Adipose and Muscle Tissue Gene Expression of Two Genes (NCAPG and LCORL) Located in a Chromosomal Region Associated with Cattle Feed Intake and Gain

Lindholm‐Perry, A. K.; Kuehn, L. A.; Oliver, W. T.; Sexten, Andrea K.; Miles, Jeremy R.; Rempel, Lea A.; Cushman, Robert A.; Freetly, H. C.

doi:10.1371/journal.pone.0080882

Cited by 60 publications

(38 citation statements)

References 24 publications

(44 reference statements)

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“…Isolated mouse homologs, Mlr1 and Mlr2, were identified as transcription factors with Mlr1 predominantly expressed in spermatocytes of the testis and suggesting a role in spermatogenesis (31). The LCORL/NCAPG genes have already been identified in other association studies for height in humans, cattle, and horses (13,30,32,34,37,41,43,48,56,58,62,63,66). In humans and horses no causative mutation in the coding sequence of LCORL or NCAPG has been identified (13,56).…”

Section: Discussionmentioning

confidence: 97%

Skeletal variation in Tennessee Walking Horses maps to theLCORL/NCAPGgene region

Staiger

Al-Abri

Pflug

et al. 2016

Physiological Genomics

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Conformation has long been a driving force in horse selection and breed creation as a predictor for performance. The Tennessee Walking Horse (TWH) ranges in size from 1.5 to 1.7 m and is often used as a trail, show, and pleasure horse. To investigate the contribution of genetics to body conformation in the TWH, we collected DNA samples, body measurements, and gait/training information from 282 individuals. We analyzed the 32 body measures with a principal component analysis. Principal component (PC)1 captured 28.5% of the trait variance, while PC2 comprised just 9.5% and PC3 6.4% of trait variance. All 32 measures correlated positively with PC1, indicating that PC1 describes overall body size. We genotyped 109 horses using the EquineSNP70 bead chip and marker association assessed the data using PC1 scores as a phenotype. Mixed-model linear analysis (EMMAX) revealed a well-documented candidate locus on ECA3 (raw P = 3.86 × 10−9) near the LCORL gene. A custom genotyping panel enabled fine-mapping of the PC1 body-size trait to the 3′-end of the LCORL gene ( P = 7.09 × 10−10). This position differs from other reports suggesting single nucleotide polymorphisms (SNPs) upstream of the LCORL coding sequence regulate expression of the gene and, therefore, body size in horses. Fluorescent in situ hybridization analysis defined the position of a highly homologous 5 kb retrogene copy of LCORL (assigned to unplaced contigs of the EquCab 2.0 assembly) at ECA9 q12-q13. This is the first study to identify putative causative SNPs within the LCORL transcript itself, which are associated with skeletal size variation in horses.

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Section: Discussionmentioning

confidence: 97%

Skeletal variation in Tennessee Walking Horses maps to theLCORL/NCAPGgene region

Staiger

Al-Abri

Pflug

et al. 2016

Physiological Genomics

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“…Lindholm‐Perry et al . (2013) reported a negative correlation between average feed intake and LCORL transcript abundance in adipose tissue from cows ( n = 81, P = 0.02) and heifers ( n = 94, P = 0.045), while a positive correlation was detected between average feed intake and LCORL transcript abundance ( P = 0.04) or protein level ( P = 0.01) in muscle tissues from steers ( n = 31). In muscle tissues from cows ( n = 86), NCAPG transcript abundance was associated with average daily gain ( P = 0.009) (Lindholm‐Perry et al .…”

Section: Ncapg‐lcorlmentioning

confidence: 98%

“…In muscle tissues from cows ( n = 86), NCAPG transcript abundance was associated with average daily gain ( P = 0.009) (Lindholm‐Perry et al . 2013). Weikard et al .…”

Section: Ncapg‐lcorlmentioning

confidence: 99%

PLAG1 and NCAPG‐LCORL in livestock

Takasuga

2015

Animal Science Journal

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A recent progress on stature genetics has revealed simple genetic architecture in livestock animals in contrast to that in humans. PLAG1 and/or NCAPG‐LCORL, both of which are known as a locus for adult human height, have been detected for association with body weight/height in cattle and horses, and for selective sweep in dogs and pigs. The findings indicate a significant impact of these loci on mammalian growth or body size and usefulness of the natural variants for selective breeding. However, association with an unfavorable trait, such as late puberty or risk for a neuropathic disease, was also reported for the respective loci, indicating an importance to discriminate between causality and association. Here I review the recent findings on quantitative trait loci (QTL) for stature in livestock animals, mainly focusing on the PLAG1 and NCAPG‐LCORL loci. I also describe our recent efforts to identify the causative variation for the third major locus for carcass weight in Japanese Black cattle.

