Jeffrey B. Endelman
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View article: Potato dihaploids uncover diverse alleles to facilitate diploid potato breeding
Potato dihaploids uncover diverse alleles to facilitate diploid potato breeding Open
Commercial potato in North America is a clonal autotetraploid crop, which complicates breeding. Efforts are underway to convert potato to a diploid inbred-hybrid crop that is amenable to additional breeding strategies and allows breeders t…
View article: Erratum to: Targeted genotyping‐by‐sequencing of potato and data analysis with R/polyBreedR
Erratum to: Targeted genotyping‐by‐sequencing of potato and data analysis with R/polyBreedR Open
View article: Genomic prediction for potato ( <i>Solanum tuberosum</i> ) quality traits improved through image analysis
Genomic prediction for potato ( <i>Solanum tuberosum</i> ) quality traits improved through image analysis Open
Potato ( Solanum tuberosum L.) is the most widely grown vegetable in the world. Consumers and processors evaluate potatoes based on quality traits such as shape and skin color, making these traits important targets for breeders. Achieving …
View article: Genomic prediction of heterosis, inbreeding control, and mate allocation in outbred diploid and tetraploid populations
Genomic prediction of heterosis, inbreeding control, and mate allocation in outbred diploid and tetraploid populations Open
Breeders have long appreciated the need to balance selection for short-term genetic gain with maintaining genetic variance for long-term gain. For outbred populations, the method called Optimum Contribution Selection (OCS) chooses parental…
View article: Targeted genotyping‐by‐sequencing of potato and data analysis with R/polyBreedR
Targeted genotyping‐by‐sequencing of potato and data analysis with R/polyBreedR Open
Mid‐density targeted genotyping‐by‐sequencing (GBS) combines trait‐specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato ( Solanum tuberosu…
View article: Genotype-by-environment interactions and local adaptation shape selection in the US National Chip Processing Trial
Genotype-by-environment interactions and local adaptation shape selection in the US National Chip Processing Trial Open
Key message We find evidence of selection for local adaptation and extensive genotype-by-environment interaction in the potato National Chip Processing Trial (NCPT). Abstract We present a novel method for dissecting the interplay between s…
View article: Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR
Targeted genotyping-by-sequencing of potato and data analysis with R/polyBreedR Open
Mid-density targeted genotyping-by-sequencing (GBS) combines trait-specific markers with thousands of genomic markers at an attractive price for linkage mapping and genomic selection. A 2.5K targeted GBS assay for potato was developed usin…
View article: Development of KASP markers for the potato virus Y resistance gene<i>Rychc</i>using whole-genome resequencing data
Development of KASP markers for the potato virus Y resistance gene<i>Rychc</i>using whole-genome resequencing data Open
Potato virus Y is the most important potato virus worldwide, affecting tuber yield and quality. The resistance gene Rychc , derived from the potato wild relative Solanum chacoense , provides broad spectrum and durable resistance to the vir…
View article: Clonal diploid and autopolyploid breeding strategies to harness heterosis: insights from stochastic simulation
Clonal diploid and autopolyploid breeding strategies to harness heterosis: insights from stochastic simulation Open
View article: Epigenetic Modifications Related to Potato Skin Russeting
Epigenetic Modifications Related to Potato Skin Russeting Open
Potato tuber skin is a protective corky tissue consisting of suberized phellem cells. Smooth-skinned varieties are characterized by a clean, shiny appearance compared to the darker hue of russeted potatoes. The rough skin of russeted culti…
View article: Using haplotype and QTL analysis to fix favorable alleles in diploid potato breeding
Using haplotype and QTL analysis to fix favorable alleles in diploid potato breeding Open
At present, the potato ( Solanum tuberosum L.) of international commerce is autotetraploid, and the complexity of this genetic system creates limitations for breeding. Diploid potato breeding has long been used for population improvement, …
View article: Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection
Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection Open
Key message R/StageWise enables fully efficient, two-stage analysis of multi-environment, multi-trait datasets for genomic selection, including support for dominance heterosis and polyploidy. Abstract Plant breeders interested in genomic s…
View article: A KASP Marker for the Potato Late Blight Resistance Gene<i>RB</i>/<i>Rpi-blb1</i>
A KASP Marker for the Potato Late Blight Resistance Gene<i>RB</i>/<i>Rpi-blb1</i> Open
The disease late blight is a threat to potato production worldwide, making genetic resistance an important target for breeding. The resistance gene RB / Rpi-blb1 is effective against most strains of the causal pathogen, Phytophthora infest…
View article: Genomic selection and genome‐wide association studies in tetraploid chipping potatoes
Genomic selection and genome‐wide association studies in tetraploid chipping potatoes Open
Potato is a major food crop in the United States and around the world. Most potatoes grown in the United States are destined for processing. Genomic selection can speed up breeding progress for important traits, including those with comple…
