ANALYSIS OF NUCLEI FLUORESCENCE HISTOGRAMS USING NON-LINEAR FUNCTIONS OR WAVELETS

Histograms based on 5,000 nuclei from cells (Chinese hamster ovary cells, bone marrow cells) are used to determine the coefficient of variation (CV) of observations surrounding the highest peak. The cells are subjected to various treatments, for example exposure to herbicides. By eyeballing the histogram, an interval under the highest peak is determined. The CV calculated from the histogram on the eyeballed interval is the response variable in an ANOVA. To avoid the subjectivity of eyeballing the histogram, non-linear functions such as the Gaussian density function can be used to model the histogram. The CV may then be determined from the parameter estimates. In many experiments nonlinear functions modeling the histograms smooth away differences in CV s obtained this way, though visually the histograms appear to be different. Then nonlinear functions or wavelets can be used to obtain intervals for calculating CV s of the histograms restricted to these intervals. The nonlinear models require close initial values for each histogram, while the wavelets just require choice of wavelet and level of decomposition

Phenotypic and Biomass Yield Variations in Natural Populations of Prairie Cordgrass (Spartina pectinata Link) in the USA

Prairie cordgrass (Spartina pectinata Link) is a productive warm-season, C4 perennial grass native to most of North America having tolerance to wet, cold, and saline growing conditions. Excellent stress tolerance, along with high biomass yields, makes prairie cordgrass a good candidate as a dedicated energy crop on marginal land. However, there is little information available on genetic variation, including yield potential, of native populations in the USA. The objectives of this study were to evaluate biomass yield and to identify the nature and extent of genetic variation in natural populations of prairie cordgrass by comparing endemic strains collected throughout the USA. Forty-two prairie cordgrass populations were collected from prairie-remnant sites in 13 states and evaluated at the University of Illinois in Urbana, IL. The 4-year field study of prairie cordgrass revealed extensive variations in biomass yield and phenotypic traits associated with biomass yield among these populations. Strong correlations were observed between the phenotypic values and origins of the populations. Path coefficient analysis indicated that tiller mass, tiller density, heading date, plant height, and phytomer number positively affected biomass yield directly or indirectly. However, the phenotypic traits including biomass yield showed significant variation among years except for phytomer number and heading date. With the extensive genetic variability and high biomass yield potential demonstrated in this experiment, prairie cordgrass could become a highly productive bioenergy crop by developing a well-planned breeding program

Insight Into Genomic Changes Accompanying Divergence: Genetic Linkage Maps and Synteny of Lucania goodei and L. parva Reveal a Robertsonian Fusion

Linkage maps are important tools in evolutionary genetics and in studies of speciation. We performed a karyotyping study and constructed high-density linkage maps for two closely related killifish species, Lucania parva and L. goodei, that differ in salinity tolerance and still hybridize in their contact zone in Florida. Using SNPs from orthologous EST contigs, we compared synteny between the two species to determine how genomic architecture has shifted with divergence. Karyotyping revealed that L. goodei possesses 24 acrocentric chromosomes (1N) whereas L. parva possesses 23 chromosomes (1N), one of which is a large metacentric chromosome. Likewise, high-density single-nucleotide polymorphism−based linkage maps indicated 24 linkage groups for L. goodei and 23 linkage groups for L. parva. Synteny mapping revealed two linkage groups in L. goodei that were highly syntenic with the largest linkage group in L. parva. Together, this evidence points to the largest linkage group in L. parva being the result of a chromosomal fusion. We further compared synteny between Lucania with the genome of a more distant teleost relative medaka (Oryzias latipes) and found good conservation of synteny at the chromosomal level. Each Lucania LG had a single best match with each medaka chromosome. These results provide the groundwork for future studies on the genetic architecture of reproductive isolation and salinity tolerance in Lucania and other Fundulidae

L.parva joinmap file for all families

This excel file contains the joinmap data for all of the families used to resolve the L. parva linkage map. Each F2 family is listed on a separate excel sheet. The joinmap code for each individual at each SNP marker is listed. The individuals are the progeny of an F2 cross between two L. parva populations (Indian River Lagoon, FL and Pecos River, TX populations). Also, the segregation type and the phase of each marker is listed. These are joinmap codes

Data from: Insight into genomic changes accompanying divergence: genetic linkage maps and synteny of Lucania goodei and L. parva reveal a Robertsonian fusion

Linkage maps are important tools in evolutionary genetics and in studies of speciation. We performed a karyotyping study and constructed high-density linkage maps for two closely related killifish species, Lucania parva and Lucania goodei, that differ in salinity tolerance and still hybridize in their contact zone in Florida. Using SNPs from orthologous EST contigs, we compared synteny between the two species to determine how genomic architecture has shifted with divergence. Karyotyping revealed that L. goodei possesses 24 acrocentric chromosomes (1N) while L. parva possesses 23 chromosomes (1N), one of which is a large metacentric chromosome. Likewise, high-density SNP-based linkage maps indicated 24 linkage groups for L. goodei and 23 linkage groups for L. parva. Synteny mapping revealed two linkage groups in L. goodei that were highly syntenic with the largest linkage group in L. parva. Together, this evidence points to the largest linkage group in L. parva being the result of a chromosomal fusion. We further compared synteny between Lucania with the genome of a more distant teleost relative medaka (Oryzias latipes) and found good conservation of synteny at the chromosomal level. Each Lucania linkage group had a single best match with each medaka chromosome. These results provide the groundwork for future studies on the genetic architecture of reproductive isolation and salinity tolerance in Lucania and other Fundulidae

L.goodei_contigs

This file contains 454 EST sequences that were used as a reference for assembling our new Illumina reads. These EST sequences were created using pooled DNA from several populations. See the ReadMe file for further details. Dassanayake M, Haas JS, Bohnert HJ, Cheeseman JM (2009) Shedding light on an extremophile lifestyle through transcriptomics. New Phytologist 183, 764-775

L. goodei joinmap file for all families

This excel file contains the joinmap data for all of the families used to resolve the L. goodei linkage map. Each family is listed on a separate excel sheet. The joinmap code for each individual at each SNP marker is listed. The individuals are the progeny of an F2 cross between two L. goodei populations (Upper Bridge River of the Wakulla River and Everglades populations). Also, the segregation type and the phase of each marker is listed. These are joinmap codes