Biology subjects

Endelman, J. B.

Publications and source records attributed to Endelman, J. B..

4 recordsLinked to original sources

bioRxiv2020

QTL Mapping in Outbred Tetraploid (and Diploid) Diallel Populations

Over the last decade, multiparental populations have become a mainstay of genetics research in diploid species. Our goal was to extend this paradigm to autotetraploids by developing software for quantitative trait locus (QTL) mapping in connected F1 populations derived from a set of shared parents. For QTL discovery, phenotypes are regressed on the dosage of parental haplotypes to estimate additive effects. Statistical properties of the model were explored by simulating half-diallel diploid and tetraploid populations with different population sizes and numbers of parents. Across scenarios, the number of progeny per parental haplotype (pph) largely determined the statistical power for QTL detection and accuracy of the estimated haplotype effects. Multi-allelic QTL with heritability 0.2 were detected with 90% probability at 25 pph and genome-wide significance level 0.05, and the additive haplotype effects were estimated with over 90% accuracy. Following QTL discovery, the software enables a comparison of models with multiple QTL and non-additive effects. To illustrate, we analyzed potato tuber shape in a half-diallel population with 3 tetraploid parents. A well-known QTL on chromosome 10 was detected, for which the inclusion of digenic dominance lowered the Deviance Information Criterion (DIC) by 17 points compared to the additive model. The final model also contained a minor QTL on chromosome 1, but higher order dominance and epistatic effects were excluded based on the DIC. In terms of practical impacts, the software is already being used to select offspring based on the effect and dosage of particular haplotypes in breeding programs.

genetics↗

bioRxiv2020

Haplotype Reconstruction in Connected Tetraploid F1 Populations

In diploid species, many multi-parental populations have been developed to increase genetic diversity and quantitative trait loci (QTL) mapping resolution. In these populations, haplotype reconstruction has been used as a standard practice to increase QTL detection power in comparison with the marker-based association analysis. To realize similar benefits in tetraploid species (and eventually higher ploidy levels), a statistical framework for haplotype reconstruction has been developed and implemented in the software PolyOrigin for connected tetraploid F1 populations with shared parents. Haplotype reconstruction proceeds in two steps: first, parental genotypes are phased based on multi-locus linkage analysis; second, genotype probabilities for the parental alleles are inferred in the progeny. PolyOrigin can utilize genetic marker data from single nucleotide polymorphism (SNP) arrays or from sequence-based genotyping; in the latter case, bi-allelic read counts can be used (and are preferred) as input data to minimize the influence of genotype call errors at low depth. To account for errors in the input map, PolyOrigin includes functionality for filtering markers, inferring inter-marker distances, and refining local marker ordering. Simulation studies were used to investigate the effect of several variables on the accuracy of haplotype reconstruction, including the mating design, the number of parents, population size, and sequencing depth. PolyOrigin was further evaluated using an autotetraploid potato dataset with a 3x3 half-diallel mating design. In conclusion, PolyOrigin opens up exciting new possibilities for haplotype analysis in tetraploid breeding populations.

bioinformatics↗

bioRxiv2020

Characterization of a late blight resistance gene homologous to R2 in potato variety Payette Russet

Breeding for late blight resistance has traditionally relied on phenotypic selection, but as the number of characterized resistance (R) genes has grown, so have the possibilities for genotypic selection. One challenge for breeding russet varieties is the lack of information about the genetic basis of resistance in this germplasm group. Based on observations of strong resistance by Payette Russet to genotype US-23 of the late blight pathogen Phytophthora infestans in inoculated experiments, we deduced the variety must contain at least one major R gene. To identify the gene(s), 79 F1 progeny were screened using a detached leaf assay and classified as resistant vs. susceptible. Linkage mapping using markers from the potato SNP array revealed a single resistant haplotype on the short arm of chromosome group 4, which coincides with the R2/Rpi-abpt/Rpi-blb3 locus. PCR amplification and sequencing of the gene in Payette revealed it is homologous to R2, and transient expression experiments in Nicotiana benthamiana confirmed its recognition of the Avr2 effector. Sequencing of a small diversity panel revealed a SNP unique to resistant haplotypes at the R2 locus, which was converted to a KASP marker that showed perfect prediction accuracy in the F1 population and diversity panel. Although many genotypes of P. infestans are virulent against R2, even when defeated this gene may be valuable as one component of a multi-genic approach to quantitative resistance.

genetics↗

bioRxiv2019

Image-based Phenotyping and Genetic Analysis of Potato Skin Set and Color

Image-based phenotyping offers new opportunities for fast, objective, and reliable measurement for breeding and genetics research. In the current study, image analysis was used to quantify potato skin color and skin set, which are critical for the marketability of new varieties. A set of 15 red potato varieties and advanced breeding lines was evaluated over two years at a single location, with two harvest times in the second year. After mechanical harvest and grading, 7-8 representative tubers per plot were photographed, and the photos were analyzed with ImageJ to measure skinning (as % surface area) and skin color using the Hue, Chroma and Lightness (HCL) representation. The plot-based heritability was consistently high (> 0.77) across traits and environments; the genetic correlation between environments was also high, ranging from 0.81 to 0.98. Significant increases in Lightness and Chroma, as well as a decrease in skinning, were observed at the late compared to early harvest, while the opposite trends for color were observed after six weeks of storage. The three color traits were unexpectedly collinear in this study, with the first principal component explaining 86% of the variation. This result may reflect the physiology of red color in potato, but the highly selected nature of the 15 genotypes may also be a factor. Image-based phenotyping offers new opportunities to advance genetic gain and understanding for tuber appearance traits that have been difficult to precisely measure in the past.

genetics↗