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Gene discovery for rice tolerance to saline and phosphorus-deficient soils
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Gene discovery for rice tolerance to saline and phosphorus-deficient soils

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Revitalizing Marginal Lands: Discovery of Genes for Tolerance of Saline and P-Deficient Soils to Enhance and Sustain Productivity …

Revitalizing Marginal Lands: Discovery of Genes for Tolerance of Saline and P-Deficient Soils to Enhance and Sustain Productivity

Ismael Abdelbagi, IRRI

GCP Project G3005.02: Progress and expected impacts of Saltol and Pup1 QTLs on rice improvement

6th Asian Crop Science Association Conference and the 2nd International Conference on Rice for the Future, organised by BioAsia in Bangkok, Thailand

November 2007

Published in: Technology, Business
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  • 1. Revitalizing Marginal Lands:Discovery of Genes for Toleranceof Saline and P-Deficient Soils toEnhance and Sustain Productivity GCP Project #2 Progress and expected impacts of Saltol and Pup1 QTLs on rice improvementIRRI
  • 2. Project Breeding ObjectivesPrecision mapping of Saltol & Pup1 lociDevelop/validate markers for both QTLs & aMAB system for introgressing them intopopular varieties and elite linesIdentify and validate the candidate genesinvolved at the two lociFunctional confirmation and assessment ofpositive and any negative impacts using NILsStrengthen the capacity of NARES partnersin MAB and other relevant technologies
  • 3. Salinity: Crop type and target Regions Salinity affect > 21 m ha in S and SE rice areas and considerably reduce productivity Target areas: Salt affected coastal areas (coastal Bangladesh) Inland saline and alkaline areas
  • 4. Salt stress in rice emergence of Germination radicle tolerant & primary leaf grain ripening tolerant Tolerance at seedling stage does not SeedlingFlowering/ ensure tolerance sensitivepollination sensitive during reproduction Active tillering tolerant panicle exertion panicle initiation stem elongation sensitive Sensitive
  • 5. Phosphorus deficiency: Crop type and target RegionsPhosphorus deficiency affectsabout 50% of rice areasTarget areas: Uplands of South and South East Asia (Indonesia) Other P-deficient soils (acid, alkaline, peat soils) Drought-prone areas
  • 6. Outputs and productsA Marker Aided Breeding system toincorporate major QTLs associated withtoleranceBetter understanding of tolerancemechanismsEfficient large-scale phenotyping systemTrained NARES capable of applying MABpackage in their breedingPopular varieties tolerant to salinity andphosphorus deficiency developed anddisseminated in target areas
  • 7. A MAB system for Pup1 and Saltol Salinity P-def +P -PMajor QTLs identified for both stresses QTL Ch R2 LOD IntervalSaltol 1 ~ 65% >8 ~ 1.2 Mb Pup1 12 ~ 80% 16.5 ~ 0.3 Mb
  • 8. MAB strategy1 2 3 4 1 2 3 4 1 2 3 4 Target Target gene + gene flanking markers Foreground Recombinant Background markers markers markers
  • 9. MAB for P-deficiency tolerance > 20-fold difference in P Mapping population developed uptake with traditional from Nipponbare x Kasalath varieties being superior and used in QTL mapping 14 Kasalath 12 Kasalath 10P uptake (mg plant-1) 8 6 Nipponbare 4 Nippobare 2 0
