Detection and Analysis of RXFP2 Gene SNPs Related to Horn Trait of Oula Sheep

doi:10.7668/hbnxb.20194458

Abstract

Abstract:

The aim of this study was to analyze the regulatory effect of RXFP2 gene on horned phenotype and related SNP markers in horned and hornless Oula sheep populations,in order to provide technical support for genetic improvement and breed breeding of Oula sheep.DNA was extracted from 100 ewe blood samples of healthy adult Oula sheep in Henan County,Qinghai Province,including 50 blood samples with horns and 50 blood samples without horns,respectively,15 samples with and without horns were randomly selected for whole genome sequencing,and then all blood samples were amplified by multiple PCR to verify the SNPs of RXFP2 gene.Genome-wide detection results showed that there were strong selection signals in chromosome 10 of Oula sheep,including RXFP2 gene,and the strongest selection signals appeared in the RXFP2 gene segment.Multiple PCR tests verified the accuracy of the 4 coding SNPs screened by whole genome resequencing.Seven high frequency SNPs in the intron region of RXFP2 gene were detected in Oula sheep(29508704G>A,29509428A>C,29509766G>A,29512170G>A,2951276G>A,29514968T>A,29521377C>A).The genotypes of the 7 SNP loci were separated in hornless phenotypes.100% of homozygous genotypes appeared horned or hornless trait,89.66% of heterozygous genotypes were hornless trait and 10.34% were horned trait.The frequency of mutant alleles was less than that of wild alleles,and the population showed an unbalanced state of Hardy-Weinberg,which meant subject to high artificial selection intensity,but the content of polymorphic information was moderate,and the potential of breeding and improvement was still large.In conclusion,the present study confirmed the strong regulatory effect of RXFP2 gene on horn trait in Oula sheep,and filtered out 7 molecular markers of RXFP2 gene on horn trait in Oula sheep population.The relevant results can be used as molecular markers for genetic improvement of the hornless population of Oula sheep.

Key words: Oula sheep, RXFP2 gene, SNPs polymorphic site, Horn trait, Molecular marker

ZHANG Qianglong, WU Sen, DUOJIE Cairang, TANG Yanhua, MA Jie. Detection and Analysis of RXFP2 Gene SNPs Related to Horn Trait of Oula Sheep[J]. Acta Agriculturae Boreali-Sinica, 2024, 39(2): 200-208. doi: 10.7668/hbnxb.20194458.

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References 26

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位点 Location	引物序列(5'—3') Primer sequences(5'—3')	长度/bp Length	退火温度/℃ Tm
Exon1	F:GGGACTGCAGCTAGTTCACTTT	751	60.3
	R:GGCACTTCTATCCATGGCTCTAT
Exon2	F:CATGCACAAGTAGGACAATCACT	743	64.5
	R:CAGAAGGAAGTGGTCATCGTTTA
Exon3	F:GCTTTTCCTTCCTTACCATTGTC	597	58.0
	R:TCTAGTGGAGCCATGTGAGGTAT
Exon4	F:GCCTTTCTGTGCCATTCAATTA	697	64.5
	R:AACCTGGACAATCCAACATACAG
Exon5	F:AAATCACCGTAGATGTTCCAGTC	667	60.3
	R:ACCACTCTTCCAGGTTAAAAAGC
Exon6	F:ACTTTGGTGGGTTCAAGTCAGAG	659	58.0
	R:TTGCAGCAGGATTCTTTACTACTG
Exon7	F:CCCCAGTGCATTATTTCTGG	738	64.5
	R:TGGGGTAGAGACCACAAAGG
Exon8	F:GAGCCCATAATCAGCCAATAAA	842	58.0
	R:CTAGAATTTTCAGTGACTCTTGCTG
Exon9	F:GGCTGTATGATGCTGGTAATGA	811	64.5
	R:GATAAGAATCCTCCAGCCAATG
Exon10	F:CCATGTCTAAGTGTCAGGCAGA	871	64.5
	R:GCAGCAACACTAACCACTTTCA
Exon11	F:CTTTGCTCTTTCTGGCCTTCT	804	60.1
	R:CATTCAGCAAACTTCAACTGAG
Exon12-13	F:CCTAAAACAGAGGAAACGAATG	835	60.1
	R:TTGTGAGAACCGTAAGATGAGA
Exon14	F:TCAAGCTACAGAGCCAATTTCA	765	62.0
	R:CATCTTTCTTCCTAAGGGCTCA
Exon15	F:TATAACACCCCCAGAGAACCAC	825	65.8
	R:TAATTTTCTGGGCTTGAGGAAC
Exon16	F:TGTGGGTGTTTTCATTAGTTCG	851	64.5
	R:AACTTGGAAGGGTCACAGGAC
Exon17	F:TATCTTTTTGATCTGGCGAACC	842	65.4
	R:ACATGGGTTTGATTTCTGGTCT
Exon18	F:TGACTCCAAACCAGAAGATTCC	962	64.5
	R:TGCTGCAGAGATAGAGATCCAC

