Paternal genetic diversity, differentiation and phylogeny of three white yak breeds/populations in China

doi:10.21203/rs.3.rs-1846119/v2

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Paternal genetic diversity, differentiation and phylogeny of three white yak breeds/populations in China

https://doi.org/10.21203/rs.3.rs-1846119/v2

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The white yak, a unique and valuable farm animal of the Qinghai-Tibetian Plateau, is mainly distributed in Tianzhu (County of Gansu Province), Menyuan, Huzhu and Ledu (three Counties of Qinghai Province) in China. In the present study, the Y-chromosomal based genetic diversity, differentiation and phylogeny of three Chinese white yak breeds/populations (Tianzhu, Huzhu and Menyuan) were comprehensively explored using five Y-SNPs (SRY4, USP9Y, UTY19, AMELY3 and OFD1Y10) and one Y-STR (INRA189) markers. The results of this study showed that six Y-haplotypes (H1Y1, H9Y1, H10Y1, H11Y2, H12Y2 and H13Y2) were identified in 97 male yaks from three white yak breeds/populations. Among haplotypes, H1Y1, H10Y1 and H11Y2 were shared haplotypes for all of breeds/populations and H12Y2 was shared by Tianzhu and Huzhu populations. However, H9Y1 and H13Y2 haplotypes were only detected in Menyuan and Tianzhu white yak populations, respectively. The Y-haplotype diversity was maximum in Huzhu white yak (0.7500±0.0349), the medium in Tianzhu white yak (0.6881±0.0614) and lowest in Menyuan white yak (0.5720±0.0657), respectively. The total Y-haplotype diversity of three white yak breeds/populations was 0.7567±0.0233, indicating rich paternal genetic diversity in white yak. The F_ST values showed a moderate differentiation between Tianzhu and Menyuan (F_ST =0.0763, P<0.05) populations, weak differentiation between Huzhu and Tianzhu white yak breeds/populations (F_ST =0.0186, P>0.05) and Huzhu and Menyuan (F_ST =-0.005, P>0.05) populations. The clustering analysis showed a close genetic relationship between Huzhu and Menyuan white yaks and far from Tianzhu white yak breed. The phylogenetic analyses showed that white yak had two Y-haplogroups/lineages (Y1 and Y2) with two potential paternal origins. The data of present study could contribute to the conservation and utilization of special white yak genetic resources.

White yak

Y chromosome markers

genetic diversity

differentiation

phylogeny

The white yak (Bos grunniens) is a unique bovine specie that inhabits in the Qinghai-Tibetan plateau (QTP) and adjacent mountains or subalpine mountainous of China. It is known for its better adaptability in the harsh environmental conditions such as high altitude, severe cold, strong ultraviolet radiations, scarce forage and deprived oxygen level¹. The white yak, is a rare ecological type in domestic yak, produces two types of white fiber (coarse outer hair and a fine down fiber) with relatively high economic value ². Since 1970s, the down fiber has been used extensively by the textile industry as an alternative to other fine animal fibers in China¹. Currently, the white yak is mainly distributed on both sides of the Qilian Mountains in QTP, including Tianzhu County in Gansu Province, and Huzhu, Menyuan Counties in Qinghai Province of China³.

The mammalian Y chromosome is considered as symbol of maleness with the characteristics of paternal inheritance, lower mutation rate and less susceptible to recombination and reverse mutation^4–5. It has been used to explore the paternal genetic diversity, origin and population genetic structure of domestic animals. In recent years, two kinds of molecular markers including Y chromosome microsatellites (Y-STRs) and single nucleotide polymorphisms (Y-SNPs) had been used to study the yak paternal population genetics which showed that Chinese yak breeds/populations own rich paternal genetic diversity with two different lineages^6–10. In our recent maternal genetic study, we found that each of three Chinese white yak breeds/populations (Menyuan, Huzhu and Tianzhu) owned special maternal genetic information with relatively rich genetic diversity¹¹. However, to date, there is no comprehensive paternal genetic analysis about these three Chinese white yak breeds/populations. In this context, the present study explored the Y chromosomal based genetic diversity, differentiation and phylogeny of three Chinese white yak breeds/populations. The tools of Y-SNP and Y-STR markers was used to clarify the status of white yak genetic resources and to provide theoretical basis for the protection and utilization of white yak populations for future breeding planes and policies.

