26
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: found
      Is Open Access

      Identification of genome-wide SNP-SNP interactions associated with important traits in chicken

      research-article

      Read this article at

      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          Background

          In addition to additive genetic effects, epistatic interactions can play key roles in the control of phenotypic variation of traits of interest. In the current study, 475 male birds from lean and fat chicken lines were utilized as a resource population to detect significant epistatic effects associated with growth and carcass traits.

          Results

          A total of 421 significant epistatic effects were associated with testis weight (TeW), from which 11 sub-networks (Sub-network1 to Sub-network11) were constructed. In Sub-network1, which was the biggest network, there was an interaction between GGA21 and GGAZ. Three genes on GGA21 ( SDHB, PARK7 and VAMP3) and nine genes ( AGTPBP1, CAMK4, CDC14B, FANCC, FBP1, GNAQ, PTCH1, ROR2 and STARD4) on GGAZ that might be potentially important candidate genes for testis growth and development were detected based on the annotated gene function. In Sub-network2, there was a SNP on GGA19 that interacted with 8 SNPs located on GGA10. The SNP (Gga_rs15834332) on GGA19 was located between C-C motif chemokine ligand 5 ( CCL5) and MIR142. There were 32 Refgenes on GGA10, including TCF12 which is predicted to be a target gene of miR-142-5p. We hypothesize that miR-142-5p and TCF12 may interact with one another to regulate testis growth and development. Two genes ( CDH12 and WNT8A) in the same cadherin signaling pathway were implicated as potentially important genes in the control of metatarsus circumference (MeC). There were no significant epistatic effects identified for the other carcass and growth traits, e.g. heart weight (HW), liver weight (LW), spleen weight (SW), muscular and glandular stomach weight (MGSW), carcass weight (CW), body weight (BW1, BW3, BW5, BW7), chest width (ChWi), metatarsus length (MeL).

          Conclusions

          The results of the current study are helpful to better understand the genetic basis of carcass and growth traits, especially for testis growth and development in broilers.

          Electronic supplementary material

          The online version of this article (10.1186/s12864-017-4252-y) contains supplementary material, which is available to authorized users.

          Related collections

          Most cited references43

          • Record: found
          • Abstract: found
          • Article: not found

          Convergence of Wnt, beta-catenin, and cadherin pathways.

          W Nelson (2004)
          The specification and proper arrangements of new cell types during tissue differentiation require the coordinated regulation of gene expression and precise interactions between neighboring cells. Of the many growth factors involved in these events, Wnts are particularly interesting regulators, because a key component of their signaling pathway, beta-catenin, also functions as a component of the cadherin complex, which controls cell-cell adhesion and influences cell migration. Here, we assemble evidence of possible interrelations between Wnt and other growth factor signaling, beta-catenin functions, and cadherin-mediated adhesion.
            Bookmark
            • Record: found
            • Abstract: found
            • Article: not found

            DJ-1, a novel oncogene which transforms mouse NIH3T3 cells in cooperation with ras.

            We have isolated and characterized the cDNA encoding a novel protein designated DJ-1. DJ-1, sharing no significant homology with the sequences so far reported, did not show transactivation activity in the Gal4 recombinant system, but transformed mouse NIH3T3 cells by itself. Furthermore, DJ-1 showed a cooperative transforming activity with H-Ras, more than 3 times as strong as the activity of ras/myc combination. DJ-1 was ubiquitously expressed in various human tissues, and the expression was induced by growth stimuli. Moreover, DJ-1 translocated from cytoplasm to nuclei in the S phase of the cell cycle. DJ-1 is thus suggested to be a novel mitogen-dependent oncogene product involved in a Ras-related signal transduction pathway.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              Sertoli cell signaling by Desert hedgehog regulates the male germline.