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“…Apart from the PLAG1 signature, several others include genes involved in morphology and growth: RUNX3 ), STARD3NL ), and RASSF2 are involved in bone development; NCAPG and/or LCORL match a large QTL for many growth traits in cattle, horses, and sheep Weikard et al 2010;Lindholm-Perry et al 2011;Makvandi-Nejad et al 2012;SignerHasler et al 2012;Lindholm-Perry et al 2013;Metzger et al 2013;Tetens et al 2013;Kijas 2014;Randhawa et al 2015;Sahana et al 2015;Xu et al 2015); and CTNNBL1 ) is associated with obesity traits in humans.…”

Section: Hapflk Signatures Of Soft or Incomplete Sweepsmentioning

confidence: 99%

Uncovering Adaptation from Sequence Data: Lessons from Genome Resequencing of Four Cattle Breeds

et al. 2016

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Detecting the molecular basis of adaptation is one of the major questions in population genetics. With the advance in sequencing technologies, nearly complete interrogation of genome-wide polymorphisms in multiple populations is becoming feasible in some species, with the expectation that it will extend quickly to new ones. Here, we investigate the advantages of sequencing for the detection of adaptive loci in multiple populations, exploiting a recently published data set in cattle (Bos taurus). We used two different approaches to detect statistically significant signals of positive selection: a within-population approach aimed at identifying hard selective sweeps and a population-differentiation approach that can capture other selection events such as soft or incomplete sweeps. We show that the two methods are complementary in that they indeed capture different kinds of selection signatures. Our study confirmed some of the well-known adaptive loci in cattle (e.g., MC1R, KIT, GHR, PLAG1, NCAPG/LCORL) and detected some new ones (e.g., ARL15, PRLR, CYP19A1, PPM1L). Compared to genome scans based on medium-or high-density SNP data, we found that sequencing offered an increased detection power and a higher resolution in the localization of selection signatures. In several cases, we could even pinpoint the underlying causal adaptive mutation or at least a very small number of possible candidates (e.g., MC1R, PLAG1). Our results on these candidates suggest that a vast majority of adaptive mutations are likely to be regulatory rather than protein-coding variants.KEYWORDS F ST ; domestication; linkage disequilibrium; next-generation sequencing; selective sweeps D ETECTING the molecular basis of adaptation in natural species is one of the major questions in population genetics. With the spectacular progress of genotyping and sequencing technologies, genome-wide scans for positive selection have been performed in multiple species and populations within the last decade. Livestock species provide a considerable resource for these selection scans, because they have been subjected to strong artificial selection since their initial domestication, leading to a large variety of breeds with distinct morphology, coat color, or specialized production. In addition, the economic value of these species and the need to improve them has motivated the development of standardized single-nucleotide polymorphism (SNP) chips and the genotyping of millions of animals using these chips, providing considerable data for population genetics analyses. For instance, in taurine cattle, at least 21 genomic scans for selection have already been published and were reviewed in GutierrezGil et al. (2015). Numerous genomic scans for selection have also been published in other livestock species; see de Simoni Gouveia et al. (2014) for a review.The regions detected by these studies are generally convincing, because they contain interesting positional and functional candidate genes (e.g., Fariello et al. 2014) and/or are statistically enriched with ...

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Adipose and Muscle Tissue Gene Expression of Two Genes (NCAPG and LCORL) Located in a Chromosomal Region Associated with Cattle Feed Intake and Gain

Cited by 60 publications

References 24 publications

Skeletal variation in Tennessee Walking Horses maps to theLCORL/NCAPGgene region

Skeletal variation in Tennessee Walking Horses maps to theLCORL/NCAPGgene region

PLAG1 and NCAPG‐LCORL in livestock

Uncovering Adaptation from Sequence Data: Lessons from Genome Resequencing of Four Cattle Breeds

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