Genetic characterization of the Cy transposable element system at the Bz locus of Zea mays L.

The unstable bz-rcy allele arose by the insertion of a receptor element, rcy, into the Bz locus of a single gamete from the TEL population. Mutability of bz-rcy is controlled by the independently segregating regulatory element Cy (Cycler). In the absence of Cy, bz-rcy conditions a stable bronze aleurone. In the presence of Cy, bz-rcy conditions many small fully colored spots on a bronze background. These two elements, rcy and Cy, were previously undescribed;Genetic tests have established a relationship between Cy and the Mutator system. Cy is not functionally homologous to any of the non-Mutator transposable element systems;The number of genetically active Cy elements in a plant can increase or decrease via Cy transposition;Nonresponsive derivatives of bz-rcy have been isolated. A model has been established to explain the loss of the distal markers C and Sh coincident with the origin of some of these derivatives;The original isolate of bz-rcy often generates derivative alleles (states) that condition altered spotting patterns, e.g., reduced numbers of spots and/or larger and smaller spots, that reflect alterations in the frequency and timing of rcy excisions from bz-rcy. In contrast to receptors of the Ac and En(Spm) systems, which undergo changes of state only in the presence of the appropriate regulatory element, bz-rcy can undergo changes of state in the absence of an active Cy;Cy changes of state occur less frequently than those of bz-rcy. States of Cy have been isolated that induce reduced rates (but not altered timing) of rcy excision from bz-rcy. Many of the Cy states show progressive loss of function over succeeding generations;Many bz-rcy states and some Cy states have the ability to revert to fine-high spotting (cycling). Cycling is developmentally regulated and occurs only in the presence of Cy. A model has been proposed which evokes a form of reversible DNA modification to explain the cycling phenomenon and the origin of bz-rcy states in the absence of Cy;Of 47 diverse maize lines assayed, only two sources were found to contain strong Cy elements, i.e., Mutator-related stocks and the TEL population. Of the remaining lines, six, contained weak Cy elements and the rest lacked genetically detectable Cy elements

Harnessing Phenotypic Plasticity to Improve Maize Yields

Plants can produce different phenotypes when exposed to different environments. Understanding the genetic basis of these plastic responses is crucial for crop breeding efforts. We discuss two recent studies that suggest that yield plasticity in maize has been under selection but is controlled by different genes than yield

tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci

Conventional genotyping-by-sequencing (cGBS) strategies suffer from high rates of missing data and genotyping errors, particularly at heterozygous sites. tGBS® genotyping-by-sequencing is a novel method of genome reduction that employs two restriction enzymes to generate overhangs in opposite orientations to which (single-strand) oligos rather than (double-stranded) adaptors are ligated. This strategy ensures that only doubledigested fragments are amplified and sequenced. The use of oligos avoids the necessity of preparing adaptors and the problems associated with inter-adaptor annealing/ligation. Hence, the tGBS protocol simplifies the preparation of high-quality GBS sequencing libraries. During polymerase chain reaction (PCR) amplification, selective nucleotides included at the 3\u27-end of the PCR primers result in additional genome reduction as compared to cGBS. By adjusting the number of selective bases, different numbers of genomic sites are targeted for sequencing. Therefore, for equivalent amounts of sequencing, more reads per site are available for SNP calling. Hence, as compared to cGBS, tGBS delivers higher SNP calling accuracy (\u3e97–99%), even at heterozygous sites, less missing data per marker across a population of samples, and an enhanced ability to genotype rare alleles. tGBS is particularly well suited for genomic selection, which often requires the ability to genotype populations of individuals that are heterozygous at many loci

