Identification and Validation of Candidate Genes Conferring Resistance to Downy Mildew in Maize (Zea mays L.)

Abstract

Downy mildew (DM) is a major disease of maize that causes significant yield loss in subtropical and tropical regions around the world. A variety of DM strains have been reported, and the resistance to them is polygenically controlled. In this study, we analyzed the quantitative trait loci (QTLs) involved in resistance to Peronosclerospora sorghi (sorghum DM), P. maydis (Java DM), and Sclerophthora macrospora (crazy top DM) using a recombinant inbred line (RIL) from a cross between B73 (susceptible) and Ki11 (resistant), and the candidate genes for P. sorghi, P. maydis, and S. macrospora resistance were discovered. The linkage map was constructed with 234 simple sequence repeat (SSR) and restriction fragment length polymorphism (RFLP) markers, which was identified seven QTLs (chromosomes 2, 3, 6, and 9) for three DM strains. The major QTL, located on chromosome 2, consists of 12.95% of phenotypic variation explained (PVE) and a logarithm of odds (LOD) score of 14.12. Sixty-two candidate genes for P. sorghi, P. maydis, and S. macrospora resistance were obtained between the flanked markers in the QTL regions. The relative expression level of candidate genes was evaluated by quantitative real-time polymerase chain reaction (qRT-PCR) using resistant (CML228, Ki3, and Ki11) and susceptible (B73 and CML270) genotypes. For the 62 candidate genes, 15 genes were upregulated in resistant genotypes. Among these, three (GRMZM2G028643, GRMZM2G128315, and GRMZM2G330907) and AC210003.2_FG004 were annotated as leucine-rich repeat (LRR) and peroxidase (POX) genes, respectively. These candidate genes in the QTL regions provide valuable information for further studies related to P. sorghi, P. maydis, and S. macrospora resistance.Genes 2020, 11, 191 2 of 20 is spread by oospores that survive in the soil [7] and can be spread through infected seeds or from plant-to-plant by airborne conidia. Because of the systemic nature of DM, susceptible lines usually die when infected in the seedling emergence stage, and when plants are infected during later growth stages, they cannot develop the maize ear despite having survived. At least six pathogens that cause DM infection of maize in Asia have been reported, including sorghum DM (P. sorghi (Weston & Uppal)), Philippine DM (P. philippinensis (Weston) Shaw), Java DM (P. maydis (Raciborski)), sugarcane DM (P. sacchari (Miyabe) Shirai and Hara), brown stripe DM (Sclerophthora rayssiae var. zeae), crazy top DM (S. macrospora), and Rajasthan DM (P. heteropogoni) [2,6,[8][9][10][11][12][13][14][15]. DM is widespread in tropical regions, although its origin is conjectural, and because of the diversity of the DM pathogens and their systemic nature, the development of resistant varieties is needed. Moreover, a renewed emphasis on cost-effectiveness and environmental safety that has brought about the application of DM management by the development of resistant varieties. According to studies on the interaction of maize and the pathogens, resistance to DM is polygenically controlled [7,13,[16][17][18]...

QTL Mapping linked to downy mildew resistance genes in maize (Zea mays)

“…Based on previous study, Kim et al (2017) and Ruswandi et al (2015) have identified QTL for downy resistance on chromosome 1 using F2 and BC1F2 populations, respectively. Furthermore, it was also reported by Jampatong et al (2013) that QTL related to Pp in the RILs, Lohithaswa et al (2015) found QTL related to Ps (Peronosclerospora sorghi) in F2 population, and QTL linked Ph (Peronosclerospora heteropogoni) character was obtained BC1F2 population (Kim et al 2020). Based on this study, we conclude that response of 198 F3:4 lines on the DM disease in the field varied from highly resistance to highly succeptible and the DM resistance related QTLs found in present study would give new insight on the future molecular maize breeding program for resistant against downy mildew disease.…”

“…In order to obtain a high-density linkage map, therefore, it is suggested that in future work more polymorphic markers between the two adjacent markers are needed to explore. The magnitude of the linkage map formed in this study was about 39.75% of the total maize genome in comparison to the maize genetic map reported by Kim et al (2020).…”

“…Some of the factors causing the low productivity of maize in Indonesia are the limited amount of maize germplasm, changing environmental conditions in each region, and the markers linked to less specific resistance genes, especially the downy mildew disease (DM). Downy Mildew is caused by the fungus Peronosclerospora which is one of the most important diseases in maize and can cause serious damage in crops throughout the world, especially in tropical Asia (Rashid et al 2018;Kim et al 2020). Daryono et al (2018) reported that the level of this pathogen attack reached ± 90% in South of Sulawesi.…”

Breeding for Prolificacy, Total Carotenoids and Resistance to Downy Mildew in Small-Ear Waxy Corn by Modified Mass Selection

“…The results in this study suggested that the crosses between resistant and susceptible varieties showed moderate resistance (Nei9008/BK-24-9-B) and resistance (TY/TF-33-1-B) to downy mildew. Difference in resistance levels among corn varieties is due to polygenic inheritance of resistance [9]. Additive and non-additive effects are equally important in the inheritance of resistance [59].…”

“…More recently, two species of DM including Peronosclerospora sorghi and P. maydis have been reported to infect corn in the country [8]. Polygenic inheritance of DM resistance has been reported [9] and additive and non-additive gene effects were equally important in the inheritance of DM resistance in maize [10,11]. Therefore, improvement of small-ear waxy corn genotypes for DM resistance is possible.…”