Jianyu Wu

Combined Linkage and Association Mapping Reveals QTL and Candidate Genes for Plant and Ear Height in Maize

Plant height (PH) and ear height (EH) are two very important agronomic traits related to the population density and lodging in maize. In order to better understand of the genetic basis of nature variation in PH and EH, two bi-parental populations and one genome-wide association study (GWAS) population were used to map quantitative trait loci (QTL) for both traits. Phenotypic data analysis revealed a wide normal distribution and high heritability for PH and EH in the three populations, which indicated that maize height is a highly polygenic trait. A total of 21 QTL for PH and EH in three common genomic regions (bin 1.05, 5.04/05, and 6.04/05) were identified by QTL mapping in the two bi-parental populations under multiple environments. Additionally, 41 single nucleotide polymorphisms (SNPs) were identified for PH and EH by GWAS, of which 29 SNPs were located in 19 unique candidate gene regions. Most of the candidate genes were related to plant growth and development. One QTL on Chromosome 1 was further verified in a near-isogenic line (NIL) population, and GWAS identified a C2H2 zinc finger family protein that maybe the candidate gene for this QTL. These results revealed that nature variation of PH and EH are strongly controlled by multiple genes with low effect and facilitated a better understanding of the underlying mechanism of height in maize.

The Genetic Basis of Natural Variation in Kernel Size and Related Traits Using a Four-Way Cross Population in Maize

Kernel size is an important component of grain yield in maize breeding programs. To extend the understanding on the genetic basis of kernel size traits (i.e., kernel length, kernel width and kernel thickness), we developed a set of four-way cross mapping population derived from four maize inbred lines with varied kernel sizes. In the present study, we investigated the genetic basis of natural variation in seed size and other components of maize yield (e.g., hundred kernel weight, number of rows per ear, number of kernels per row). In total, ten QTL affecting kernel size were identified, three of which (two for kernel length and one for kernel width) had stable expression in other components of maize yield. The possible genetic mechanism behind the trade-off of kernel size and yield components was discussed.

Genomic Dissection of Leaf Angle in Maize (Zea mays L.) Using a Four-Way Cross Mapping Population.

Increasing grain yield by the selection for optimal plant architecture has been the key focus in modern maize breeding. As a result, leaf angle, an important determinant of plant architecture, has been significantly improved to adapt to the ever-increasing plant density in maize production over the past several decades. To extend our understanding on the genetic mechanisms of leaf angle in maize, we developed the first four-way cross mapping population, consisting of 277 lines derived from four maize inbred lines with varied leaf angles. The four-way cross mapping population together with the four parental lines were evaluated for leaf angle in two environments. In this study, we reported linkage maps built in the population and quantitative trait loci (QTL) on leaf angle detected by inclusive composite interval mapping (ICIM). ICIM applies a two-step strategy to effectively separate the cofactor selection from the interval mapping, which controls the background additive and dominant effects at the same time. A total of 14 leaf angle QTL were identified, four of which were further validated in near-isogenic lines (NILs). Seven of the 14 leaf angle QTL were found to overlap with the published leaf angle QTL or genes, and the remaining QTL were unique to the four-way population. This study represents the first example of QTL mapping using a four-way cross population in maize, and demonstrates that the use of specially designed four-way cross is effective in uncovering the basis of complex and polygenetic trait like leaf angle in maize.

The Maize AAA-Type Protein SKD1 Confers Enhanced Salt and Drought Stress Tolerance in Transgenic Tobacco by Interacting with Lyst-Interacting Protein 5

ATPase associated with various cellular activities (AAA) proteins are important regulators involved in diverse cellular functions. To date, the molecular mechanisms of AAA proteins involved in response to salt and drought stresses in plants are largely unknown. In this study, a putative SKD1 (suppressor of K + transport growth defect 1) ortholog from Zea mays (ZmSKD1), which encodes a putative AAA protein, was isolated. The transcript levels of ZmSKD1 were higher in aerial tissues and were markedly up-regulated by salt or drought stress. Over-expression of ZmSKD1 in tobacco plants enhanced their tolerances not only to salt but to drought. Moreover, reactive oxygen species accumulations in ZmSKD1 transgenic lines were relative less than those in wild-type plants during salt or PEG-induced water stress. The interaction between ZmSKD1 and NtLIP5 (Lyst-Interacting Protein 5 homolog from Nicotiana tabacum) was confirmed by both yeast two-hybrid and immuno-precipitation assays; moreover, the α-helix-rich domain in the C-terminus of ZmSKD1 was identified to be required for its interaction with NtLIP5 using truncation mutations. Collectively, these data demonstrate that ZmSKD1could be involved in salt and drought stress responses and its over-expression enhances salt or drought stress tolerance possibly through interacting with LIP5 in tobacco. This study may facilitate our understandings of the biological roles of SKD1-mediated ESCRT pathway under stress conditions in higher plants and accelerate genetic improvement of crop plants tolerant to environmental stresses.

