scholarly journals Identification of Caprine KRTAP28-1 and Its Effect on Cashmere Fiber Diameter

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 121 ◽  
Author(s):  
Jiqing Wang ◽  
Huitong Zhou ◽  
Jon G. H. Hickford ◽  
Mengli Zhao ◽  
Hua Gong ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Fiber Diameter ◽  
Single Strand Conformation Polymorphism ◽  
Chromosome 1 ◽  
Polymorphism Analysis ◽  
Gene Encoding ◽  
Banding Patterns ◽  
Reading Frame ◽  
Associated Proteins ◽  
Cashmere Goats

The keratin-associated proteins (KAPs) are constituents of cashmere fibers and variation in many KAP genes (KRTAPs) has been found to be associated with fiber traits. The gene encoding the high-sulphur KAP28-1 has been described in sheep, but it has not been identified in the goat genome. In this study, a 255-bp open reading frame on goat chromosome 1 was identified using a search of similar sequence to ovine KRTAP28-1, and that would if transcribed and translated encode a high sulphur KAP. Based on the analysis of polymerase chain reaction amplicons for the goat nucleotide sequences in 385 Longdong cashmere goats in China, five unique banding patterns were detected using single strand conformation polymorphism analysis. These represented five DNA sequences (named variants A to E) and they had the highest resemblance to KRTAP28-1 sequences from sheep, suggesting A–E are variants of caprine KRTAP28-1. DNA sequencing revealed a 2 or 4-bp deletion and eleven nucleotide sequence differences, including four non-synonymous substitutions. Of the four common variants (A, B, C and D) found in these goats, the presence of variant A was associated with decreased mean fiber diameter and this effect appeared to be additive. These results indicate that caprine KRTAP28-1 variation might have value as a molecular marker for reducing cashmere mean fiber diameter.

scholarly journals Identification of the Ovine Keratin-Associated Protein 2-1 Gene and Its Sequence Variation in Four Chinese Sheep Breeds

Genes ◽  
2020 ◽  
Vol 11 (6) ◽  
pp. 604
Author(s):  
Jianqing Wang ◽  
Huitong Zhou ◽  
Jon G. H. Hickford ◽  
Yuzhu Luo ◽  
Hua Gong ◽  
...  
Keyword(s):  
Single Strand Conformation Polymorphism ◽  
Local Alignment ◽  
Polymorphism Analysis ◽  
Chromosome 11 ◽  
Gene Encoding ◽  
Reading Frame ◽  
Sheep Breeds ◽  
Wool Fibers ◽  
Associated Proteins ◽  
Search Tool

Keratin-associated proteins are important components of wool fibers. The gene encoding the high-sulfur keratin-associated protein 2-1 has been described in humans, but it has not been described in sheep. A basic local alignment search tool nucleotide search of the Ovine Genome Assembly version 4.0 using a human keratin-associated protein 2-1 gene sequence revealed a 399-base pair open reading frame, which was clustered among nine previously identified keratin-associated protein genes on chromosome 11. Polymerase chain reaction–single strand conformation polymorphism analysis revealed four different banding patterns, with these representing four different sequences (A–D) in Chinese sheep breeds. These sequences had the highest similarity to human keratin-associated protein 2-1 gene, suggesting that they represent variants of ovine keratin-associated protein 2-1 gene. Nine single nucleotide variations were detected in the gene, including one non-synonymous nucleotide substitution. Differences in variant frequencies between fine-wool sheep breeds and coarse-wool sheep breeds were detected. The gene was found to be expressed in various tissues, with the highest expression level in skin, and moderate expression levels in heart and lung tissue. These results reveal that the ovine keratin-associated protein 2-1 gene is variable and suggest the gene might affect variation in mean fiber diameter.

scholarly journals The Mean Staple Length of Wool Fibre Is Associated with Variation in the Ovine Keratin-Associated Protein 21-2 Gene

