Genome-wide SNP discovery and evaluation of genetic diversity among six Chinese indigenous cattle breeds in Sichuan

Wang, Wei; Gan, Jia; Fang, Donghui; Tang, Hui; Huai, Wang; Yi, Jun; Fu, Maozhong

doi:10.1371/journal.pone.0201534

Cited by 24 publications

(14 citation statements)

References 23 publications

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“…Nucleotide diversities were also lower in Iberian wild goats than in domestic goats. Moreover, nucleotide diversities of domestic goats were similar to those observed in other livestock populations (Luigi‐Sierra et al, 2020 ; Wang et al, 2018 ). Nucleotide diversity estimated on a per‐site basis (–site‐pi), as we have done in the current work, yields values that are different from those obtained by considering windows of 1000 bp (–window‐pi), as previously discussed by Luigi‐Sierra et al ( 2020 ).…”

Section: Discussionsupporting

confidence: 81%

Assessing the levels of intraspecific admixture and interspecific hybridization in Iberian wild goats (Capra pyrenaica)

Cardoso

Luigi-Sierra

Castelló

et al. 2021

Evolutionary Applications

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Iberian wild goats (Capra pyrenaica, also known as Iberian ibex, Spanish ibex, and Spanish wild goat) underwent strong genetic bottlenecks during the 19th and 20th centuries due to overhunting and habitat destruction. From the 1970s to 1990s, augmentation translocations were frequently carried out to restock Iberian wild goat populations (very often with hunting purposes), but they were not systematically planned or recorded. On the other hand, recent data suggest the occurrence of hybridization events between Iberian wild goats and domestic goats (Capra hircus). Augmentation translocations and interspecific hybridization might have contributed to increase the diversity of Iberian wild goats. With the aim of investigating this issue, we have genotyped 118 Iberian wild goats from Tortosa‐Beceite, Sierra Nevada, Muela de Cortes, Gredos, Batuecas, and Ordesa and Monte Perdido by using the Goat SNP50 BeadChip (Illumina). The analysis of genotypic data indicated that Iberian wild goat populations are strongly differentiated and display low diversity. Only three Iberian wild goats out from 118 show genomic signatures of mixed ancestry, a result consistent with a scenario in which past augmentation translocations have had a limited impact on the diversity of Iberian wild goats. Besides, we have detected eight Iberian wild goats from Tortosa‐Beceite with signs of domestic goat introgression. Although rare, hybridization with domestic goats could become a potential threat to the genetic integrity of Iberian wild goats; hence, measures should be taken to avoid the presence of uncontrolled herds of domestic or feral goats in mountainous areas inhabited by this iconic wild ungulate.

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Section: Discussionsupporting

confidence: 81%

Assessing the levels of intraspecific admixture and interspecific hybridization in Iberian wild goats (Capra pyrenaica)

Cardoso

Luigi-Sierra

Castelló

et al. 2021

Evolutionary Applications

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“…iN VeTeRiNARy ScieNce Vol 2, No 1, 2019 Background With the rapid advancement in high-throughput (HT) next-generation genome sequencing (NGS), numerous studies were performed in last decade, to discovery the de novo and reference-based Single nucleotide polymorphisms (SNPs) discovery in cattle and pig domesticated animals [1][2][3][4][5][6][7][8][9]. The SNPs are generally the single nucleotide variations (SNVs) caused either by transitions (C/T or G/A) or transversions (C/G, C/A, or T/A, T/G), in the same position between individual genomic DNA sequences [10][11].…”

