Genomics for cereal nutrition and quality in a changing ...Nock C, Waters DLE, Edwards MA, Bowen S,...

Queensland Alliance for Agriculture and Food Innovation

Genomics for cereal nutrition

and quality in a changing climate

Robert Henry


Food and Nutritional Security


-0.80

-0.60

-0.40

-0.20

0.00

0.20

0.40

0.60

0.80

1.00

1860 1880 1900 1920 1940 1960 1980 2000 2020

Yea r

Te

mp

era

ture

0C

Global temperature


World Population


Progress in crop production

Ray et al. (2013) PLOS One 8: ee66428


Whole genome sequencing

Amplicon sequencing

Transcriptome sequencing

Gene enriched genome sequencing

Organelle sequencing

Population sequencing

Mutant sequencing

Advances in sequencing

creating new opportunities


Oryza sativa japonica, rice genome

DNA base pairs

%

chloroplast 134,551

0.04

mitochondrial 490,669

0.13

nuclear 382,151,945

99.84

Total 100 382,776,165

Sources of total plant DNA

Analysis of plant genomes

Nock C, Waters DLE, Edwards MA, Bowen S, Rice N, Cordeiro GM, Henry RJ (2011) Chloroplast

genome sequence from total DNA for plant identification. Plant Biotechnology Journal. 9: 328-333.


Ion Torrent sequencing


Variation within genotypes

Pattemore JA, Rice N, Marshall DF,

Waugh R, Henry RJ (2010) Cereal

Variety Identification using MALDI-

TOF mass spectrometry SNP

Genotyping. Journal of Cereal

Science 52: 356-361.


Cereal Identification and Purity Analysis

Genomics Key Outcomes

• Grain Genomics:

Improved wheat yields by removal of constraints on yield due to

quality selection

Improved price and market share for wheat due to higher value to

customers

lower cost processing; higher value products…

Knowledge of genes controlling

-processing

-end use quality

-nutritional traits


Aleurone

Endosperm

Pericarp

Embryo

Protein, Starch

Minerals, Vitamins

Dietary Fibre

Antioxidants

Processed Fibre

Bioactives

Next Generation Wheat Initiative


Gene expression in the

developing aleurone

and starchy endosperm

of wheat

Plant Biotechnology Journal

pages no-no, 5 JUN 2012 DOI: 10.1111/j.1467-7652.2012.00705.x

http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00705.x/full#f6

http://onlinelibrary.wiley.com/doi/10.1111/j.1467-7652.2012.00705.x/full





Gene expression in the developing aleurone and starchy endosperm of

wheat


DOI: 10.1111/j.1467-7652.2012.00705.x


6 pda 9dpa 14 dpa






Wheat transcriptome

Gillies S, Furtado A, Henry RJ

(2012) Gene expression in the

developing aleurone and

starchy endosperm of wheat.


i10; 668-679.


Gene expression in the developing

aleurone and starchy endosperm of wheat


pages no-no, 5 JUN 2012 DOI: 10.1111/j.1467-7652.2012.00705.x


aleurone endosperm






Novel wheat gene expression in maize


Germplasm

A wide range of

germplasm was

evaluated


Correlation of gene expression

with milling yield

S/R Flour Ext. %

80.0

79.0

78.0

77.0

76.0

75.0

74.0

73.0

72.0

71.0

70.0

69.0

68.0

67.0

66.0

65.0

S/R Flour Ext %30

20

10

0

Std. Dev = 2.36

Mean = 75.6

N = 100.00


Genetics of Bioprocessing

BP/H2O BP/Dry H2O/Dry


Bread quality


Bread quality


Chapatti quality


Genes determining end use quality


Food security

Rice


Cereal Starches

Wheat relative

A and B type Granules

A: <10µM

B: 10-50µM

Rice like Granules

Rigid dodecahedrons

2-5µM

Compound granules

Sorghum granules

10-30µM

Spherical to

non-uniform polyhedral


Cereal starches

ADP glucose pyrophosphorylase (AGPase) Granule bound starch synthases (GBSSI and GBSSII) Starch synthases (SSI, SSIIa, SSIIb, SSIIIa, SSIIIb, SSIVa, SSIVb) Branching enzymes (BEI, BEIIa, BEIIb) Debranching enzymes (IAS1, ISA2, pullulanase) Starch phosphorylase (SPHOL) Glucose phosphate-6-translocator (GPT1)

,

Kharabian-Masouleh A, Waters DLE, Reinke RF, Ward R, Henry RJ (2012) SNP in starch

biosynthesis genes associated with nutritional and functional properties of rice.

