Large-effect pleiotropic or closely linked QTL segregate within and across ten US cattle breeds

Saatchi, Mahdi; Schnabel, Robert D.; Taylor, Jeremy F.; Garrick, Dorian J.

doi:10.1186/1471-2164-15-442

Cited by 198 publications

(194 citation statements)

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“…2012; Saatchi et al . 2014). The association may be explained by an increase in birth weight and length due to the height‐increasing allele, although the authors mentioned other candidate genes.…”

Section: Ncapg‐lcorlmentioning

confidence: 99%

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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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Section: Ncapg‐lcorlmentioning

confidence: 99%

“…In cattle, several major loci including PLAG1 and NCAPG‐LCORL explained more than a third of genetic variance in a breed (Saatchi et al . 2014). In horses, only the LCORL region explained 11% and 18% of the phenotypic variance in Franches‐Montagnes and German Warmblood, respectively (Signer‐Hasler et al .…”

Section: Genetic Architecture For Staturementioning

confidence: 99%

PLAG1 and NCAPG‐LCORL in livestock

Takasuga

2015

Animal Science Journal

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“…Although not reported in Table 3 due to P-values slightly .10 24 ; five other suggestive polymorphisms are located within MAGI1 introns. One of these, at position 36,011,838, is located within a highly conserved region according to a multiple alignment of 36 eutherian mammals (www.ensembl.org).…”

Section: Hard-sweep Signalsmentioning

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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“…Interestingly, the results showed that 47 of 61 candidate genes located in QTL regions were associated with meat and carcass traits, and 11 of 61 candidate genes were reported to be associated with meat and carcass traits on the basis of GWAS data. All these 11 genes were present in the 47 candidate genes in QTL regions associated with meat and carcass traits, including chromosome 8 open reading frame 22, CA8, gamma-glutamyl hydrolase, neuropeptides B/W receptor 1, opioid receptor, kappa 1, PCMTD1, RAB2A, RB1-inducible coiled-coil 1, tocopherol (alpha) transfer protein, leucine rich adaptor protein 1-like, and tyrosinase-related protein-1 (Doran et al, 2014;McClure et al, 2012;Nalaila et al, 2012;Nishimura et al, 2012;Saatchi et al, 2014;Veneroni-Gouveia et al, 2012). These results suggested that the Jinnan breed has high genetic potential for beef cattle breeding.…”

Section: Discussionmentioning

confidence: 99%