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

Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Wild potato species serve as a resource for the introgression of important agronomic traits into cultivated potato. One key species is Solanum chacoense and the diploid, inbred clone M6, which is self-compatible and has desirable tuber market quality and disease resistance traits. Sequencing and assembly of the genome of the M6 clone of S. chacoense generated an assembly of 825,767,562 bp in 8,260 scaffolds with an N50 scaffold size of 713,602 bp. Pseudomolecule construction anchored 508 Mb of the genome assembly into 12 chromosomes. Genome annotation yielded 49,124 high confidence gene models representing 37,740 genes. 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 three potato species. Analysis of single nucleotide polymorphisms across the M6 genome revealed enhanced residual heterozygosity on chromosomes 4, 8 and 9 relative to the other chromosomes. Access to the M6 genome provides a resource for identification of key genes for important agronomic traits and aids in genome-enabled development of inbred diploid potatoes with the potential to accelerate potato breeding.

栽培马铃薯（Solanum tuberosum L.）属于高度杂合的同源四倍体，其基因组分析与育种工作均面临诸多挑战。野生马铃薯种质资源可作为重要农艺性状渐渗至栽培马铃薯的遗传材料来源，其中查科马铃薯（Solanum chacoense）及其二倍体自交克隆M6是关键物种之一。该克隆具备自交亲和性，同时拥有优良的块茎商品品质与抗病性状。研究团队对查科马铃薯M6克隆的基因组进行测序与组装，最终获得总长度为825,767,562 bp、包含8260个支架（scaffold）的基因组组装结果，其支架N50长度达713,602 bp。通过伪分子（Pseudomolecule）构建，将508 Mb的基因组组装序列锚定至12条染色体上。基因组注释共得到49,124个高置信度基因模型，对应37,740个功能基因。将M6基因组与其余6个茄科物种开展比较分析，共鉴定得到158,367个茄科核心基因，以及仅存在于3个马铃薯物种中的1,897个特有基因。对M6基因组的单核苷酸多态性分析显示，相较于其余染色体，其第4、8和9号染色体上存在更高水平的残余杂合性。M6基因组序列的公开，为重要农艺性状关键基因的挖掘提供了资源支撑，同时有助于推动基于基因组学的二倍体自交马铃薯品种培育，进而加速马铃薯育种进程。