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Ma Z, Xia X, Chen S, Bai M, Lei C, Han J. A Global Analysis of Y-STR INRA189 Polymorphism in Chinese Domestic Yak Breeds/Populations. Animals (Basel) 2020; 10:ani10030393. [PMID: 32121109 PMCID: PMC7142920 DOI: 10.3390/ani10030393] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 02/22/2020] [Accepted: 02/25/2020] [Indexed: 11/18/2022] Open
Abstract
Simple Summary Y chromosome-specific markers have been widely used in studying the origin, migration, diversity, and population relationship in several mammalian species. So far, the investigations on yak paternal genetics were mostly based on Y-SNPs information, but very few on Y-STR markers. In this study, we comprehensively investigated the polymorphism of Y-STR INRA189 locus, identified the geographical distribution pattern of its alleles in 15 Chinese domestic yak breeds/populations, and provided basic data for yak paternal genetic analysis. Our results showed that INRA189 is an intermediate polymorphic Y-STR marker with six alleles present among 15 Chinese domestic yak breeds/populations and that the variation among six alleles was due to different numbers of repetitions of a TG dinucleotide motif. Abstract The objective of this study was to probe into the polymorphism of Y-STR INRA189 and identify the geographical distribution pattern of its alleles in the Chinese domestic yak gene pool. We examined the variation at INRA189 locus in 682 male yaks representing 15 breeds/populations in China. The results showed that six alleles, including five reported previously (149, 155, 157, 159, and 161 bp) and a new one identified in this study (139 bp), were detected at INRA189 locus based on genotyping analysis. The frequencies of six alleles varied among the 15 yak breeds/populations with a clear phylogeographical pattern, which revealed the paternal genetic difference among Chinese yak breeds/populations. The average polymorphism information content (PIC) among the 15 yak breeds/populations was 0.32, indicating INRA189 to be an intermediate polymorphic Y-STR marker (0.25 < PIC < 0.5) in yak. Sequence alignment revealed that the variations among six alleles at INRA189 were defined by a TG dinucleotide repeat motif, which repeated for 12, 17, 20, 21, 22, and 23 times, corresponding to the alleles of 139, 149, 155, 157, 159, and 161 bp, respectively. Therefore, we believe that the polymorphic yak Y-STR INRA189 can be used to characterize male-mediated genetic events, including paternal genetic origin, diversity, and evolution.
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Affiliation(s)
- Zhijie Ma
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China;
- Correspondence: ; Tel.: +86-139-971-576-25
| | - Xiaoting Xia
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (X.X.); (C.L.)
| | - Shengmei Chen
- Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, China;
| | - Ma Bai
- Bureau of Animal Husbandry and Veterinary, Diqing Tibetan Autonomous Prefecture of Yunnan Province, Shangri-La 674400, China;
| | - Chuzhao Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; (X.X.); (C.L.)
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China;
- International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
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Han H, Chen N, Jordana J, Li C, Sun T, Xia X, Zhao X, Ji C, Shen S, Yu J, Ainhoa F, Chen H, Lei C, Dang R. Genetic diversity and paternal origin of domestic donkeys. Anim Genet 2017; 48:708-711. [PMID: 28929497 DOI: 10.1111/age.12607] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2017] [Indexed: 11/30/2022]
Abstract
Numerous studies have been conducted to investigate genetic diversity, origins and domestication of donkey using autosomal microsatellites and the mitochondrial genome, whereas the male-specific region of the Y chromosome of modern donkeys is largely uncharacterized. In the current study, 14 published equine Y chromosome-specific microsatellites (Y-STR) were investigated in 395 male donkey samples from China, Egypt, Spain and Peru using fluorescent labeled microsatellite markers. The results showed that seven Y-STRs-EcaYP9, EcaYM2, EcaYE2, EcaYE3, EcaYNO1, EcaYNO2 and EcaYNO4-were male specific and polymorphic, showing two to eight alleles in the donkeys studied. A total of 21 haplotypes corresponding to three haplogroups were identified, indicating three independent patrilines in domestic donkey. These markers are useful for the study the Y-chromosome diversity and population genetics of donkeys in Africa, Europe, South America and China.
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Affiliation(s)
- H Han
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - N Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - J Jordana
- Facultat de Veterinària, Department Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Barcelona, Bellaterra, 08193, Spain
| | - C Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - T Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - X Xia
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - X Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - C Ji
- Donge Ejiao Company Limited by Shares, Donge, Shandong, 252299, China
| | - S Shen
- Donge Ejiao Company Limited by Shares, Donge, Shandong, 252299, China
| | - J Yu
- Donge Ejiao Company Limited by Shares, Donge, Shandong, 252299, China
| | - F Ainhoa
- Facultat de Veterinària, Department Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Barcelona, Bellaterra, 08193, Spain
| | - H Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - C Lei
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
| | - R Dang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, 712100, China
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