Donald L. Auger

Understanding mechanisms of novel gene expression in polyploids

Polyploidy has long been recognized as a prominent force shaping the evolution of eukaryotes, especially flowering plants. New phenotypes often arise with polyploid formation and can contribute to the success of polyploids in nature or their selection for use in agriculture. Although the causes of novel variation in polyploids are not well understood, they could involve changes in gene expression through increased variation in dosage-regulated gene expression, altered regulatory interactions, and rapid genetic and epigenetic changes. New research approaches are being used to study these mechanisms and the results should provide a more complete understanding of polyploidy.

In Search of the Molecular Basis of Heterosis

Heterosis, or hybrid vigor, refers to the phenomenon that progeny of diverse inbred varieties exhibit greater biomass, speed of development, and fertility than the better of the two parents ([Figure 1][1]). This phenomenon has been exploited extensively in crop production and has been a powerful

Rapid Invasion of a Great Lakes Coastal Wetland by Non-native Phragmites australis and Typha

ABSTRACT Great Lakes coastal wetlands are subject to water level fluctuations that promote the maintenance of coastal wetlands. Point au Sauble, a Green Bay coastal wetland, was an open water lagoon as of 1999, but became entirely vegetated as Lake Michigan experienced a prolonged period of below-average water levels. Repeat visits in 2001 and 2004 documented a dramatic change in emergent wetland vegetation communities. In 2001 non-native Phragmites and Typha were present but their cover was sparse; in 2004 half of the transect was covered by a 3 m tall, invasive Phragmites and non-native Typha community. Percent similarity between plant species present in 2001 versus 2004 was approximately 19% (Jaccards coefficient), indicating dramatic changes in species composition that took place in only 3 years. The height of the dominant herbaceous plants and coverage by invasive species were significantly higher in 2004 than they were in 2001. However, floristic quality index and coefficient of conservatism were greater in 2004 than 2001. Cover by plant litter did not differ between 2001 and 2004. The prolonged period of below-average water levels between 1999 and early 2004 exposed unvegetated lagoon bottoms as mud flats, which provided substrate for new plant colonization and created conditions conducive to colonization by invasive taxa. PCR/RFLP analysis revealed that Phragmites from Point au Sauble belongs to the more aggressive, introduced genotype. It displaces native vegetation and is tolerant of a wide range of water depth. Therefore it may disrupt the natural cycles of vegetation replacement that occur under native plant communities in healthy Great Lakes coastal wetlands.

Genomic dosage effects on heterosis in triploid maize

The genetic basis of hybrid vigor or heterosis has been debated for more than a century. A popular hypothesis to explain this phenomenon is that there are different slightly deleterious recessive homozygous alleles in the two parents and that these alleles are complemented in the hybrid so that the biomass and fertility exceed both parents. To address the complementation hypothesis in a direct manner, heterosis was examined in diploid inbreds and reciprocal hybrids and compared with matched triploid inbred derivatives and two types of triploid hybrids that differ in the number of genomes from the different parents. Complementation of recessive mutations would occur equally in the two types of triploid hybrids predicting that, if this complementation were the sole basis of the heterotic response, the two types of triploid hybrids would be equivalent for hybrid vigor. However, the reciprocal diploid hybrids were similar for six of nine measured traits, but the two types of triploid hybrids differed significantly for eight of the same traits. Importantly, the triploid hybrids differed in the level of high-parent heterosis relative to the derived triploid inbreds. Also, the differences observed between the reciprocal triploid hybrids correlated strongly with differences observed between the inbreds, either at the diploid or triploid level, in a manner explicable by genome dosage rather than parent of origin effects. The findings of this study suggest that a major component of heterosis is a mechanism that is modulated by dosage-sensitive factors that involves allelic diversity across the genome.

Minichromosomes derived from the B chromosome of maize.

Fourteen minichromosomes derived from the B chromosome of maize are described. The centromeric region of the B chromosome contains a specific repetitive DNA element called the B repeat. This sequence was used to determine the transmission frequency of the different types of minichromosomes over several generations via Southern blot analysis at each generation. In general, the minichromosomes have transmission rates below the theoretical 50% frequency of a univalent chromosome. The gross structure of each minichromosome was determined using fluorescence in situ hybridization (FISH) on root tip chromosome spreads. The presence of the B centromeric repeat and of the adjacent heterochromatic knob sequences was determined for each minichromosome. In two cases, the amount of the centromeric knob repeat is increased relative to the progenitor chromosome. Other isolates have reduced or undetectable levels of the knob sequence. Potential uses of the minichromosomes are discussed.

A test for a metastable epigenetic component of heterosis using haploid induction in maize.

