Seeds of Discovery (SeeD): An initiative to systematically explore

and mobilize novel genetic variation into maize and wheat breeding

programs Sarah Hearne, Sukhwinder Singh, Peter Wenzl, Marc Ellis, Martha

Willcox, Carolina Saint-Pierre, Matthew Reynolds, Samuel Trachsel, John Hickey, Jiankang Wang, Juan Burgueño, Ky

Mathews, Gregor Gorjanc, Janez Jenco, Armando Espinoza Banda, Alejandro Ortega Corona

“Genebanks are not museums”

● Most of the requests to banks with maize germplasm holdings are for described elite lines or landraces / wild relatives with some publication history

● Most breeders would not “touch” an un-described landrace and would have to be “desperate” to use one with very good characterisation

Bridging the divide

Information Knowledge Germplasm

Maize  

Maize  strategy  

Molecular Atlas

GWAS/GS of 4500

testcrosses

Per-se evaluation

Germplasm development

Genomic  selection  MABC,  MAS,  DH  

Large  and  small-­‐effect  alleles  

Small  and  large  effect  alleles  

Breeding  programs  (line  and  landrace  improvement)  

Information  

Germplasm  

Partners:  Mexican  genebanks  (INIFAP,  UAAAN,  UdeG,  UACH),  Langebio,  DArT,  AMAIZING    

Partners:  INFAP,  UdeG,  UAAN,  CINVESTAV,  Langebio  

Partners:  Cornell  Univ.,  INIFAP,  UAAAN,  UdeG  

Thank you

Modified GBS procedure Obtain population level fingerprints PCA of CMLs Green- highland Yellow- Sub-tropical Red- Lowland tropical 20k accessions end 2013

Molecular Atlas

GWAS/GS training panel Single plant from accession x single cross hybrid Accession parent genotyped using high density GBS (850k) Modified testcrosses from 4000 accessions phenotyped for a range of abiotic, biotic and quality traits:- Drought, heat, low N, Turcicum, Tar spot, Cercospora, ear rot, stalk rot, quality Per-se (accession direct testing) Using GIS selected accessions which were collected in areas with a prevalence of abiotic stress of interest- e.g. drought. Assumption that accessions will have through evolutionary pressures accumulated alleles favourable to stress tolerance over time -Stresses include drought and heat stress -Quality, specifically tortilla, pozole and azules also evaluated

GWAS/GS and Per-se; phenotyping intensive approaches

Pre-breeding; current activities activities

  “Re-packaging alleles”   Fixed background - DH   Shifting useful traits

from accessions or other un-adapted germplasm into early generation material that a breeder can adopt without high amounts of genetic drag - GS

3m To go from this To this

Accession Inducer line X

Each ♀ ear kept separate

Colchicine Self

Doubled haploids

DH lines

  Great when you need a fixed source quickly

  Bi-parental pops

Pre-breeding- GWAS/GS

X GBS genotype 4000 accessions Testcross phenotype 4000 testcrosses

The G-matrix is a matrix of additive genetic variances and covariances. It describes to what extent traits have genetic variation and whether or not different traits are genetically correlated with one another

Determine the genomic relationship matrix (G-matrix; like pedigree matrix) based on all markers (assigns value to markers but not effects) In un-phenotyped materials take ALL genotypic data and predict GEBV for each line using statistical models, use as proxy for phenotypic ranking GWAS is working

Assessment of options; simulations G

enetic merit

Conclusions (up to now …)

● Approach �  Lower accuracy in initial selection using test-cross materials

but higher genetic merit in C4 (beware of reconstructing the tester!!!)

�  More gain up to C4 using landrace DH than segregating materials but add two more seasons for making DH (lower rate of gain)

● Genotyping platform �  larger chip seems to be better (GBS10x10K not enough with

large Ne=10K)

●  Retraining �  Improves accuracy and gain (40 individuals likely enough)

●  Test more seeds per landrace �  3 per landrace better for GS applications than looking across

more backgrounds

Pre-breeding- GWAS/GS   G-matrix   Statistical model   Phenotypic ranking of

the 4000 testcrosses   Description of

adaptation, colour, “heterotic pattern” not A/B

  Selection of best 20 accessions per adaptation per colour/heterotic group

Pre-breeding- GWAS/GS

1 2 3 4 20

Pre-breeding- GWAS/GS Using GEBVs select highest ranking 20 plants

Select 40 high ranking plants and form testcrosses

Repeat 4 times

Use phenotype and genotype to re-estimate model

Use new model to select best 5 and backcross to same elite line. Genotype BC1 and hand best materials to breeders

