Polymorphic sequence in the D-loop region of equine mitochondrial DNA.
Abstract: The D-loop regions in equine mitochondrial DNA were cloned from three thoroughbred horses by polymerase chain reaction (PCR). The total number of bases in the D-loop region were 1114 bp, 1115 bp and 1146 bp. The equine D-loop region is A/T rich like many other mammalian D-loops. The large central conserved sequence block and small conserved sequence blocks 1, 2 and 3, that are common to other mammals, were observed. Between conserved sequence blocks 1 and 2 there were tandem repeats of an 8 bp equine-specific sequence TGTGCACC, and the number of tandem repeats differed among individual horses. The base composition in the unit of these repeats is G/C rich as are the short repeats in the D-loops of rabbit and pig. Comparing DNA sequences between horse and other mammals, the difference in the D-loop region length is mostly due to the difference in the number of DNA sequences at both extremities. The similarities of the DNA sequences are in the middle part of the D-loop. In comparison of the sequences among three thoroughbred horses, it was determined that the region between tRNA(Pro) and the large central conserved sequence block was the richest in variation. PCR primers in the D-loop region were designed and the expected maternal inheritance was confirmed by PCR-RFLP (restriction fragment length polymorphism).
Publication Date: 1994-08-01 PubMed ID: 7985837DOI: 10.1111/j.1365-2052.1994.tb00196.xGoogle Scholar: Lookup
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Summary
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This study focused on understanding the differences and similarities in the D-loop regions of mitochondrial DNA in three thoroughbred horses. The researchers cloned these regions and analysed them, finding differences in base pairs, repeat sequences, and other factors. They also designed primers for this region and confirmed maternal inheritance using a specific technique known as PCR-RFLP.
Understanding the D-Loop Region
- This research delved into the study of D-loop regions in the mitochondrial DNA of horses. These regions have variable lengths and are responsible for controlling the replication and transcription of the mitochondrial genome.
- Three Thoroughbred horses were used in the study. The D-loop regions were cloned and it was found that they contained 1114, 1115 and 1146 base pairs (bp) respectively.
- The researchers noted that, just like in other mammals, the equine D-loop region is rich in Adenine (A) and Thymine (T) bases.
Discovering Conserved and Variant Sequences
- The large central conserved sequence block along with the three small conserved sequence blocks common to other mammals were also seen in the equine D-loop region.
- Interestingly, there were tandem repeats of a particular 8 base pair sequence, TGTGCACC, present between the first and second conserved sequence blocks. The number of repeats differed among individual horses.
- This repeat sequence was found to be rich in Guanine (G) and Cytosine (C) bases, similar to the short repeats seen in other mammals including rabbits and pigs.
Comparative Analysis
- Comparative analysis of the DNA sequences from the D-loop regions of the horses and other mammals indicated that the length difference is mainly due to variation in the DNA sequences at both ends of the region.
- On the other hand, sequence similarities among species were found in the middle part of the D-loop.
- On examination of the sequences among the three horses, the area between the tRNA(Pro) and the large central conserved sequence block showed the most variation.
PCR-RFLP Confirmation
- In the last part of the study, the researchers designed PCR primers specific to the D-loop region.
- Using these primers, they were able to confirm the expected maternal inheritance using a technique called PCR-RFLP (Polymerase Chain Reaction-Restriction Fragment Length Polymorphism).
- This technique helped the researchers confirm that the variation they had observed in the D-loop regions was indeed inherited maternally, as it should be for mitochondrial DNA.
Cite This Article
APA
Ishida N, Hasegawa T, Takeda K, Sakagami M, Onishi A, Inumaru S, Komatsu M, Mukoyama H.
(1994).
Polymorphic sequence in the D-loop region of equine mitochondrial DNA.
Anim Genet, 25(4), 215-221.
https://doi.org/10.1111/j.1365-2052.1994.tb00196.x Publication
Researcher Affiliations
- Laboratory of Molecular and Cellular Biology, Japan Racing Association, Tokyo.
MeSH Terms
- Animals
- Base Sequence
- Cloning, Molecular
- DNA, Mitochondrial
- Female
- Horses / genetics
- Male
- Molecular Sequence Data
- Pedigree
- Polymerase Chain Reaction
- Polymorphism, Genetic
Citations
This article has been cited 18 times.- Sheikh A. Mitochondrial DNA sequencing of Kehilan and Hamdani horses from Saudi Arabia.. Saudi J Biol Sci 2023 Sep;30(9):103741.
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- Xia J, Chang L, Xu D, Jia Y, Ding Y, Cao C, Geng Z, Jin S. Next-Generation Sequencing of the Complete Huaibei Grey Donkey Mitogenome and Mitogenomic Phylogeny of the Equidae Family.. Animals (Basel) 2023 Feb 2;13(3).
- Nikbakhsh M, Varkoohi S, Seyedabadi HR. Mitochondrial DNA D-loop hyper-variable region 1 variability in Kurdish horse breed.. Vet Med Sci 2023 Mar;9(2):721-728.
- Myćka G, Klecel W, Stefaniuk-Szmukier M, Jaworska J, Musiał AD, Ropka-Molik K. Mitochondrial Whole D-Loop Variability in Polish Draft Horses of Sztumski Subtype.. Animals (Basel) 2022 Jul 22;12(15).
- Dell AC, Curry MC, Yarnell KM, Starbuck GR, Wilson PB. Mitochondrial D-loop sequence variation and maternal lineage in the endangered Cleveland Bay horse.. PLoS One 2020;15(12):e0243247.
- Othman OE, Mahrous KF, Shafey HI. Mitochondrial DNA genetic variations among four horse populations in Egypt.. J Genet Eng Biotechnol 2017 Dec;15(2):469-474.
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