位点 Location	引物序列(5'—3') Primer sequences(5'—3')	长度/bp Length	退火温度/℃ Tm
Exon1	F:GGGACTGCAGCTAGTTCACTTT	751	60.3
	R:GGCACTTCTATCCATGGCTCTAT
Exon2	F:CATGCACAAGTAGGACAATCACT	743	64.5
	R:CAGAAGGAAGTGGTCATCGTTTA
Exon3	F:GCTTTTCCTTCCTTACCATTGTC	597	58.0
	R:TCTAGTGGAGCCATGTGAGGTAT
Exon4	F:GCCTTTCTGTGCCATTCAATTA	697	64.5
	R:AACCTGGACAATCCAACATACAG
Exon5	F:AAATCACCGTAGATGTTCCAGTC	667	60.3
	R:ACCACTCTTCCAGGTTAAAAAGC
Exon6	F:ACTTTGGTGGGTTCAAGTCAGAG	659	58.0
	R:TTGCAGCAGGATTCTTTACTACTG
Exon7	F:CCCCAGTGCATTATTTCTGG	738	64.5
	R:TGGGGTAGAGACCACAAAGG
Exon8	F:GAGCCCATAATCAGCCAATAAA	842	58.0
	R:CTAGAATTTTCAGTGACTCTTGCTG
Exon9	F:GGCTGTATGATGCTGGTAATGA	811	64.5
	R:GATAAGAATCCTCCAGCCAATG
Exon10	F:CCATGTCTAAGTGTCAGGCAGA	871	64.5
	R:GCAGCAACACTAACCACTTTCA
Exon11	F:CTTTGCTCTTTCTGGCCTTCT	804	60.1
	R:CATTCAGCAAACTTCAACTGAG
Exon12-13	F:CCTAAAACAGAGGAAACGAATG	835	60.1
	R:TTGTGAGAACCGTAAGATGAGA
Exon14	F:TCAAGCTACAGAGCCAATTTCA	765	62.0
	R:CATCTTTCTTCCTAAGGGCTCA
Exon15	F:TATAACACCCCCAGAGAACCAC	825	65.8
	R:TAATTTTCTGGGCTTGAGGAAC
Exon16	F:TGTGGGTGTTTTCATTAGTTCG	851	64.5
	R:AACTTGGAAGGGTCACAGGAC
Exon17	F:TATCTTTTTGATCTGGCGAACC	842	65.4
	R:ACATGGGTTTGATTTCTGGTCT
Exon18	F:TGACTCCAAACCAGAAGATTCC	962	64.5
	R:TGCTGCAGAGATAGAGATCCAC

