Development and utilization of molecular markers to study genetic diversity of smooth cordgrass and cold tolerance sugarcane

Smooth cordgrass (Spartina alterniflora Loisel) and sugarcane (Saccharum spp. hybrids) are both grasses that belong to the family Poaceae and have significant impact on Louisiana environment and economy. Coastal Louisiana accounts to ~80% of the national wetland loss through natural and human interventions; (re)vegetation is considered an important component of coastal restoration efforts. Smooth cordgrass, a warm season marsh grass, is used as an ecosystem engineer to stabilize and restore Louisiana coastal marshes. In this study, genetic diversity was determined among 13 elite smooth cordgrass accessions of Louisiana through 276 polymorphic markers generated by 23 SSR and 32 RAPD primers. AMOVA results showed that sufficient variation existed among smooth cordgrass accessions for further exploitation in breeding program. A few genetic markers unique to specific smooth cordgrass accession(s) were also developed. Sugarcane, the number one row crop in Louisiana, is sensitive to cold; so cold tolerance is desirable to expand its cultivation in more northern environments. Cold tolerance alleles of Saccharum spontaneum can be exploited to develop sugarcane clones tolerant to low temperatures. To this end, forty differentially expressed genes (DEGs; 29 up-regulated and 11 down-regulated) were identified in a cold-tolerant clone Ho02-144 and a cold-sensitive clone L79-1002 under cold stress, using annealing control primer system. Reverse-transcription PCR (RT-PCR) analysis of the cold-responsive DEGs revealed distinctive expression profiles in the tolerant and sensitive clone. Mining of the cold-responsive DEGs yielded 12 sequences with simple sequence repeats (SSRs), which were used to design eSSR primers. Genotyping of 48 Louisiana sugarcane clones and 16 ancestral parents with these eSSRs generated 170 polymorphic markers that could classify cultivated sugarcane clones from their ancestral S. spontaneum clones at 0.23 similarity coefficient. The cold responsive genes will be useful for breeding cold tolerant sugarcane either through genetic engineering or selection through the use of gene-based markers