Enabling Molecular Breeding

Among the major food crops, potato is unique for being autotetraploid and clonally propagated. Autotetraploid genomes are organized in groups of four homologous chromosomes, which gives rise to more complex patterns of inheritance than in diploid crops. We are developing new methods and practical software solutions to enable molecular breeding in potato and other autotetraploids, such as alfalfa and blueberry.

Zheng et al. (2021) Haplotype reconstruction in connected tetraploid F1 populations

Amadeu et al. (2021) QTL mapping in outbred tetraploid (and diploid) diallel populations

Rosyara et al. (2016) Software for genome-wide association studies in autopolyploids and its application to potato

Genomic selection aims to predict the performance of new breeding lines based on phenotypes from related germplasm and genome-wide markers. We are using this technology to shorten the breeding cycle while maintaining selection accuracy in potato.

Endelman (2023) Fully efficient, two-stage analysis of multi-environment trials with directional dominance and multi-trait genomic selection.

Schmitz Carley et al. (2019) Genetic covariance of environments in the Potato National Chip Processing Trial.

Endelman et al. (2018) Genetic variance partitioning and genome-wide prediction with allele dosage information in autotetraploid potato.

Image-based Phenotyping

The Endelman Lab is using image analysis to increase the automation and reliability of phenotyping for several traits of importance to potato breeding. One application is characterizing the appearance and integrity of potato tuber skin, which has a major influence on marketability. Another example is the evaluation of fry color and defects in potato chips. We are also using unmanned aerial vehicles to collect images throughout the growing season for improved measurements of canopy development and maturity.

Caraza-Harter and Endelman (2022) The genetic architectures of vine and skin maturity in tetraploid potato.

Caraza-Harter and Endelman (2020) Image-based phenotyping and genetic analysis of potato skin set and color. 

Matias et al. (2020) FIELDimageR: An R package to analyze orthomosaic images from agricultural field trials.


Diploid Breeding & Genetics

At present, commercial potato varieties and elite breeding stocks are heterozygous, autotetraploid clones maintained in vitro. This genetic complexity is an impediment to rapid breeding progress, and the biology of vegetative production in potato imposes limits on the multiplication rate and economics of seed production. Our goal is to create a new paradigm for potato breeding based on inbred, diploid lines that can be sexually hybridized to generate true potato seed (TPS) of F1 hybrid varieties. There are many benefits of inbred lines for breeding and genetics research, including more rapid discovery and introgression of beneficial genes from exotic germplasm, more efficient storage of germplasm as true seed, and more economical genotyping. The phytosanitary and freight advantages of TPS have been recognized for decades, but previous attempts to commercialize TPS-varieties based on autotetraploid parents have been unsuccessful.

Song and Endelman (2023) Using haplotype and QTL analysis to fix favorable alleles in diploid potato breeding

Endelman and Jansky (2016) Genetic mapping with an inbred line-derived F2 population in potato