Transcript Molecular marker technologies for plant breeding in Latvia

APPLICATION OF MOLECULAR
MARKERS FOR CHARACTERIZATION
OF LATVIAN CROP PLANTS
Nils Rostoks
University of Latvia
2012.05.31.
Vienošanās
Nr.
1
2009/0218/1DP/1.1.1.2.0/09/APIA/VIAA/099
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
3
Genomics and plant breeding
Genomics
Genetic map
Physical map
Genome sequence
Allelic diversity
Plant breeding
Phenotype
Gene function
2012.05.31.
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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
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
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Oat DArT
0.35
0.30
0.25
PCo2 (9.2%)
0.20
0.15
LV hulless
0.10
LV hulled
0.05
Foreign hulless
0.00
Foreign hulled
-0.05
-0.10
-0.15
-0.20
-0.10
0.00
0.10
0.20
0.30
PCo1 (18.7%)
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Oat DArT
0.1
31929
Pob14391-93
30104
31652
BOR88322
Bug
Hja82371
31292
31995
31769
32055
31960
NSC-3076-76
D104
31709
31029
Endspurt
Laima
31142
31231
PCU-32
StendesDarta
31124
31959
Korol
31611
Lia1313-137
Migla
31143
30020
Lia1313-100
31869
32013
31945
Belinda
Freja
Kazstan
31851
Kirovec
Jumbo
Parsival
Zlatak
31824
P4707
31800
Straļec
29427
Skakun
P4690
Pennuda
StendesVelas
StendesDzeltenas
32224
StendesLiva
31353
31759
Arta
Hecht
31901
31906
D101EP2
S-156
31790
Stmara
SW96269
31367
Edit
Selma
Bor-1426
Katri
32190
32191
Bor88601
30629
29149
Izak
OA-504-5
Belorusskijgolozernij
Adam
Mernime
28167
28168
Abel
31868
30616
30638
30636
NosNacht
31796
GA931015
IL85-2069
GA921098
Panther
8
2012.05.31.
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
Trait mapping
Fine mapping
QTL 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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LV breding line
50
100
150
200
Distance between markers (cM)
Foreign accession
13
Interchromosomal
Intrachromosomal
LV variety
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LD (r2)
L-2532
Priekulu1 Agra
0
0
-0.2
PCo1 (10.6%)
0.4
0.2
0
-0.1
-0.2
-0.4
0.1
PCo2 (6.4%)
Dzintars
Vairogs
No-79 Daghestanicum-PI330504
No-51
1079488-45
PR-3749
Druvis
L24
ZNCF
PR-5108
PR-5109
V-08-83
Lawina
PR-5112
HeilsHanna
PR-5127
BZ14-90
BZ14-99
BZ14-12
PR-4803
Primus
3280-14-1-4
PR-5105
BZ12-86
BZ12-93
69-Clho11319
Komabainieris
PR-4832
LatvijasVietejie
PR-3274
PR-3005
PR-5131
1268498-3
PR-3134
Danuta
PR-3885
Tocada
PR-4822
Otira
PR-3512
PR-3518
Annabell
Justina
743-09
Heris
Roxana
SZD4748
Nuevo
12811
PR-4362
PR-4368
PR-4115
PR-4121
PR-3421
PR-3473
PR-3527
PR-3474
PR-3475
PR-3464
797877-39
768678-28
827580-15
1163691-34
L-2630
901683-48
Rasa
Leeni
250-PI436150
Aura
L-2529
L-2295
PR-3245
Gate
PR-3528
PR-3416
PR-3414
PR-3415
L-400
PR-3467
PR-3522
918683-13
PR-3223
Sencis
Thuringia
Hellana
Steffi
12820
PR-3345
PR-3348
Kristaps
Vienna
BZ12-63
PR-3282
Eunova
PR-3335
PR-3520
1272500-36
754277-27
1273300-50
Peggy
PR-4760
1267199-30
L-2544
Camila
Vada
12825
G-131
M9
Lysiba
Anni
Betzes
Pervonez
L-2735
Alsa
Verena
718676-19
PR-3300
PR-3515
Ula
PR-3807
PR-3494
L13
PR-3534
Maaren
PR-3351
Inari
1268799-2
L-2332
Mik1
738177-41
Golf
PR-4181
828680-15
1012786-41
Malva
720076-34
742977-10
1271100-26
Klinta
813380-13
Stendes
Ilga
Pallas
Priekulu60
PR-3605
PR-4814
B-93
L-3008
PR-3487
Ruja
12819
803877-15
PR-5137
PR-5135
L-2406
Abava
Ansis
Divosnoje
Iakub
Run8-458
PR-3448
PR-3537
PR-3438
PR-3440
PR-3297
PR-3353
L-3101
Balga
Linga
1263098-13
PR-5145
BZ12-83
Rubiola
PR-4810
PR-4812
PR-4144
PR-3636
PR-4835
Bor88377
PR-5117
L-2233
L-2985 1
H130
Imula
L14
Dziugiai
Idumeja
0.2
1
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0.3
0.1
SNP diversity in Latvian barley
germplasm
0.4
2H
3H
6H
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2009/0218/1DP/1.1.1.2.0/09/APIA/VIAA/099
Preliminary results of association
mapping
• BOPA1 genotypes, phenotypes from biological
and conventional trials 2010 – 2011
Resistance to loose
smut
b-glucan content
8
60
7
6H, 55.7 cM
50
7H, 34.8 cM
40
- Log P
5
4
3
30
20
2
10
1
2012.05.31.
1
47
93
139
185
231
277
323
369
415
461
507
553
599
645
691
737
783
829
875
921
967
1013
1059
0
0
1
45
89
133
177
221
265
309
353
397
441
485
529
573
617
661
705
749
793
837
881
925
969
1013
1057
- Log P
6
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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
Centromere
ABC15612
~0.2 cM
Mla
538P8
Telomere
~0.15 cM
RGH1bcd
(mla)
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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
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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
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