Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity

• DOI: 10.1016/j.molp.2022.01.003
• Publication Date: 2022-01-10T17:05:19Z
• Authors: Genevieve Hoopes; Xiaoxi Meng; John P. Hamilton; Sai Reddy Achakka...; Fernanda de Alves...; Marie E. Bolger; Joseph J. Coombs; Danny Esselink; Natalie R. Kaiser; Linda Kodde; Maria Kyriakidou; Brian Lavrijssen; Natascha van Lies...; Rachel Shereda; Heather K. Tuttle; Brieanne Vaillanc...; Joshua C. Wood; Jan M. de Boer; Nolan Bornowski; Peter Bourke; David Douches; Herman J. van Eck; Dave Ellis; Max J. Feldman; Kyle M. Gardner; Johannes C.P. Hopman; Jiming Jiang; Walter S. De Jong; Joseph C. Kuhl; Richard G. Novy; Stan Oome; Vidyasagar Sathuv...; Ek Han Tan; Remco A. Ursum; M. Isabel Vales; Kelly Vining; Richard G.F. Visser; Jack Vossen; G. Craig Yencho; Noelle L. Anglin; Christian W.B. Ba...; Jeffrey B. Endelman; Laura M. Shannon; Martina V. Strömvik; Helen H. Tai; Björn Usadel; C. Robin Buell; Richard Finkers
• Keywords: Germ plasm

Cultivated potato is a clonally propagated autotetraploid species with highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome revealed extensive allelic diversity, altered coding and transcript sequences, preferential allele expression, structural variation that collectively result in complex transcriptome predicted proteome, which are distributed across the homologous chromosomes. Wild contribute to diversity tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts. As undergoes limited meiosis, dysfunctional deleterious alleles not purged potato. Nearly quarter loci bore mutations have high negative impact on protein function, complicating breeder's efforts reduce genetic load. The StCDF1 locus controls maturity, analysis genomes 12 variants correlated maturity dosage-dependent manner. Knowledge complexity its rampant embedded will be key only implementing precision but also construction homozygous, diploid germplasm containing favorable capitalize heterosis F1 hybrids.