              In mammals, testis development is initiated in the embryo in response to the expression of the sex determining gene, Sry, in Sertoli cell precursors. Subsequently, Sertoli cells are thought to play a central role in male-specific cell interactions, including those that occur during spermatogenesis. However, the molecular nature of these interactions is poorly understood. Desert hedgehog (Dhh) encodes a signaling molecule expressed in the testis, but not the ovary, and may therefore play a role in the regulation of spermatogenesis. Dhh expression is initiated in Sertoli cell precursors shortly after the activation of Sry and persists in the testis into the adult. Female mice homozygous for a Dhh-null mutation show no obvious phenotype, whereas males are viable but infertile, owing to a complete absence of mature sperm. Examination of the developing testis in different genetic backgrounds suggests that Dhh regulates both early and late stages of spermatogenesis. Patched, a likely target of Hedgehog signaling, also displays male-specific transcription in the gonad. This expression is restricted to a second somatic lineage, the Leydig cells. The expression of Patched is lost in Dhh mutants. Dhh expression in pre-Sertoli cells is one of the earliest indications of male sexual differentiation. Analysis of a null mutant demonstrates that Dhh signaling plays an essential role in the regulation of mammalian spermatogenesis. Loss of Patched expression in Dhh mutants suggests a conservation in the Hedgehog signaling pathway between flies and mice, and indicates that Leydig cells may be the direct target of Dhh signaling.
                Bookmark

                Author and article information

                Contributors
                huizhang@neau.edu.cn
                yujiaqiang5259@163.com
                yanglili5259@163.com
                lmkramer@iastate.edu
                xinyanglucy@sina.com
                nawei19861102@163.com
                jreecy@iastate.edu
                lihui@neau.edu.cn
                Journal
                BMC Genomics
                BMC Genomics
                BMC Genomics
                BioMed Central (London )
                1471-2164
                21 November 2017
                21 November 2017
                2017
                : 18
                : 892
                Affiliations
                [1 ]ISNI 0000 0004 0369 6250, GRID grid.418524.e, Key Laboratory of Chicken Genetics and Breeding, Ministry of Agriculture, ; Harbin, 150030 People’s Republic of China
                [2 ]ISNI 0000 0004 1760 1136, GRID grid.412243.2, Key Laboratory of Animal Genetics, Breeding and Reproduction, Education Department of Heilongjiang Province, ; Harbin, 150030 People’s Republic of China
                [3 ]ISNI 0000 0004 1760 1136, GRID grid.412243.2, College of Animal Science and Technology, , Northeast Agricultural University, ; Harbin, 150030 People’s Republic of China
                [4 ]ISNI 0000 0004 1936 7312, GRID grid.34421.30, Department of Animal Science, , Iowa State University, ; 2255 Kildee Hall, Ames, IA 50011 USA
                Article
                4252
                10.1186/s12864-017-4252-y
                5698929
                29162033
                987f2b6c-d628-4b33-b084-dd6e8183f2d6
                © The Author(s). 2017

                Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License ( http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver ( http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

                History
                : 18 May 2017
                : 31 October 2017
                Funding
                Funded by: National 863 Project of China
                Award ID: 2013AA102501
                Award Recipient :
                Funded by: National Natural Science Foundation of China (CN)
                Award ID: 31301960
                Award Recipient :
                Funded by: FundRef http://dx.doi.org/10.13039/501100002858, China Postdoctoral Science Foundation;
                Award ID: 2015M581421
                Award Recipient :
                Funded by: Heilongjiang Postdoctoral Financial Assistance
                Award ID: LBH-TZ0612
                Award Recipient :
                Funded by: University Nursing Program for Young Scholars with Creative Talents in Heilongjiang Province
                Award ID: UNPYSCT-2015007
                Award Recipient :
                Categories
                Research Article
                Custom metadata
                © The Author(s) 2017

                Genetics
                carcass and growth traits,testis,epistasis,snp-snp interaction,chicken
                Genetics
                carcass and growth traits, testis, epistasis, snp-snp interaction, chicken

                Comments

                Comment on this article