| Literature DB >> 25049869 |
Xinhong Luan1, Zhongzan Cao1, Wen Xu1, Ming Gao1, Laiyou Wang1, Shuwei Zhang1.
Abstract
Huoyan goose is a Chinese local breed famous for its higher laying performance, but the problems of variety degeneration have emerged recently, especially a decrease in the number of eggs laid. In order to better understand the molecular mechanism that underlies egg laying in Huoyan geese, gene profiles in the pituitary gland of Huoyan geese taken during the laying period and ceased period were investigated using the suppression subtractive hybridization (SSH) method. Total RNA was extracted from pituitary glands of ceased period and laying period geese. The cDNA in the pituitary glands of ceased geese was subtracted from the cDNA in the pituitary glands of laying geese (forward subtraction); the reverse subtraction was also performed. After sequencing and annotation, a total of 30 and 24 up and down-regulated genes were obtained from the forward and reverse SSH libraries, respectively. These genes mostly related to biosynthetic process, cellular nitrogen compound metabolic process, transport, cell differentiation, cellular protein modification process, signal transduction, small molecule metabolic process. Furthermore, eleven genes were selected for further analyses by quantitative real-time PCR (qRT-PCR). The qRT-PCR results for the most part were consistent with the SSH results. Among these genes, Synaptotagmin-1 (SYT1) and Stathmin-2 (STMN2) were substantially over-expressed in laying period compared to ceased period. These results could serve as an important reference for elucidating the molecular mechanism of higher laying performance in Huoyan geese.Entities:
Keywords: Ceased; Huoyan Goose; Laying; Pituitary Gland; Quantitative Real-time PCR; Suppression Subtractive Hybridization
Year: 2013 PMID: 25049869 PMCID: PMC4093504 DOI: 10.5713/ajas.2013.13083
Source DB: PubMed Journal: Asian-Australas J Anim Sci ISSN: 1011-2367 Impact factor: 2.509
Primers used for the quantitative real-time PCR analysis
| Putative gene symbols | Forward primer sequence (5′-3′) | Reverse primer sequence (5′-3′) | Amplicon size (bp) |
|---|---|---|---|
| CAMTA1 | TTTCATATCTCCTGCTGGAAG | AGCAATATACCATGACACCC | 111 |
| ENPP2 | CACTGGGTGGATGATGAC | TGCACGGAAACCATCAAC | 102 |
| SMOC2 | AGTGTGTAAATTGCTGTTGAC | GTTGCATTCTCATTGCATGAT | 128 |
| VAMP4 | ACCATAAATAATGTCTTCGGGA | CAGAAGAGAAACGTGCCACTA | 134 |
| CDK5R1 | ATGACACAGTCTGTCAGG | GTTGACCAAATTGGTGGG | 115 |
| PAK2 | TCACACAGCAAGCACTGA | TTAGTGTACTTAGGAGACGGT | 105 |
| PCDH9 | GAGAGTCAAGTAGAGGTCCATA | TCTGATTTCTGCATTGCTTCC | 105 |
| SPRED1 | ACAAGAAAGACGTTACCACT | GCTGCTACTCTGGTTGATT | 109 |
| STMN2 | CCGAGGTAAGAGGCAACAAATA | TGGCTGTTTGGCATCATTTAG | 128 |
| SYT1 | TTCAGTCTGGCAGTGTAGG | TCAGTTGTTCATTCAGGATAGC | 101 |
| VAPA | TGCAACTGACACTTGCTAT | GCTTTGCCTTTAATGATCTCG | 111 |
| ACTB | CCTGGCACCTAGCACAATGA | TGGGTGTTGGTAACAGTCCG | 194 |
Identities of differentially expressed cDNA clones from the SSH forward library
| NCBI BLAST gene name | Accession number | Species | E-value |
|---|---|---|---|
| Contactin associated protein-like 2 (CNTNAP2) | NM_001193337.1 | Taeniopygia guttata | 3.00E-23 |
