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ARS Home » Pacific West Area » Aberdeen, Idaho » Small Grains and Potato Germplasm Research » Research » Publications at this Location » Publication #385374

Research Project: Potato Genetic Improvement for Enhanced Tuber Quality and Greater Productivity and Sustainability in Western U.S. Production

Location: Small Grains and Potato Germplasm Research

Title: Phased, chromosome-scale genome assemblies of tetraploid potato reveals a complex genome, transcriptome, and proteome landscape that underpin phenotypic diversity

Author
item Anglin, Noelle
item Novy, Richard - Rich
item FINKERS, RICHARD - Wageningen University
item SHANNON, LAURA - University Of Minnesota
item TAI, HELEN - Agriculture And Agri-Food Canada
item STROMVIK, MARTINA - McGill University - Canada
item ENDELMAN, JEFF - University Of Wisconsin
item BACHEM, CHRISTIAN - Wageningen University
item BUELL, ROBIN - University Of Michigan
item HOOPES, GENEVIEVE - University Of Michigan
item DOUCHES, DAVE - University Of Michigan
item OOME, STAN - Hzpc Research Bv
item VOSSEN, JACK - Wageningen University
item KYRIAKIDOU, MARIA - McGill University - Canada
item KAISER, NATALIE - University Of Michigan
item VIDYASAGAR, SATHUVALLI - Oregon State University
item VANLIESHOUT, NATASCHA - Wageningen University
item USADEL, BJORN - Forschungszentrum Juelich Gmbh
item ELLIS, DAVE - International Potato Center
item TUTTLE, HEATHER - University Of Minnesota
item VALES, M ISABEL - Texas A&M University
item VISSER, RICHARD - Wageningen University
item DE JONG, WALTER - Cornell University - New York
item VINING, KELLY - Oregon State University
item YENCHO, G CRAIG - North Carolina State University
item GARDNER, KYLE - Agriculture And Agri-Food Canada
item COOMBS, JOSEPH - University Of Michigan
item ACHAKKAGARI, SAI - McGill University - Canada
item KUHL, JOESEPH - University Of Idaho
item HAMILTON, JOHN - University Of Michigan
item VAILLANCOURT, BRIEANNE - University Of Michigan
item WOOD, JOSHUA - University Of Michigan
item DEALVESFREITASGUESDE, FERNANDA - Wageningen University
item TAN, EK HAN - University Of Maine
item MENG, XIAOXI - University Of Minnesota
item BOLGER, MARIE - Forschungszentrum Juelich Gmbh
item Feldman, Max
item DE BOER, JAN - Averis Seeds Bv
item LAVRIJSSEN, BRIAN - Wageningen University
item ESSELINK, DANNY - Wageningen University
item HOPMAN, JOHANNES CP - Averis Seeds Bv
item KODDE, LINDA - Wageningen University
item BOURKE, PETER - Wageningen University
item SHEREDA, RACHEL - Michigan State University

Submitted to: Molecular Plant
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/7/2022
Publication Date: N/A
Citation: N/A

Interpretive Summary: Cultivated potato has a very complex genetic constitution with four copies of chromosomes and a high level of genetic diversity, making its genetic analysis and the development of a blueprint of its assemblage of chromosomes a significant challenge. In this study, the assemblage of chromosomes, transcribed genes, and cellular organelles for six potato cultivars were sequenced, assembled, and phased. The six cultivars chosen for this study, are important in the European and the North American markets allowing a comparison of the genetic basis for market class traits and the similarities among them. Sequence data from 20 wild potato species were also utilized to examine if DNA from them had been incorporated into cultivated potato. All wild species examined had signatures within the cultivated material suggesting significant gene exchange over time. The data obtained allowed an assessment of the genetic variability and chromosomal structural variation in cultivars which demonstrated high genetic diversity, dysfunctional alleles, and significant wild species integration. The data reinforces the notion that potato has a complex assemblage of chromosomes, perhaps the most complex analyzed and released to date among cultivated crops.

Technical Abstract: Cultivated potato is a clonally propagated autotetraploid species with a highly heterogenous genome. Construction of phased, chromosome-scale assemblies of multiple cultivars revealed extensive allelic diversity including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and resulting proteome distributed across the homologous chromosomes. Wild species introgressions further contribute to allelic diversity demonstrating ancestral introgressions prior to modern breeding efforts. As an autotetraploid that undergoes limited meiosis, dysfunctional and deleterious alleles are not purged and nearly a quarter of loci bore mutations predicted to have high negative impact on protein function complicating breeder’s efforts to reduce genetic load. The locus StCDF1 controls maturity and analysis of six tetraploid genomes revealed eight allelic variants, of which, allele dosage was correlated maturity. Knowledge of the complexity of a tetraploid genome with its embedded deleterious and dysfunctional alleles will be key to constructing diploid potato homozygous for favorable alleles that can then be combined in an F1 hybrid to capture heterosis.