Barley and Climate Change: - PowerPoint Presentation

Slide1

Barley and Climate Change: The Intersections of Low Temperature Tolerance and Growth Habit

Slide2

Fall-sown crops and resiliency

Optimum use of available precipitation

Escape summer diseasesDouble cropping opportunities

Slide3

Low temperature toleranceAcclimation

Vegetative stage

Slide4

Regulating the vegetative to reproductive transition

Vernalization sensitivity

Sort day photoperiod sensitivity

Slide5

The challenges of phenotyping

LTT

VRNSd-PPD

Slide6

The QTLs/genes Low temperature tolerance

FR-H1

FR-H2FR-H3

Vernalization sensitivity

VRN-H1

VRN-H2

VRN-H3

Photoperiod sensitivity

PPD-H2 (

sd

)PPD-H1 (ld)

Slide7

Facultative growth habit – theoretical framework

LTT +

VRN -sdPPD +

Winter

Facultative

Spring

Low temperature tolerance

Yes

Yes

No

Vernalization

sensitivity

Yes

No

No

Photoperiod sensitivity (short day)

Varies:

insurance

Varies:

necessary

Varies:

value?

Slide8

Facultative growth habit – evidence it can work

Biparental mapping

GWASVarieties

Fall planted Thunder (left) and Lightning (right) Corvallis, OR 2020

Plant in fall and cold tolerant

Plant in spring and no vernalization required

Slide9

Slide10

The TCAP LTT Project

882 accessions

21 barley breeding/genetics programs2 years

Illumina 9K

KASP allele-specific genotyping

LTT (as winter survival)

VRN sensitivity (days to flowering without vernalization)

Slide11

Phenotypes

Slide12

Phenotypes

Slide13

Phenotypes

Slide14

2-row/6-row; g

eographic origin phenotypes + genotypes

PC1

(11.4%)

PC2

(8.0%)

PC1

(11.4%)

PC2

(8.0%)

2 rows

6 rows

Asia

Europe

North America

A.

B.

Slide15

The top 5% for LTT - phenotype and genotype

I 61%

II 59%

III 58%

IV 60%

V 62%

VI 65%

VII 59%

Slide16

GWAS

Slide17

KASP

Slide18

The TCAP LTT Project – Conclusions

LTT and VRN

The top 5%PPD-H2

PPD-H1

Slide19

The TCAP LTT Project – Implications and next steps

Facultative growth habit

FR-H3

Slide20

FR-H3 in barley

Muñoz-Amatriain et al. (2020)

SNP (WS)

chr

bp

cM

(Pop/9K)

BOPA2_12_30336

1H

31676923

40.08

SCRI_RS_114047

1H

31685164

40.08

SNP (WS)

chr

bp

cM

(Pop/9K)

BOPA2_12_31467

1H

66,850,934

46.46

BOPA1_4473-309

1H

11,259,897

17.85

Fisk et al 2013

Gene Name

chr

bp

Description

HORVU1Hr1G012680

1H

31672910

UDP-Glycosyltransferase superfamily protein

HORVU1Hr1G012690

1H

31684461

Tetraspanin

family protein

HORVU1Hr1G012710

1H

31944906

Low temperature-induced protein lt101.2

Slide21

FR-3 in wheat

Fowler et al 2018

Three bi-parental mapping populations

Geno: 90K.

Pheno

: FSI and LT

50

Baga

et al 2007

Two bi-parental mapping populations

Geno: Different types of markers.

