Construction of a high-density genetic linkage map and QTL analysis for hazelnut breeding

Hazelnut breeding is a slow activity due to the long lifecycle of the plant, the long time between pollination and reliable phenotype observation in the progeny, the presence of self-incompatibility and the high level of heterozygosity. Improved knowledge on the hazelnut genome and the development of marker-assisted selection would greatly facilitate breeding programs. Objective of this study was the construction of high-density genetic maps and the detection of QTL (quantitative trait loci) related to phenological, vegetative and productive traits, by using an F1 progeny obtained by crossing ‘Tonda Gentile delle Langhe’ (female parent, hereafter TGdL) with ‘Merveille de Bollwiller’ (syn. ‘Hall’s Giant’ male parent, MB). Genotyping-by-sequencing (GBS), followed by SNP mining using a Samtools-based pipeline, yielded 7,980 SNP markers. Independent linkage maps were constructed for each parent on the basis of the double pseudo-testcross mapping strategy. The linkage map for TGdL consisted of 1,236 markers covering a total genetic length of 900.4 cM, with a mean inter-marker distance of 0.83 cM. A reciprocal translocation was detected in TGdL between two non-homologous chromosomes. The linkage map for MB was based on segregation at 1,211 markers covering a total genetic length of 899.1 cM, with a mean inter-marker distance of 0.82 cM. Plant and nut traits were recorded during five years and statistically analyzed with molecular data to identify marker/QTL associations for flowering and bud burst time, sucker habit and nut traits, such as nut and seed size, roundness index, percent kernel and ease of pellicle removal.