  • 10. Four QTLs for P uptake detected on chromosomes 2,6,10,12 Pup11 2 3 4 5 6 7 8 9 10 11 12 C445 C112 C 1 4 70 R 1 9 25 C597 R 2 8 69 C261 R 1 9 63 C711 C701 R 1 5 06 C901 C107 R 1 9 62 C 1 0 57 R 2 6 62 R 1 1 64 C950 C 1 4 45 R 1 9 27 R 1 4 27 G 1 40 6 R117 R830 C82 C 1 2 21 R 3 2 26 C 1 9 1B C502 R 1 9 33 R 1 6 87 C 1 0 69 R 3 1 66 G 3 76 R 1 6 18 C 1 0 16 C498 R 2 1 74 G 2 75 C 1 0 12 2 G 1 46 5 R 1 7 09 C742 C 1 4 54 C595 G 2 35 R 1 8 38 R 1 9 54 R565 R 2 1 94 C560 C50 R 2 7 08 R514 S 1 0 0 12 G 1 03 C189 C944 R 2 4 14 C249 L6 8 8 C 1 1 72 G 2 14 0 C 1 4 08 C 1 1 00 C86 C746 R79 G 2 00 R202 R 1 6 29 S2260 R418 R 1 7 83 R566 C136 R 2 4 01 R 2 6 76 R 3 3 93 R 2 1 47 G 2 57 R 1 7 51 C443 R374 R 2 5 58 C 1 4 78 G 1 87 C747 R 1 4 88 R728 R617 C813 R250 C335 G 1 07 3 G 3 85 R 4 8 0A G 1 45 8 C39 G 2 02 R 2 4 17 R19 R727 R 3 3 75 C513 R372 R 2 4 47 C424 R 2 1 71 C 1 2 26 R 2 2 72 C3 R93 R 1 4 36 C347 C 1 2 86 R 2 6 72 C 1 3 70 R 1 8 26 R 1 4 40 G44 G 3 32 R 2 2 89 R 2 1 23 R 2 3 81 R 2 6 38 C 1 3 36 C891 C 1 3 69 C535 R26 R 2 6 54 G 1 04 C80 C975 C 1 2 68 C609 R642 C122 C499 R437 R 3 0 89 R 1 8 77 S2137 C 1 1 07 R 1 5 53 C 1 2 63 C 1 1 16 A R886 C214 C488 G 3 20 G 1 31 4 B R 1 8 13 C 1 6 77 G 1 22 C570 R 2 3 16 C732 C624 C 1 1 21 R716 R674 C451 C808 C361 R902 C506 C477 G 1 93 C128 C809 C734 R 1 4 85 R 2 1 70 R 2 5 49 R 1 3 57 C166 G 2 93 G 2 4B C 1 3 50 R 2 6 35 C 1 1 35 C 1 0 18 G 1 27 C358 R 1 2 45 C 7 9 4A R288 C905 G 1 32 R 3 1 56 C466 C223 C556 C847 C390 R 3 2 02 C777 C 1 4 88 C246 C946 R 2 0 71 C 1 4 12 R 1 4 66 R 1 9 28 R 1 9 43 R 1 8 43 C63 R521 R11 R 2 2 53 R 1 8 54 R 1 7 89 C 1 2 30 R 1 8 88 R77 C596 C563 R 2 3 73 R 1 6 08 C213 10 cM R712 C607 C728 C25 R 1 1 67 C178 G 2 27 R 2 3 29 C515 C365 P uptake P use efficiency R210 C132 C 1 2 11 G 1 32 7 C955 C885 C421 G 3 65 R 1 9 44 R 1 6 13 R 2 5 10 C970 C161 The one on chromosome 12 is a major QTL (~13 cM)
  • 11. NIL NIL 14-4 14-6 (Mb in Nip.) RM27815 (7.47) 12 (cM) G124A (30.0) C732Fine mapping S2572 G124A S10520 (40.3) RM27090 (12.20)of Pup1 locus S10520 P96 (47.9) RM28002 (12.95)on chr 12 C443 S10704 (49.3) T5-4 (15.32) C443 (50.5) S14025 (51.8) RM28073 (14.95) G2140 S13126 (55.1) Pup1 S13752 (56.0) RM28102 (15.91) S1436 (57.4) C449 RM465 (16.75) C61722 (58.9) Ba76H14_7154 RM511 (17.40) (15.47) RM1261 (17.53) C2808 G2140 (63.7) RM28195 (18.08) W326 V124 (70.7) RM519 (19.90) C901 C449 (72.5) T S Pup1 fine-mapped to within 272 kb and sequenced Candidate genes short listed and are being analyzed through RNAi and overexpression
  • 12. Gene- & allele-specific markers for Pup1 Kasalath (272007bp) 39 T5-4 4/5 1418 21 26 38 43 45 50 59 Ba76H14_7154 40 42 22/24 67 SSR3 T5-4 Ba76H14_7154 (15.32Mb) (15.47Mb) Nipponbare (154071bp) over 95% 90~95% 80~90%Kasalath allele-specific Candidate gene-specific Sequence similaritydominant markers Co-dominant markersSSR markers developed to be developed for candidate genesMarkers (SSRs, gene-specific) developed & are beingused to transfer Pup1 into 3 popular upland varieties,Dodokan, Situ Bagendit, and BaturNine sets of crosses madeBC1F1 populations genotyped (Foreground, recombinant& background) and BC2F1 developed for further analysis
  • 13. MAB for salinity tolerance 1 2 3 4 5 6 7 8 9 10 11 12 Saltol = seedling salt tolerance = Na+ exclusion = Δ13CSaltol is fine-mapped, annotatedgenes are being further analyzed
  • 14. Different types of markers were developed (SSRs, SFPs, gene-specific)11.1 11.2 11.3 11.4 11.5 11.6 B1146F03 P0552C05 OsJNBb- OsJNOa173H09 P0475H04 0022N24 OsJNBa0008D05 AP003206 AP002873 (1,288-137,047) AP002871 (69,518-136,586) AP003567 AP006856 AP007204 (32,660-143,337) (60,200-124,062) (33,026-39,054) (1-134,776) S21150 E4175 C11732 RM10711 RM8094 RM10719 RM10720 RM10725 RM3412 (AGG)9 (AT)31 (CCG)8 (AT)34 (AC)25 (AG)17 LOC_Os01g19694 LOC_Os01g19800 homeobox protein PIT1 retrotransposons retrotransposons retrotransposons OSH1 (KNOX) (zinc-finger) LOC_Os01g19770 LOC_Os01g19850 LOC_Os01g19970 LOC_Os01g20720 stress-inducible cation-chloride myb-like retrotransposons NBS-LRR membrane pore protein co-transporter transcription factor (CCC1-like) LOC_Os01g19820 LOC_Os01g20160 retrotransposons universal stress cation transporter OsHKT8 protein (ER6) (SKC1)
