Jack C. Comstock

Natural Allelic Variations in Highly Polyploidy Saccharum Complex

Sugarcane (Saccharum spp.) is an important sugar and biofuel crop with high polyploid and complex genomes. The Saccharum complex, comprised of Saccharum genus and a few related genera, are important genetic resources for sugarcane breeding. A large amount of natural variation exists within the Saccharum complex. Though understanding their allelic variation has been challenging, it is critical to dissect allelic structure and to identify the alleles controlling important traits in sugarcane. To characterize natural variations in Saccharum complex, a target enrichment sequencing approach was used to assay 12 representative germplasm accessions. In total, 55,946 highly efficient probes were designed based on the sorghum genome and sugarcane unigene set targeting a total of 6 Mb of the sugarcane genome. A pipeline specifically tailored for polyploid sequence variants and genotype calling was established. BWA-mem and sorghum genome approved to be an acceptable aligner and reference for sugarcane target enrichment sequence analysis, respectively. Genetic variations including 1,166,066 non-redundant SNPs, 150,421 InDels, 919 gene copy number variations, and 1,257 gene presence/absence variations were detected. SNPs from three different callers (Samtools, Freebayes, and GATK) were compared and the validation rates were nearly 90%. Based on the SNP loci of each accession and their ploidy levels, 999,258 single dosage SNPs were identified and most loci were estimated as largely homozygotes. An average of 34,397 haplotype blocks for each accession was inferred. The highest divergence time among the Saccharum spp. was estimated as 1.2 million years ago (MYA). Saccharum spp. diverged from Erianthus and Sorghum approximately 5 and 6 MYA, respectively. The target enrichment sequencing approach provided an effective way to discover and catalog natural allelic variation in highly polyploid or heterozygous genomes.

Identifying Quantitative Trait Loci (QTLs) and Developing Diagnostic Markers Linked to Orange Rust Resistance in Sugarcane (Saccharum spp.)

Sugarcane (Saccharum spp.) is an important economic crop, contributing up to 80% of table sugar used in the world and has become a promising feedstock for biofuel production. Sugarcane production has been threatened by many diseases, and fungicide applications for disease control have been opted out for sustainable agriculture. Orange rust is one of the major diseases impacting sugarcane production worldwide. Identifying quantitative trait loci (QTLs) and developing diagnostic markers are valuable for breeding programs to expedite release of superior sugarcane cultivars for disease control. In this study, an F1 segregating population derived from a cross between two hybrid sugarcane clones, CP95-1039 and CP88-1762, was evaluated for orange rust resistance in replicated trails. Three QTLs controlling orange rust resistance in sugarcane (qORR109, qORR4 and qORR102) were identified for the first time ever, which can explain 58, 12 and 8% of the phenotypic variation, separately. We also characterized 1,574 sugarcane putative resistance (R) genes. These sugarcane putative R genes and simple sequence repeats in the QTL intervals were further used to develop diagnostic markers for marker-assisted selection of orange rust resistance. A PCR-based Resistance gene-derived maker, G1 was developed, which showed significant association with orange rust resistance. The putative QTLs and marker developed in this study can be effectively utilized in sugarcane breeding programs to facilitate the selection process, thus contributing to the sustainable agriculture for orange rust disease control.

Discovering the desirable alleles contributing to the lignocellulosic biomass traits in saccharum germplasm collections for energy cane improvement

