Association of single nucleotide polymorphisms with form traits in three New Zealand populations of radiata pine in the presence of genotype by environment interactions

Associations of single nucleotide polymorphisms (SNP) with the form traits, branch cluster frequency and stem straightness, were studied in three radiata pine (Pinus radiata D. Don) breeding populations. For branch cluster frequency, high genotype by environment (G×E) interactions were found between two sites of the POP1 trial series (Tarawera and Glenledi) and between two sites of the POP2 trial series (Tarawera and Woodhill). For stem straightness, high G×E interactions were found between two sites (Tarawera and Woodhill) in both the POP2 and POP3 trial series. Thirty-two and 26 SNPs were associated with branch cluster frequency and stem straightness respectively, across a number of sites and trial series in a genetic model assuming heterogeneous additive genetic variances across sites. These SNPs had significant associations with branch cluster frequency or stem straightness either in one site only, across sites within a trial series or across different trial series. Seven SNPs had significant associations with branch cluster frequency and seven SNPs with stem straightness across two of three trial series. One SNP had significant association with stem straightness across all three trial series. Strong G×E interactions resulted in fewer significant SNPs in common across the sites among which there were large effect differences. The percentage of genetic variance explained by SNPs showing significant associations ranged from 0.23 to 8.76 % for branch cluster frequency and from 0.37 to 12.75 % for stem straightness. This study showed that SNP effects for a trait change across environments if G×E interactions exist for that trait.