*3.4. GWAS of Mesocotyl Lengths*

As Bonferroni correction was extremely conservative, a compromised threshold of –log10(*P*) ≥ 6.0 was used as the threshold for significantly associated SNPs. The Manhattan plots for the markers significantly associated with mesocotyl length under different conditions were shown in Figure 4. A total of 16 unique loci were detected, which explained the phenotypic variations ranged from 6.3% to 15.9%. Totally, 12 loci for mesocotyl length were identified on chromosomes 1, 2, 3, 5, 6, 8, 9 and 12 in sand, and each explained phenotypic variation ranged from 6.6 to 15.7%. Besides, seven loci were detected on chromosomes 2, 3, 5, 6 and 9 under water culture, which explain phenotypic variations ranging from 7.8 to 15.5%. There were remarkable differences among three sowing depths under soil culture. As far as the 2 cm sowing depth, a total of seven notable loci were detected on chromosomes 1, 4, 5, 7, 9 and 12, each explaining 7.6 to 15.7% of the phenotypic variation. When coming to the sowing depth of 4 and 6 cm, only two (chromosomes 1 and 12) and three (chromosomes 2, 6 and 12) loci were detected respectively, with an explanation rate of 14.4–14.8% and 6.3–15.9%.

Among all the above QTLs, 12 on chromosomes 1, 2, 3, 5 and 9 were identified under two or more environments. The loci located on chromosomes 1 (14.1–17.3 Mb) and 12 (13.3–15.0 Mb) were identified in sand, soil (2 cm) and soil (6 cm); whereas the locus on chromosome 12 (4.4-4.5 Mb) was detected in sand, soil (4 cm) and soil (6 cm). Besides, five loci on chromosomes 2 (5.6–8.7 Mb), 3 (15.2–15.3 Mb), 5 (5.8–6.3 Mb), 6 (7.3–9.7 Mb) and 9 (1.3–2.8 Mb) were identified in water and sand; two loci identified on chromosomes 5 (10.6–12.0 Mb) and 9 (7.1–9.1 Mb) were detected in sand and soil (6 cm); the locus on chromosome 6 (15.3–16.6 Mb) was identified on sand and soil (4 cm); the locus on chromosomes 2 (11.7–15.4 Mb) was identified on water and soil (4 cm) (Table 2, Table S2, Figure 4).

**Figure 4.** Genome-wide association studies for mesocotyl length among three culture media. Manhattan plots and Quantile-quantile plots of mesocotyl lengths in sand culture (**a**), water (**b**) and soil culture with a sowing depths of 2 cm (**c**), 4 cm (**d**) and 6 cm (**e**), respectively. Negative log10-transformed *p* values from a genome-wide scan are plotted against position on each of 12 chromosomes. The red horizontal dashed lines indicate the genome-wide significance threshold. Blue stripes show important signals in different GWAS.


**Table 2.** Loci significantly associated with mesocotyl length under different environment.
