Serving as a community resource, Panzea () is the bioinformatics arm of the Molecular and Functional Diversity in the Maize Genome project. Maize, a classical model for genetic studies, is an important crop species and also the most diverse crop species known. On average, two randomly chosen maize lines have one single-nucleotide polymorphism every ∼100 bp; this divergence is roughly equivalent to the differences between humans and chimpanzees. This exceptional genotypic diversity underlies the phenotypic diversity maize needs to be cultivated in a wide range of environments. The Molecular and Functional Diversity in the Maize Genome project aims to understand how selection has shaped molecular diversity in maize and then relate molecular diversity to functional phenotypic variation. The project will screen 4000 loci for the signature of selection and create a wide range of maize and maize–teosinte mapping populations. These populations will be genotyped and phenotyped, permitting high-power and high-resolution dissection of the traits and relating the molecular diversity to functional variation. Panzea provides access to the genotype, phenotype and polymorphism data produced by the project through user-friendly web-based database searches and data retrieval/visualization tools, as well as a wide variety of information and services related to maize diversity.

/pdf/panzea-a-database-and-resource-for-molecular-and-functional-1lf2fid6g1.pdf

Panzea: a database and resource for molecular and functional diversity in the maize genome - eScholarship

Flowering time is an important agronomic trait of crops and significantly affects plant adaptation and seed production. Flowering time varies greatly among maize (Zea mays) inbred lines, but the genetic basis of this variation is not well understood. Here, we report the comprehensive genetic architecture of six flowering time-related traits using a recombinant inbred line (RIL) population obtained from a cross between two maize genotypes, B73 and Abe2, and combined with genome-wide association studies to identify candidate genes that affect flowering time.Our results indicate that these six traits showed extensive phenotypic variation and high heritability in the RIL population. The flowering time of this RIL population showed little correlation with the leaf number under different environmental conditions. A genetic linkage map was constructed by 10,114 polymorphic markers covering the whole maize genome, which was applied to QTL mapping for these traits, and identified a total of 82 QTLs that contain 13 flowering genes. Furthermore, a combined genome-wide association study and linkage mapping analysis revealed 17 new candidate genes associated with flowering time.In the present study, by using genetic mapping and GWAS approaches with the RIL population, we revealed a list of genomic regions and candidate genes that were significantly associated with flowering time. This work provides an important resource for the breeding of flowering time traits in maize. 

/pdf/linkage-mapping-combined-with-gwas-revealed-the-genetic-pj5gl66v.pdf

Linkage mapping combined with GWAS revealed the genetic structural relationship and candidate genes of maize flowering time-related traits

Brown midrib (BMR) maize (Zea mays L.) harbors mutations that result in lower lignin levels and higher feed digestibility, making it a desirable silage market class for ruminant nutrition. Northern leaf blight (NLB) epidemics in upstate New York highlighted the disease susceptibility of commercially grown BMR maize hybrids. We found the bm1, bm2, bm3, and bm4 mutants in a W64A genetic background to be more susceptible to foliar fungal (NLB, gray leaf spot [GLS], and anthracnose leaf blight [ALB]) and bacterial (Stewart's wilt) diseases. The bm1, bm2, and bm3 mutants showed enhanced susceptibility to anthracnose stalk rot (ASR), and the bm1 and bm3 mutants were more susceptible to Gibberella ear rot (GER). Colocalization of quantitative trait loci (QTL) and correlations between stalk strength and disease traits in recombinant inbred line families suggest possible pleiotropies. The role of lignin in plant defense was explored using high‐resolution, genome‐wide association analysis for resistance to NLB in the Goodman diversity panel. Association analysis identified 100 single and clustered single‐nucleotide polymorphism (SNP) associations for resistance to NLB but did not implicate natural functional variation at bm1–bm5. Strong associations implicated a suite of diverse candidate genes including lignin‐related genes such as a β‐glucosidase gene cluster, hct11, knox1, knox2, zim36, lbd35, CASP‐like protein 8, and xat3. The candidate genes are targets for breeding quantitative resistance to NLB in maize for use in silage and nonsilage purposes.

