SoyMapII

About the project

The resources presented here are part of the NSF project SoyMap II: Leveraging untapped genetic diversity in soybean, 0822258-DFBI. This project is determining important parts of the genome sequences of seven wild relatives of soybean, in order to better understand how these wild relatives have been are able to adapt to the harsh conditions where they grow - and to understand how this group of species has evolved over the several million years since they separated from their common ancestor.

These page gives access to the survey sequencing from the project, and to the twelve focus regions in the project, which are being sequenced and studied in detail. The NSF project SoyMap II also give the opportunity for undergraduate students to conduct research in plant genomics, molecular biology, bioinformatics and computer science during the SoyMap Summer Research Program 2015 (archived web page available at the Internet Archive).

Seven wild perennial Glycine species were included in the SoyMap II project because of interesting traits. G. tomentella was included because it has successfully crossed with G. max (Newell et al., 1987). G. canescens was included due to reported resistance to various pathogens (Hartman et al., 2000). G. stenophita and G. syndetika were chosen because they have each contributed genomes to recent perennial polyploids (Doyle et al., 2004). This project is evaluating genomic diversity by sequencing twelve ~half-megabase genomic regions selected to include many traits with potential utility for soybean improvement.

Click here to view more information about the seven wild perennial Glycine species.

Project Objectives

Previous research has shown that the genetic base within the soybean germplasm is exceedingly narrow (Hyten, D.L. et al 2006). A key goal of the SoyMap2 project is to develop tools and resource that can assist in improving the genetic diversity of soybeans.

The following specific objectives will help us reach our key goal:

Generate diversity maps using genomic clones from a set of wild perennial Glycine species.
Explore genome evolution within the genus Glycine at both the chromosomal and sequence
level to gather a better understanding of the polyploidy and diploidization.
Sequence target regions and homologs across the set of wild perennial Glycine species
in order to gain a better understand of linkage disequilibrium and genetic diversity.

Data for this project

NCBI BioProject for SoyMapII (with links to Illumina HiSeq data in SRA)

BAC-end sequencing data in NCBI SRA

Species	SRA Study Accession
Glycine canescens	SRP202503
Glycine cyrtoloba	SRP202504
Glycine dolichocarpa	SRP202505
Glycine falcata	SRP202506
Glycine soja	SRP202507
Glycine stenophita	SRP202508
Glycine syndetika	SRP202509
Glycine tomentella	SRP202510

Regions of Interest - assembly v2.0

Region-Pair Nickname	Region Interest	chrA	start	end	chrB	start	end
SCN1 & SCN2	nematode resistance	Gm18	1,666,460	2,000,762	Gm11	32,603,866	32,940,400
seed protein	seed composition	Gm20	33,343,658	33,641,332	Gm10	37,621,924	37,921,195
LG E & A2	structural traits	Gm15	50,347,696	50,653,388	Gm08	12,128,367	12,550,870
Dt1 & Dt2	morphological	Gm19	45,033,356	50,013,023	Gm03	40,372,379	40,668,152
Rpp1 & Rpp2	ASR resistance	Gm18	51,379,854	51,682,831	Gm09	48,099,948	48,398,414
isoflavone synthase	seed composition	Gm07	37,011,571	37,320,614	Gm13	28,594,532	28,895,103

Regions of Interest - assembly v1.0