Skip to main content
ARS Home » Research » Publications at this Location » Publication #163497
Title: SNP DISCOVERY IN LEGUME SPECIES USING PRIMERS DERIVED FROM SOYBEAN UNIGENES

Author
item CHOI, IK-YOUNG - KOREA
item Hyten, David
item MATUKUMALLI, L - GEORGE MASON UNIVERSITY
item YI, SEUNG YI - KOREA
item Cregan, Perry

Submitted to: BARC Poster Day
Publication Type: Abstract Only
Publication Acceptance Date: 3/20/2003
Publication Date: 3/20/2003
Citation: Choi, I., Hyten, D.L., Matukumalli, L.K., Yi, S., Cregan, P.B. 2003. Snp discovery in legume species using primers derived from soybean unigenes [abstract]. BARC Poster Day. Abstract 09.

Interpretive Summary:

Technical Abstract: Soybean unigene data were used as the source of sequence to discover SNPs (single nucleotide polymorphisms) in soybean as well as in several other Legume species. PCR primers to 1518 soybean unigenes successfully amplified a product from which readable DNA sequence traces were obtained in soybean. 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% 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) while nucleotide diversity of common bean and pea were the highest, (theta) = 0.0048 and 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 here can serve as genetic markers for genetic mapping in each Legume species as well as for initial comparative mapping across species.