Genetic diversity of Chinese laboratory macaques based on 2b‐RAD simplified genome sequencing

Min, Fangui; Xu, Fengjiao; Huang, Shuwu; Wu, Ruike; Zhang, Lan; Wang, Jing

doi:10.1111/jmp.12571

Cited by 6 publications

(5 citation statements)

References 13 publications

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“…High-flux mutation detection technologies such as genome sequencing and chipping are widely used in the research of livestock genetic structure, kinship, inbreeding, etc. [5]. And significant progress has been made in this area, which has important reference value for the formulation of livestock breeding and seed conservation strategies.…”

Section: Introductionmentioning

confidence: 99%

Analysis of the Genetic Relationship and Inbreeding Coefficient of the Hetian Qing Donkey through a Simplified Genome Sequencing Technology

Liu,

Gong,

Tulafu

et al. 2024

Genes

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The Hetian Qing donkey is an excellent local donkey breed in Xinjiang. It is of great significance to accelerate breeding and the speed of breeding and rejuvenation, as well as to understand the genetic basis of the strategies and population. This study collected a total of 4 male donkeys and 28 female donkeys. It then obtained genotype data through Simplified Genomic Sequencing (GBS) technology for data analysis. The results detected a total of 55,399 SNP loci, and the genotype detection rate of individuals was ≥90%. A total of 45,557 SNP loci were identified through quality control, of which 95.5% were polymorphic. The average minimum allele frequency was 0.250. The average observed heterozygosity was 0.347. The average expected heterozygosity was 0.340. The average IBS (state homologous) genetic distance was 0.268. ROH: 49 (homozygous fragments), with 73.47% of the length between 1 and 5 Mb. The average per-strip ROH length was 1.75 Mb. The mean inbreeding coefficient was 0.003. The 32 Hetian green donkeys could be divided into six families. The number of individuals in each family is significant. To sum up, the Hetian Qing donkey population has low heterozygosity, few families, and large differences in the number of individuals in each family, which can easily cause a loss of genetic diversity. In the subsequent process of seed protection, seed selection should be conducted according to the divided pedigree to ensure the long-term protection of the genetic resources of Hetian green donkeys.

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Section: Introductionmentioning

confidence: 99%

Analysis of the Genetic Relationship and Inbreeding Coefficient of the Hetian Qing Donkey through a Simplified Genome Sequencing Technology

Liu,

Gong,

Tulafu

et al. 2024

Genes

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“…In recent years, with the continuous progress of molecular biological technology and the substantial reduction in the cost of mutation detection, a large amount of SNPs information has become easier to obtain. Highflux mutation detection technologies, such as genome sequencing and chips, are widely used in the research of livestock genetic structure, kinship, and inbreeding [3]. Significant progress has been made, which has important reference value for the formulation of strategies for livestock breeding and seed conservation.…”

Section: Introductionmentioning

confidence: 99%

Analysis of genetic relationship and inbreeding coefficient of Hetian Qing donkey based on simplified genome sequencing

Liu

Hanikezi

Zhang

et al. 2023

Preprint

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A total of 32 individual samples of Hetian Qing donkeys were collected in this study, including 4 male donkeys and 28 female donkeys. Genotype data were collected by the Simplified Genome Sequencing (GBS) technology, and then genetic diversity, genetic structure, inbreeding degree and family analysis were carried out. The results showed that a total of 55399 SNP loci were detected, and the genotype detection rate of individuals was ≥ 90%; There are 45557 SNP loci through quality control, of which 95.5% are polymorphic; The average effective allele number is 0.048, the polymorphism information content is 0.273, and the average minimum allele frequency is 0.250; The average observed heterozygosity was 0.347, and the average expected heterozygosity was 0.340; The average IBS (state homology) genetic distance was 0.268; There are 49 ROHs (homozygous fragments of genome length), 73.47% of which are between 1 and 5 Mb in length. The average length of each ROH is 1.75 Mb, and the average inbreeding coefficient is 0.003; The 32 Hetian Qing donkeys can be divided into 6 families, and the individual number of each family is significantly different. To sum up, the Hetian Qing donkey population has low heterozygosity, low inbreeding degree, few families, and large differences in the number of individuals in each family, which is easy to cause the loss of genetic diversity.

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“…As one of the most effective methods for single-nucleotide polymorphism (SNP) identification, restriction-site associated DNA (RAD) sequencing has been widely used in population genetic studies of aquatic animals. The 2b-RAD technology has the advantage of simplicity and flexibility as a means of providing genome-wide genotyping information [ 21 ]. For instance, based on 2b-RAD sequencing, the low genetic diversity of five golden-backed carp ( Cyprinus carpio var.…”

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Population Structure of Coilia nasus Revealed by 2b-RAD Sequencing

Zhang

Luo

et al. 2023

Biology

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Coilia nasus is a threatened migratory species in the Yangtze River Basin. To reveal the genetic diversity of natural and farmed populations of C. nasus and the status of germplasm resources in the Yangtze River, the genetic diversity and structure of two wild populations (Yezhi Lake: YZ; Poyang Lake: PY) and two farmed populations (Zhenjiang: ZJ; Wuhan: WH) of C. nasus were analyzed using 44,718 SNPs obtained via 2b-RAD sequencing. The results indicate that both the wild and farmed populations had low genetic diversity, and germplasm resources have undergone varying degrees of degradation. Population genetic structure analyses indicated that the four populations may have come from two ancestral groups. Different amounts of gene flow were identified among WH, ZJ, and PY populations, but gene flow among YZ and other populations was low. It is speculated that the river–lake isolation of Yezhi Lake is the main cause of this phenomenon. In conclusion, this study revealed that genetic diversity reduction and germplasm resource degradation had occurred in both wild and farmed C. nasus, suggesting that conservation of its resources is of great urgency. This study provides a theoretical basis for the conservation and rational exploitation of germplasm resources for C. nasus.

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Genetic diversity of Chinese laboratory macaques based on 2b‐RAD simplified genome sequencing

Cited by 6 publications

References 13 publications

Analysis of the Genetic Relationship and Inbreeding Coefficient of the Hetian Qing Donkey through a Simplified Genome Sequencing Technology

Analysis of the Genetic Relationship and Inbreeding Coefficient of the Hetian Qing Donkey through a Simplified Genome Sequencing Technology

Analysis of genetic relationship and inbreeding coefficient of Hetian Qing donkey based on simplified genome sequencing

Genetic Diversity and Population Structure of Coilia nasus Revealed by 2b-RAD Sequencing

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