Table II. Summary of significant loci identified by GWAS analysis using two approaches (CMLM and MLMM) for 33 traits across five categories (A–E) in control (C) and water-deficit (WD) conditions and for phenotypic plasticity (PP) of traits as a relative measure.

Values in parentheses are loci associated with more than one trait (Supplemental Table S6), and values in square brackets are percentages of loci out of total loci detected by both CMLM and MLMM approaches. The total a priori genes are predicted in the expected LD block of peak SNP/SNPs.

Trait Classification	C	WD	PP
(A) Shoot morphological traits	6	11	8
(B) Physiological traits	16	6	6
(C) Root morphological traits	34	52	33
(D) Root anatomical traits	14	17	15
(E) Dry matter traits	34	20	14
Total loci	104 (22)	106 (10)	76 (9)
Loci detected by the CMLM approach	39 [32%]	26 [24%]	19 [25%]
Loci detected by the MLMM approach	42 [40%]	45 [42%]	36 [47%]
Loci detected by both approaches	23 [22%]	35 [33%]	21 [27%]
Total predicted a priori genes	296	284	233
Genes responsive to abiotic stress stimulus	48	61	38