Maize Rough Dwarf Disease Resistance Research Articles

ZmGLK36 transcription factor bestows viral resistance in rice and wheat

Maize rough dwarf disease (MRDD) threatens the sustainable production of major cereal crops. Recently, Xu et al. reported a new resistance gene, ZmGLK36, which promotes MRDD resistance in maize by increasing jasmonic acid (JA)-mediated defence. This discovery provides opportunities to develop resistance to rice black-streaked dwarf virus (RBSDV) in other cereal crops such as rice and wheat.

Targeted generation of Null Mutants in ZmGDIα confers resistance against maize rough dwarf disease without agronomic penalty.

Targeted generation of Null Mutants in ZmGDIα confers resistance against maize rough dwarf disease without agronomic penalty.

Identification and Fine-Mapping of a Novel QTL, qMrdd2, That Confers Resistance to Maize Rough Dwarf Disease.

Maize rough dwarf disease (MRDD) is caused by a virus and seriously affects maize quality and yield worldwide. MRDD can be most effectively controlled with disease-resistant hybrids of corn. Here, MRDD-resistant (Qi319) and -susceptible (Ye478) parental inbred maize lines and their 314 recombinant inbred lines (RILs) that were derived from a cross between them were evaluated across three environments. A stable resistance QTL, qMrdd2, was identified and mapped using best linear unbiased prediction (BLUP) values to a 0.55-Mb region between the markers MK807 and MK811 on chromosome 2 (B73 RefGen_v3) and was found to explain 8.6 to 11.0% of the total phenotypic variance in MRDD resistance. We validated the effect of qMrdd2 using a chromosome segment substitution line (CSSL) that was derived from a cross between maize inbred Qi319 as the MRDD resistance donor and Ye478 as the recipient. Disease severity index of the CSSL haplotype II harboring qMrdd2 was significantly lower than that of the susceptible parent Ye478. Subsequently, we fine-mapped qMrdd2 to a 315-kb region flanked by the markers RD81 and RD87, thus testing recombinant-derived progeny using selfed backcrossed families. In this study, we identified a novel QTL for MRDD resistance by combining the RIL and CSSL populations, thus providing important genetic information that can be used for breeding MRDD-resistant varieties of maize.

Marker-assisted selection of qMrdd8 to improve maize resistance to rough dwarf disease.

Maize rough dwarf disease (MRDD) is caused by viruses in the Fijivirus genus in the family Reoviridae. MRDD resistance can be improved by a combination of marker-assisted selection (MAS) and conventional breeding strategies. In our previous study, we fine-mapped a major QTL qMrdd8 and developed the functional Indel marker IDP25K. In the present study, qMrdd8 from the donor parent X178 was introgressed into elite inbred lines derived from the three corn heterotic groups using multi-generation backcrossing and MAS. Recipient lines included Huangzao4, Chang7-2, Ye478, Zheng58, Zhonghuang68, B73, and Ji846. Markers used for foreground selection included IDRQ4, IDRQ47, IDP25K, and IDP27K. Background selection was carried out in the BC3 or BC4 using 107 SSR markers to select lines with the highest rate of recovery of the particular recurrent parent genome. Plants from BC4F2 and BC3F2 that carried the shortest qMrdd8 interval from X178 and those with the highest rate of recovery of the recurrent parent genome were then selected to create converted homozygous inbred lines. In 2017, seven converted inbred lines and five hybrids exhibited enhanced resistance to MRDD, while other agronomic traits were not affected under nonpathogenic stress conditions. Thus, the MRDD resistance allele at the qMrdd8 locus, or IDP25K, should be valuable for maize breeding programs in China.

Identification of QTLs for resistance to maize rough dwarf disease using two connected RIL populations in maize.

Maize rough dwarf disease (MRDD) is a significant viral disease caused by rice black-streaked dwarf virus (RBSDV) in China, which results in 30% yield losses in affected summer maize-growing areas. In this study, two connected recombinant inbred line (RIL) populations were constructed to elucidate the genetic basis of resistance during two crop seasons. Ten quantitative trait loci (QTLs) for resistance to MRDD were detected in the two RILs. Individual QTLs accounted for 4.97–23.37% of the phenotypic variance explained (PVE). The resistance QTL (qZD-MRDD8-1) with the largest effect was located in chromosome bin 8.03, representing 16.27–23.37% of the PVE across two environments. Interestingly, one pair of common significant QTLs was located in the similar region on chromosome 4 in both populations, accounting for 7.11–9.01% of the PVE in Zheng58×D863F (RIL-ZD) and 9.43–13.06% in Zheng58×ZS301 (RIL-ZZ). A total of five QTLs for MRDD resistance trait showed significant QTL-by-Environment interactions (QEI). Two candidate genes associated with resistance (GDSL-lipase and RPP13-like gene) which were higher expressed in resistant inbred line D863F than in susceptible inbred line Zheng58, were located in the physical intervals of the major QTLs on chromosomes 4 and 8, respectively. The identified QTLs will be studied further for application in marker-assisted breeding in maize genetic improvement of MRDD resistance.