Brown midrib mutant and genome‐wide association analysis uncover lignin genes for disease resistance in maize

Despite lignin having long been viewed as an impediment to the processing of biomass for the production of paper, biofuels, and high-value chemicals, the valorization of lignin to fuels, chemicals, and materials is now clearly recognized as a critical element for the lignocellulosic bioeconomy. However, the intended application for lignin will likely require a preferred lignin composition and form. To that end, effective lignin valorization will require the integration of plant biology, providing optimal feedstocks, with chemical process engineering, providing efficient lignin transformations. Recent advances in our understanding of lignin biosynthesis have shown that lignin structure is extremely diverse and potentially tunable, while simultaneous developments in lignin refining have resulted in the development of several processes that are more agnostic to lignin composition. Here, we review the interface between in planta lignin design and lignin processing and discuss the advances necessary for lignin valorization to become a feature of advanced biorefining. 

Enabling Lignin Valorization Through Integrated Advances in Plant Biology and Biorefining

Bacterial leaf streak (BLS) of maize is an emerging foliar disease of maize in the Americas. It is caused by the gram-negative non-vascular bacterium Xanthomonas vasicola pv. vasculorum (Xvv). There are no chemical controls available for BLS, and thus, host resistance is crucial for managing Xvv. The objective of this study was to examine the genetic determinants of resistance to Xvv in maize, as well as the relationship between other defense-related traits and BLS resistance. Specifically, we examined the correlations among BLS severity, severity for three fungal diseases, flg-22 response, hypersensitive response and auricle color. We conducted quantitative trait locus (QTL) mapping for Xvv resistance using the maize recombinant inbred line population Z003 (B73 × CML228). We detected three QTL for BLS resistance. In addition to the disease resistance QTL, we detected a single QTL for auricle color. We observed significant, yet weak, correlations among BLS severity, levels of pattern-triggered immunity (PTI) response and leaf flecking. These results will be useful for understanding resistance to Xvv and mitigating the impact of BLS on maize yields. 

Exploring the relationship between pattern-triggered immunity and quantitative resistance to Xanthomonas vasicola pv. vasculorum in maize

Genome-wide association (GWA) studies can identify quantitative trait loci (QTL) putatively underlying traits of interest, and nested association mapping (NAM) can further assess allelic series. Near-isogenic lines (NILs) can be used to characterize, dissect and validate QTL, but the development of NILs is costly. Previous studies have utilized limited numbers of NILs and introgression donors. We characterized a panel of 1270 maize NILs derived from crosses between 18 diverse inbred lines and the recurrent inbred parent B73, referred to as the nested NILs (nNILs). The nNILs were phenotyped for flowering time, height and resistance to three foliar diseases, and genotyped with genotyping-by-sequencing. Across traits, broad-sense heritability (0.4-0.8) was relatively high. The 896 genotyped nNILs contain 2638 introgressions, which span the entire genome with substantial overlap within and among allele donors. GWA with the whole panel identified 29 QTL for height and disease resistance with allelic variation across donors. To date, this is the largest and most diverse publicly available panel of maize NILs to be phenotypically and genotypically characterized. The nNILs are a valuable resource for the maize community, providing an extensive collection of introgressions from the founders of the maize NAM population in a B73 background combined with data on six agronomically important traits and from genotyping-by-sequencing. We demonstrate that the nNILs can be used for QTL mapping and allelic testing. The majority of nNILs had four or fewer introgressions, and could readily be used for future fine mapping studies.

