366 SEX IDENTIFICATION OF PORCINE EMBRYOS BY PCR BASED ON THE AMELOGENIN GENE

2007 ◽  
Vol 19 (1) ◽  
pp. 298
Author(s):  
S. Senbon ◽  
S.-I. Suzuki ◽  
D.-I. Fuchimoto ◽  
M. Iwamoto ◽  
T. Kawarasaki ◽  
...  

The amelogenin (AMEL) gene exists on both X and Y chromosomes in various mammalian species. The non-coding region of this gene is different between X and Y chromosomes. The use of this gene has made sex determination much less complicated, since only one pair of primers is required to amplify the different size fragments of the AMEL gene. Therefore, AMEL had been successfully used to determine the sex in cattle, sheep, and humans. The difference of AMEL genomic sequences between X and Y chromosomes has also been found in pig. In this study, we designed primers that identified AMEL of both chromosomes. The amplicons were isolated and sequenced, and showed a length polymorphism characteristic for the X and Y chromosome in pigs. Furthermore we examined whether a single oocyte or embryo could be sexed. Genomic DNA samples were collected from various breeds of pigs (European breeds: Landrace, Large White, Duroc, Berkshire; Chinese breeds: Meishan, Jinhua). DNA was extracted from ears, tails, or leukocytes using the salting-out method and then dissolved in TE buffer. We used one set of primers for amplifying the pig AMEL gene. The polymerase chain reaction (PCR) procedure was performed with initial denaturation at 94�C for 2 min, followed by 40 cycles of one denaturation step at 98�C for 10 s, primer annealing at 60�C for 30 s, and primer extension at 72�C for 30 s in 20 �L of reaction mixture containing 50 ng genomic DNA. The PCR products were electrophoresed and documented. Some amplicons were isolated and sequenced, and showed a length polymorphism characteristic for the X and Y chromosome in every breed. Next, we tried sexing of pig oocytes and embryos. Cumulus–oocyte complexes (COCs) were aspirated from ovaries recovered from prepubertal gilts. COCs were matured in modified NCSU-37 medium for 44 h, fertilized in vitro, and then cultured in PZM5. The pre-implantation embryos were sampled at 1, 2, 3, 4, and 5–6 days after insemination. Day 1–4 embryos were treated in 5 �L of lysis solution; whole solution were used for subsequent PCR. After Day 5–6 of insemination, only blastocysts were treated in 20 �L of lysis solution, and 5 �L were used for PCR. GV oocytes and electro-activated embryos were sampled as controls. PCR amplification yielded the expected 480-bp and 301-bp products. Male pigs in all breeds are expected to show 2 bands (480 bp and 301 bp), whereas all females, one band only (480 bp). The comparison of AMEL gene DNA sequences among pig breeds showed over 99% homology for the PCR products in both the AMEL-X and the AMEL-Y gene, except for several single-base substitutions. Within GV oocytes and electro-activated embryos, 98% and 96–99% of those examined displayed one band of 480 bp. In IVF groups, 49–55% of those embryos had 2 bands, with no difference between the number of embryos displaying one band and two bands. In conclusion, our findings show that the PCR assay based on the AMEL gene is reliable for sex identification in every pig breed. The advantage of this assay is its capability of identifying sex using a genomic DNA sequence as small as that contained within a single cell such as an oocyte.

2020 ◽  
Vol 160 (5) ◽  
pp. 264-271
Author(s):  
Juana Gutierrez ◽  
Gael Aleix-Mata ◽  
Juan A. Marchal ◽  
María Arroyo ◽  
Riccardo Castiglia ◽  
...  

The Talpidae family has a highly stable karyotype. Most of the chromosome studies in this mammal group, however, employed classical cytogenetic techniques. Molecular cytogenetic analyses are still scarce and, for example, no repeated DNA sequences have been described to date. In this work, we used sequence analysis, chromosomal mapping of a LINE1 retroelement sequence, as well as chromosome painting with a whole Y chromosome probe of T. occidentalis to compare the karyotypes of 3 species of the genus Talpa (T. occidentalis, T. romana, and T. aquitania). Our results demonstrate that in Talpa genomes LINE1 sequences are widely distributed on all chromosomes but are enriched in pericentromeric C-band-positive regions. In addition, these LINE1 accumulate on the Y chromosomes of the 3 Talpa species regardless of their euchromatic or heterochromatic condition. Chromosome painting shows that the Y chromosomes in these 3 species are highly conserved. Interestingly, they share sequences with heterochromatic blocks on chromosome pairs 14 and 16 and, to a lesser degree, with the pericentromeric regions of other autosomes. Together, our analyses demonstrate that the repetitive DNA content of chromosomes from Talpa species is highly conserved.


