Overview of developments

Nested Association Mapping (NAM)

Jianming Yu, James B. Holland, Michael D. McMullen and Edward S. Buckler, Genetics, Vol. 178, 539-551, 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 valuesTo 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

UNEAKWorkflow

TASSEL workflow

marker’

trait

filter convert impute PCA

impute

K

Q

GLM GLMstructure MLM

marker filter

Hybrid workflow

csv

qtlConvert

qtlcart

csvr

Qtl Cartographer

mm

MapMaker QTL Network

csv2plink

Plink

ped, map

tped

vbay

Tassel

GenABEL

Fast-LMM

RandomJungle

RqtlRmap

Rcross

Prune

MapMaker map file

SRmapqtl

Zmapqtl

Eqtl

Preplot

GNUplot

QTL Cartographer Workflow