Skip to main content
ARS Home » Research » Publications at this Location » Publication #171548
Title: SNP DISCOVERY AND COMPARATIVE SEQUENCE ANALYSIS IN LEGUME SPECIES USING PRIMERS DERIVED FROM SOYBEAN UNIGENES

Author
item CHOI, IK-YOUNG - REPUBLIC OF KOREA
item Hyten, David
item MATUKUMALLI, L - GEORGE MASON UNIVERSITY
item YOON, M - REPUBLIC OF KOREA
item Cregan, Perry

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 2/28/2005
Publication Date: 2/28/2005
Citation: Choi, I., Hyten, D.L., Matukumalli, L.K., Yoon, M.S., Cregan, P.B. 2005. Snp discovery and comparative sequence analysis in legume species using primers derived from soybean unigenes. Meeting Abstract. Plant & Animal Genome XIII Abstract. P426.

Interpretive Summary:

Technical Abstract: Unigenes derived from soybean EST data were used as a source of sequence to discover SNPs in soybean as well as several other legume species. PCR primers to 1518 soybean unigenes successfully amplified a product from which readable DNA sequence data were obtained in soybean. 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 in order to assist in the development of a legume-wide universal set of PCR-based markers. The soybean-derived STSs were used to amplify two genotypes (mapping parents) of each species to determine the transferability to the other species and to discover mappable SNPs. Sequencable products were obtained for 15.6, 14.0, 6.2, 5.6, 2.7, 2.7 and 2.1% of the 1204 primer sets from amplification of genomic DNA of P. vulgaris, V. unigiculata, C. arietinum, M. truncatula, P. sativum A. hypogea and L. japonicus , respectively. Sequence comparison of the two genotypes from each species indicated that nucleotide diversity (theta) was the lowest in soybean (0.001), cowpea (0.00095) and Lotus (0.0001). The nucleotide diversity of common bean and pea were the highest, 0.0048 and 0.0042, respectively. The across-species SNP markers discovered here can serve as useful genetic markers as well as a tool for the study of comparative legume genomics.