1
|
Huang HL, Liu HL, Cheng YS. A new DNA marker of the TMIGD1 gene used to identify high fertilization rates in Tsaiya ducks (Anas platyrhynchos). J Reprod Dev 2018; 64:529-534. [PMID: 30305481 PMCID: PMC6305851 DOI: 10.1262/jrd.2018-071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
In a prior study, comparisons of individuals of Anas platyrhynchos with higher/lower reproductive performances showed that the expression of the transmembrane and immunoglobulin domain containing 1 (TMIGD1) gene significantly differed between the two groups. Here, we demonstrate that ducks with the TMIGD1 GG genotype have a significantly higher fertilization rate than other TMIGD1 genotypes. Primers designed based on the TMIGD1 sequence of Pekin duck were able to successfully amplify a TMIGD1 fragment from Tsaiya ducks, and sequencing results indicated that a single nucleotide polymorphism (SNP) of the TMIGD1 gene existed. We also developed a cost-effective method of restriction fragment length polymorphism. Using the above methods, ducks were classified into three genotypes. To identify the relationships between genotypes and traits, we recorded the ducks’ performance; to ensure the coverage of the entire duration of the fertile period, the egg collection period was extended to 18 days, and therefore, lower than usual fertilization rates were observed. Further assessment using a high-throughput system showed that the ducks with the GG genotype exhibited the highest fertilization rates among genotypes (P < 0.05). We suggest that TMIGD1 may affect the release of sperm protection factors from the female genital tract, and thus alter fertilization rate. In conclusion, the results of this study demonstrate that the TMIGD1 GG genotype can be used as a new DNA marker to identify animals with high fertilization rates at a young age, a process which could improve farming efficiency.
Collapse
Affiliation(s)
- Hsiu-Lin Huang
- Department of Animal Science, National Chung Hsing University, Taichung 402, Taiwan
| | - Hsiao-Lung Liu
- Livestock Research Institute, Council of Agriculture, Hsin-Hua, Tainan 712, Taiwan
| | - Yu-Shin Cheng
- Livestock Research Institute, Council of Agriculture, Hsin-Hua, Tainan 712, Taiwan
| |
Collapse
|
2
|
Lin CW, Kuo JC, Liu HL, Cheng YS, Huang HL. A new method for detection of single nucleotide polymorphism in a female reproduction-associated gene, tmigd1, of Anas platyrhynchos using a strip biosensor with gold nanoparticles. Poult Sci 2018; 97:3456-3462. [DOI: 10.3382/ps/pey240] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 05/23/2018] [Indexed: 12/14/2022] Open
|
3
|
Wu SJ, Cheng YS, Liu HL, Wang HH, Huang HL. Global transcriptional expression in ovarian follicles from Tsaiya ducks (Anas platyrhynchos) with a high-fertilization rate. Theriogenology 2016; 85:1439-1445.e1. [PMID: 26861074 DOI: 10.1016/j.theriogenology.2016.01.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 11/06/2015] [Accepted: 01/04/2016] [Indexed: 02/07/2023]
Abstract
Novel candidates for biomarkers of a high-fertilization rate were identified here through global transcriptional profiling of ovarian follicles. Some other differentially expressed candidate genes were first noted to influence animal reproduction in our previous cDNA microarray analysis and are now recognized as markers for marker-assisted selection. In the present study, we compared gene expression in ovarian follicles from animals with high- and low-fertilization rates using an oligonucleotide array. On the basis of a fold change of greater than 1.2 and less than -1.2, a difference of >100 Affymetrix arbitrary units between the two groups, and a P value of less than 0.05, 47 genes were found to be associated with fertilization rate. GOEAST and MetaCore software were further used to identify the functional categories of genes that were differentially expressed. Then, we focused on three interesting genes associated with a high-fertilization rate: one of these genes was discovered to participate in signaling pathways of fertilization, and two genes take roles in lipid metabolism. An oligonucleotide array showed that the levels of orthodenticle homeobox 2 (OTX2) and lecithin:cholesterol acyltransferase (LCAT) gene expression were 1.62-fold and 1.95-fold higher in the high-fertilization rate group than in the low-fertilization rate group, respectively (P < 0.05). The level of apolipoprotein A-I (APOA1) gene expression was also higher in the high-fertilization rate group, with a difference of 2.31-fold (P < 0.05). The data were validated through quantitative polymerase chain reaction analysis. These results confirm the usefulness of the array technique and data mining methods in the discovery of new biomarkers and add knowledge to our understanding of the factors affecting fertilization rates in ovarian follicles.
