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Genome-Wide Scans for Detecting the Selection Signature of the Jeju-Island Native Pig in Korea

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Genome-Wide Scans for Detecting the Selection Signature of the Jeju-Island Native Pig in Korea Open Access Asian-Australas J Anim Sci Vol. 33, No. 4:539-546 April 2020 https://doi.org/10.5713/ajas.19.0026 pISSN 1011-2367 eISSN 1976-5517 Genome-wide scans for detecting the selection signature of the Jeju-island native pig in Korea Young-Sup Lee1,a, Donghyun Shin1,2,a, Kyeong-Hye Won1, Dae Cheol Kim3, Sang Chul Lee4,*, and Ki-Duk Song1,2,* * Corresponding Authors: Objective: The Jeju native pig (JNP) found on the Jeju Island of Korea is a unique black pig Sang Chul Lee Tel: +82-43-716-2300, Fax: +82-43-716-2301, known for high-quality meat. To investigate the genetic uniqueness of JNP, we analyzed the E-mail: [email protected] selection signature of the JNP in comparison to commercial pigs such as Berkshire and Ki-Duk Song Yorkshire pigs. Tel: +82-63-219-5523, Fax: +82-63-270-2937, E-mail: [email protected] Methods: We surveyed the genetic diversity to identify the genetic stability of the JNP, using the linkage disequilibrium method. A selective sweep of the JNP was performed to identify 1 Department of Animal Biotechnology, Jeonbuk the selection signatures. To do so, the population differentiation measure, Weir-Cockerham’s National University, Jeonju 54896, Korea 2 The Animal Molecular Genetics and Breeding Center, Fst was utilized. This statistic directly measures the population differentiation at the variant Jeonbuk National University, Jeonju 54896, Korea level. Additionally, we investigated the gene ontologies (GOs) and genetic features. 3 Livestock Promotion Agency, Jeju Special Self- Results: Compared to the Berkshire and Yorkshire pigs, the JNP had lower genetic diversity Governing Province, Jeju 63122, Korea 4 Cronex Co., Cheongju 28174, Korea in terms of linkage disequilibrium decays. We summarized the selection signatures of the JNP as GO. In the JNP and Berkshire pigs, the most enriched GO terms were epithelium a The authors equally contributed to this work. development and neuron-related. Considering the JNP and Yorkshire pigs, cellular response ORCID to oxygen-containing compound and generation of neurons were the most enriched GO. Young-Sup Lee Conclusion: The selection signatures of the JNP were identified through the population https://orcid.org/0000-0001-9267-0850 differentiation statistic. The genes with possible selection signatures are expected to play a Donghyun Shin role in JNP’s unique pork quality. https://orcid.org/0000-0002-0819-0553 Kyeong-Hye Won https://orcid.org/0000-0001-8112-2840 Keywords: Jeju Island Native Pig; Berkshire Pig; Linkage Disequilibrium; Population Dae Cheol Kim Differentiation Statistic; Selection Signatures; Yorkshire Pig https://orcid.org/0000-0002-4740-0154 Sang Chul Lee https://orcid.org/0000-0002-9341-3255 Ki-Duk Song https://orcid.org/0000-0003-2827-0873 Submitted Jan 10, 2019; Revised May 3, 2019; INTRODUCTION Accepted Jun 11, 2019 Of the various pig breeds, the Jeju native pig (JNP) can be considered as one of the repre- sentatives of Korean native black pig (KNBP) [1]. The JNP has black skin, erect, unfolded ears and is well-known for its tender and juicy meat. Consumers prefer JNP meat because of its superior taste, tenderness and marbling quality compared to the meat from western breeds [2]. JNP meat can be regarded as one of the best pork in Korea. The uniqueness of the JNP meat may come from the distinct climate of Jeju Island of Korea and the life pattern of the people of Jeju Island. Notably, the winter temperature on Jeju Island remains above zero and the JNP are used to dispose of human waste. These factors might change the allele patterns in the JNP genome compared to other pig breeds. JNP has problems of lower feed efficiency and smaller litter sizes as compared to Berkshire pig breeds [2]. Thus to under- stand the uniqueness of the JNP and JNP pork quality, a comparative genomic study between the JNP and other commercial pig breeds like Berkshire or Yorkshire pigs, is needed. In a previous study, Ghosh et al [3] used RNA-seq to identify pork quality-related genes. Population differentiation (subdivision) is a fundamental process of evolution and its infer- Copyright © 2020 by Asian-Australasian Journal of Animal Sciences This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and repro- www.ajas.info duction in any medium, provided the original work is properly cited. 