Academic journal article Genetics

Sequence Conservation of Homeologous Bacterial Artificial Chromosomes and Transcription of Homeologous Genes in Soybean (Glycine Max L. Merr.)

Academic journal article Genetics

Sequence Conservation of Homeologous Bacterial Artificial Chromosomes and Transcription of Homeologous Genes in Soybean (Glycine Max L. Merr.)

Article excerpt

ABSTRACT

The paleopolyploid soybean genome was investigated by sequencing homeologous BAC clones anchored by duplicate N-hydroxycinnamoyl/benzoyltransferase (HCBT) genes. The homeologous BACs were genetically mapped to linkage groups C1 and C2. Annotation of the 173,747- and 98,760-bp BACs showed that gene conservation in both order and orientation is high between homeologous regions with only a single gene insertion/deletion and local tandem duplications differing between the regions. The nucleotide sequence conservation extends into intergenic regions as well, probably due to conserved regulatory sequences. Most of the homeologs appear to have a role in either transcription/DNA binding or cellular signaling, suggesting a potential preference for retention of duplicate genes with these functions. Reverse transcriptase-PCR analysis of homeologs showed that in the tissues sampled, most homeologs have not diverged greatly in their transcription profiles. However, four cases of changes in transcription were identified, primarily in the HCBT gene cluster. Because a mapped locus corresponds to a soybean cyst nematode (SCN) QTL, the potential role of HCBT genes in response to SCN is discussed. These results are the first sequenced-based analysis of homeologous BACs in soybean, a diploidized paleopolyploid.

GENE duplication, arising from region-specific duplication or genomewide polyploidization, is a prominent feature of genome evolution. Gene and genome duplication have been shown to provide morphological and fitness advantages, create genetic redundancy, expand genome size, and provide a source for forming diverse/novel gene functions (W endel 2000). Although found across most eukaryotic lineages, gene duplication appears to occur at an elevated rate in plants with up to 100% of all angiosperms having a polyploid or paleopolyploid history (Masterson 1994; Lockton and Gaut 2005). The high incidence of gene duplication in plants is probably due to its impact on genetic diversity and adaptation (Lawton-Rauh 2003).

Increased evidence of paleopolyploidy in plants once thought to be purely diploid has come to light in recent years. Comparative mapping studies as well as genome-sequencing efforts have revealed that both Arabidopsis and rice are paleopolyploids (Lynch and Conery 2000; Tagi 2000; Vision et al. 2000; Goff et al. 2002; S imillion et al. 2002; Blanc et al. 2003; Yu et al. 2003). Expressed sequence tag (EST)-based analyses of several plant genomes have also revealed evidence for large-scale genome duplications in a wide range of genera, including soybean (Blanc and Wolfe 2004a; Schlueter et al. 2004).

Further evidence of paleopolyploidy has been identified in soybean specifically. Soybean (Glycine max L. Merr.) is a member of the papilionoid Leguminosae tribe Phaseoleae. While most genera of the Phaseoleae have a genome complement of 2n ¼ 22, soybean has a chromosome number of 2n ¼ 40 (Hadley and Hymowitz 1973; Lackey 1980). Studies of soybean gene families have also suggested that soybean is a paleopolyploid (Lee and Verma 1984; Hightower and Meagher 1985;Grandbastien et al. 1986;Nielsen et al. 1989). Additionally, combined data from nine mapping populations uncovered extensive homeologous relationships among linkage groups, with 90% of soybean RFLP probes detecting more than two fragments (Shoemaker et al. 1996). In many cases nested duplications were observed, suggesting at least two rounds of duplication and diploidization (Shoemaker et al. 1996; Lee et al. 1999, 2001).

The most compelling evidence to date is from an analysis of duplicate genes identified from ESTs. Large numbers of conserved duplicate gene pairs with similar levels of divergence from one another allowed the identification of at least twomajor genome duplications in soybean (Blanc and Wolfe 2004a; Schlueter et al. 2004). These gene pairs are referred to as homeologs since they most likely resulted from a polyploidy event and not from single gene duplications. …

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