RNA-seq-based genetic mapping in European beech. CKS

The objective of this study was to establish a SNP-based genetic linkage map of European beech (Fagus sylvatica) using a genotyping-by-sequencing approach. This map was further used to validate a chromosome scale assembly of the beech genome. The mapping population consisted of 200 half-sibs from a single tree (accession MSSB) used as a reference genotype within the BEECHGENOME project funded by ANR. The selected tree is located in Saint-Symphorien (44° 25' 41.138" N 0° 29' 23.125" W) in the south-west of France. RNA-seq data (Illumina short-reads) were obtained from bud RNA extracted from each offspring. A unigene set established for MSSB was available to detect heterozygous sites in transcribed sequences segregating 1:1 in the progeny. Paternity test allows identifying two full-sib families to precisely estimate genetic distances and order SNP markers in each linkage group. The alignment of the linkage map to the beech genome sequence validated the chromosome scale assembly of this genome. Beechnuts were collected using a net under an adult tree (accession MSSB) located in the southern range of the species in the south-west of France (Saint-Symphorien 44° 25' 41.138" N 0° 29' 23.125" W). Seeds were germinated and raised the following springs at the National Forest Office nursery in Guemene-Penfao (47° 37' 59.99" N -1° 49' 59.99" W) and then planted at the Nouzilly (47° 32′ 36″ N 0° 45′ 0″ E) experimental unit of INRAE. Vegetative buds were sampled the 28th of February 2018 in Nouzilly at the ecodormancy stage from 200 genotypes (i.e. 200 half-sibs that constitute the mapping population). They were immediately frozen on dry ice and then stored at -80°C. RNA was extracted from bud scale free leaves. Noteworthy, these 200 genotypes included two relatively large full-sib families comprising 49 full-sibs (family MSSBxSSP12) and 37 full-sibs (family MSSBxMSSH). Tissues were immediately frozen in liquid nitrogen and stored at -80°C before RNA extraction.