The roles of aldehyde dehydrogenases (ALDHs) in the PDH bypass of Arabidopsis

<p>Abstract</p> <p>Background</p> <p>Eukaryotic aldehyde dehydrogenases (ALDHs, EC 1.2.1), which oxidize aldehydes into carboxylic acids, have been classified into more than 20 families. In mammals, Family 2 ALDHs detoxify acetaldehyde. It has been hypothesized that plant Family 2 ALDHs oxidize acetaldehyde generated via ethanolic fermentation, producing acetate for acetyl-CoA biosynthesis via acetyl-CoA synthetase (ACS), similar to the yeast pathway termed the "pyruvate dehydrogenase (PDH) bypass". Evidence for this pathway in plants has been obtained from pollen.</p> <p>Results</p> <p>To test for the presence of the PDH bypass in the sporophytic tissue of plants, Arabidopsis plants homozygous for mutant alleles of all three Family 2 ALDH genes were fed with ¹⁴C-ethanol along with wild type controls. Comparisons of the incorporation rates of ¹⁴C-ethanol into fatty acids in mutants and wild type controls provided direct evidence for the presence of the PDH bypass in sporophytic tissue. Among the three Family 2 ALDHs, one of the two mitochondrial ALDHs (ALDH2B4) appears to be the primary contributor to this pathway. Surprisingly, single, double and triple ALDH mutants of Arabidopsis did not exhibit detectable phenotypes, even though a Family 2 ALDH gene is required for normal anther development in maize.</p> <p>Conclusion</p> <p>The PDH bypass is active in sporophytic tissue of plants. Blocking this pathway via triple ALDH mutants does not uncover obvious visible phenotypes.</p

Intragenic Meiotic Crossovers Generate Novel Alleles with Transgressive Expression Levels

Meiotic recombination is an evolutionary force that generates new genetic diversity upon which selection can act. Whereas multiple studies have assessed genome-wide patterns of recombination and specific cases of intragenic recombination, few studies have assessed intragenic recombination genome-wide in higher eukaryotes. We identified recombination events within or near genes in a population of maize recombinant inbred lines (RILs) using RNA-sequencing data. Our results are consistent with case studies that have shown that intragenic crossovers cluster at the 5\u27 ends of some genes. Further, we identified cases of intragenic crossovers that generate transgressive transcript accumulation patterns, that is, recombinant alleles displayed higher or lower levels of expression than did nonrecombinant alleles in any of ~100 RILs, implicating intragenic recombination in the generation of new variants upon which selection can act. Thousands of apparent gene conversion events were identified, allowing us to estimate the genome-wide rate of gene conversion at SNP sites (4.9 X 10-5). The density of syntenic genes (i.e., those conserved at the same genomic locations since the divergence of maize and sorghum) exhibits a substantial correlation with crossover frequency, whereas the density of nonsyntenic genes (i.e., those which have transposed or been lost subsequent to the divergence of maize and sorghum) shows little correlation, suggesting that crossovers occur at higher rates in syntenic genes than in nonsyntenic genes. Increased rates of crossovers in syntenic genes could be either a consequence of the evolutionary conservation of synteny or a biological process that helps to maintain synteny

Meta-analysis identifies pleiotropic loci controlling phenotypic trade-offs in sorghum

Community association populations are composed of phenotypically and genetically diverse accessions. Once these populations are genotyped, the resulting marker data can be reused by different groups investigating the genetic basis of different traits. Because the same genotypes are observed and scored for a wide range of traits in different environments, these populations represent a unique resource to investigate pleiotropy. Here, we assembled a set of 234 separate trait datasets for the Sorghum Association Panel, a group of 406 sorghum genotypes widely employed by the sorghum genetics community. Comparison of genome-wide association studies (GWAS) conducted with two independently generated marker sets for this population demonstrate that existing genetic marker sets do not saturate the genome and likely capture only 35–43% of potentially detectable loci controlling variation for traits scored in this population. While limited evidence for pleiotropy was apparent in cross-GWAS comparisons, a multivariate adaptive shrinkage approach recovered both known pleiotropic effects of existing loci and new pleiotropic effects, particularly significant impacts of known dwarfing genes on root architecture. In addition, we identified new loci with pleiotropic effects consistent with known trade-offs in sorghum development. These results demonstrate the potential for mining existing trait datasets from widely used community association populations to enable new discoveries from existing trait datasets as new, denser genetic marker datasets are generated for existing community association populations