Current Projects

Sugarcane (Saccharum spp.), Florida’s largest field crop, is also ranked number one in sugarcane production nationwide. Currently, sugarcane production is declined by orange rust disease caused by Puccinia kuehnii. Sugarcane orange rust was first observed in Florida and in the U.S., in 2007 (Comstock et al, 2008). Economic losses caused by orange rust in a single season have been estimated at US$40 million in Florida. Using disease resistant cultivars is the best approach to control the disease and a strong genetic basis exists for disease resistance. Cultivar development through marker-assisted selection (MAS) can accelerate the breeding process and improve breeding efficiency. Remarkable advances in molecular genetics, genomic technologies, specifically next generation sequencing (NGS) technologies, and massive biological databases provide an opportunity to mine valuable alleles underlying disease resistance in the Saccharum germplasm. The objectives of this project are to 1) Identify major quantitative trait loci (QTLs) contributing to disease resistance and markers linked to by using genotype by sequencing (GBS) and exome sequencing of a bi-parental segregating population; 2) to develop PCR-based markers for MAS of orange rust resistant clones in sugarcane breeding program.

Developing markers linked to genes controlling sugarcane orange rust disease resistance

Funded by Florida Sugarcane League

Discovering the desirable alleles contributing to biomass traits in Saccharum spp for energy cane improvement.

Funded by DOE and USDA Biomass Genomics Research

In the Southern US, energy cane has great potential as a biofuel feedstock and shows competitive advantage in producing lignocellulosic biomass. Energy canes, just as sugarcanes, are interspecific hybrids derived from crosses between species primarily within the genus Saccharum in Poaceae family. Energy cane cultivars are selected from the interspecific hybrids for high biomass, high fiber but low sucrose content, while sugarcane cultivars are selected for high sugar content.  Energy cane cultivars out-yield many other biofuel feedstocks, such as Miscanthus, Arundo donax or switchgrass in Southern Florida field trials. However, energy cane breeding programs are very primitive compared to those of other field crops due to 1) limited or poorly characterized genetic resources resulting in failure to reach the highest biomass potential and 2) lack of genetic and genomic information of the breeding materials, which leads to inefficient breeding processes.
This funded project aims to 1) genetically and phenotypically identify a core collection of approximately 300 accessions from the world sugarcane germplasm collection that captures the greatest extent of molecular and phenotypic diversity; 2) discover desirable alleles contributing to biomass composition in Saccharum spp. through association analysis between allelic variation and lignocellulosic biomass components and cell wall composition variation;  3) develop energy cane cultivars through marker assisted selection. This funding allows our research program to evaluate the world germplasm collection of Saccharum spp for efficiently utilizing the genetic resources and to study the genetic and genomic variance of the genes contributing to biomass and many other important traits in Saccharum spp.

Dissecting the genetic components underlying the flowering time and biomass in elephant grass.

Funded by UF-IFAS Plant Molecular Breeding Initiative

Elephant grass (Pennisetum purpureum, Schumach), is one of the most promising feedstocks for lignocellulosic biofuel production in the southeastern US due to its exceptionally high biomass yield and persistence. It also provides alternative use options as forage due to its high forage quality. Evaluation of elephant grass and pearl millet (Pennisetum glaucum) germplasm as well as their interspecific hybridization have recently demonstrated significant improvements of both biomass yield and biosafety in the interspecific hybrids (also called king grass). The formation of wind dispersed seeds in elephant grass is the main factor that contributes to its invasive potential. Therefore, combining reproductive sterility caused by the triploid cytotype of king grass with late flowering is the most promising strategy to ensure the biosafety of this feedstock. To maximize both biomass yield and biosafety of elephant grass and king grass, we are identifying QTLs underlying flowering time in elephant grass through GBS and QTL-seq, comparative genomics, and candidate gene approaches.

Characterizing and understanding the molecular genetic mechanisms of spotted wilt resistance in peanut. 

Funded by Southeastern Peanut Research Initiative and Plant Molecular Breeding Initiative

Peanut (Arachis hypogaea L.) is the world’s fifth most important oilseed crop and second most important legume crop (after soybean) serving as an important oil and food source for millions of people. However, since it was discovered in the 1990's, spotted wilt caused by tomato spotted wilt virus (TSWV) has severely impacted US peanut production. Up to now, no commercial peanut cultivars or genotypes can prevent the TSWV infection completely. The Florida peanut breeding program has identified breeding lines nearly “immune” to the spotted wilt in the infected field in an effort to develop spotted wilt resistant cultivars. To understand the genetic basis of this significant resistance in these breeding lines and improve the efficiency of breeding TSWV resistant cultivars, we intend to genetically map the TSWV resistance gene loci and develop markers linked with the resistance. Ultimately, we will fine map and clone the underlying genes conferring resistance to the spotted wilt and understand the molecular functions of the virus-immune genes in peanut.

Characterizing and understanding the molecular genetic mechanisms of peanut nodulation.

Funded by UF IFAS seed grant and Florida Peanut

Legumes are benefited by fixing substantial amounts of atmospheric nitrogen through root nodules, which allows the plants to grow well in N-deficient soils and eliminate N fertilizer application. Biologically fixed N by legume species accounts for about 65% N utilization in the current global agriculture and N fixation is becoming increasingly imperative in sustainable crop production systems. Peanut (Arachis hypogaea L.), as one of the world’s most important warm season legume crops for oil production and protein sources, can be infected by rhizobia to form nodules and fix N. However, the N fixed by this symbiosis process in peanut can only supply 55% N needs for optimal plant growth. Compared to other legumes, the N fixation efficiency through symbiosis is relatively low in peanuts, thus leave a big gap for improvement. The molecular mechanism of peanut symbiosis is largely unknown. Peanut nodulation doesn’t show root hair infection processes as in the model legume species. Instead, the rhizobia enter the peanut root through a crack tentatively at the sites of lateral root emergence. The rhizobia species colonizing peanuts for symbiosis are different from those colonizing model legume species. Studies on peanut- rhizobium symbiosis may reveal novel insights on nodule organogenesis in non-model legume species, since specific host provides specific genetic background for the infection mode and nodule organogenesis. Deep understanding of the plant genes involved in nodulation and symbiotic nitrogen fixation specifically through crack entry infection is critical in order to develop true nodulating cereal crops.
The ultimate goals of this research are to clone the nodulation genes in peanut and to understand the molecular genetic basis of peanut nodulation. The Specific objectives of this project are 1) to evaluate phenotypic and yield effects of non-nodulating inbred lines compared with near isogenic nodulating inbred lines and their parents; 2) to identify the differentially expressed genes in the nodulating and non-nodulating near isogenic inbred lines through RNA-seq; and 3) to map genes controlling non- nodulation in peanut genome to build the foundation for map-based cloning of the peanut nodulation genes.