Genetic diversity of male specific region of Y chromosome in Tibetan antelope

doi:10.16829/j.slxb.150688

Abstract

Abstract:

Genetic diversity is an important indicator of population health, especially for assessing population recovery of endangered species. To characterize the genetic diversity of Tibetan antelope(Pantholops hodgsonii) populations, we used muscle and placental tissues from accidentally killed Tibetan antelopes in Qinghai and Xinjiang and screened 11 Tibetan antelope Y-SNP-specific loci from 30 published polymorphic Y-SNP loci in bovids, of which AMELY3 (g.723 C > T) and SRYOY1 (g.167 G > A) 2 pairs of primers were polymorphic. Based on the AMELY3 locus, the haplotype diversity of Tibetan antelope Y chromosome was 0.048 ± 0.045 and the nucleotide polymorphism was 0.00006 ± 0.00005. According to the SRYOY1 locus, Tibetan antelope was divided into two haplotypes, of which H1 (g.167 G) was the dominant haplotype. Maximum likelihood tree suggests that Tibetan antelope might have two paternal origins. The haplotype diversity of Tibetan antelope Y chromosome was 0.439 ± 0.050 and the nucleotide polymorphism was 0.0008 ± 0.0004. The genetic differentiation index showed that the F_ST value between the male population of Tibetan antelope in Qinghai and Xinjiang was 0.6846 ± 0.0389, suggesting a strong population genetic differentiation. Therefore, integrated conservation across regions and research on sex chromosomes need more attention in the future conservation of Tibetan antelope.

Key words: Tibetan antelope, Y chromosome, Single nucleotide polymorphism (SNP), Genetic diversity

关键词: 藏羚, Y染色体, 单核苷酸多态性, 遗传多样性

CLC Number:

Ruotong CHENG, Yibo CHEN, Xiangqiong MENG, Jiarui CHEN, Qing WEI. Genetic diversity of male specific region of Y chromosome in Tibetan antelope[J]. ACTA THERIOLOGICA SINICA, 2022, 42(5): 609-614.

成若通, 陈一博, 孟祥琼, 陈家瑞, 魏青. 藏羚Y染色体雄性特异区遗传多样性[J]. 兽类学报, 2022, 42(5): 609-614.

Figures/Tables 4

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引物 Primer	序列（5′ ‒ 3′） Sequence（5′ ‒ 3′）	退火温度 Annealing temperature （℃）	参考文献 Reference
SRY6	F： CTCACAAATTCATGGTACAGAG	54	Nijman et al.， 2008
SRY6	R： GATCTTGTTTATCCCATCCC	54	Nijman et al.， 2008
SRYOY1	F： TCAGTAGCTTAGGTACATTCA	56	Meadows et al.， 2004
SRYOY1	R： GTGCTACATAAATATGATCTGC	56	Meadows et al.， 2004
SRY4	F： GTCTGCTGCACCTTCATC	55	Nijman et al.， 2008
SRY4	R： CTTATTGTGGCCCAGGCTTGTC	55	Nijman et al.， 2008
AMELY4	F： TGGTTGGCTCTGGCGTAG	55	Li et al.， 2014
AMELY4	R： TCCTGCCCTCCAAACTCC	55	Li et al.， 2014
ZFY2	F： ATATGCTTGAAGAGACGACAAC	50	Nijman et al.， 2008
ZFY2	R： AGTCAGAAGACAAATGTCACA	50	Nijman et al.， 2008
AMELY3	F： ACTTACACCTCTGAAGTGGTAT	53.2	Meadows et al.， 2004
AMELY3	R： CCATCCACCAACGGGTTCATAG	53.2	Meadows et al.， 2004
DDX3Y7	F： TTGAAAGCTGTGAAGGTAGGG	55	Ginja et al.， 2009
DDX3Y7	R： GATACTGTTTACGGCGTCCA	55	Ginja et al.， 2009
DDX3Y	F： ACACTGGCACTTGAATGTTG	53.2	Meadows et al.， 2004
DDX3Y	R： CCTTGGCATGTTATAGTTTC	53.2	Meadows et al.， 2004
USP9Y	F： AAACCCTTCAAGGTAATAAAACAAAA	46.9	Bonfiglio et al.， 2012
USP9Y	R： CACAGCTCCTCAAAACCAGA	46.9	Bonfiglio et al.， 2012
UTY19	F： TGATGCCTATATTAGCCATTGACA	45.1	Gotherstrom et al.， 2005
UTY19	R： AAAATTCTTTATGATGTTCCATCC	45.1	Gotherstrom et al.， 2005
ZFY3	F：TTCTAATTTGAAGACGCATGTG	47.5	Nijman et al.， 2008
ZFY3	R：CAACTTCTTTATGGTGTCGTG	47.5	Nijman et al.， 2008

引物 Primer	序列（5′ ‒ 3′） Sequence（5′ ‒ 3′）	退火温度 Annealing temperature （℃）	参考文献 Reference
SRY6	F： CTCACAAATTCATGGTACAGAG	54	Nijman et al.， 2008
SRY6	R： GATCTTGTTTATCCCATCCC	54	Nijman et al.， 2008
SRYOY1	F： TCAGTAGCTTAGGTACATTCA	56	Meadows et al.， 2004
SRYOY1	R： GTGCTACATAAATATGATCTGC	56	Meadows et al.， 2004
SRY4	F： GTCTGCTGCACCTTCATC	55	Nijman et al.， 2008
SRY4	R： CTTATTGTGGCCCAGGCTTGTC	55	Nijman et al.， 2008
AMELY4	F： TGGTTGGCTCTGGCGTAG	55	Li et al.， 2014
AMELY4	R： TCCTGCCCTCCAAACTCC	55	Li et al.， 2014
ZFY2	F： ATATGCTTGAAGAGACGACAAC	50	Nijman et al.， 2008
ZFY2	R： AGTCAGAAGACAAATGTCACA	50	Nijman et al.， 2008
AMELY3	F： ACTTACACCTCTGAAGTGGTAT	53.2	Meadows et al.， 2004
AMELY3	R： CCATCCACCAACGGGTTCATAG	53.2	Meadows et al.， 2004
DDX3Y7	F： TTGAAAGCTGTGAAGGTAGGG	55	Ginja et al.， 2009
DDX3Y7	R： GATACTGTTTACGGCGTCCA	55	Ginja et al.， 2009
DDX3Y	F： ACACTGGCACTTGAATGTTG	53.2	Meadows et al.， 2004
DDX3Y	R： CCTTGGCATGTTATAGTTTC	53.2	Meadows et al.， 2004
USP9Y	F： AAACCCTTCAAGGTAATAAAACAAAA	46.9	Bonfiglio et al.， 2012
USP9Y	R： CACAGCTCCTCAAAACCAGA	46.9	Bonfiglio et al.， 2012
UTY19	F： TGATGCCTATATTAGCCATTGACA	45.1	Gotherstrom et al.， 2005
UTY19	R： AAAATTCTTTATGATGTTCCATCC	45.1	Gotherstrom et al.， 2005
ZFY3	F：TTCTAATTTGAAGACGCATGTG	47.5	Nijman et al.， 2008
ZFY3	R：CAACTTCTTTATGGTGTCGTG	47.5	Nijman et al.， 2008

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