Collapse
Affiliation(s)
- Shyh-Jong Wu
- Department of Medical Laboratory Science and Biotechnology, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yu-Shin Cheng
- Livestock Research Institute, Council of Agriculture, Tainan, Taiwan
| | - Hsiao-Lung Liu
- Livestock Research Institute, Council of Agriculture, Tainan, Taiwan
| | - Hsing-He Wang
- Department of Post-Modern Agriculture, MingDao University, Changhua, Taiwan
| | - Hsiu-Lin Huang
- Department of Post-Modern Agriculture, MingDao University, Changhua, Taiwan.
| |
Collapse
|
4
|
Lin R, Du X, Peng S, Yang L, Ma Y, Gong Y, Li S. Discovering All Transcriptome Single-Nucleotide Polymorphisms and Scanning for Selection Signatures in Ducks (Anas platyrhynchos). Evol Bioinform Online 2015; 11:67-76. [PMID: 26819540 PMCID: PMC4721680 DOI: 10.4137/ebo.s21545] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Revised: 11/02/2015] [Accepted: 11/08/2015] [Indexed: 12/21/2022] Open
Abstract
The duck is one of the most economically important waterfowl as a source of meat, eggs, and feathers. Characterizing the genetic variation in duck species is an important step toward linking genes or genomic regions with phenotypes. Human-driven selection during duck domestication and subsequent breed formation has likely left detectable signatures in duck genome. In this study, we employed a panel of >1.4 million single-nucleotide polymorphisms (SNPs) identified from the RNA sequencing (RNA-seq) data of 15 duck individuals. The density of the resulting SNPs is significantly positively correlated with the density of genes across the duck genome, which demonstrates that the usage of the RNA-seq data allowed us to enrich variant functional categories, such as coding exons, untranslated regions (UTRs), introns, and downstream/upstream. We performed a complete scan of selection signatures in the ducks using the composite likelihood ratio (CLR) and found 76 candidate regions of selection, many of which harbor genes related to phenotypes relevant to the function of the digestive system and fat metabolism, including TCF7L2, EIF2AK3, ELOVL2, and fatty acid-binding protein family. This study illustrates the potential of population genetic approaches for identifying genomic regions affecting domestication-related phenotypes and further helps to increase the known genetic information about this economically important animal.
Collapse
Affiliation(s)
- Ruiyi Lin
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Xiaoyong Du
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China.; College of Informatics, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Sixue Peng
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Liubin Yang
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yunlong Ma
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yanzhang Gong
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shijun Li
- Key Lab of Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, People's Republic of China
| |
Collapse
|
5
|
Liu HC, Huang JF, Lee SR, Liu HL, Hsieh CH, Huang CW, Huang MC, Tai C, Poivey JP, Rouvier R, Cheng YS. Selection for Duration of Fertility and Mule Duck White Plumage Colour in a Synthetic Strain of Ducks (Anas platyrhynchos). ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:605-11. [PMID: 25715691 PMCID: PMC4412989 DOI: 10.5713/ajas.14.0740] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 10/23/2014] [Accepted: 11/08/2014] [Indexed: 11/27/2022]
Abstract
A synthetic strain of ducks (Anas platyrhynchos) was developed by introducing genes for long duration of fertility to be used as mother of mule ducklings and a seven-generation selection experiment was conducted to increase the number of fertile eggs after a single artificial insemination (AI) with pooled Muscovy semen. Reciprocal crossbreeding between Brown Tsaiya LRI-2 (with long duration of fertility) and Pekin L-201 (with white plumage mule ducklings) ducks produced the G0. Then G1 were intercrossed to produce G2 and so on for the following generations. Each female duck was inseminated 3 times, at 26, 29, and 32 weeks of age. The eggs were collected for 14 days from day 2 after AI. Individual data regarding the number of incubated eggs (Ie), the number of fertile eggs at candling at day 7 of incubation (F), the total number of dead embryos (M), the maximum duration of fertility (Dm) and the number of hatched mule ducklings (H) with plumage colour were recorded. The selection criterion was the breeding values of the best linear unbiased prediction animal model for F. The results show high percentage of exhibited heterosis in G2 for traits to improve (19.1% for F and 12.9% for H); F with a value of 5.92 (vs 3.74 in the Pekin L-201) was improved in the G2. Heritabilities were found to be low for Ie (h (2) = 0.07±0.03) and M (h (2) = 0.07±0.01), moderately low for Dm (h (2) = 0.13±0.02), of medium values for H (h (2) = 0.20±0.03) and F (h (2) = 0.23±0.03). High and favourable genetic correlations existed between F and Dm (rg = 0.93), between F and H (rg = 0.97) and between Dm and H (rg = 0.90). The selection experiment showed a positive trend for phenotypic values of F (6.38 fertile eggs in G10 of synthetic strain vs 5.59 eggs in G4, and 3.74 eggs in Pekin L-201), with correlated response for increasing H (5.73 ducklings in G10 vs 4.86 in G4, and 3.09 ducklings in Pekin L-201) and maximum duration of the fertile period without increasing the embryo mortality rate. The average predicted genetic response for F was 40% of genetic standard deviation per generation of selection. The mule ducklings' feather colour also was improved. It was concluded that this study provided results for a better understanding of the genetics of the duration of fertility traits in the common female duck bred for mule and that the selection of a synthetic strain was effective method of improvement.
