Adaptation to new environments

Transcription

1 Adaptation to new environments

2 adaptation to new environments requires the generation and / or selection of alleles that improve survival or performance Can we use the products of post domestication eco geographical adaptation to identify genes that have been under selection?

3 The domestication and spread of cultivated barley Scandanavia o Cmax Fertile Crescent o Cmax o Cmin o Cmin precip 20 Precip

4 Growth Habit genes identified in cereals PPDH1 VRNH3 PPDH2 VRNH1 VRNH2

5 EARLINESS per se (EPS)?

6 Growth Habit genes identified in cereals PPDH1 VRNH3 PPDH2 MAT C EPS2 VRNH1 MAT A EPS1 VRNH2 MAT I

7 Genetic Platform: Multi parent population c. 900 spring and winter 2 row barley cultivars

8 Molecular Markers The James Hutton Institute

9 Genetic Diversity The James Hutton Institute PCO 1 vs 2 PCO 1 vs PCO 1: % PCO 2: 5.31 % PCO 3: 3.62 % 0.7

10 Divergent Selection The James Hutton Institute PCO 1 vs. 2 PCO 1 vs PCO 1: % PCO 2: 5.31 % PCO 3: 3.62 % 0.2

11 Estimating locus by locus genetic differentiation Ф PT via AMOVA is a measure of the degree of gene differentiation among populations in terms of allele frequencies (analogous to Wrights F statistic, Fst) Ф PT is calculated as the proportion of the variance among populations (V AP ) relative to the total variance (V WP ): Ф PT = V AP V AP + V WP 0 1 No differentiation Complete differentiation

12 Ф PT at 9K SNPs Winter vs. Spring 1.0 PhiPT H 2H 3H 4H 5H 6H 7H Jordi Comadran

13 GWAS flowering time (MABDE) log10(fp value) 1H 2H 3H 4H 5H 6H 7H 19 trials (Spain, Morocco, Algeria, Syria, Jordan, Italy, Turkey...) / average h Effect on heading date: % genetic variance Effect on yield: 8.29 % genetic variance

14 Divergent selection centromere 2H PhiPT Barley genetic distance cm Rice gene order ~300 gene models phosphatidyl ethanolamine binding protein (PEBP) (FT, TFL1, CENTRORADIALIS)

15 PEBP s FT and TFL1 have opposing functions FD FT FD TFL1 FD AP1 AP1 AP1 BarleyPEBP is most closely related to AmCENRORADIALIS a homolog of TFL1 From Ahn et al. The EMBO Journal (2006) 25, HvCEN

16 QTL mapping flowering time / HvCEN 118 Nure (winter) x Tremois (spring) DH lines HvCEN 66% genotypic variation log10(p) H 2H 3H 4H 5H 6H 7H EPS2 (13 Mediterranean environments / six countries / 2 years) Tondelli, Pecchioni et al

17 Phenotypic effect of Nure (winter) HvCEN allele in Mediterranean Environments Yield +0.26t/ha (5) TCW +3.8g (9) Flowering 4.7 Days (13)

18 Proving HvCEN/TFL1 is EPS2

19 PREMATURUM C (mat c) mutants are early Flowering and map at EPS2 The James Hutton Institute

20 Flowering time mat c mutants Days to flower

21 EPS2 is HvCEN c.770 ATG (27) c.943 P S (52) c bp del C9.3 D N (71) c.966 D N (73) c.93 S N (78) c.1115 R W (83) c.94 Splice site c.1114 Splice site c.32 P L (113) c.907 G D (116) c.400 D W (139) c.881 ATG P135A

22 How does a single amino acid change have this effect?

23 FT/TFL1 Domain Swaps in ft tfl1 mutants FT TFL1 Early Late etc. Early Early Early Early Early Late Late Late Late Late Exon 4 responsible for opposing activities in vivo From Ahn et al. The EMBO Journal (2006) 25,

24 FT/TFL1 Domain Swaps in ft tfl1 mutants FT TFL1 Early Late etc. Early Late Late Late Early Early Domain B responsible for opposing activities in vivo From Ahn et al. The EMBO Journal (2006) 25,

25 PEBP protein structure hpebp Ligand Binding site External Loop (Domain B) General architecture of a PEBP

26 Barley HvCEN variants P135 FD A135 FD AP1 AP1

27 adaptation to new environments required the selection of alleles that improved survival or performance. Do we see evidence for changes in allele frequency across geographical/environmental clines

28 Haplotypes in 1143 geo referenced wild, landrace and cultvated accessions Benjamin Kilian H. Spontaneum H. agriocrithon H. vulgare (cultivar) H. vulgare (Landrace) Hap_I CACTATTTGCCCGC Hap_II..T.G..AT...C. Hap_III..T.G... Hap_IV..T.G..AT.T.C. Hap_V..T.G...T.. Hap_VI..T.G..AT...CT Hap_VII...T... Hap_VIII..TCG... Hap_IX..T.G...C. Hap_X..T.GC...C. Hap_XI.GT.G..AT...C. Hap_XII G.T.G... Hap_XIII..T.G.C...C.

29 Geographical distribution of Haplotypes Spring Barley Winter Barley Haplotype I Haplotype I Haplotype II Haplotype II Haplotype III Haplotype III Benjamin Kilian

30 A135P was unique to barley Clade 1 (incl. Tremois) Hordeum vulgare Lineage 13 Triticum and Aegilops species Clade 2 (Incl. Nure) Benjamin Kilian

31 Summary HvCEN Ive shown how we can use genetics to identify gene s(and loci) that have undergone selection during post domestication range extension I showed that new and legacy A collections B of Cmutants proved to be an excellent validation strategy for candidate genes Information from other biological systems allowed us to pinpoint the likely quantitative trait nucleotide responsible By using geo referenced wild, landrace, cultivated genebank accessions and related species the causal QTN was selected from the wild genepool (rather than a post domestication mutation) and that it only happened in the Hordeum lineage.