Ethical approval

This study was conducted with the guidelines of the Council of China and animal welfare requirements. Based on the recommendations of the Regulations for the Administration of Affairs Concerning Experimental Animals of China, the Institutional Animal Care and Use Committee of Qinghai Academy of Animal Science and Veterinary Medicine approved all animal experiments. Specific consent procedures were not required for this study following the recommendation of the Regulations for the Administration of Affairs Concerning Experimental Animals of China.

Sample collection and genomic DNA extraction

The blood samples from 34, 32 and 31 male white yaks were randomly collected by jugular venipuncture from Tianzhu County of Gansu Province, Huzhu and Menyuan Counties of Qinghai Province in China, respectively (Table 1, Figure 1). The genomic DNA was extracted using blood DNA extraction kit (Aidlab Biotechnologies Co., Ltd, China) and stored at -20 ℃ for future use.

PCR amplification, sequencing and data analysis

By referring the reported information on five Y-SNP markers (SRY4, USP9Y, UTY19, AMELY3 and OFD1Y10) and one Y-STR marker (INRA189)^9,12, the six pairs of primers were synthesized and were used to amplified these regions as previously stated. The purified PCR products were sequenced and typed commercially (Shanghai Sangon Biotech Co., Ltd,) respectively. The CHROMAS 2.3 was used for sequencing output, while, BIOEDIT 7.2.5 was used for multiple sequence alignment^13-14. Meanwhile, the typing results of Y-STR (INRA189 marker) were analyzed with GENEMARKER 1.91 to determine its allele size¹⁵. The Y chromosome haplotypes/haplogroups of each male white yak were determined by combined analysis of two kinds of molecular markers. The number of Y chromosome haplotype of white yak was determined by DNASP 5.10.01 and ARLEQUIN 3.11 software^16-17. The Y chromosome haplotype diversity (Hd) evaluated the paternal genetic diversity of three white yak breeds/populations. The pairwise fixation index (F_ST) value was calculated using ARLEQUIN 3.11 software to evaluate differentiation degree amongst the breeds/populations. The UPGMA (unweighted pair-group method with arithmetic means, UPGMA) tree was constructed using MEGA 7.0 based on F_ST to reveal genetic relationship among white yak breeds/populations¹⁸. Based on nucleotide variations between different haplotypes, the median-joining (MJ) network was drawn using NETWORK 10.1 to reveal the phylogenetic relationship among haplotypes/haplogroups¹⁹.

Identification of Y-haplotype/haplogroup in white yak

The fragment lengths of the five Y-SNPs markers (SRY4, USP9Y, UTY19, AMELY3 and OFD1Y10) were 969 bp, 470 bp, 290 bp, 971 bp and 763 bp, respectively. The sequencing results of each Y-SNPs marker were analyzed by multiple sequence alignment and 10 previously reported Y-SNPs were also detected¹⁰.In the typing analysis of Y-STR (INRA189) marker, three alleles of 155bp, 157bp and 161bp were detected. However, the allele of 161bp was only detected in Tianzhu white yak, while, others were found in all three populations (Table S1).

The haplotypes/haplogroups were jointly identified based on the alleles of Y-SNPs and Y-STR. According to previous judgment criterion for yak Y-haplotype (Y-chromosome-specific haplotype, Y-haplotype), a total of six haplotypes were determined in white yak, namely H1Y1, H9Y1, H10Y1, H11Y2, H12Y2 and H13Y2, respectively (Table 1, Table S1). The six haplotypes could be further divided into two haplogroups (Y1 and Y2): Y1 haplogroup included three haplotypes (H1Y1, H9Y1 and H10Y1), whereas, Y2 haplogroup contain H11Y2, H12Y2 and H13Y2 haplotypes.

