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

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

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  1. 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

  2. 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

  3. Consumer Preferences in West Africa 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

  4. Experiments Conducted 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.

  5. Data collected for the Quality tests 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

  6. Heading (days) 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

  7. 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

  8. Yield (kg/ha) 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

  9. 100 seeds (g) 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

  10. US variety CCDR and African improved WAB 56-104 CCDR 7004 kg/ha 74 days 99.25 cm WAB 56-104 4540 kg/ha 69 days 127 cm

  11. African Landrace Gninni Zeba and interspecific NERICA 5 Gninni Zeba 3063 kg/ha 105 days 162 cm NERICA 5 6229 kg/ha 69 days 109 cm

  12. % Total Mill-Top 10 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

  13. 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)

  14. Aroma Content 2-AP (ng/g) ofCultivars grown in the USA

  15. 9.5 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)

  16. Amylose classes and Waxy 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

  17. Distribution of Waxy Alleles in WARDA Materials Grown in Africa Conv. LG DXBL PB/Canning Soft Cooking

  18. 30 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

  19. Marker Associations with Cooking Quality Traits 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

  20. ----- (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)

  21. 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

  22. PCR Primers Used for Molecular Marker Analysis 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.

  23. Single Factor Analysis for the 3 Markers used for Associations Study R^2= Total Phenotypic explanation (%)

  24. Summary and Conclusions • 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

  25. Summary and Conclusions (cont.) • 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.

  26. Acknowledgements I wish to express my sincere gratitude to: • WARDA • Rockefeller foundation • Texas A&M (Soil and Crop Sciences) • USDA-ARS Beaumont

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