  • 15. RM3252 RM243 10.4 Mb RM10655 Saltol RM1287 RM10694 10.9 RM10649 10.3Saltol RM10696 RM10701 RM10711 fine-map RM10713 AP3206QTL RM8094 11.3 RM10720 15.3 RM10927 RM3412 11.5 SKC1 Centromere RM10748 RM10772 RM24 RM493 12.1 RM10773 30 SSRs and 12.2 RM140 gene-based RM10793 RM9 RM8115 12.7 RM10800 markers across RM10825 the Saltol region RM10829 13.7 RM5461 RM10843 13.8 SalT RM10852 RM7643 RM10864 RM562 14.6 RM10871 RM10890 RM7075 15.1 RM10927 15.3 Chromosome 1 Background markers developed for a set of recipient varieties
  • 16. MAB scheme for Saltol BR28/FL478 // BR28Recipient varieties: BC1F1 IR64 (widely grown), BR11 and BRRI dhan 28 Selected BC1F1 (Bangladesh), swarna BC1F1 / BR28Donors: BC2F1 Pokkali, FL478 and FL378 Selected BC2F1MAB is used to transfer BC2F1 / BR28Saltol: BC2F2 BC3F1 Foreground and recombinant markers used for selection Selected BC3F1 after each cross X SSRs for background BC3F2 selection
  • 17. Saltol MAB for BRRI dhan 28• Goal: Saltol QTL line with BR28 background• Current status: – SSR-selected BC2F1 individuals were backcrossed to BR28 – 1,500 BC3F1 plants now growing at IRRI – Markers are being used to select individuals to advance to BC3F2• Confirmation: – BC3F2 seeds will be used to confirm the Saltol effect in the BR28 background
  • 18. Saltol MAB for BR11Goal: Saltol QTL line withBR11 backgroundCurrent status: 90 BC1F1 individuals currently being screened for salinity tolerance Tolerant plants will be rescued and backcrossed to BR11 to BC2F1 BC2F1 plants will be genotyped with markers for foreground and background selection
  • 19. Progress in MAB in Bangladesh BR11 X FL378 Out of 248 F 1 185 were confirmed by using a primer Methionine Synthatase F1 (185) X BR11Parents: BC1F1 (251) FOREGROUND SELECTIONRecurrent: (RM3412 & RM493) BR11 (T.Aman/WS) Selected BC 1F1 (135) BRRI dhan28 (Boro/DS) RECOMBINANT SELECTION ( RM490 & RM7075)Donor Selected BC 1F1 (39) FL378 (NIL from BACKGROUND SELECTION ( 60 SSR DISTRIBUTED WHOLE GENOME) IR29 x Pokkali) BC1F1 (2/3) X BR11 Backcrosses: BRRI Again do the similar selection scheme with more primers. DNA isolation, marker BC2F1 analysis: DU If recovery of RPG is > 90% then selfing of selected plants, otherwise, another backcross (BC3)
  • 20. Transfer plansTraining of NARES in MAS and other relevanttechnologies Training workshop in MAB (2005) On-job training Degree trainingParticipatory varietal selection (PVS) networks INGER Salinity network Farmers field daysOut-scaling and up-scaling Large-scale seed production and dissemination Support and involvement of policy makers and development organizations
  • 21. Constraints to plans of product transferMAB is efficient but expensiveCapacity of National programs in MAB Additional degree training In-country workshops Infrastructure (equipments, storage etc) Supplies: availability and funds
  • 22. Constraints ….Product delivery Production of sufficient certified seeds for PVS trials Out-scaling on a large scale require varieties to be released first National policies for release of MAB products still the same as that for varieties developed conventionally
  • 23. Research TeamIRRI NARES ARIsAbdelbagi Ismail Indonesia JIRCASMike Thomson M. Bustamam M. WissuwaSigrid Heuer M. Sugiono UCDDave Mackill Joko Prasetiyono Ed BlumwaldGlenn Gregorio Bangladesh Ellen TumimbangRK Singh Zeba SerajX. Lu MA SalamHei Leung Collaborators Korea USDA Jukon Kim Clyde Wilson Linghe Zeng UCR Tim Close ABRII, Iran Harkamal Walia G. Hosseini Xinping Cui NIAS M. Yano

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