Pheno

: Freeze tests (LT

50

)

LT50: Temperature at which 50% of the plants are killed by LT stress

FSI: field survival index

BLAST FR-H3 genes based on IWGSC on 1B

Wheat

gene

chr

bp

cM

(Pop/90K)

Barley gene

TraesCS1B02G080300

1B

62,681,652

HORVU1Hr1G012710

TraesCS1B02G080400

1B

62,723,385

HORVU1Hr1G012680

TraesCS1B02G080500

1B

63,050,981

HORVU1Hr1G012690

Wheat

gene

chr

bp

cM

(Pop/90K)

Barley gene

TraesCS1D02G062800

1D

42,762973

HORVU1Hr1G012680

TraesCS1D02G062900

1D

42,845631

HORVU1Hr1G012710

TraesCS1D02G063000

1D

43,123697

HORVU1Hr1G012690

BLAST FR-H3 genes based on IWGSC on 1D

Slide22

FR-H3 in TCAP

1:3

1:21

Ratio

7:1

TOP 5%

BOTTOM 5%

Whole Population

Slide23

FR-H3 in TCAP

TOP 5% by Origin

SP1 (65)

Asia-6R-W

SP2 (178)

PNW 6R-W/F

SP3 (323)

EU-2R-W

SP4 (202)

EU/USA (OH-NB)

6R-W

SP5 (37)

MW-6R-F

SP1 (65)

Asia 6R-W

SP2 (178)

PNW-6R-W/F

SP3 (323)

EU-2R-W

SP4 (202)

EU/USA (OH-NB)

6R-W

SP5 (37)

MW-6R-F

BOTTOM 5% by Origin

TOP 5% by Head Type

BOTTOM 5% by Head Type

Slide24

Barley Pan-genome to target FR-H3

Jayakodi

et al 2020.

Slide25

FR-H3 in Pan-genome

Gene Name

chr

bp

Description

HORVU1Hr1G012680

1H

31672910

UDP-Glycosyltransferase superfamily protein

HORVU1Hr1G012690

1H

31684461

Tetraspanin

family protein

HORVU1Hr1G012710

1H

31944906

Low temperature-induced protein lt101.2

31944109

31946518

HORVU1Hr1G012710

Low temperature-induced protein lt101.2

Igri

Morex

Hv21599

H

ordeum

s

pontaneum

Hv3081

Hv3365

FRH3

BLASTn

Golden Promise

Barke

Winter

Growth Habit

Spring

Growth Habit

Slide26

FR-H3 Alignment of CDS regions

S

S

S

W

W

W

W

Hs

HORVU1Hr1G012680

SSS

W

W

W

W

Hs

HORVU1Hr1G012690

S

S

S

W

W

W

W

Hs

HORVU1Hr1G012710

Slide27

FR-H3 alignment of promoter regions

S

SSWWWWHs

HORVU1Hr1G012680

S

S

S

W

W

W

WHsHORVU1Hr1G012690**SSSWWWWHsHORVU1Hr1G012710

-103

-478

Tetraspanin

family is comprised of evolutionarily conserved integral membrane proteins

Important functions in plant development, reproduction and stress responses

In silico screening for

cis

-regulatory elements in the 1 kb promoter region of rice gene

OsTETs

revealed motifs responsive to temperature (heat and cold)

Reimann et al 2017

Gene Name

chr

bp

Description

HORVU1Hr1G012690

1H

31684461

Tetraspanin

family protein

Slide28

FR-H3 - future research

Experiment 1: Allelic variation in Nebraska lines

Due to the limited variation at the sequence level among lines retrieved from the pan-genome, allele sequencing of the three candidate genes (Hv680, Hv690, and Hv710) will be performed on

NE lines identified as high LTT in the TCAP panel

Parents used in Fisk et al. (2013) and lines from OSU in the TCAP LTT panel, with potential introgressions from NE lines, will be also used for sequencing and alignment

All retrieved sequences compared with three spring lines (

Morex

, Golden Promise and

Barke

)

Experiment 2. Expression analysis in targeted germplasm with contrasting LTT

Subset of NE, OSU, and controls

High genetic similarity, but with large LTT differences

Gene expression under low temperature conditions targeting the three candidate genes

Primers designed based on

Igri

,

Morex

, and germplasm identified in Experiment 1

Global gene expression under low temperature conditions

Focus on genes in the Fr-H3 region

Find other genome region with expression differences

Slide29

Thanks!Questions?