Detection of Selection Signatures Based on the Integrated Haplotype Score in Chinese Jinnan Cattle

Zhang, Yuan Qing; He, Dong Chang; Cheng, Jing; Xu, Fang; Li, Bo; Jin, Guang; Zhang, Xi Zhong

doi:10.9755/ejfa.2016-06-761

Cited by 3 publications

(4 citation statements)

References 27 publications

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“…We used three methods to detect signatures of selection: two haplotype-based ( iHS and Rsb ) and one F ST based method. The first two methods are based on extended haplotype homozygosity ( EHH ), which correspond to the probability that two randomly chosen chromosomes carrying the core haplotype are identical by descent 83 , 84 . The first method is the intra-population standardized integrated haplotype score ( iHS ) 41 ; the second is the inter-population standardized log-ratio of integrated EHH ( iES ) between pairs of populations ( Rsb ) 42 .…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus)

Cádiz

López

Díaz-Domínguez

et al. 2020

Sci Rep

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Nile tilapia belongs to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs and domestication process of Nile tilapia may have modified the genome through selective pressure, leaving signals that can be detected at the molecular level. In this work, signatures of selection were identified using genomewide SNP data, by two haplotype-based (iHS and Rsb) and one F ST based method. Whole-genome re-sequencing of 326 individuals from three strains (A, B and C) of farmed tilapia maintained in Brazil and Costa Rica was carried out using Illumina HiSeq 2500 technology. After applying conventional SNP-calling and quality-control filters, ~ 1.3 M high-quality SNPs were inferred and used as input for the iHS, Rsb and F ST based methods. We detected several candidate genes putatively subjected to selection in each strain. A considerable number of these genes are associated with growth (e.g. NCAPG, KLF3, TBC1D1, TTN), early development (e.g. FGFR3, PFKFB3), and immunity traits (e.g. NLRC3, PIGR, MAP1S). These candidate genes represent putative genomic landmarks that could be associated to traits of biological and commercial interest in farmed nile tilapia. Nile tilapia (Oreochromis niloticus) is a teleost fish of the Cichlidae family native to Africa and the Middle East. The geographic range of the species extends from 8°N to 32°N 1. The first record of domestication is dated around 3,500 years ago as evidenced in paintings at the Theban tombs in Egypt 2. Nowadays, this species is the second most cultivated group of fish in the world 3. Favorable characteristics for production include rapid growth, adaptability to different culture conditions, tolerance to high densities, disease resistance, easy reproduction, and tolerance to low concentrations of oxygen 4. Genetic improvement programs (GIPs) for Nile tilapia began in 1988 as an approach to counteract the production decrease generated by introgressions with Mozambique tilapia (Oreochromis mossambicus) 5,6. Since then, nearly twenty GIPs have been established for Nile tilapia around the world 7,8. GIPs aim to improve traits of commercial interest, such as growth rate, disease resistance, cold and salinity tolerance 7. The GIFT (Genetic Improvement of Farmed Tilapia) 9 Nile tilapia strain was developed by the ICLARM (International Centre for Living Aquatic Resources Management, now the WorldFish Center), in collaboration with the Norwegian Institute of Aquaculture Research (AKVAFORSK, now NOFIMA Marin) 1. The implementation of GIPs for the GIFT population has been successful, because growth rate in Nile tilapia has doubled in five generations, showing that this species had a positive response to selection 1 .

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Section: Methodsmentioning

confidence: 99%

“…The iHS method compares EHH values between alleles within one population, i.e. the area under the curve of the derived and ancestral alleles 84 . This procedure requires the identification of the ancestral allele for each SNP, which is automatically inferred by the REHH package (polarize_vcf = FALSE).…”

Section: Signatures Of Selectionmentioning

confidence: 99%

Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus)

Cádiz

López

Díaz-Domínguez

et al. 2020

Sci Rep

View full text Add to dashboard Cite

show abstract

“…The third method was the standardized Integrated Haplotype Score (iHS) [24], which is included in the R package REHH v3.1.2 [50]. This method is based on extended haplotype homozygosity (EHH) and corresponds to the probability that two randomly chosen chromosomes carrying the core haplotype are identical by descent [50,51]. The iHS compares the EHH between alleles within the same population [51].…”

Section: Signatures Of Selectionmentioning

confidence: 99%

Detection of selection signatures in the genome of a farmed population of anadromous rainbow trout (Oncorhynchus mykiss)

Cádiz¹,

López²,

Díaz-Domínguez³

et al. 2021

Genomics

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“…The iHS test can avoid the impact of heterogeneous recombination rates across whole genome of cattle. This iHS method is best performed when the selected allele segregates at intermediate frequencies in the population (Zhang et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

Identification of Selection Signals Through Haplotype Structure in Genome of Dual-Purpose Breeds

Olšanská¹,

Kasarda²,

Trakovická³

et al. 2020

AgricultForest

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The aim of this study was to analyse the selection signals by the integrated haplotype homozygosity score (iHS) in dual-purpose Slovak Spotted cattle in order to clarify the effects of natural or artificial selection. Overall, 85 animals genotyped by a high-density SNP array were included in the analysis. After quality control, 35995 autosomal loci with an average adjacent SNP spacing of 69.3 kb were included in the analysis. Then, haplotypes were reconstructed for each chromosome. Next, the R package rehh was used to compute the score based on a matrix of integrated extended haplotype homozygosity statistics for both ancestral and derived alleles. The average iHS score across the genome was 0.83. The selection signals in the genome had positive iHS values. A common iHS score (higher than 2.5) was chosen to indicate genomic regions with extreme iHS frequency due to outliers (according to the boxplot distribution). In each region with selection signals, quantitative trait loci (QTLs) were identified. For BTA s 3, 6, 8 and 21, signals were identified in regions of milk production. Marbling scores, QTLs and signals within BTA 12 were placed around QTLs for calving ease. Based on the results, we can conclude that the identified regions in the genome that are affected by positive selection correspond to the breeding goals for Slovak Spotted cattle.

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Detection of Selection Signatures Based on the Integrated Haplotype Score in Chinese Jinnan Cattle

Cited by 3 publications

References 27 publications

Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus)

Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus)

Detection of selection signatures in the genome of a farmed population of anadromous rainbow trout (Oncorhynchus mykiss)

Identification of Selection Signals Through Haplotype Structure in Genome of Dual-Purpose Breeds

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