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

RACEDO, J.; GUTIERREZ, L.; PERERA, M. F.; OSTENGO, S.; PARDO, E. M.; CUENYA, M. I.; WELIN, B. AND CASTAGNARO, A. P.

BMC PLANT BIOLOGY

BIOMED CENTRAL LTD

Lugar: Londres; Año: 2016

1471-2229

Background: Molecular markers associated with relevant agronomic traits could7 significantly reduce the time and cost involved in developing new sugarcane varieties.Previous sugarcane genome-wide association analyses (GWAS) have found few9 molecular markers associated with relevant traits at plant-cane stage. The aim of this10 study was to establish an appropriate GWAS to find molecular markers associated with11 yield related traits consistent across harvesting seasons in a breeding population.12 Sugarcane clones were genotyped with DArT (Diversity Array Technology) and TRAP13 (Target Region Amplified Polymorphism) markers, and evaluated for cane yield (CY)14 and sugar content (SC) at two locations during three successive crop cycles. GWAS15 mapping was applied within a novel mixed-model framework accounting for16 population structure with Principal Component Analysis scores as random component.17 Results: A total of 43 markers significantly associated with CY in plant-cane, 42 in first18 ratoon, and 41 in second ratoon were detected. Out of these markers, 20 were19 associated with CY in two years. Additionally, 38 significant associations for SC were20 detected in plant-cane, 34 in first ratoon, and 47 in second ratoon. For SC, one marker21trait association was found significant for the three years of the study, while twelve22 markers presented association for two years. In the multi-QTL model several markers23 with large allelic substitution effect were found. Sequences of four DArT markersshowed high similitude and e-value with coding sequences 1 of Sorghum bicolor,2 confirming the high gene microlinearity between sorghum and sugarcane.3 Conclusions: In contrast with other sugarcane GWAS studies reported earlier, the4 novel methodology to analyze multi-QTLs through successive crop cycles used in the5 present study allowed us to find several markers associated with relevant traits.6 Combining existing phenotypic trial data and genotypic DArT and TRAP marker7 characterizations within a GWAS approach including population structure as random8 covariates may prove to be highly successful. Moreover, sequences of DArT marker9 associated with the traits of interest were aligned in chromosomal regions where10 sorghum QTLs has previously been reported. This approach could be a valuable tool to11 assist the improvement of sugarcane and better supply sugarcane demand that has12 been projected for the upcoming decades.