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

Abstract

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.

Genome-wide association studies dissect the genetic architecture of seed shape and size in common bean

“…Despite its modest size, the panel embodies broad genetic diversity (see Perseguini et al 2015 and Diniz et al 2018 ) and is considered a high-variability repository for many important traits, including seed morphology and composition, and resistance to biotic and abiotic stresses. Furthermore, this panel was recently used to successfully map genomic regions associated with the common bean’s response to root-knot nematodes ( Giordani et al 2021 ), further evidence of its suitability for GWAS.…”

“…The development of next-generation sequencing technologies significantly improved genotyping capacity and cut costs ( Varshney et al 2009 ), boosting the popularity of GWAS, which takes advantage of the historical accumulation of recombination events, obviating the need to synthesize segregating populations. This approach has enabled researchers to explore a wider genetic base and provide higher mapping resolution for studies focused on understanding the genetic underpinnings of quantitative traits (see Zhu et al 2008 ; Korte and Farlow 2013 ; Huang and Han 2014 ; Giordani et al 2021 ). Furthermore, high-throughput approaches involving image acquisition and analysis have also decisively favored GWAS, allowing large mapping populations, germplasm collections, and other breeding resources to be screened with progressively greater precision and accuracy for several phenotypic traits, including seed attributes (see Mir et al 2019 ).…”

Transcriptome analysis of two tobacco varieties with contrast resistance to Meloidogyne incognita in response to PVY MSNR infection

“…Root-knot nematode (RKN) infection is among the most prevalent diseases of tobacco worldwide and seriously hinders the improvement of tobacco yield and quality. A cost-effective, environmentally friendly, and economical method of controlling RKN damage is to select and promote RKN-resistant varieties; however, laborious phenotyping procedures make it difficult for breeding programs to assess nematode resistance ( Giordani et al., 2022 ), and the identification of RKN-resistant tobacco is the premise and basis for the breeding of RKN-resistant tobacco varieties.…”

Perfil transcricional de genótipos de feijoeiro-comum contrastantes para a resposta à infecção por >i<Meloidogyne incognita>/i<

“…Nessa avaliação, destacaram-se os genótipos 'IAC-Tybatã' e 'Branquinho', para a resistência e suscetibilidade, respectivamente. Neste mesmo estudo, foi feita a detecção de regiões genômicas associadas à resposta do feijoeiro ao nematoide das galhas, via mapeamento associativo, permitindo avançar no entendimento da arquitetura genética da interação(Giordani et al 2021).Neste cenário, no presente estudo, se pretende avaliar o perfil transcricional dos genótipos contrastantes, IAC-Tybatã (R) e Branquinho (S), e identificar os genes diferencialmente expressos envolvidos na resistência. Em resumo, se busca compreender o mecanismo molecular envolvido na complexa interação do feijoeiro-comum e o nematoide das galhas, reconhecendo as vias de sinalização e rotas específicas ativadas em reações compatíveis e incompatíveis, e indicar genes candidatos à resistência.…”