APPLICATION OF MOLECULAR MARKERS FOR CHARACTERIZATION OF LATVIAN CROP PLANTS Nils Rostoks University of Latvia 2012.05.31. 1 Vienošanās Nr. 2009/0218/1DP/1.1.1.2.0/09/APIA/VIAA/09 9
Feb 24, 2016
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APPLICATION OF MOLECULAR MARKERS FOR CHARACTERIZATION OF LATVIAN CROP PLANTS
Nils Rostoks University of Latvia
2012.05.31. Vienošanās Nr. 2009/0218/1DP/1.1.1.2.0/09/APIA/VIAA/099
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Outline of the talk
• Genomics and plant breeding • DArT un SNP genotyping systems for
characterization of plant genomes • Trait mapping using association with SNP
markers • Markers for marker assisted selection
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Conventional plant breeding
2012.05.31. From Poehlman (1959) Breeding field crops 2012.05.31. 32012.05.31. 3
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Genomics and plant breeding
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Geno
mic
s
Plan
t bre
edin
g
Phenotype
Genetic map
Physical map
Genome sequence
Gene function
Allelic diversity
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DNA-based molecular markers
• Type of variation: - point mutations - insertions/deletions - repeat number variation - copy number variation
• Genotyping technology: - RFLP - AFLP - RAPD, ISSR - CAPS - SSAP, IRAP, REMAP - SSCP
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Variation in anonymous genomic regions or variation in transcribed regions (genes)
Throughput and level of automation of the genotyping technology
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DArT
• DArT genotyping available as service from the Diversity Arrays Technologies, Australia
• Dominant marker system, based on randomly digested polymorphic genomic DNA clones
• DArT platform available for barley, wheat, rice, oat and potato
• DArT genotyping done for Latvian barley, oat and potato accessions
2012.05.31.
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Oat DArT
2012.05.31.
-0.20 -0.15 -0.10 -0.05 0.00 0.05 0.10 0.15 0.20 0.25 0.30-0.15
-0.10
-0.05
0.00
0.05
0.10
0.15
0.20
0.25
0.30
0.35
LV hullessLV hulledForeign hullessForeign hulled
PCo1 (18.7%)
PCo2
(9.2
%)
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Oat DArT
2012.05.31.
0.1
31929Pob14391-93
3010431652
BOR88322Bug
Hja8237131292
3199531769
3205531960NSC-3076-76
D1043170931029
EndspurtLaim
a3114231231
PCU-32StendesDarta
3112431959Korol31611
Lia1313-137M
igla31143
30020Lia1313-100
3186932013
31945Belinda
FrejaKazstan31851
KirovecJum
boParsival
31796Zlatak31824
GA931015IL85-2069
GA921098P470731800
Straļec29427Skakun
P4690Panther
PennudaStendesVelas
StendesDzeltenas32224
StendesLiva31353
31759Arta
Hecht3190131906D101EP2
S-15631790Stm
araSW
9626931367
EditSelm
aBor-1426
Katri3219032191
Bor8860130629
29149Izak
OA-504-5Belorusskijgolozernij
AdamM
ernime28167
28168Abel
3186830616
3063830636NosNacht
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Genomics for plant breeding
• Identification of genes encoding specific traits and characterization of gene function
• Assessment of allelic diversity in specific genes to link diversity and the gene function
• Markers for specific traits allowing to create varieties with defined properties
• Assessment of genetic diversity in germplasm available to plant breeders for new varieties with novel characteristics
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Development of molecular markers
- SNP discovery by resequencing- eSNP discovery from ESTs
Development of mapping populations
- Experimental populations - Natural populations
High-throughput genotyping Phenotyping
QTL mappingTrait mapping
Fine mapping
Development of low cost, robust markers linked to
specific traits
Chromosome walking/landing
Gene cloning Gene-based marker
development
Marker Assisted Selection
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Illumina SNP genotyping
• Genotyping technology developed by Illumina • Barley genotyping assays (BOPA1 and BOPA2)
developed by The James Hutton Institute, University of California, Riverside and The Leibniz Institute of Plant Genetics and Crop Plant Research
• 2 x 1536 SNP • Most of the SNPs mapped
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SNP diversity in Latvian barley germplasm
• 95 Latvian barley varieties and breeding lines genotyped with BOPA1 (1536 SNP)
• 96 Latvian and foreign accessions genotyped with BOPA1 and BOPA2 (2 x 1536 SNP)
• Assessement of genetic diversity based on BOPA1
• Association mapping in a set of 153 accessions genotyped with BOPA1
