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NBS-LRR proposal

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Prepared in 2007.

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NBS-LRR proposal

  1. 1. SAMEER KHANAL DEPARTMENT OF CROP AND SOIL SCIENCES THE UNIVERSITY OF GEORGIA DEVELOPMENT OF AN A-GENOME DIPLOID MODEL FOR COMPARATIVE GENOMICS IN PEANUT AND OTHER LEGUMES
  2. 2. BACKGROUN D OBJECTIVE S SUMMARY
  3. 3. IMPORTANCE OF PEANUT Among food legumes, second in national and global economic importance United States World Crop Area Harvested (ha) Production (Mg) Area Harvested (ha) Production (Mg) Soybean 28,842,260 82,820,048 91,386,621 209,531,558 Peanut 650,340 2,112,700 25,217,201 36,492,147 Source: compiled from faostat.fao.org
  4. 4. PEANUT PRODUCTION CONSTRAINTS Abiotic Constraints Drought High Temperature www.gapeanuts.com/news/2006/092906.asp southeastfarmpress.com/news/091106-peanut-markets/ www.washingtonpost.com/wp- dyn/content/article/2006/07/29/AR2006072900414_pf.html
  5. 5. Abiotic Constraints Drought High Temperature Biotic Constraints Diseases Insect-Pests PEANUT PRODUCTION CONSTRAINTS Source: Diseases compiled from plantpathology.tamu.edu/Texlab/Fiber/Peanuts/atlas-toc.html edis.ifas.ufl.edu/IN176
  6. 6. Third most important source of vegetable protein Among food legumes, second in national and global economic importance IMPORTANCE OF PEANUT Fourth most important source of vegetable oil Twelfth most important food crop in the world Source: ICRISAT (www.icrisat.org) and the UN-FAO
  7. 7. PEANUT IMPROVEMENT CONSTRAINTS • POLYPLOIDY (YOUNG ET AL., 1996) • AUTOGAMY (HALWARD ET AL., 1991) • NARROW GENETIC BASE (KNAUFT & GORBET, 1989) AA BBX AB AABB PARENTS: INTERSPECIFIC HYBRIDIZATION F1 HYBRID: SPONTANEOUS CHROMOSOME DOUBLING ALLOTETRAPLOI D PEANUT : LOW GENETIC VARIABILITY
  8. 8. PEANUT IMPROVEMENT CONSTRAINTS LACK OF SOURCES OF RESISTANCE TO SEVERAL ABIOTIC/BIOTIC STRESSES IN CULTIVATED PEANUT Source: peanut.tamu.edu/peanut_photos.htm
  9. 9. PEANUT IMPROVEMENT CONSTRAINTS DIFFICULT TO INTROGRESS RESISTANCE GENES FROM DIPLOID WILD SPECIES WARRANTS COMPLEX CROSSES OR GENETIC TRANSFORMATION LAGGING IN GENOMIC RESOURCES AND APPLICATION OF MOLECULAR BREEDING SOLUTIONS TO THE PERTINENT PROBLEMS Source: peanut.tamu.edu/peanut_photos.htm
  10. 10. REALIZATIONS - A CONSENSUS MAP FOR ARACHIS - MAPPING PHENOTYPIC AND QUANTITATIVE TRAIT LOCI (QTLs) - MARKERS LINKED TO THE GENES OF INTEREST FOR MARKER ASSISTED SELECTION (MAS) CROP IMPROVEMENT THROUGH MOLECULAR BREEDING TECHNIQUES REQUIRE:
  11. 11. OBJECTIVES INCREASING THE FREQUENCY OF HIGH-THROUGHPUT DNA MARKERS IN THE A-GENOME FIRST OBJECTIVE GOAL A MICROSATELLITE-ENRICHED LINKAGE MAP FOR A-GENOME
