Association mapping in forage crop grasses Leif Skøt.

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Presentation transcript:

Association mapping in forage crop grasses Leif Skøt

Potential for high-resolution mapping Evaluation of many alleles Complements linkage mapping Control for population structure Association mapping in Lolium perenne

Traits Water soluble carbohydrates Ruminant productivity Abiotic stress tolerance (drought, cold) Flowering time Plant development Forage quality traits Seed production

Turner et al. New Phytol Fructose and Glucose Alkaline Invertase locus map to QTL for Glucose and Fructose

Invertases: 1. Acid (vacuolar and Cell wall) 2. Alkaline Vacoule Sucrose Glucose Fructose Glucose Fructose Glucose Fructose Acid Invertase Fructan Fructosyl- transferase Alkaline Invertase Sucrose Acid Invertase Chloroplast / Amyloplast Starch -substrates for respiration -biosynthesis of primary and secondary compounds - regulation of gene expression by sugars Cytosol -sugar storage -osmoregulation -response to cold stress Cell Wall

Effect of sucrose accumulation on gene expression Depleted in soluble carbohydrate Plants - low light short photoperiod Excised Leaves Sucrose solution Sorbitol solution (osmotic Control) Dark Water 24h Actin Suc W Sor Alk Inv.

TLC - Water Soluble Carbohydrates Photoperiod Sucrose Alkaline invertase expression along the developing leaf Ct

SNPs in Alkaline Invertase Locus of Lolium perenne LG 6 1 kb M-L D-N SNPNo Indel6 Syn13 Non-syn8 Non-coding65 Total92

LD in candidate genes Alkaline Invertase

LD in Alkaline invertase locus

Pop Inferred clusters Population structure 70 AFLP markers

SNPWSCNDMD SNP Association analysis Alkaline Invertase and WSC Linear mixed model (WSC) ANOVA

E38M INV1:2 R2869 B6102b CDO545 OSW LpF2 LpF1 LpF3 C764 LpF4 ACA_CTA_254ACA_CTA_321 E40M5909 RZ144S2539 ACA_CAC_225 E39M4910 E37M5601 GSY60.1 CDO385.1 PSR690 E41M5710 RZ952 C390 LtemCOa LtemCOb E39M5802 E41M5701 ACA_CAC_246 ACA_CTA_204 ACP CAT ACA_CTA_254 ACA_CTA_321 C764 S2539 ACA_CAC_ LOD AFLP markers associated with flowering time in Lolium perenne Fructan epistatic QTL

Properties of LpCO gene Synteny with rice HD1 locus Homologous to CONSTANS Complements Arabidopsis co-2 mutant (Martin et al. 2004, PMB 56: 159) Upregulated in response to LD Map to major QTL for flowering time

N-I CAA[C/A]A V-M HD1 Peroxidase SNPs in HD1 locus in Lolium perenne LG7 1 kb SNPNo Indel0 Syn2 Non-syn2 Non-coding8 Total12

LD in candidate genes HD1

Association analysis HD1 locus and flowering time SNPFlowering timeWSC <0.05< Linear mixed model (pops random effect)

SNPBa9955Ba10113Ba10158Ba10278Ba10284Ba10732Ba10870Ba11304Ba *** 1475**** 2118***** 2389* 4443************ ******* Association analysis HD1 locus and flowering time ANOVA * P<0.05; ** P<0.01; *** P<0.001

N-I CAA[C/A]A V-M HD1 Peroxidase SNP 4443 in HD1 locus 1 kb CAACA Consensus recognition sequence for RAV1/AP2…

Acknowledgements IGER Janet Humphreys Mervyn Humphreys Joe Gallagher Danny Thorogood Ian Armstead Sue Heywood Mark Hirst Ruth Sanderson Lesley Turner University of Birmingham Zewei Luo Mike Kearsey