Collapse
Affiliation(s)
- H C Liu
- Ilan Branch, Livestock Research Institute, Council of Agriculture, Ilan 26845, Taiwan
| | - J F Huang
- Ilan Branch, Livestock Research Institute, Council of Agriculture, Ilan 26845, Taiwan
| | - S R Lee
- Ilan Branch, Livestock Research Institute, Council of Agriculture, Ilan 26845, Taiwan
| | - H L Liu
- Livestock Rescarch Institute, Council of Agriculture, Tainan 71246, Taiwan
| | - C H Hsieh
- Livestock Rescarch Institute, Council of Agriculture, Tainan 71246, Taiwan
| | - C W Huang
- Department of Aquaculture, National Taiwan Ocean University, Keelung 20024, Taiwan
| | - M C Huang
- Department of Animal Science, National Chung Hsing University, Taichung 40227, Taiwan
| | - C Tai
- Southern Taiwan University of Science and Technology, Tainan 71005, Taiwan
| | - J P Poivey
- Institut National de la Recherche Agronomique, Station d'Amélioration Génétique des Animaux, 31326 Castanet-Tolosan, France
| | - R Rouvier
- Institut National de la Recherche Agronomique, F-34000 Montpellier, France
| | - Y S Cheng
- Livestock Rescarch Institute, Council of Agriculture, Tainan 71246, Taiwan
| |
Collapse
|
6
|
Huang HL, Cheng YS. A novel minisequencing single-nucleotide polymorphism marker of the lysozyme gene detects high hatchability of Tsaiya ducks (Anas platyrhynchos). Theriogenology 2014; 82:1113-20. [DOI: 10.1016/j.theriogenology.2014.07.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2014] [Revised: 07/16/2014] [Accepted: 07/22/2014] [Indexed: 10/25/2022]
|
7
|
Huang HL, Huang LT, Cheng YS. A novel SNP marker of ovalbumin gene in association with duck hatchability. Theriogenology 2013; 79:1218-1223.e1. [PMID: 23528974 DOI: 10.1016/j.theriogenology.2013.02.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 02/16/2013] [Accepted: 02/16/2013] [Indexed: 12/25/2022]
Abstract
Our previous transcriptome analysis using a cDNA microarray identified differentially-expressed transcripts in Tsaiya ducks (Anas platyrhynchos); we concluded that the ovalbumin gene might be involved in duck hatchability. In the present study, associations of single nucleotide polymorphism (SNP) genotypes of the duck ovalbumin gene with hatchability were investigated. To confirm the cDNA microarray analysis, real-time polymerase chain reaction (PCR) and Western blot analysis were used to validate ovalbumin gene expression. The messenger RNA and protein expression of the ovalbumin gene were higher (P < 0.05) in the low-hatchability group (1.00 ± 0.19; 30.36 ± 3.51 arbitrary units) than in high-hatchability counterparts (0.56 ± 0.07; 8.53 ± 2.97 arbitrary units), consistent with the previous cDNA microarray analysis. The PCR products (506 base pairs) of ovalbumin gene amplified by the primer pair of TovaF and TovaR from the genomic DNA templates of 10 ducks were sequenced and a g.385 C>T SNP site in the 506-base pair sequence of the ovalbumin gene identified. Genotyping of SNP of 187 ducks was then carried out by PCR restriction fragment length polymorphism and minisequencing methods. Based on SNP genotypes of the duck ovalbumin gene, there were three types: CC, TT, and CT. Birds with the CC and TT genotypes had higher hatchability (79.59 ± 3.40, 76.35 ± 1.77) (P < 0.05) than those with a CT genotype (65.77 ± 2.07). In conclusion, the ovalbumin gene was an important candidate gene that can be used for marker-assisted selection to increase hatchability in Tsaiya ducks.
