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Rapid and Targeted Introgression of Traits via Genome Elimination


  • Comai Lab: Luca Comai (PI), Han Tan (co-PI), Kirk Amundson, Peter Lynagh, Livingstone Nganga, Benny Ordonez. Ek Han Tan was co-PI during 2015-2016 and is now at the University of Maine.
  • Britt Lab: Anne Britt (co-PI), Ross Johnson
  • CIP, Peru: Merideth Bonierbale (co-PI), Monica Santayana. Awais Khan was co-PI during 2015-2016 and is now at Cornell University.
  • Collaborators: Ek Han Tan (University of Maine); Ravi Maruthachalam (IISER-TVM, India)


A common plant breeding procedure involves moving valuable traits, such as disease resistance, from wild relatives to crop varieties. To achieve this, breeders cross a wild variety to a crop variety. The result is called a hybrid, and it mixes genes from both parents. Most of the genes from the wild variety, however, are unsuited for agriculture and must be cast away. This is done by repeated crossing to the crop variety, coupled to selection for the trait of interest, a process called backcrossing that often requires as many as 10 years. This constitutes a dramatic bottleneck to developing new varieties. Therefore, shortening the development time is particularly critical in the face of unexpected crop challenges when human sustenance depends on the rapid development of new, improved varieties. This project addresses this need. It aims at developing a method for rapid deployment of useful traits into crops, using potato as the experimental system. The collaboration between University of California-Davis and the International Potato Center will also train graduate and undergraduate students in genomic-based breeding. The method developed will be applicable in many crop species and will be useful for both basic and applied research.

Haploid induction, a process that generates plants with a single genome instead of the two parental ones, can significantly shorten the time it takes to make new varieties. However, no methods have resolved the problem of overcoming linkage drag, the common, negative association of deleterious genes with desirable ones. The project team discovered a method to facilitate the transfer of selected genomic regions to a target variety, providing a novel solution to make breeding faster and more efficient. The work plan combines rapid testing in the model plant Arabidopsis with exploration of natural and engineered haploid inducer systems in potato to develop methods for rapid and simple introgression of new traits in crops. The specific objectives are to 1) Exploit and develop haploid induction systems in potato, based on the S. tuberosum phureja haploid inducer as well as on manipulation of centromeric histone H3. 2) Engineer introgression of defined chromosomal segments from a donor to a recipient genome using different types of recombination mechanisms. Useful potato and Arabidopsis lines produced by this work will be deposited in, respectively, GRIN NRSP-6 ( and the ABRC (https:/ stock centers. Progress and resources will also be linked here.

The project started on Sep 2015. We are making good progress on all fronts.




NSF, IOS, Division Of Integrative Organismal Systems. Award Number:1444612

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