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Association genetics of traits controlling lignin and cellulose biosynthesis in black cottonwood ( Populus trichocarpa , Salicaceae) secondary xylem
Author(s) -
Wegrzyn Jill L.,
Eckert Andrew J.,
Choi Minyoung,
Lee Jennifer M.,
Stanton Brian J.,
Sykes Robert,
Davis Mark F.,
Tsai ChungJui,
Neale David B.
Publication year - 2010
Publication title -
new phytologist
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.742
H-Index - 244
eISSN - 1469-8137
pISSN - 0028-646X
DOI - 10.1111/j.1469-8137.2010.03415.x
Subject(s) - populus trichocarpa , biology , linkage disequilibrium , single nucleotide polymorphism , genetics , nucleotide diversity , salicaceae , association mapping , haplotype , population , genetic association , candidate gene , gene , botany , allele , genome , genotype , woody plant , demography , sociology
Summary• An association genetics approach was used to examine individual genes and alleles at the loci responsible for complex traits controlling lignocellulosic biosynthesis in black cottonwood ( Populus trichocarpa ). Recent interest in poplars as a source of renewable energy, combined with the vast genomic resources available, has enabled further examination of their genetic diversity. • Forty candidate genes were resequenced in a panel of 15 unrelated individuals to identify single nucleotide polymorphisms (SNPs). Eight hundred and seventy‐six SNPs were successfully genotyped in a clonally replicated population (448 clones). The association population (average of 2.4 ramets per clone) was phenotyped using pyrolysis molecular beam mass spectrometry. Both single‐marker and haplotype‐based association tests were implemented to identify associations for composite traits representing lignin content, syringyl : guaiacyl ratio and C6 sugars. • Twenty‐seven highly significant, unique, single‐marker associations (false discovery rate Q < 0.10) were identified across 40 candidate genes in three composite traits. Twenty‐three significant haplotypes within 11 genes were discovered in two composite traits. • Given the rapid decay of within‐gene linkage disequilibrium and the high coverage of amplicons across each gene, it is likely that the numerous polymorphisms identified are in close proximity to the causative SNPs and the haplotype associations reflect information present in the associations between markers.