Examining the history and impact of gene content variation in sunflower

The proposed research will contribute to new resources for the sunflower genomics community including new draft genome assemblies and annotations for wild Helianthus annuus and an early domesticate. We will also test our hypothesis that copy number variation has been an important contributor to sunflower domestication, and by combining this knowledge with our gene expression datasets and published trait mapping datasets, we may highlight variants useful for further improvement of agronomic traits like yield, oil content, and stress resistance. Finally, this project will test whether the applications of optical mapping can be extended to identifying large chromosomal variants that distinguish pools of DNAs. In addition to the use of this approach to examine the historical action of divergent selection on these variants as proposed here, this application could also be applied for bulk segregant mapping of trait variation in crosses developed from contemporary germplasm. Finally, the collaboration will train junior scientists, enrich ongoing and future research projects by the collaborating labs, and expand the range and quality of services of the primary French facility for agricultural genomics.

One of the most impactful insights gained from the onslaught of sequence data being generated for plant genomes using high-throughput genomic sequencing technologies is a single individual’s genome may contain just half of the total gene set present across all individuals of the species as a whole. In other words, a substantial portion of the genes present in one individual’s genome may be absent from the genome of another individual or vice versa. Consequently, the pan-genome, or the total functional gene sequence present among all individuals of a species, is far larger than the content annotated in a single reference genome. These gene presence/absence polymorphisms segregating among individuals within species arise through large duplication, insertion, or deletion events and can be important sources of variation that have contributed in the past to crop domestication or adaptation of wild populations to local habitats. Moreover, this form of variation is also a critical source of genetic diversity to draw upon in the future to improve crop yields in the face of changing climates, especially as losses of diversity during the history of cultivation may have disproportionately removed variants favorable under stressful environments from the gene pool. Here we propose a collaboration to develop advanced genomic resources for wild and domesticated accessions of the common sunflower, Helianthus annuus, to facilitate greater understanding of the role of gene content variation in its history and breeding potential.

Collaborators

Dr. Benjamin Blackman - University of California, Berkeley (UC Berkeley) - 111 Koshland Hall #3102 - Berkeley, CA 94720 -  United States  

http://plantandmicrobiology.berkeley.edu/profile/bblackman

https://nature.berkeley.edu/blackmanlab/Blackman_Lab/Welcome.html

Responsible

William Marande