Browsing by Author "Jansky, Shelley H."

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    Meiotic crossovers are associated with open chromatin and enriched with Stowaway transposons in potato
    Marand, Alexandre P.; Jansky, Shelley H.; Zhao, Hainan; Leisner, Courtney P.; Zhu, Xiaobiao; Zeng, Zixian; Crisovan, Emily; Newton, Linsey; Hamernik, Andy J.; Veilleux, Richard E.; Buell, C. Robin; Jiang, Jiming (Biomed Central, 2017-10-30)
    Background: Meiotic recombination is the foundation for genetic variation in natural and artificial populations of eukaryotes. Although genetic maps have been developed for numerous plant species since the late 1980s, few of these maps have provided the necessary resolution needed to investigate the genomic and epigenomic features underlying meiotic crossovers. Results: Using a whole genome sequencing-based approach, we developed two high-density reference-based haplotype maps using diploid potato clones as parents. The vast majority (81%) of meiotic crossovers were mapped to less than 5 kb. The fine-scale accuracy of crossover detection was validated by Sanger sequencing for a subset of ten crossover events. We demonstrate that crossovers reside in genomic regions of “open chromatin”, which were identified based on hypersensitivity to DNase I digestion and association with H3K4me3-modified nucleosomes. The genomic regions spanning crossovers were significantly enriched with the Stowaway family of miniature inverted-repeat transposable elements (MITEs). The occupancy of Stowaway elements in gene promoters is concomitant with an increase in recombination rate. A generalized linear model identified the presence of Stowaway elements as the third most important genomic or chromatin feature behind genes and open chromatin for predicting crossover formation over 10-kb windows. Conclusions: Collectively, our results suggest that meiotic crossovers in potato are largely determined by the local chromatin status, marked by accessible chromatin, H3K4me3-modified nucleosomes, and the presence of Stowaway transposons.
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    Reinventing Potato as a Diploid Inbred Line-Based Crop
    Jansky, Shelley H.; Charkowski, Amy O.; Douches, David S.; Gusmini, Gabe; Richael, Craig; Bethke, Paul C.; Spooner, David M.; Novy, Richard G.; De Jong, Hielke; De Jong, Walter S.; Bamberg, John B.; Thompson, A. L.; Bizimungu, Benoit; Holm, David G.; Brown, Chuck R.; Haynes, Kathleen G.; Sathuvalli, Vidyasagar R.; Veilleux, Richard E.; Miller, J. Creighton Jr.; Bradeen, Jim M.; Jiang, Jiming (2016-07)
    The third most important food crop worldwide, potato (Solanum tuberosum L.) is a tetraploid outcrossing species propagated from tubers. Breeders have long been challenged by polyploidy, heterozygosity, and asexual reproduction. It has been assumed that tetraploidy is essential for high yield, that the creation of inbred potato is not feasible, and that propagation by seed tubers is ideal. In this paper, we question those assumptions and propose to convert potato into a diploid inbred line-based crop propagated by true seed. Although a conversion of this magnitude is unprecedented, the possible genetic gains from a breeding system based on inbred lines and the seed production benefits from a sexual propagation system are too large to ignore. We call on leaders of public and private organizations to come together to explore the feasibility of this radical and exciting new strategy in potato breeding.
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    Retrospective View of North American Potato (Solanum tuberosum L.) Breeding in the 20th and 21st Centuries
    Hirsch, Candice N.; Hirsch, Cory D.; Felcher, Kimberly J.; Coombs, Joseph J.; Zarka, Dan; Van Deynze, Allen; De Jong, Walter S.; Veilleux, Richard E.; Jansky, Shelley H.; Bethke, Paul C.; Douches, David S.; Buell, C. Robin (Genetics Society of America, 2013-06-01)
    Cultivated potato (Solanum tuberosum L.), a vegetatively propagated autotetraploid, has been bred for distinct market classes, including fresh market, pigmented, and processing varieties. Breeding efforts have relied on phenotypic selection of populations developed from intra-and intermarket class crosses and introgressions of wild and cultivated Solanum relatives. To retrospectively explore the effects of potato breeding at the genome level, we used 8303 single-nucleotide polymorphism markers to genotype a 250-line diversity panel composed of wild species, genetic stocks, and cultivated potato lines with release dates ranging from 1857 to 2011. Population structure analysis revealed four subpopulations within the panel, with cultivated potato lines grouping together and separate from wild species and genetic stocks. With pairwise kinship estimates clear separation between potato market classes was observed. Modern breeding efforts have scarcely changed the percentage of heterozygous loci or the frequency of homozygous, single-dose, and duplex loci on a genome level, despite concerted efforts by breeders. In contrast, clear selection in less than 50 years of breeding was observed for alleles in biosynthetic pathways important for market class-specific traits such as pigmentation and carbohydrate composition. Although improvement and diversification for distinct market classes was observed through whole-genome analysis of historic and current potato lines, an increased rate of gain from selection will be required to meet growing global food demands and challenges due to climate change. Understanding the genetic basis of diversification and trait improvement will allow for more rapid genome-guided improvement of potato in future breeding efforts.