Identifying Marker-Trait Associations for Fiber Components in Sugarcane with Simple Sequence Repeat Markers

Modern   sugarcane   varieties   are   derived   from   interspecific hybridization   between  Saccharum   officinarum   and   Saccharum   spontaneum, resulting in highly polyploid and aneuploid plants with chromosome number ranging from 80 to 140. The identification of marker-trait associations can expedite breeding programs by reducing the cycle of selection through the indirect identification of plants with desirable traits. Here we describe 26 marker-trait associations to lignin and cellulose content in 250 individuals derived from a bi-parental cross between two elite clones from the CTC’s (Centro de Tecnologia Canavieira) breeding program (Brazil). Lignin and cellulose content analyses were performed at the plant cane and first ratoon stages by Near Infrared. Seventy Expressed Sequence Tags Single Sequence Repeats (EST-SSR), obtained from the lignin and cellulose biochemical pathways, and 15 genomic Single Sequence Repeats (gSSR) were screened in the population, producing 157 polymorphic markers. Only single dose markers were considered, in a total of 64. A Single-Marker Analysis for both lignin and cellulose content was performed by maximum likelihood tests in models considering one marker at a time. Overall, 26 marker-trait associations were found at P<0.05 (13 markers with cellulose and 13 with lignin). Ten markers (38%) were aligned to the sorghum genome and mapped in the chromosomes 1, 2, 4 and 7. There are evidences that, in sorghum, chromosome 1 is related to cellulose and chromosomes 2, 4 and 7 to hemicellulose content, thus confirming that SSRs, conserved in sugarcane and sorghum, would be informative for mapping quantitative trait loci in sugarcane. Multiple linear regression determined the ratio of phenotypic variance explained by the association between SSR markers and traits (R2). These SSRs are explaining 18% in Lignin content and 27% in Cellulose content. These markers can be useful if applied in marker-assisted selection and genomic studies.