Overview of developments

Nested Association Mapping (NAM) Jianming Yu, James B. Holland, Michael D. McMullen and Edward S. Buckler, Genetics, Vol. 178, , January 2008

More about NAM line ~1.6 million SNPs for each of the 26 founder lines 1106 markers for each of the 5000 RILs – Distributed across 10 chromosome – Chromosome 1 has 175 markers but chromosome 10 has only 77 markers Phenotype data are the residuals from a linear model containing joint linkage QTL for all but the chromosome targeted

Projecting SNP values To project a SNP, use its physical position, snp.pos, to find the flanking NAM markers, based on agp_pos from the NAM map. For each NAM line in the residuals file, find its projected SNP value as follows: 1.Determine the parent number for the line 2.Find the parent SNP value for that line from the fastphase file 3.Determine the proportional distance, pd, of SNP from its left and right flanking markers as pd = (snp.pos - left marker agp_pos) / (right marker agp_pos – left marker agp_pos) 4.If the parent value = 0, set the snp.value = 0 for that line. 5.If the parent value = 1, set snp.value = left marker value * (1 - pd) + right marker value * pd

Genotyping by Sequencing < 450 bp ApeKI site (GCWGC) ( ) 64-base sequence tag B73 Reduced genome representation; Reads can be aligned without reference genome;

GBS Workflow

UNEAK Workflow

TASSEL workflow marker’ trait filterconvertimputePCA impute K Q GLMGLMstructureMLM markerfilter

Hybrid workflow csv qtlConvert qtlcart csvr Qtl Cartographer mm MapMaker QTL Network csv2plink Plink ped, map tped vbay Tassel GenABEL Fast-LMM Random Jungle

Rqtl Rmap Rcross Prune MapMaker map file SRmapqtl Zmapqtl Eqtl Preplot GNUplot QTL Cartographer Workflow