<em>PINUS</em> <em>ARMANDII</em> GROWTH GENE IDENTIFICATION USING GENOME-WIDE ASSOCIATION STUDY APPROACHES

Abstract

In the study to identify key genes and molecular markers related to Pinus armandii Franch growth and to obtain shorten breeding cycles, we selected 209 single plants from six seed sources from a clonal P. armandii seed orchard on Zixi Mountain, Chuxiong City, Yunnan Province, China and examined tree height and diameter at breast height (DBH) traits. We then studied single nucleotide polymorphisms (SNP) markers related to tree height and DBH using Genome-Wide Association Studies (GWAS) and predicted candidate genes associated with growth traits using quantitative polymerase chain reaction (qPCR) to preliminarily verify these genes. We identified 13 SNP loci in the population, of which six and seven SNPs were related to DBH and tree height, respectively. We also identified a candidate gene caffeoyl- CoA-O-methyltransferase (CCoAOMT) which has important roles in lignin monomer synthesis. Another candidate gene cellulose synthase A2 (CesA2) was involved in cellulose synthesis in different organs, tissue, and the cell wall. The SNP marker (Marker227806) was associated with DBH, the genotypes of marker227806 in 209 samples of P. armandii. In total, 175 samples had homozygous (GG) and 34 had heterozygous (GT) genotypes, and average DBH values were 23.80 cm and 26.10 cm, respectively, indicating significant differences between two genotypes for DBH (P = 0.037, < 0.05), which could be used for optimal DBH selection. The candidate genes CCoAOMT and CesA2 were evaluated by qPCR and AT5G42190 was selected as an internal reference gene. Needle (ZY), bark (SP), root (SG), phloem (RP), and xylem (MZ) tissues from 15 samples were used to analyze gene expression, with CCoAOMT and CesA2 identified in all tissue, but expression was highest in RP and relatively low in SP tissue, with significant differences observed. Both genes were preliminarily
related to P. armandii growth traits and may be implicated in DBH and tree height. Our study provides important information for the genetic improvement of P. armandii.