Blackcurrant breeding at the James Hutton Institute:Blackcurrant breeding at the James Hutton Institute: present and future prospects
Rex Brennan, Fruit Breeding Group, JHI
Norway, Sept. 2011
Ribes BreedingRibes Breeding
Ribes – member of Saxifragaceae (no related crop members)
All spp. diploid
Blackcurrant world production ca. 137k tonnes
Added value through processingAdded value through processing
Breeding at SCRI for juice processing since 1970
Also breeding for fresh market since 2006
SCRI cultivars commercially successful globally
Recent SCRI Blackcurrant Cultivars
Ben Gairn Ben VaneBig Ben*Ben Avon Ben Dorain
Ben StaravBen KlibreckBen Hope Ben Maia* Ben Finlay
* Fresh market cv.
Breeding ObjectivesFruit quality
Brix/acid ratio
Agronomic
Environmental resilienceBrix/acid ratio
Low total acidity
Anthocyanin levels (dephinidins
Environmental resilience
Pest resistance for low‐input
growingAnthocyanin levels (dephinidins
preferred)
Vitamin C (AsA)
Acceptable yield
Sensory traits
Trial seedlings from GSK/JHI breeding programmeg / g p g
JHI 9265‐6
Late mid season cv.
Tall vigorous growth
Good yields at Ben Hope/Alder levelslevels
Early mid season
Yi ld d i t i l i 2009 & 2010
JHI 92127‐1
Yields good in trials in 2009 & 2010
Very stocky upright growth, with dense foliage High anthocyanins, medium AsA
Good `hangability’ (only 10% drop after 14 days)Good hangability (only 10% drop after 14 days)
Marker targetsMarker targets
Ribes‐specific traits
Single gene traits, eg. pest resistance
Quantitative traits eg nutritional components inQuantitative traits, eg. nutritional components in fruit (AsA, Acy)
GenericGeneric
Quantitative traits, eg. dormancy
Linkage Map Development
2 2 P1 2 P2E45M40-2220E41M42-3882gmr4E40M43-236 E40M41-1218E41M40-2229g1-G06 E41M41-163E41M43-17911gr1-F07a g2-J08_166E45M39-156 E40M42-22613E40M40 219 E40M61 263
log HB
W
2
E41M42-3882E40M41-1218g1-G0611E40M61-263 SNPctig258
1 P01 213 E45M39 21314
SG
2_P1
E45M40-2220gmr4E40M43-236 E40M41-1218E41M40-2229g1-G06 E41M41-163E41M43-17911gr1-F07a g2-J08 16613
AsA
2_P2
E40M40-219 E40M61-263SNPctig258 g1-P01_213E45M39-213 g1-B02
14
E40M43-289 E41M43-370E45M61-262 E33M55-17716E40M55-35017E45M50-19124SNPctig22125E45M58-23226E45M41-41027E41M41-37528E45M40 27031
(21.7%)
g1-P01_213 E45M39-213g1-B02
14
E41M43-370 E45M61-262E33M55-17716E40M55-35017E45M50-19124E45M58-23226E41M41-37528E33M55-20136E40M41-14842E45M39 11747
(19.3%)
gr1 F07a g2 J08_166E45M39-156 E40M42-22613E40M40-219 SNPctig258g1-B0214E40M43-28916SNPctig22125E45M41-41027E45M40-27031E45M42-22832
(14.4%)
E45M40-27031E45M42-22832E33M55-20136E40M41-14842E45M39-11747
E45M39-11747
• Map based on SSR, AFLP and SNP data
Brennan, Hackett, Jorgensen, Gordon and Russell, 2009 Euphytica
Blackcurrant Gall Mite (Cecidophyopsis ribis Westw.)( p y p )
Highly host‐specific eriophyid mite, producing galling of buds (`big bud’)
l f l k ( ) S i h hSole vector of Blackcurrant Reversion Virus (BRV)
Difficult to control
• Until 1990 – Endosulfan
Section through mite‐infested bud
• 1990‐2005 – Fenpropathrin
• 2005 – present – sulphur
Resistance derived from gooseberry (R. grossularia), controlled by single gene Ce
Introgressed into blackcurrant (R. nigrum) in 1970s at East Malling
Extensive backcrossing to restore key fruit quality traitsExtensive backcrossing to restore key fruit quality traits
Now at BC9 ‐ commercial releases now emerging (`Ben Finlay’, 2009)
