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Title: Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity

item LEISNER, COURTNEY - Michigan State University
item HAMILTON, JOHN - Michigan State University
item CRISOVAN, EMILY - Michigan State University
item MANRIQUE-CARPINTERO, NORMA - Michigan State University
item MARAND, ALEXANDRE - University Of Wisconsin
item NEWTON, LINSEY - Michigan State University
item PHAM, GINA - Michigan State University
item JIANG, JIMING - University Of Wisconsin
item DOUCHES, DAVID - Michigan State University
item Jansky, Shelley
item BUELL, C - Michigan State University

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/1/2018
Publication Date: 4/17/2018
Citation: Leisner, C., Hamilton, J., Crisovan, E., Manrique-Carpintero, N., Marand, A.P., Newton, L., Pham, G.M., Jiang, J., Douches, D.S., Jansky, S.H., Buell, C.R. 2018. Genome sequence of M6, a diploid inbred clone of the high glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity. Plant Journal. (94):562–570.

Interpretive Summary: The genome of the cultivated potato has been sequenced. However, high quality sequence data for wild potato relatives are lacking. This paper presents sequence data on a highly inbred clonof the wild relative S. chacoense, named M6. This is an important clone for breeding, as it is a source of tuber quality and disease resistance. In addition, M6 is serving as a foundation for a diploid inbred-hybrid breeding system in potato, so this genome sequence data set will be important for mapping and genome-wide selection.

Technical Abstract: Background: Potato (Solanum tuberosum) is the world’s most important vegetable crop and central to global food security. Cultivated potato is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Numerous wild potato species serve as a resource for introgression of agronomic traits into cultivated potato such as disease resistance, abiotic stress tolerance, and tuber quality. One key species is Solanum chacoense and the diploid, inbred clone M6 is self-compatible, resistant to several important potato pathogens, and has good tuber market quality traits. Findings: Sequencing and assembly of the genome of the M6 clone of S. chacoense generated an assembly of 825,701,819 bp in 8,192 scaffolds with an N50 scaffold size of 714,946 bp. From the genome assembly, 12 pseudomolecules were constructed, anchoring 508 Mb of the genome assembly to chromosomes. Annotating the genome assembly yielded 37,740 high confidence representative gene models and a total of 49,124 high confidence gene models. Genes involved in steroidal glycoalkaloid biosynthesis and regulation were found in gene clusters on chromosomes six and nine. Comparative analyses of the M6 genome with six other Solanaceae species revealed a core set of 158,367 Solanaceae genes and 1,897 genes unique to potato as represented by three potato species. Analysis of single nucleotide polymorphisms (SNPs) across the M6 genome identified retained heterozygosity on chromosomes 4, 8 and 9 at levels higher than expected for a clone inbred for seven generations. Conclusions: Access to the M6 genome provides a resource for identification of key genes and alleles that confer disease resistance, processing quality and self-compatibility. It also provides the foundation for genome-enabled development of inbred diploid potatoes that have the potential to accelerate potato breeding efficiencies