13 MEI 2013

KLUB JURNAL

13 MEI 2013

SNP Linkage Disequilibrium (LD) map Association mapping

Key words :

SNPs

A single base change in a DNA sequence that occurs in a significant proportion (more than 1 percent) of a large population (Anand et al, 2003)A difference between the nucleotide at a corresponding locus in one genome as compared to another (Mc Nally et al, 2008).Variation can be

ith A t G C t T t iti

a SNP is a Single Nucleotide Polymorphism

either A to G or C to T transitions or A/G to C/T transversions.

the bulk of genetic variation is due to SNPs

Transitions are interchanges of two-ring purin (A G) or of one-ring pyrimidines (C T): they therefore involve bases of similar shape. Transversions are interchanges of purine for pyrimidine bases, which therefore involve exchange of one-ring and two-ring structures.

Transition are generated at higher frequency than Transversions.

Where Result Effect

In codingregion

May be silent, o.g.,UUG→CUG, leu in both cases sSNP Usually no change inphenotype

In coding region

May change amino acid sequence, e.g., UUC→UUA,phe to leu, Some characterize these as the leastcommon and most valuable SNPs, Many beingpatented

cSNP Phenotype change(may be subtledepending on aminoacid replacement andposition)

SNP effect (Shastry (2009) ; Mammadov, (2012)

In coding region

May create a "Stop"codon, e. g., UCA→UGA,ser to stop

Phenotype change

In coding region

May affect the rate of transcription(up-or down-regulate)

cSNP Possible phenotypeChange

Other regions

No affect on gene products(7).May act as genetic markers for multi-componentdiseases. These are sometimes called anonymous SNPsand are the most common.

rSNP

LD Mapping & Association Genetics

(linking genotypes with phenotypes)( g g yp p yp )

Linkage Equilibrium     vs    Linkage Disequilibrium

(Zhu et al, 2008)

• Bi-allelic nature results in easier genotyping as opposed to SSRs • Allelic variation might be indicative of function• Association of alleles (2-states) with one another and with phenotypes is easily tested.• Easy to estimate linkage equilibrium/ disequilibrium (gametic phase)

Why use SNPs for mapping and association?

(McNally et al, 2008)

Article : GWAS mapping reveals a rich genetic GWAS mapping reveals a rich genetic

architecture of complex traits in architecture of complex traits in O.sativaO.sativapp

44K (44,100) SNP-Chip

High quality (< 4,5% missing data)~1 SNP per 10kb in 12 chromosomesSummary : Private SNP (spesific); Polymorphic SNP; MAF 0.05

Population structure

Distribution of subpopulation 413 O sativa PCA cluster of subpopulations

Allele sharing across subpopulations and phenotype variation

Allele sharing clearly tracks subpopulation ~ PCA analysis

Mean IBS (Identical by State) value : TrJ~TempJ : 0,80I~Aus : 0,64

genetic & cultured barries in different subpopulation

TrJ

Indica

Aro

TempJ

IBS between Indv

Aus

Phenotype distribution : morphology, yield component and quality highly domestication

Idv based on phenotype

Naïve vs Mixed model : Phenotype distribution and GWAS for plant height

EMMA Prog : Mixed : adjusment on different level of pop, eliminate low PvalNaïve : no adjusment, high false +

Naïve & Mixed : detected SD1

Naive : detected DGL1 (chr1) and OsBAK1 (chr8)

Naïve : alleles segregate in only 1 subpopulation

Mixed : alleles segregate across subpopulation

Heterogenity in panicle length GWAS for flowering time

GWAS for panicle length :Indica : OsTB1, SLR1 & OsBRI1Aus : FZP, SSD1TrJ: OsLIC & MOC1

Heterogenity in O.sativa

HD1 detected in 3 environment

Summary of association significant locus

Research Progress in BB Biogen : GWAS mapping reveals heading and yield GWAS mapping reveals heading and yield

component traits in Indonesian rice (component traits in Indonesian rice (O.sativaO.sativa) ) germplasmgermplasmgermplasmgermplasm

,1536-SNP BIO RiceOPA-1 : Short heading & Yield component

1536-SNP Chip : Universal 32Universal 32

Material genetic : 

Wild species, 11

Genotyping : 467 acc, 1535 SNP-

chip, GoldenGateplatform

Released , 29

Introduction, 95

NIL, 34

Local , 136 Double Haploid, 104

Breeding lines, 47

Mutant, 11

Improved lines, 162

Diversity and LD Mapping

JaponicaIndicaAromaticAromatic Indica Trop.Jap

Graphical genotyping : Track Introgression 

Adv Var

Chr1 Chr2 Chr3 Chr4

Chr5 Chr6 Chr7 Chr8

Chr9 Chr10 Chr11 Chr12

Landraces

Chr1 Chr2 Chr3 Chr4

Chr5

Chr9

Chr6

Chr10

Chr7

Chr11

Chr8

Chr12

0

50

0 10 20 30 40 50

million

Marka SNP Bunga Lapang Bunga Rm KacaGabah Isi Panjang Malai Bunga Lapang MLM

GWAS Heading Date in Indonesian Rice Germplasm

Preliminary Results  

-50Chr1

SNP Locus : TBGI068738; Trait : Date to flowering LOC_Os01g72220 (Chr1: 41,837,949‐41,880,601)  : WD domain, G‐beta repeat domain  Function : progression of the flower over time, from its formation to the mature structure. 

Genotipe : FWS22‐2‐2; Silugonggo dan Dodokan