/pdf/genotypic-and-phenotypic-characterization-of-a-large-diverse-2u6x4544az.pdf

Genotypic and phenotypic characterization of a large, diverse population of maize near‐isogenic lines

Brown midrib (BMR) maize harbors mutations that result in lower lignin levels and higher feed digestibility, making it a desirable silage market class for ruminant nutrition. Northern leaf blight (NLB) epidemics in upstate NY highlighted the disease susceptibility of commercially grown BMR maize hybrids. We found the bm1, bm2, bm3 and bm4 mutants in a W64A genetic background to be more susceptible to foliar fungal (NLB, gray leaf spot, and anthracnose leaf blight) and bacterial (Stewart’s wilt) diseases. The bm1, bm2 and bm3 mutants showed enhanced susceptibility to anthracnose stalk rot, and the bm1 and bm3 mutants were more susceptible to Gibberella ear rot. Co-localization of quantitative trait loci and correlations between stalk strength and disease traits in recombinant inbred line families suggest possible pleiotropies. The role of lignin in plant defense was explored using high-resolution, genome-wide association analysis for resistance to NLB in the Goodman diversity panel. Association analysis identified 100 single and clustered SNP associations for resistance to NLB, but did not implicate natural functional variation at bm1-bm5. Strong associations implicated a suite of diverse candidate genes, including lignin-related genes such as a β-glucosidase gene cluster, hct11, knox1, knox2, zim36, lbd35, CASP-like protein 8, and xat3. The candidate genes are targets for breeding quantitative resistance to NLB in maize for use in silage and non-silage purposes. Core Ideas Brown midrib mutants (bm1-bm4) in maize, characterized as mutations with reduced lignin content, are susceptible to a range of foliar pathogens. Several brown midrib mutants in maize show enhanced susceptibility to stalk rot and ear rot pathogens. Genome wide association analysis identified a number of diverse candidate genes associated with resistance to northern leaf blight in maize, including lignin-related genes involved in the monolignol pathway, developmental genes and transcription factors. Association analysis for resistance to NLB implicated a β-glucosidase gene cluster, including Zmbglu24 and Zmbglu25 known for targeting monolignols and contributing to ∼15% phenotypic variation. hct11, which plays an important role in the monolignol pathway, was implicated for resistance to northern leaf blight in maize with potential for multiple stress tolerance.

Uncovering the roles of lignin-related genes in disease resistance in maize using mutant and association analysis

Sorghum grain mold (SGM) is an important multifungal disease complex affecting sorghum (Sorghum bicolor) production systems worldwide. SGM-affected sorghum grain can be contaminated with potent fumonisin mycotoxins produced by Fusarium verticillioides, a prevalent SGM-associated taxon. Historically, efforts to improve resistance to SGM have achieved only limited success. Classical approaches to evaluating SGM resistance are based solely on disease severity, which offers little insight regarding the distinct symptom manifestations within the disease complex. In this study, three novel phenotypes were developed to facilitate assessment of SGM symptom manifestation. A sorghum diversity panel composed of 390 accessions was inoculated with endogenous strains of F. verticillioides and evaluated for these phenotypes, as well as for the conventional panicle grain mold severity rating phenotype, in South Carolina, U.S.A., in 2017 and 2019. Distributions of phenotype values were examined, broad-sense heritability was estimated, and relationships to botanical race were explored. A typology of SGM symptom manifestations was developed to classify accessions using principal component analysis and k-means clustering, constituting a novel option for basing breeding decisions on SGM outcomes more nuanced than disease severity. Genome-wide association studies were performed using SGM trait data, resulting in the identification of 19 significant single nucleotide polymorphisms in linkage disequilibrium with a total of 86 gene models. Our findings provide a basis of exploratory evidence regarding the genetic architecture of SGM symptom manifestation and indicate that traits other than disease severity could be tractable targets for SGM resistance breeding.

Host Determinants of Fungal Species Composition and Symptom Manifestation in the Sorghum Grain Mold Disease Complex.

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Papers

Genotypic and phenotypic characterization of a large, diverse population of maize near‐isogenic lines

Brown midrib mutant and genome‐wide association analysis uncover lignin genes for disease resistance in maize

Uncovering the roles of lignin-related genes in disease resistance in maize using mutant and association analysis

Host Determinants of Fungal Species Composition and Symptom Manifestation in the Sorghum Grain Mold Disease Complex.