Target region amplification polymorphism (TRAP) is a fairly new PCR-based molecular marker technique which uses gene-based information for primer design. The objective of this study was to evaluate the utility of TRAP markers for assessing genetic diversity and interrelationships in sugarcane germplasm collections. Thirty genotypes from the genera Saccharum, Miscanthus, and Erianthus were used in the study. Among the genus Saccharum were the species, S. officinarum L., S. barberi Jesw., S. sinense Roxb., S. spontaneum L., S. robustum Brandes and Jeswiet ex Grassl, cultivars, cultivar-derived mutants and interspecific hybrids between S. officinarum and S. spontaneum. Six fixed primers, designed from sucrose-and cold tolerance-related EST (expressed sequence tags) sequences, paired with three arbitrary primers, were used to characterize the germplasm. Both the cluster and principal coordinate (PCoA) analyses placed the Erianthus spp. and Miscanthus spp. genotypes distinctly from each other and from the Saccharum species, thus, supporting their taxonomic classification as separate genera. Genotypes of the low sucrose and cold tolerant species, S. spontaneum, formed one distinct group, while the rest of the Saccharum species formed one interrelated cluster with no distinct subgroups. Sequence analysis of TRAP bands derived from a S. spontaneum genotype revealed homology with known gene sequences from other grass species including Sorghum. A BLASTn search using the homologous sequences from Sorghum matched with the S. officinarum GenBank accession from which the fixed TRAP primer was designed. These results ratify TRAP as a potentially useful marker technique for genetic diversity studies in sugarcane.

‘L 79‐1002’ (Reg. No. CV‐132, PI 651501) sugarcane (a complex hybrid of Saccharum officinarum L., S. spontaneum L., S. barberi Jeswiet, and S. sinense Roxb. amend. Jeswiet) was released on 26 Apr. 2007 by the Louisiana State University Agricultural Center in cooperation with the USDA‐ARS and the American Sugarcane League, Inc. The cross for L 79‐1002, a F1 hybrid, was made in 1974 using ‘CP 52‐68’ as the female parent and Tainan, a S. spontaneum clone, as the male parent. Initial clonal selection was done in single stools. Testing was done from 1976 through 1983 in yield trials conducted in the traditional sugarcane growing area in south Louisiana and in the colder, non‐sugarcane growing regions of north Louisiana. Yield testing was resumed in 2002 through 2005 as interest in biofuels research renewed. L 79‐1002 was released for an emerging biofuels industry because of its high fiber content and biomass (cane yield) potential. Average fiber content for L 79‐1002 is approximately 257 g kg−1 The new cultivar also has excellent vigor and ratooning ability. Experiments conducted at Bossier City, Louisiana (32.1° N lat) indicated a broader range of adaptability than sugarcane cultivars grown for the production of sucrose.

Sugarcane hybrids are complex aneu-polyploids (2n = 100-130) derived from inter-specific hybridization between ancestral polyploid species, namely S. officinarum L. and S. spontaneum L. Efforts to understand the sugarcane genome have recently been enhanced through the use of new molecular marker technologies. A framework genetic linkage map of Louisiana's popular cultivar LCP 85-384 was constructed using the selfed progeny and based on polymorphism derived from 64 AFLP, 19 SSR and 12 TRAP primer pairs. Of 1,111 polymorphic markers detected, 773 simplex (segregated in 3:1 ratio) and 182 duplex (segregate in 77:4 ratio) markers were used to construct the map using a LOD value of ≥ 4.0 and recombination threshold of 0.44. The genetic distances between pairs of markers linked in the coupling phase was computed using the Kosambi mapping function. Of the 955 markers, 718 simplex and 66 duplex markers were assigned to 108 co-segregation groups (CGs) with a cumulative map length of 5,617 cM and a density of 7.16 cM per marker. Fifty-five simplex and 116 duplex markers remained unlinked. With an estimated genome size of 12,313 cM for LCP 85-384, the map covered approximately 45.6% of the genome. Forty-four of the 108 CGs were assigned into 9 homo(eo)logous groups (HGs) based on information from locus-specific SSR and duplex markers, and repulsion phase linkages detected between CGs. Meiotic behavior of chromosomes in cytogenetic studies and repulsion phase linkage analysis between CGs in this study inferred the existence of strong preferential chromosome pairing behavior in LCP 85-384. This framework map marks an important beginning for future mapping of QTLs associated with important agronomic traits in the Louisiana sugarcane breeding programs.

Brown rust, caused by the fungus Puccinia melanocephala, poses an increasing threat to sugarcane industries worldwide. Recently, markers R12H16 and 9020-F4 were developed for a major resistance gene Bru1 that contributes to a significant proportion of brown rust resistance in multiple sugarcane industries. Marker-assisted screening of Louisiana sugarcane germplasm showed a low frequency (4.3%, five out of 117 clones) of Bru1 among sugarcane cultivars and elite breeding clones. Likewise, among progeny of crosses involving wild/exotic germplasm, only 14 of 208 clones (6.7%) tested Bru1 positive. However, Bru1 frequency was higher (28.7%, 52 of 181 clones) in wild/exotic germplasm, which indicated that diverse genetic resources are available for Bru1 introgression. Commercial Bru1-positive cultivar, 'L 01-299', was resistant to brown rust. However, Bru1-positive cultivar, 'L 10-146', was susceptible while Bru1-negative cultivars, such as 'L 99-233', showed resistance to brown rust. Bru1-negative clones with brown rust resistance offer an opportunity to identify alternate sources of resistance, which can be pyramided with Bru1 for effective and durable resistance in sugarcane against the changing pathogen.

Framework genetic linkage maps of two progenitor species of cultivated sugarcane, Saccharum officinarum 'La Striped' (2n = 80) and S. spontaneum 'SES 147B' (2n = 64) were constructed using amplified fragment length polymorphism (AFLP), sequence related amplified polymorphism (SRAP), and target region amplification polymorphism (TRAP) markers. The mapping population was comprised of 100 F 1 progeny derived from the interspecific cross. A total of 344 polymorphic markers were generated from the female (S. officinarum) parent, out of which 247 (72%) were single-dose (segregating in a 1:1 ratio) and 33 (9%) were double-dose (segregating in a 3.3:1 ratio) markers. Sixty-four (19%) markers deviated from Mendelian segregation ratios. In the S. spontaneum genome, out of a total of 306 markers, 221 (72%) were single-dose, 43 (14%) were double-dose, and 42 markers (14%) deviated from Mendelian segregation ratios. Linkage maps with Kosambi map distances were constructed using a LOD score C5.0 and a recombination threshold of 0.45. In Saccharum officinarum, 146 markers were linked to form 49 linkage groups (LG) spanning 1732 cM whereas, in S. spontaneum, 121 markers were linked to form 45 LG spanning 1491 cM. The estimated genome size of S. officinarum 'La Striped' was 2448 cM whereas that of S. spontaneum 'SES 147B' was 3232 cM. Based on the two maps, genome coverage was 69% in S. officinarum and 46% in S. spontaneum. The S. officinarum parent 'La Striped' behaved like an auto-allopolyploid whereas S. spontaneum 'SES 147B' behaved like a true autopolyploid. Although a large disparity exists between the two genomes, the existence of simple duplex markers, which are heterozygous in both parents and segregate 3:1 in the progeny, indicates that pairing and recombination can occur between the two genomes. The study also revealed that, compared with AFLP, the SRAP and TRAP markers appear less effective at generating a large number of genome-wide markers for linkage mapping in sugarcane. However, SRAP and TRAP markers can be useful for QTL mapping because of their ability to target gene-rich regions of the genome, which is a focus of our future research.