Prepared in 2007.

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. BACKGROUN
D
OBJECTIVE
S
SUMMARY

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. 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. 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. 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. 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. PEANUT IMPROVEMENT CONSTRAINTS
LACK OF SOURCES OF RESISTANCE TO SEVERAL ABIOTIC/BIOTIC
STRESSES IN CULTIVATED PEANUT
Source: peanut.tamu.edu/peanut_photos.htm

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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. OBJECTIVES
IDENTIFY NBS-LRR ALLELES INTROGRESSED FROM WILD DIPLOID INTO
CULTIVATED TETRAPLOID LINES
THIRD OBJECTIVE
GOAL
IDENTIFY AND CHARACTERIZE SEVERAL NBS-LRR GENES

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. 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. 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. END OF THE PRESENTATION
THANK YOU