1993 ◽  
Vol 37 (1) ◽  
Author(s):  
H.J. Breukelman ◽  
J.J. Beintema ◽  
E. Confalone ◽  
C. Costanzo ◽  
M.P. Sasso ◽  
...  

1990 ◽  
Vol 10 (12) ◽  
pp. 6619-6623
Author(s):  
S Y Tam ◽  
E N Geissler ◽  
S L Graw ◽  
D E Housman

The entire 33-kb coding region of the mouse Na,K-ATPase alpha 1 subunit gene was cloned in two overlapping cosmids which contain inserts of 40 kb. To assess the functional expression of the mouse alpha 1 gene, the two cosmids were cotransfected into ouabain-sensitive CV-1 monkey cells yielding an average of 64 resistant colonies per 10(6) cells per microgram of DNA. Analysis of the DNA transferred to the ouabain-resistant transformants by the two cosmids suggests that the generation of a functional gene can occur by homologous recombination between the two introduced segments, as demonstrated by generation of a novel diagnostic restriction fragment. The ability to reconstruct the intact mouse alpha 1 gene in a heterologous host cell and to monitor its functional expression with a selection protocol permits direct identification and isolation of regulatory sequences for the gene.


Genome ◽  
2000 ◽  
Vol 43 (3) ◽  
pp. 580-583
Author(s):  
Joaquina de la Torre ◽  
Angel Martínez-Ramírez ◽  
José Luis Fernández ◽  
José Luis Díez-Martín ◽  
Alfonso Gómez-Pineda ◽  
...  

A 154-bp PCR product amplified from human female DNA mapped onto the Y chromosome under high-stringency in situ hybridization conditions. The female DNA sequence revealed an 89% homology with the HSDYZ1 sequence. When the same primers were used to amplify male DNA, a 154-bp DNA fragment was also obtained, showing a 98% homology with HSDYZ1. However, although the HSDYZ1 sequence is widely distributed along the long arm of the Y chromosome, both of these particular PCR products are di-regionally localized within this distal block of constitutive heterochromatin. In situ hybridization under lower stringency showed that these 154-bp sequences map both onto the autosomes and the Y chromosome. Overall, this paper shows (i) a new class of DNA sequences shared by the autosomes and the Y chromosome; and (ii) a substructured organization of some DNA repeats within the DYZ1 family that forms a large part of the constitutive heterochromatin of the Y chromosome.Key words: human satellite DNA, satellite 3, DYZ1, Y chromosome.


1990 ◽  
Vol 10 (12) ◽  
pp. 6619-6623 ◽  
Author(s):  
S Y Tam ◽  
E N Geissler ◽  
S L Graw ◽  
D E Housman

The entire 33-kb coding region of the mouse Na,K-ATPase alpha 1 subunit gene was cloned in two overlapping cosmids which contain inserts of 40 kb. To assess the functional expression of the mouse alpha 1 gene, the two cosmids were cotransfected into ouabain-sensitive CV-1 monkey cells yielding an average of 64 resistant colonies per 10(6) cells per microgram of DNA. Analysis of the DNA transferred to the ouabain-resistant transformants by the two cosmids suggests that the generation of a functional gene can occur by homologous recombination between the two introduced segments, as demonstrated by generation of a novel diagnostic restriction fragment. The ability to reconstruct the intact mouse alpha 1 gene in a heterologous host cell and to monitor its functional expression with a selection protocol permits direct identification and isolation of regulatory sequences for the gene.


2009 ◽  
Vol 75 (22) ◽  
pp. 7163-7172 ◽  
Author(s):  
Tomasz A. Leski ◽  
Clayton C. Caswell ◽  
Marcin Pawlowski ◽  
David J. Klinke ◽  
Janusz M. Bujnicki ◽  
...  

ABSTRACT The Bacillus cereus group includes three closely related species, B. anthracis, B. cereus, and B. thuringiensis, which form a highly homogeneous subdivision of the genus Bacillus. One of these species, B. anthracis, has been identified as one of the most probable bacterial biowarfare agents. Here, we evaluate the sequence and length polymorphisms of the Bacillus collagen-like protein bcl genes as a basis for B. anthracis detection and fingerprinting. Five genes, designated bclA to bclE, are present in B. anthracis strains. Examination of bclABCDE sequences identified polymorphisms in bclB alleles of the B. cereus group organisms. These sequence polymorphisms allowed specific detection of B. anthracis strains by PCR using both genomic DNA and purified Bacillus spores in reactions. By exploiting the length variation of the bcl alleles it was demonstrated that the combined bclABCDE PCR products generate markedly different fingerprints for the B. anthracis Ames and Sterne strains. Moreover, we predict that bclABCDE length polymorphism creates unique signatures for B. anthracis strains, which facilitates identification of strains with specificity and confidence. Thus, we present a new diagnostic concept for B. anthracis detection and fingerprinting, which can be used alone or in combination with previously established typing platforms.


