Whole-genome association study for the roan coat color in an intercrossed pig population between Landrace and Korean native pig

Cho, In-Cheol; Zhong, Tao; Seo, Bo-Young; Jung, Eun Ji; Yoo, Chae-Kyoung; Kim, Jaehwan; Lee, Jae-Bong; Lim, Hyun‐Tae; Kim, Byoung-Woo; Lee, Jun Heon; Ko, Moon-Suck; Jeon, Jin-Tae

doi:10.1007/s13258-010-0108-4

Cited by 12 publications

(14 citation statements)

References 33 publications

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“…Characterization of the equine KIT locus has found multiple independent mutations that are presumed to be responsible for dominant white-spotting (Haase et al 2007) Furthermore, cattle breeds carrying different putative alleles at the spotting locus show genetic heterogeneity within the KIT gene (Fontanesi et al 2010). KIT has been implicated in white-spotting patterns in many species but also in roan coat color in horses and pigs (Marklund et al 1999;Cho et al 2011).…”

Section: Discussionmentioning

confidence: 99%

The Genetic Inheritance of the Blue-eyed White Phenotype in Alpacas (Vicugna pacos)

Jackling¹,

Johnson²,

Appleton³

2012

JHERED

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White-spotting patterns in mammals can be caused by mutations in the gene KIT, whose protein is necessary for the normal migration and survival of melanocytes from the neural crest. The alpaca (Vicugna pacos) blue-eyed white (BEW) phenotype is characterized by 2 blue eyes and a solid white coat over the whole body. Breeders hypothesize that the BEW phenotype in alpacas is caused by the combination of the gene causing gray fleece and a white-spotting gene. We performed an association study using KIT flanking and intragenic markers with 40 unrelated alpacas, of which 17 were BEW. Two microsatellite alleles at KIT-related markers were significantly associated (P < 0.0001) with the BEW phenotype (bew1 and bew2). In a larger cohort of 171 related individuals, we identify an abundance of an allele (bew1) in gray animals and the occurrence of bew2 homozygotes that are solid white with pigmented eyes. Association tests accounting for population structure and familial relatedness are consistent with a proposed model where these alleles are in linkage disequilibrium with a mutation or mutations that contribute to the BEW phenotype and to individual differences in fleece color.

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Section: Discussionmentioning

confidence: 99%

The Genetic Inheritance of the Blue-eyed White Phenotype in Alpacas (Vicugna pacos)

Jackling¹,

Johnson²,

Appleton³

2012

JHERED

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“…The candidacy of this gene was established based on findings in other animals. The KIT gene has been identified or implicated to be related to white color or white-spotting in alpacas (Jackling et al, 2014), cows (Fontanesi et al, 2010), yaks (Zhang et al, 2014), pigs (Cho et al, 2011), goats (Nazari-Ghadikolaei et al, 2018), horses (Hauswirth et al, 2013), donkeys (Haase et al, 2015), cats (David et al, 2014), dogs (Wong et al, 2012), mice (Geissler et al, 1988), and rabbits (Fontanesi et al, 2014). Thus, applying a candidate gene approach to camels requires the presence of the phenotype in other mammals and a manageable number of candidate genes to be sequenced.…”

Section: Introductionmentioning

confidence: 99%

Cdrom Archive: A Gateway to Study Camel Phenotypes

Alhaddad

Alhajeri

2019

Front. Genet.

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Camels are livestock that exhibit unique morphological, biochemical, and behavioral traits, which arose by natural and artificial selection. Investigating the molecular basis of camel traits has been limited by: (1) the absence of a comprehensive record of morphological trait variation (e.g., diseases) and the associated mode of inheritance, (2) the lack of extended pedigrees of specific trait(s), and (3) the long reproductive cycle of the camel, which makes the cost of establishing and maintaining a breeding colony (i.e., monitoring crosses) prohibitively high. Overcoming these challenges requires (1) detailed documentation of phenotypes/genetic diseases and their likely mode of inheritance (and collection of related DNA samples), (2) conducting association studies to identify phenotypes/genetic diseases causing genetic variants (instead of classical linkage analysis, which requires extended pedigrees), and (3) validating likely causative variants by screening a large number of camel samples from different populations. We attempt to address these issues by establishing a systematic way of collecting camel DNA samples, and associated phenotypic information, which we call the “Cdrom Archive.” Here, we outline the process of building this archive to introduce it to other camel researchers (as an example). Additionally, we discuss the use of this archive to study the phenotypic traits of Arabian Peninsula camel breeds (the “Mezayen” camels). Using the Cdrom Archive, we report variable phenotypic traits related to the coat (color, length, and texture), ear and tail lengths, along with other morphological measurements.

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“…To detect mutations in the coding region of the porcine KIT gene, eight F2 animals expressing representative coat colors were selected from an F2 population resulting from the interbreeding of Landrace and KNP swine (Cho et al, 2010). Two animals were randomly selected for the detection of tissue-specific AS patterns.…”

Section: Preparation Of Animals and Nucleic Acidsmentioning

confidence: 99%

“…The molecular basis of this phenotype has not been explored, although these animals have been confirmed to possess a single KIT copy without a splice mutation, as the recessive wild type i contributes to a solid or wild coat color. Recently, a novel allele, I Rn , associated with a roan phenotype has been identified in an interbred population of Landrace and Korean Native pigs (Cho et al, 2010).…”

Section: Introductionmentioning

confidence: 99%

Characterization of an alternative splicing by a NAGNAG splice acceptor site in the porcine KIT gene

et al. 2011

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The KIT gene has been shown to have multiple functions in hematopoiesis, melanogenesis, and gametogenesis. In addition, mutations of this gene cause pigmentation disorders in humans and mice and are responsible for coat color differences in pigs. While characterizing polymorphisms in the porcine KIT gene, we detected alternative splicing (AS) of the NAGNAG splice acceptor site at the boundary of intron 4 and exon 5. This AS event generated the E and I isoforms, characterized by insertion or deletion, respectively, of CAG at the borders of coding sequence. AS patterns measured in tissue samples from two randomly selected animals did not identified any tissue-specific outcomes. Analysis of AS patterns using three breeds demonstrated that Landrace and Large White pigs expressed both the E and I isoforms. In contrast, a subset of specimens from Korean Native Pigs (KNP) yielded a single I isoform. Alignment of the sequence from several species revealed that the region between the branch point sequence (BPS) and 3′ acceptor site is conserved. However, it is appeared that the selection of either the proximal or distal splice site varied between species. To test the breed specificity the NAGNAG splice acceptor site, we constructed two lineages of minigenes from KNP and Landrace pigs harboring breed-specific mutations. The minigene splicing assay demonstrated that both types of minigenes expressed both the E and I isoforms in two host cell lines, and no differences were detected in the AS pattern between the two breeds. We conclude that the AS at the NAGNAG splice acceptor site on intron 4/exon 5 in the porcine KIT gene is the result of noise selection at the splice site by the splicing machinery. Therefore, this AS event in the porcine KIT gene is unlikely to have any relationship with the coat color variations of Landrace and KNP breeds.

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Whole-genome association study for the roan coat color in an intercrossed pig population between Landrace and Korean native pig

Cited by 12 publications

References 33 publications

The Genetic Inheritance of the Blue-eyed White Phenotype in Alpacas (Vicugna pacos)

The Genetic Inheritance of the Blue-eyed White Phenotype in Alpacas (Vicugna pacos)

Cdrom Archive: A Gateway to Study Camel Phenotypes

Characterization of an alternative splicing by a NAGNAG splice acceptor site in the porcine KIT gene

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