Mapping and fine mapping of quantitative trait loci for the number of vertebrae in a <scp>W</scp>hite <scp>D</scp>uroc × <scp>C</scp>hinese <scp>E</scp>rhualian intercross resource population

Ren, D. R.; Ren, Jun; Ruan, Guorong; Guo, Yuanmei; Wu, Lihua; Yang, Guoqiang; Zhou, Lisheng; Li, L.; Zhang, Z. Y.; Huang, Lusheng

doi:10.1111/j.1365-2052.2011.02313.x

Cited by 44 publications

(46 citation statements)

References 32 publications

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“…In zebrafish, Prox2 is mainly expressed in the brain and involved in eye development [56]. Notably, both Vertnin and Prox2 have recently been proposed as candidates for the number of vertebrae in a White Duroc x Chinese Erhualian intercross, that also carries two different haplotypes for increased teat number [57]. …”

Section: Discussionmentioning

confidence: 99%

High-resolution association mapping of number of teats in pigs reveals regions controlling vertebral development

et al. 2014

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BackgroundSelection pressure on the number of teats has been applied to be able to provide enough teats for the increase in litter size in pigs. Although many QTL were reported, they cover large chromosomal regions and the functional mutations and their underlying biological mechanisms have not yet been identified. To gain a better insight in the genetic architecture of the trait number of teats, we performed a genome-wide association study by genotyping 936 Large White pigs using the Illumina PorcineSNP60 Beadchip. The analysis is based on deregressed breeding values to account for the dense family structure and a Bayesian approach for estimation of the SNP effects.ResultsThe genome-wide association study resulted in 212 significant SNPs. In total, 39 QTL regions were defined including 170 SNPs on 13 Sus scrofa chromosomes (SSC) of which 5 regions on SSC7, 9, 10, 12 and 14 were highly significant. All significantly associated regions together explain 9.5% of the genetic variance where a QTL on SSC7 explains the most genetic variance (2.5%). For the five highly significant QTL regions, a search for candidate genes was performed. The most convincing candidate genes were VRTN and Prox2 on SSC7, MPP7, ARMC4, and MKX on SSC10, and vertebrae δ-EF1 on SSC12. All three QTL contain candidate genes which are known to be associated with vertebral development. In the new QTL regions on SSC9 and SSC14, no obvious candidate genes were identified.ConclusionsFive major QTL were found at high resolution on SSC7, 9, 10, 12, and 14 of which the QTL on SSC9 and SSC14 are the first ones to be reported on these chromosomes. The significant SNPs found in this study could be used in selection to increase number of teats in pigs, so that the increasing number of live-born piglets can be nursed by the sow. This study points to common genetic mechanisms regulating number of vertebrae and number of teats.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-542) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

High-resolution association mapping of number of teats in pigs reveals regions controlling vertebral development

et al. 2014

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“…A phenotypic correlation of 0.24 between NT and number of thoracic vertebrae has been estimated [42], and a larger number of vertebrae is associated with an increase in carcass length and number of ribs [46], [47]. Thus, the region is of great interest for pig breeders with favourable pleiotropic effects on economically important traits, including mothering ability of the sows due to the increase in NT, and increased pork production per animal due to longer carcasses.…”

Section: Discussionmentioning

confidence: 99%

“…VRTN encodes a potential DNA binding factor and has been described as an essential factor for development of the embryo in different species [48]. Due to its biological function, this gene has been indicated as a candidate gene for number of vertebrae [42], [48], [49]. Recently, Fan et al .…”

Section: Discussionmentioning

confidence: 99%

A Genome-Wide Association Study Reveals Dominance Effects on Number of Teats in Pigs

et al. 2014

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Dominance has been suggested as one of the genetic mechanisms explaining heterosis. However, using traditional quantitative genetic methods it is difficult to obtain accurate estimates of dominance effects. With the availability of dense SNP (Single Nucleotide Polymorphism) panels, we now have new opportunities for the detection and use of dominance at individual loci. Thus, the aim of this study was to detect additive and dominance effects on number of teats (NT), specifically to investigate the importance of dominance in a Landrace-based population of pigs. In total, 1,550 animals, genotyped for 32,911 SNPs, were used in single SNP analysis. SNPs with a significant genetic effect were tested for their mode of gene action being additive, dominant or a combination. In total, 21 SNPs were associated with NT, located in three regions with additive (SSC6, 7 and 12) and one region with dominant effects (SSC4). Estimates of additive effects ranged from 0.24 to 0.29 teats. The dominance effect of the QTL located on SSC4 was negative (−0.26 teats). The additive variance of the four QTLs together explained 7.37% of the total phenotypic variance. The dominance variance of the four QTLs together explained 1.82% of the total phenotypic variance, which corresponds to one-fourth of the variance explained by additive effects. The results suggest that dominance effects play a relevant role in the genetic architecture of NT. The QTL region on SSC7 contains the most promising candidate gene: VRTN. This gene has been suggested to be related to the number of vertebrae, a trait correlated with NT.

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“…Necks contain cervical and thoracic vertebrae whereas loin cuts include lumbar, sacral and caudal vertebrae. Total number of vertebrae was correlated with total number of vertebrae, rib number, body length and body weight (Borchers et al, 2004;Ren et al, 2012). The QTL on SSC7 centred on VRTN affects mainly thoracic and total number of vertebrae (Mikawa et al, 2005;Ren et al, 2012).…”

Section: Vrtn Polymorphism In Pigsmentioning

confidence: 99%

“…Total number of vertebrae was correlated with total number of vertebrae, rib number, body length and body weight (Borchers et al, 2004;Ren et al, 2012). The QTL on SSC7 centred on VRTN affects mainly thoracic and total number of vertebrae (Mikawa et al, 2005;Ren et al, 2012). According to these studies, the lack of association between VRTN and LC we observed may be explained by the fact that there might be a negative or poor correlation between the length of lean cuts and their weight as, usually, shorter loins have a larger Longissimus dorsi area (Buttazzoni et al, unpublished results).…”

Section: Vrtn Polymorphism In Pigsmentioning

confidence: 99%

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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Mapping and fine mapping of quantitative trait loci for the number of vertebrae in a White Duroc × Chinese Erhualian intercross resource population

Cited by 44 publications

References 32 publications

High-resolution association mapping of number of teats in pigs reveals regions controlling vertebral development

High-resolution association mapping of number of teats in pigs reveals regions controlling vertebral development

A Genome-Wide Association Study Reveals Dominance Effects on Number of Teats in 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

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