QTL mapping and colocalization analysis reveal novel candidate genes for multiple disease resistance in maize

Abstract

Unpredictable pathogen pressures resulting from changing climatic patterns have required plant breeders to breed crop cultivars with durable resistance to multiple plant pathogens. The genetic basis of multiple disease resistance (MDR) is an important component in building durable resistance in crop plants. Maize (Zea mays L.) inbred NY22613, developed at Cornell University, has shown resistance to northern leaf blight (NLB), gray leaf spot (GLS), common rust, and Stewart's wilt (SW). In order to unravel the genetic basis of MDR in NY22613, quantitative trait locus (QTL) mapping and colocalization studies were conducted. A BC3S3 biparental mapping population (resistant inbred NY22613 and susceptible recurrent inbred Oh7B) was used to map the QTL responsible for disease resistance. The analysis revealed that 16 QTL were associated with NLB resistance, 17 QTL with GLS resistance, and 16 QTL with SW resistance. No QTL were colocalized for all three diseases. Three QTL were shared for NLB and GLS in chromosomes 7, 9, and 10 and one QTL was shared for GLS and SW in chromosome 2. These QTL contain the following genes that have been previously associated with disease resistance: Zm00001d002005 (lg1, liguleless1), Zm00001d024007, Zm00001d024008, LOC103642379, and LOC103641009. These regions also contain the following novel genes, which have not been associated with any function: LOC541757, Zm00001d044974, Zm00001d044975, and LOC109941121. To select individuals with MDR, a novel selection method was developed that combines phenotypic data, QTL data, and high‐density marker information in a cluster analysis designated as the high‐density marker phenotype (HEMP) QTL selection strategy.

Advanced backcross QTL analysis and comparative mapping with RIL QTL studies and GWAS provide an overview of QTL and marker haplotype diversity for resistance to Aphanomyces root rot in pea (Pisum sativum)

“…BC 2 or BC 3 , allow to develop recombinant lines genetically less similar to the donor parental line, accelerating the transfer of wild alleles into agronomic lines. Transfer of disease resistance traits has been successfully achieved through AB-QTL analysis in several major field crops, like barley ( Haas et al., 2016 ), maize ( Palanichamy and Smith, 2022 ), rice ( Jiang et al., 2020 ), sunflower ( Talukder et al., 2022 ), and wheat ( Naz et al., 2015 ). GWAS is a powerful tool to investigate complex genetic determinism and identify exotic or agronomic alleles in plant natural diversity panels.…”

Brown midrib mutant and genome‐wide association analysis uncover lignin genes for disease resistance in maize

“…Analysis of NILs and mutants have implicated a remorin‐like gene (Jamann et al., 2016) for resistance to NLB that also affects flowering time. The use of a genome‐wide association study (GWAS) in a set of nested NILs along with mutant analysis implicated a role of the liguleless1 gene in resistance to NLB (Kolkman et al., 2020) that appears to be independent of leaf angle and confirmed via expression analysis (Palanichamy & Smith, 2022). Genome‐wide association studies in maize diversity panels indicate that a large number of small‐effect genes across the genome are segregating in these populations (Wisser et al., 2011; Van Inghelandt et al., 2012; Ding et al., 2015; Schaefer & Bernardo, 2013; Rashid et al., 2020).…”