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SNP diversity in Latvian barley germplasm
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0.1 DzintarsVairogs
L-2532Priekulu1
AgraN
o-79Daghestanicum
-PI330504N
o-511079488-45PR-3749
DruvisL24ZN
CFPR-5108
PR-5109V-08-83
Lawina
PR-5112HeilsHanna
PR-5127BZ14-90
BZ14-99BZ14-12
PR-4803Prim
us3280-14-1-4PR-5105BZ12-86BZ12-93
69-Clho11319Kom
abainierisPR-4832LatvijasVietejie
PR-3274PR-3005PR-5131
1268498-3PR-3134
DanutaPR-3885Tocada
PR-4822O
tiraPR-3512
PR-3518AnnabellJustina743-09
HerisRoxana
SZD4748Nuevo
12811PR-4362PR-4368
PR-4115PR-4121PR-3421
PR-3473PR-3527
PR-3474PR-3475PR-3464
797877-39768678-28
827580-151163691-34
L-2630901683-48
RasaLeeni250-PI436150
AuraL-2529
L-2295PR-3245G
atePR-3528PR-3416PR-3414PR-3415L-400
PR-3467PR-3522
918683-13PR-3223SencisThuringiaH
ellanaSteffi
12820PR-3345
PR-3348Kristaps
ViennaBZ12-63
PR-3282EunovaPR-3335PR-3520
1272500-36754277-27
1273300-50PeggyPR-4760
1267199-30L-2544Cam
ilaVada12825
G-131
M9LysibaAnni
BetzesPervonez
L-2735AlsaVerena
718676-19PR-3300
PR-3515U
laPR-3807PR-3494
L13PR-3534M
aarenPR-3351
Inari1268799-2
L-2332M
ik1738177-41
GolfPR-4181828680-15
1012786-41M
alva720076-34
742977-101271100-26
Klinta813380-13
StendesIlga
PallasPriekulu60
PR-3605PR-4814
B-93L-3008
PR-3487Ruja
12819803877-15
PR-5137PR-5135L-2406
AbavaAnsisDivosnoje
IakubRun8-458
PR-3448PR-3537PR-3438
PR-3440PR-3297
PR-3353L-3101
BalgaLinga
1263098-13PR-5145
BZ12-83Rubiola
PR-4810PR-4812
PR-4144PR-3636PR-4835
Bor88377PR-5117L-2233
L-2985 1H
130Im
ulaL14
DziugiaiIdum
eja
PCo2 (6.4%)
-0.2
-0.1
0
0.1
0.2
0.3
0.4
-0.4 -0.2 0 0.2 0.4
PCo1 (10.6%)
Foreign accession LV breding line
LV variety
LD (r
2)
0.10.20.30.40.50.60.70.80.9
1
0 50 100 150 200Distance between markers (cM)
Intrachromosomal Interchromosomal
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2H
3H
6H
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Preliminary results of association mapping
• BOPA1 genotypes, phenotypes from biological and conventional trials 2010 – 2011
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b-glucan content
1 70 139 208 277 346 415 484 553 622 691 760 829 898 96710360
10
20
30
40
50
60
- Log
P
7H, 34.8 cM
1 70 139 208 277 346 415 484 553 622 691 760 829 898 96710360
1
2
3
4
5
6
7
8
- Log
P
Resistance to loose smut
6H, 55.7 cM
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Molecular markers and genetic diversity
• Genetic diversity is both the basis for development of varieties with different traits, and a tool to distinguish the varieties and map and transfer traits
• DNA-based markers directly assess genetic diversity in a genome
• Gene-based molecular markers allow to assess allelic diversity in genes providing direct link to functional diversity
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Markers for plant breeding • Any marker that allows to select for a specific trait is
useful in plant breeding • Molecular markers detect differences between individuals
or varieties at molecular (protein and DNA) level • Molecular markers that are linked to certain traits form
the basis for marker-assisted selection (MAS) • Essentially, molecular markers are just another way of
achieving what breeders have been doing for years – combine traits of interest in a novel variety in the most efficient way
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Markers for breeding
• Powdery mildew resistance in barley – Mla case
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Centromere ABC15612~0.2 cM ~0.15 cM
538P8
RGH1bcd mla( )
Mla Telomere
Mla19 GB
Mla18 GB
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Outlook
• Association mapping in barley using SNP markers and phenotyping data collected within European Social Fund project
• Development of assays for published and new molecular markers for specific traits that can be used by breeders with a focus on traits important in organic farming
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Acknowledgements
• Plant molecular genetics group at the University of Latvia
• State Priekuli Plant Breeding Institute • State Stende Plant Breeding Institute • Funding – European Social Fund project
2009/0218/1DP/1.1.1.2.0/09/APIA/VIAA/099
2012.05.31.
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Acknowledgements
• Collaborators at the James Hutton Institute Dr. Robbie Waugh, Dr. William Thomas
• Collaborators at University of California, Riverside Dr. Timothy Close
• Diversity Arrays Technology Dr. Andrzej Kilian
2012.05.31.