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Differentiation of the Historic Alfalfa Germplasm Sources
Using MicrosatillitesC. He, Z.L. Xia, T.A. Campbell, and G. Bauchan,
Soybean Genomics and Improvement Lab
USDA-ARS, Plant Sciences Institute
Beltsville, MD 20705
Objectives
To develop SSR from alfalfa genomic
library
To determine the genetic relationships
among
ten historically recognized alfalfa
germplasm
sources
Materials and Methods
Genomic library
DNA from pest resistant germplasm
“W10”
Size-selected fragments: 400-900 bp
Vector: pUC19
Transformation and colony lift
Colony hybridization and signal
development
DNA sequencing
Primer design and germplasm screening
(1) Primary screening
(2) Secondary screening
(3) Tertiary screening
single colony/well
1-3 colonies/well
Screening process based on DNA hybridization
PCR amplification of the DNA
inserts
(Colonies showing positive
signals)
480 bp
(CT)15 (AT)20
DNA sequencing
Dinucleotide (CT)Positive signals: 94
Unuseful DNA sequences(no SSR, terminal SSR, unreadable): 41Useful DNA sequences: 53
Redundant DNA sequences: 11Unique DNA sequence: 42
PCR primers designed: 42Workable primer pairs: 39 (93%)
Polymorphic SSR loci: 29 (69%)
Trinucleotide (CAT, GAT)
Positive signals: 24Unuseful DNA sequences(no SSR, terminal SSR, unreadable): 11Useful DNA sequences: 13
Redundant DNA sequences: 1Unique DNA sequence: 12
PCR primers designed: 12Workable primer pairs: 12 (100%)
Polymorphic SSR loci: 7 (58%)
The profile of SSR development from an alfalfa genomic library
Number Germplasm Source Cultivar Name Accession
1 African African NSL 4142 2 African Moapa NSL 4123 3 Chilean Arizona Common
NSL 4144 4 Falcata WISFAL PI 560333 5 Falcata Wild tetraploid ssp.falcata PI 214218 6 Flemish DuPuit PI 206103 7 Indian Sirsa Type 9 PI 235736 8 Ladak Ladak NSL 4164 9 Peruvian Hairy Pervian NSL 4143 10 Turkistan Kaysari PI 17172111 Arabian Very Nondormant
UC-1887 12 Arabian Very Nondormant UC-146513 Varia Grimm NSL 4162 14 M. sativa ssp. caerulea Wild diploid alfalfaPI577548 15 M. sativa ssp. falcata Wild diploid ssp. falcata
PI258754 16 M. truncatula JemalongPI442895
Germplasm of M. sativa and M. truncatula used for screening
SSR primers
MFV
T
IL
F
A
C
CP
R
MF = FalcataL = LadakV = VariaF = FlemishT = TurkistanC = ChileanP = PeruvianI = IndianA = AfricanR = Arabian
Distribution of historical alfalfa germplasm
Banding patterns generated bythree SSR primer pairs
2 alleles
2 alleles
Multiple alleles
No. alleles No. SSR loci%
1 15 29.4 2 9 17.6 3 5 9.8 4 10 19.6 5 3 5.9 6 6 11.8 7 2 3.9 10 1 2.0
Allelic variation for the 51 SSR loci with CT, CAT and GAT
repeats
Polymorphic primers
Including M. truncatula: 70.6%
Within M. sativa: 58.8%
Truncatula (PI 442895)
2X Falcata (PI 258754)
2x Alfalfa (PI 577548)
Falcata (PI 560333)
Falcata (PI 214218)
African (NSL 4123)
Arabian (UC-1465)
Arabian (UC-1887)
Turkistan (PI 171721)
Varia (NSL 4162)
African (NSL 4142)
Peruvian (NSL 4143)
Chilean (NSL 4144)
Ladak (NSL 4164)
Flemish (PI 206103)
Indian (PI 235736)
0.7 0.6 0.5 0.4 0.3 0.2 0.1Genetic distance
4x M. sativa
2x M. sativa
2x M. truncatula
Summary
In developing SSRs, 118 colonies with
positive signals were identified and
sequenced for the repeats of CT, CAT and
GAT, 54 primer pairs were obtained;
About 70% of the 51 SSRs were
polymorphic among the germplasm and
produced 154 different alleles;
Summary (continue)
The number of alleles generated from the
36
polymorphic SSR primer pairs ranged from
1-10;
The dendrogram largely represents the
true
relationship among the 24 germplasm.
Acknowledgements
Soybean Genomics & Improvement Lab.,
Beltsville, MD Dr. Perry Cregan
Dr. Qijian Song
Edward Fickus
Kristina Pilitt