Genetic evidence for the introgression of Western <i>NR6A1</i> haplotype into Chinese Licha breed associated with increased vertebral number

Resequencing a number of individuals of various breeds as reference population and imputing the whole-genome sequences of individuals that were genotyped with medium-density chips to perform an association study is a very efficient strategy. Previously, we performed a genome-wide association study (GWAS) of lumbar number using 60K SNPs from the porcine Illumina chips in 418 Sutai pigs and did not detect any significant signals. Therefore, we imputed the whole-genome sequences of 418 Sutai individuals from 403 deeply resequenced reference individuals and performed association tests. We identified a quantitative trait locus (QTL) for lumbar number in SSC1 with a P value of 9.01E-18 that was close to the potential causative gene of NR6A1. The result of conditioning on the top SNP association test indicated that only one QTL was responsible for this trait in SSC1. The linkage disequilibrium (LD) drop test result for the condition of the reported potential causative mutation (c.575T > C missense mutation of NR6A1) indicated that this mutation was probably not the underlying mutation that affected lumbar number in our study. As the first trial of imputed whole-genome sequence GWAS in swine, this approach can be also powerful to investigate complex traits in pig like in human and cattle.

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“…41 . Briefly, a 360 bp segment was amplified and cut into two pieces of 183 and 177 bp for allele C at the position of 299,084,752 bp on SSC1.…”

Section: Methodsmentioning

confidence: 99%

Imputation-Based Whole-Genome Sequence Association Study Rediscovered the Missing QTL for Lumbar Number in Sutai Pigs

Yan

Qiao

Zhang

et al. 2017

Sci Rep

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“…Mikawa et al (2007) showed that a missense mutation in the nuclear receptor subfamily 6, group A, member 1 (NR6A1) gene is the most probable causative mutation for the QTL on SSC1. This mutation is fixed for the allele associated with larger number of thoracic and lumbar vertebrae in most commercial pig breeds (Mikawa et al, 2007;Yang et al, 2009;Ruben et al, 2012), including Italian Large White (Fontanesi et al, manuscript in preparation). Therefore, this polymorphism is not suitable for association studies with production traits in these breeds.…”

Section: Introductionmentioning

confidence: 96%

Investigation of a Short Interspersed Nuclear Element Polymorphic Site in the PorcineVertninGene: Allele Frequencies and Association Study With Meat Quality, Carcass and Production Traits in Italian Large White pigs

Scotti

Buttazzoni²,

Dall’Olio

et al. 2014

Italian Journal of Animal Science

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A 291 bp short interspersed nuclear element (SINE) insertion in the porcine vertnin (VRTN) gene on porcine chromosome 7 was shown to affect vertebral number and several production traits: allele Q (with the insertion) increases vertebral number compared to the wild type allele (WT, without insertion). In this study we genotyped this polymorphism in eight pig breeds (Italian Large White, Italian Duroc, Italian Landrace, Cinta Senese, Mora Romagnola, Casertana, Apulo Calabrese, and Nero Siciliano) and in Italian wild boars to evaluate allele frequency distribution of the two alleles. Allele Q was the most frequent in Italian Landrace and Italian Duroc (0.738 and 0.545, respectively) whereas it was the less frequent in all other breeds and was absent in wild boars. Association study was carried out in two Italian Large White samples. These two groups of animals were constituted by performance tested pigs for which estimated breeding values (EBV) and random residuals (RR) for several traits (average daily gain, back fat thickness, feed:gain ratio, lean cuts and ham weight) were calculated: i) 270 pigs chosen without any criteria (random group), that were also measured for several meat quality traits; ii) 560 gilts with extreme and divergent EBV for back fat thickness. For these animals vertebral number was not available. Results of the association analyses indicated that allele Q was associated with a lower ham weight, confirming indirectly, the negative correlation reported by other studies between vertebral number and this trait. No other trait was associated with the analysed VRTN polymorphism.

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“…However, genetic variation of NR6A1 / GCNF was not detected in today's commercial-breed pigs, and they have no fewer than 20 vertebrae. Interestingly, the number-increasing-type (Leu-type) alleles were also detected in some Chinese indigenous breeds, in which introgression of Western germplasm has occurred with aim of improving their productivity and the number of vertebrae has increased [8]. …”

Section: Introductionmentioning

confidence: 99%

Identification of a second gene associated with variation in vertebral number in domestic pigs

Mikawa

Sato

Nii³

et al. 2011

BMC Genet

120

147

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BackgroundThe number of vertebrae in pigs varies and is associated with body size. Wild boars have 19 vertebrae, but European commercial breeds for pork production have 20 to 23 vertebrae. We previously identified two quantitative trait loci (QTLs) for number of vertebrae on Sus scrofa chromosomes (SSC) 1 and 7, and reported that an orphan nuclear receptor, NR6A1, was located at the QTL on SSC1. At the NR6A1 locus, wild boars and Asian local breed pigs had the wild-type allele and European commercial-breed pigs had an allele associated with increased numbers of vertebrae (number-increase allele).ResultsHere, we performed a map-based study to define the other QTL, on SSC7, for which we detected genetic diversity in European commercial breeds. Haplotype analysis with microsatellite markers revealed a 41-kb conserved region within all the number-increase alleles in the present study. We also developed single nucleotide polymorphisms (SNPs) in the 450-kb region around the QTL and used them for a linkage disequilibrium analysis and an association study in 199 independent animals. Three haplotype blocks were detected, and SNPs in the 41-kb region presented the highest associations with the number of vertebrae. This region encodes an uncharacterized hypothetical protein that is not a member of any other known gene family. Orthologs appear to exist not only in mammals but also birds and fish. This gene, which we have named vertnin (VRTN) is a candidate for the gene associated with variation in vertebral number. In pigs, the number-increase allele was expressed more abundantly than the wild-type allele in embryos. Among candidate polymorphisms, there is an insertion of a SINE element (PRE1) into the intron of the Q allele as well as the SNPs in the promoter region.ConclusionsGenetic diversity of VRTN is the suspected cause of the heterogeneity of the number of vertebrae in commercial-breed pigs, so the polymorphism information should be directly useful for assessing the genetic ability of individual animals. The number-increase allele of swine VRTN was suggested to add an additional thoracic segment to the animal. Functional analysis of VRTN may provide novel findings in the areas of developmental biology.

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Genetic evidence for the introgression of Western NR6A1 haplotype into Chinese Licha breed associated with increased vertebral number

Cited by 43 publications

References 8 publications

Imputation-Based Whole-Genome Sequence Association Study Rediscovered the Missing QTL for Lumbar Number in Sutai Pigs

Imputation-Based Whole-Genome Sequence Association Study Rediscovered the Missing QTL for Lumbar Number in Sutai Pigs

Investigation of a Short Interspersed Nuclear Element Polymorphic Site in the PorcineVertninGene: Allele Frequencies and Association Study With Meat Quality, Carcass and Production Traits in Italian Large White pigs

Identification of a second gene associated with variation in vertebral number in domestic pigs

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