Pinot clones resequencing

Structural variants (SVs) are a common source of genetic variation in plants, and can give rise to mosaic organs. Mosaicism is caused by post-zygotic mutations occurring in a proportion of somatic cells, is widespread in all living organisms, and is particularly abundant in fruit crops. Cultivated grapevines (Vitis vinifera) are ancient seedlings immortalized by vegetative propagation. The most popular varieties are propagated by millions of cuttings every year, facilitating the occurrence of bud sports carrying mosaic variants and displaying unique phenotypes.Mosaic SVs cause deviations from the expected 1:1 ratio in heterozygous positions, thus leading to reduction of heterozygosity (ROH). We present ?-scan, a software package using ROH signal across multiple SNPs to identify mosaic SVs. ?-scan can detect SVs using high coverage sequencing data by comparing relative allele frequencies in populations of cells present in two samples derived from the same zygote. We demonstrated ?-scan capabilities by detecting a mosaic SV in Pinot gris and one in Pinot blanc, both known to be associated with berry color variation. ?-scan will help the identification of mosaic structural variants possibly associated with novel phenotypic variation in several crop species, thus enhancing marker assisted breeding. ?-scan is freely available at https://bitbucket.org/dscaglione/xscan.