Collapse
Affiliation(s)
- Hsiu-Lin Huang
- Department of Biotechnology, MingDao University, Pettow, ChangHua, Taiwan.
| | | | | |
Collapse
|
8
|
Li S, Wang C, Yu W, Zhao S, Gong Y. Identification of genes related to white and black plumage formation by RNA-Seq from white and black feather bulbs in ducks. PLoS One 2012; 7:e36592. [PMID: 22615785 PMCID: PMC3352928 DOI: 10.1371/journal.pone.0036592] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Accepted: 04/03/2012] [Indexed: 01/19/2023] Open
Abstract
To elucidate the genes involved in the formation of white and black plumage in ducks, RNA from white and black feather bulbs of an F(2) population were analyzed using RNA-Seq. A total of 2,642 expressed sequence tags showed significant differential expression between white and black feather bulbs. Among these tags, 186 matched 133 annotated genes that grouped into 94 pathways. A number of genes controlling melanogenesis showed differential expression between the two types of feather bulbs. This differential expression was confirmed by qPCR analysis and demonstrated that Tyr (Tyrosinase) and Tyrp1 (Tyrosinase-related protein-1) were expressed not in W-W (white feather bulb from white dorsal plumage) and W-WB (white feather bulb from white-black dorsal plumage) but in B-B (black feather bulb from black dorsal plumage) and B-WB (black feather bulb from white-black dorsal plumage) feather bulbs. Tyrp2 (Tyrosinase-related protein-2) gene did not show expression in the four types of feather bulbs but expressed in retina. C-kit (The tyrosine kinase receptor) expressed in all of the samples but the relative mRNA expression in B-B or B-WB was approximately 10 fold higher than that in W-W or W-WB. Additionally, only one of the two Mitf isoforms was associated with plumage color determination. Downregulation of c-Kit and Mitf in feather bulbs may be the cause of white plumage in the duck.
Collapse
Affiliation(s)
- Shijun Li
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Cui Wang
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Wenhua Yu
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Shuhong Zhao
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| | - Yanzhang Gong
- Key Lab of Agriculture Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, People's Republic of China
| |
Collapse
|
9
|
Frankenberg S, Fenelon J, Dopheide B, Shaw G, Renfree MB. A novel MSMB-related microprotein in the postovulatory egg coats of marsupials. BMC Evol Biol 2011; 11:373. [PMID: 22208949 PMCID: PMC3268785 DOI: 10.1186/1471-2148-11-373] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2011] [Accepted: 12/30/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Early marsupial conceptuses differ markedly from those of eutherian mammals, especially during cleavage and early blastocyst stages of development. Additionally, in marsupials the zona pellucida is surrounded by two acellular layers, the mucoid coat and shell, which are formed from secretions from the reproductive tract. RESULTS We report the identification of a novel postovulatory coat component in marsupials, which we call uterinesecreted microprotein (USM). USM belongs to a family of disulfide-rich microproteins of unconfirmed function that is found throughout deuterostomes and in some protostomes, and includes β-microseminoprotein (MSMB) and prostate-associated microseminoprotein (MSMP). We describe the evolution of this family in detail, including USM-related sequences in other vertebrates. The orthologue of USM in the tammar wallaby, USM1, is expressed by the endometrium with a dynamic temporal profile, possibly under the control of progesterone. CONCLUSIONS USM appears to have evolved in a mammalian ancestor specifically as a component of the postovulatory coats. By analogy with the known properties of MSMB, it may have roles in regulating sperm motility/survival or in the immune system. However, its C-terminal domain is greatly truncated compared with MSMB, suggesting a divergent function.
Collapse
Affiliation(s)
- Stephen Frankenberg
- ARC Centre of Excellence for Kangaroo Genomics and Department of Zoology, University of Melbourne, Parkville, Victoria, Australia.
| | | | | | | | | |
Collapse
|