Enhancing maize's nitrogen-fixing potential through ZmSBT3, a gene suppressing mucilage secretion.

Maize (Zea mays) requires substantial amounts of nitrogen, posing a challenge for its cultivation. Recent work discovered that some ancient Mexican maize landraces harbored diazotrophic bacteria in mucilage secreted by their aerial roots. To see if this trait is retained in modern maize, we conducted a field study of aerial root mucilage (ARM) in 258 inbred lines. We observed that ARM secretion is common in modern maize, but the amount significantly varies, and only a few lines have retained the nitrogen-fixing traits found in ancient landraces. The mucilage of the high-ARM inbred line HN5-724 had high nitrogen-fixing enzyme activity and abundant diazotrophic bacteria. Our genome-wide association study identified 17 candidate genes associated with ARM across three environments. Knockouts of one candidate gene, the subtilase family gene ZmSBT3, confirmed that it negatively regulates ARM secretion. Notably, the ZmSBT3 knockout lines had increased biomass and total nitrogen accumulation under nitrogen-free culture conditions. High ARM was associated with three ZmSBT3 haplotypes that were gradually lost during maize domestication, being retained in only a few modern inbred lines such as HN5-724. In summary, our results identify ZmSBT3 as a potential tool for enhancing ARM, and thus nitrogen fixation, in maize.

Evaluation and Identification of Resistance Lines and QTLs of Maize to Seedborne Fusarium verticillioides.

Internal fungal contamination in cereal grains may affect plant growth and result in health concerns for humans and animals. Fusarium verticillioides is a seedborne fungus that can systemically infect maize. However, few efforts had been devoted to studying the genetics of maize resistance to seedborne F. verticillioides. In this study, we developed a disease evaluation method to identify resistance to seedborne F. verticillioides in maize, by which a set of 121 diverse maize inbred lines were evaluated. A 160 F10-generation recombinant inbred line (RIL) population derived from a cross of the resistant (BT-1) and susceptible (N6) inbred line was further used to identify major quantitative trait loci (QTLs) for seedborne F. verticillioides resistance. Eighteen inbred lines with a high resistance to seedborne F. verticillioides were characterized and could be used as potential germplasm resources for genetic improvement of maize resistance. Six QTLs with high heritability across multiple environments were detected on chromosomes 3, 4, 6, and 10, among which was a major QTL, qISFR4-1. Located on chromosome 4 at the interval of 12922609-13418025, qISFR4-1 could explain 16.63% of the total phenotypic variance. Distinct expression profiles of eight candidate genes in qISFR4-1 between BT-1 and N6 inbred lines suggested their pivotal regulatory roles in seedborne F. verticillioides resistance. Taken together, these results will improve our understanding of the resistant mechanisms of seedborne F. verticillioides and would provide valuable germplasm resources for disease resistance breeding in maize.

Linkage mapping and genome-wide association study reveals conservative QTL and candidate genes for Fusarium rot resistance in maize.

BACKGROUND: Fusarium ear rot (FER) caused by Fusarium verticillioides is a major disease of maize that reduces grain yield and quality globally. However, there have been few reports of major loci for FER were verified and cloned. RESULT: To gain a comprehensive understanding of the genetic basis of natural variation in FER resistance, a recombinant inbred lines (RIL) population and one panel of inbred lines were used to map quantitative trait loci (QTL) for resistance. As a result, a total of 10 QTL were identified by linkage mapping under four environments, which were located on six chromosomes and explained 1.0-7.1% of the phenotypic variation. Epistatic mapping detected four pairs of QTL that showed significant epistasis effects, explaining 2.1-3.0% of the phenotypic variation. Additionally, 18 single nucleotide polymorphisms (SNPs) were identified across the whole genome by genome-wide association study (GWAS) under five environments. Compared linkage and association mapping revealed five common intervals located on chromosomes 3, 4, and 5 associated with FER resistance, four of which were verified in different near-isogenic lines (NILs) populations. GWAS identified three candidate genes in these consistent intervals, which belonged to the Glutaredoxin protein family, actin-depolymerizing factors (ADFs), and AMP-binding proteins. In addition, two verified FER QTL regions were found consistent with Fusarium cob rot (FCR) and Fusarium seed rot (FSR). CONCLUSIONS: These results revealed that multi pathways were involved in FER resistance, which was a complex trait that was controlled by multiple genes with minor effects, and provided important QTL and genes, which could be used in molecular breeding for resistance.

Linkage mapping and genome-wide association reveal candidate genes conferring thermotolerance of seed-set in maize.

It is predicted that high-temperature stress will increasingly affect crop yields worldwide as a result of climate change. In order to determine the genetic basis of thermotolerance of seed-set in maize under field conditions, we performed mapping of quantitative trait loci (QTLs) in a recombinant inbred line (RIL) population using a collection of 8329 specifically developed high-density single-nucleotide polymorphism (SNP) markers, combined with a genome-wide association study (GWAS) of 261 diverse maize lines using 259 973 SNPs. In total, four QTLs and 17 genes associated with 42 SNPs related to thermotolerance of seed-set were identified. Among them, four candidate genes were found in both linkage mapping and GWAS. Thermotolerance of seed-set was increased significantly in near-isogenic lines (NILs) that incorporated the four candidate genes in a susceptible parent background. The expression profiles of two of the four genes showed that they were induced by high temperatures in the maize tassel in a tolerant parent background. Our results indicate that thermotolerance of maize seed-set is regulated by multiple genes each of which has minor effects, with calcium signaling playing a central role. The genes identified may be exploited in breeding programs to improve seed-set and yield of maize under heat stress.

Genetic analysis of cob resistance to F. verticillioides: another step towards the protection of maize from ear rot.

KEY MESSAGE: We lay the foundation for further research on maize resistance to Fusarium verticillioides cob rot by identifying a candidate resistance gene. Fusarium verticillioides ear rot is the most common type of maize ear rot in the Huanghuaihai Plain of China. Ear rot resistance includes cob and kernel resistance. Most of the current literature concentrates on kernel resistance, and genetic studies on cob resistance are scarce. We aimed on identifying the QTLs responsible for F. verticillioides cob rot (FCR) resistance. Twenty-eight genes associated with 48 single nucleotide polymorphisms (SNPs) were identified (P < 10-4) to correlate with FCR resistance using a whole-genome association study. The major quantitative trait locus, qRcfv2, for FCR resistance was identified on chromosome 2 through linkage mapping and was validated in near-isogenic line populations. Two candidate genes associated with two SNPs were detected in the qRcfv2 region with a lower threshold (P < 10-3). Through real-time fluorescence quantitative PCR, one candidate gene was found to have no expression in the cob but the other was expressed in response to F. verticillioides. These results lay a foundation for research on the resistance mechanisms of cob and provide resources for marker-assisted selection.

Field Inoculation and Classification of Maize Ear Rot Caused by Fusarium verticillioides.

Maize ear rot is a worldwide fungal disease mainly caused by Fusarium verticillioides and Fusarium graminearum. Maize planted in the field was inoculated with Fusarium verticillioides at the filling stage, 15 days after pollination. Two milliliters of spore suspension with a concentration of 5 x 106/ml was injected into the middle of the top ear using pricking ear method to cause maize ear rot. The thirty days after inoculation was the most suitable time for phenotypic evaluation of Fusarium resistance.