2010. Genome organization and genetic diversity of wildrice (Zizania palustris L.)

2010. Genome organization and genetic diversity of wildrice (Zizania palustris L.)

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ABSTRACT

The large amount of molecular marker and DNA sequence information in rice (Oryza sativa L.) has allowed for comparative genetics between rice and wildrice (Zizania palustris L.). In particular, rice simple sequence repeat (SSR) markers were used to develop an SSR-based linkage map in wildrice and to determine the amount of genetic diversity within and among populations of the species. The same set of markers was analyzed in a wildrice population segregating for the pistillate trait to find marker genotypes that correlated with the trait. Rice genome DNA sequences for three well-characterized genes were used to determine the relatedness between Oryza species and wildrice.

Six-hundred-eleven rice SSR markers were tested in wildrice. Approximately 42% of the markers can be amplified in wildrice and about 30% of those markers exhibit polymorphism in the newly developed SRT X BRL mapping population. SRT is a shattering resistant tester line used in the wildrice breeding program. BRL is a breeding line resulting from selection on a population collected from Big Rice Lake in Cass County, Minnesota. An additional 36 SSR markers were developed in Zizania palustris using DNA sequences from the endangered wildrice species Z. texana. About 47% of these markers exhibited co-dominant polymorphism and 23% dominant polymorphism in the SRT X BRL mapping population. In all, seventy-five of these polymorphic markers were used to develop the first SSR-based molecular genetic map of wildrice.

In contrast to the RFLP-based wildrice map, the SSR-based map indicates little synteny between rice and wildrice. This difference may be due to some non-specific amplification with the rice SSR markers. It may also be an indication of the amount of DNA sequence conservation between the two species as the RFLP markers were generated from cDNAs representing expressed DNA sequences. The majority of the rice SSR markers were generated from genomic DNA sequences where SSR motifs are largely in intron or even non-genic sequences. Such regions of eukaryotic genomes are known to be subject to rearrangement which may be reflected in what appears to be a reduced level of detected synteny (Langham et al. 2004).

A molecular genetic marker was identified to be associated with the pistillate gene. Using this genetic marker to select for the pistillate gene would be useful for developing significantly larger mapping populations than are currently possible in wildrice allowing for more precise mapping and QTL studies. In the short-term, use of pistillate wildrice could benefit the wildrice breeding program by increasing cultivar yields as much as 50%. In the long-term, a true breeding pistillate wildrice could facilitate the development of recombinant inbred lines and near isogenic lines for use in producing wildrice hybrids and genetic stocks. Zizania palustris is more closely related to wild Oryza species than to the cultivated species Oryza sativa based on direct comparison of gene sequences from Adhl, Waxy and MatK.

The Rc gene is known to control rice seed pericarp color via the presence of a 14-bp indel sequence. Comparison of the Rc gene sequence among Zizania palustris, Oryza. rufipogon and O. sativa revealed that wildrice contains the indel sequence conferring red pericarp color in O. rufipogon. Further comparative genetics between Z. palustris and wild Oryza species such as O. brachyantha, O. granulata and O. rufipogon may uncover greater synteny than with O. sativa.

Genetic diversity studies of recently collected natural wildrice from lakes in Minnesota and Wisconsin do not appear to correlate with geographic distribution. The assessment of the available genetic diversity in wildrice is important for continued improvements in wildrice breeding. Generally, wildrice 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 the unique environment of each lake. Further diversity analysis using a larger set of populations may lead to a greater understanding of specific alleles involved in wildrice adaptation that could be utilized to produce varieties that would be more uniformly adapted to the varying cultivated conditions in northern Minnesota  .