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United States Department of Agriculture

Agricultural Research Service

Research Project: IMPROVEMENT OF PEST RESISTANCE AND QUALITY TRAITS OF SOYBEAN Title: Development of soybean aphid genomic SSR markers using next generation sequencing

Authors
item Jun, Tae-Hwan -
item Michel, Andrew -
item Mian, Rouf

Submitted to: Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 15, 2010
Publication Date: May 1, 2011
Repository URL: http://hdl.handle.net/10113/50065
Citation: Jun, T., Michel, A.P., Mian, R.M. 2011. Development of soybean aphid genomic SSR markers using next generation sequencing. Genome. 54:360-367.

Interpretive Summary: DNA markers such as simple sequence repeats (SSRs) or microsatellites are very useful molecular markers for studying agriculturally important pests. The soybean aphid (Aphis glycines Matsumura) has become the most damaging insect pest of soybean [Glycine max (L.) Merr.] in North America since it was first found in the Midwest of USA in 2000. Biotypes (race) of the soybean aphid capable of colonizing newly developed aphid resistant soybean cultivars were discovered recently. Genetic resources, including molecular markers, to study soybean aphids are currently severely lacking. The objectives of this study were (1) to develop and characterize genomic SSR markers from soybean aphid genomic sequences generated by next generation sequencing technology and (2) to evaluate the utility of the SSRs for genetic diversity or relationship analyses. One hundred twenty eight SSR primer pairs were designed from sequences generated by Illumina GAII from a reduced representation library of A. glycines. Nearly 94% (120) of the markers amplified SSR alleles of expected size and 24 SSR loci were polymorphic among three aphid samples from three populations. The polymorphic SSRs were successfully used to differentiate among 24 soybean aphids from Ohio and South Dakota. These markers should be particularly useful for genetic differentiation among aphids collected from soybean fields at different localities and regions. These SSR markers provide the soybean aphid research community with the first set of PCR based co-dominant markers developed from the genomic sequences of A. glycines. Due to the quick adaptation and evolution of soybean aphids into new biotypes, these SSR markers will serve as very important molecular resource in combating the soybean aphids in North America.

Technical Abstract: Simple sequence repeats (SSRs) or microsatellites are very useful molecular markers due to locus-specific co-dominant and multi-allelic nature, high abundance in the genome, and high rates of transferability across species. The soybean aphid (Aphis glycines Matsumura) has become the most damaging insect pest of soybean [Glycine max (L.) Merr.] in North America since it was first found in the Midwest of USA in 2000. Biotypes of the soybean aphid capable of colonizing newly developed aphid resistant soybean cultivars were discovered recently. Genetic resources, including molecular markers, to study soybean aphids are severely lacking. Recently developed next generation sequencing platforms offer opportunities for high-throughput and inexpensive genome sequencing and rapid marker development. The objectives of this study were (1) to develop and characterize genomic SSR markers from soybean aphid genomic sequences generated by next generation sequencing technology and (2) to evaluate the utility of the SSRs for genetic diversity or relationship analyses. One hundred twenty eight SSR primer pairs were designed from sequences generated by Illumina GAII from a reduced representation library of A. glycines. Nearly 94% (120) of the primer pairs amplified SSR alleles of expected size and 24 SSR loci were polymorphic among three aphid samples from three populations. The polymorphic SSRs were successfully used to differentiate among 24 soybean aphids from Ohio and South Dakota. Sequencing of PCR products of two SSR markers from 4 aphid samples revealed that the allelic polymorphism was due to variation in the SSR repeats among the aphids. These markers should be particularly useful for genetic differentiation among aphids collected from soybean fields at different localities and regions. These SSR markers provide the soybean aphid research community with the first set of PCR based co-dominant markers developed from the genomic sequences of A. glycines.

Last Modified: 11/28/2014
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