Genome-wide Detection of Residual Heterozygosity in Solanum chacoense Inbred Lines

Most wild tuber-bearing Solanum species are diploid (2n =2x = 24) and self-sterile due to the presence of a genetically based gametophytic self-incompatibility system. In some members of one species, S. chacoense, self-compatibility is determined by the presence of a dominant allele of a self-incompatibility locus inhibitor (Sli) gene.  A series of selfed diploid potato lines (S6 and S7) derived from S. chacoense were characterized.  DNA from a set of twenty S6 and S7 lines was genotyped with the SolCAP Infinium 8303 SNP array to examine the genome wide level of SNP heterozygosity.  Average SNP heterozygosity ranged from 2 to 10%.  Of 6931 SNPs evaluated, 1243 SNPs were heterozygous in at least one line.  The heterozygosity was distributed throughout the genome and along the chromosome arms. There were 72 SNPs with high frequency of heterozygosity across the lines examined.  The observed level of heterozygosity is well above the expected level for S6 and S7 derived lines.  Further SNP genotyping of additional lines and selfed generations is underway to better understand the high levels of residual heterozygosity in S. chacoense lines.