1990 ◽  
Vol 38 (3) ◽  
pp. 421-426 ◽  
Author(s):  
H U Weier ◽  
R Segraves ◽  
D Pinkel ◽  
J W Gray

We describe the use of in vitro DNA amplification for production of double-stranded, biotin-labeled DNA probes. Specifically, a 124 BP DNA segment of the Y chromosome-specific 3.4 KB repeat was amplified in preparations of human genomic DNA using the polymerase chain reaction (PCR) and a thermostable DNA polymerase. The PCR products were amplified further in the presence of a molar excess of biotin-11-dUTP. The resulting double-stranded DNA segments showed a high amount of incorporated biotin-11-dUTP. The probes were used in DNA-DNA hybridization experiments without further purification. When DNA sequences flanking the target region are known, probe generation by enzymatic amplification offers a rapid and efficient alternative to molecular cloning and nick translation.


2005 ◽  
Vol 03 (03) ◽  
pp. 677-696 ◽  
Author(s):  
YINHE CAO ◽  
WEN-WEN TUNG ◽  
J. B. GAO ◽  
YAN QI

With the completion of the human and a few model organisms' genomes, and with the genomes of many other organisms waiting to be sequenced, it has become increasingly important to develop faster computational tools which are capable of easily identifying the structures and extracting features from DNA sequences. One of the more important structures in a DNA sequence is repeat-related. Often they have to be masked before protein coding regions along a DNA sequence are to be identified or redundant expressed sequence tags (ESTs) are to be sequenced. Here we report a novel recurrence time-based method for sequence analysis. The method can conveniently study all kinds of periodicity and exhaustively find all repeat-related features from a genomic DNA sequence. An efficient codon index is also derived from the recurrence time statistics, which has the salient features of being largely species-independent and working well on very short sequences. Efficient codon indices are key elements of successful gene finding algorithms, and are particularly useful for determining whether a suspected EST belongs to a coding or non-coding region. We illustrate the power of the method by studying the genomes of E. coli, the yeast S. cervisivae, the nematode worm C. elegans, and the human, Homo sapiens. Our method requires approximately 6 · N byte memory and a computational time of N log N to extract all the repeat-related and periodic or quasi-periodic features from a sequence of length N without any prior knowledge on the consensus sequence of those features, hence enables us to carry out sequence analysis on the whole genomic scale by a PC.


Author(s):  
Kuldeepsingh A. Kalariya ◽  
Ram Prasnna Meena ◽  
Lipi Poojara ◽  
Deepa Shahi ◽  
Sandip Patel

Abstract Background Squalene synthase (SQS) is a rate-limiting enzyme necessary to produce pentacyclic triterpenes in plants. It is an important enzyme producing squalene molecules required to run steroidal and triterpenoid biosynthesis pathways working in competitive inhibition mode. Reports are available on information pertaining to SQS gene in several plants, but detailed information on SQS gene in Gymnema sylvestre R. Br. is not available. G. sylvestre is a priceless rare vine of central eco-region known for its medicinally important triterpenoids. Our work aims to characterize the GS-SQS gene in this high-value medicinal plant. Results Coding DNA sequences (CDS) with 1245 bp length representing GS-SQS gene predicted from transcriptome data in G. sylvestre was used for further characterization. The SWISS protein structure modeled for the GS-SQS amino acid sequence data had MolProbity Score of 1.44 and the Clash Score 3.86. The quality estimates and statistical score of Ramachandran plots analysis indicated that the homology model was reliable. For full-length amplification of the gene, primers designed from flanking regions of CDS encoding GS-SQS were used to get amplification against genomic DNA as template which resulted in approximately 6.2-kb sized single-band product. The sequencing of this product through NGS was carried out generating 2.32 Gb data and 3347 number of scaffolds with N50 value of 457 bp. These scaffolds were compared to identify similarity with other SQS genes as well as the GS-SQSs of the transcriptome. Scaffold_3347 representing the GS-SQS gene harbored two introns of 101 and 164 bp size. Both these intronic regions were validated by primers designed from adjoining outside regions of the introns on the scaffold representing GS-SQS gene. The amplification took place when the template was genomic DNA and failed when the template was cDNA confirmed the presence of two introns in GS-SQS gene in Gymnema sylvestre R. Br. Conclusion This study shows GS-SQS gene was very closely related to Coffea arabica and Gardenia jasminoides and this gene harbored two introns of 101 and 164 bp size.


Sign in / Sign up

Export Citation Format

Share Document