An enriched sugarcane diversity panel for utilization in genetic improvement of sugarcane.

Sugarcane crop is important for both sugar and biofuels. A world collection of sugarcane and related grasses (WCSRG) maintained at Miami, FL contains > 1,200 non-redundant clones of different species and genera within the Saccharum complex. However, linkage of undesirable alleles with useful genes in wild species has hindered its efficient utilization in sugarcane breeding. A core collection developed previously with smaller number of clones representing WCSRG did not take into account > 120 wild/exotic clones maintained at the USDA-ARS Sugarcane Research Unit in Houma, Louisiana. Moreover, the genome complexity and sub-tropical to temperate growing climate of Louisiana warrant a region-specific core collection that can be used for base-broadening breeding aimed at efficient introgression of desirable alleles. Genetic diversity of 1,485 clones within WCSRG and Louisiana (commercials, wild/exotic) using 423 SSR alleles showed an average gene diversity (h) at 0.208 among all species groups where Erianthus-like Saccharum species (ELSS), Miscanthus spp., and S. spontaneum each formed a distinct cluster, Saccharum robustum, S. officinarum, hybrid cultivars, and S. edule grouped together in a major cluster, and Saccharum sinense and S. barberi formed distinct grouping. A 309-clone diversity panel (SDP1) was developed that captured the genetic diversity based on the combination of maximum length subtree and manual selection to maximize representation of Louisiana clones and minimize import of clones from Miami. SDP1 shared 324 alleles out of the 423 alleles in the entire population of 1,485 clones and captured the genetic diversity of the entire collection with an average gene diversity (h) at 0.163. The variation within (11-17%) and among (83-89%) the populations in SDP1 were comparable with the entire population of 1,485 clones (9-15% and 85-91%, respectively). The breadth of the genetic variation of SDP1 was exemplified by the intra- and inter-specific diversity of a 190-clone mini-core collection with markers derived from known cold-responsive genes. SDP1 will facilitate genome-wide association studies for identification of trait-specific markers for use in marker-assisted breeding in Louisiana and elsewhere.

Genome-wide association mapping identifies markers associated with cane yield components and sucrose traits in the Louisiana sugarcane core collection.

Sugarcane is an economically important crop for both food and biofuel industries. Marker-assisted breeding in sugarcane is becoming a reality with the recent development and deployment of markers linked with disease resistance genes. Large linkage disequilibrium in sugarcane makes genome-wide association studies (GWAS) a better alternative to biparental mapping to identify markers associated with agronomic traits. GWAS was conducted on a Louisiana core collection to identify marker-trait associations (MTA) for 11 cane yield and sucrose traits using single nucleotide polymorphism (SNP) and insertion-deletion (Indel) markers. Significant (P < .05) MTAs were identified for all traits where the top ranked markers explained up to 15% of the total phenotypic variation. High correlations (0.732 to 0.999) were observed between sucrose traits and 56 markers were found consistent across multiple traits. These markers following validation in more diverse populations could be used in marker-assisted selection of clones in sugarcane breeding program in Louisiana and elsewhere.

Identification of cold-responsive genes in energycane for their use in genetic diversity analysis and future functional marker development.

Breeding for cold tolerance in sugarcane will allow its cultivation as a dedicated biomass crop in cold environments. Development of functional markers to facilitate marker-assisted breeding requires identification of cold stress tolerance genes. Using suppression subtractive hybridization, 465 cold-responsive genes were isolated from the cold-tolerant energycane Ho02-144. Predicted gene interactions network indicated several associated pathways that may coordinately regulate cold tolerance responses in energycane. Expression analysis of a select set of genes, representing signaling and transcription factors, genes involved in polyamine and antioxidant biosynthesis, protein degradation and in the repair of damaged proteins in the cytosol, showed their time-dependent regulation under cold-stress. Comparative expression profiles of these genes between Ho02-144 and a cold-sensitive clone (L79-1002) showed that almost all genes were induced immediately upon imposition of cold stress and maintained their expression in Ho02-144 whereas they were either downregulated or their upregulation was very low in L79-1002. Simple sequence repeat markers derived from 260 cold-responsive genes showed allelic diversity among the cold-sensitive commercial hybrids that were distinct from the Saccharum spontaneum clones. Future efforts will target sequence polymorphism information of these genes in our ongoing QTL and association mapping studies to identify functional markers associated with cold tolerance in sugar/energycane.