Genome-wide Association Study of the Cone Number Character in Pinus armandii Based on SLAF-seq

PurposeTo excavate genes related to the number of cones in Pinus armandii.

MethodsBased on the phenotypic data of cone number of P. armandii, the high and low cone number individual plants were screened. Combined with phenotypic data, single-nucleotide polymorphism (SNP) markers developed previously were used to genome-wide association study (GWAS), and the phylogenetic tree of P. armandii samples was constructed, the SNP markers and candidate genes related to cone number of P. armandii were excavated, and the tissue-specific expression of qPCR gene was further analyzed in six parts of P. armandii, such as needles, xylem, phloem, bark, young cones and roots.

ResultsThe phylogenetic tree showed that the individual plants of the same provenance were basically in a similar position, while the individual plants from Weishan were widely distributed in each population, which was basically consistent with the results of principal component analysis. A total of 12 SNP loci significantly associated with cone number were detected by GWAS. It was found that the sequence of Marker193307 was highly similar to the cellulose synthesis related gene Korrigan (KOR1, encoding transmembrane endo-β-1,4-D glucanase) (74.74%). The tissue-specific expression of qPCR results showed that the expression level of the gene was the highest in the phloem of branches, followed by the young cones, and the least in the roots. It was preliminarily judged that the gene was related to the number of cones.

ConclusionP. armandii provenance close to the individual basically in a similar position. The materials of Weishan provenance have more extensive genetic variation than other provenances. GWAS only retrieves one gene (KOR1) related to plant cellulose synthesis, which may be involved in the expression of cone number.