539 Lee et al (2020) Asian-Australas J Anim Sci 33:539-546 ence is required for genetics, phylogeography and conservation Structure analysis and linkage disequilibrium 105 diversity of the JNP, Berkshire and Yorkshire pigs. Linkage disequilibrium is the nonrandom biology. It can be recognized as “fundamental” because every To understand the characteristics of the JNP, Berkshire and 105 diversity of the JNP, Berkshire and Yorkshire pigs. Linkage disequilibrium is the nonrandom 106 speciesassociations unavoidably of alleles undergoes at two population loci, A and differentiation, B. Linkage disequilbrium Yorkshire is usuallypig populations, used to assess structure the analysis genetic was performed and it may lead to new106 speciation associations or extinction of alleles under certainat two loci, Awith and theB. Linkagestructure disequilbrium program [8]. Weis usually set the used5,000 to iterations assess the genetic 107 conditions.diversity Additionally, of a given genetic population, differentiation estimation of ofpopulations effective populationafter the size burn-in and population 5,000 iterations genetic and stability. K = 3, 4, and 5. We eval- can be the result of uneven107 (nonrandom)diversity of a spatialgiven population,distribu- estimationuated the of JNP’s effective purity population and structure size analysis and population showed that genetic the stability. 2 108 tionUsing of genetic the variationR package and “LDc alleleorSV”, frequencies we examined in a species. all105 pairwise diversityJNP r wasdecay mixedofs withthe with JNP,100 Berkshire SNPBerkshire bins in part.along and Thus, theYorkshire we eliminated pigs. Linkage disequilibrium is the nonrandom 2 The fixation index, Fst108, is the Usingmeasure the of R population package “LDcdiffer-orSV”, impurewe examined JNP individuals all pairwise for the r nextdecay analysis.s with 100 SNP bins along the 109 entiationphysical [4]. distance [9]. The formula based on this is as105106 follow diversityassociations s: The correlation of ofthe alleles JNP, coefficient at Berkshire two loci, of Atheand and linkage YorkshireB. Linkage disequilibrium pigs. disequilbrium Linkage isdisequilibriu usually usedm tois assess the nonrandomthe genetic In previous study, Kim109 et al physical[5], used distancethe cross-population [9]. The formula based(r2) was on computed this is as followto assesss: the genetic diversity of the JNP, 110 extended haplotype homozygosity (XP-EHH) and cross pop106107- associationsdiversityBerkshire of and aof given Yorkshire alleles population, at pigs.two loci,Linkage estimation A and disequilibrium B. of Linkage effective disequilbriumis thepopulation size is usually and population used to assess genetic the stability. genetic ulation composite likelihood110 ratio (XP-CLR) to identify the nonrandom associations of alleles at two loci, A and B. Linkage 2 111 putative selection signature causes of meat quality of JNP. The107108 diversityUsingdisequilibrium the of R a packagegiven is usually population, “LDc usedorSV”, to estimation assess we the examined genetic of effective diversityall pairwise population r decay size ands with population 100 SNP genetic bins along stability. the 2 (1) 2 111 XP-EHH statistic examines the haplotype difference2 between of (1)a given population, estimation of effective population 2 = 108109 Usingphysical the distance R package [9]. The“LDc formulaorSV”, basedwe examined on this is all as pairwisefollows: r decays with 100 SNP bins along the 112 two populations and detects alleles that2 have increased in fre- size and population genetic stability. Using the R package = 2 quency at the point of fixation112 or near-fixation. The haplotypes “LDcorSV”, we examined all pairwise r decays with 100 109110 physical distance [9]. The formula based on this is as follows: 113 that warehere frequent isand the have linkage longer disequilibrium than expected of values two alleles are A, BSNP and bins PX isalong the frequencythe physical of distance major allele [9]. The X formula based regarded as being positively selected. Alternatively, XP-CLR on this is as follows: 2 113 where is the linkage disequilibrium110 of two alleles A, B and PX is the frequency of major allele X 111 114 evaluatesand P Xthe is allelethe frequency frequency of differentiation minor allele2 x. between two 2 (1) 2 populations to assess 114the candidateand PX regions is the frequency of the selective of minor allele x. 111 = (1) 115 sweeps. Selective sweep regions can be considered to be highly112 2 (1) positive-selected. Oh 115et al [6], used the F of the microsatel- 2 st = 116 lite markersPopulation of JNP differentiation to assess meat analysisquality. Our approach was112113 wwherehere isis the the linkage linkage disequilibrium disequilibrium of of two two alleles alleles A, A,B B and PX is the frequency of major allele X 116 to use Fst of single nucleotide polymorphismPopulation differentiation (SNP) markers. analysisand PX is2 the frequency of major allele X and PX is the fre- 117 InWe this used study, the we population aimed to revealdifferentiation genomic differencesstatistic (F stand)113114 to find wandselectionquencyhere PX is of thesignature minor is frequency the allele linkages of x. the of disequilibriumminorJNP breeds allele. x.The of two alleles A, B and PX is the frequency of major allele X the selective sweep regions117 of Wethe usedJNP inthe comparison population to differentiation the statistic2 (Fst) to find selection signatures of the JNP breeds. The 118 reference pig breeds were Berkshire and Yorkshire. Berkshire and Yorkshire pigs are worldwide Berkshire and Yorkshire breeds using the fixation index. 114115The and Population PX is the differentiationfrequency of minor analysis allele x.
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