Y-chromosome haplotype diversity of white yak

The frequencies of six haplotypes were different among three white yak breeds /populations (Figure 1, Table 1). In total the H11Y2 haplotype was predominant (37.1%) and H13Y2 (1.0%) was scarce in white yak. Three haplotypes (H1Y1, H10Y1 and H11Y2) were common and shared amongst three white yak breeds/populations; however, H12Y2 was just shared by Tianzhu and Huzhu white yak populations. The H9Y1 and H13Y2 haplotype were exclusively found in Menyuan and Tianzhu white yaks, respectively. These results showed that Menyuan and Tianzhu white yak breeds/populations possessed unique paternal genetic information. In our previous study, 5, 3 and 43 specific maternal haplotypes were detected in Menyuan, Huzhu and Tianzhu white yak breeds/populations, respectively¹¹. Based on the studies of maternal and paternal genetic markers, it can be concluded that Menyuan and Tianzhu white yak populations possess specific genetic information; therefore, the conservation and application should be independent for this genetic unit in the future.

In this study, the total haplotype diversity (H_d) of three white yak populations was 0.7567±0.0233. The current study showed that white yak had higher haplotype diversity than previously reported 15 other Chinese domestic yak breeds/populations (0.6964±0.0143) and lower than the wild yak population (0.8214±0.1007) comparing to the previous report¹⁰. This total haplotype diversity revealed that white yak also owned rich paternal genetic diversity. The haplotype diversities of Huzhu, Tianzhu and Menyuan white yak breeds/populations were 0.7500±0.0349, 0.6881±0.0614 and 0.5720±0.0657, respectively (Table 1). Surprisingly, the haplotype diversity of Huzhu white yak was higher than that of the all other Chinese domestic yak breeds/populations (0.1174-0.7273) but only lower than that of the wild yak population (0.8214±0.1007). At the same time, the haplotype diversities of Menyuan and Tianzhu white yak population were also higher than the most Chinese domestic yak breeds/populations (0.1174-0.7273). The present results indicated a rich paternal genetic diversity in all three Chinese white yak breeds/populations; however, Huzhu white yak showed the highest level of paternal genetic diversity.

Differentiation and clustering relationship among white yak populations

The genetic differentiation index (F_ST) was used to evaluate the differentiation degree among white yak breeds/populations. The F_ST values ranged from -0.0050-0.0763, whereas, R_ST values (linearized F_ST values) ranged from 0-0.0826 (Table S2) indicating the variable differentiation degree amongst the three white yak breeds/populations. Refer to Wright's standard²⁰, the F_ST values indicated moderate differentiation between Tianzhu and Menyuan white yak breeds/populations (0.0763, P<0.05), however, the Huzhu white yak population displayed a weaker genetic differentiation with Tianzhu white yak (0.0186, P>0.05) and Menyuan white yak (-0.0050, P>0.05) (Table S2).

Phylogenetic and network analysis of white yak

The UPGMA phylogenetic tree (Figure S1) was constructed using R_ST values between populations for cluster analysis. The result showed that Huzhu and Menyuan white yak populations clustered together firstly and then clustered with Tianzhu white yak. The results of genetic relationship revealed that there is a close relationship between Huzhu and Menyuan white yaks and far genetic relationship with Tianzhu white yak.

