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Characterization of Novel Rice Germplasm from West Africa and Genetic Marker Associations with Rice Cooking Quality. Dr. Karim Traore IER, Mali Dr. Anna McClung USDA Beaumont, TX Dr. Robert Fjellstrom USDA Beaumont, TX.

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Slide1 l.jpg

Characterization of Novel Rice Germplasm from West Africa and Genetic Marker Associations with Rice Cooking Quality

Dr. Karim Traore IER, Mali

Dr. Anna McClung USDA Beaumont, TX

Dr. Robert Fjellstrom USDA Beaumont, TX


Consumers around the world have different preferences in rice cooking quality l.jpg
Consumers Around the World Have Different Preferences in Rice Cooking Quality

  • The Japanese people prefer soft and sticky rice with short grain (japonica types)

  • In the USA, medium and long grain rice varieties are preferred

  • In South America and the Middle East, people prefer firm and non-sticky rice

  • Thai people prefer long grain soft and nonsticky

  • In India, Pakistan, fragrant or scented rice is preferred

  • In Brazil, people prefer long, slender, and translucent grain


Consumer preferences in west africa l.jpg
Consumer Preferences in West Africa Rice Cooking Quality

In West Africa consumers prefer:

  • long, slender, intermediate amylose

  • Aroma

  • Sticky rice to make rice porridge

  • Parboiled rice

  • Brokens

  • Farmers like rice that is slow to digest giving longer satisfaction


Experiments conducted l.jpg
Experiments Conducted Rice Cooking Quality

1. Conduct genotypic and phenotypic evaluation of West African germplasm for agronomic and quality traits to identify characteristics that can benefit WA and USA rice breeding programs.

2. Determine genetic marker associations with key cooking quality traits that can be used in rice cultivar improvement programs.


Data collected for the quality tests l.jpg
Data collected for the Quality tests Rice Cooking Quality

Alkali Spreading Value (ASV)- qualitative indicator of starch gelatinization temperature, dispersion of milled grain in 1.5% KOH solution

Apparent Amylose Content (AA), Soluble Amylose (SA)- indicator of cooked rice texture, using wet chemistry auto analyzer

Rapid Visco Analyzer (RVA)- determines the viscosity of rice flour pasting subjected to cycles of heating and cooling

Differential Scanning Calorimetry DSC- quantitativeindicator of starch gelatinization temperature, using DSC 6 analyzer determines the temperature and heat of gelatinization

Cooking Time- time required for 10 milled rice grains to be completely gelatinized

Total and Whole Milling Yield – indicator of crop value, using McGill#2 Mill for 1 min.

Grain dimensions- indicator of crop value, using WinSEEDLE

Crude Protein Content-indicator of nutritional value, using nitrogen gas analyzer LECO 528

Aroma (2-Acetyl-1-pyrroline)-indicator of market value, using gas chromatography


Heading from the agronomic evaluation field of wa germplasm l.jpg

Heading (days Rice Cooking Quality)

120

100

80

60

40

20

0

IMP

INT

LOC

USA

Heading from the Agronomic Evaluation Field of WA Germplasm

IMP = Improved Africa(6)

Land = Landrace(13)

INT = Interspecific (7)

USA = checks (8)

103

102

76

74

Same color =

No differences


Plant height from the agronomic evaluation field of wa germplasm l.jpg
Plant Height from the Agronomic Evaluation Field of WA Germplasm

IMP = Improved Africa(6)

Land = Landrace(13)

INT = Interspecific (7)

USA = checks (8)

Plots: 6 rows of 4.57 m length; spacing

17.78 cm between rows

RCBD, 4 rep.