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 148
Author(s):  
Shaobin Li ◽  
Huitong Zhou ◽  
Hua Gong ◽  
Fangfang Zhao ◽  
Jiqing Wang ◽  
...  
Keyword(s):  
Fibre Diameter ◽  
Single Strand Conformation Polymorphism ◽  
Amino Acid Sequences ◽  
Chromosome 1 ◽  
Wool Fibre ◽  
Gene Marker ◽  
Reading Frame ◽  
Associated Proteins ◽  
Fleece Weight ◽  
Staple Length

Wool and hair fibres consist of a variety of proteins, including the keratin-associated proteins (KAPs). In this study, a putative ovine homologue of the human KAP21-2 gene (KRTAP21-2) was identified. It was located on chromosome 1 as a 201-bp open reading frame (ORF) in the ovine genome assembly from a Texel sheep (v.4 NC_019458.2: nt122932727 to 122932927). A polymerase chain reaction- single strand conformation polymorphism (PCR-SSCP) analysis of this ORF, and subsequent DNA sequencing, identified five sequences (named A-E). The putative amino acid sequences that would be produced, shared some identity with each other and with other KAPs, but they were most similar to ovine KAP21-1, and phylogenetically related to human KAP21-2. The location of the ovine KRTAP21-2 sequence was consistent with the location of human KRTAP21-2, and this suggests they represent different variant forms of ovine KRTAP21-2. Variation in this gene was investigated in 389 Merino (sire) × Southdown-cross (ewe) lambs. These were derived from four independent sire-lines. The sequence variation was found to be associated with variation in five wool traits: including mean staple length (MSL), mean fibre diameter (MFD), fibre diameter standard deviation (FDSD), prickle factor (PF), and greasy fleece weight (GFW). The most persistent effect of KRTAP21-2 variation was with variation in MSL; with the MSL of sheep of genotype AC being 12.5% greater than those of genotype CE. A similar effect was observed from individual variant absence/presence models. This suggests that KRTAP21-2 should be further investigated as a possible gene-marker for improving MSL.

scholarly journals Variation in the Caprine Keratin-Associated Protein 27-1 Gene is Associated with Cashmere Fiber Diameter

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 934
Author(s):  
Mengli Zhao ◽  
Huitong Zhou ◽  
Yuzhu Luo ◽  
Jiqing Wang ◽  
Jiang Hu ◽  
...  
Keyword(s):  
Nucleotide Sequence ◽  
Fiber Diameter ◽  
Single Strand Conformation Polymorphism ◽  
Chromosome 1 ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Longissimus Dorsi Muscle ◽  
Cashmere Goats ◽  
Kidney Liver ◽  
Conformation Polymorphism

Variation in some caprine keratin-associated protein (KAP) genes has been associated with cashmere fiber traits, but many KAP genes remain unidentified in goats. In this study, we confirm the identification of a KAP27-1 gene (KRTAP27-1) and describe its effect on cashmere traits in 248 Longdong cashmere goats. A polymerase chain reaction–single strand conformation polymorphism (PCR-SSCP) analysis was used to screen for sequence variation in this gene, and three sequence variants (named A to C) were found. These sequences have the highest similarity (77% identity) to a human KRTAP27-1 sequence, while sharing some homology with a predicted caprine KRTAP27-1 sequence ENSCHIG00000023347 in the goat genome construct (ARS1:CM004562.1) at chromosome 1 position 3,966,193–3,973,677 in the forward strand. There were two single nucleotide polymorphisms (SNPs) detected in the coding sequence, including one nonsynonymous SNP (c.413C/T; p.Ala138Val) and one synonymous SNP (c.495C/T). The C variant differed from A and B at c.413C/T, having cytosine in its nucleotide sequence, while the B variant differed from A and C at c.495C/T, having thymine in its nucleotide sequence. Goats of the genotypes AB and BB produced cashmere fibers of higher mean fiber diameter (MFD) than goats of genotype AA, but no difference in MFD was detected between the AB and BB goats. These results suggest that B is associated with increased MFD. Expression of the caprine KRTAP27-1 sequence was predominantly detected in the skin tissue of goats but not or only weakly detected in other tissues, including longissimus dorsi muscle, heart, kidney, liver, lung and spleen.

scholarly journals Variation in the Caprine KAP24-1 Gene Affects Cashmere Fibre Diameter

