Detecting selection signatures on the X chromosome of the Chinese Debao pony.
Abstract: The X chromosome shows a special interaction between demographic factors and genetic variation, and the analysis of X-linked genomic variation can therefore provide insights into the unique effects of demography and selection on the horse genome that cannot be readily detected by autosomal markers. Debao (DB) ponies have experienced intense selective pressure for the development of their small stature (<106 cm at adult height). To identify selective sweeps on the X chromosome of the DB pony, we performed a genome-wide scan of three Chinese horse breeds using an Equine SNP70 BeadChip. Using Yili and Mongolian horses (>134 cm at adult height) as reference groups, both FST and XP-EHH revealed that five regions on the X chromosome were under strong selection, resulting in 95 overlapping genes. Seven of these genes, SMS, PHEX, ACSL4, CHRDL1, CACNA1F, DKC1 and CDKL5, are involved in bone development, growth hormone secretion and fat deposition. The region showing the strongest selection pressure was located at the position of 86.6-87.5 Mb. The subsequent genome-wide association analysis of the adult height of three Chinese horse breeds detected the two most significant SNPs in the same region, and these two SNPs overlapped with the gene CHRDL1. As a member of the bone morphogenetic protein (BMP) superfamily, CHRDL1 antagonizes the function of BMP4 and plays an important role in embryonic bone formation and cartilage generation. Our results provide new insights into the X-linked selection in Chinese Debao pony.
© 2018 Blackwell Verlag GmbH.
Publication Date: 2018-01-19 PubMed ID: 29345071DOI: 10.1111/jbg.12314Google Scholar: Lookup
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- Journal Article
Summary
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The researchers conducted a study to identify the genetic factors that influenced the small stature of the Debao pony breed by looking at its X chromosome. The study showed that certain genes related to bone and growth development are under strong selection pressure which influences the small stature of these ponies.
Objectives of the Research
- The researchers aimed to understand the effects of demography and selection on the horse genome by specifically focusing on the X chromosome.
- They intended to identify genetic markers and regions on the X chromosome under selection pressure that contribute to the small stature of Debao ponies.
- The study aimed to provide more genetic insights into the Debao pony breed and horses in general.
Methodology of the Research
- The researchers collected and analyzed genomic data from three different Chinese horse breeds using an Equine SNP70 BeadChip. They used Yili and Mongolian horses, which are larger in stature, as reference groups.
- They performed a genome-wide scan to identify selective sweeps or regions in the genome where advantageous mutations have increased in frequency due to selection.
- They also performed genome-wide association analysis to identify the most significant SNPs (single nucleotide polymorphisms) related to adult height.
Results of the Research
- The genome-wide scan revealed five regions on the X chromosome under strong selection pressure leading to 95 overlapping genes. Seven of these genes were identified to be involved with bone development, growth hormone secretion, and fat deposition, which likely contribute to the Debao pony’s small stature.
- The region with the strongest selection pressure was located at a position of 86.6-87.5 Mb on the X chromosome.
- The genome-wide association analysis identified two significant SNPs that overlapped with the CHRDL1 gene, which is part of the bone morphogenetic protein (BMP) superfamily. CHRDL1 antagonizes the function of BMP4, affecting embryonic bone formation and cartilage generation.
Significance of the Research
- The study provides a new understanding of the unique genetic selection happening on the X chromosome of Debao ponies, providing an explanation for their small stature.
- These findings can enlighten future breeding strategies and conservation efforts for the Debao pony breed and other horse species.
- Overall, the research contributes to a broader understanding of equestrian genetics, which can be used to inform animal breeding and veterinary practices.
Cite This Article
APA
Liu XX, Pan JF, Zhao QJ, He XH, Pu YB, Han JL, Ma YH, Jiang L.
(2018).
Detecting selection signatures on the X chromosome of the Chinese Debao pony.
J Anim Breed Genet, 135(1), 84-92.
https://doi.org/10.1111/jbg.12314 Publication
Researcher Affiliations
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- International Livestock Research Institute (ILRI), Nairobi, Kenya.
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- State Key Laboratory of Animal Nutrition, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.
MeSH Terms
- Animals
- Evolution, Molecular
- Genome-Wide Association Study
- Genomics
- Haplotypes
- Heterozygote
- Horses / anatomy & histology
- Horses / genetics
- Polymorphism, Single Nucleotide
- Selection, Genetic
- X Chromosome / genetics
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