Height (cm)

180

162

160

119

122

140

105

120

100

80

60

40

20

0

IMP

INT

Land

USA

Same color =

No differences


Grain yield from the agronomic evaluation of wa germplasm l.jpg

Yield (kg/ha Germplasm)

7000

6000

5000

4000

3000

2000

1000

0

IMP

INT

Land

USA

Grain Yield from the Agronomic Evaluation of WA Germplasm

IMP = Improved Africa(6)

Land = Landrace(13)

INT = Interspecific (7)

USA = checks (8)

6200

4579

4342

2586

Same color =

No differences


Grain weight from the agronomic evaluation field of wa germplasm l.jpg

100 seeds (g) Germplasm

3

2.5

2

1.5

1

.5

0

IMP

INT

Land

USA

Grain weight from the Agronomic Evaluation Field of WA Germplasm

IMP = Improved Africa(6)

Land = Landrace(13)

INT = Interspecific (7)

USA = checks (8)

2.78

2.59

2.51

2.37

Same color =

No difference


Us variety ccdr and african improved wab 56 104 l.jpg
US variety CCDR and African improved WAB 56-104 Germplasm

CCDR

7004 kg/ha

74 days

99.25 cm

WAB 56-104

4540 kg/ha

69 days

127 cm


African landrace gninni zeba and interspecific nerica 5 l.jpg
African Landrace Gninni Zeba and interspecific NERICA 5 Germplasm

Gninni Zeba

3063 kg/ha

105 days

162 cm

NERICA 5

6229 kg/ha

69 days

109 cm


Total and whole milling yield of varieties grown in the usa l.jpg

% Total Mill-Top 10 Germplasm

Gnanle Gnan-Man (78)

Baldo (77)

Bengal (76.6)

Nerica 2 (76.5)

Mahafin (76.4)

Nerica 5 (76.2)

ZHE733(BMT) (76)

Nerica 1 (76)

Mokossi (76)

Nerica 3 (76)

% Whole Mill-Top 10

Bengal (70)

CPRS (68)

Saber (68)

Nerica 3 (67.7)

Saber (BMT) (67.5)

Cheniere (66.7)

Nerica 4 (66.5)

WAB 638-1 (66.1)

Bakue Danane (66.05)

CCDR (65)

Total and Whole Milling Yield of Varieties Grown in the USA

Plots: 3 rows of 4.57 m length; spacing 17.78 cm between rows

RCBD, 4 Rep


Grain characteristics like grain width and total mill can affect cooking time l.jpg
Grain Characteristics like Grain Width and Total Mill can affect Cooking time

1% change in breakage can cause a $100,000 difference in profit for an

average-sized rice mill (Hosney 1998)


Aroma content 2 ap ng g of cultivars grown in the usa l.jpg
Aroma Content 2-AP (ng/g) of affect Cooking timeCultivars grown in the USA


Protein content of cultivars grown in the usa l.jpg

9.5 affect Cooking time

9

+1 SD

8.5

8

Mean

protein

7.5

7

-1 SD

6.5

6

5.5

Observations

Protein Content (%) ofCultivars Grown in the USA

Cheniere (9.1)

Jaya (9)

Nerica 2 (9)

ZHE733 (BMT)(9)

ZHE733 (8.8)

IITA 123(a) (8.8)

Bengal (8.7)

BG 90-2 (b) (8.6)

IITA 123 (b) (8.5)


Amylose classes and waxy gene l.jpg
Amylose classes and affect Cooking timeWaxy gene

  • Starch = amylose + amylopectin (60-80%) of edible weight of cereal.

  • Starch comprises 90% of the total dry matter of milled rice (Bao et al. 2002). The cooking and eating quality of rice is mainly influenced by the properties of starch.

  • Smith et al. (1997): GBSS= wx protein is the product of waxy gene, plays roles in the synthesis of amylose.

  • Starch branching enzyme, soluble starch synthase, and starch debranching enzyme plays major role in the synthesis of amylopectin.

  • No amylose (waxy): very soft and extremely sticky (0%)

  • Low amylose: firm, separate, non sticky (10-19%)

  • Intermediate: (20-24%)

  • High amylose: extra firm, low solid loss during processing, superior kernel stability (>24%)

Glucose molecule

Amylopectin

Amylose


Distribution of waxy alleles in warda materials grown in africa l.jpg
Distribution of affect Cooking timeWaxy Alleles in WARDA Materials Grown in Africa

Conv. LG

DXBL

PB/Canning

Soft Cooking


Distribution of the waxy allele among the interspecifics grown in africa l.jpg

30 affect Cooking time

26.1

25.3

24.7

23.6

23.5

22.6

25

22.2

21.7

21.1

20

15

10

5

0

CG14

NERICA 3

NERICA 7

NERICA 4

NERICA 6

NERICA 2

NERICA 5

NERICA 1

WAB 56-104

Distribution of the Waxy allele among the interspecifics Grown in Africa

AA

%

Waxy 124

Waxy 103-105


Marker associations with cooking quality traits l.jpg
Marker Associations with Cooking Quality Traits affect Cooking time

Cocodrie CCDR: Cypress//L-202/Tebonnet at Louisiana in

1990.

