Genome-wide association study identified three major QTL for carcass weight including the PLAG1-CHCHD7 QTN for stature in Japanese Black cattle

Nishimura, Syoyo; Watanabe, Toshio; Mizoshita, Kazunori; Tatsuda, Ken; Fujita, Tatsuo; Watanabe, Naoto; Sugimoto, Yoshikazu; Takasuga, Akiko

doi:10.1186/1471-2156-13-40

Cited by 141 publications

(193 citation statements)

References 30 publications

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“…In Japanese Black cattle, we detected the strongest association for carcass weight in an 830‐kb interval containing PLAG1 (Nishimura et al . 2012). Target resequencing revealed that the Q haplotype in Japanese Black shared only QTNs with the Q haplotype of the F1 sires reported by Karim et al .…”

Section: Plag1mentioning

confidence: 99%

“…2012). Imputation of the 50K genotypes from the GWAS to high‐density SNP genotypes and a haplotype‐based association analysis highlighted a 3.3 Mb interval as a candidate region (Takasuga A, 2014, unpublished data).…”

Section: Genetic Architecture For Staturementioning

confidence: 99%

“…For example, the causative variations at the PLAG1 locus were located within a GC‐rich region and were not covered by target resequencing (Nishimura et al . 2012). …”

Section: Genetic Architecture For Staturementioning

confidence: 99%

“…2009; Nishimura et al . 2012). The three loci together explained approximately one‐third of genetic variance of the GWAS population (Nishimura et al .…”

Section: Introductionmentioning

confidence: 99%

“…The three loci together explained approximately one‐third of genetic variance of the GWAS population (Nishimura et al . 2012). The PLAG1 and NCAPG‐LCORL regions were also detected for an association in different cattle breeds and other livestock species (Tables 1 and 2).…”

Section: Introductionmentioning

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: Plag1mentioning

confidence: 99%

Section: Genetic Architecture For Staturementioning

confidence: 99%

“…For example, the causative variations at the PLAG1 locus were located within a GC‐rich region and were not covered by target resequencing (Nishimura et al . 2012). …”

Section: Genetic Architecture For Staturementioning

confidence: 99%

“…2009; Nishimura et al . 2012). The three loci together explained approximately one‐third of genetic variance of the GWAS population (Nishimura et al .…”

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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PLAG1 and NCAPG‐LCORL in livestock

Takasuga

2015

Animal Science Journal

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GWAS analysis using interspecific backcross progenies reveals superior blue catfish alleles responsible for strong resistance against enteric septicemia of catfish

et al. 2018

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Infectious diseases pose significant threats to the catfish industry. Enteric septicemia of catfish (ESC) caused by Edwardsiella ictaluri is the most devastating disease for catfish aquaculture, causing huge economic losses annually. Channel catfish and blue catfish exhibit great contrast in resistance against ESC, with channel catfish being highly susceptible and blue catfish being highly resistant. As such, the interspecific backcross progenies provide an ideal system for the identification of quantitative trait locus (QTL). We previously reported one significant QTL on linkage group (LG) 1 using the third-generation backcrosses, but the number of founders used to make the second- and third-generation backcross progenies was very small. Although the third-generation backcross progenies provided a greater power for fine mapping than the first-generation backcrosses, some major QTL for disease resistance may have been missing due to the small numbers of founders used to produce the higher generation backcrosses. In this study, we performed a genome-wide association study using first-generation backcrosses with the catfish 690 K SNP arrays to identify additional ESC disease resistance QTL, especially those at the species level. Two genomic regions on LG1 and LG23 were determined to be significantly associated with ESC resistance as revealed by a mixed linear model and family-based association test. Examination of the resistance alleles indicated their origin from blue catfish, indicating that at least two major disease resistance loci exist among blue catfish populations. Upon further validation, markers linked with major ESC disease resistance QTL should be useful for marker-assisted introgression, allowing development of highly ESC resistant breeds of catfish.

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Genome-wide association analysis of intra-specific QTL associated with the resistance for enteric septicemia of catfish

et al. 2018

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Disease resistance is one of the most important traits for aquaculture industry. For catfish industry, enteric septicemia of catfish (ESC), caused by the bacterial pathogen Edwardsiella ictaluri, is the most severe disease, causing enormous economic losses every year. In this study, we used three channel catfish families with 900 individuals (300 fish per family) and the 690K catfish SNP array, and conducted a genome-wide association study to detect the quantitative trait loci (QTL) associated with ESC resistance. Three significant QTL, with two of located on LG1 and one on LG26, and three suggestive QTL located on LG1, LG3, and LG21, respectively, were identified to be associated with ESC resistance. With a well-assembled- and -annotated reference genome sequence, genes around the involved QTL regions were identified. Among these genes, 37 genes had known functions in immunity, which may be involved in ESC resistance. Notably, nlrc3 and nlrp12 identified here were also found in QTL regions of ESC resistance in the channel catfish × blue catfish interspecific hybrid system, suggesting this QTL was operating within both intra-specific channel catfish populations and interspecific hybrid backcross populations. Many of the genes of the Class I MHC pathway, for mediated antigen processing and presentation, were found in the QTL regions. The positional correlation found in this study and the expressional correlation found in previous studies indicated that Class I MHC pathway was significantly associated with ESC resistance. This study validated one QTL previously identified using the second and fourth generation of the interspecific hybrid backcross progenies, and identified five additional QTL among channel catfish families. Taken together, it appears that there are only a few major QTL for ESC disease resistance, making marker-assisted selection an effective approach for genetic improvements of ESC resistance.

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Genome-wide association study identified three major QTL for carcass weight including the PLAG1-CHCHD7 QTN for stature in Japanese Black cattle

Cited by 141 publications

References 30 publications

PLAG1 and NCAPG‐LCORL in livestock

PLAG1 and NCAPG‐LCORL in livestock

GWAS analysis using interspecific backcross progenies reveals superior blue catfish alleles responsible for strong resistance against enteric septicemia of catfish

Genome-wide association analysis of intra-specific QTL associated with the resistance for enteric septicemia of catfish

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