investigation of candidate loci associated with maize ...€¦ · key words perennialism...

Investigation of Candidate

Loci Associated with Maize

Perennialism

Anjun Ma

Key Words

Perennialism

Single-nucleotide-polymorphism (SNP)

Genotype-by-sequencing (GBS)

TASSEL pipeline

Genotype-phenotype association study

Workflow

SNP

Reference

Sequence

A

C

5’

5’

3’

3’

T

G

SNP

CTTACGGTGACTGGTGAATGGTTATCGTG

CTTACGGTGACTGGTGAATGGTTATCGTG

CTTACGGTGACTGGTGCATGGTTATCGTG

CTTACGGTGACTGGTGCATGGTTATCGTG

CTTACGGTGACTGGTGAATGGTTATCGTG

CTTACGGTGACTGGTGAATGGTTATCGTG

CTTACGGTGACTGGTGAATGGTTATCGTG

CTTACGGTGACTGGTGAATGGTTATCGTG

CTTACGGTGACTGGTGAATGGTTATCGTG

CTTACGGTGACTGGTGCATGGTTATCGTG

CTTACGGTGACTGGTGCATGGTTATCGTG

CTTACGGTGACTGGTGCATGGTTATCGTG

CTTACGGTGACTGGTGCATGGTTATCGTG

CTTACGGTGACTGGTGCATGGTTATCGTG

CTTACGGTGACTGGTGCATGGTTATCGTG

CTTACGGTGACTGGTGCATGGTTATCGTG

AA x AA

AC x AC

Reference

Sample A

Sample C

Sample B

GBS

Pros:

Highly reduced genome size (methylation-sensitive RE)

Inexpensive (~$1,700 per lane)

Good for SNP detection and GWAS analysis

Cons:

large amount of missing data (~40-80% with ApeKI)

Difficult to call heterozygotes in highly heterozygous

Technical missing is confounded with biological missing

GBS Library

TASSEL Pipeline

SNP Filters and Scoring

The 1st SNP filter

GBSHapMapFiltersPlugin [Remove minimum allele

frequency (MAF) < 0.01]

The 2nd SNP filter

Remove missing data ratio > 20%

The 3rd SNP filter

Keep SNP with χ2 < 9.49

The 4th SNP filter

Remove neighboring SNPs with the same genotype

pattern

714,158

37,925

10,431

946

597

Candidate Loci &

Verification

90% = 3.84

S7_5,862,253*

2,566 positions: 597 SNP + 1,969 simulation

S2_27,934,73999% = 4.89

95% = 4.17

Gene Position Annotation

GRMZM2G002642 27,769,950 to 27,776,452 Polypeptide: Ankyrin-like protein

Zm00001d002943 27,769,845 to 27,779,192 NA

AC199765.4_FGT008 27,777,537 to 27,779,027 Enzyme: Cellulase

Zm00001d002944 27,779,321 to 27,782,869 NA

• 2-1A primer set targets the 27,773,017

bp on chromosome 2

• χ2 = 9.16 (P=0.057), df = 4

Next Step

Test for gene-gene interactions

Identify candidate gene function and

annotation

Gene-expression to regulatory pathway

Current Work

Bicluster review

Background & publication reading

R/QUBIC package exercise

Revise

Regulatory response to acid-stress in Lactococcus lactis

MG1363

An application of biclustering

Revision and reconstruction

Thank You