Table.

Traits amenable to high-throughput phenotyping (HTP) and their potential for coapplication with GS for sugarcane breeding. The applicability of HTP and /or GS for these traits has been demonstrated in sugarcane experimentally^a.

Traits		Genotyping technology	Marker systems b	Sensor systems	Application	Genomics-phenomics integration potential	Current status
Genomics	Phenomics
Cane yield	Cane yield	AAS array, DArT, and GBS	SNP markers and DArT markers	Multidimensional RGB, LiDAR, and multispectral imaging	Crop yield improvement, crop growth assessment	High	Limited institutional capacity and marker cost still limit wider application; targeted implementation efforts underway
Sugar content	Sugar content	AAS array, DArT, and GBS	SNP markers and DArT markers	NIR	Crop yield improvement	Medium to high	As above, hyperspectral imaging research for HTP
Fiber content	Fiber content	AAS array, DArT, and GBS	SNP markers and DArT markers	NIR	Stalk quality and energy cane	Medium to high	Moderate high-throughput currently
Stalk height, stalk number, and biomass	Stalk height, stalk number, and biomass	AAS array, DArT, and GBS	SNP markers and DArT markers	LiDAR and multidimensional RGB	Crop yield, stalk weight, rationability, and crop establishment	Medium to high	Used for crop growth monitoring and crop management
	Canopy cover and canopy architecture			LiDAR and multidimensional RGB	Canopy filling, crop gap, light interception, and water use	Limited genomics research	Extensively used for crop growth modeling and crop monitoring
Brown rust	Brown rust	AAS array and DArT	Bru gene	RGB and multispectral imaging	Brown rust resistance	High	Currently limited implementation in breeding programs
Orange rust, smut, and red rot		AAS array	SNP markers		Diseases resistance	Limited phenomics research	Application of smut markers for GS underway
Flowering	Flowering	AAS array	SNP markers	RGB and multispectral imaging	Flowering time and flowering propensity	High	Breeding application not reported
	Canopy conductance and canopy temperature			IR temperature sensors and thermal camera	Crop water use and thermal and water stress tolerance	Little genomics research on this trait	A valuable trait for breeding sugarcane for water-limited environments
	Early-stage crop vigor			RGB and multispectral imaging	Early-stage clone selection in breeding	Little genomics research on this trait	Value of this trait for improving early-stage clone selection demonstrated

^a References for the traits listed in this table can be found in [5,8,10,11,13–15,18,19].

^b These are the most frequently tested sugarcane DNA marker systems, but other polymerase-chain-reaction-based and single-gene marker systems with high-throughput screening potential have been reported for sugarcane by different groups.

AAS array, Affimetrix Axiom SNP array; DArT, Diversity Array Technology; GBS, genotyping by sequencing; RGB, red, green and blue; LiDAR, light detection and ranging; NIR, near-infrared.