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.

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 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 Variation in the caprine keratin-associated protein 15-1 (KAP15-1) gene affects cashmere fibre diameter

2019 ◽  
Vol 62 (1) ◽  
pp. 125-133 ◽  
Author(s):  
Mengli Zhao ◽  
Huitong Zhou ◽  
Jon G. H. Hickford ◽  
Hua Gong ◽  
Jiqing Wang ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Fibre Diameter ◽  
Kidney Tissue ◽  
Single Strand Conformation Polymorphism ◽  
Hair Follicles ◽  
Pcr Analysis ◽  
Nucleotide Polymorphisms ◽  
Chain Reaction ◽  
Association Analyses ◽  
Polymerase Chain

Abstract. Keratin-associated proteins (KAPs) are a structural component of cashmere fibre, and variation in some KAP genes (KRTAPs) has been associated with a number of caprine fibre traits. In this study, we report the identification of KRTAP15-1 in goats. Sequence variation in the gene was detected using the polymerase chain reaction single-strand conformation polymorphism (PCR-SSCP) technique in 250 Longdong goats, and six variants (named A to F) containing eight single nucleotide polymorphisms (SNPs) were identified. Five of the SNPs were non-synonymous and would lead to putative amino acid changes. Reverse-transcription polymerase chain reaction (RT-PCR) analysis revealed that KRTAP15-1 was expressed in secondary hair follicles but not in heart tissue, liver tissue, lung tissue, kidney tissue or the longissimus dorsi muscle. Despite being rich in cysteine, the caprine KAP15-1 protein possesses a high content of serine and moderate content of glycine and phenylalanine. Association analyses revealed that KRTAP15-1 variant A was associated with decreased mean fibre diameter (MFD), and this effect appeared to be dominant; while variant C was found to be associated with increased MFD, the effect being recessive. The findings suggest that caprine KRTAP15-1 is highly polymorphic and that variation in this gene affects cashmere MFD.

scholarly journals Lingrong Bai 1,†, Jing Wang 2,†, Huitong Zhou 3, Hua Gong 3, Jinzhong Tao 1,* and Jon G. H. Hickford 3,*

Animals ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 142 ◽  
Author(s):  
Lingrong Bai ◽  
Jing Wang ◽  
Huitong Zhou ◽  
Hua Gong ◽  
Jinzhong Tao ◽  
...  
Keyword(s):  
Chromosome Region ◽  
Mammalian Species ◽  
Fibre Diameter ◽  
Start Codon ◽  
Wool Fibre ◽  
Gene Marker ◽  
Nucleotide Polymorphisms ◽  
Repeat Polymorphism ◽  
Reading Frame ◽  
Associated Proteins

Keratin-associated proteins (KAPs) are a diverse group of proteins and form a matrix that cross-links keratin intermediate filaments in hair and wool fibres. From over 100 KAP genes (KRTAPs) identified in mammalian species, KRTAP25-1 is a high sulphur (HS)-KAP gene, which has recently been described in humans. Here, we report the absence of KRTAP25-1 in sheep, and describe a new HS-KRTAP (named KRTAP28-1) in the chromosome region where KRTAP25-1 was expected to be found. Six variants (A−F) of KRTAP28-1 containing eight single nucleotide polymorphisms (SNPs) and a TG repeat polymorphism were detected. One was positioned 30 bp upstream of the transcription start codon and all the others were non-synonymous SNPs, including a nonsense SNP. The TG repeat polymorphism would lead to a reading frame shift at the carboxyl-terminal end. The effect of KRTAP28-1 on wool traits was investigated with 383 Southdown × Merino-cross lambs from seven sire lines. Of the four genotypes with a frequency of over 5%, lambs of genotypes AB and BD produced wool of a smaller MFD than lambs of genotype BC. This shows that KRTAP28-1 is associated with wool fibre diameter, and that variation in this gene might have potential for use as a gene marker for reducing wool fibre diameter.

scholarly journals Failure To Differentiate Cryptosporidium parvum from C. meleagridis Based on PCR Amplification of Eight DNA Sequences

