Presentation during IITA R4D week 2015 (23 - 27 Nov. 2015). By: Al Brown

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Towards molecular breeding in banana: challenges
and opportunities working with perennial polyploid
crops.
Al Brown

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Quick Introduction
NARITA 1
NARITA 5
NARITA 7
NARITA 19
NARITA 17
• Univ. Minnesota (Sweet Corn)
– Conventional Breeding
• New Mexico State (Chile Peppers)
– Conventional Breeding
• Univ. Illinois (Broccoli)
– Marker Assisted Breeding
• Washington State/USDA (Peas)
– Marker assisted breeding
• USDA Parlier CA (Prickly Pear)
• N. Carolina State (Broccoli, Blueberry)
– Marker assisted, genomics bioinformatics

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Blueberry Banana

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Banana
• Triploid
• Clonally propagated
• Perennial (suckers)
• Spacing 2 to 2.5 m
• 2-3 years before
evaluation
• Limited genetic/genomic
resources
• Inbreeding not feasible
Blueberry
• Tetraploid, Hexaploid
• Clonally propagated
• Perennial (canes)
• Spacing 1.5 to 2 m
• 3+ years before
evaluation
• Limited genetic/genomic
resources
• Inbreeding not feasible
due to inbreeding
depression

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Conventional breeding: slow and expensive
3x4x
2x
2x3x
10 – 17 years

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Conventional breeding: slow and expensive
1 plant per 6 m2
Playing with ploidy
Parthenocarpy
Unpredictable seed production (3x)
Poor seed/embryo germination
Field Tissue culture
Screenhouse Field
First selection after 2-3 years
99.9% of the hybrids discarded in EET

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Suggestions
NARITA 1
NARITA 5
NARITA 7
NARITA 19
NARITA 17
• Resource development (takes the most time)
– Utilizing random molecular markers the fastest but generally the
least informative approach
– Utilizing information, conserved sequences from related crops
– Generating de novo resources (takes the longest, requires the
greatest cash outlay and bioinformatic expertise
Before you build the house, you need the tools

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Blueberry Tool building
2007
• ~50 SSR Markers
• 20,000 ESTs
• 1 incomplete linkage map
• No sequence information
• No BAC Library
• No database
2015
• >42,000 SSR Markers
• Several RNA SEQ
Libraries
– Multiple tissues, conditions
• 3 Genetic linkage maps
– MSU, USDA, UFL)
• Draft assembly 8,000
scaffolds, N50 =250 kb
• 1 BAC Library (w/ UFL)
• Vaccinium.org (w/ WSU)

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Gupta, Brown et al. GigaScience (2015) 4:5

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Mol. Breeding (2014) 34:675–689

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Northern High Bush
Southern High Bush
Canker resistance

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Utilizing information from related crops
NARITA 1
NARITA 5
NARITA 7
NARITA 19
NARITA 17
• Illumina 60K SNP array Brassica napus AACC (Rapeseed,
canola)
– Generated first saturated linkage map of B. oleracea (CC) (broccoli)
– Multiple QTL studies impacting health-related compounds
– Most effective for closely related crops
– Information currently used by Monsanto and General Mills (Green
Giant) Proprietary issues.

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Brown et al., 2015. Theor Appl Genet 128:1431-7

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Suggestions
NARITA 1
NARITA 5
NARITA 7
NARITA 19
NARITA 17
• Partnering with Industry (Dole, Monsanto, General Mills)
– Identify common goals, objectives and concessions
– Address Intellectual property issues at the onset
– Bring your own lawyer to the table!

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Suggestions
NARITA 1
NARITA 5
NARITA 7
NARITA 19
NARITA 17
• Wider crosses
– Increase the time needed to obtain finished product
– Greater potential gains, multiple purposes
– Expand phenotyping beyond narrow specific targets
– automate?
– Glucosinolates, Carotenoids,
– Polyphenolics, Mineral accumulation, sugars, amino acids

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• QTL analysis in diploid populations
– Fusarium wilt
– Weevil
– Nematode
– Dwarfness
• Genomic selection
– Yield
– Agronomic traits
• GWAS
– Drought
– Parthenocarpy
Speeding up selection

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• Gene expression
– Drought
• Genomics
– Sequencing of matooke and plantain breeding
material (100 accessions each): AOCC, ICRAF
• Others
– Metabolomics
– Flower biology
– Vitamin and mineral content
– Chromosome doubling (2x doubled to 4x)
– Heterosis
Speeding up selection

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Progress: Genomic selection
NARITA 1
NARITA 5
NARITA 7
NARITA 19
NARITA 17
• Phenotypic data:
– 320 genotypes:
– Since 2012
– 2 fields in Sendusu with contrasting management
– 1 field in Mbarara
– Yield-related traits (fruit feeling, suckering behavior,
bunch weight, etc.)
– Data collection for 2 to 3 cycles
– About 60% of data collected

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• Each crop is different and often requires modifications
to strategies, however, important to learn from the
experiences (good and bad) of colleagues
• Banana presents challenging but not insurmountable
problems that will require innovative approaches
• Banana is quickly shifting from resource building to
utilization of these tools
• The current strategy is to utilize multiple approaches,
evaluate effectiveness, and modify as necessary
• We are not re-inventing the wheel but determining
which wheel fits our car.
Conclusions

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