released in 2017 and 2019, respectively. The panel was genotyped using the BeadChip Illumina technology by BARCBean6K_3, with 5,398 SNPs [ 68 ], and validated for GWAS by Almeida et al [ 69 ] and successfully used to identify QRL associated with angular leaf spot by Almeida et al [ 70 ]. All the information on the CDP is given in S1 Table of the Supplementary Materials, including the phenotypic and genotypic data.…”

“…For linkage mapping, the AM genetic map estimated from 1,114 SNPs genotyped by GBS (genotyping by sequencing) in the AM segregating population BC 2 F 3 ({[(♀AND-277 × ♂IAC-Milênio) × IAC-Milênio] × IAC-Milênio}) was used. The AM population was developed and validated for genetic mapping by Almeida et al [ 70 ] and was composed of 91 inter-pool lines selected according to the carioca grain ideotype. All the information on the genotypes of the AM population is presented in S1 Table in the Supplementary Materials, including the phenotypic and genotypic data.…”

“…The AM genetic map, constructed by Almeida et al [ 70 ], was used for the linkage mapping. The identification of QRL followed the approach described by the authors using the OneMap package [ 81 ].…”

Marker‐assisted backcrossing for disease resistance and agronomic traits in Carioca beans

“…Brown, is one of the most devastating diseases of beans and can lead to production losses of more than 80% (Nay et al, 2019). Studies on the inheritance of common bean resistance to ALS have identified several resistance loci, of both greater and lesser effects, showing a predominance of quantitative resistance to the disease (Almeida et al, 2021;Bassi et al, 2017;Keller et al, 2015;Oblessuc et al, 2012;Pereira et al, 2015). In a recent study using 144 Brazilian commercial accessions, only 7% showed resistance to ALS in the V3 phenological stage .…”

Genetic mapping reveals complex architecture and candidate genes involved in common bean response to Meloidogyne incognita infection

“…To perform QTL mapping, a linkage map previously constructed for a BC 2 F 3 population was used. This map was built using the software OneMap v2.1.3 (Margarido et al., 2007), which was modified to fit the genetic structure of this specific population (de Almeida et al., 2021). In brief, markers were tested for the expected Mendelian frequencies (1/8:7/8), and those exhibiting segregation distortion were excluded.…”