GBS 200 seeds. Using GEBVs select high ranking 20 plants

Pre-breeding; plans   DH continuation

  Disease traits   Abiotic traits with excellent per-se validation

  GS   More populations from GWAS/GS panel and

from per-se and molecular atlas   Bi-parental pops

  Target diseases   Per-se

  `MABC and pyramiding for specific traits   Outputs from GWAS

Wheat

1.  Molecular  atlas  of  genetic  diversity  

Identification  of  underexplored  sources  of  

genetic  variation,  synthetics  

 

3.  Identify  ‘good’  accessions  and  

beneficial  alleles  Evaluate  key  agricultural  

traits;  genome-­‐wide  association  studies    

4.  Introgression  of  exotic  alleles  into  adapted  backgrounds  

Populations  of  linked  topcross  families  for  joint  linkage/association  mapping  in  elite  

genetic  backgrounds  

Breeding  programs:  Development  of  new  

cultivars  

Software  tools,  genetic-­‐analysis  service  (SAGA)  

Wheat  strategy  

Red: Iranian landraces Purple: Breadwheat

synthetics

Blue: Elite spring wheats

Green: Mexican landraces

Initial diversity survey of 11,000 accessions

Sukhwinder Singh, Marc Ellis, Huihui Li, Andrzej Kilian et al.

●  50,000 accessions grown in 35 field trials (220,000 plots in total) to evaluate the following characters: �  Heat and drought tolerance �  Disease resistances (tan spot, spot blotch, karnal bunt) �  Tolerance to soil infertility (low P) �  Grain quality characters

�  Adaptation to agroecological zones in Mexico

Phenotypic characterization

Carolina Saint-Pierre, Matthew Reynolds, Tom Payne, Guillermo Fuentes, Pawan Singh, Ivan Ortíz, Javier Peña, Ernesto Solis, Sergio Cortéz, Gaspar Estrada, Pedro Figueroa, Victor Hernández, Javier Ireta, Javier Lozano, Gustavo Martínez, Leodegario Osorio, Eduardo Villaseñor, Victor Zamora et al.

Maria Tattaris, Mathew Reynolds, Carolina Saint-Pierre et al.

Heat tolerance of 28,000 accessions

Drought tolerance of 46,000 accessions

“Donor accessions” for pre-breeding programs

Large-scale heat/drought screens

Matthew Reynolds, Ky Matthews, Carolina Saint-Pierre et al.

0

5

10

15

20

25

30

35

1 2 3 4 5 6 7 8 9 10

Freq

uenc

y (%

)

Fe (mg/kg)

Mexican landraces

25 27.5 30 32.5 35 37.5 40 42.5 45

0

5

10

15

20

25

30

35

1 2 3 4 5 6 7 8 9 10 11 12 13 14

Zn (mg/kg) 17.5 20 22.5 25 27.5 30 32.5 35 37.5 40 42.5 45 47.5 50

0

5

10

15

20

25

30

35

Freq

uenc

y (%

)

Iranian landraces

0

5

10

15

20

25

30

35

Elite line (Sokoll)

Grain micronutrient content

Javier Peña et al.

Ø Nature  of  plant  breeding  =  narrowing  genetic  diversity  with  high  precision:  few  large  families  

Ø Nature  of  a  project  like  SeeD  =  broadly  sampling  genetic  diversity  with  lower  precision:  many  more  small  families  §  Objective:  a  representation  of  allelic  diversity  of  exotic  wheats  in  

a  population  of  families  with  predominantly  elite  genetic  backgrounds  

 

Introgression  Strategy

Genetic  diversity  

Population  advancement  

Breeding  programs

SeeD

Linked  Topcross  Panel  (LTP)  

Exotic  1  

50:50  

25:75  

SSD  

Elite 1

Elite 2

Yield,  heat,  drought  trials   …  

Exotic  2  

50:50  

25:75  

Elite 2

Elite 3

SSD  

Yield,  heat,  drought  trials  

àà  “Co-­‐analyzable  network  of  several  200  small  TC  families Sukhwinder Singh et al.

LTP: Genetic analysis & pre-breeding

Ø  Joint  linkage/association  mapping  to  increase  odds  of  detecting  rare,  beneficial  alleles    §  Association  mapping:  low  statistical  power  to  detect  effects  

of  rare  alleles  §  Large,  bi-­‐parental  populations:  low  probability  of  capturing  

rare  alleles  because  only  few  accessions  can  be  sampled  by  crossing  

§  LTP:  Rare  alleles  of  parents  are  “amplified”  within  topcross  families  à  balance  between  AM  and  bi-­‐parental  populations  

Many thanks!

Seeds of Discovery – opening the black box of genetic diversity http://seedsofdiscovery.org seed@masagro.org