A Rice Black-Streaked Dwarf Virus Replication Curve Model to Evaluate Maize Rough Dwarf Disease Resistance.

Resistance to maize rough dwarf disease (MRDD), a major cause of crop losses, depends on external conditions such as the virus transmission period and the rate of viruliferous small brown planthoppers, Laodelphax striatellus. The precise identification of MRDD contributes to the utilization of resistant germplasm and the cloning of resistant genes. In this study, eight maize varieties were artificially inoculated in a greenhouse with viruliferous planthoppers. The viral titers in maize seedlings were detected by quantitative fluorescence RT-PCR, and the viral replication curves were analyzed by regression. A logistic model fit the Rice black-streaked dwarf virus (RBSDV) replication data for five susceptible varieties well, whereas a linear model fit the data for three resistant varieties. Among the five susceptible varieties, the time points with the maximum replication rates (tIP) of the highly susceptible Ye478 and XH6 were significantly earlier than those of the three susceptible varieties, Mo17, Zheng58, and Zhengdan958. P138, the most highly resistant variety, had the lowest slope of the best fit line, followed by moderately resistant Chang7-2 and Dan 340. The RBSDV replication curve model developed in this study can accurately identify the resistance of maize germplasm to MRDD at the molecular level. Our results also suggested that tIP and the slope of the RBSDV replication curve can be considered new criteria to evaluate maize resistance to MRDD.

Comparative proteomics analysis of maize (Zea mays) leaves infected by small brown planthopper (Laodelphax striatellus)

Maize rough dwarf disease (MRDD) is a viral disease caused by brown planthopper infestation, and leads to great yield loss, especially in China. Comparative proteomics was performed using maize inbred line Zheng 58 and LN 287. MRDD pathogen was detected as rice black-streaked dwarf virus (RBSDV) by quantitative real time PCR (qRT-PCR) in Shandong Province, China. The modified trichloroacetic acid (TCA)/acetone method was used for soluble protein extraction from leaves. Two-dimensional electrophoresis (2-DE) analysis was performed on 24-cm long, pH 4–7 linear immobilized pH gradient (IPG) strips, and gels were stained with silver and coomassie brilliant blue. We identified 944 proteins expressed in RBSDV infected maize leaves by proteomics approaches. Among these, 44 protein spots that revealed a 1.5-fold difference in intensity were identified by mass spectrometry between mock-inoculated and RBSDV infected samples. Among these, 17 and 26 spots were up-regulated, and 27 and 18 spots were down-regulated in the virus infected samples of Zheng 58 and LN 287, respectively. Differential protein spots were analyzed by mass spectrometry identification, which could be divided into six categories. Furthermore, the expression of stress-related proteins was detected and confirmed by qRT-PCR. This study lays the foundation for further investigations, enabling the enhancement of MRDD resistance in maize.

Identification of a locus conferring dominant resistance to maize rough dwarf disease in maize

Maize rough dwarf disease (MRDD) is a severe viral disease of maize that occurs worldwide, particularly in the summer maize-growing areas in China, resulting in yield losses and quality deterioration in susceptible maize varieties. An effective solution to control MRDD is to use resistance genes to improve the behavior of susceptible genotypes. Here, we employed maize F2 populations derived from a cross between susceptible line S221 and resistant line K36 for the deep sequencing of the two DNA pools containing extremely resistant and susceptible F2 individuals, and used traditional linkage analysis to locate the resistance-related genomic region. The results showed that MRDD resistance in K36 was controlled by a single dominant locus, and an associated region was identified within the genomic interval of 68,396,487 bp and 69,523,478 bp on chromosome 6. Two simple sequence repeat (SSR) markers 6F29R29 and 6F34R34 were tightly linked to the MRDD resistance locus. The findings of the present study improve our understanding of the inheritance patterns of MRDD resistance, and should inform MRDD-resistant maize breeding programs.

