Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array

Jun, Ma; Gao, Xue; Li, Junya; Gao, Huijiang; Wang, Zezhao; Zhang, Lupei; Xu, Lingyang; Gao, Han; Li, Hongwei; Wang, Yahui; Zhu, Bo; Cai, Wentao; Wang, Congyong; Yan, Chen

doi:10.3390/ani11123469

Cited by 10 publications

(4 citation statements)

References 82 publications

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“…Genetic diversity is an important index to measure the degree of population variation and the status of germplasm resources [19]. Jianli pigs had Ho of 0.21 and He of 0.22, which were comparable with those of most Chinese indigenous breeds.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide detection of selection signatures in Jianli pigs reveals novel cis-regulatory haplotype for two-end black coat color

Xu,

Wu,

Zhang

et al. 2023

Preprint

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Background:Jianli pig, a renowned indigenous breed in China, has the characteristics of a two-end black (TEB) coat color, excellent meat quality, strong adaptability and increased prolificacy. However, there is limited information available regarding the genetic diversity, population structure and genomic regions under selection of Jianli pig. On the other hand, the genetic mechanism of TEB coat color has remained largely unknown. Results: In this study, the whole genome resequencing of 30 Jianli pigs within a context of 153 individuals representing 13 diverse breeds was performed. The population structure analysis revealed that Jianli pigs have close genetic relationships with the Tongcheng pig breed, their geographical neighbors. Three methods (observed heterozygosity, expected heterozygosity, and runs of homozygosity) implied a relatively high level of genetic diversity and, a low inbreeding coefficient in Jianli compared with other pigs. We used Fst and XP-EHH to detect the selection signatures in Jianli pigs compared with Asian wild boar. A total of 451 candidate genes influencing meat quality (CREBBP, ADCY9, EEPD1 and HDAC9), reproduction (ESR1 and FANCA), and coat color (EDNRB, MITF and MC1R), were detected by gene annotation analysis. Finally, to fine-map the genomic region for the two-end black (TEB) coat color phenotype in Jianli pigs, we performed three signature selection methods between the TEB coat color and no-TEB coat color pig breeds. The current study, further confirmed that the EDNRB gene is a candidate gene for TEB color phenotype found in Chinese pigs, including Jinhua pigs, and the haplotype harboring 25 SNPs was a strong candidate causative mutation that regulates the TEB coat color phenotype by altering enhancer function. Conclusion: Our results advanced the understanding of the genetic mechanism behind artificial selection, and provided further resources for the protection and breeding improvement of Jianli pigs.

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Section: Discussionmentioning

confidence: 99%

Genome-wide detection of selection signatures in Jianli pigs reveals novel cis-regulatory haplotype for two-end black coat color

Xu,

Wu,

Zhang

et al. 2023

Preprint

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“…SNPs are a common type of genetic variation present throughout the genome. They are extensively utilized for various research purposes, including the evaluation of germplasm resources, analysis of genetic diversity, and the study of phylogenetic evolution [ 15 – 17 ]. Current SNP typing methods commonly include whole genome sequencing (WGS), genotyping by sequencing (GBS), and commercial SNP chips.…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity analysis of Inner Mongolia cashmere goats (Erlangshan subtype) based on whole genome re-sequencing

Wang,

et al. 2024

BMC Genomics

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Background Inner Mongolia cashmere goat (IMCG), renowned for its superior cashmere quality, is a Chinese indigenous goat breed that has been developed through natural and artificial selection over a long period. However, recently, the genetic resources of IMCGs have been significantly threatened by the introduction of cosmopolitan goat breeds and the absence of adequate breed protection systems. Results In order to assess the conservation effectiveness of IMCGs and efficiently preserve and utilize the purebred germplasm resources, this study analyzed the genetic diversity, kinship, family structure, and inbreeding of IMCGs utilizing resequencing data from 225 randomly selected individuals analyzed using the Plink (v.1.90), GCTA (v.1.94.1), and R (v.4.2.1) software. A total of 12,700,178 high-quality SNPs were selected through quality control from 34,248,064 SNP sites obtained from 225 individuals. The average minor allele frequency (MAF), polymorphic information content (PIC), and Shannon information index (SHI) were 0.253, 0.284, and 0.530, respectively. The average observed heterozygosity (Ho) and the average expected heterozygosity (He) were 0.355 and 0.351, respectively. The analysis of the identity by state distance matrix and genomic relationship matrix has shown that most individuals’ genetic distance and genetic relationship are far away, and the inbreeding coefficient is low. The family structure analysis identified 10 families among the 23 rams. A total of 14,109 runs of homozygosity (ROH) were identified in the 225 individuals, with an average ROH length of 1014.547 kb. The average inbreeding coefficient, calculated from ROH, was 0.026 for the overall population and 0.027 specifically among the 23 rams, indicating a low level of inbreeding within the conserved population. Conclusions The IMCGs exhibited moderate polymorphism and a low level of kinship with inbreeding occurring among a limited number of individuals. Simultaneously, it is necessary to prevent the loss of bloodline to guarantee the perpetuation of the IMCGs’ germplasm resources.

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“…Therefore, the detection of selection signals is vital to uncover the genes related to economic traits and explore the adaptation mechanism of domestication. In recent years, several statistical methods have been used to detect recent selection footprints in composite populations, including comprehensive haplotype score (iHS), complex likelihood ratio (CLR), crosspopulation extended haplotype homozygosity (XP-EHH), and interpopulation relatively comprehensive haplotype homozygosity (Rsb) [15,16]. For example, based on the Illumina BovineLD v2 BeadChip data, van der Nest.…”

Section: Introductionmentioning

confidence: 99%

“…Ma. et al identified potentially selected genes at the genome-wide level in Huaxi cattle, which related to ion binding and muscle growth and differentiation [15].…”

Section: Introductionmentioning

confidence: 99%

Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array

Jiang

Lai

et al. 2023

Animals

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Chinese Red Steppe Cattle (CRS), a composite cattle breed, is well known for its milk production, high slaughter rate, carcass traits, and meat quality. Nowadays, it is widely bred in Jilin and Hebei Province and the Inner Mongolia Autonomous region. However, the population structure and the genetic basis of prominent characteristics of CRS are still unknown. In this study, we systematically describe their population structure, genetic diversity, and selection signature based on genotyping data from 61 CRS individuals with GGP Bovine 100 K chip. The results showed that CRS cattle had low inbreeding levels and had formed a unique genetic structure feature. Using two complementary methods (including comprehensive haplotype score and complex likelihood ratio), we identified 1291 and 1285 potentially selected genes, respectively. There were 141 genes annotated in common 106 overlapping genomic regions covered 5.62 Mb, including PLAG1, PRKG2, DGAT1, PARP10, TONSL, ADCK5, and BMP3, most of which were enriched in pathways related to muscle growth and differentiation, milk production, and lipid metabolism. This study will contribute to understanding the genetic mechanism behind artificial selection and give an extensive reference for subsequent breeding.

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Assessing the Genetic Background and Selection Signatures of Huaxi Cattle Using High-Density SNP Array

Cited by 10 publications

References 82 publications

Genome-wide detection of selection signatures in Jianli pigs reveals novel cis-regulatory haplotype for two-end black coat color

Genome-wide detection of selection signatures in Jianli pigs reveals novel cis-regulatory haplotype for two-end black coat color

Genetic diversity analysis of Inner Mongolia cashmere goats (Erlangshan subtype) based on whole genome re-sequencing

Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array

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