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

Hazelnut breeding is slow due to 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 of the hazelnut genome and the development of marker-assisted selection (MAS) would greatly facilitate breeding programs. The objective of this study was the construction of a high-density genetic map and the detection of quantitative trait loci (QTL) related to phenological, vegetative and productive traits using an F1 family obtained from crossing ‘Tonda Gentile delle Langhe’ (TGdL) as the female parent with ‘Hall’s Giant’ (HG) as the male parent. Genotyping-by-sequencing (GBS) was used to discover single nucleotide polymorphism (SNP) markers. Raw reads were analyzed after filtering out contaminant substrings and removing reads with poor quality ends (Q<30). SNP mining was conducted using a Samtools-based pipeline. A total of 7,980 SNPs were identified. 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 (1,216 SNP markers and 20 SSR 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 HG consisted of 1,211 markers (1,192 SNP markers and 19 SSR 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 the molecular data to identify marker/QTL associations for flowering and bud burst time, sucker habit and nut traits, including nut and kernel size, roundness index, percent kernel and ease of pellicle removal. The analysis identified a series of major QTLs that will be useful in MAS. The research was carried out with the contribution of Ferrero Hazelnut Company HCO.