Genotyping by Sequencing Reveals Genetic Relatedness of Southwestern U.S. Blue Maize Landraces.

Maize has played a key role in the sustenance and cultural traditions of the inhabitants of the southwestern USA for many centuries. Blue maize is an important component of the diverse landraces still cultivated in the region but the degree to which they are related is unknown. This research was designed to ascertain the genotypic, morphological, and phenotypic diversity of six representative southwestern blue maize landraces. Their genotypic diversity was examined using tunable genotyping-by-sequencing (tGBS™). A total of 81,038 high quality SNPs were identified and obtained through tGBS. A total of 45 morphological and biochemical traits were evaluated at two locations in New Mexico. The varieties Los Lunas High and Flor del Rio were genetically less related with other southwestern landraces whereas diffusion between Navajo Blue, Hopi Blue, Yoeme Blue, and Taos Blue demonstrated that these landraces were genetically related. Phenotypic variability was highest for kernel traits and least for plant traits. Plant, ear, and kernel traits were fairly consistent within and across locations. Principal component analysis and tGBS showed that Corn Belt variety 'Ohio Blue' was distinctly different from southwestern landraces. Genotypic analysis displayed that southwestern landraces are genetically closely related, but selection has resulted in differing phenotypes. This study has provided additional insight into the genetic relatedness of southwestern blue maize landraces.

Compositional Analyses Reveal Relationships among Components of Blue Maize Grains.

One aim of this experiment was to develop NIR calibrations for 20-grain components in 143 pigmented maize samples evaluated in four locations across New Mexico during 2013 and 2014. Based on reference analysis, prediction models were developed using principal component regression (PCR) and partial least squares (PLS). The predictive ability of calibrations was generally low, with the calibrations for methionine and glycine performing best by PCR and PLS. The second aim was to explore the relationships among grain constituents. In PCA, the first three PCs explained 49.62, 22.20, and 6.92% of the total variance and tend to align with nitrogen-containing compounds (amino acids), carbon-rich compounds (starch, anthocyanin, fiber, and fat), and sulfur-containing compounds (cysteine and methionine), respectively. Correlations among traits were identified, and these relationships were illustrated by a correlation network. Some relationships among components were driven by common synthetic origins, for example, among amino acids derived from pyruvate. Similarly, anthocyanins, crude fat, and fatty acids all share malonyl CoA in their biosynthetic pathways and were correlated. In contrast, crude fiber and starch have similar biosynthetic origins but were negatively correlated, and this may have been due to their different functional roles in structure and energy storage, respectively.

Quantitative and qualitative evaluation of kernel anthocyanins from southwestern United States blue corn.

BACKGROUND: Anthocyanin-rich blue corn is an emerging specialty crop in the USA. The antioxidant properties of blue corn offer health benefits in the human diet. The objectives of this study were to identify, characterize and quantify the anthocyanins from blue corn. Hypotheses tested were that total anthocyanin content was similar among southwestern US accessions and that it would vary across locations. It was also examined whether different anthocyanin components were unique to certain genotypes. RESULTS: Across all locations and accessions, an average of 0.43 g kg(-1) total anthocyanin content (TAC) was observed. Accessions Santa Clara Blue and Ohio Blue displayed the highest TAC. The TAC of accession Flor del Rio was lower by nearly a factor of six. A total of five anthocyanin components were identified. Cyanidin 3-glucoside was the most abundant, followed by pelargonidin and peonidin 3-glucoside. Succinyl and disuccinyl glycosidic forms of cyanidin were also identified. Cyanidin 3-disuccinylglucoside was newly identified as a novel form of anthocyanin. CONCLUSION: Quantitative and qualitative anthocyanin expression was determined to be relatively stable across multiple southwestern environments. Increased expression of red and purple pigmentation in accession Flor del Rio appeared to be associated more with reduced TAC and cyanidin 3-glucoside than with elevated pelargonidin per se. A previously unreported anthocyanin component in blue corn, cyanidin 3-disuccinylglucoside, is present in southwestern landraces. © 2016 Society of Chemical Industry.

The bacterium Pantoea stewartii uses two different type III secretion systems to colonize its plant host and insect vector.