Fine mapping of a quantitative trait locus conferring resistance to maize rough dwarf disease.

A QTL qMrdd8 that confers resistance to MRDD was fine mapped into an interval of 347kb; one SNP and two InDels identified in the interval were significantly associated with resistance to MRDD. Maize rough dwarf disease (MRDD) is highly prevalent in the summer maize-growing areas in China, and leads to significant yield losses in maize (Zea mays L.). In this study, the quantitative trait locus (QTL) qMrdd8, which confers resistance to MRDD, was fine mapped. Initially, qMrdd8 was consistently identified in the interval between the simple sequence repeat markers umc1617 and phi121 in three F2 sub-populations derived from a cross between the resistant recombinant inbred line NL203 and the susceptible line B73. Subsequently, qMrdd8 was fine mapped into an interval of 347kb defined by the markers IDRQ2 and IDRQ20 using a recombinant-derived progeny test strategy. Based on single nucleotide polymorphism (SNP) genotypes identified using the MaizeSNP50 BeadChip, a long haplotype including qMrdd8 was identified in four resistant inbred lines. One SNP, the 2549-bp insertion/deletion polymorphism (InDel) InDel25, and the 2761-bp InDel27, which all were significantly associated with resistance to MRDD in a set of 226 maize inbred lines (P<0.05), were detected within qMrdd8. Furthermore, two candidate genes, CG1 and CG2, were detected in the interval using RNA sequencing (RNA-Seq), and InDel25 was localized within the candidate gene CG1. In conclusion, the fine mapping of qMrdd8 will be helpful in cloning the resistance gene, and the three polymorphic markers identified in this study could be used to improve MRDD resistance via a marker-assisted selection approach.

Genome-Wide Association Implicates Candidate Genes Conferring Resistance to Maize Rough Dwarf Disease in Maize.

Maize rough dwarf disease (MRDD) is a destructive viral disease in China, which results in 20–30% of the maize yield losses in affected areas and even as high as 100% in severely infected fields. Understanding the genetic basis of resistance will provide important insights for maize breeding program. In this study, a diverse maize population comprising of 527 inbred lines was evaluated in four environments and a genome-wide association study (GWAS) was undertaken with over 556000 SNP markers. Fifteen candidate genes associated with MRDD resistance were identified, including ten genes with annotated protein encoding functions. The homologous of nine candidate genes were predicted to relate to plant defense in different species based on published results. Significant correlation (R2 = 0.79) between the MRDD severity and the number of resistance alleles was observed. Consequently, we have broadened the resistant germplasm to MRDD and identified a number of resistance alleles by GWAS. The results in present study also imply the candidate genes in defense pathway play an important role in resistance to MRDD in maize.

Identification of significant single nucleotide polymorphisms for resistance to maize rough dwarf disease in elite maize (Zea mays L.) inbred lines

Maize rough dwarf disease (MRDD) is a devastating viral disease that causes considerable yield losses in maize worldwide. Identifying quantitative trait loci underlying resistance to MRDD is important for genetic improvement of maize. In this study, 184 elite maize inbred lines from modern breeding programs were evaluated in three years to identify QTLs for MRDD resistance using 3072 single-nucleotide polymorphisms (SNPs) via genome-wide association analysis. The analysis revealed abundant phenotypic diversity in the studied population. All tested maize inbred lines were divided into two subpopulations based on a Bayesian model, and the linkage disequilibrium (LD) level differed among chromosomes, with an intra-chromosomal average of 1,000–1,500 kb. After correction for multiple testing, 21 SNPs were identified for MRDD resistance in different years as well as for BLUPs (the best linear unbiased predictions) of MRDD resistance based on the MLM model, one SNP of PZE-101245575 was stably possessed the most promising association. Several SNPs were located in or close to previously reported quantitative trait loci for MRDD resistance. The significant SNPs identified in this study will be helpful for further understanding the genetic basis of MRDD resistance, and might facilitate the pyramiding of favorable alleles for high resistance to MRDD in future marker-assisted selection schemes in maize.

