Genome organization and genetic diversity of wildrice (Zizania palustris L.)

Molecular marker and DNA sequence information in rice (Oryza saliva L.) has allowed for comparative genetics between rice and wildrice (Zizania palustris L.). Rice simple sequence repeat (SSR) markers were mapped in wildrice. Approximately 42% of the tested markers amplified in wildrice and about 35% of those were polymorphic in the SRT X BRL mapping population. SRT is a shattering resistant line and BRL is a line originally collected from Big Rice Lake in Minnesota. An additional 36 SSR markers were developed in Z. palustris using DNA sequences from Z. texana. About 56% of these markers were polymorphic in the same mapping population. In all, seventy-nine markers were placed on the first SSR-based molecular genetic map of wildrice. In contrast to the previous RFLP-based wildrice map, the SSR-based map indicates little synteny between rice and wildrice. This may be because the RFLP markers were generated from cDNA sequences and most of the SSR markers were generated from genomic DNA sequences.;One SSR marker correlated with the pistillate trait. Pistillate type wildrice could benefit the breeding program by increasing yields as much as 50%. A true breeding pistillate wildrice could facilitate development of recombinant inbred lines and near isogenic lines for producing wildrice hybrids and genetic stocks.;The Rc gene controls rice pericarp color via the presence of a 14-bp indel. Comparison of the Rc gene sequences among Zizania palustris, Oryza rufipogon and O. sativa revealed that wildrice contains the indel sequence.;Rice DNA sequences for the Adh1, Waxy and MatK genes were used to determine the relatedness between Oryza species and wildrice. Zizania palustris is more closely related to wild Oryza species than to the cultivated Oryza sativa.;Wildrice genetic diversity studies are important for continued improvements in wildrice breeding. A subset of SSR markers was used to determine genetic diversity within and among wildrice populations. Generally, genetic diversity analysis has shown that allele uniqueness and frequency are specific to a given natural population. This may be a result of adaptation to specific environments. Further diversity analysis may lead to a greater understanding of specific alleles involved in wildrice adaptation.