Comparative Study of the Zinc Finger Sequences of Prdm9 Gene in Three Black Sheep Populations in Liangshan Prefecture,Sichuan

doi:10.7668/hbnxb.20193737

Abstract

Abstract:

It aimed to explore the kinship between three black sheep populations in Sichuan by determining the sequence of the zinc finger domain of Prdm9.Anticoagulated whole blood was collected from the black sheep population,genomic DNA was extracted,and the zinc finger domain of the Prdm9 was specifically amplified by PCR,and further sequenced by cloning to analyze genetic diversity.The results showed that nine types of zinc fingers were identified in black sheep,with 1—5 amino acid differences between zinc fingers,constituting five Prdm9 zinc finger domains,defined as different alleles(A,B,C,D and E),of which A to D contained eight zinc fingers,which were the main types of Prdm9 zinc finger domains in the tested black sheep,and E contained nine zinc fingers and was only found in Yanyuan black sheep,with an allele frequency of 0.050.These alleles formed six genotypes,including AA,AC,BB,BD,CC and EE,and four genotypes were detected in both Butuo and Puge black sheep,while six were found in Yanyuan black sheep,and BB and EE were only observed in this population.The Prdm9 allele frequencies and PIC values varied among the three black sheep populations,with richer genetic polymorphisms,of which the Yanyuan black sheep were relatively the most abundant.The allele frequency distribution of the Prdm9 zinc finger domain in all three black sheep populations deviated significantly from Hardy-Weinberg equilibrium(P<0.01),suggesting that they were influenced by artificial selection in breeding.In conclusion,Prdm9 has rich genetic diversity in the black sheep population,and all three populations are closely related to each other.

Key words: Black sheep, Prdm9, Zinc finger, Clonal sequencing, Relationship

ZHANG Fenfen, HUANG Weiping, HUANG Lin, JIN Suyu, ZHENG Yucai. Comparative Study of the Zinc Finger Sequences of Prdm9 Gene in Three Black Sheep Populations in Liangshan Prefecture,Sichuan[J]. Acta Agriculturae Boreali-Sinica, 2023, 38(S1): 408-412. doi: 10.7668/hbnxb.20193737.

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Figures/Tables 7

Fig.1 Agarose gel electrophoresis of PCR amplification products of Prdm9 gene fragments in black sheep M.DNA Marker; 1—6.PCR products from 6 black sheep.

Fig.2 Nine Prdm9 zinc fingers detected in black sheep 1—9.Different Prdm9 zinc fingers,each containing 28 amino acids; five amino acid variant sites are at -9,-5,-1,+3,+6 of the zinc finger sequence,where ★ is a positive selection site.

Fig.3 Schematic structure of the Prdm9 zinc finger domain in black and common sheep ZF1—ZF9 are the zinc finger sequences in Prdm9 gene.A total of five zinc finger domain structures containing eight to nine zinc fingers are shown in the figure,among which ZFD is the common sheep Prdm9 zinc finger domain structure(GenBank No.KX109932.1)and ZFD1—ZFD5 are the Prdm9 zinc finger domain structures of this study black sheep,the sequence and number of each zinc finger are shown in Fig.2.

Tab.1 Allele frequencies of the Prdm9 gene in three black sheep populations

等位基因 Alleles	锌指数量 Number	布拖黑绵羊 Butuo black sheep (n=20)	普格黑绵羊 Puge black sheep (n=20)	盐源黑绵羊 Yanyuan black sheep(n=20)	平均值 Average (n=60)
A	8	0.375 0	0.300 0	0.275 0	0.317 0
B	8	0.050 0	0.075 0	0.250 0	0.125 0
C	8	0.525 0	0.550 0	0.375 0	0.483 0
D	8	0.050 0	0.075 0	0.050 0	0.058 0
E	9	0.000 0	0.000 0	0.050 0	0.017 0

Tab.2 Genotype frequencies of the Prdm9 gene in three black sheep populations

基因型 Genotype	布拖黑绵羊 Butuo black sheep (n=20)	普格黑绵羊 Puge black sheep (n=20)	盐源黑绵羊 Yanyuan black sheep(n=20)	平均值 Average (n=60)
AA	0.100 0	0.100 0	0.150 0	0.117 0
AC	0.550 0	0.400 0	0.250 0	0.400 0
BB	0.000 0	0.000 0	0.200 0	0.067 0
BD	0.100 0	0.150 0	0.100 0	0.117 0
CC	0.250 0	0.350 0	0.250 0	0.283 0
EE	0.000 0	0.000 0	0.050 0	0.016 0

Tab.3 Genetic variation of the Prdm9 gene in three black sheep populations

参数 Parameter	布拖黑绵羊 Butuo black sheep	普格黑绵羊 Puge black sheep	盐源黑绵羊 Yanyuan black sheep
等位基因数Number of alleles	4	4	5
基因型数Number of genotypes	4	4	6
有效等位基因数Effective number of alleles	2.374	2.477	3.524
观察杂合度Observed heterozygosity	0.650 0	0.550 0	0.350 0
期望杂合度Expected heterozygosity	0.579 0	0.596 0	0.716 0
多态信息含量Polymorphism information contents	0.497 0	0.533 0	0.665 0

Fig.4 N-J evolutionary trees of three black sheep populations

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