Analysis of GJB6 and PRKAA1 Genes Polymorphisms and Their Association with Lambing Number in Huai Goats

doi:10.7668/hbnxb.20193872

Abstract

Abstract:

To investigate the effects of GJB6 and PRKAA1 genes on the reproductive performance of Huai goats,122 Huai goats with different lambing number were selected as research objects.The primers were designed based on the reference sequences of GJB6 and PRKAA1 genes from the NCBI database.Single nucleotide polymorphisms (SNPs)were screened by PCR and sequencing methods.The genetic diversity,population genetic parameters and association analyses between different genotypes and lambing number were conducted.As a result,two SNPs (g.50694819 C>T and g.50694816 T>C) were detected in GJB6 gene,and both SNPs were synonymous mutations.Three SNPs(g.33691489 T>C,g.33693395 A>T and g.33693100 T>C)were detected in PRKAA1 gene,and they were all located in non-coding regions.The results of polymorphic information content indicated that g.50694819 C>T locus of GJB6 gene and g.33693100 T>C locus of PRKAA1 gene showed low degree of polymorphism,g.50694816 T>C locus of GJB6 gene,g.33691489 T>C and g.33693395 A>T loci of PRKAA1 gene showed moderate degree of polymorphism.The χ² test showed that the five loci were all in Hardy-Weinberg equilibrium.The results of the association analysis between different genotypes and lambing number for the two SNPs from GJB6 gene showed that the differences were not significant,indicating that these two SNPs were not suitable for multiple lambing traits selection in Huai goats.The lambing number produced by goats with the TC genotype at g.33691489 T>C of PRKAA1 gene was significantly higher than goats with the CC genotype,and the lambing number produced by individuals with the AT genotype at g.33693395 A>T was significantly higher than goats with the AA,TT genotypes(P<0.05).Linkage disequilibrium analysis revealed a strong linkage equilibrium between the g.33691489 T>C and g.33693395 A>T loci(D'>0.8,r²>0.33).Haplotype correlation analysis showed that the lambing number of goats with haplotype TCA was significantly higher than that with haplotypes CTA,CTT,and TTA(P<0.05).The results showed that Huai goats with the TC genotype at the g.33691489 T>C locus,the AT genotype at the g.33693395 A>T locus and TCA haplotype of PRKAA1 gene had higher lambing number,indicating that these two SNPs could be used as candidate molecular markers for lambing number selection in Huai goats.

Key words: Huai goats, PRKAA1 gene, GJB6 gene, SNP, Lambing number

HAN Haoyuan, LI Tao, LI Shikai, SONG Xiaoyu, LI Jun, HA Si, ZHAO Jinyan, WEI Hongfang, QUAN Kai. Analysis of GJB6 and PRKAA1 Genes Polymorphisms and Their Association with Lambing Number in Huai Goats[J]. Acta Agriculturae Boreali-Sinica, 2023, 38(4): 225-232. doi: 10.7668/hbnxb.20193872.

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References 23

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基因名称 Gene name	引物序列(5'—3') Sequence of primers(5'—3')	产物长度/bp Product length	退火温度/℃ Tm
GJB6	1F:GCGTGAACAAGCACTCCAC	321	57.6
	1R:CCAGGTCCTTGAACTCACTCC
	2F:GTGGCCTACTACAGGCACG	504	57.0
	2R:TTAACTGGGAAACCCGGTGAT
	3F:ATGAGCTGATTTCCGAGGGC	477	56.7
	3R:ACCCTAACAGCCAAGACAGC
PRKAA1	1F:ATGCGCAGACTCAGTTCCTG	618	60.0
	1R:TACCTCTGGGCCAGCATACA
	2F:TGCTGCACCAGAAGTAATTTCA	779	58.5
	2R:GATTCTTCCTCCGAACACGC
	3F:TGAATGGAAGGTTGTAAACCCG	645	59.5
	3R:TCAAGTGAGCCTGAGAGACCT
	4F:TGCGCAATGAATTATAGGTCTCT	719	55.0
	4R:ACCAGACATTCCTGCATACAGTT
	5F:CACAGAGTCCTCTCTCCTAATCA	644	56.0
	5R:TGGGCAGTTCCCATAATGCT
	6F:GTCACATTTGCTTTGGATTTTCATT	693	55.0
	6R:TCCCCACAACAGGTCAGAGA
	7F:TCCTAGTGTTAAGAACAGAAGACTG	626	55.0
	7R:CCCAGTCCCCCAACCTGATA

