nbs-lrr proposal
TRANSCRIPT
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SAMEER KHANALDEPARTMENT OF CROP AND SOIL SCIENCES
THE UNIVERSITY OF GEORGIA
DEVELOPMENT OF AN A-GENOME DIPLOID MODEL FOR COMPARATIVE GENOMICS IN
PEANUT AND OTHER LEGUMES
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BACKGROUND
OBJECTIVES SUMMARY
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IMPORTANCE OF PEANUT
Among food legumes, second in national and global economic importance
United States World
Crop AreaHarvested
(ha)
Production(Mg)
AreaHarvested
(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
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PEANUT PRODUCTION CONSTRAINTS
Abiotic Constraints
Drought
High Temperaturewww.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
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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
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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
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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
ALLOTETRAPLOID
PEANUT :
LOW GENETIC VARIABILITY
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PEANUT IMPROVEMENT CONSTRAINTS
LACK OF SOURCES OF RESISTANCE TO SEVERAL ABIOTIC/BIOTIC STRESSES IN CULTIVATED PEANUT
Source: peanut.tamu.edu/peanut_photos.htm
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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
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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:
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OBJECTIVES
INCREASING THE FREQUENCY OF HIGH-THROUGHPUT DNA MARKERS IN THE A-GENOME
FIRST OBJECTIVE
GOALA MICROSATELLITE-ENRICHED LINKAGE MAP FOR A-GENOME
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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
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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
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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
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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
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OBJECTIVES
GENETIC MAPPING OF NUCLEOTIDE BINDING SITE – LEUCINE RICH REPEATS (NBS-LRR) REGISTANCE GENE CANDIDATE (RGC) LOCI
SECOND OBJECTIVE
GOALMAPPING OF 100-150 NBS-LRR RGCs
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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 LRR
TIR/CCN C
RESISTANCE GENES IN PLANTS
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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
DU
R25
DU
R35
BA
T6
BA
T8
HY
P-G
TC-9
HY
P-A
100
HY
P-A
EQ
-2
HY
P-P
RV
-1H
YP
-TifrunnerH
YP
-HIR
-3H
YP
-GTC
-20H
YP
-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
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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
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OBJECTIVES
IDENTIFY NBS-LRR ALLELES INTROGRESSED FROM WILD DIPLOID INTO CULTIVATED TETRAPLOID LINES
THIRD OBJECTIVE
GOALIDENTIFY AND CHARACTERIZE SEVERAL NBS-LRR GENES
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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
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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
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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
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END OF THE PRESENTATION
THANK YOU