Genome Wide Association Analysis of Litter Size in Pigs

doi:10.7668/hbnxb.20192808

Abstract

Abstract:

The objective of the study was to screen the candidate genes and SNP markers for the total number born(TNB)and number born alive(NBA)in pigs,so as to prepare for the next step of improving the reproduction traits,and breeding new high-proliferation of Canadian line of large white pigs. Illumina porcine 50K chip was used to do a genome-wide SNP scan on 186 Canadian line of large white sows in one pig farm,followed by quality control,beagle fill and SNP genotyping. Combined with the phenotypic traits and population structure analysis results of these experimental pigs,genome-wide association study(GWAS)was carried out. The results of population structure analysis showed that there was no population stratification in the pig samples used in the experiment. A total of 36 867 effective SNP markers were obtained on 18 pairs(36)of autosomes for GWAS analysis of experimental pigs. The results of GWAS showed that NBA in all parities of these Canadian large white pigs was significantly associated with two SNPs:seq-rs323899658 and seq-rs329781338,respectively. The SNP of seq-rs329781338 was annotated with three genes:SSBP1,WEE2 and KIAA1147,respectively. NBA was significantly associated with 7 SNPs,namely:seq-rs81238474,seq-rs321377412,seq-rs340736313,seq-rs80782154,seq-rs81244816,seq-rs81467772 and seq-rs329781338. Five out of seven SNPs had gene annotation,and a total of 22 genes were annotated:EphA1, TAS2R60, FAM131B, CLCN1, CASP2, TMEM139, TRBV21OR9-2, PRSS2, TRBV19, TRBV24-1, U6, SSBP1, WEE2, KIAA1147, NKX2-8, ALKBH3, HSD17B12, U6, HOMER2, WHAMM, FSD2 and SCARNA15. The results of GO function and KEGG pathway analysis showed that the most significant biological process of GO function of these genes was the regulation of multi biological process,the molecular function was non transmembrane/transmembrane protein tyrosine kinase activity,and the KEGG pathway was mismatch repair.Combined with GWAS and gene function annotation results,WEE2 and EphA1 genes could be used as key candidate genes to increase the TNB and NBA of Canadian large white pigs,and provide some reference for the precise cultivation of high-yield pigs in the future.

Key words: Pig, GWAS, Litter size, SNP, Chip

FU Yanfeng, ZHAO Weimin, LI Hui, LI Bixia, CHENG Jinhua, XU Xiaobo, REN Shouwen. Genome Wide Association Analysis of Litter Size in Pigs[J]. Acta Agriculturae Boreali-Sinica, 2022, 37(4): 232-238. doi: 10.7668/hbnxb.20192808.

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References 23

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胎次 Parity	窝数 Litter	总产仔数 TNB	产活仔数 NBA	健仔数 NH	断奶仔猪数 NW	出生窝质量/kg WB	出生个体均质量/kg AIWB
1	186	11.53±0.15c	10.04±0.20c	9.85±0.21c	9.60±0.22a	14.33±0.30bc	1.44±0.02a
2	186	12.35±0.15b	11.04±0.15ab	10.91±0.16ab	10.06±0.20a	15.81±0.26a	1.43±0.01a
3	186	12.92±0.18ab	11.50±0.18a	11.19±0.20a	9.68±0.24a	15.68±0.29a	1.37±0.01b
4	141	13.17±0.22ab	11.44±0.22a	11.18±0.22a	9.84±0.26a	15.49±0.33a	1.36±0.01b
5	116	12.91±0.23ab	10.91±0.23ab	10.63±0.24ab	9.50±0.27a	14.77±0.31ab	1.35±0.02b
6	77	13.30±0.30a	11.29±0.23ab	10.94±0.23ab	9.47±0.35a	15.37±0.37a	1.36±0.02b
7	51	12.67±0.40ab	10.65±0.42b	10.27±0.41bc	8.67±0.42b	13.61±0.57c	1.29±0.02c
8	17	12.94±0.70ab	-	-	-	-	-
合计Total	186	12.52±0.09ab	10.94±0.09ab	10.65±0.09ab	9.60±0.10a	14.94±0.13ab	1.37±0.01b

胎次 Parity	窝数 Litter	总产仔数 TNB	产活仔数 NBA	健仔数 NH	断奶仔猪数 NW	出生窝质量/kg WB	出生个体均质量/kg AIWB
1	186	11.53±0.15c	10.04±0.20c	9.85±0.21c	9.60±0.22a	14.33±0.30bc	1.44±0.02a
2	186	12.35±0.15b	11.04±0.15ab	10.91±0.16ab	10.06±0.20a	15.81±0.26a	1.43±0.01a
3	186	12.92±0.18ab	11.50±0.18a	11.19±0.20a	9.68±0.24a	15.68±0.29a	1.37±0.01b
4	141	13.17±0.22ab	11.44±0.22a	11.18±0.22a	9.84±0.26a	15.49±0.33a	1.36±0.01b
5	116	12.91±0.23ab	10.91±0.23ab	10.63±0.24ab	9.50±0.27a	14.77±0.31ab	1.35±0.02b
6	77	13.30±0.30a	11.29±0.23ab	10.94±0.23ab	9.47±0.35a	15.37±0.37a	1.36±0.02b
7	51	12.67±0.40ab	10.65±0.42b	10.27±0.41bc	8.67±0.42b	13.61±0.57c	1.29±0.02c
8	17	12.94±0.70ab	-	-	-	-	-
合计Total	186	12.52±0.09ab	10.94±0.09ab	10.65±0.09ab	9.60±0.10a	14.94±0.13ab	1.37±0.01b

