Genome-wide association mapping uncovers sex-associated copy number variation markers and female hemizygous regions on the W chromosome in Salix viminalis

Table 1 Characteristics and positions of Salix viminalis scaffolds that contain significantly sex-associated markers (Bonferroni-corrected p < 0.05, Fisher’s exact test)

S. viminalis scaffold^a	Scaffold length (bp)	Chr based on S. viminalis linkage mapping^b	Center position in S. viminalis linkage map, if on Chr15 (cM)^b	Chr in S. purpurea v5.1,^c	Number of sex-associated markers
0702	768,110	Chr15	69.0	Chr15W	10
0535	622,702	Chr15	57.2	Chr15W	9
1391	539,124	Chr15	70.4	Chr15W	5
1541	2553,872	Chr15	68.0	Chr15W	4
1658	116,437	NA	NA	NA	3
0302	814,410	Chr15	58.0	Chr15W	2
0724	541,616	NA	NA	Chr15W	2
1236	355,459	Chr15	67.6	Chr15W	2
0779	3,309,791	Chr05	NA	Chr15W	1
1114	392,477	NA	NA	Chr15W	1
1491	291,271	NA	NA	Chr16	1
1649	120,404	NA	NA	NA	1
1730	2,005,520	Chr14	NA	Chr14	1
1839	54,690	NA	NA	NA	1
2018	1,314,944	Chr11	NA	Chr11	1
2040	3,822,569	Chr02	NA	Chr02	1
2041	1,625,512	Chr17	NA	Chr17	1
2173	26,877	NA	NA	NA	1
2218	1,126,343	Chr14	NA	Chr14	1
1112^d	7,166,859	Chr09	NA	Chr09	0

^aAbbreviated names for scaffolds in the S. viminalis genome assembly are used in the table, e.g. ENA|CAADRP010000702|CAADRP010000702.1 will be called 0702 etc
^bMajority of map markers. Linkage mapping markers described in [40]
^cPosition of that chromosome/scaffold in the S. purpurea genome v5.1, majority. For each hit on chromosome 15W, there were always also slightly less significant hits found on chromosome 15Z
^dScaffold 1112 is included here since it contains a highly similar secondary blast hit for the tag sequence of the highest ranking SA markers