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

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Towards molecular breeding in banana: challenges

and opportunities working with perennial polyploid

crops.

Al Brown


Quick Introduction

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• 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


Blueberry Banana


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


Conventional breeding: slow and expensive

3x 4x

2x

2x 3x

10 – 17 years


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


Suggestions

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• 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


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)


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


Mol. Breeding (2014) 34:675–689


Northern High Bush

Southern High Bush

Canker resistance


Utilizing information from related crops

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• 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.


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


Suggestions

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• 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!


Suggestions

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• 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


• QTL analysis in diploid populations

– Fusarium wilt

– Weevil

– Nematode

– Dwarfness

• Genomic selection

– Yield

– Agronomic traits

• GWAS

– Drought

– Parthenocarpy

Speeding up selection


• 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


Progress: Genomic selection

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• 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


• 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

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

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