High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus

• DOI: 10.1186/s12864-015-1215-z
• Publication Date: 2015-01-23T19:46:07Z
• Authors: Wellington Muchero; Jianjun Guo; Stephen P DiFazio; Jin-Gui Chen; Priya Ranjan; Gancho T Slavov; Lee E Gunter; Sara Jawdy; Anthony C Bryan; Robert Sykes; Angela Ziebell; Jaroslav Klápště; Ilga Porth; Oleksandr Skyba; Faride Unda; Yousry A El-Kassaby; Carl J Douglas; Shawn D Mansfield; Joel Martin; Wendy Schackwitz; Luke M Evans; Olaf Czarnecki; Gerald A Tuskan
• Keywords: Populus trichocarpa; Candidate gene; Association mapping; Genetic linkage; Positional cloning; Centimorgan

QTL cloning for the discovery of genes underlying polygenic traits has historically been cumbersome in long-lived perennial plants like Populus. Linkage disequilibrium-based association mapping proposed as a tool, and recent advances high-throughput genotyping whole-genome resequencing enable marker saturation to levels sufficient with no priori candidate gene selection. Here, multiyear multienvironment evaluation cell wall phenotypes was conducted an interspecific P. trichocarpa x deltoides pseudo-backcross pedigree two partially overlapping populations unrelated genotypes using pyrolysis molecular beam mass spectrometry, saccharification, and/ or traditional wet chemistry. high-density genetic map 3,568 SNP markers. As fine-mapping approach, chromosome-wide targeting hot-spot on linkage group XIV performed populations. Both were genotyped 34 K Populus Infinium array one facilitated marker-saturation intervals identification. Five QTLs ranging size from 0.6 1.8 Mb mapped lignin content, syringyl guaiacyl (S/G) ratio, 5- 6-carbon sugars pedigree. Six loci exhibiting significant associations identified within intervals. These reproducible across multiple environments, independent platforms, different plant growth stages. cDNA sequencing allelic variants three six polymorphisms leading variable length poly glutamine (PolyQ) stretch transcription factor annotated ANGUSTIFOLIA C-terminus Binding Protein (CtBP) premature stop codons KANADI well protein kinase. Results protoplast transient expression assays suggested that each conferred differences activation cellulose, hemicelluloses, pathway genes. This study illustrates utility complementary tools proof concept organism opens up opportunities novel determinants economically important but complex plants.