Data from: Genome-wide association mapping of quantitative traits in a breeding population of sugarcane

Background: Molecular markers associated with relevant agronomic traits
could significantly reduce the time and cost involved in developing new
sugarcane varieties. Previous sugarcane genome-wide association analyses
(GWAS) have found few molecular markers associated with relevant traits at
plant-cane stage. The aim of this study was to establish an appropriate
GWAS to find molecular markers associated with yield related traits
consistent across harvesting seasons in a breeding population. Sugarcane
clones were genotyped with DArT (Diversity Array Technology) and TRAP
(Target Region Amplified Polymorphism) markers, and evaluated for cane
yield (CY) and sugar content (SC) at two locations during three successive
crop cycles. GWAS mapping was applied within a novel mixed-model framework
accounting for population structure with Principal Component Analysis
scores as random component. Results: A total of 43 markers significantly
associated with CY in plant-cane, 42 in first ratoon, and 41 in second
ratoon were detected. Out of these markers, 20 were associated with CY in
2 years. Additionally, 38 significant associations for SC were detected in
plant-cane, 34 in first ratoon, and 47 in second ratoon. For SC, one
marker-trait association was found significant for the 3 years of the
study, while twelve markers presented association for 2 years. In the
multi-QTL model several markers with large allelic substitution effect
were found. Sequences of four DArT markers showed high similitude and
e-value with coding sequences of Sorghum bicolor, confirming the high gene
microlinearity between sorghum and sugarcane. Conclusions: In contrast
with other sugarcane GWAS studies reported earlier, the novel methodology
to analyze multi-QTLs through successive crop cycles used in the present
study allowed us to find several markers associated with relevant traits.
Combining existing phenotypic trial data and genotypic DArT and TRAP
marker characterizations within a GWAS approach including population
structure as random covariates may prove to be highly successful.
Moreover, sequences of DArT marker associated with the traits of interest
were aligned in chromosomal regions where sorghum QTLs has previously been
reported. This approach could be a valuable tool to assist the improvement
of sugarcane and better supply sugarcane demand that has been projected
for the upcoming decades.