Open AccessDemonstration of Genome-Wide Association Studies for Identifying Markers for Wood Property and Male Strobili Traits in Cryptomeria japonica
Author(s) -
Kentaro Uchiyama,
Hiroyoshi Iwata,
Yoshinari Moriguchi,
Tokuko UjinoIhara,
S. Ueno,
Yuriko Taguchi,
Miyoko Tsubomura,
Kentaro Mishima,
Taiichi Iki,
Atsushi Watanabe,
Norihiro Futamura,
Kenji Shinohara,
Yoshihiko Tsumura
Publication year - 2013
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0079866
Subject(s) - strobilus , cryptomeria , biology , japonica , genome wide association study , single nucleotide polymorphism , quantitative trait locus , genetics , haplotype , genetic association , gene , genotype , botany
Genome-wide association studies (GWAS) are an alternative to bi-parental QTL mapping in long-lived perennials. In the present study, we examined the potential of GWAS in conifers using 367 unrelated plus trees of Cryptomeria japonica D. Don, which is the most widely planted and commercially important tree species in Japan, and tried to detect significant associations between wood property traits and quantity of male strobili on the one hand, and 1,032 single nucleotide polymorphisms (SNPs) assigned to 1,032 genes on the other. Association analysis was performed with the mixed linear model taking into account kinship relationships and subpopulation structure. In total, 6 SNPs were found to have significant associations with the variations in phenotype. These SNPs were not associated with the positions of known genes and QTLs that have been reported to date, thus they may identify novel QTLs. These 6 SNPs were all found in sequences showing similarities with known genes, although further analysis is required to dissect the ways in which they affect wood property traits and abundance of male strobili. These presumptive QTL loci provide opportunities for improvement of C. japonica , based on a marker approach. The results suggest that GWAS has potential for use in future breeding programs in C. japonica .