Phenotyping Methods: The accessions (which includes 21 taxa and 1,177 accessions) in the World Collection of Sugarcane and Related Grasses (WCSRG) was evaluated for the following traits: arenchyma, internode length and diameter, pubescence, pith, Brix, stalk number and fiber. A core of 300 accessions that included each species in the World Collection was selected by using the Maximization Strategy in MStrat software. Results: The core had a higher diversity rating than random selections of 300 accessions. The Shannon–Weaver Diversity Index scores of the core and whole collection were similar indicating that the majority of the diversity was captured by the core collection. The ranges and medians between the core and WCSRG were similar; only two of the trait medians were not significant at P = 0.05 using the non-parametric Wilcoxon method and the coincidence rate (CR % = 96.2) was high (>80) indicating that extreme values were retained. Thus, the phenotypic diversity of these traits in the WCSRG was well represented by the core collection. Associations Methods: Genotypic and phenotypic data were collected for 1002 accessions of the WCSRG including 209 SSR markers. Association analysis was performed using both General Linear (GLM) and Maximum Likelihood (MLM) models. Different core collectionsmorexa0» with 300 accessions each were selected based on genotypic, phenotypic and combined data based on the Maximization Strategy in MStrat software. Results: A major portion of the genotyping involving SNPs is being conducted by Dr. Jianping Wang of the University of Florida under the DOE award DE-FG 02-11ER 65214 and the genotypic and phenotypic associations will be reported separately next year. In the current, study forty one and seventeen markers were found to be associated with traits using the GLM and MLM methods respectively including associations with arenchyma, internode length and diameter, pubescence, pith, and Sugar Cane Yellow Leaf Virus. The data indicates that each of the cores and the World Collection are similar to each other genotypically and phenotypically, but the core that was selected using only genotypic data was significantly different phenotypically. This indicates that there is not enough association between the genotypic and phenotypic diversity as to select using only genotypic diversity and get the full phenotypic diversity. Core Collection: Creation and Phenotyping Methods: To evaluate this germplasm for breeding purposes, a representative diversity panel selected from the WCSRG of approximately 300 accessions was planted at Canal Point, FL in three replications. These accessions were measured for stalk height and stalk number multiple times throughout the growing season and Brix and fresh biomass during harvest in 2013 and, stalk height, stalk number, stalk diameter, internode length, Brix and fresh and dry biomass was determined in the ratoon crop harvest in 2014. Results: In correlations of multiple measurements, there were higher correlations for early measurements of stalk number and stalk height with harvest traits like Brix and fresh weight. Hybrids had higher fresh mass and Brix while Saccharum spontaneum had higher stalk number and dry mass. The heritability of hybrid mass traits was lower in the ratoon crop. According to the principal component analysis, the diversity panel was divided into two groups. One group had accessions with high stalk number and high dry biomass like S. spontaneum and the other groups contained accessions with higher Brix and fresh biomass like S. officinarum. Mass traits correlated with each other as expected but hybrids had lower correlations between fresh and dry mass. Stalk number and the mass traits correlated with each other except in S. spontaneum and hybrids in the first ratoon. There were 110 accessions not significantly different in Brix from the commercial sugarcane checks including 10 S. spontaneum accessions. There were 27 dry and 6 fresh mass accessions significantly higher than the commercial sugarcane checks. Core Collection: Fiber analysis Methods: A biomass sample was taken from each accession then shredded and dried. Fiber analysis was then performed on each sample. The acetyl groups, acid insoluble lignin, acid soluble lignin, arabinan, glucan, holocellulose, total lignin, structural ash, and xylan were quantified on a % fiber basis and nonstructural ash on a % total basis. Results: There were significant, but not large differences between species for holocellulose, lignin, acetyl, acid soluble lignin, nonstructural ash, and glucan. For each trait, S. spontaneum had significantly more holocellulose, glucan, lignin, and nonstructural ash and less acetyl and acid soluble lignin than the other species. In all populations, glucan and was positively correlated with holocellulose were positively correlated and glucan and and holocellulose were negatively correlated with lignin. In hybrids, internode length correlated positively with holocellulose and nonstructural ash and negatively with lignin. The heritability estimates for each of the fiber component traits is low indicating that environment is an important factor in fiber composition. Principal component analysis indicated that a large amount of diversity exists within each of the species.«xa0less

Report of the VIIth ISSCT Pathology Workshop Louisiana, USA 11–16 May, 2003

The Vllth ISSCT pathology workshop was held in Louisiana (USA) from 11 to 16 May 2003 and was hosted by the American Society of Sugar Cane Technologists (ASSCT) in collaboration with the Louisiana State University (LSU) Agricultural Centre and the US Department of Agriculture Sugar Cane Research Unit. The theme of the workshop was Advances and challenges in sugar cane pathology. The workshop was followed by a post workshop tour in Florida (USA) from 19 to 20 May 2003. The theme of the post workshop was Florida pathology: research programmes and industrys disease concerns.