Quantitative Proteomic Analyses Identify ABA-Related Proteins and Signal Pathways in Maize Leaves under Drought Conditions

Drought stress is one of major factors resulting in maize yield loss. The roles of abscisic acid (ABA) have been widely studied in crops in response to drought stress. However, more attention is needed to identify key ABA-related proteins and also gain deeper molecular insights about drought stress in maize. Based on this need, the physiology and proteomics of the ABA-deficient maize mutant vp5 and its wild-type Vp5 under drought stress were examined and analyzed. Malondialdehyde content increased and quantum efficiency of photosystem II decreased under drought stress in both genotypes. However, the magnitude of the increase or decrease was significantly higher in vp5 than in Vp5. A total of 7051 proteins with overlapping expression patterns among three replicates in the two genotypes were identified by Multiplex run iTRAQ-based quantitative proteomic and liquid chromatography-tandem mass spectrometry methods, of which the expression of only 150 proteins (130 in Vp5, 27 in vp5) showed changes of at least 1.5-fold under drought stress. Among the 150 proteins, 67 and 60 proteins were up-regulated and down-regulated by drought stress in an ABA-dependent way, respectively. ABA was found to play active roles in regulating signaling pathways related to photosynthesis, oxidative phosphorylation (mainly related to ATP synthesis), and glutathione metabolism (involved in antioxidative reaction) in the maize response to drought stress. Our results provide an extensive dataset of ABA-dependent, drought-regulated proteins in maize plants, which may help to elucidate the underlying mechanisms of ABA-enhanced tolerance to drought stress in maize.

The Mechanisms of Maize Resistance to Fusarium verticillioides by Comprehensive Analysis of RNA-seq Data

Fusarium verticillioides is the most commonly reported fungal species responsible for ear rot of maize which substantially reduces grain yield. It also results in a substantial accumulation of mycotoxins that give rise to toxic response when ingested by animals and humans. For inefficient control by chemical and agronomic measures, it thus becomes more desirable to select more resistant varieties. However, the molecular mechanisms underlying the infection process remain poorly understood, which hampers the application of quantitative resistance in breeding programs. Here, we reveal the disease-resistance mechanism of the maize inbred line of BT-1 which displays high resistance to ear rot using RNA high throughput sequencing. By analyzing RNA-seq data from the BT-1 kernels before and after F. verticillioides inoculation, we found that transcript levels of genes associated with key pathways are dramatically changed compared with the control treatment. Differential gene expression in ear rot resistant and susceptible maize was confirmed by RNA microarray and qRT-PCR analyses. Further investigation suggests that the small heat shock protein family, some secondary metabolites, and the signaling pathways of abscisic acid, jasmonic acid, or salicylic acids (SA) may be involved in the pathogen-associated molecular pattern-triggered immunity against F. verticillioides. These data will not only provide new insights into the molecular resistant mechanisms against fungi invading, but may also result in the identification of key molecular factors associated with ear rot resistance in maize.

Genome-Wide Association Study and QTL Mapping Reveal Genomic Loci Associated with Fusarium Ear Rot Resistance in Tropical Maize Germplasm

Fusarium ear rot (FER) incited by Fusarium verticillioides is a major disease of maize that reduces grain quality globally. Host resistance is the most suitable strategy for managing the disease. We report the results of genome-wide association study (GWAS) to detect alleles associated with increased resistance to FER in a set of 818 tropical maize inbred lines evaluated in three environments. Association tests performed using 43,424 single-nucleotide polymorphic (SNPs) markers identified 45 SNPs and 15 haplotypes that were significantly associated with FER resistance. Each associated SNP locus had relatively small additive effects on disease resistance and accounted for 1–4% of trait variation. These SNPs and haplotypes were located within or adjacent to 38 candidate genes, 21 of which were candidate genes associated with plant tolerance to stresses, including disease resistance. Linkage mapping in four biparental populations to validate GWAS results identified 15 quantitative trait loci (QTL) associated with F. verticillioides resistance. Integration of GWAS and QTL to the maize physical map showed eight colocated loci on chromosomes 2, 3, 4, 5, 9, and 10. QTL on chromosomes 2 and 9 are new. These results reveal that FER resistance is a complex trait that is conditioned by multiple genes with minor effects. The value of selection on identified markers for improving FER resistance is limited; rather, selection to combine small effect resistance alleles combined with genomic selection for polygenic background for both the target and general adaptation traits might be fruitful for increasing FER resistance in maize.