Plant- and animal-pathogenic bacteria utilize phylogenetically distinct type III secretion systems (T3SS) that produce needle-like injectisomes or pili for the delivery of effector proteins into host cells. Pantoea stewartii subsp. stewartii (herein referred to as P. stewartii), the causative agent of Stewart's bacterial wilt and leaf blight of maize, carries phylogenetically distinct T3SSs. In addition to an Hrc-Hrp T3SS, known to be essential for maize pathogenesis, P. stewartii has a second T3SS (Pantoea secretion island 2 [PSI-2]) that is required for persistence in its flea beetle vector, Chaetocnema pulicaria (Melsh). PSI-2 belongs to the Inv-Mxi-Spa T3SS family, typically found in animal pathogens. Mutagenesis of the PSI-2 psaN gene, which encodes an ATPase essential for secretion of T3SS effectors by the injectisome, greatly reduces both the persistence of P. stewartii in flea beetle guts and the beetle's ability to transmit P. stewartii to maize. Ectopic expression of the psaN gene complements these phenotypes. In addition, the PSI-2 psaN gene is not required for P. stewartii pathogenesis of maize and is transcriptionally upregulated in insects compared to maize tissues. Thus, the Hrp and PSI-2 T3SSs play different roles in the life cycle of P. stewartii as it alternates between its insect vector and plant host.

Mapping resistance quantitative trait Loci for three foliar diseases in a maize recombinant inbred line population-evidence for multiple disease resistance?

Southern leaf blight (SLB), gray leaf spot (GLS), and northern leaf blight (NLB) are all important foliar diseases impacting maize production. The objectives of this study were to identify quantitative trait loci (QTL) for resistance to these diseases in a maize recombinant inbred line (RIL) population derived from a cross between maize lines Ki14 and B73, and to evaluate the evidence for the presence genes or loci conferring multiple disease resistance (MDR). Each disease was scored in multiple separate trials. Highly significant correlations between the resistances and the three diseases were found. The highest correlation was identified between SLB and GLS resistance (r = 0.62). Correlations between resistance to each of the diseases and time to flowering were also highly significant. Nine, eight, and six QTL were identified for SLB, GLS, and NLB resistance, respectively. QTL for all three diseases colocalized in bin 1.06, while QTL colocalizing for two of the three diseases were identified in bins 1.08 to 1.09, 2.02/2.03, 3.04/3.05, 8.05, and 10.05. QTL for time to flowering were also identified at four of these six loci (bins 1.06, 3.04/3.05, 8.05, and 10.05). No disease resistance QTL was identified at the largest-effect QTL for flowering time in bin 10.03.

Genetic control of photoperiod sensitivity in maize revealed by joint multiple population analysis.

Variation in maize for response to photoperiod is related to geographical adaptation in the species. Maize possesses homologs of many genes identified as regulators of flowering time in other species, but their relation to the natural variation for photoperiod response in maize is unknown. Candidate gene sequences were mapped in four populations created by crossing two temperate inbred lines to two photoperiod-sensitive tropical inbreds. Whole-genome scans were conducted by high-density genotyping of the populations, which were phenotyped over 3 years in both short- and long-day environments. Joint multiple population analysis identified genomic regions controlling photoperiod responses in flowering time, plant height, and total leaf number. Four key genome regions controlling photoperiod response across populations were identified, referred to as ZmPR1-4. Functional allelic differences within these regions among phenotypically similar founders suggest distinct evolutionary trajectories for photoperiod adaptation in maize. These regions encompass candidate genes CCA/LHY, CONZ1, CRY2, ELF4, GHD7, VGT1, HY1/SE5, TOC1/PRR7/PPD-1, PIF3, ZCN8, and ZCN19.

Validation of consensus quantitative trait loci associated with resistance to multiple foliar pathogens of maize.

Maize production in sub-Saharan Africa incurs serious losses to epiphytotics of foliar diseases. Quantitative trait loci conditioning partial resistance (rQTL) to infection by causal agents of gray leaf spot (GLS), northern corn leaf blight (NCLB), and maize streak have been reported. Our objectives were to identify simple-sequence repeat (SSR) molecular markers linked to consensus rQTL and one recently identified rQTL associated with GLS, and to determine their suitability as tools for selection of improved host resistance. We conducted evaluations of disease severity phenotypes in separate field nurseries, each containing 410 F2:3 families derived from a cross between maize inbred CML202 (NCLB and maize streak resistant) and VP31 (a GLS-resistant breeding line) that possess complimentary rQTL. F2:3 families were selected for resistance based on genotypic (SSR marker), phenotypic, or combined data and the selected F3:4 families were reevaluated. Phenotypic values associated with SSR markers for consensus rQTL in bins 4.08 for GLS, 5.04 for NCLB, and 1.04 for maize streak significantly reduced disease severity in both generations based on single-factor analysis of variance and marker-interval analysis. These results were consistent with the presence of homozygous resistant parent alleles, except in bin 8.06, where markers were contributed by the NCLB-susceptible parent. Only one marker associated with resistance could be confirmed in bins 2.09 (GLS) and 3.06 (NCLB), illustrating the need for more robust rQTL discovery, fine-mapping, and validation prior to undertaking marker-based selection.

Shades of gray: the world of quantitative disease resistance.