SNP	位置/bp Position	候选基因 Candidate gene					距离/bp Distance	P值 P-value
SNP	位置/bp Position	基因ID Gene ID	所在染色体 Chr	起始物理位置/bp Start	终止物理位置/bp End	名称 Name	距离/bp Distance	P值 P-value
seq-rs329781338	8 435 604	ENSSSCG00000016488	18	8 450 516	8 460 500	SSBP1	14 912	2.94E-06
seq-rs329781338	8 435 604	ENSSSCG00000016489	18	8 463 648	8 488 381	WEE2	28 044	2.94E-06
seq-rs329781338	8 435 604	ENSSSCG00000016491	18	8 497 971	8 547 784	KIAA1147	62 367	2.94E-06

SNP	位置/bp Position	候选基因 Candidate gene					距离/bp Distance	P值 P-value
SNP	位置/bp Position	基因ID Gene ID	所在染色体 Chr	起始物理位置/bp Start	终止物理位置/bp End	名称 Name	距离/bp Distance	P值 P-value
seq-rs329781338	8 435 604	ENSSSCG00000016488	18	8 450 516	8 460 500	SSBP1	14 912	2.94E-06
seq-rs329781338	8 435 604	ENSSSCG00000016489	18	8 463 648	8 488 381	WEE2	28 044	2.94E-06
seq-rs329781338	8 435 604	ENSSSCG00000016491	18	8 497 971	8 547 784	KIAA1147	62 367	2.94E-06

SNP	位置/bp Position	候选基因Candidate gene					距离/bp Distance	P值 P-value
SNP	位置/bp Position	基因ID Gene ID	所在染色体 Chr	起始物理位置/bp Start	终止物理位置/bp End	名称 Name	距离/bp Distance	P值 P-value
seq-rs81244816	7 124 607	ENSSSCG00000016458	18	7 045 247	7 046 597	TAS2R60	78 010	2.15E-06
seq-rs81244816	7 124 607	ENSSSCG00000016459	18	7 081 288	7 098 452	EPHA1	26 155	2.15E-06
seq-rs81244816	7 124 607	ENSSSCG00000028274	18	7 134 211	7 145 293	FAM131B	9 604	2.15E-06
seq-rs81244816	7 124 607	ENSSSCG00000016462	18	7 145 222	7 181 268	CLCN1	20 615	2.15E-06
seq-rs81244816	7 124 607	ENSSSCG00000016464	18	7 187 327	7 206 997	CASP2	62 720	2.15E-06
seq-rs81244816	7 124 607	ENSSSCG00000016465	18	7 211 800	7 214 244	TMEM139	87 193	2.15E-06
seq-rs81467772	7 848 618	ENSSSCG00000016476	18	7 756 189	7 823 672	TRBV21OR9-2	24 946	3.11E-06
seq-rs81467772	7 848 618	ENSSSCG00000016478	18	7 761 371	7 764 639	PRSS2	83 979	3.11E-06
seq-rs81467772	7 848 618	ENSSSCG00000016479	18	7 776 934	7 777 450	TRBV19	71 168	3.11E-06
seq-rs81467772	7 848 618	ENSSSCG00000016477	18	7 811 001	7 811 502	TRBV24-1	37116	3.11E-06
seq-rs81467772	7 848 618	ENSSSCG00000018482	18	7 849 585	7 849 678	U6	967	3.11E-06
seq-rs329781338	8 435 604	ENSSSCG00000016488	18	8 450 516	8 460 500	SSBP1	14 912	4.69E-06
seq-rs329781338	8 435 604	ENSSSCG00000016489	18	8 463 648	8 488 381	WEE2	28 044	4.69E-06
seq-rs329781338	8 435 604	ENSSSCG00000016491	18	8 497 971	8 547 784	KIAA1147	62 367	4.69E-06
seq-rs80782154	68 369 751	ENSSSCG00000001944	7	68 332 624	68 334 022	NKX2-8	35 729	1.15E-05
seq-rs81238474	20 130 547	ENSSSCG00000025731	2	20 010 994	20 048 322	ALKBH3	82 225	1.33E-05
seq-rs81238474	20 130 547	ENSSSCG00000021739	2	20 061 566	20 211 950	HSD17B12	0	1.33E-05
seq-rs81238474	20 130 547	ENSSSCG00000028702	2	20 088 399	20 088 502	U6	42 045	1.33E-05
seq-rs340736313	57 657 259	ENSSSCG00000001804	7	57 489 036	57 582 494	HOMER2	74 765	2.01E-05
seq-rs340736313	57 657 259	ENSSSCG00000001805	7	57 596 454	57 627 963	WHAMM	29 296	2.01E-05
seq-rs340736313	57 657 259	ENSSSCG00000001806	7	57 653 600	57 679 877	FSD2	0	2.01E-05
seq-rs340736313	57 657 259	ENSSSCG00000020586	7	57 683 211	57 683 337	SCARNA15	25 952	2.01E-05

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