| P21 protein (Cdc42/Rac)-activated kinase 2, transcript variant 2 (PAK2) | XM_422671.2 | Gallus gallus | 1.00E-92 |
| Phytanoyl-CoA 2-hydroxylase interacting protein-like (PHYHIPL) | NM_001199504.1 | Gallus gallus | 1.00E-97 |
| Solute carrier family 5 (sodium/glucose cotransporter), member 11 (SLC5A11), | XM_414862.3 | Gallus gallus | 0.000006 |
| Serine/arginine-rich splicing factor 3 (SRSF3), | NM_001195554.1 | Gallus gallus | 2.00E-171 |
| Legumain (LGMN) | XM_421328.3 | Gallus gallus | 2.00E-84 |
| Stathmin-2-like (STMN2) | XM_003205132.1 | Meleagris gallopavo | 2.00E-75 |
| O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase) (OGT) | NM_001006317.2 | Meleagris gallopavo | 0 |
| Glutamate-ammonia ligase (GLUL) | NM_205493.1 | Gallus gallus | 8.00E-109 |
| Cytochrome c oxidase subunit I (COX1) gene, mitochondrial | GU179002.1 | Anser | 6.00E-170 |
| Cytochrome c oxidase subunit III (COX3) gene, mitochondrial | GU179010.1 | Anser | 0 |
| Synaptotagmin-1-like SYT1 | XM_003202102.1 | Meleagris gallopavo | 0.0003 |
| Ribosomal protein, large, P0 (RPLP0) | NM_204987.1 | Gallus gallus | 1.00E-171 |
| Poly(A) binding protein interacting protein 2 (PAIP2) | NM_001007832.1 | Gallus gallus | 8.00E-109 |
| Minichromosome maintenance complex component 6 (MCM6) | NM_001006527.1 | Gallus gallus | 7.00E-150 |
| Sprouty-related, EVH1 domain containing 1 (SPRED1), | NM_152594.2 | Homo sapiens | 2.00E-49 |
| Protocadherin 20 (PCDH20) | XM_003980439.1 | G | 8.00E-14 |
| Protocadherin 9 (PCDH9) | XM_003640560.1 | Gallus gallus | 0 |
| Vesicle-associated membrane protein-associated protein A-like (VAPA) | XM_003204959.1 | Meleagris gallopavo | 0 |
| Solute carrier family 4, sodium bicarbonate cotransporter, member 4, (SLC4A4) | XM_003641192.1 | Meleagris gallopavo | 1.00E-161 |
| ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit (ATP5O) | XM_416717.3 | Meleagris gallopavo | 0 |
| Four and a half LIM domains 2 (FHL2), | XM_416924.3 | Meleagris gallopavo | 1.00E-112 |
| Major facilitator superfamily domain containing 2A (MFSD2A) | XM_417826.3 | Meleagris gallopavo | 0.0001 |
| SDA1 domain containing 1 (SDAD1) | XM_420597.3 | Meleagris gallopavo | 0.0005 |
| Anser albifrons mitochondrion, complete genome | AF363031.1 | Anser | 7.00E-170 |
| anser clone goosePiSSHFmixIB05 pituitary gland-expressed unknown gene 8 mRNA sequence | DQ836037.1 | Anser | 8.00E-55 |
| Voucher BISE-Aves24 cytochrome oxidase subunit 1 (COI) gene,mitochondrial | GU571728.1 | Anser anser | 6.00E-165 |
| Meleagris gallopavo myelin proteolipid protein-like | XM_003205647.1 | Meleagris gallopavo | 0 |
| Chondroitin polymerizing factor 2 (CHPF2), | XM_003214253.1 | Meleagris gallopavo | 2.00E-178 |
| Reticulon 4 (RTN4) | XM_003640893.1 | Gallus gallus | 3.00E-143 |
Accession numbers are from the National Center for Biotechnology Information (NCBI) nonredundant nucleotide database.
Expected (E) value is a parameter when searching a sequence of particular size in a database (http://www.ncbi.nlm.nih.gov/BLAST/tutorial/Altschul-1.html). It is used to test the hypothesis of a random match to the bases in the database, the closer the E-value to zero, the lower the possibility of mistake in a gene identity.
