A significant quantitative trait locus on chromosome Z and its impact on egg production traits in seven maternal lines of meat-type chicken

Ding, Jiqiang; Ying, Fan; Li, Qinghe; Zhang, Gaomeng; Zhang, Jin; Liu, Ranran; Zheng, Maiqing; Wen, Jie; Zhao, Guiping

doi:10.1186/s40104-022-00744-w

Journal of Animal Science and Biotechnology

Table 4 Annotation of SNPs with significance associated with egg number traits in 627 of line W2 hens

From: A significant quantitative trait locus on chromosome Z and its impact on egg production traits in seven maternal lines of meat-type chicken

Traits^a	rs	GGA^b	Position^c	Allele	AF	β^d	P-value	Gene	Gap, kb^e
EN2	rs315536207	24	4,203,575	G/A	0.41	−0.84	4.84E-06	THY1	Instron
EN2	rs316053320	Z	10,263,677	A/G	0.11	−1.00	4.60E-06	ADAMTS12	Instron
EN2, EN3, TEN	rs318154184	Z	10,661,667	T/A	0.46	1.97	4.08E-06	PRLR	Instron
EN2, EN3, TEN	rs13769886	Z	10,672,563	G/C	0.46	1.97	4.08E-06	PRLR	Instron
EN2, EN3, TEN	rs313325646	Z	10,706,318	A/G	0.46	1.97	4.08E-06	PRLR	U 26.6 KB
EN2, TEN	rs317829338	Z	11,039,011	C/A	0.11	−1.07	3.92E-07	RANBP3L	Instron
EN2, TEN	rs317316870	Z	11,049,964	C/G	0.11	−1.07	3.92E-07	NADK2	U 25.3 KB
EN2, TEN	rs16130829	Z	11,138,239	G/A	0.11	−1.04	7.72E-07	SLC1A3	D 34.0 KB
EN2, TEN	rs313925951	Z	11,181,202	A/G	0.11	−1.04	7.72E-07	SLC1A3	Instron
EN2, TEN	rs315242894	Z	11,250,945	G/A	0.11	−1.04	7.72E-07	SLC1A3	U 16.7 KB
EN2, TEN	rs315141712	Z	11,295,727	G/A	0.11	−1.04	7.72E-07	SLC1A3	D 58.6 KB
EN2, TEN	rs313907922	Z	11,336,593	A/G	0.1	−0.97	3.87E-06	SLC1A3	D 98.5 KB
EN2, TEN	rs314230546	Z	11,360,621	T/A	0.12	−1.03	8.51E-07	CPLANE1	D 106.3 KB
EN2, TEN	rs316797236	Z	11,583,068	T/A	0.09	−1.06	1.39E-06	WDR70	Instron
EN2, TEN	rs318193135	Z	11,775,041	A/G	0.09	−1.12	3.46E-07	GDNF	U 30.6 KB
EN2, TEN	rs14786300	Z	11,823,333	A/G	0.09	−1.12	3.46E-07	GDNF	U 77.9 KB
EN2, TEN	rs14786270	Z	11,831,103	G/A	0.09	−1.12	3.46E-07	GDNF	U 85.5 KB
EN2, TEN	rs14786427	Z	11,995,193	A/G	0.09	−1.13	6.28E-07	EGFLM	D 2.7 KB
EN2, TEN	rs317925374	Z	12,003,955	T/A	0.1	−1.03	1.23E-06	LIFR	D 3.33 KB
EN2, TEN	rs16131724	Z	12,481,249	A/G	0.12	−1.07	2.36E-07	DAB2	U 117.9 KB
EN2, TEN	rs317751736	Z	12,614,891	A/G	0.12	−1.07	2.36E-07	OTGER4	D 219.8 KB
EN2	rs14756086	Z	12,901,024	G/A	0.16	−0.84	2.22E-06	PRKAA1	Instron
EN2, TEN	rs317744265	Z	12,965,710	A/G	0.11	−1.03	7.63E-07	C6	D 0.7 KB
EN2	rs14756790	Z	13,656,667	A/G	0.13	−0.93	1.40E-06	HMGCS1	Instron
EN2	rs316455929	Z	13,662,376	A/G	0.13	−0.93	1.40E-06	HMGCS1	Instron
EN2	rs313666070	Z	79,095,862	G/A	0.26	0.63	6.28E-06	FEM1C	D 22.0 KB
EN3	rs14485191	4	66,642,445	A/G	0.22	−3.06	3.29E-06	CORIN	Instron
EN3	rs318004733	4	66,681,294	G/A	0.22	−3	4.29E-06	CORIN	Instron
TEN, EN4	rs14319456	3	6,449,298	G/A	0.2	−0.92	2.11E-05	NRXN1	D 706.6 KB

^aEN2, EN3, EN4, and TEN represent egg numbers at four stages (from 196 to 227 d, from 228 to 307 d, from 308 to 354 d, and from onset of laying eggs to 354 d, respectively)
^bGallus gallus chromosome
^cGallus_gallus-6.0 source
^dAllele substitution effect was the additive effect estimated by GEMMA
^eU and D indicate that the SNP is upstream and downstream of a gene, respectively

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ISSN: 2049-1891

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