ARS | Publication request: SEQUENCE ANALYSIS OF BAC104J7 AND THE I LOCUS IN WILLIAMS 82

Submitted to: Plant Animal and Microbe Genomes Conference
Publication Type: Proceedings
Publication Acceptance Date: January 15, 2003
Publication Date: N/A

Technical Abstract: Plants produce a wide variety of complex secondary compounds such as lignin, anthocyanins, phytoalexins, and flavones that provide structural strength, color, and defense against aggressors. The synthesis of many of these compounds stem from the phenylpropanoid pathway. A key enzyme of this anabolic pathway is chalcone synthase (CHS), which catalyzes the conversion of p-coumaroyl-CoA to chalcone. In soybeans, CHS is present as a gene family consisting of at least seven members. We used a fragment of CHS4 to probe soybean BAC filters of Williams 82 genomic DNA. Several different BACs hybridized to the CHS probe and one clone, BAC104J7 was chosen to be sequenced. BAC104J7 was restriction digested with MunI, EcoRI, or HindIII and fragments were subcloned into the vector pGEM3Zf+. A diagnostic sequence was obtained by sequencing all subclones with universal primers off the vector. This sequence data was used to identify unique clones and to verify that soybean DNA was present. Unique clones were fully sequenced by primer walking and contigged using the software program Sequencher. Gaps were filled by either sequencing directly off the BAC, or by identification of new subclones using different restriction enzymes (either SstI, SstII, Sau3A, PstI, or AccI). Sequence data reveal that the I-locus, consisting of CHS4, CHS3, and CHS1, is present on BAC104J7 in duplication, which has complicated sequencing efforts. BAC104J7 is genes rich, containing at least 15 putative coding sequences, for which soybean ESTs have been found for more that half. Annotation of the entire BAC will be presented.