Animals ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 15 ◽  
Author(s):  
Jiqing Wang ◽  
Huitong Zhou ◽  
Yuzhu Luo ◽  
Mengli Zhao ◽  
Hua Gong ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Fibre Diameter ◽  
Pcr Amplification ◽  
Pcr Primers ◽  
Single Strand Conformation Polymorphism ◽  
Chromosome 1 ◽  
Start Codon ◽  
Nucleotide Polymorphisms ◽  
Coding Region ◽  
Cashmere Goats

The keratin-associated proteins (KAPs) are structural components of cashmere fibres. The gene encoding the high-sulphur (HS)-KAP24-1 (KRTAP24-1) has been identified in humans and sheep, but it has not been described in goats. In this study, we report the identification of caprine KRTAP24-1, describe variation in this gene, and investigate the effect of this variation on cashmere traits. A search for sequences orthologous to the ovine gene in the goat genome revealed a 774 bp open reading frame on chromosome 1, which could encode an HS-KAP. Based on this goat genome sequence and comparison with ovine KRTAP24-1 sequences, polymerase chain reaction (PCR) primers were designed to amplify an 856 bp fragment that would contain the entire coding region of the putative caprine KRTAP24-1. Use of this PCR amplification with subsequent single-strand conformation polymorphism (SSCP) analysis of the amplicons identified four distinct patterns of DNA bands on gel electrophoresis, with these representing four different DNA sequences (A to D), in 340 Longdong cashmere goats reared in China. The variant sequences had the highest similarity to KRTAP24-1 sequences from sheep and humans, suggesting that they are variants of caprine KRTAP24-1. Nine single-nucleotide polymorphisms (SNPs) were detected in the gene, including four non-synonymous SNPs and an SNP in proximity to the ATG start codon. Of the three common genotypes (AA, AB, and BB) found in these Longdong cashmere goats, cashmere fibres from goats of genotype AA had lower mean fibre diameter (MFD) than did those of genotype AB, and cashmere fibres from goats of genotype AB had lower MFD than did those from goats of genotype BB.

Short Communication: A highly polymorphic caprine keratin-associated protein gene identified and its effect on cashmere traits

2021 ◽  
Author(s):  
Shaobin Li ◽  
Qiming Xi ◽  
Fangfang Zhao ◽  
Jiqing Wang ◽  
Zhaohua He ◽  
...  
Keyword(s):  
Sequence Similarity ◽  
Fibre Diameter ◽  
Single Strand Conformation Polymorphism ◽  
Chromosome 1 ◽  
Wool Fibre ◽  
Polymorphism Analysis ◽  
Coding Region ◽  
Nucleotide Substitutions ◽  
Cashmere Goats ◽  
Conformation Polymorphism

Abstract Five keratin-associated protein 6 genes (KRTAP6) have been identified in sheep and variation in some KRTAP6 has been associated with wool fibre diameter-related traits, but none of these homologues has been identified in goats. In this study, we reported the identification of the sheep KRTAP6-5 homologue on goat chromosome 1 and PCR-single strand conformation polymorphism analysis in 300 Longdong cashmere goats revealed the existence of twelve variant sequences. Both coding region and 3’UTR of the putative caprine KRTAP6-5 displayed a biggest sequence similarity to ovine KRTAP6-5 gene. This suggested that the gene represents caprine KRTAP6-5 sequences, and these sequences composed twenty three genotypes which was the most polymorphism gene in KRTAPs that have been studied. Among these sequences, fifteen nucleotide substitutions and a 24-bp insertion/detection were identified. Variation in goat KRTAP6-5 was associated with variation in mean fibre diameter, suggesting that KRTAP6-5 is worthy of further study in the context of variation in cashmere traits.