The network analysis showed that six Y chromosome haplotypes is dividable into two haplogroups/lineages (Y1 and Y2) that suggesting two paternal origins of the white yak. The current observation is consistent with the previous research findings on wild and other domestic yak breeds¹⁰. In the present study, Y1 and Y2 lineages have 3 haplotypes in each lineage, respectively (Figure 2). The Y1 lineage observed in 48.45% (47/97) individuals and Y2 lineage in 51.55% (50/97) individuals (Table 1) which indicate that Y2 is a dominant lineage in white yaks. Meanwhile, the proportion of Y1 in Menyuan, Huzhu and Tianzhu white yaks was 41.94%, 43.75% and 58.82%, respectively; however, the proportion of Y2 in Menyuan, Huzhu and Tianzhu white yaks was observed to be 58.06%, 56.25% and 41.18%, respectively (Table 1). The observed data indicate the dominancy of Y1 haplogroups in Tianzhu white yak and Y2 lineage in the Menyuan and Huzhu white yak populations. Previous studies represented that Y1 lineage as a dominant haplogroup in most of domestic and wild yaks except for the Pali yak breed¹⁰. The present findings showed that the population structure composition of Menyuan and Huzhu white yaks is different from most of other Chinese domestic yak breeds but similar to Pali yak breed.

Table 1

Frequencies and diversities of haplotypes in three Chinese white yak breeds/populations.

Breeds/Populations	No.	Haplotype/haplogroups						Nh	Hd±SD
		Y1			Y2
		H1Y1	H9Y1	H10Y1	H11Y2	H12Y2	H13Y2
Tianzhu	34	0.500（17）		0.088 （3）	0.177（6）	0.206（7）	0.029（1）	5	0.6881±0.0614
Huzhu	32	0.250 (8)		0.188 (6)	0.375(12)	0.188(6)		4	0.7500±0.0349
Menyuan	31	0.032 (1)	0.323 (10)	0.065 (2)	0.581(18)			4	0.5720±0.0657
Total	97	0.268（26）	0.103（10）	0.113 (11)	0.371(36)	0.134(13)	0.010(1)	6	0.7567±0.0233

Note: Nh: Number of haplotype; Hd: Haplotype diversity; SD: standard deviation.

In conclusion, the white yaks in China showed a rich paternal genetic diversity. Menyuan and Tianzhu white yak breeds/populations possessed unique haplotype with a medium differentiation level. The Huzhu white yak and Menyuan white yaks have closer genetic relationship and far relationship to Tianzhu white yak. The Chinese white yak owned two haplogroups/lineages of Y1 and Y2 with dominance of Y2 haplogroup/lineage which is an indication of two paternal origins. The population structure composition of Menyuan and Huzhu white yaks was different from most of other Chinese domestic yak breeds but similar to Pali yak breed. Given paternal genetic diversity, genetic differentiation and clustering relationship between white yak populations, it is suggested that the conservation of white yak genetic resources should be strengthened to protect their unique and excellent genetic characteristics and make reasonable utilization. The Huzhu and Menyuan white yaks in Qinghai Province and Tianzhu white yaks in Gansu Province should be considered as different genetic units.

Data availability

The executable codes and datasets are available from the corresponding author on reasonable request.

ORCID

Jing Luo http://orcid.org/0000-0002-9077-1807

Xudong Wei https://orcid.org/0000-0001-5608-2365

Zhijie Ma http://orcid.org/0000-0001-7544-3533

Acknowledgements

This study was supported by the National Natural Science Foundation of China [31960656] and CAS “Light of West China” Program (3-1).

Author contributions

Zhijie Ma conceived and designed the project. Zhijie Ma, Jing Luo, Xudong Wei, Shengmei Chen, Wenxian Liu, Wenping Sun and Chuzhao Lei carried out sampling. Jing Luo, Xudong Wei and Zhijie Ma performed the experiment and data analyses. Jing Luo wrote the original manuscript. Zhijie Ma and Zulfiqar Ahmed revised the manuscript. All authors reviewed and approved the final manuscript.

Competing interests

No potential conflict of interest was reported by the author(s).

Correspondence and requests for materials should be addressed to Z.M.

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Paternal genetic diversity, differentiation and phylogeny of three white yak breeds/populations in China

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