Identities of differentially expressed cDNA clones from the SSH reverse library
| NCBI BLAST gene name | Accession number | Species | E-value |
|---|---|---|---|
| Muscleblind-like 3 (Drosophila) (MBNL3), transcript variant 1 | NM_001163338.1 | Gallus gallus | 0.00E+00 |
| NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4 (NDUFA4) | XM_001234600.2 | Gallus gallus | 7.00E-148 |
| N(alpha)-acetyltransferase 20, NatB catalytic subunit (NAA20) | XM_422177.3 | Gallus gallus | 5.00E-57 |
| Solute carrier family 1 (glial high affinity glutamate transporter), member 3 (SLC1A3) | XM_425011.2 | Gallus gallus | 0 |
| Ectonucleotide pyrophosphatase/phosphodiesterase 2 (ENPP2) | NM_001198662.1 | Gallus gallus | 8.00E-110 |
| Nuclear factor I/B (NFIB), transcript variant 2 | NM_001190738.1 | Homo sapiens | 0 |
| voucher IPMB 7137 NADH dehydrogenase subunit 2 (nd2) gene, mitochondrial | EU585683.1 | Anser rossii | 2.00E-115 |
| Ferritin, heavy polypeptide 1 (FTH1), mRNA | NM_205086.1 | Gallus gallus | 1.00E-34 |
| Phosphatidylinositol-5-phosphate 4-kinase, type II, alpha (PIP4K2A) | NM_001030971.1 | Gallus gallus | 4.00E-62 |
| Microfibrillar-associated protein 3 (MFAP3) | NM_001012784.2 | Gallus gallus | 0 |
| Intraflagellar transport 74 homolog (Chlamydomonas) (IFT74) | XM_003643070.1 | Gallus gallus | 2.00E-50 |
| Transmembrane emp24 domain trafficking protein 2 (TMED2) | NM_001006186.1 | Gallus gallus | 2.00E-76 |
| Profilin 2 (PFN2) | NM_001079760.1 | Gallus gallus | 0 |
| Amyloid beta (A4) precursor-like protein 2 (APLP2) | NM_001006317.2 | Gallus gallus | 2.00E-56 |
| Cyclin-dependent kinase 5, regulatory subunit 1 (p35) (CDK5R1) | NM_003885.2 | Homo sapiens | 1.00E-49 |
| Ribosomal protein L39 (RPL39) | NM_204272.1 | Gallus gallus | 0.00000005 |
| Vacuolar protein sorting 37 homolog B | XM_415126 | Gallus gallus | 4.00E-103 |
| Vesicle-associated membrane protein 4 (VAMP4) | XM_001233851.2 | Gallus gallus | 7.00E-21 |
| Rho guanine nucleotide exchange factor (GEF) 37 (ARHGEF37) | XM_414480.3 | Gallus gallus | 1.00E-78 |
| Acetyl-CoA acetyltransferase 1 (ACAT1) | XM_417162.3 | Gallus gallus | 4.00E-57 |
| Calmodulin binding transcription activator 1 (CAMTA1) | XM_417530.3 | Gallus gallus | 0 |
| SPARC related modular calcium binding 2 (SMOC2) | XM_419600.3 | Gallus gallus | 2.00E-123 |
| Mitochondrion, complete genome | AF363031.1 | Anser albifrons | 6.00E-170 |
| hypothetical protein | AJ720212.1 | Gallus gallus | 1.00E-172 |
| Dynein, axonemal, light chain 1 (DNAL1) | NM_001199681.1 | Gallus gallus | 3.00E-158 |
Accession numbers are from the National Center for Biotechnology Information (NCBI) nonredundant nucleotide database.
Expected (E) value is a parameter when searching a sequence of particular size in a database (http://www.ncbi.nlm.nih.gov/BLAST/utorial/Altschul-1.html). It is used to test the hypothesis of a random match to the bases in the database, the closer the E-value to zero, the lower the possibility of mistake in a gene identity.
Figure 1.Gene ontology (GO) classification of the differentially expressed ESTs in the forward and reverse SSH libraries. Based on the GO terms, the ESTs are categorized into putative functional groups. The black and white columns represent the up- and down-regulated genes from forward and reverse libraries, respectively.
Figure 2.Quantitative real-time PCR validation. The gene expression level of 11 randomly selected ESTs, including 6 from SSH forward library (the black column) and 5 from SSH reverse library (the white column), was tested using qRT-PCR. The relative gene expression level in the laying period was normalized to the ceased period. Data are presented as mean±SE. Asterisks denote significant gene expression differences between the laying period and ceased period, as determined by the student’s t tests (* p<0.05).