Polymerase chain reaction based mapping of rye involving repeated DNA sequences

Genome ◽  
1992 ◽  
Vol 35 (4) ◽  
pp. 621-626 ◽  
Author(s):  
Peter M. Rogowsky ◽  
Ken W. Shepherd ◽  
Peter Langridge
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
Chromosome 1 ◽  
Repeated Dna ◽  
Chain Reaction ◽  
Pcr Marker ◽  
Banding Patterns ◽  
Repeated Dna Sequences ◽  
Cereal Rye ◽  
Polymerase Chain

A novel type of polymerase chain reaction (PCR) marker was developed for the mapping of cereal rye (Secale cereale). Primer pairs were synthesized targeting the insertion sites of three individual copies of the R173 family of rye specific repeated DNA sequences. While one primer was derived from a sequence within the respective R173 element, the second primer corresponded to a flanking region. The complex banding patterns obtained in rye allowed not only the mapping of the three R173 elements to certain chromosome regions of 1RS (the short arm of rye chromosome 1) but also the mapping of an additional 3–10 easily identifiable bands per primer pair to other rye chromosomes. Linkage mapping of a polymorphic 1R band derived from three rye cultivars demonstrated the presence of nonallelic, dominant markers in two independent crosses. Because of the high copy number of the R173 family (15 000 copies per diploid rye genome), its dispersion over the entire length of all chromosomes and the high number of markers obtained per primer pair, PCR markers based on the R173 family provide an almost unlimited source for well-spaced markers in rye mapping.Key words: polymerase chain reaction, mapping, repetitive DNA sequences, wheat, rye.

scholarly journals Variation in a Newly Identified Caprine KRTAP Gene Is Associated with Raw Cashmere Fiber Weight in Longdong Cashmere Goats

Genes ◽  
2021 ◽  
Vol 12 (5) ◽  
pp. 625
Author(s):  
Mengli Zhao ◽  
Huitong Zhou ◽  
Yuzhu Luo ◽  
Jiqing Wang ◽  
Jiang Hu ◽  
...  
Keyword(s):  
Chemical Properties ◽  
Single Strand Conformation Polymorphism ◽  
Nucleotide Polymorphisms ◽  
Longissimus Dorsi Muscle ◽  
Associated Proteins ◽  
Cashmere Goats ◽  
Fiber Traits ◽  
Fleece Weight ◽  
Main Components ◽  
Physical And Chemical

Keratin-associated proteins (KAPs) and keratins determine the physical and chemical properties of cashmere fibers as they are the main components of the fibers. It has been reported that ovine KRTAP1-2 affects clean fleece weight, greasy fleece weight and yield in sheep, but the gene has not been described in goats and its effects on fiber traits are unknown. In this study, we identify the keratin-associated protein 1-2 gene (KRTAP1-2) in the goat genome and describe its effect on cashmere fiber traits in 359 Longdong cashmere goats. Six sequence variants (named CAPHI-KRTAP1-2*A to CAPHI-KRTAP1-2*F) were revealed using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis. These sequences have the highest homology with ovine KRTAP1-2 sequences. There were a 60-bp deletion, a 15-bp insertion and five single nucleotide polymorphisms (SNPs) including two non-synonymous SNPs in the coding sequence. The caprine KRTAP1-2 gene was expressed in the skin tissue, but a signal was not observed for the kidneys, liver, lungs, spleen, heart and longissimus dorsi muscle. Variation in caprine KRTAP1-2 was found to be associated with raw cashmere fiber weight, but not with fiber diameter and length.

Evaluation of PCR–Single-Strand Conformational Polymorphism Analysis for Identification of Gram-Negative Histamine-Producing Bacteria Isolated from Fish

2007 ◽  
Vol 70 (5) ◽  
pp. 1200-1205 ◽  
Author(s):  
HAJIME TAKAHASHI ◽  
MIKI SATO ◽  
BON KIMURA ◽  
TATSUYA ISHIKAWA ◽  
TATEO FUJII
Keyword(s):  
Histidine Decarboxylase ◽  
Single Strand Conformation Polymorphism ◽  
Single Strand ◽  
Sscp Analysis ◽  
Polymorphism Analysis ◽  
Single Strand Conformational Polymorphism ◽  
Banding Patterns ◽  
Gram Negative ◽  
Fish Samples ◽  
Conformation Polymorphism

