Biology subjects

Ivan Baxter

Publications and source records attributed to Ivan Baxter.

6 recordsLinked to original sources

bioRxiv2016

Genome-Wide Association Study of Ionomics Traits on Diverse Soybean Populations from Germplasm Collections

The elemental content of a soybean seed is a determined by both genetic and environmental factors and is an important component of its nutritional value. The elemental content is chemically stable, making the samples stored in germplasm repositories an intriguing source of experimental material. To test the efficacy of using samples from germplasm banks for gene discovery, we analyzed the elemental profile of seeds from 1653 lines in the USDA Soybean Germplasm Collection. We observed large differences in the elemental profiles based on where the lines were grown, which lead us to break up the genetic analysis into multiple small experiments. Despite these challenges, we were able to identify candidate SNPs controlling elemental accumulation as well as lines with extreme elemental accumulation phenotypes. Our results suggest that elemental analysis of germplasm samples can identify SNPs in linkage disequilibrium to genes, which can be leveraged to assist in crop improvement efforts.

Genetics↗

bioRxiv2016

The Interaction of Genotype and Environment Determines Variation in the Maize Kernel Ionome

Plants obtain soil-resident elements that support growth and metabolism via water-mediated flow facilitated by transpiration and active transport processes. The availability of elements in the environment interact with the genetic capacity of organisms to modulate element uptake through plastic adaptive responses, such as homeostasis. These interactions should cause the elemental contents of plants to vary such that the effects of genetic polymorphisms influencing elemental accumulation will be dramatically dependent on the environment in which the plant is grown. To investigate genotype by environment interactions underlying elemental accumulation, we analyzed levels of elements in maize kernels of the Intermated B73 x Mo17 (IBM) recombinant inbred population grown in 10 different environments spanning a total of six locations and five different years. In analyses conducted separately for each environment, we identified a total of 79 quantitative trait loci controlling seed elemental accumulation. While a set of these QTL were found in multiple environments, the majority were specific to a single environment, suggesting the presence of genetic by environment interactions. To specifically identify and quantify QTL by environment interactions (QEIs), we implemented two methods: linear modeling with environmental covariates and QTL analysis on trait differences between growouts. With these approaches, we found several instances of QEI, indicating that elemental profiles are highly heritable, interrelated, and responsive to the environment.\n\nAuthor SummaryPlants take up elements from the soil, a process that is highly regulated by the plants genome. To investigate how maize alters its elemental uptake in response to different environments, we analyzed the kernel elemental content of a population derived from a cross grown 10 different times in six locations. We found that environment had a profound effect on which genetic loci were important for elemental accumulation in the kernel. Our results suggest that to have a full understanding of elemental accumulation in maize kernels and other food crops, we will need to understand the interactions identified here at the level of the genes and the environmental variables that contribute to loading essential nutrients into seeds.

Plant Biology↗

bioRxiv2016

Forward genetics by sequencing EMS variation induced inbred lines.

In order to leverage novel sequencing techniques for cloning genes in eukaryotic organisms with complex genomes, the false positive rate of variant discovery must be controlled for by experimental design and informatics. We sequenced five lines from three pedigrees of EMS mutagenized Sorghum bicolor, including a pedigree segregating a recessive dwarf mutant. Comparing the sequences of the lines, we were able to identify and eliminate error prone positions. One genomic region contained EMS mutant alleles in dwarfs that were homozygous reference sequence in wild-type siblings and heterozygous in segregating families. This region contained a single non-synonymous change that cosegregated with dwarfism in a validation population and caused a premature stop codon in the sorghum ortholog encoding the giberellic acid biosynthetic enzyme ent-kaurene oxidase. Application of exogenous giberillic acid rescued the mutant phenotype. Our method for mapping did not require outcrossing and introduced no segregation variance. This enables work when line crossing is complicated by life history, permitting gene discovery outside of genetic models.This inverts the historical approach of first using recombination to define a locus and then sequencing genes. Our formally identical approach first sequences all the genes and then seeks co-segregation with the trait. Mutagenized lines lacking obvious phenotypic alterations are available for an extention of this approach: mapping with a known marker set in a line that is phenotypically identical to starting material for EMS mutant generation.