Genome-wide association study of resistance to rough dwarf disease in maize

Maize rough dwarf disease (MRDD), caused by the Maize rough dwarf virus (MRDV) is highly prevalent across summer at maize-growing areas in China. To investigate the genetic architecture underlying this viral disease, a set of 236 Chinese maize inbred lines was evaluated for resistance to MRDD in 2010 and 2011. Based on 41,101 single-nucleotide polymorphism (SNP) markers with minor allele frequencies (MAF) greater than 5 %, a genome-wide association study (GWAS) was employed to identify genomic loci for resistance to MRDD. A total of 73 SNPs were found to be associated with resistance to MRDD at a significance threshold of -log10 (P) > 4 controlling the false discovery rate (FDR) at α = 0.1. Fourteen of these SNPs were detected in both of the two environments tested. A total of 48 SNPs were identified in linkage disequilibrium (LD) blocks containing candidate resistance genes, including protein kinase genes. Using the pedigree information and whole-genome SNP analysis of five highly resistant inbred lines derived from the hybrid ‘P78599’, nine derivative fragments harbouring SNPs associated with MRDD resistance were detected. One 81.57 Mb fragment in particular located in bin 8.03, which contained six SNPs associated with MRDD resistance, and included the major quantitative trait loci (QTL) that had been identified in the previous study. These results suggest that the SNPs and fragments associated with MRDD resistance, especially those in bin 8.03, could be used for fine mapping of resistance genes and developing resistant varieties in maize.

Identification of promoter motifs regulating ZmeIF4E expression level involved in maize rough dwarf disease resistance in maize (Zea Mays L.)

Maize rough dwarf disease (MRDD, a viral disease) results in significant grain yield losses, while genetic basis of which is largely unknown. Based on comparative genomics, eukaryotic translation initiation factor 4E (eIF4E) was considered as a candidate gene for MRDD resistance, validation of which will help to understand the possible genetic mechanism of this disease. ZmeIF4E (orthologs of eIF4E gene in maize) encodes a protein of 218 amino acids, harboring five exons and no variation in the cDNA sequence is identified between the resistant inbred line, X178 and susceptible one, Ye478. ZmeIF4E expression was different in the two lines plants treated with three plant hormones, ethylene, salicylic acid, and jasmonates at V3 developmental stage, suggesting that ZmeIF4E is more likely to be involved in the regulation of defense gene expression and induction of local and systemic resistance. Moreover, four cis-acting elements related to plant defense responses, including DOFCOREZM, EECCRCAH1, GT1GAMSCAM4, and GT1CONSENSUS were detected in ZmeIF4E promoter for harboring sequence variation in the two lines. Association analysis with 163 inbred lines revealed that one SNP in EECCRCAH1 is significantly associated with CSI of MRDD in two environments, which explained 3.33 and 9.04% of phenotypic variation, respectively. Meanwhile, one SNP in GT-1 motif was found to affect MRDD resistance only in one of the two environments, which explained 5.17% of phenotypic variation. Collectively, regulatory motifs respectively harboring the two significant SNPs in ZmeIF4E promoter could be involved in the defense process of maize after viral infection. These results contribute to understand maize defense mechanisms against maize rough dwarf virus.

Identification of a major quantitative trait locus for resistance to maize rough dwarf virus in a Chinese maize inbred line X178 using a linkage map based on 514 gene-derived single nucleotide polymorphisms

Maize rough dwarf disease (MRDD) is a worldwide viral disease and causes significant yield losses in maize (Zea mays L.) production. In this study, we mapped and characterized quantitative trait loci (QTL) conferring resistance to MRDD using 89 F8 recombinant inbred lines derived from a cross between X178 (resistant parent) and B73 (susceptible). The population was evaluated for MRDD resistance in Baoding, Hebei Province, China (a hot spot of MRDD incidence) under natural infection in 2008 and 2009 and artificial inoculation in 2010. Genotypic variances for disease severity index (DSI) were highly significant in the population. Heritability estimates for DSI evaluation were 0.472 and 0.467 in 2008 and 2009, respectively. The linkage map was constructed using 514 gene-derived single nucleotide polymorphisms (SNPs) and 72 simple sequence repeat markers, spanning a genetic distance of 1,059.72 cM with an average interval of 1.8 cM between adjacent markers. Multiple-QTL model mapping detected a major QTL for MRDD resistance on chromosome 8, explaining 24.6–37.3% of the phenotypic variation across three environments. In 2010, an additional QTL was detected on chromosome 10, explaining 15.8% of the phenotypic variation. The major QTL on chromosome 8 and the SNP markers (SNP31, SNP548, and SNP284) co-located with the QTL peak have potential for further functional genomic analysis and use in molecular marker-assisted selection for MRDD resistance in maize.