Unlocking new alleles for leaf rust resistance in the Vavilov wheat collection Adnan Riaz1, Naveenkumar Athiyannan1,2, Sambasivam K. Periyannan1,2, Olga Afanasenko3, Olga P.

Mitrofanova4, Gregory J. Platz5, Elizabeth A. B. Aitken6, Rod J. Snowdon7, Evans S. Lagudah2, Lee T.

Hickey1*, Kai P. Voss-Fels1,7*

1The University of Queensland, Queensland Alliance for Agriculture and Food Innovation (QAAFI), St Lucia, Australia2Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture & Food, Canberra ACT, Australia3Department of Plant Resistance to Diseases, All-Russian Research Institute for Plant Protection, St Petersburg, 196608, Russia4N. I. Vavilov Institute of Plant Genetic Resources, St Petersburg, 190000, Russia5Department of Agriculture, Fisheries and Forestry Hermitage Research Facility, Warwick, Australia6The University of Queensland, School of Agriculture and Food Science (SAFS), Saint Lucia, Australia7Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University Giessen, Germany

Will we meet the future demand?

Causal agent of wheat leaf rust: Puccinia triticina

Annual yield loss 10% to 70%(Huerta-Espino et al. 2011)

P. triticina germinated spore

Most common and widespread wheat disease

(Huerta-Espino et al. 2011; Kolmer et al. 2012; RustTracker.org, 2014)

Brazil

Canada

Spain

Germany

France

UK

Ukraine

Italy

Leaf rust in Australia

(ACRCP, 2016)

• Six different clonal lineages in Australia:

• 10-1,3,9,10,12

• 53-1,(6),(7),11

• 64-(6),(7),(10),11

• 76-1,3,5,10,12

• 104-(2),3,(6),(7)

• 122-1,2, 3, (6),(7), 11

• From 2000 to 2016

• 30 pathotypes

Seedling vs Adult plant resistance• Also referred to as: “All stage

resistance”

• Often single gene with major effect

• Often hypersensitive response

• Race specific

• Pathogen overcomes easily

• Adult plant stage

• Single gene with large effect or multiple genes with minor effect

• Partial resistance

• Race-nonspecific

• Often additive effect

+Lr28-Lr28 Photo: (Herrera-Foessel et al 2012)

Lr68

Lr34

Lr46

Genetic resistance

Variety 2014

Gregory R-MR

Suntop R

Crusader R

Livingston R

Wylie R

Spitfire MS

Wallup MRMS

2015

MR

MRMS

MRMS

MS

MS

S

SVS

2016

MR

MRMS

RMR

MSS

MS

S

SVS

Falkner** NA NA MRMS

Suntime** NA NA SVS

Viking* NA SVS

Mitch* NA SVS

Sunmate* NA MS

** released in 2016* released in 2015

Popular wheat cultivars in the eastern wheat-belt of Australia

(National variety trial, 2014; 2015; 2016)

MSS

SVS

MS

Resistant

Suscep

tible

To identify new genomic regions underpinning leaf rust resistance inVavilov wheat diversity panel through genome-wide association studies.

Objective

The Vavilov wheat diversity panel

295 diverse bread wheat accessions from VIR

Collected from 28 countries, spanning from 1920–1990

Genotyped with >56,000 DArTseq GBS markers

(Riaz et al. 2017, Genetic Resources and Crop Evolution)

N. I. Vavilov Institute of Plant Genetic

Resources (VIR), St Petersburg, Russia

Evaluating diversity panel

Growth Stage Environment Year Tested Leaf rust pathotype used

Seedling Glasshouse 2014 104–1,2,3,(6),(7),11,13

Adult plant stage Glasshouse 2014 104–1,2,3,(6),(7),11,13

Field 2014* 104–1,2,3,(6),(7),11,13

Field 2015* 104–1,2,3,(6),(7),11,13

76–1,3,5,7,9,10,12,13+ Lr37

Field 2016* 104–1,2,3,(6),(7),11,13

76–1,3,5,7,9,10,12,13+ Lr37

104–1,3,4,6,7,8,10,12+ Lr37

*Multiple readings were recorded in each field environment

Disease response of diversity panel

Dis

ea

se

re

sp

on

se

• 10,748 polymorphic markers in GenABel pakage in R

• -log10(p) > 3.5 threshold

• MAF 3%

• 52 highly associated markers 31 QTL total

• 1 seedling QTL: 3A

• 1 all-stage resistance: 2B

• 29 APR QTL: 1A, 1B, 2A, 2B, 3A, 3B, 4A, 5A, 5B, 6A, 6B, 7A, 7B, 7D

Summary of Genome wide association studies (GWAS)

Alignment to previously reported studies

• 14 QTL aligned with previously reported studies

• 4 co-located with the catalogued Lr genes

• 13 QTL were considered new loci

• Two QTL on chromosome 3A and 7B were selected for further analysis

Seedling resistance QTL on 3A

qNV.Lr-3A.1

qNV.Lr-3A.3

qNV.Lr-3A.2

47.73 109.54 116.70-117.01Distance

(cM)

Haplotype analysis: 3A QTL

Geographic distribution: 3A QTL

Adult plant resistance QTL on 7B

126.0-130.6 cM

Genetic Map length: 0.75cM

Distance (cM)

Haplotype analysis QTL on 7B

Pyramiding effect: resistance alleles in the field

LRi =

𝑘

𝑛 𝑖𝑛𝑑𝑖𝑣𝑖𝑑𝑢𝑎𝑙 𝐷𝑖𝑠. 𝑠𝑐𝑜𝑟𝑒[𝑘

𝑚𝑒𝑎𝑛 𝐷𝑖𝑠. 𝑠𝑐𝑜𝑟𝑒 [𝑘

Outcomes

• Historical accessions provide a great source of genetic diversity for resistance to leaf rust

• GWAS identified a large number of genomic regions conferring APR to leaf rust (some novel)

• Landraces carry multiple QTL conferring resistance to leaf rust

• Stable resistance can be achieved via QTL pyramiding

Riaz et al. (2017) Unlocking new alleles for leaf rust resistance in the Vavilov wheat collection.

Theoretical and Applied Genetics (Accepted)

Acknowledgements

Contact for follow up questions:

a.riaz@uq.edu.au

Twitter:@adnanriaz7