Scientific Reports 2, 557


Australian Wild

Rice

Distribution of Oryza species in

Australia as indicated by Australian

Herbarium records

Henry RJ, Rice N, Waters DLE, Kasem S, Ishikawa R, Dillon SL, Crayn D, Wing R,

Vaughan D (2010) Australian Oryza: Utility and conservation. Rice. 3: 235-241.


Asian and Australian rice

Oryza meridionalis

Species A

Species B

Oryza australiensis

Asian

Australian


Asian and Australian rice

Species A

Species B

Asian

Australian

Oryza meridionalis

Oryza australiensis


Wild rice chloroplast


Species A


Species B


Impact of climate change

on biodiversity

Cronin, JK, Bundock, PC, Henry, RJ and Nevo, E (2007) Adaptive Climatic Molecular

Evolution in Wild Barley at the Isa Defense Locus. Proceedings of the National Academy

of Science USA, 104: 2773-2778.


Climate and biodiversity: Collection sites from sea level to mountain tops

Fitzgerald TL, Shapter FM, McDonald S, Waters DLE, Chivers IH, Drenth A, Nevo E and Henry RJ

(2011) Genome diversity in wild grasses under environmental stress. Proceeding of the National

Academy of Science USA 108, 21139-21144.


Genome diversity

• Greatest in hotter dryer sites

• Chloroplast and nuclear genome


International Climate-Resilient Crop Genomics Consortium

(ICRCGC)


Website

http://www.climatechangegenomics.org/index.php

.


Domestication of New Crops

Henry RJ (2011) Next generation

sequencing for understanding and

accelerating crop domestication. Briefings

in Functional Genomics 11: 51-56.


Gene isolation whole genome

sequencing strategy

1

Homologues mining in M. stipoides for domestication

related genes from genus Oryza

UPM SSPM

18 Genbank entries from genus Oryza

18 Genbank entries from genus Oryza

17 genes with homologous sequence in other

Poacaeae

1 gene without homologous sequence in other Poaceae

18 genes with between 30-74% homology to the

reference genes

12 genes sufficient for primer design (21 fragments)

5 genes insufficient for primer design

2 genes insufficient for primer design

5 genes non-degenerate universal primers

(fragments)

5 genes combination universal primers

(fragments)

2 gene degenerate universal primers

(fragments)

16 genes sufficient for non-degenerate primer design

(24 fragments)

12 non-specific PCR products (>2 fragments)

12 PCR products with ≤2 fragments

12 confirmed sequences

Align M stipoides MPS sequence data to rice reference

genes Blastn search for 18 rice genes

Malory S, Shapter FM, Elphinstone MS, Chivers IH and Henry RJ (2011)

Characterizing homologues of crop domestication genes in poorly described wild relatives

by high-throughput sequencing of whole genomes.

Plant Biotechnology Journal 9: 1131-1140.


Fragrance in Plants and Foods

2-acetyl-1-pyrroline

Popcorn

Tortillas

Baguettes

Ham

Cheese

Mung bean

Green tea

Wine

Lobster

Pearl millet

Potatoes

Bradbury LMT, Fitzgerald TL, Henry RJ, Jin Q, Waters DLE (2005) The Gene for

Fragrance in Rice. Plant Biotechnology Journal 3: 363-370.


Conflict between human

and natural selection Fragrance

Bradbury LME, Gillies SA, Brushett D, Waters DLE, Henry RJ (2008) Inactivation of an

aminoaldehyde dehydrogenase is responsible for fragrance in rice. Plant Molecular

Biology 68: 439-449.



Genomics outcomes

Improved yields by removal of constraints on yield due to

quality selection

Climate resilient genotypes

Crop diversification

Grain foods with enhanced nutritional and functional

properties



QAAFI is funded by the

University of Queensland and the Queensland Government

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Genomics for cereal nutrition and quality in a changing ...Nock C, Waters DLE, Edwards MA, Bowen S,...

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