Abstract
BackgroundMolecular 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.ResultsA 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.ConclusionsIn 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0829-x) contains supplementary material, which is available to authorized users.
Highlights
Molecular markers associated with relevant agronomic traits could significantly reduce the time and cost involved in developing new sugarcane varieties
In contrast with others sugarcane genome-wide association analyses (GWAS) studies reported earlier involving yield related traits [27, 28] where analyzes were conducted at plant-cane stage, the novel methodology to analyze multi-Quantitative trait loci (QTL) through successive crop cycles used in the present study allowed us to find several markers associated with relevant traits
This study demonstrated that association mapping in elite germplasm seems to have a clear potential for improving sugarcane, especially for complex traits such as cane yield (CY) and sugar content (SC), for which measurements are costly and time consuming
Summary
Molecular markers associated with relevant agronomic traits could significantly reduce the time and cost involved in developing new sugarcane varieties. The highest tonnage crop among cultivated plants, plays a substantial role in the global economy Nowadays, this crop has gained great importance for its traditional use as food (80 % of world’s sugar is produced from sugarcane) and for ethanol and biomass production. The initial interspecific hybrids were repeatedly backcrossed to S. officinarum clones or to other hybrids in order to recover high sugar content, a process known as “nobilization”. These modern cultivars are highly polyploid and often aneuploid, with chromosome numbers ranging from 100 to 130 [2]. Due to this genetic complexity, the application of both conventional and molecular breeding is a challenge in sugarcane
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