Inter and Intra Variation of Potato Yellow Vein Virus in Three Potato Species From Colombia

Potato yellow vein virus (PYVV), (family Closteroviridae, genus Crinivirus) is a re-emergent virus in Andean countries. Low inter-isolate variation has been reported for PYVV CP gene, but there are no reports for intra-isolate variation. Inter- and intra-isolate variability in CP from a population of PYVV was studied. Samples of 216 symptomatic potato plants (115 Solanum tuberosum subsp. andigena (STA), 100 Solanum phureja (SPH) and 1 Solanum chaucha (SCH)) were collected in five Colombian departments. Viral isolates were amplified by RT-PCR and the amplicons were analyzed by single-strand conformation polymorphism (SSCP). Six different migration SSCP patterns (A to F) with different complexities were observed among the population. Pattern A was detected in the five departments in 66% of the isolates. Pattern E was found only in the department of Cundinamarca with a frequency of 0.09%. Patterns B, C, D and F were found in similar proportions of from 13% to 5.6% and were present in the five departments. Homology at the nucleotide level of 75% of the sequence of the CP gene was greater than 99% and the dN/dS ratio (no-synonymous/synonymous changes) was 0.002. Amplicons of the whole CP gene of eight selected isolates representing the six SSCP patterns were cloned and the SSCP analysis showed that, in all cases, more than one variant was present. The sequence analysis of the 35 clones confirmed intra-isolate variability of PYVV. The existence of several variants in a single field isolate was demonstrated and negative selection against amino acid changes of the CP was suggested.

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Genetic variability of glutamate-gated chloride channel genes in ivermectin-susceptible and -resistant strains of Cooperia oncophora

Parasitology ◽

10.1017/s0031182004006183 ◽

2004 ◽

Vol 129 (6) ◽

pp. 741-751 ◽

Cited By ~ 40

Author(s):

A. I. NJUE ◽

R. K. PRICHARD

Keyword(s):

Genetic Variability ◽

Chloride Channels ◽

Field Isolate ◽

Single Strand Conformation Polymorphism ◽

High Sequence Identity ◽

Cooperia Oncophora ◽

Resistant Strains ◽

High Degree ◽

Pcr Techniques ◽

Conformation Polymorphism

The glutamate-gated chloride channels (GluCls) are members of the ligand-gated ion channel superfamily that are thought to be involved in the mode of action of ivermectin and mechanism of resistance. Using reverse-transcriptase PCR techniques, 2 full-length GluCl cDNAs, encoding GluClα3 and GluClβ subunits, were cloned from Cooperia oncophora, a nematode parasite of cattle. The two sequences show a high degree of identity to similar subunits from other nematodes. The C. oncophora GluClα3 subunit is most closely related to the Haemonchus contortus GluClα3B subunit, while C. oncophora GluClβ subunit shares high sequence identity with the H. contortus GluClβ subunit. Using single-strand conformation polymorphism, the genetic variability of these two genes was analysed in an ivermectin-susceptible isolate and an ivermectin-resistant field isolate of C. oncophora. Statistical analysis suggested an association between the C. oncophora GluClα3 gene and ivermectin resistance. No such association was seen with the GluClβ gene.

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W14.383 Validation of single strand conformation polymorphism (SSCP) analysis in the detection of mutations in genes such as that coding for the LDL receptor

Atherosclerosis ◽

10.1016/s0021-9150(04)90382-6 ◽

2004 ◽

Vol 5 (1) ◽

pp. 88-89

Author(s):

P NISSEN

Keyword(s):

Ldl Receptor ◽

Single Strand Conformation Polymorphism ◽

Single Strand ◽

Sscp Analysis ◽

Detection Of Mutations ◽

Conformation Polymorphism

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Sequence Variations in the Bovine Growth Hormone Gene Characterized by Single-Strand Conformation Polymorphism (SSCP) Analysis and Their Association with Milk Production Traits in Holsteins

Genetics ◽

10.1093/genetics/144.4.1809 ◽

1996 ◽

Vol 144 (4) ◽

pp. 1809-1816 ◽

Cited By ~ 1

Author(s):

Jianbo Yao ◽

Samuel E Aggrey ◽

David Zadworny ◽

J Flan Hayes ◽

Urs Kühnlein

Keyword(s):

Growth Hormone ◽

Milk Production ◽

Milk Yield ◽

Single Strand Conformation Polymorphism ◽

Sscp Analysis ◽

Bovine Growth Hormone ◽

Production Traits ◽

Milk Production Traits ◽

Sequence Variations ◽

Conformation Polymorphism

Sequence variations in the bovine growth hormone (GH) gene were investigated by single strand conformation polymorphism (SSCP) analysis of seven amplified fragments covering almost the entire gene (2.7 kb). SSCPs were detected in four of these fragments and a total of six polymorphisms were found in a sample of 128 Holstein bulls. Two polymorphisms, a T→C transition in the third intron (designated GH4.1) and an A→C transversion in the fifth exon (designated GH6.2), were shown to be associated with milk production traits. GH4.1c/GH4.1c bulls had higher milk yield than GH4.1c/GH4.1t (P ≤ 0.005) and GH4.1t/GH4.1t (P ≤ 0.0022) bulls. GH4.1c/GH4.1c bulls had higher kg fat (P ≤ 0.0076) and protein (P ≤ 0.0018) than GH4.1c/GH4.1t bulls. Similar effects on milk production traits with the GH6.2 polymorphism were observed with the GH6.2a allele being the favorable allele. The average effects of the gene substitution for GH4.1 and GH6.2 are similar, with ±300 kg for milk yield, ±8 kg for fat content and ±7 kg for protein content per lactation. The positive association of GH4.1c and GH6.2a with milk production traits may be useful for improving milk performance in dairy cattle.

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