Cell wall composition and biomass digestibility diversity in Mexican maize (Zea mays L) landraces and CIMMYT inbred lines

Maize is one of the most important crops worldwide. Historically, breeding efforts in this crop have been primarily focused on the improvement of grain yield and stability and just recently also on the potential utility of maize stover (above ground biomass excluding the grain) as a source of biomass for the production of feed, fiber and cellulosic ethanol. The International Maize and Wheat Improvement Center (CIMMYT) holds one of the largest maize germplasm collections in the world and therefore is an important source of phenotypic and genetic diversity for many traits. Our objectives were to assess the phenotypic diversity for cell wall composition and biomass digestibility in Mexican tropical, subtropical and highland maize landraces and elite maize lines (CMLs) in the CIMMYT germplasm collection, as well as to evaluate the relationship between place of origin of these materials and phenotypic expression of biomass compositional traits. The range of variation for neutral detergent fiber for three groups of landraces was from 47 to 73%. Slightly larger levels of phenotypic variation were observed for this trait in the set of CMLs evaluated (42 to 78%). Some of the inbred lines, such as CML 507, presented superior characteristics in terms of cell wall composition and digestibility. The Tuxpeño tropical-subtropical race, widely used in CIMMYT breeding programs, formed a cluster characterized by high cell wall content and low biomass digestibility. The CIMMYT germplasm collection appears to be a vast source of untapped genetic and phenotypic variation for the improvement of maize biomass composition

A high-throughput core sampling device for the evaluation of maize stalk composition

<p>Abstract</p> <p>Background</p> <p>A major challenge in the identification and development of superior feedstocks for the production of second generation biofuels is the rapid assessment of biomass composition in a large number of samples. Currently, highly accurate and precise robotic analysis systems are available for the evaluation of biomass composition, on a large number of samples, with a variety of pretreatments. However, the lack of an inexpensive and high-throughput process for large scale sampling of biomass resources is still an important limiting factor. Our goal was to develop a simple mechanical maize stalk core sampling device that can be utilized to collect uniform samples of a dimension compatible with robotic processing and analysis, while allowing the collection of hundreds to thousands of samples per day.</p> <p>Results</p> <p>We have developed a core sampling device (CSD) to collect maize stalk samples compatible with robotic processing and analysis. The CSD facilitates the collection of thousands of uniform tissue cores consistent with high-throughput analysis required for breeding, genetics, and production studies. With a single CSD operated by one person with minimal training, more than 1,000 biomass samples were obtained in an eight-hour period. One of the main advantages of using cores is the high level of homogeneity of the samples obtained and the minimal opportunity for sample contamination. In addition, the samples obtained with the CSD can be placed directly into a bath of ice, dry ice, or liquid nitrogen maintaining the composition of the biomass sample for relatively long periods of time.</p> <p>Conclusions</p> <p>The CSD has been demonstrated to successfully produce homogeneous stalk core samples in a repeatable manner with a throughput substantially superior to the currently available sampling methods. Given the variety of maize developmental stages and the diversity of stalk diameter evaluated, it is expected that the CSD will have utility for other bioenergy crops as well.</p

Data from: Insights into the maize pan-genome and pan-transcriptome

Genomes at the species level are dynamic, with genes present in every individual (core) and genes in a subset of individuals (dispensable) that collectively constitute the pan-genome. Using transcriptome sequencing of seedling RNA from 503 maize (Zea mays) inbred lines to characterize the maize pan-genome, we identified 8681 representative transcript assemblies (RTAs) with 16.4% expressed in all lines and 82.7% expressed in subsets of the lines. Interestingly, with linkage disequilibrium mapping, 76.7% of the RTAs with at least one single nucleotide polymorphism (SNP) could be mapped to a single genetic position, distributed primarily throughout the nonpericentromeric portion of the genome. Stepwise iterative clustering of RTAs suggests, within the context of the genotypes used in this study, that the maize genome is restricted and further sampling of seedling RNA within this germplasm base will result in minimal discovery. Genome-wide association studies based on SNPs and transcript abundance in the pan-genome revealed loci associated with the timing of the juvenile-to-adult vegetative and vegetative-to-reproductive developmental transitions, two traits important for fitness and adaptation. This study revealed the dynamic nature of the maize pan-genome and demonstrated that a substantial portion of variation may lie outside the single reference genome for a species

Transcript assemblies for representative transcripts generated in a joint assembly across 503 diverse maize inbred lines.

The assembly was generated from reads that could not be mapped to the maize v2 reference sequence. Only the representative transcript assembly for each locus, defined as the longest transcript within the locus, is presented in the file

Imputed Genotype Scores 438K Single Nucleotide Polymorphisms across 503 diverse maize inbred lines

The file is a CSV file with a header that contains genotype scores imputed using GAPIT

Fragments per kilo base of exon model perl million fragments mapped (FPKM) values for 503 diverse maize inbred lines.

This file is a tab delimited file with a header line. The columns in the file are gene name, chromosome, gene start, and gene stop followed by the expression data for the 503 inbred lines

Genome wide association study (GWAS) results for growing degree days to pollen shed, growing degree days to silk, and last leaf with juvenile wax.

The file is a tab delimated file with a header that contains GWAS results presented as p-values for ~438K SNPs. The columns in the file are SNP, chromosome, position, growing degree days to pollen shed p- values, growing degree days to silk p-values, and last leaf with juvenile wax p-values

Single Nucleotide Polymorphisms (SNPs) for 503 diverse maize inbred lines.

This is a tab delimited file with a header line that contains raw SNP data for 485,179 SNPs across 503 diverse maize inbred lines. The file contains a column for chromosome, position, the reference B73 v2 allele, number of missing data points, and observed alleles across the 503 inbred lines, followed by the data for the 503 inbred lines