Browsing by Author "Jiang, Jiming"

Now showing 1 - 3 of 3
  • Thumbnail Image
    Genome Reduction in Tetraploid Potato Reveals Genetic Load, Haplotype Variation, and Loci Associated With Agronomic Traits
    Manrique-Carpintero, Norma C.; Coombs, Joseph J.; Pham, Gina M.; Laimbeer, F. Parker E.; Braz, Guilherme T.; Jiang, Jiming; Veilleux, Richard E.; Buell, C. Robin; Douches, David S. (2018-07-03)
    The cultivated potato (Solanum tuberosum) has a complex genetic structure due to its autotetraploidy and vegetative propagation which leads to accumulation of mutations and a highly heterozygous genome. A high degree of heterozygosity has been considered to be the main driver of fitness and agronomic trait performance in potato improvement efforts, which is negatively impacted by genetic load. To understand the genetic landscape of cultivated potato, we constructed a gynogenic dihaploid (2n = 2x = 24) population from cv. Superior, prior to development of a high-density genetic map containing 12,753 single nucleotide polymorphisms (SNPs). Common quantitative trait loci (QTL) were identified for tuber traits, vigor and height on chromosomes 2, 4, 7, and 10, while specific QTL for number of inflorescences per plant, and tuber shape were present on chromosomes 4, 6, 10, and 11. Simplex rather than duplex loci were mainly associated with traits. In general, the Q allele (main effect) detected in one or two homologous chromosomes was associated with lower mean trait values suggesting the importance of dosage allelic effects, and the presence of up to two undesired alleles in the QTL region. Loss of heterozygosity has been associated with a lower rate of fitness, yet no correlation between the percent heterozygosity and increased fitness or agronomic performance was observed. Based upon linkage phase, we reconstructed the four homologous chromosome haplotypes of cv. Superior. revealing heterogeneity throughout the genome yet nearly duplicate haplotypes occurring among the homologs of particular chromosomes. These results suggest that the potentially deleterious mutations associated with genetic load in tetraploid potato could be mitigated by multiple loci which is consistent with the theory that epistasis complicates the identification of associations between markers and phenotypic performance.
  • Thumbnail Image
    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.
  • Thumbnail Image
    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.