A thorough understanding of quantitative disease resistance (QDR) would contribute to the design and deployment of durably resistant crop cultivars. However, the molecular mechanisms that control QDR remain poorly understood, largely due to the incomplete and inconsistent nature of the resistance phenotype, which is usually conditioned by many loci of small effect. Here, we discuss recent advances in research on QDR. Based on inferences from analyses of the defense response and from the few isolated QDR genes, we suggest several plausible hypotheses for a range of mechanisms underlying QDR. We propose that a new generation of genetic resources, complemented by careful phenotypic analysis, will produce a deeper understanding of plant defense and more effective utilization of natural resistance alleles.

Heritability and Components of Resistance to Cercospora zeae-maydis Derived from Maize Inbred VO613Y.

ABSTRACT Gray leaf spot (GLS), caused by the fungus Cercospora zeae-maydis, is one of the most important foliar diseases of maize. This study was undertaken to estimate heritability of C. zeae-maydis resistance and examine the relationship between previously identified resistance loci and certain components of resistance including incubation period, lesion number, and maximum lesion length. Partially inbred progenies arising from hybridization between maize inbred lines VO613Y (high level of partial resistance) and Pa405 (susceptible) were examined in Ohio and South Africa. Heritability estimates of resistance were calculated based on severity and incubation period values. The range of heritability estimates based on severity was broad, with values ranging from approximately 0.46 to 0.81 (mean = 0.59). Estimates of mean heritability for incubation period were lowest (0.18), indicating that this component would likely be unsuitable for selection of germ plasm intended for deployment in diverse regions. Length of GLS lesions was significantly affected by host genotype, with resistant genotypes having shorter lesions from one site in Ohio during two seasons. Genotype also had a significant effect on incubation period and lesion number; the lower values for these components also were associated with resistant genotypes. The combined action of these resistance components resulted in lower overall disease severity.

Effect of environment on resistance to the European corn borer (Lepidoptera: Crambidae) in maize.

The European corn borer, Ostrinia nubilalis (Hübner) (Lepidoptera: Crambidae), is a major pest of maize, Zea mays L., in many temperate parts of the world. Genotype-by-environment interaction effects can make relative performance unpredictable and may hamper selection for resistance to European corn borer. The objective of this study was to determine the effect of environment on genotypic reaction to European corn borer resistance in maize. A set of 12 maize inbred lines was chosen to represent a range of European corn borer responses. Eleven testing environments ranged from Delaware, Ohio, Illinois, Iowa, Nebraska, Missouri, to Mississippi. For length of stalk tunneling, environmental and genotypic main effects (estimated by restricted maximum likelihood) were >20- and 10-fold larger than their interaction effect, respectively. Length of tunneling means for genotypes (across environments) ranged from 10.1 to 35.4 cm. Several putatively resistant genotypes grouped with the susceptible checks, B73 and Mol7. By breaking factors and the interaction into single degree of freedom components, we observed that GEMS-0001 had significant crossover interactions toward less susceptibility in both Mississippi and the Nebraska environments. Environments displaying several crossover interactions indicated that European corn borer screening at these sites would not necessarily apply to other locations, whether due to small differences in experimental conduct and/or environmental effects. The five most resistant genotypes were fairly consistent across environments. Because all environments except Illinois used larvae from the same insectary, and these environments differed in damage intensity and rankings, it is unlikely that insect biotype was a factor contributing to genotype-by-environment effects.

Expression and nucleotide sequence of an INS (3) P1 synthase gene associated with low-phytate kernels in maize (Zea mays L.).

Most of the phosphorus (P) in maize (Zea mays L.) kernels is in the form of phytic acid. A low phytic acid (lpa) maize mutant, lpa1-1, displays levels reduced by 66%. A goal of genetic breeding is development of low phytic acid feedstocks to improve P nutrition of nonruminant animals and reduce the adverse environmental impacts of excess P in manure. The genetic basis of the lpa1-1 mutation is not known, but previous genetic mapping has shown both the mutant phenotype and the Ins (3) P(1) synthase (MIPS) gene, which encodes the first enzyme, myo-inositol phosphate synthase, in the phytic acid biosynthetic pathway, map to the same chromosomal region in maize. Research was conducted to determine the expression of the MIPS gene in lpa1-1 and wild-type kernels with similar genetic backgrounds and to ascertain if variation in the MIPS coding sequence could be inferred to be the basis of the mutation. MIPS enzyme activity determined by TLC was reduced 2-3-fold in mutant kernels. RT-PCR-based experiments using primers specific for the 1S-MIPS sequence indicated gene expression was reduced 50-60% in the mutant. Sequence analysis of the MIPS genomic sequence revealed 10 exons and 9 introns that are identical in both mutant and wild-type developing kernels. These findings support an association between reduced MIPS gene activity and low phytic acid content, but additional research should examine the promoter, the 5'UTR, or transcriptional controlling elements of the MIPS gene to ascertain the possible presence of a genetic lesion in those regions.