Dixiebelle DXBL: RU8303181/CB801 at Beaumont in 1983

Brown rice was used for DNA extraction using Qiagen

Kit. PCR was used for amplification followed by evaluation for

polymorphisms using ABI sequencer


Slide20 l.jpg

----- affect Cooking time(CT)n--

G/TTATAC-

Diagrammatic Representation of the Waxy Gene

Exon 6:

A  C transversion and substitution changes a Tyrosine to Serine

Differences in DNA sequence of Rexmont, JODON, and Toro-2 from lemont

-intermediate

-High/low

Larkin and Park. 2003

Exon 10:

C  T transition and substitution changes a Proline to Serine. Differences in DNA sequence of Rexmont from Jodon, Toro-2 and Lemont.

-high amyl.strong RVA

-others

Larkin and Park (2003)

Exon 1

G  T substitution is associated with low amylose varieties.

-interm. /high

-low amylose

Ayres et al. (1997)

CT repeats associated with apparent amylose content

(CT)10 & (CT)11= high

(CT)14 & (CT) 20= int

(CT)17 & (ct)18= low

Ayres et al. (1997)

Bergman et al. (2001)

Rexmont= high amylose strong RVA

Lemont= intermediate amylose

Jodon, L202= high amylose, weak RVA

Toro-2= low amylose

Adapted from Chen (2004)


Ccdr et dxbl ont la m me teneur en amylose 26 mais diff rent en rva l.jpg
CCDR et DXBL ont la même teneur en Amylose (~26%) mais Diffèrent en RVA

105

400

Temperature profile

DXBL

Peak

Cool

90

300

CCDR

RVU

75

Temp oC

200

Hot

60

100

Bkdn=Peak- hot

Stbk= Cool-Peak

CS= Cool- Hot

45

0

0

0

3

6

9

12

15

15

Time minutes


Pcr primers used for molecular marker analysis l.jpg
PCR Primers Used for Molecular Marker Analysis Diff

21 PCR markers were selected and screened for marker association study. The markers were either:-near starch metabolism (like SSS, SBE )-at a map position with significant effects on starch properties (like amylose content, or RVA pasting properties

Waxy, exon10, and AB26285 showed association with the amylose and RVA properties.


Single factor analysis for the 3 markers used for associations study l.jpg
Single Factor Analysis for the 3 Markers used for Associations Study

R^2= Total Phenotypic explanation (%)


Summary and conclusions l.jpg
Summary and Conclusions Associations Study

  • Interspecifics were found interesting for reduced water rice growing, more studies can elucidate these findings

  • Nerica 2 had good agronomic and milling characteristics

  • Bakue Danane, Cocote, WAB 638-1 had strong aroma

  • Jaya, Nerica 2, BG 90-2, IITA 123 had high level of Protein


Summary and conclusions cont l.jpg
Summary and Conclusions (cont.) Associations Study

  • Soluble Amylose (SA) explained more the difference in RVA profile than the Apparent Amylose (AA).

  • Different GBSS alleles may produce the same amount of total amylose but different proportions of soluble and insoluble amylose.

  • The Waxy microsatellite and waxy exon 10 SNP markers are now useful molecular markers for rapid and efficient identification of cooking quality traits that can be difficult to separate with only physico-chemical data.


Acknowledgements l.jpg
Acknowledgements Associations Study

I wish to express my sincere gratitude to:

  • WARDA

  • Rockefeller foundation

  • Texas A&M (Soil and Crop Sciences)

  • USDA-ARS Beaumont