  12. 12. MICROSATELLITE-BASED LINKAGE MAP FOR THE AA-GENOME - DIPLOID RFLP MAP PRODUCED FROM AN INTERSPECIFIC (A. duranensis x A. stenosperma) HYBRID (HALWARD ET AL., 1993) - TETRAPLOID RFLP MAP PRODUCED FROM HYBRID BETWEEN A. hypogaea AND A ‘SYNTHETIC’ AMPHIDIPLOID [A. batizocoi x A. diogoi)] (BUROW ET AL., 2002) - RECENTLY FIRST MICROSATELLITE-BASED MAP IS PUBLISHED IN Arachis (MORETZSOHN ET AL., 2005). LINKAGE MAPPING IN DIFFERENT PEANUT SPECIES
  13. 13. MICROSATELLITE-BASED LINKAGE MAP FOR THE AA-GENOME MICROSATELLITES OR SIMPLE SEQUENCE REPEATS (SSRs) ARE MULTIPLE REPEATING UNITS OF 1 TO 4 BASE PAIRS EXAMPLE: (A)5, (AT)7, (CGG)9, (ACGG)6 - SCREENING SEQUENCES FROM GENOMIC LIBRARY - SCREENING SSR ENRICHED LIBRARY - SCREENING EST SEQUENCES - SCREENING OF SSRs AGAINST DIFFERENT GENOTYPES SSR DEFINITION SSR DEVELOPMENT POLYMORPHISM DETECTION
  14. 14. MICROSATELLITE-BASED LINKAGE MAP FOR THE AA-GENOME - 720 MARKERS SCREENED AMONG 18 ELITE AND 14 EXOTIC GERMPLAM ACCESSIONS - 556 SSR MARKERS FOUND POLYMORPHIC - 336 (60.4%) WERE POLYMORPHIC IN (A. Kuhlmanii x A. diogoi) - 82 OUT OF 336 HAVE ALREADY BEEN MAPPED (MORETZSOHN ET AL., 2005) Source: Ma (Communication) SCREENING AVAILABLE SSR MARKERS FOR POLYMORPHISMS
  15. 15. MICROSATELLITE-BASED LINKAGE MAP FOR THE AA-GENOME - MAPPING POPULATION OF A. kuhlmanii X A. diogoi - GENOTYPING 82 PREVIOUSLY MAPPED AND 254 PREVIOUSLY UNMAPPED SSR MARKER LOCI - THREE FOLD INCREASE IN THE DENSITY OF DNA MARKER LOCI IN THE A-GENOME RESEARCH OVERVIEW FOR THE FIRST OBJECTIVE
  16. 16. OBJECTIVES GENETIC MAPPING OF NUCLEOTIDE BINDING SITE – LEUCINE RICH REPEATS (NBS-LRR) REGISTANCE GENE CANDIDATE (RGC) LOCI SECOND OBJECTIVE GOAL MAPPING OF 100-150 NBS-LRR RGCs
  17. 17. GENETIC MAPPING OF NBS-LRR RGC LOCI - GROUPED INTO SEVERAL FAMILIES - MOST R-GENE PROTEINS CHARACTERIZED BY NUCLEOTIDE BINDING SITE LEUCINE RICH REPEATS - 150 NBS-LRR-ENCODING GENES IN Arabidopsis thaliana AND >400 IN Oryza sativa Source: McHale et al. 2006 NBS LR R TIR/CCN C RESISTANCE GENES IN PLANTS
  18. 18. GENETIC MAPPING OF NBS-LRR RGC LOCI INDEL AND SSCP MARKERS BEING DEVELOPED NBS-LRR TEMPLETES: BERTIOLI ET AL. (2004), YUSKEL ET AL. (2005), COOK ET AL. (UNPUBLISHED DATA) SCREENING: 58 NBS-LRR TEMPLETES SCREENED SO FAR EIGHT CULTIVATED PEANUT (AABB) : HIGHLY MONOMORPHIC FOUR DIPLOID GENOTYPES: HIGHLY POLYMORPHIC RGC7 RGC4 RGC8 DUR25 DUR35 BAT6 BAT8 HYP-GTC-9 HYP-A100 HYP-AEQ-2 HYP-PRV-1 HYP-Tifrunner HYP-HIR-3 HYP-GTC-20 HYP-FST-3 DUR BAT - AFLP-BASED MAPPING OF RESISTANCE TO APHID VECTOR (HERSELMAN ET AL., 2004) - THREE SMALL MAP SETS WITH MARKERS FOR ROOT KNOT NEMATOD RESISTANCE (JESUBATHAM AND BUROW, 2006) RESISTANT GENE MAPPING IN PEANUT MARKERS USED FOR MAPPING NBS-LRR RGC LOCI
