Identification of Loci That Confer Resistance to Bacterial and Fungal Diseases of Maize

Abstract

Crops are hosts to numerous plant pathogenic microorganisms. Maize has several major disease issues; thus, breeding multiple disease resistant (MDR) varieties is critical. While the genetic basis of resistance to multiple fungal pathogens has been studied in maize, less is known about the relationship between fungal and bacterial resistance. In this study, we evaluated a disease resistance introgression line (DRIL) population for the foliar disease Goss's bacterial wilt and blight (GW) and conducted quantitative trait locus (QTL) mapping. We identified a total of ten QTL across multiple environments. We then combined our GW data with data on four additional foliar diseases (northern corn leaf blight, southern corn leaf blight, gray leaf spot, and bacterial leaf streak) and conducted multivariate analysis to identify regions conferring resistance to multiple diseases. We identified 20 chromosomal bins with putative multiple disease effects. We examined the five chromosomal regions (bin 1.05, 3.04, 4.06, 8.03, and 9.02) with the strongest statistical support. By examining how each haplotype effected each disease, we identified several regions associated with increased resistance to multiple diseases and three regions associated with opposite effects for bacterial and fungal diseases. In summary, we identified several promising candidate regions for multiple disease resistance in maize and specific DRILs to expedite interrogation.

How Well Can Multivariate and Univariate GWAS Distinguish Between True and Spurious Pleiotropy?

“…With the recent acquisition of high-throughput phenotype and genotype data, it is now possible to directly identify pleiotropic causal mutations (Wagner and Zhang, 2011 ). The abundance of such high-throughput data in conjunction with a plethora of tools available for quantifying genotype-to-phenotype associations (Marchini et al, 2007 ; Purcell et al, 2007 ; Lipka et al, 2012 ; Zhou and Stephens, 2014 ) is providing increasing evidence for pleiotropic genes involved in evolution (Smith, 2016 ; Auge et al, 2019 ), disease resistance (Wisser et al, 2011 ; Lopez-Zuniga et al, 2019 ; Qiu et al, 2020 ), yield (Ward et al, 2019 ), and many other traits (Jiang et al, 2019 ; Rice et al, 2020 ). These analyses have also led to opposing views for (Boyle et al, 2017 ) and against (Wray et al, 2018 ) the ubiquitousness of pleiotropy in complex trait variation, particularly in the form of the omnigenic model.…”

Spatiotemporal Dynamics of Maize (Zea mays L.) Root Growth and Its Potential Consequences for the Assembly of the Rhizosphere Microbiota

“…Although the optimization of microbial formulas using synthetic communities is advancing, crop breeding programs have not yet incorporated the selection of beneficial traits of rhizosphere microorganisms ( Trivedi et al, 2020 ). The perhaps most promising trait in this respect is pathogen resistance ( Zhao et al, 2004 ; Qiu et al, 2020 ), where the rhizosphere community has proved helpful ( Compant et al, 2005 ; Hohmann and Messmer, 2017 ). For instance, a common bean cultivar resistant to Fusarium oxysporum selects for a particular rhizosphere microbiome with enriched functional traits related to the first line of defense against the pathogen, biosynthesis machineries for antifungal phenazines, and fungal membrane damaging small molecules, rhamnolipids ( Mendes et al, 2018 ).…”

Genomics-Assisted Breeding for Quantitative Disease Resistances in Small-Grain Cereals and Maize

“…Currently, a multiple diseases approach instead of analyzing single disease resistances is increasingly getting attention. Different authors combined the localization of single-disease QTLs finding candidate regions for MDR on the following bins: 1.02, 1.05/1.06, 3.04, 4.06, 7.02, 8.03, 8.05 and 9.02 [ 29 , 90 , 100 , 113 , 114 , 115 , 116 , 117 ]. Some of these regions overlap with hotspots for resistance to NCLB presented in Figure 2 .…”

“…Obviously, some mechanisms underlying QDR are unspecific and common for several diseases. Some regions also presented contrasting effects for resistances to bacterial and fungal diseases [ 115 ].…”

“…Another hotspot seems to be maize bins 1.05/1.06, where resistance to NCLB, Stewart’s wilt, SCLB, common rust, GLS, and ear and stalk rot caused by multiple fungi have been detected [ 90 , 100 , 112 , 114 , 115 , 120 ]. The bin 1.06 was reported by several authors for NCLB resistance (rf.…”