Section: Translational Researchmentioning

confidence: 99%

RNA-seq based SNP discovery in gluteus medius muscle of Polish Landrace pigs

Pierzchała

Ogłuszka

Poławska

et al. 2019

TRVS

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Background: Single nucleotide polymorphisms (SNPs) are the well-known molecular markers in genetics and breeding studies applied to veterinary sciences and livestock production. Advancement of next generation sequencing (NGS) provides a high-throughput means of potential putative SNP discovery. The aim of the study was to identify the putative genetic variants in gluteus medius muscle transcriptome of Polish Landrace pigs.Methods. RNA-seq based NGS experiment was performed on Polish Landrace pigs fed with omega-6 and omega-3 polyunsaturated fatty acids (and normal diets. Isolation of total RNA from gluteus medius muscle was performed PUFAs dietary of Polish Landrace pigs. The RNA-seq libraries were constructed by mRNA enrichment, mRNA fragmentation, second strand cDNA synthesis, adaptor ligation, size selection and PCR amplification using the illumina TruSeq RNA Sample Prep Kit v2 (Illumina, San Diego CA, USA), followed by NGS sequencing on MiSeq illumina platform. The quality control of raw RNA-seq data was performed using the Trimmomatic and FastQC tools. High QC pairedend RNA-seq data of gluteus medius muscle transcriptome were mapped to the reference genome Sus scrofa v.10.2. Finally, the SNPs discovery was performed using GATK and SAMtools bioinformatics SNPs caller tools. Results:The Fastq RNA-seq data generated from two pooled paired-end libraries (151bp) of gluteus medius muscle tissue of Polish Landrace pigs were submitted to NCBI SRA database (https://www.ncbi.nlm.nih.gov/sra). Study identified a total of 50.5 million pairedend reads (32.5 million low PUFAs dietary group and 18 million reads high PUFAs dietary group) of gluteus medius muscle transcriptome of Polish Landrace pigs. SNP discovery identified a total of 35436 homozygous and 28644 heterozygous cSNPs in gluteus medius muscle transcriptomes representing both dietary groups of Polish Landrace pig. Moreover, a total of 25187 and 5488 cSNP were identified as synonymous SNPs, and 18005 and 4780 cSNP were identified as nonsynonymous SNPs. Finally, single nucleotide variation (SNV) representing substitutions of all four possibilities (A,T,G,C) were identified ranging 2935 to 3227 SNVs (high PUFAs) and 3528 to 3882 SNVs (low PUFAs) for the heterozygous cSNPs and 2712 to 4058 (high PUFAs) and 4169 to 5692 SNVs (low PUFAs) for the heterozygous SNPs in gluteus medius muscle transcriptomes of Polish Landrace pigs. Conclusions.Study concluded that identification of cSNPs dataset representing the gluteus medius muscle transcriptome of Polish Landrace pigs fed with a control diet (low) and pigs fed with a PUFAs diet (high) may be helpful to develop a new set of genetic markers specific to Polish Landrace pig breed. Such cSNP markers eventually can be utilized in genome-wide association studies (GWAS) and to finally implement on marker assisted selection (MAS) and genomics selection (GS) program in active breeding population of Polish Landrace pigs in Poland.

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“…For example, Li et al [ 13 ] used RAD-seq for genome SNP typing of 618 sows to accurately predict of genome breeding value and evaluate the accuracy of breeding value prediction. Moreover, Wang et al [ 14 ] successfully employed RAD-seq to explore genome-wide SNPs among six breeds of Sichuan cattle.…”

Section: Introductionmentioning

confidence: 99%

Exploring the genomic resources of seven domestic Bactrian camel populations in China through restriction site-associated DNA sequencing

et al. 2021

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The domestic Bactrian camel is a valuable livestock resource in arid desert areas. Therefore, it is essential to understand the roles of important genes responsible for its characteristics. We used restriction site-associated DNA sequencing (RAD-seq) to detect single nucleotide polymorphism (SNP) markers in seven domestic Bactrian camel populations. In total, 482,786 SNPs were genotyped. The pool of all remaining others were selected as the reference population, and the Nanjiang, Sunite, Alashan, Dongjiang, Beijiang, Qinghai, and Hexi camels were the target populations for selection signature analysis. We obtained 603, 494, 622, 624, 444, 588, and 762 selected genes, respectively, from members of the seven target populations. Gene Ontology classifications and Kyoto Encyclopedia of Genes and Genomes enrichment analyses were performed, and the functions of these genes were further studied using Genecards to identify genes potentially related to the unique characteristics of the camel population, such as heat resistance and stress resistance. Across all populations, cellular process, single-organism process, and metabolic process were the most abundant biological process subcategories, whereas cell, cell part, and organelle were the most abundant cellular component subcategories. Binding and catalytic activity represented the main molecular functions. The selected genes in Alashan camels were mainly enriched in ubiquitin mediated proteolysis pathways, the selected genes in Beijiang camels were mainly enriched in MAPK signaling pathways, the selected genes in Dongjiang camels were mainly enriched in RNA transport pathways, the selected genes in Hexi camels were mainly enriched in endocytosis pathways, the selected genes in Nanjiang camels were mainly enriched in insulin signaling pathways, while the selected genes in Qinghai camels were mainly enriched in focal adhesion pathways; these selected genes in Sunite camels were mainly enriched in ribosome pathways. We also found that Nanjiang (HSPA4L and INTU), and Alashan camels (INO80E) harbored genes related to the environment and characteristics. These findings provide useful insights into the genes related to the unique characteristics of domestic Bactrian camels in China, and a basis for genomic resource development in this species.

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Genome-wide SNP discovery and evaluation of genetic diversity among six Chinese indigenous cattle breeds in Sichuan

Cited by 24 publications

References 23 publications

Assessing the levels of intraspecific admixture and interspecific hybridization in Iberian wild goats (Capra pyrenaica)

Assessing the levels of intraspecific admixture and interspecific hybridization in Iberian wild goats (Capra pyrenaica)

RNA-seq based SNP discovery in gluteus medius muscle of Polish Landrace pigs

Exploring the genomic resources of seven domestic Bactrian camel populations in China through restriction site-associated DNA sequencing

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