Association mapping resolving the major loci Scmv2 conferring resistance to sugarcane mosaic virus in maize

Sugarcane mosaic virus (SCMV) is one of the most damaging virus diseases in maize. Two major loci, Scmv1 and Scmv2, have been identified in many studies across a broad spectrum of germplasm by linkage mapping. In this study, we undertook a genome-wide association study (GWAS) in a maize association panel comprising 504 diverse inbred lines with over 556,000 SNP markers in three environments. Extensive phenotypic variation of resistance to SCMV was observed in the association panel. GWAS identified five genes significantly associated with resistance to SCMV. A cluster of four genes was detected near or within the Scmv2 region on chromosome 3 (bin 3.05). GRMZM2G116204, which encoded auxin binding protein and resided within the fine-mapped Scmv2 region, was predicted as the most likely candidate gene for Scmv2. In conclusion, we found that GWAS along with linkage analyses are effective approaches to the mapping of resistance to SCMV and to the subsequent identification of causal genes.

Dissecting the genetic architecture of Fusarium verticillioides seed rot resistance in maize by combining QTL mapping and genome-wide association analysis

Fusarium verticillioides can be transmitted via seeds and cause systemic infection in maize (Zea mays L.); its mycotoxin has harmful effects on animal and human health. We combined QTL mapping in recombinant inbred line (RIL) populations with a genome-wide association study (GWAS) of 217 diverse maize lines using 224,152 single nucleotide polymorphisms (SNPs) under controlled conditions to determine the genetic architecture of F. verticillioides seed rot (FSR) resistance. Our study identified 8 quantitative trait loci (QTLs) and 43 genes associated with 57 SNPs that were correlated with FSR resistance through linkage mapping and GWAS, respectively. Among these, there were three candidate genes, namely GRMZM2G0081223, AC213654.3_FG004, and GRMZM2G099255, which were detected in both linkage mapping and GWAS. Furthermore, the near-isogenic lines (NILs) containing GRMZM2G0081223, which also had a susceptible parent background, were found to have a significantly improved level of resistance. In addition, the expression profile of the three candidate genes revealed that they all respond to the infection following inoculation with F. verticillioides. These genetic analyses indicate that FSR resistance is controlled by loci with minor effect, and the polymerization breeding of lines with beneficial alleles and candidate genes could improve FSR resistance in maize.

Sulfite Oxidase is Essential for Timely Germination of Maize Seeds upon Sulfite Exposure

Acid rain adversely affects maize seed germination by sulfite toxicity. Unfortunately, the molecular mechanisms underlying seed germination inhibition by sulfite in maize are largely unknown. Previously, the involvement of sulfite oxidase (SO) in sulfite detoxification in model plants was characterized. Here, we characterized Zea mays SO (ZmSO) in transgenic maize to investigate its role during seed germination upon sulfite exposure. ZmSO was responsive to sulfite stress at the transcriptional level during germination of maize seeds. Unlike the null mutant atso-1, ZmSO-overexpressing transgenic Arabidopsis plants were tolerant to SO2 stress and could effectively rescue the susceptible phenotype of atso-1. Silencing of ZmSO could lead to seed germination delay upon sulfite exposure, but not under normal conditions; interestingly, expressions of several seed germination-related genes encoding hydrolytic enzymes such as α-amylase, β-amylase, and glucosidase were reduced markedly in germinating seeds of ZmSO-compromised lines. This indicates that embryonic SO might alleviate the inhibitory effect of toxic sulfite by sulfite oxidation and the modulation of several hydrolytic enzymes during seed germination. Collectively, these data demonstrate that embryonic SO could be essential for timely seed germination upon sulfite exposure in maize. ZmSO might be a promising target for genetic improvement of crops tolerant to acid rain in molecular breeding programs.