“tools, resources, genotyping and phenotyping” - … meetings/sm... · “tools, resources,...

“Tools, resources, genotyping and phenotyping”

Clare Lister and Simon Griffiths

30/11/2016

Thank you to:• Simon Orford, Alba Farre, Ji Zhou, Rajani Awal, Cathy Mumford and the Field Trials Team• Current and former group members previously involved• DEFRA

WGIN Projects Overview

• Crossing different combinations of genes / QTLs / mutations into a common background (Paragon) and studying the phenotypic effects

• Known as the Paragon Library

• Looking at interactions between genes x environment in Avalon x Cadenza NILs

• Generating new populations (RL crosses, Chromosome Segment Substitution Libraries and Breeding-by-Design)

• Dissecting UK drought tolerance in Paragon x Garcia

UK Drought

DEFRA “Adapting to climate change: UK Climate Projections” 2011

• UK will get warmer, more in summer than winter

• Summer precipitation tends to decrease

• Winter precipitation tends to increase.

Predictions for 2080’s

UK Drought

Met Office “Climate: Observations, Projections and Impacts” 2011

• Vulnerability to water stress is currently focussed in the south and south-east of the UK.

• These regions are projected to experience an increase in the frequency of droughts and water stress with climate change.

UK drought

• These are predictions but must explore mechanisms to cope with these scenarios, to breed resilience to climate change

• The Paragon x Garcia population was generated within WGIN to study drought tolerance

• Defra LINK Project: LK0986: Improving water use efficiency and drought tolerance in UK winter wheats (Eric Ober and colleagues )

UK drought

• LINK project evaluated 120 lines under irrigated and managed drought

• DT index (DTI), water use efficiency (WUE), yield potential and yield stability.

• Results showed that significant genotypic diversity for drought tolerance and WUE

• Wheat yields in the UK are often limited by water deficit during critical early stages of crop development

• Elsewhere in the world drought affects grain filling

Weather data courtesy of http://www.buxton-weather.co.uk/weather.htm * Buxton is 13 miles from the John Innes Centre

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Total Monthly Rain, Buxton*

2013 2014 2015

UK drought

Grain number is determined

http://www.buxton-weather.co.uk/weather.htm

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Total Monthly Rain, Buxton

2013 2014 2015

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2013 2014 2015 2016

UK drought

Unfortunately one doesn’t always get drought when you want it…!

UK drought tolerance

• LINK project indicated that the carbon isotope discrimination ratio (Delta) has a negative correlation with Drought Tolerance

• Four varieties showed consistently low values for carbon isotope discrimination ratio, which included Garcia. Paragon had a consistently high ratio

• The Paragon x Garcia population was originally generated to map this QTL

UK Drought Tolerance in Paragon x Garcia

• Paragon x Garcia (PxG) RIL population produced within WGIN to specifically target UK drought (~350 lines)

• Paragon - UK spring wheat

• Garcia - grown in southern France and northern Spain

- adapted to drought stress

Paragon Garcia


• Potentially advantageous to look for drought-tolerant characteristics in non-UK wheat varieties such as Garcia

• Genetic maps of Paragon x Garcia population available

• Genetic + phenotypic data should allow identification of regions of chromosome carrying drought tolerant genes

• NILs can be generated carrying these regions and used to validate the phenotypic effect.

• If successful could be introduced into breeding programmes to improve drought tolerance in UK wheat


• Drought Trial with selected PxG RILs (Ppd-sensitive)• Included subset of Paragon Library (9 lines)• 2 reps each of Irrigated / Not Irrigated plots

• Traits recorded/measured: Dates of Stage 31, Booting and Ear Emergence, plus Height, Yield, Specific Weight, TGWT, (Lodging and Senescence)


Irrigation of lower plots

Trial Layout


Soil water content and temperature monitoring Aerial monitoring with UAV

A

B

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BEMSW

BEM

EM-B

HTGWT

TGWT

TGWT High Value AlleleGarcia

Paragon

B BootingEM Ear EmergenceEM-BH HeightSW Specific WeightTGWT Thousand

Grain Weight

TGWT = NI and ITGWT = NI onlyTGWT = I only


Computational analysis of Genotypic + Phenotypic data: Chromosomal regions identified

3.003.103.203.303.403.503.603.703.803.904.004.104.204.304.404.504.604.704.804.905.005.105.205.305.405.505.605.705.805.906.006.106.206.306.406.506.606.70

4.00 4.10 4.20 4.30 4.40 4.50 4.60 4.70 4.80 4.90 5.00 5.10 5.20 5.30 5.40 5.50 5.60 5.70 5.80 5.90 6.00 6.10 6.20 6.30 6.40 6.50 6.60

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NOT IRRIGATED kg

Irrigated = 4.4 kg / Not Irrigated = 4.0 kg

PxG RILParagonGarciaSoisson


Analysis of Genotypic + Phenotypic data: Yield

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BEMSW

BEM

EM-B

HTGWT

TGWT

TGWT


Vrn-1A

Vrn-1B

Rht8

New combinations of genes in the Paragon Library: i.e. Rht’s and Vrn

Rht-1B

Rht-1D

• Drought Trial being repeated 2016-2017• Location: Riverside Field, Church Farm, Bawburgh• Field with lighter sandy soil and gentler slope

• WHAT I NEED NOW IS A DROUGHT!• ……… but maybe just over my field you’re probably thinking!


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