In this study, the previously established PCR–single-strand conformation polymorphism (SSCP) system for detecting and identifying gram-negative histamine-producing bacteria was evaluated. This system can detect and identify histamine-producing bacteria directly from seafood by the use of sequence polymorphisms of the histidine decarboxylase gene (hdc). First, we isolated 81 histamine-producing strains of bacteria from fish samples and analyzed the hdc gene by the PCR-SSCP system. The 22 newly obtained SSCP banding patterns were added to our database, and the utility of our modified database was tested in a second experiment consisting of 18 strains of histamine-producing bacteria isolated from 25 fish samples. Approximately 80% of the histamine-producing strains corresponded to those in the new database. Use of the database for PCR-SSCP analysis, including the band patterns newly added in this study, for the hdc gene makes it possible to more accurately identify histamine producers.

scholarly journals A DNA Sequence Corresponding to the Gene Encoding Cysteine Proteinase 5 in Entamoeba histolytica Is Present and Positionally Conserved but Highly Degenerated inEntamoeba dispar

1999 ◽  
Vol 67 (11) ◽  
pp. 5925-5929 ◽  
Author(s):  
Ute Willhoeft ◽  
Lutz Hamann ◽  
Egbert Tannich
Keyword(s):  
Entamoeba Histolytica ◽  
Dna Sequences ◽  
Common Ancestor ◽  
Cysteine Proteinase ◽  
Human Tissues ◽  
Cysteine Proteinases ◽  
Genomic Context ◽  
Entamoeba Dispar ◽  
Gene Encoding ◽  
Reading Frame

ABSTRACT Cysteine proteinases of Entamoeba histolytica are considered to be one of the most important classes of molecules responsible for the parasite's ability to destroy human tissues. Interestingly, one particular cysteine proteinase, located on the surface of E. histolytica trophozoites and designated cysteine proteinase 5 (CP5), is not expressed in the closely related but nonpathogenic species Entamoeba dispar. By comparing the E. histolytica and E. dispar genomic loci containing the gene for CP5 (cp5), it was found that the position of cp5 within the genomic context is conserved between the two organisms, but that the gene is highly degenerated inE. dispar, as it contains numerous nucleotide exchanges, insertions, and deletions, resulting in multiple stop codons within thecp5 reading frame. An alignment of all available orthologous E. histolytica and E. dispar DNA sequences suggested that cp5 started to degenerate inE. dispar coincidently when the two organisms began to diverge from a common ancestor.

Transcripts from amplified sequences of an inherited homogeneously staining region in chromosome 1 of the house mouse (Mus musculus)

1991 ◽  
Vol 11 (4) ◽  
pp. 2229-2235
Author(s):  
W A Eckert ◽  
C Plass ◽  
A Weith ◽  
W Traut ◽  
H Winking
Keyword(s):  
House Mouse ◽  
Dna Sequences ◽  
Mus Musculus ◽  
Genomic Sequence ◽  
Gene Families ◽  
Chromosome 1 ◽  
Homologous Sequence ◽  
Sequence Motifs ◽  
Reading Frame ◽  
Hybridization Data

Several populations of the house mouse, Mus musculus, are polymorphic for the presence or absence of an inherited homogeneously staining region (HSR) in chromosome 1. The HSR consists of highly amplified DNA sequences, present in low copy numbers in the HSR- genome. A cloned HSR-derived genomic sequence detected transcripts of about 1.3 and 4.5 kb on blots of poly(A)+ RNA from liver of HSR+ mice but not from that of HSR- mice. A cDNA library was established from RNA of HSR+ mice and screened with the HSR-derived genomic clone. Positive clones were isolated and shown to be complementary to the 1.3-kb RNA species and to amplified DNA sequences in the HSR+ genome. The combined sequence of four overlapping cloned cDNAs is 959 nucleotides long and includes an open reading frame encoding a putative protein of 208 amino acids. The pertinent gene is unidentified. No homologous sequence is stored in the EMBL data base. A stretch of 109 nucleotides at the 3' end of the 1.3-kb RNA homology region in the same genomic fragment, as indicated by hybridization data and sequence motifs resembling promoter elements. Thus, our data suggest that at least two genes or gene families are encoded in the HSR.

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