Table 3.

Associations between individual polymorphisms or LD groups and biomass yield and agronomic traits.

Gene	Position	Associated trait	R^2%	Identified by
PAL	947-1655LD,1	DTS	7.4%	GLM*, MLM**
4CL2	192, 217LD, 2	PHT	14.3%	GLM*, MLM*
COMT	2358	DTS	10.3%	GLM*
F5H	65	DTS	22.4%	GLM**
4CL1	454	DTS	20.2%	GLM*, MLM*
	810	DTS	6.0%	GLM*, MLM**
CCoAOMT2	75,144, 406LD,3	DMC	23.5%	GLM*, MLM*
	663	PHT	25.8%	GLM*
	663	DTS	18.5%	GLM*, MLM**
	663	DMC	10.5%	GLM*, MLM**

Positions of trait associated polymorphisms are presented according to public reference sequences.

^LD linkage group in a linkage block; ¹ the LD group contains 17 polymorphisms in complete LD in PAL and 947 and 1655 are the first and last polymorphisms; ² the LD group contains two polymorphisms which are in complete LD; ³ the LD group contains three polymorphisms with r² > 0.89. Associations identified by GLM were after controlling multiple testing, while those identified by MLM were not. Polymorphism positions are denoted by the position in our alignment; R²% is the proportion of phenotypic variance explained by the detected polymorphisms/LD group; * and ** mean P < 0.05 and P < 0.01, respectively.

4CL: 4-coumarate:CoA ligase, C3H: p-coumarate 3-hydroxylase, C4H: cinnamate 4-hydroxylase, CAD: cinnamyl alcohol dehydrogenase, CCoAOMT: caffeoyl-CoA O-methyltransferase, COMT: caffeic acid O-methyltransferase, F5H: ferulate 5-hydroxylase; PHT: plant height in cm; DTS: days from sowing to silking; DMC: % dry matter content of stover; DMY: dry matter yield of stover in tons per hectare