  19. 19. GENETIC MAPPING OF NBS-LRR RGC LOCI - MAPPING NBS-LRR RGC LOCI IN MAPPING POPULATION OF A. kuhlmanii x A. diogoi F2 PROGENY - SCREEN AND MAP AVAILABLE INDEL AND SSCP MARKERS FOR 50 NBS-LRR GENES - DEVELOP, SCREEN AND MAP ADDITIONAL MARKERS FOR 50-150 ADDITIONAL NBS-LRR GENES RESEARCH OVERVIEW FOR THE SECOND OBJECTIVE
  20. 20. OBJECTIVES IDENTIFY NBS-LRR ALLELES INTROGRESSED FROM WILD DIPLOID INTO CULTIVATED TETRAPLOID LINES THIRD OBJECTIVE GOAL IDENTIFY AND CHARACTERIZE SEVERAL NBS-LRR GENES
  21. 21. Line P.I. Number Background Reference   PI 262141 A. cardenasii Donor   PI 261942 A. hypogaea Parent   PI 261943 A. hypogaea Parent GP-NC WS 1 PI 564844  Wild Introgression Line (WIL) Stalker and Beute (1993) GP-NC WS 2 PI 564845  WIL Stalker and Beute (1993) GP-NC WS 3 PI 564846  WIL Stalker and Beute (1993) GP-NC WS 4 PI 564847  WIL Stalker and Beute (1993) TXAG-6 PI 565287  WIL Simpson et al. (1993) TXAG-7 PI 565288  WIL Simpson et al. (1993) ICGV 86699 PI 591815 (A. batizocoi/A. duranensis)//NC 2 Reddy et al. (1996) ICGV 87165 PI 594923 WIL Moss et al. (1997) ICGV SM 86715 PI 598133  WIL Moss et al. (1998) COAN PI 610452  WIL Simpson and Starr (2001) GP-NC WS 5 PI 619169 WIL Stalker et al. (2002a) GP-NC WS 6 PI 619170 WIL Stalker et al. (2002a) GP-NC WS 7 PI 619171 WIL Stalker and Lynch (2002) GP-NC WS 8 PI 619172 WIL Stalker and Lynch (2002) GP-NC WS 9 PI 619173 WIL Stalker and Lynch (2002) GP-NC WS 10 PI 619174  WIL Stalker and Lynch (2002) GP-NC WS 11 PI 619175 (NC 6//NC Ac 3033)/GP-NC WS 1 Stalker et al. (2002b) GP-NC WS 12 PI 619176 (NC 6//NC Ac 3033)/GP-NC WS 1 Stalker et al. (2002b) GP-NC WS 13 PI 619177 (NC 5//PI 270806)/GP-NC WS 4 Stalker et al. (2002b) GP-NC WS 14 PI 619178 WIL Stalker et al. (2002b) GP-NC WS 15 PI 619179 WIL Stalker et al. (2002b) NR 0817 PI 639266 AT-108/GP-NC WS 5 Anderson et a. (2006) NR 0812 PI 639267 AT-108/GP-NC WS 5 Anderson et a. (2006) N96076L PI 641950 N90004/GP-NC WS 13 Isleib et al. (2006) IDENTIFICATION AND CHARACTERIZATION OF NBS-LRR GENES
  22. 22. IDENTIFICATION AND CHARACTERIZATION OF NBS-LRR GENES -SCREENING AVAILABLE LINES FOR R-GENE INTROGRESSION -IDENTIFYING INTROGRESSED NBS-LRR ALLELES - CHARACTERIZING NOVEL NBS-LRR ALLELES RESEARCH OVERVIEW FOR THE THIRD OBJECTIVE
  23. 23. SUMMARY • WILD RELATIVES OF CULTIVATED PEANUT ARE THE SOURCES OF NOVEL RESISTANCE GENES • MOLECULAR BREEDING TOOLS FACILITATE TO TRANSFER USEFUL GENES FROM WILD DIPLOID TO CULTIVATED PEANUT SPECIES • SSR-ENRICHED LINKAGE MAP WILL BE DEVELOPED FOR AA- GENOME DIPLOID MODEL • MORE THAN 100 NBS-LRR RGC LOCI WILL BE MAPPED WITH SSCP AND INDEL MARKERS • WILD INTROGRESSION LINES WILL BE SCREENED TO IDENTIFY NBS-LRR ALLELE
  24. 24. END OF THE PRESENTATION THANK YOU

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