Kiwifruit Breeding & Genomics
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1 Kiwifruit Breeding & Genomics Luis Gea, Breeding & Genomics
2 Genetics for productivity» 3-4 years to flowering» 10 years breeding to production cycle» Progeny test + RRS» Backcross / inbreeding /sex
3 Genetics for productivity» Volume (m 3 )» Wood quality» Wood density» Spiral Grain» Stiffness» Dothistroma» Yield (trays/ha)» Fruit Quality» Dry Matter» SSC» Flavour» Psa
4 Genetics for productivity» Longevity» Climate change» n=12» Fitzroya cuppresoides (4x)» Sequoia sempervirens (6x)» Longevity» Climate change» n=29» Actinidia chinensis (2x, 4x)» A. arguta (2x, 4x, 8x)» Actinidia deliciosa (6x)
5 Germplasm Ferguson and Datson
6
7 November 2010 The killer awoke before dawn, he put his boots on he took a face from the ancient gallery And he walked on down the hall Photo: Paul Sutherland, PFR
8 November 2010
9
10 Quantitative and non-ordinal trait
11 SunGold development timeline 1995 Tetraploid Actinidia chinensis breeding programme begins 2000 Breeding team selects 6 females and 7 males as promising parents seedlings, including Gold3, are planted out in the research orchard 2004 Gold3 produces its first four fruit, identified as having superior dry matter and texture characteristics 2006 Ten selections, including Gold3, are selected for clonal trials Gold3 is transferred from the clonal development programme to pre-commercial block trials after sensory trials indicate high consumer preference Approximately 11.5 hectares of Gold3 established across the North Island and top of the South Island 206 hectares of Gold3 is released to growers. Psa is identified in New Zealand 2011 An additional 250 hectares of Gold3 is released to growers 2012 An additional 1,750 hectares of Gold3 to be released to growers to replace Hort16A ,600 hectares of Gold3 planted
12 Volume (million trays) SunGold Forecast GOLD Production by Supply Year GOLD 3 Hort16A Gold
13 Message Importance of pipeline concept Understanding that breeding a new cultivar was going to take a few years A new cultivar needs to be developed fast(er)
14 November 2010: Now what?
15 Breeding post-psa
16 Breeders pocket We cannot make progress only by increasing numbers
17 Genomics pocket» Automated DNA extraction, genotyping and scoring» High resolution melting
18 Genomics of red and Psa tolerance» Database» Pedigree» Ent» Accurate phenotyping» Genetic architecture» Structure, trial design, population size
19 Pedigrees and database * Red Whole Genome sequence
20 Database Everything? How far back? What data?
21 Accurate phenotyping G07 G08 H07 H08
22 Accurate phenotyping Peter McAtee 2015
23 Genetic architecture 100% 100% GBS 80% 60% 40% 20% 80% 60% 40% 20% % % A B C D E F G Male parent Female parent Canhong Cheng, Paul Datson
24 Tightly-Linked Myb Genes are Associated with Red Petal Colour in A. eriantha x A. chinensis Back-cross Families Fraser et al BMC Genomics. 2013; 14: 28.
25 Round 1 Marker Design List of Candidate Genes Transcription Factors Phenolic Metabolism Map Genomic Sequence BWA/Samtools Red 5 Scaffolds Filter out Non-Synonymous Variants Ensembl VEP Red5 Gene Models Design Small-Amplicon HRM
26 Red Whole Genome Sequencing-Myb210 John McCallum
27 Chrom 9 Improved assembly of Refining A. chinensis Red5 for Genetic Analysis Current Ch30 15Mb Ross Crowhurst
28 Round 2 marker design BamH1 GBS 12E Factorial WGS 12 chinensis Map to Hong Yang Map to Hong Yang Tassel Freebayes/VCFtools GS GS Logistic Regression Fst/Phasing Logistic Regression Taqman/HRM
29 Organisation of Myb Genes on Red5 Pseudo-Sanger Pseudomolecule Chromosome 9
30 Transient expression in tobacco suggests Myb210/110b may act as a repressor Myb10 + empty vector Myb110 + empty vector Myb10 + Myb210 Myb110 + Myb210 Myb210 + empty vector empty vector Mirco Montefiori
31 GBS for Red Flesh Score? Canhong Cheng, Paul Datson
32 brcrcode Psa, ploidy and bioassay rmu_367 rll_142 rld_328 rkg_376 rjz_299 rjl_302 rjl_299 rjl_297 rje_296 rje_295 rjd_307 rjd_293 rjb_307 rhr_284 rhr_283 rhr_282 rhr_281 rhq_285 rhq_283 rhq_282 rhq_280 rhp_284 rhp_282 rhp_280 GZ22 GU23 db01 da03 da01 ploidy information added remaining_percent Subprogram 2x Red 2x Yellow 4x Yellow Novel gp field inoculated
33 Mapping in a susceptible x tolerant population» 2x CK 52 seedlings clonally propagated and 200 bioassayed» Detailed phenotyping» Good reads aligned to HY and PFR reference genome assembly» 30,797 SNP sites detected; 11,211 polymorphic filtered to 6,608» Draft genetic map comprised 3,364 SNPs spanning 4,295 cm» SSR analysis at QTL peaks
34 Sus x Res mapping Sue Gardiner, John McCallum
35 T allele PSA Survival in Genotyped Commercial Red x Gold Families 36% 53 % 49 % 80 % C allele
36 Directions» Quantitative phenotypes with image analysis» Tagging markers for MAS» Integration of red with Psa» Validation» Bioassay
37 Wise monkeys?» Qualitative measurement» Low heritability» Expensive» Negatively correlated
38 Germplasm universe, the lungs of new breeding Cooper M. et al 2014
39 Acknowledgements» KRIP» Zespri» Breeding and Genomics (Te Puke, MARC, Kerikeri, Motueka, Palmerston North, Lincoln)» Plant pathology team (Te Puke, Ruakura)
40
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