Dissection of the genetic mechanisms underlying congenital anal atresia in pigs

Kai Jiang^{1, 2},
Yuyun Xing^{3
, ,},
Pan Xu³,
Qiang Yang³,
Chuanmin Qiao³,
Weiwei Liu³,
Hao Chen³,
Yuyong He³,
Jun Ren^{3, 1
, ,},
Lusheng Huang³

1.
State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China
2.
School of Life Sciences, Jinggangshan University, JiAn, 343009, China
3.
State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, 330045, China

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Corresponding author: E-mail address: xingyuyun9@hotmail.com (Yuyun Xing); E-mail address: renjunjxau@hotmail.com (Jun Ren)

Current address: College of Animal Science, South China Agricultural University, 510642, Guangzhou, China.

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Current address: College of Animal Science, South China Agricultural University, 510642, Guangzhou, China.

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Fig. 1. Pedigree, genome-wide mapping of pathogenic loci, and identification of candidate causative mutation (rs325886172) for anal atresia in the Large White pig inbred population. A: An F₃ (backcross) subfamily derived from a cross between one F₁ boar (#1033) and one affected F₂ sow. Circles and boxes indicate normal sows and boars, respectively. Filled blue boxes and circles represent affected individuals, and the blue oblique line in boxes and circles represent heterozygous individuals. n, the number of pigs. B: Transmission disequilibrium test. The dotted line represents the genome-wide significant threshold. C: The results of haplotype sharing (identical-by-descent) mapping. Red represents pathogenic haplotype 1, yellow represents pathogenic haplotype 2, and the colorless represents other haplotypes. D: Distribution of accordant SNPs across the genome. The accordant SNPs are indicated by red dots, which are consistent with the deduced genotypes of individuals in the backcross subfamily.E: Location of rs325886172, a splice mutation in intron 1 of the GLI2 gene. F: Visualization of RNA sequence reads of GLI2 using the IGV software. Alternative transcripts of affected and unaffected individuals are indicated by a red box. Red and blue lines denote sequence reads of affected and unaffected individuals, respectively. G: Amplification of GLI2 alternative transcripts. M represents DL 500-bp marker. H: Schematic diagram of the GLI2 protein encoded by the normal and alternative transcripts. I–J: GLI2 and CAPN3 mRNA expression levels in the skin of the anus and rectum terminal. ∗, P < 0.05. AA represents affected individuals and WT indicates unaffected individuals. WT, wild-type; IGV, Integrative Genomics Viewer.

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Table 1. Genotypes of two candidate causative mutations in 188 unaffected individuals.

Mutation	Genotype	GLI2 rs325886172
Mutation	Genotype	GG	AG	AA
CAPN3 rs332273097	TT	28	16	7
	TA	13	50	26
	AA	15	29	4
CAPN3 rs1108103493	del/del	30	22	10
	del/T	17	47	26
	TT	10	26	0

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