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The FAD2 Gene Family of Soybean:

Insights into the Structural and Functional Divergence of a Paleopolyploid Genome

J.A. Schlueter and R.C. Shoemaker, USDA-ARS-CICGR, Ames, IA 50011; I.F. Vasylenko-Sanders, S. Deshpande, J. Yi, M. Seigfried, and B. Roe, Dep. of Chemistry and Biochemistry, Univ. of Oklahoma, Norman, OK 73019; S.D. Schlueter, Dep. of Genetics Development and Cellular Biology, Iowa State Univ., Ames, IA 50011; B. Scheffler, USDA-ARS MSA Genomics Lab., Stoneville, MS 38776. Names are necessary to report factually on the available data; however, the USDA neither guarantees nor warrants the standard of the product, and the use of the name by the USDA implies no approval of the product to the exclusion of others that may also be suitable

View larger version (31K): [in this window] [in a new window]   Figure 1. Graphical representation of Linkage Groups I and O based on the soybean composite map at www.soybase.org (verified 13 Dec. 2006). The BACs gmw1-15k6 (FAD2-1A) and gmw1-105h23 (FAD2-1B) mapped to these linkage groups in the Glycine max A81-356022 x Glycine soja PI 468.916 mapping populations. Their locations relative to other markers are shown. Lines between markers show syntenic markers.

View larger version (32K): [in this window] [in a new window]   Figure 2. Predicted gene structures and retrotransposon insertions on soybean BACs gmw1-11j16, gmw1-15k6, gmw1-105h23, and gmw1-45m6. Each colored block arrow on the line represents a gene. Gray connecting boxes between genes show homeologs or syntenic relationships. Black arrowheads represent full-length predicted retrotransposon elements. Gray arrowheads represent fragmented remnants of retrotransposons.

View larger version (50K): [in this window] [in a new window]   Figure 3. VISTA based identity plots between gmw1-15k6 and gmw1-105h23. The plots above and below the representative BAC structures show the relative nucleotide identity between the two BACs. The light purple boxes on top of the VISTA plots correspond to exon positions.

View larger version (50K): [in this window] [in a new window]   Figure 4. RT-PCR amplification for FAD2-1A_L, FAD2-1A_S, FAD2-1B_L, FAD2-1B_S, FAD2-2B, and FAD2-2C. Positive control reactions used tubulin56. Plus symbols indicate amplification of that transcript in a particular tissue, and minus symbols indicate no amplification. Tissue types are as follows: 6–10, developing pods 6–10 d after flowering (DAF); 13, developing pods 13 DAF; 17, developing pods 17 DAF; 19, developing pods 19 DAF; 21, developing pods 21 DAF; 26, developing pods 26 DAF; C3, cotyledons 3 days after emergence (DAE); R3, roots 3 DAE; FU, furled unifoliate 3 DAE; UU, unfurled unifoliate 4 DAE; C7, cotyledons 7 DAE; R8, roots 8 DAE; FT, furled trifoliolate 11 DAE; UT, unfurled trifoliolate 15 DAE; P, pods 76 DAE. All samples with a w were grown under the warm conditions and c for cool conditions. All samples with a -RT are controls with no reverse transcriptase for mRNA amplification, but still contain Taq DNA polymerase. The final sample in each set of reactions is a Williams 82 DNA based positive control.