Identification of resistant plants – field infestation plot for 4 years
Mite infestation plot, Dundee 2006`Big bud’ symptoms
Gall mite marker
1
Maps to within 4‐5 cM of phenotype resistance on linkage map
Accuracy in test genotypes ca. 95%Mapping population
E45M40-2220
gmr4 Phenotypic resistanceMapping population
Cultivars
Trial lines
E40M43-2367GMRes_a8E41M88-2809E41M43-17910E40M40-21911E40M42-226 E45M39-156g2-J08_16612gr1-F07a g1-B02E41M41-16313
Marker
Marker now routinely deployed in SCRI breeding programmes as a breeding tool
2009 First trial lines selected using marker, seedling progenies tested during year
E40M43-28915erb2-P21_25416
erb1-B24b19
SNPctig22124progenies tested during year
Field infestation plot removed
2011 Separate plots of exclusively resistant material initiated
Material tested for other programmes, eg. ISK, Poland
E45M41-41027
Material tested for other programmes, eg. ISK, PolandE45M61-12635
Resistant Lines in Trial
Mite‐resistant cv. : Ben Finlay (released 2010)(released 2010)
Next Generation Sequencing in Ribes
Large scale 454 transcriptomic sequencing of two Ribes genotypes (9328 reference mapping parents)
526293 reads (117.9 Mbp of blackcurrant transcriptome)
Reads assembled into 46411 contigsg
7245 SNPs and 3179 SSRs discovered
Set of 384 SNPs representing heterozygous categories for one or both parents selected using `Tablet’ programme for validation on Illumina BeadXpress platform
New SNP‐based linkage map developed, markers and trait associations in progress *New SNP based linkage map developed, markers and trait associations in progress
SNP* Russell et al. (2011) Identification, utilisation and mapping of novel transcriptome based markerstranscriptome‐based markers from blackcurrant (Ribesnigrum) BMC Plant Biology(in press)
Trait associations
Fruit quality traits
Metabolomic analysis for sugars, organic acids and phenolics
Putative QTL developed on SNP map, validation in progress
Dormancy‐related traits
Differentially regulated genes identified using microarrays mapped to LG3 on
0.1
1
10
0.1
1
10
Differentially‐regulated genes identified using microarrays mapped to LG3 on original linkage map in area where QTL for budbreak and flowering is located
Ongoing analysis using SNP map and diverse germplasm including population segregating for chilling requirement with Plant and Food (NZ)
Y-axis: No 43, StageColored by: Week 12 Gene List: 1-Way ANOVA Bon 0.05 (184)
0.0 2.0 4.0 8.0 12.0 14.0 16.0
Week0.01
0.0 2.0 4.0 8.0 12.0 14.0 16.0
Week0.01
Significance for future sustainability of blackcurrant production
Summary
Marker‐assisted breeding strategies are now being used in blackcurrant
Screening using PCR‐based marker linked to gall mite resistance is now a routine part of the breeding programme at JHI, and new resistant lines are in commercial trials
SNP platform developed from NGS in Ribes offers real opportunities for developing marker‐based selection for key quality and developmental traits in a minor fruit crop
Longer‐term aim is to move breeding towards genomic selection approaches genotyping by sequencing is nowselection approaches – genotyping by sequencing is now being investigated in blackcurrant
Acknowledgements
James Hutton InstituteGenotyping ‐ Joanne Russell, Pete Hedley, Linzi Jorgensen, Jenny Morris
Ph iPhenotyping ‐ Sandra Gordon, Dorota Jarret, Ilka Abreu, Derek Stewart
Bioinformatics – Micha Bayer, Linda Milne, David Marshall
BioSSStatistical support ‐ Christine Hackett
