Short Communication Genome-wide association with residual body weight gain in Bos indicus cattle

Santana, Miguel Henrique de Almeida; Gomes, Rodrigo da Costa; Utsunomiya, Yuri Tani; Neves, Haroldo Henrique de Rezende; Novais, Francisco José de; Bonin, Michael; Fukumasu, Heidge; Garcia, José Fernando; Oliveira, G.A.; Coutinho, Luiz Lehmann; Ferraz, José Bento Sterman

doi:10.4238/2015.may.18.14

Cited by 13 publications

(11 citation statements)

References 19 publications

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“…The gene ankrd10a has been detected as a candidate gene for abdominal fat yield on GGA3 in chicken [47]. The gene iffo2 has been associated with residual body weight gain in cattle [48]. The apoer2 (also known as low-density lipoprotein receptor-related protein 8, lrp8 ) is a member of the low density lipoprotein receptor (LDLR) gene family, which is not only involved in the lipid metabolism, but also plays an important role in endocytosis and signal transduction [49].…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study for Muscle Fat Content and Abdominal Fat Traits in Common Carp (Cyprinus carpio)

Zheng

Kuang

et al. 2016

PLoS ONE

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Muscle fat content is an important phenotypic trait in fish, as it affects the nutritional, technical and sensory qualities of flesh. To identify loci and candidate genes associated with muscle fat content and abdominal fat traits, we performed a genome-wide association study (GWAS) using the common carp 250 K SNP assay in a common carp F2 resource population. A total of 18 loci surpassing the genome-wide suggestive significance level were detected for 4 traits: fat content in dorsal muscle (MFdo), fat content in abdominal muscle (MFab), abdominal fat weight (AbFW), and AbFW as a percentage of eviscerated weight (AbFP). Among them, one SNP (carp089419) affecting both AbFW and AbFP reached the genome-wide significance level. Ten of those loci were harbored in or near known genes. Furthermore, relative expressions of 5 genes related to MFdo were compared using dorsal muscle samples with high and low phenotypic values. The results showed that 4 genes were differentially expressed between the high and low phenotypic groups. These genes are, therefore, prospective candidate genes for muscle fat content: ankyrin repeat domain 10a (ankrd10a), tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2 (tanc2), and four jointed box 1 (fjx1) and choline kinase alpha (chka). These results offer valuable insights into the complex genetic basis of fat metabolism and deposition.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Association Study for Muscle Fat Content and Abdominal Fat Traits in Common Carp (Cyprinus carpio)

Zheng

Kuang

et al. 2016

PLoS ONE

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“…Abnormal pancreatic function could conceivably affect weight gain, though a role for LNX2 in the gut or in regulating some aspect of metabolism could also be responsible. Interestingly a genome-wide association study (GWAS) linked LNX2 to weight gain in cattle [67] and another study identified LNX2 as a growth-related quantificative trait locus in the Chinese mitten crab [68]. A closer analysis of organ function outside the CNS may clarify the basis for the decreased weight observed in in LNX1/2 DKO mice.…”

Section: Mammalian Lnx1 and Lnx2mentioning

confidence: 99%

LNX1/LNX2 proteins: functions in neuronal signalling and beyond

Young

2018

Neuronal Signaling

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Ligand of NUMB Protein X1 and X2 (LNX1 and LNX2) are E3 ubiquitin ligases, named for their ability to interact with and promote the degradation of the cell fate determinant protein NUMB. On this basis they are thought to play a role in modulating NUMB/NOTCH signalling during processes such as cortical neurogenesis. However, LNX1/2 proteins can bind, via their four PDZ (PSD95, DLGA, ZO-1) domains, to an extraordinarily large number of other proteins besides NUMB. Many of these interactions suggest additional roles for LNX1/2 proteins in the nervous system in areas such as synapse formation, neurotransmission and regulating neuroglial function. Twenty years on from their initial discovery, I discuss here the putative neuronal functions of LNX1/2 proteins in light of the anxiety-related phenotype of double knockout mice lacking LNX1 and LNX2 in the central nervous system (CNS). I also review what is known about non-neuronal roles of LNX1/2 proteins, including their roles in embryonic patterning and pancreas development in zebrafish and their possible involvement in colorectal cancer (CRC), osteoclast differentiation and immune function in mammals. The emerging picture places LNX1/2 proteins as potential regulators of multiple cellular signalling processes, but in many cases the physiological significance of such roles remains only partly validated and needs to be considered in the context of the tight control of LNX1/2 protein levels in vivo.

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“…Genome-wide association studies (GWAS) are robust statistical tools are that broadly identify candidate genes with significant SNPs involved in production traits [14][15][16], growth traits [17,18], carcass quality traits and fertility traits [19,20]. In beef cattle, various SNPs, genes, and haplotype blocks have been found to associate with growth, however the current GWAS-based studies focus mainly on only one growth parameter [21], such as the weaning size [22], yearling weight or stature upon slaughter [23]. Furthermore, loci controlling growth traits may be variable in different growth stages, and some loci may control traits throughout the lifetime of the animal [24].…”

Section: Introductionmentioning

confidence: 99%

Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle

Xu²,

Xia

et al. 2020

Preprint

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Background: Body size traits as one of the main breeding selection criteria was widely used to monitor cattle growth and to evaluate the selection response. In this study, body size was defined as body height (BH), body length (BL), hip height (HH), heart size (HS), abdominal size (AS), and cannon bone size (CS). We performed genome-wide association studies (GWAS) of these traits over the course of three growth stages (6, 12 and 18 months after birth) using three statistical models, singletrait GWAS, multi-trait GWAS and LONG-GWAS. The Illumina Bovine HD 770K BeadChip was used to identify genomic single nucleotide polymorphisms (SNPs) in 1217 individuals. Results: In total, 19, 29, and 10 significant SNPs were identified by the three models, respectively. Among these, 21 genes were promising candidate genes, including SOX2, SNRPD1, RASGEF1B, EFNA5, PTBP1, SNX9, SV2C, PKDCC, SYNDIG1, AKR1E2, and PRIM2 identified by single-trait analysis; SLC37A1, LAP3, PCDH7, MANEA, and LHCGR identified by multi-trait analysis; and P2RY1, MPZL1, LINGO2, CMIP, and WSCD1 identified by LONG-GWAS. Conclusions: Multiple association analysis was performed for six growth traits at each growth stage. These findings offer valuable insights for the further investigation of potential genetic mechanism of growth traits in Simmental beef cattle.

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Short Communication Genome-wide association with residual body weight gain in Bos indicus cattle

Cited by 13 publications

References 19 publications

Genome-Wide Association Study for Muscle Fat Content and Abdominal Fat Traits in Common Carp (Cyprinus carpio)

Genome-Wide Association Study for Muscle Fat Content and Abdominal Fat Traits in Common Carp (Cyprinus carpio)

LNX1/LNX2 proteins: functions in neuronal signalling and beyond

Multiple association analysis of loci and candidate genes that regulate body size at three growth stages in Simmental beef cattle

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