基因名称 Gene name	引物序列(5'—3') Sequence of primers(5'—3')	产物长度/bp Product length	退火温度/℃ Tm
GJB6	1F:GCGTGAACAAGCACTCCAC	321	57.6
	1R:CCAGGTCCTTGAACTCACTCC
	2F:GTGGCCTACTACAGGCACG	504	57.0
	2R:TTAACTGGGAAACCCGGTGAT
	3F:ATGAGCTGATTTCCGAGGGC	477	56.7
	3R:ACCCTAACAGCCAAGACAGC
PRKAA1	1F:ATGCGCAGACTCAGTTCCTG	618	60.0
	1R:TACCTCTGGGCCAGCATACA
	2F:TGCTGCACCAGAAGTAATTTCA	779	58.5
	2R:GATTCTTCCTCCGAACACGC
	3F:TGAATGGAAGGTTGTAAACCCG	645	59.5
	3R:TCAAGTGAGCCTGAGAGACCT
	4F:TGCGCAATGAATTATAGGTCTCT	719	55.0
	4R:ACCAGACATTCCTGCATACAGTT
	5F:CACAGAGTCCTCTCTCCTAATCA	644	56.0
	5R:TGGGCAGTTCCCATAATGCT
	6F:GTCACATTTGCTTTGGATTTTCATT	693	55.0
	6R:TCCCCACAACAGGTCAGAGA
	7F:TCCTAGTGTTAAGAACAGAAGACTG	626	55.0
	7R:CCCAGTCCCCCAACCTGATA

基因 Gene	多态位点 SNP	基因型(频率) Genotype (frequency)			等位基因(频率) Allele (frequency)
GJB6	g.50694819 C>T	CC(0.844 3)	CT(0.131 1)	TT(0.024 6)	C(0.909 8)	T(0.090 2)
	g.50694816 T>C	TT(0.590 2)	TC(0.344 3)	CC(0.065 6)	T(0.762 3)	C(0.237 7)
PRKAA1	g.33691489 T>C	TT(0.204 9)	TC(0.475 4)	CC(0.319 7)	T(0.442 6)	C(0.557 4)
	g.33693100 T>C	TT(0.844 3)	TC(0.131 1)	CC(0.024 6)	T(0.909 8)	C(0.090 2)
	g.33693395 A>T	AA(0.278 7)	AT(0.516 4)	TT(0.204 9)	A(0.536 9)	T(0.463 1)

基因 Gene	多态位点 SNP	基因型(频率) Genotype (frequency)			等位基因(频率) Allele (frequency)
GJB6	g.50694819 C>T	CC(0.844 3)	CT(0.131 1)	TT(0.024 6)	C(0.909 8)	T(0.090 2)
	g.50694816 T>C	TT(0.590 2)	TC(0.344 3)	CC(0.065 6)	T(0.762 3)	C(0.237 7)
PRKAA1	g.33691489 T>C	TT(0.204 9)	TC(0.475 4)	CC(0.319 7)	T(0.442 6)	C(0.557 4)
	g.33693100 T>C	TT(0.844 3)	TC(0.131 1)	CC(0.024 6)	T(0.909 8)	C(0.090 2)
	g.33693395 A>T	AA(0.278 7)	AT(0.516 4)	TT(0.204 9)	A(0.536 9)	T(0.463 1)

多态位点 SNP	卡方检验 χ²	多态信息含量 PIC	杂合度 He	有效等位基因数 Ne
g.50694819 C>T	4.912 0	0.150 6	0.164 1	1.196 3
g.50694816 T>C	0.305 7	0.296 7	0.362 4	1.568 4
g.33691489 T>C	0.162 5	0.371 7	0.493 4	1.974 0
g.33693100 T>C	4.912 0	0.150 6	0.164 1	1.196 3
g.33693395 A>T	0.180 3	0.373 6	0.497 3	1.989 1

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