A genome scan for quantitative trait loci affecting three ear traits in a White Duroc × Chinese Erhualian resource population

Ma, Junwu; Qi, Wencheng; Ren, D. R.; Duan, Yanyu; Qiao, Ruimin; Guo, Yuanmei; Yang, Zhangping; Li, L.; Milan, Denis; Ren, Jun; Huang, Lusheng

doi:10.1111/j.1365-2052.2009.01867.x

Cited by 20 publications

(25 citation statements)

References 19 publications

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“…A total of 19 annotated genes containing peroxisome proliferator-activated receptor delta ( PPARD ) are located in the 971-kb region. Similar to our results, a QTL for ear size was previously mapped to an interval of 55.08-Mb (12.74–67.82 Mb) on SSC7 using a genome scan of a White Duroc×Erhualian intercross population [4]. Further, PPARD was reported to be the responsible gene for ear size at the SSC7 locus and the G32E was identified to be the casual mutation [6].…”

Section: Resultssupporting

confidence: 86%

“…The most significant SNP was H3GA0016181 and can explain 53.09% of the phenotypic variance. An ear-size QTL has been reportedly mapped to 57.9–101.6 cM (12.7–67.8 Mb) on SSC5 [4]. The present significant SNPs were all located within this QTL interval.…”

Section: Resultsmentioning

confidence: 55%

“…Although there are large differences in the mechanisms determining ear-size diversity and ear disease (e.g., microtia), genetic research on porcine ear size can contribute to the understanding of human ear development and abnormalities. In pig, the quantitative trait loci (QTL) for ear size were mapped on Sus Scrofa Chromosome (SSC) 1, 4, 5, 6, 7, 8, 9, 11, 12, 16, and X [4], [5], and in which the two most significant QTL were on SSC5 and SSC7, respectively. Recently, a missense mutation, G32E, in PPARD in the QTL interval on SSC7 was identified as the causative mutation for ear size [6].…”

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Scan Reveals LEMD3 and WIF1 on SSC5 as the Candidates for Porcine Ear Size

et al. 2014

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The quantitative trait loci (QTL) for porcine ear size was previously reported to mainly focus on SSC5 and SSC7. Recently, a missense mutation, G32E, in PPARD in the QTL interval on SSC7 was identified as the causative mutation for ear size. However, on account of the large interval of QTL, the responsible gene on SSC5 has not been identified. In this study, an intercross population was constructed from the large-eared Minzhu, an indigenous Chinese pig breed, and the Western commercial Large White pig to examine the genetic basis of ear size diversity. A GWAS was performed to detect SNPs significantly associated with ear size. Thirty-five significant SNPs defined a 10.78-Mb (30.14–40.92 Mb) region on SSC5. Further, combining linkage disequilibrium and haplotype sharing analysis, a reduced region of 3.07-Mb was obtained. Finally, by using a selective sweep analysis, a critical region of about 450-kb interval containing two annotated genes LEMD3 and WIF1 was refined in this work. Functional analysis indicated that both represent biological candidates for porcine ear size, with potential application in breeding programs. The two genes could also be used as novel references for further study of the mechanism underlying human microtia.

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Section: Resultssupporting

confidence: 86%

Section: Resultsmentioning

confidence: 55%

Section: Introductionmentioning

confidence: 99%

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Genome-Wide Scan Reveals LEMD3 and WIF1 on SSC5 as the Candidates for Porcine Ear Size

et al. 2014

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“…Whereas pigs used to be bred for high fat deposition, in modern pig production systems lean meat is desired. AZGP1 also overlaps with a 16 Mb QTL for ear size, area and weight [38] and a 8.5 Mb QTL for vertebra number [39]. Ear morphology traits have been traditionally used to define breed standards.…”

