Be aware: diploid hybrid potatoes are coming! Pim Lindhout, Menno - - PowerPoint PPT Presentation
Be aware: diploid hybrid potatoes are coming! Pim Lindhout, Menno - - PowerPoint PPT Presentation
Be aware: diploid hybrid potatoes are coming! Pim Lindhout, Menno ter Maat and Michiel de Vries www.solynta.com Vico Equense, Italy November 15 th 18 st , 2015 Theo Schotte, breeding Pim Lindhout, R&D Johan Trouw, Seed productio
Food Valley 140313 EAPR meeting, OULU, Finland 2
Theo Schotte, breeding Hein Kruyt, business development Johan Trouw, Seed productio Pim Lindhout, R&D
Solynta staff in 2006 - 2011
Solynta staff in 2015
Hybrid breeding
Corn as example for F1 hybrid breeding
Potato today
Traditional breeding Hybrid breeding Introduction one trait Trait stacking Phytophthora resistance Multiplication Seed health Conclusion
Hybrid breeding has great advantages
15 – 50 years Impossible > 50 years Vegetative > 5 y contaminated 2 – 3 years 3 – 7 years 4 years ½ year clean Dynamic introductions
- f innovative products
Value creation Disruptive change Russet Burbank (1876)
400.000 plants = 10 ha commercial potato field ~ 200 gram seeds = envelope ~ 25 ton seed tubers = big sea container
The first draft potato genome sequence
The first draft potato genome sequence
- Frequency of SNPs in DNA
comparing man and chimpanzee
- Frequency of SNPs in DNA
comparing the two genomes of the heterozygous diploid RH 1 per 80 bp 1 per 28 bp So, potato has tremendous genetic variation
Potato is an extremely heterozygous crop, that harbours many deleterious alleles, which are the cause of inbreeding depression Proof of Principle:
- Generate inbred lines
- Make hybrid by crossing these inbreds
Conclusion:
Homozygocity increase by selfing is much faster in diploids as compared to tetraploids
Abbr. Short description H Sli locus donor+ fertility+ homozygosity D1 Y (yellow flesh), Qcook D2 Early, Y, Qcook D3 R3, Nematode H1, Gpa2, virus RXadg, Y D4 Nematode Grp1, early, long (shape) D5 Early, long, Y, Qfry D6 Long, Y, Qfry, H1, Qcook D7 Early, long, Y, H1, Qcook, Zep (orange flesh) D8 Early, y (white flesh) D9 Qstarch, Y D10 Wild species hybrid: late blight Rpi-avl (S. avilesi) D11 Wild species hybrid: late blight Rpi-rch (S. rechei) D12 Round (shape), Qcook, Qfry D13 Early, round, Zep (orange flesh), Y, spectacled, Qcook, blue anthocyans D14 Wild species hybrid: late blight Rpi-tar (S tarijense) D15 Early, late blight Rpi-vnt1 (S. venturii), round, Y, H1 D16 Early, round, y (white flesh)
diploid germplasm
Donor Sli gene
The donor material is weak: bad germination, slow emergence, weak seedling growth, late and poor flowering, fragile flowers, limited pollen production, lack
- f vigour, poor tuber shape
and quality and low tuber yield. Proof of inbreeding depression or basis for developing good performing inbred clones?
Sli parent Elite clone F3 progeny clones
2009: Proof of principle F1 hybrid breeding
Hybrid breeding
Requirements: Diploid germplasm Self-compatibility (Sli-gene) Goal: homozygous self-compatible lines
EAPR meeting, OULU, Finland EAPR meeting, OULU, Finland EAPR meeting, OULU, Finland
Breeding started in 2010
Planting mechanisation
(Ex-)minister of Agriculture Sharon Dijksma supporting Solynta breeding in greenhouse
SNP markers in inbred development in diploid potato
F1 F2 F3 parents
% homozygocity
F1 F2 F3 parents
- bserved
expected DS parent 98 D2 parent 39 F1 30 - 38 31 F2 27 - 70 65 F3 58 - 87 82 F4 49 - 96 91 F5 65 - 97 95
98% 99%
2012: Essentially homoygous inbreds
Good performance, not good enough for parent
Solynta breeding germplasm
F2 F2 F3
What about the genetic compostion
- f the breeding germplasm?
diploid germplasm
Abbr. Short description H Sli locus donor+ fertility+ homozygosity D1 Y (yellow flesh), Qcook D2 Early, Y, Qcook D3 R3, Nematode H1, Gpa2, virus RXadg, Y D4 Nematode Grp1, early, long (shape) D5 Early, long, Y, Qfry D6 Long, Y, Qfry, H1, Qcook D7 Early, long, Y, H1, Qcook, Zep (orange flesh) D8 Early, y (white flesh) D9 Qstarch, Y D10 Wild species hybrid: late blight Rpi-avl (S. avilesi) D11 Wild species hybrid: late blight Rpi-rch (S. rechei) D12 Round (shape), Qcook, Qfry D13 Early, round, Zep (orange flesh), Y, spectacled, Qcook, blue anthocyans D14 Wild species hybrid: late blight Rpi-tar (S tarijense) D15 Early, late blight Rpi-vnt1 (S. venturii), round, Y, H1 D16 Early, round, y (white flesh)
17 original diploid donor genotypes 2010 – 2015: Breeding for good performing homozygous self-compatible inbred lines Present Solynta breeding germplasm: Genetically biased progenies
Is genetic bottleneck driving hybrid breeding into similar genotypes?