群体 Group	染色体 Chromosome	起始位点 Start site	SNP数量 SNP number	Tajima's D检验 Tajima's D test
无角型欧拉羊	NC_019477.2	50280000	160	3.960 54
The hornless Oula sheep	NC_019484.2	66800000	226	3.957 48
	NC_019463.2	90200000	111	3.932 68
	NC_019467.2	42100000	110	3.929 81
	NC_019460.2	130080000	194	3.920 43
	NC_019484.2	66940000	111	3.905 65
	NC_019484.2	66960000	103	3.903 45
	NC_019484.2	67060000	62	3.896 94
	NC_019471.2	14220000	126	3.887 90
	NC_019474.2	58000000	242	3.874 20
有角型欧拉羊	NC_019467.2	32440000	142	3.952 12
The horn Oula sheep	NC_019458.2	109560000	152	3.934 47
	NC_019484.2	76280000	98	3.928 91
	NC_019484.2	84160000	167	3.920 42
	NC_019467.2	41860000	82	3.919 64
	NC_019458.2	199560000	187	3.905 77
	NC_019467.2	41840000	97	3.896 65
	NC_019458.2	109580000	183	3.894 97
	NC_019467.2	41700000	171	3.887 07

群体 Group	染色体 Chromosome	起始位点 Start site	SNP数量 SNP number	Tajima's D检验 Tajima's D test
无角型欧拉羊	NC_019477.2	50280000	160	3.960 54
The hornless Oula sheep	NC_019484.2	66800000	226	3.957 48
	NC_019463.2	90200000	111	3.932 68
	NC_019467.2	42100000	110	3.929 81
	NC_019460.2	130080000	194	3.920 43
	NC_019484.2	66940000	111	3.905 65
	NC_019484.2	66960000	103	3.903 45
	NC_019484.2	67060000	62	3.896 94
	NC_019471.2	14220000	126	3.887 90
	NC_019474.2	58000000	242	3.874 20
有角型欧拉羊	NC_019467.2	32440000	142	3.952 12
The horn Oula sheep	NC_019458.2	109560000	152	3.934 47
	NC_019484.2	76280000	98	3.928 91
	NC_019484.2	84160000	167	3.920 42
	NC_019467.2	41860000	82	3.919 64
	NC_019458.2	199560000	187	3.905 77
	NC_019467.2	41840000	97	3.896 65
	NC_019458.2	109580000	183	3.894 97
	NC_019467.2	41700000	171	3.887 07

群体 Group	染色体 Chromosome	起始位点 Start site	终止位点 End site	SNP数量 SNP number	π值 π value
无角型欧拉羊	NC_019464.2	22640001	22680000	1 281	0.002 218 53
The hornless Oula sheep	NC_019475.2	57520001	57560000	1 006	0.002 367 82
	NC_019464.2	22620001	22660000	972	0.002 187 53
	NC_019464.2	22660001	22700000	989	0.001 798 51
	NC_019460.2	205440001	205480000	927	0.001 593 17
	NC_019460.2	206780001	206820000	900	0.001 169 72
	NC_019458.2	96920001	96960000	836	0.001 220 93
	NC_019470.2	36880001	36920000	749	0.001 442 71
	NC_019464.2	22560001	22600000	867	0.001 033 39
	NC_019460.2	205420001	205460000	837	0.001 196 61
有角型欧拉羊	NC_019464.2	22640001	22680000	1 286	0.011 804 10
The horn Oula sheep	NC_019475.2	57520001	57560000	1 003	0.009 558 05
	NC_019464.2	22660001	22700000	1 000	0.008 712 36
	NC_019464.2	22620001	22660000	966	0.008 669 54
	NC_019460.2	205440001	205480000	929	0.008 469 74
	NC_019458.2	96920001	96960000	828	0.007 802 66
	NC_019460.2	205420001	205460000	835	0.007 780 87
	NC_019460.2	206780001	206820000	896	0.007 728 59
	NC_019472.2	45640001	45680000	898	0.007 637 26
	NC_019470.2	36880001	36920000	726	0.007 569 19

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