We conducted a test to detect if there is a heritable epigenetic component to hybrid vigor and/or inbreeding depression. The impetus for this work was a classical study of the effect of homozygosis on the expression of the maize red color (r1) locus. It had been shown that maintaining R1 mottling alleles in the homozygous state over several generations produces a progressive decrease of their paternally imprinted expression. This effect is reversed by R1/r1 allele heterozygosity. If this behavior were characteristic of many regulatory genes, then such a phenomenon could contribute to inbreeding depression and heterosis. To examine this question, inbreds of Mo17 and B73 and the two reciprocally produced hybrids were crossed by Stock 6 to generate four classes of maternal haploids. The mature haploid plants were measured for several quantitative traits. If inbreeding depression results from an accumulating heritable effect that is reversed by the hybrid state, one would expect the haploids derived from the hybrids to perform better than those derived from the inbred lines. The hybrid-derived haploids did not exhibit greater average performance than the inbred-derived haploids. These data fail to support the hypothesis that inbreeding depression and heterosis have a metastable epigenetic component.

A test for ectopic exchange catalyzed by Cre recombinase in maize

A maize line expressing Cre recombinase as well as the recipient line without the transgene were assayed for evidence of ectopic recombination within the maize genome. Such a test is valuable for understanding the action of Cre as well as for its use to recombine two target lox sites present in the chromosomes. Pollen examination and seed set tests of material expressing Cre provided no evidence of ectopic recombination, which would be manifested in the production of translocations or inversions and result in pollen abortion and reduced seed set. Root-tip chromosome karyotype analysis was also performed on material with and without Cre expression. Chromosomal aberrations in Cre+ material were not observed above the background level.

Plant Chromosomal Deletions, Insertions, and Rearrangements

With the exception of a small subset found within mitochondria and chloroplasts, the genes of plants are arranged along an essential set of chromosomes that are found in the nucleus. Within a species, the placement of genes along the chromosomes is expected to be the same in all individuals. This chapter is a primer on several major aberrations of gene order. These aberrations have consequences not only to the individual that harbors them but also to the population at large in terms of genome evolution. Here, we limit our discussion mainly to the effects on the individual. We are particularly interested in the use of these aberrations as experimental tools and include some discussions to that effect.

The genetics and genome-wide screening of perennialism loci in Zea diploperennis

Perennialism is common among the higher plants, yet we know little about its inheritance. To address this, six hybrids were made by reciprocally crossing perennial Zea diploperennis Iltis, Doebley & R. Guzman with three varieties/inbred lines of annual maize (Z. mays L. spp. mays). We specifically focused on the plants ability to regrow after flowering and senescence. All the F1 plants demonstrated senescence and regrowth for several cycles, indicating a dominant effect of the Z. diploperennis alleles. The regrowth ability was stably transmitted to progeny of the hybrids in segregation ratios that suggested the trait was controlled by two dominant, complementary loci. Genome-wide screening with genotyping-by-sequencing (GBS) identified two major regrowth loci reg1 and reg2 on chromosomes 2 and 7, respectively. GBS results were validated using a larger F2 population and PCR markers derived from the single nucleotide polymorphisms within the locus intervals. These markers will be employed to select near-isogenic lines for the two loci and to identify candidate genes in the loci in Z. diploperennis.Perennialism is common among the higher plants, yet little is known about its inheritance. To address this, six hybrids were made by reciprocally crossing perennial Zea diploperennis Iltis, Doebley & R. Guzman with inbred lines B73 and Mo17 and Rhee Flint, a heirloom variety, of Z. mays L. ssp. mays. All the F1 plants demonstrated several cycles of growth, flowering, senescence and regrowth into normal flowering plants, indicating a dominant effect of the Z. diploperennis alleles. The regrowability (i.e. the plants’ ability to regrow after senescence) was stably transmitted to progeny of the hybrids, so we focused on this trait. Segregation ratios in the F2 generations are consistent with the trait controlled by two dominant, complementary loci, but do not exclude the influence of other modifiers or environment. Genome-wide screening with genotyping-by-sequencing (GBS) indicated two major regrowth loci, regrowth 1 and regrowth 2, were on chromosomes 2 and 7, respectively. These findings lay the foundation for further exploration of the molecular mechanism of regrowth in Z. diploperennis. Significance Statement This study contributes to the general understanding of inheritance of perennialism in the higher plants. Previous genetic studies of the perennialism in Zea have yielded contradictory results. We take a reductionist approach by specifically focusing on one trait, the plant’s ability to restart a new life cycle after senescence on the same body. While traits, such as rhizome formation, tillering and dormancy may be important to converting Z. mays to becoming truly perennial, understanding the conditions for regrowth after senescence will be substantial first step. Importantly, our data indicate that there is no major barrier to transferring this trait into maize or other grass crops for perennial crop development with proper technology, which enhances sustainability of grain crop production in an environmentally friendly way. This manuscript was previously deposited as a preprint at http://dx.doi.org/10.1101/388256.