Some F5 populations
High level of homozygosity, but still genetic variation among and within populations
What about inbreeding depression?
Inbreeding depression and hybrid vigour
1 1,5 2 2,5 3 3,5 4 4,5 5 F2 F3 F4 F5 F6 F7 F8 F1 Average Plant Vigour
- Inbreeding depression is still
present but declining
- It will take decades before
inbred lines are at same level as hybrids
What about level of homozygosity?
D1 × DS AGV008-0206 AGV009-048 D1 SOL011-357 SOL012-1312 SOL013-304 SOL014-1025 SOL015-0044 SOL015-0046 SOL015-0047 SOL015-0053 SOL015-3034 SOL015-3733 SOL015-3734 SOL015-3735 × × × × × × × × × × × × × ×
F1 F2 BC1F1 BC1F2 BC1F3 BC1F4 BC1F5 BC1F6 BC1F7
6 years 1 year
Development of homozygous inbred lines
SNP genotyping – marker distribution
- 180 SNP markers used polymorphic between D1 and DS
07
SOT08-01078910 SOT08-05438901 SOT08-11695077 SOT08-18393399 SOT08-23895193 SOT08-34342007 SOT08-38666935 SOT08-43993811 SOT08-46167248 SOT08-50484929 SOT08-52832533 SOT08-53836906 SOT08-5562111108
SOT09-02142413 SOT09-02470833 SOT09-07835623 SOT09-11805410 SOT09-15572748 SOT09-20712307 SOT09-21044695 SOT09-34192084 SOT09-47586990 SOT09-47587566 SOT09-52408174 SOT09-55501417 SOT09-58582477 SOT09-60565011 SOT09-6057064309
SOT10-00197674 SOT10-03908993 SOT10-06151401 SOT10-11539446 SOT10-17630382 SOT10-20101484 SOT10-27379373 SOT10-29626410 SOT10-36225437 SOT10-36743832 SOT10-38722150 SOT10-44048179 SOT10-48721966 SOT10-49584558 SOT10-53707878 SOT10-5967512410
SOT11-00786787 SOT11-03072948 SOT11-05051415 SOT11-09379722 SOT11-11001175 SOT11-15009691 SOT11-20780633 SOT11-22213990 SOT11-34059404 SOT11-34061926 SOT11-41840983 SOT11-4542190111
SOT12-04399051 SOT12-09356334 SOT12-20336319 SOT12-30582910 SOT12-48851340 SOT12-53989918 SOT12-53990411 SOT12-56878727 SOT12-59957346 SOT12-5997959112
34
Development of homozygous line
SOL015-0044-231
01
46.702
48.2 56.3 56.303
64.1 64.204 05 06 07
5.4 18.4 38.7 53.808
2.509 10
9.4 15.0 22.211
4.4 20.3 38.5 48.912
BC1F6 still three heterozygous regions
SOL015-3034-1002
01 02 03 04 05 06 07 08 09 10 9.4 11 12BC1F7 no heterozygous regions
Development of homozygous line
SOL015-3034-1002
01 02 03 04 05 06 07 08 09 10
9.4
11 12
Homozygous by using 180 informative SNP markers Sequencing to define homozygosity
BC1F7 no heterozygous regions
Homozygous lines available for research purposes:
- Segregating populations (F2, BC, RIL, IL, etc) fot
genetic studies
- Nearly isogenic lines (NILs) for functional
studies
- Mutant population to identify new alleles
- Development and testing of isogenic series of
hybrid varities
What about the hybrid varieties?
Yield trials in 2015
Control (4n) F2×F2 F2×F2 F3
Some breeding germplasm
Diploid Hybrids and Inbred lines vs 4n Checks
Genotype
L a d y R
- s
e t t a F e l s i n a L a d y A n a M
- z
a r t S O L 1 5
- 6
2 7 S O L 1 5
- 5
7 5 S O L 1 5
- 6
3 5 S O L 1 5
- 5
7 9 S O L 1 5
- 6
1 2 S O L 1 5
- 6
3 1 S O L 1 5
- 1
9 1 S O L 1 5
- 1
6 8 S O L 1 5
- 2
3 S O L 1 5
- 6
3 S O L 1 5
- 6
8 S O L 1 5
- 1
8 9
Tuber Yield (gr/plant)
200 400 600 800 1000 Checks
Hybrids Inbreds
LSD α=0,05
Diploid Hybrids and Inbred lines vs 4n Checks
Genotype
Lady rosetta Felsina Lady anna Mozart SOL015-0635 SOL015-0627 SOL015-0612 SOL015-0579 SOL015-0575 SOL015-0631 SOL015-0063 SOL015-0230 SOL015-0068 SOL015-0168 SOL015-0189 SOL015-0191
Frying colour index
2 4 6 8 10 Checks Hybrids Inbreds LSD α=0,05
EU demonstration project: Marker assisted backcrossing in potato
Desiree + GM
Desiree, healthy crop Desiree, susceptible Desiree, one R-gene Desiree, two R-genes
Geert Kessel
10 20 30 40 50 60 70
Delay in late blight onset, GM Desiree (2015)
Jack Vossen
Objective for 2017: Double stack Phytophthora resistant varieties
NB: Combination of resistance genes involved in diferent steps of the pathogenesis may render more durable resistance