Genotyping by Genome Reducing and Sequencing for Outbred Animals

Chen, Qiang; Ma, Yufang; Yang, Yumei; Chen, Zhenliang; Liao, Rongrong; Xie, Xiaoxian; Wang, Zhen; He, Pengfei; Tu, Yanan; Zhang, Xiangzhe; Yang, Changsuo; Yang, Hongjie; Yu, Fuqing; Zheng, Yun; Zhang, Zhiwu; Wang, Qishan; Pan, Yuchun

doi:10.1371/journal.pone.0067500

Cited by 64 publications

(81 citation statements)

References 11 publications

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“…Sequencing data from 284 individuals (parts of these data were published by Wang et al, 2015) that belonged to four swine breeds (161 Chinese Meishan, 49 Duroc, 37 Landrace and 37 Yorkshire pigs) were used to identify pleiotropic SNPs in Meishan and European pigs. The DNA samples were sequenced and genotyped using the genotyping by genome reducing and sequencing protocol (http://klab.sjtu.edu.cn/GGRS/) (Chen et al, 2013). A quality control test was performed based on the criterion that minor allele frequency should be >0.01.…”

Section: Identification Of Pleiotropic Single Nucleotide Polymorphismmentioning

confidence: 99%

Identification of pleiotropic genes and gene sets underlying growth and immunity traits: a case study on Meishan pigs

Zhang

Wang

Yang

et al. 2016

animal

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Both growth and immune capacity are important traits in animal breeding. The animal quantitative trait loci (QTL) database is a valuable resource and can be used for interpreting the genetic mechanisms that underlie growth and immune traits. However, QTL intervals often involve too many candidate genes to find the true causal genes. Therefore, the aim of this study was to provide an effective annotation pipeline that can make full use of the information of Gene Ontology terms annotation, linkage gene blocks and pathways to further identify pleiotropic genes and gene sets in the overlapping intervals of growth-related and immunity-related QTLs. In total, 55 non-redundant QTL overlapping intervals were identified, 1893 growth-related genes and 713 immunity-related genes were further classified into overlapping intervals and 405 pleiotropic genes shared by the two gene sets were determined. In addition, 19 pleiotropic gene linkage blocks and 67 pathways related to immunity and growth traits were discovered. A total of 343 growth-related genes and 144 immunity-related genes involved in pleiotropic pathways were also identified, respectively. We also sequenced and genotyped 284 individuals from Chinese Meishan pigs and European pigs and mapped the single nucleotide polymorphisms (SNPs) to the pleiotropic genes and gene sets that we identified. A total of 971 high-confidence SNPs were mapped to the pleiotropic genes and gene sets that we identified, and among them 743 SNPs were statistically significant in allele frequency between Meishan and European pigs. This study explores the relationship between growth and immunity traits from the view of QTL overlapping intervals and can be generalized to explore the relationships between other traits.

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Section: Identification Of Pleiotropic Single Nucleotide Polymorphismmentioning

confidence: 99%

Identification of pleiotropic genes and gene sets underlying growth and immunity traits: a case study on Meishan pigs

Zhang

Wang

Yang

et al. 2016

animal

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“…Next-generation sequencing (NGS) technology has provided a great impulse to the genetic study of animals, for which genotyping by genome reducing and sequencing (GGRS) approach (Chen et al, 2013) was developed to enable discovery and genotyping of a great number of genetic markers across the genome at low cost. Therefore, the objective of this study was to use various strategies based on GGRS data to explore the uniqueness of the PW breed via exploration of the genetic relationships among PW, other Taihu and western pig breeds, in addition of determination of the genetic structure of PW, and to provide data to inform further research into the genetic origins, biodiversity and evolutionary history of this breed.…”

Section: Introductionmentioning

confidence: 99%

Pudong White pig: a unique genetic resource disclosed by sequencing data

Xiao

Zhang

Sun

et al. 2017

Animal

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Pudong White (PW) pigs are distributed in the Taihu region of China and are characterized by their completely white coats. A heated debate concerning this genetic resource and its relationship to Taihu and western pig breeds has arisen, due to the white coat of the animals. To determine whether PW is a unique genetic resource, we performed a detailed assessment of the genetic relationships among PW, six breeds from the Taihu population and three western pig breeds, based on whole-genome single nucleotide polymorphism (SNP) data. A total of 68 102 SNPs were identified in the genomes of the tested populations by nextgeneration sequencing technology, of which, 64 were determined as the potentially specific to PW breed. The genetic distance between PW pigs and the Taihu population was shorter than that between PW and western breeds. The genetic distance within the PW population was small and neighbour-joining tree analysis revealed that all PW individuals clustered into a separated group, indicating a close genetic relationship among PW individuals which may result from a small effective population size ( N e ) and inbreeding. The results of both principal component analysis and evaluation using fastSTRUCTURE demonstrated that PW was clearly differentiated from other breeds. Together, these results indicate that PW is a distinctive genetic resource with a unique genetic structure separate from other Taihu and western pig breeds. Furthermore, this genome-wide comprehensive survey of the relationships among PW, Taihu and western pig breeds, demonstrates the rationality of the current breed classification of PW. The results also provide evidence about the unique genetic resource of PW, based on genome-wide genetic markers. These data will improve our understanding of the genetic structure and current state of PW breed, and facilitate the development of a national project for the conservation and utilization of these pigs.

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“…The DNA samples were genotyped using the genotyping by genome reducing and sequencing (GGRS) protocol (http://klab.sjtu.edu.cn/GGRS/) (Chen et al . 2013) (Appendix S1). A total of 581 401 615 good reads with an average depth of 11× and an average coverage of 2.16% were generated (Table 1).…”

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Genetic variation and genetic structure of five Chinese indigenous pig populations in Jiangsu Province revealed by sequencing data

et al. 2017

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SummaryIn this study, we investigated the genetic variants, including SNPs and indels (short insertions or deletions, less than 50 bp in length), in the genomes and genetic structures of five pig populations (in the northern Taihu Lake region, Jiangsu Province) using the genotyping by genome reducing and sequencing (GGRS) approach. A total of 581 million good reads with an average depth of 11× and an average coverage of 2.16% were used to call variants. In general, 202 106 SNPs and 34 415 indels were obtained, of which 2690 SNPs and 224 indels were capable of inducing protein‐coding changes. The genes containing these variants were extracted for functional annotation. The results of gene enrichment analysis revealed that the SNPs under investigation may be associated with reproduction, disease resistance, meat quality and adipose tissue traits, whereas the indels were associated mainly with adipose tissue and disease. Analysis of the genetic structure showed that each population displayed comparable, large differentiations from the others, indicating their uniqueness. In conclusion, the results of our study provide the first genomic overview of the genetic variants and population structures of five Chinese indigenous pig populations.

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Genotyping by Genome Reducing and Sequencing for Outbred Animals

Cited by 64 publications

References 11 publications

Identification of pleiotropic genes and gene sets underlying growth and immunity traits: a case study on Meishan pigs

Identification of pleiotropic genes and gene sets underlying growth and immunity traits: a case study on Meishan pigs

Pudong White pig: a unique genetic resource disclosed by sequencing data

Genetic variation and genetic structure of five Chinese indigenous pig populations in Jiangsu Province revealed by sequencing data

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