Analysis of Genetic Diversity and Population Structure of Tarim and Junggar Bactrian Camels Based on Simplified GBS Genome Sequencing
In view of the severe reduction in Bactrian camel germplasm resources, scientific evaluation, protection, and utilization is particularly important. Therefore, it is necessary to investigate the genetic diversity and genetic structure of this species, and identify the genes that have played importan...
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MDPI AG
2023-07-01
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| author | Weikun Tao Lazat Aniwar Azat ZuliPicar Hanikzi Tulafu Rongyin Zhang Bo Liu Weiwei Wu Juncheng Huang |
| author_facet | Weikun Tao Lazat Aniwar Azat ZuliPicar Hanikzi Tulafu Rongyin Zhang Bo Liu Weiwei Wu Juncheng Huang |
| author_sort | Weikun Tao |
| collection | DOAJ |
| description | In view of the severe reduction in Bactrian camel germplasm resources, scientific evaluation, protection, and utilization is particularly important. Therefore, it is necessary to investigate the genetic diversity and genetic structure of this species, and identify the genes that have played important roles in its evolution. In this study, 21,971 SNPs were identified in 118 domestic Bactrian camels from the Tarim (<i>n</i> = 60) and Junggar (<i>n</i> = 58) populations using simplified GBS genome sequencing. The results show that Tarim and Junggar Bactrian camels have high nucleotide diversity. A phylogenetic tree constructed using structural analysis, principal component analysis (PCA), and the adjacency method (NJ) showed that Tarim and Junggar Bactrian camels were clustered together. The selection signals revealed that the Tarim and Junggar Bactrian camels shared 108 genes under positive selection, including WNT1, WNT10B, CD14, SEC61A2, DPAGT1, FOXO6, etc. These selected genes were widely involved in the immune system, embryonic development, lipid metabolism, and other processes. From a genomic analysis perspective, the genetic relationship between TLM and ZGE camels is close, with an average Fst of 0.048 and a relatively low average differentiation coefficient between the two populations. In addition, shared selected genes in the long-term depression pathway were significantly enriched in Tarim and Junggar. These findings will offer support and assistance for the exploration of genetic resource preservation, economically significant traits, and the mechanisms underlying biological characteristics, molecular breeding, and disease. |
| first_indexed | 2024-03-11T01:22:31Z |
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| language | English |
| last_indexed | 2024-03-11T01:22:31Z |
| publishDate | 2023-07-01 |
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| series | Animals |
| spelling | doaj.art-697b133de15b4de987deee65145c48a42023-11-18T18:01:09ZengMDPI AGAnimals2076-26152023-07-011314234910.3390/ani13142349Analysis of Genetic Diversity and Population Structure of Tarim and Junggar Bactrian Camels Based on Simplified GBS Genome SequencingWeikun Tao0Lazat Aniwar1Azat ZuliPicar2Hanikzi Tulafu3Rongyin Zhang4Bo Liu5Weiwei Wu6Juncheng Huang7Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, ChinaInstitute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, ChinaInstitute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, ChinaInstitute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, ChinaInstitute of Quality Standards, Xinjiang Academy of Animal Husbandry Sciences, Urumqi 830000, ChinaInstitute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, ChinaInstitute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, ChinaInstitute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi 830000, ChinaIn view of the severe reduction in Bactrian camel germplasm resources, scientific evaluation, protection, and utilization is particularly important. Therefore, it is necessary to investigate the genetic diversity and genetic structure of this species, and identify the genes that have played important roles in its evolution. In this study, 21,971 SNPs were identified in 118 domestic Bactrian camels from the Tarim (<i>n</i> = 60) and Junggar (<i>n</i> = 58) populations using simplified GBS genome sequencing. The results show that Tarim and Junggar Bactrian camels have high nucleotide diversity. A phylogenetic tree constructed using structural analysis, principal component analysis (PCA), and the adjacency method (NJ) showed that Tarim and Junggar Bactrian camels were clustered together. The selection signals revealed that the Tarim and Junggar Bactrian camels shared 108 genes under positive selection, including WNT1, WNT10B, CD14, SEC61A2, DPAGT1, FOXO6, etc. These selected genes were widely involved in the immune system, embryonic development, lipid metabolism, and other processes. From a genomic analysis perspective, the genetic relationship between TLM and ZGE camels is close, with an average Fst of 0.048 and a relatively low average differentiation coefficient between the two populations. In addition, shared selected genes in the long-term depression pathway were significantly enriched in Tarim and Junggar. These findings will offer support and assistance for the exploration of genetic resource preservation, economically significant traits, and the mechanisms underlying biological characteristics, molecular breeding, and disease.https://www.mdpi.com/2076-2615/13/14/2349Bactrian camelgenetic diversitygroup structurecluster analysisfunctional gene selection |
| spellingShingle | Weikun Tao Lazat Aniwar Azat ZuliPicar Hanikzi Tulafu Rongyin Zhang Bo Liu Weiwei Wu Juncheng Huang Analysis of Genetic Diversity and Population Structure of Tarim and Junggar Bactrian Camels Based on Simplified GBS Genome Sequencing Animals Bactrian camel genetic diversity group structure cluster analysis functional gene selection |
| title | Analysis of Genetic Diversity and Population Structure of Tarim and Junggar Bactrian Camels Based on Simplified GBS Genome Sequencing |
| title_full | Analysis of Genetic Diversity and Population Structure of Tarim and Junggar Bactrian Camels Based on Simplified GBS Genome Sequencing |
| title_fullStr | Analysis of Genetic Diversity and Population Structure of Tarim and Junggar Bactrian Camels Based on Simplified GBS Genome Sequencing |
| title_full_unstemmed | Analysis of Genetic Diversity and Population Structure of Tarim and Junggar Bactrian Camels Based on Simplified GBS Genome Sequencing |
| title_short | Analysis of Genetic Diversity and Population Structure of Tarim and Junggar Bactrian Camels Based on Simplified GBS Genome Sequencing |
| title_sort | analysis of genetic diversity and population structure of tarim and junggar bactrian camels based on simplified gbs genome sequencing |
| topic | Bactrian camel genetic diversity group structure cluster analysis functional gene selection |
| url | https://www.mdpi.com/2076-2615/13/14/2349 |
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