View article: Using Haplotype and QTL Analysis to Fix Favorable Alleles in Diploid Potato Breeding
Using Haplotype and QTL Analysis to Fix Favorable Alleles in Diploid Potato Breeding Open
At present, the potato of international commerce is autotetraploid, and the complexity of this genetic system creates limitations for breeding. Diploid potato breeding has long been used for population improvement, and thanks to improved u…
View article: Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection
Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection Open
Plant breeders interested in genomic selection often face challenges to fully utilizing the multi-trait, multi-environment datasets they rely on for selection. R package StageWise was developed to go beyond the capabilities of most special…
View article: Clonal breeding strategies to harness heterosis: insights from stochastic simulation
Clonal breeding strategies to harness heterosis: insights from stochastic simulation Open
To produce genetic gain, hybrid crop breeding can change the additive as well as dominance genetic value of populations, which can lead to utilization of heterosis. A common hybrid breeding strategy is reciprocal recurrent selection (RRS),…
View article: The genetic architectures of vine and skin maturity in tetraploid potato
The genetic architectures of vine and skin maturity in tetraploid potato Open
Potato vine and skin maturity, which refer to foliar senescence and adherence of the tuber periderm, respectively, are both important to production and therefore breeding. Our objective was to investigate the genetic architectures of these…
View article: Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity
Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity Open
Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity, includin…
View article: Optimal Compost Rates for Organic Crop Production Based on a Decay Series
Optimal Compost Rates for Organic Crop Production Based on a Decay Series Open
One of the more challenging aspects of organic farming is the development of an appropriate fertility plan, which may include crop rotation, cover crops, and/or soil amendments. When fertility is maintained by applying manure and/or compos…
View article: QTL mapping in outbred tetraploid (and diploid) diallel populations
QTL mapping in outbred tetraploid (and diploid) diallel populations Open
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 co…
View article: Haplotype reconstruction in connected tetraploid F1 populations
Haplotype reconstruction in connected tetraploid F1 populations Open
In diploid species, many multiparental 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 …
View article: QTL Mapping in Outbred Tetraploid (and Diploid) Diallel Populations
QTL Mapping in Outbred Tetraploid (and Diploid) Diallel Populations Open
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 co…
View article: Haplotype Reconstruction in Connected Tetraploid F1 Populations
Haplotype Reconstruction in Connected Tetraploid F1 Populations Open
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…
View article: Characterization of a late blight resistance gene homologous to<i>R2</i>in potato variety Payette Russet
Characterization of a late blight resistance gene homologous to<i>R2</i>in potato variety Payette Russet Open
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 v…
View article: FIELDimageR: An R package to analyze orthomosaic images from agricultural field trials
FIELDimageR: An R package to analyze orthomosaic images from agricultural field trials Open
Remote sensing is revolutionizing the phenotyping of agricultural field trials, but for many researchers, the extraction of plot‐level results is a bottleneck. We have developed the R package FIELDimageR as a user‐friendly tool to analyze …
View article: Expected Genotype Quality and Diploidized Marker Data from Genotyping‐by‐Sequencing of <i>Urochloa</i> spp. Tetraploids
Expected Genotype Quality and Diploidized Marker Data from Genotyping‐by‐Sequencing of <i>Urochloa</i> spp. Tetraploids Open
Core Ideas Introduced concept of expected genotype quality (EGQ) and software to calculate it Provided read depth guidelines for GBS in tetraploids Developed software to generate diploidized genotype calls from VCF files Demonstrated value…
View article: Image-based Phenotyping and Genetic Analysis of Potato Skin Set and Color
Image-based Phenotyping and Genetic Analysis of Potato Skin Set and Color Open
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…
View article: Genomic Prediction of Autotetraploids; Influence of Relationship Matrices, Allele Dosage, and Continuous Genotyping Calls in Phenotype Prediction
Genomic Prediction of Autotetraploids; Influence of Relationship Matrices, Allele Dosage, and Continuous Genotyping Calls in Phenotype Prediction Open
Estimation of allele dosage, using genomic data, in autopolyploids is challenging and current methods often result in the misclassification of genotypes. Some progress has been made when using SNP arrays, but the major challenge is when us…
View article: Expected Genotype Quality and Diploidized Marker Data from Genotyping-by-Sequencing of <i>Urochloa</i> spp. Tetraploids
Expected Genotype Quality and Diploidized Marker Data from Genotyping-by-Sequencing of <i>Urochloa</i> spp. Tetraploids Open
Although genotyping-by-sequencing (GBS) is a well-established marker technology in diploids, the development of best practices for tetraploid species is a topic of current research. We determined the theoretical relationship between read d…