Application Datasets
Polymorphism analysis was performed at Soybean Genomics
and Improvement Laboratory at the USDA, ARS, Beltsville to analyze
more than 3000 STS. Zhu et al. 2003 have analyzed >76
kbp of soybean sequence and identified 281 polymorphisms. DNA sequences
amplified from genomic DNA using PCR primers designed to complete
genes, cDNAs and random genomic sequence. 28.7 kbp of coding sequence,
37.9 kbp of noncoding perigenic DNA and 9.7kbp of random genomic
sequence to identify polymorphisms and thereby estimate sequence
variation in different regions of the genome. They calculated the
nucleotide diversity expressed as Watterson’s q as 0.00097
with 0.00053 in coding and 0.00111 in non coding perigenic regions.
From the haplotype analysis it was observed that 6 genotypes represented
75% of all sequence variations in 25 genotypes and 90% of commonly
identified polymorphisms.
Choi et al.,(Choi et al. 2003) identified approximately 5000 polymorphisms
by the random 3’ sequence amplification method. PCR primer
success rate was 57%. 44% of the succesfully amplified sequences
had at least one intron. Nucleotide diversity (θ) in introns
is 1.456 ×10-3, in exons 0.834 ×10-3 57% of the polymorphisms
found are in exon regions. These polymorphisms will be very useful
in mapping and characterizing the genes for important agronomic
traits. Approximately 1000 polymorphisms were identified by targeted
sequence amplification method.
Choi et al (Choi et al. 2004) analyzed chromatogram data
from several legumes amplified from soybean primers using this software.
In order to assist in the development of a legume-wide universal
set of PCR-based markers, 1204 of these soybean-derived sequence
tagged sites ( STS) were used to attempt amplification in other
legume species including common bean (Phaseolus vulgaris), cowpea
(Vigna ungiculata) chickpea (Cicer arietinum) pea (Pisum sativum),
peanut (Arachis hypogea), barrel medic (Medicago truncatula) and
Lotus japonicus. Two commonly used mapping parents of each species
were used in SNP discovery. Sequenable products were obtained for
15.6, 14.0., 6.2, 5.6, 2.7, 2.7 and 2.1% respectively. Sequence
comparison of the two genotypes from each species indicated that
nucleotide diversity (θ) was the lowest in soybean (0.001),
cowpea (0.00095) and Lotus (0.0001) while nucleotide diversity of
common bean and pea were the highest, θ = 0.0048 and θ
= 0.0042, respectively. A total of 23 primer sets were discovered
as universal primers in five legume species; soybean, common bean,
cowpea, chickpea and barrel medic. The SNP markers discovered from
this study can serve as genetic markers for each legume species
mapping.
Publications / Poster Presentations
- Matukumalli L. K, 2004.
Development of bioinformatics applications for prediction and validation of polymorphisms in soybean (Glycine max) genome using EST data.
Doctoral Thesis submitted to George Mason University, Aug 2004.
- Choi, I.-Y., D.L. Hyten, L. K. Matukumalli, S.-I. Yi, and P.B.
Cregan, 2004.
SNP Discovery in Legume Species Using Primers Derived from Soybean
Unigenes
Beltsville Agriculture Research Center Poster Day, Beltsville, MD
- Ik-young Choi, DL Hyten, Matukumalli LK , P.B.Cregan, 2003.
Single Nucleotide Polymorphism discovery in 3’ EST sequence of soybean,
PAG XI The International Conference on the Status of Plant & Animal Genome Research, San Diego, CA
- Lakshmi K. Matukumalli ., John J. Grefenstette., Curtis P. Van Tassell., Ik-Young Choii and Perry B Cregan. 2004
In silico prediction and validation of polymorphisms in soybean genome using EST data.
Beltsville Agriculture Research Center Poster Day, Beltsville, MD.
- Zhu Y.L, Song Q.J, Hyten D.L, Van Tassell C.P, Matukumalli L.K,
Grimm D.R, Hyatt S.M,
Fickus E.W, Young N.D, Cregan P.B. 2003.
Single-nucleotide polymorphisms in soybean. Genetics 163:1123-1134.
- Matukumalli, LK., Grefenstette, JJ., Van Tassell, CP., Choi, I-Y.,
Cregan, PB.
Development of Algorithms for prediction and validation of polymorphisms
in polyploids (soybean) using EST data.
TIGR GSAC Conference 2004.
- Eun-Young Hwang, Kyujung Van, Moon Young Kim, Lakshmi Kumar, Suk-Ha
Lee, Gary Stacey, Perry B Cregan, 2004.
Single Nucleotide Polymorphisms Using Primers Designed To Methyl-Filtrated Clones In Soybean PAG XIII The International
Conference on the Status of Plant & Animal Genome Research,
San Diego, CA
- Ik-Young Choi , David L. Hyten , Lakshmi K. Matukumalli , Eun-Young
Hwang , Perry B. Cregan, 2004.
SNP Discovery In 3'-EST Sequence Of Soybean
PAG XIII The International Conference on the Status of Plant &
Animal Genome Research, San Diego, CA
- Lakshmi K Matukumalli, John J Grefenstette, Curtis P Van Tassell,
Ik-Young Choii, Perry B Cregan, 2004.
Application of Machine Learning programs towards Accelerating
Polymorphisms Discovery
7th Annual Conference on Computational Genomics
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