Section: Discussionmentioning

confidence: 99%

Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds

et al. 2014

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BackgroundA major concern in conservation genetics is to maintain the genetic diversity of populations. Genetic variation in livestock species is threatened by the progressive marginalisation of local breeds in benefit of high-output pigs worldwide. We used high-density SNP and re-sequencing data to assess genetic diversity of local pig breeds from Europe. In addition, we re-sequenced pigs from commercial breeds to identify potential candidate mutations responsible for phenotypic divergence among these groups of breeds.ResultsOur results point out some local breeds with low genetic diversity, whose genome shows a high proportion of regions of homozygosis (>50%) and that harbour a large number of potentially damaging mutations. We also observed a high correlation between genetic diversity estimates using high-density SNP data and Next Generation Sequencing data (r = 0.96 at individual level). The study of non-synonymous SNPs that were fixed in commercial breeds and also in any local breed, but with different allele, revealed 99 non-synonymous SNPs affecting 65 genes. Candidate mutations that may underlie differences in the adaptation to the environment were exemplified by the genes AZGP1 and TAS2R40. We also observed that highly productive breeds may have lost advantageous genotypes within genes involve in immune response – e.g. IL12RB2 and STAB1–, probably as a result of strong artificial in the intensive production systems in pig.ConclusionsThe high correlation between genetic diversity computed with the 60K SNP and whole genome re-sequence data indicates that the Porcine 60K SNP Beadchip provides reliable estimates of genomic diversity in European pig populations despite the expected bias. Moreover, this analysis gave insights for strategies to the genetic characterization of local breeds. The comparison between re-sequenced local pigs and re-sequenced commercial pigs made it possible to report candidate mutations to be responsible for phenotypic divergence among those groups of breeds. This study highlights the importance of low input breeds as a valuable genetic reservoir for the pig production industry. However, the high levels of ROHs, inbreeding and potentially damaging mutations emphasize the importance of the genetic characterization of local breeds to preserve their genomic variability.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-601) contains supplementary material, which is available to authorized users.

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“…[5] identified two significant QTL with a major effect on ear size on SSC5 and SSC7 in a Large White × Meishan F 2 resource population. Another study involving a White Duroc × Erhualian F 2 intercross also detected two major QTL for ear size on the same chromosomes, which explained more than 45% and 17% of the phenotypic variance, respectively [6]. Although the genetic positions of the QTL were different (51 cM vs. 70 cM on SSC5 and 70 cM vs. 58 cM on SSC7), the 95% confidence interval of both QTL overlapped partly in the two studies.…”

Section: Introductionmentioning

confidence: 99%

Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene

Xiao

Wei

et al. 2012

Genet Sel Evol

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BackgroundEar size and shape are distinct conformation characteristics of pig breeds. Previously, we identified a significant quantitative trait locus (QTL) influencing ear surface on pig chromosome 5 in a White Duroc × Erhualian F2 resource population. This QTL explained more than 17% of the phenotypic variance.MethodsFour new markers on pig chromosome 5 were genotyped across this F2 population. RT-PCR was performed to obtain expression profiles of different candidate genes in ear tissue. Standard association test, marker-assisted association test and F-drop test were applied to determine the effects of single nucleotide polymorphisms (SNP) on ear size. Three synthetic commercial lines were also used for the association test.ResultsWe refined the QTL to an 8.7-cM interval and identified three positional candidate genes i.e. HMGA2, SOX5 and PTHLH that are expressed in ear tissue. Seven SNP within these three candidate genes were selected and genotyped in the F2 population. Of the seven SNP, HMGA2 SNP (JF748727: g.2836 A > G) showed the strongest association with ear size in the standard association test and marker-assisted association test. With the F-drop test, F value decreased by more than 97% only when the genotypes of HMGA2 g.2836 A > G were included as a fixed effect. Furthermore, the significant association between g.2836 A > G and ear size was also demonstrated in the synthetic commercial Sutai pig line. The haplotype-based association test showed that the phenotypic variance explained by HMGA2 was similar to that explained by the QTL and at a much higher level than by SOX5. More interestingly, HMGA2 is also located within the dog orthologous chromosome region, which has been shown to be associated with ear type and size.ConclusionsHMGA2 was the closest gene with a potential functional effect to the QTL or marker for ear size on chromosome 5. This study will contribute to identify the causative gene and mutation underlying this QTL.

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A genome scan for quantitative trait loci affecting three ear traits in a White Duroc × Chinese Erhualian resource population

Cited by 20 publications

References 19 publications

Genome-Wide Scan Reveals LEMD3 and WIF1 on SSC5 as the Candidates for Porcine Ear Size

Genome-Wide Scan Reveals LEMD3 and WIF1 on SSC5 as the Candidates for Porcine Ear Size

Whole-genome sequence analysis reveals differences in population management and selection of European low-input pig breeds

Fine mapping of a QTL for ear size on porcine chromosome 5 and identification of high mobility group AT-hook 2 (HMGA2) as a positional candidate gene

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