Table 4 Information on the 14 candidate SVs used for the XX DSD pig cohort validation

Inversion

TBP

1:1-5433

5,433 bp

This gene is associated with spermatogenesis [80].

Deletion

PITX1*

2:137200501–137,209,200

8,700 bp

PITX1 regulates the synthesis of reproductive hormones and the expression of related genes, including LHβ, FSHβ, and GNRHR [81, 82].

Deletion

PDGFA/PRKAR1B/DNAAF5*

3:231801–479,100

247,300 bp

PDGFA is associated with Leydig cell development and testosterone synthesis [83].

Duplication

SRD5A2

3:107856801–107,907,700

50,900 bp

Variants in this gene cause 46, XY DSD [3].

Duplication

SHC1*

4:94822101–94,826,100

4,000 bp

SHC1 is involved in oocyte maturation [50].

Duplication

RORC

4:97372801–97,377,100

4,300 bp

Key regulators involved in steroid metabolism [84].

Duplication

WNT2B

4:107914901–107,923,000

8,100 bp

This gene functions in the Wnt/β-catenin signalling pathway and regulates the proliferation of ovarian granulosa cells [85,86].

Inversion

SYCE3

5:185339–186,259

921 bp

Syce3 regulate testosterone and dihydrotestosterone synthesis via steroidogenic pathways in Sertoli and Leydig cells [87].

Deletion

WWOX*

6:9669113–9,669,182

70 bp

WWOX plays a role in sex hormone synthesis and gonadal development; associated with human and dog DSD [2, 66,68].

Deletion

CCDC85C

120,582,001–120,616,000

34,000 bp

This gene is involved in the beta-collagen signalling pathway [88].

Inversion

NXPH1

9:79527380–79,534,749

7,370 bp

This gene is associated with ovarian development [89].

Deletion

EGFR

9:139446401–139,499,300

52,900 bp

This gene is located in the EGFR Signaling Pathway and is associated with testicular development [90, 91].

Duplication

SOX9*

12:8562001–8,572,600

10,600 bp

SOX9 plays an important role in male sex determination and differentiation; variants in this gene cause DSD in mammals [3, 20].

Deletion

WNT6*

15:120911501–120,914,400

2,900 bp

WNT6 activates the WNT/β-catenin signalling pathway [92]; involved in spermatogenesis [54].