Dissecting the control of shoot development in grapevine: genetics and genomics identify potential regulators

A F2 population consisting of 337 individuals was derived from the inter-specific cross of V. vinifera cv. Cabernet-Sauvignon (CS) x V. riparia cv. Riparia Gloire de Montpellier (RGM). This population, named CS x RGM_F2, resulted from the self-fertilization of the F1_148 individual of the F1 CS X RGM1995-1 described by Marguerit et al. (2009). Simple sequence repeat (SSR) markers were mainly chosen from the markers used to construct the map of the F1 CS X RGM1995-1 population (Marguerit et al., 2009, https://doi.org/10.1007/s00122-009-0979-4). In addition, 46 new SSR markers were designed using the grape genome 12X sequence (http://www.genoscope.cns.fr/externe/GenomeBrowser/Vitis/). Primers were designed with PRIMER 0.5 software (Whitehead Institute for Biomedical Research). The map was constructed using the software CarthaGene (de Givry et al., 2005, https://doi.org/ 10.1093/bioinformatics/bti222) at a logarithm of the odds (LOD) value of 5.0 and at a maximal distance threshold of 35 cM. Validation of the map obtained was done using the software JoinMap® 3.0 (Stam, 1993) using a Kosambi’s mapping function. The marker order obtained was checked according to the consensus map of the F1 population CS x RGM1995-1 and to the 12X genome sequence. About 1.5 µg of DNA from both BACs VVCS1H018A11 and VVCS1H006A20 were pooled and sequenced using the standard Pacific Biosciences library preparation protocol for 10 kb libraries. Assembly of the PacBio reads was performed following the HGAP workflow (https://github.com/PacificBiosciences/Bioinformatics-Training/wiki/HGAP). The SMRT® Analysis (v2.3.0) software suite was used for HGAP implementation (https://github.com/PacificBiosciences/SMRT-Analysis). Reads were first aligned by BLASR (https://github.com/PacificBiosciences/blasr) against “Escherichia coli strain K12 substrain DH10B complete genome”. The Quiver algorithm (https://github.com/PacificBiosciences/GenomicConsensus/blob/master/doc/QuiverFAQ.rst) was used to enrich the quality scores embedded in Pacific Biosciences bas.h5 files. The “polished assemblies” were identified by matching their BAC end sequences with BLAST. Read coverage was obtained by aligning the raw reads on the assembled sequences with BLASR.