Genetics↗

bioRxiv2016

Phosphorus acquisition efficiency in arbuscular mycorrhizal maize is correlated with the abundance of root-external hyphae and the accumulation of transcripts encoding PHT1 phosphate transporters

O_LIPlant interactions with arbuscular mycorrhizal fungi have long excited interest for their potential to promote more efficient use of mineral resources in agricultural production. Their use, however, remains limited, in part because of a lack of understanding of the factors that determine symbiotic outcome. In this work, variation in response to arbuscular mycorrhizal colonization was characterized a panel of genetically diverse maize inbred lines.\nC_LIO_LIThe parents of the maize Nested Association Mapping population were evaluated, with and without colonization, in early vegetative stages. Subsequently, six lines with contrasting phenotypes were selected for further characterization, including quantification of fungal colonization, mycorrhiza-mediated phosphorus uptake, and accumulation of transcripts encoding plant PHT1 family phosphate transporters.\nC_LIO_LIThe relative growth of lines changed between non-inoculated and inoculated plants, indicative of variation in host capacity to profit from symbiosis. Patterns of Pht1 transcript accumulation varied among lines, and were correlated with outcome.\nC_LIO_LILarger growth responses were correlated with more extensive development of root-external hyphae, increased accumulation of specific Pht1 transcripts and a high level of mycorrhiza-mediated phosphorus uptake. The data suggest that host genetic factors influence fungal growth strategy with subsequent impact on plant biomass production.\nC_LI

Plant Biology↗

bioRxiv2016

Canopy position has a profound effect on soybean seed composition

Although soybean seeds appear homogeneous, their composition (protein, oil and mineral concentrations) can vary significantly with the canopy position where they were produced. In studies with 10 cultivars grown over a 3-yr period, we found that seeds produced at the top of the canopy have higher concentrations of protein but less oil and lower concentrations of minerals such as Mg, Fe, and Cu compared to seeds produced at the bottom of the canopy. Among cultivars, mean protein concentration (average of different positions) correlated positively with mean concentrations of S, Zn and Fe, but not other minerals. Therefore, on a whole plant basis, the uptake and allocation of S, Zn and Fe to seeds correlated with the production and allocation of reduced N to seed protein; however, the reduced N and correlated minerals (S, Zn and Fe) showed different patterns of allocation among node positions. For example, while mean concentrations of protein and Fe correlated positively, the two parameters correlated negatively in terms of variation with canopy position. Altering the microenvironment within the soybean canopy by removing neighboring plants at flowering increased protein concentration in particular at lower node positions and thus altered the node-position gradient in protein (and oil) without altering the distribution of Mg, Fe and Cu, suggesting different underlying control mechanisms. Metabolomic analysis of developing seeds at different positions in the canopy suggests that availability of free asparagine may be a positive determinant of storage protein accumulation in seeds and may explain the increased protein accumulation in seeds produced at the top of the canopy. Our results establish node-position variation in seed constituents and provide a new experimental system to identify genes controlling key aspects of seed composition. In addition, our results provide an unexpected and simple approach to link agronomic practices to improve human nutrition and health in developing countries because food products produced from seeds at the bottom of the canopy contained higher Fe concentrations than products from the top of the canopy. Therefore, using seeds produced in the lower canopy for production of iron-rich soy foods for human consumption could be important when plants are the major source of protein and human diets can be chronically deficient in Fe and other minerals.

Plant Biology↗

bioRxiv2015

Integration of experiments across diverse environments identifies the genetic determinants of variation in Sorghum bicolor seed element composition

AbstractSeedling establishment and seed nutritional quality require the sequestration of sufficient element nutrients. Identification of genes and alleles that modify element content in the grains of cereals, including Sorghum bicolor, is fundamental to developing breeding and selection methods aimed at increasing bioavailable element content and improving crop growth. We have developed a high throughput workflow for the simultaneous measurement of multiple elements in sorghum seeds. We measured seed element levels in the genotyped Sorghum Association Panel (SAP), representing all major cultivated sorghum races from diverse geographic and climatic regions, and mapped alleles contributing to seed element variation across three environments by genome-wide association. We observed significant phenotypic and genetic correlation between several elements across multiple years and diverse environments. The power of combining high-precision measurements with genome wide association was demonstrated by implementing rank transformation and a multilocus mixed model (MLMM) to map alleles controlling 20 element traits, identifying 255 loci affecting the sorghum seed ionome. Sequence similarity to genes characterized in previous studies identified likely causative genes for the accumulation of zinc (Zn) manganese (Mn), nickel (Ni), calcium (Ca) and cadmium (Cd) in sorghum seed. In addition to strong candidates for these four elements, we provide a list of candidate loci for several other elements. Our approach enabled identification of SNPs in strong LD with causative polymorphisms that can be evaluated in targeted selection strategies for plant breeding and improvement.\n\nOne sentence summaryHigh-throughput measurements of element accumulation and genome-wide association analysis across multiple environments identified novel alleles controlling seed element accumulation in Sorghum bicolor.\n\nThis project was partially funded by the iHUB Visiting Scientist Program (http://www.ionomicshub.org), Chromatin, Inc., NSF EAGER (1450341) to I.B. and BPD, NSF IOS 1126950 to IB, NSF IOS-0919739 to EC, and BMGF (OPP 1052924) to B.P.D.

Genetics↗