1998 ◽  
Vol 64 (4) ◽  
pp. 1454-1458 ◽  
Author(s):  
Dominique Champliaud ◽  
Philippe Gobet ◽  
Muriel Naciri ◽  
Odile Vagner ◽  
José Lopez ◽  
...  
Keyword(s):  
Cryptosporidium Parvum ◽  
Dna Sequences ◽  
Target Genes ◽  
Pcr Amplification ◽  
Dna Amplification ◽  
Pcr Primers ◽  
18S Rrna Gene ◽  
Rrna Gene ◽  
Restriction Enzyme Digestion ◽  
Human Pathogens

ABSTRACT In order to determine the specificities of PCR-based assays used for detecting Cryptosporidium parvum DNA, eight pairs of previously described PCR primers targeting six distinct regions of theCryptosporidium genome were evaluated for the detection ofC. parvum, the agent of human cryptosporidiosis, andC. muris, C. baileyi, and C. meleagridis, three Cryptosporidium species that infect birds or mammals but are not considered to be human pathogens. The four Cryptosporidium species were divided into two groups: C. parvum and C. meleagridis, which gave the same-sized fragments with all the reactions, and C. muris and C. baileyi, which gave positive results with primer pairs targeting the 18S rRNA gene only. In addition to being genetically similar at each of the eight loci analyzed by DNA amplification, C. parvum and C. meleagridiscouldn’t be differentiated even after restriction enzyme digestion of the PCR products obtained from three of the target genes. This study indicates that caution should be exercised in the interpretation of data from water sample analysis performed by these methods, since a positive result does not necessarily reflect a contamination by the human pathogen C. parvum.

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.

Hopanoid lipids inFrankia: identification of squalene-hopene cyclase gene sequences

2001 ◽  
Vol 47 (6) ◽  
pp. 535-540 ◽  
Author(s):  
Svetlana V Dobritsa ◽  
Dan Potter ◽  
Timothy E Gookin ◽  
Alison M Berry
Keyword(s):  
Polymerase Chain Reaction ◽  
Dna Sequences ◽  
Oxygen Diffusion ◽  
Root Nodules ◽  
Pcr Primers ◽  
Coding Region ◽  
Chain Reaction ◽  
Wide Range ◽  
Oxygen Protection ◽  
Polymerase Chain

In Frankia, the microsymbiont in actinorhizal root nodules, nitrogen fixation takes place in specialized structures called vesicles. The lipidic vesicle envelope forms a barrier to oxygen diffusion, an essential part of the nitrogenase oxygen protection system. We have shown previously that the vesicle envelope is composed primarily of two species of hopanoid lipids, sterol-like molecules that are synthesized in a wide range of bacteria, including Frankia, several cyanobacteria, and rhizobia. The levels of hopanoid found in Frankia are among the highest of any organism known to date. Here we report that short (328-bp) DNA sequences from several strains of Frankia spp. have been identified that are homologous to a portion of the coding region of squalene-hopene cyclase (shc) genes. The fragments and corresponding polymerase chain reaction (PCR) primers can be used in phylogenetic comparisons of Frankia, both within Frankiaceae and among bacteria that synthesize hopanoids.Key words: Frankia, squalene-hopene cyclase, shc, hopanoid, phylogeny, actinorhizal.

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.

scholarly journals The Association Between Novel Polymorphisms of Gremlin Genes and Egg-Laying Performance Traits in Chinese Village Dagu Hens

2018 ◽  
Vol 18 (2) ◽  
pp. 361-373 ◽  
Author(s):  
Thobela Louis Tyasi ◽  
Ning Qin ◽  
Dehui Liu ◽  
Xiaotian Niu ◽  
Hongyan Zhu ◽  
...  
Keyword(s):  
Amino Acids ◽  
Egg Production ◽  
Single Strand Conformation Polymorphism ◽  
Synonymous Substitution ◽  
Egg Laying ◽  
Nucleotide Polymorphisms ◽  
Production Traits ◽  
Coding Region ◽  
Laying Performance ◽  
Performance Traits

Abstract Gremlin (GREM1, GREM2) genes are the known bone morphogenetic proteins (BMPs) inhibitors, but their genetic diversity in animal species remains unknown. The current study was conducted to investigate single nucleotide polymorphisms (SNPs) in chicken GREM1 and GREM2 genes, and their association with egg production traits using polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) and deoxyribonucleic acid (DNA) sequencing. The results discovered novel SNPs and, among these variations, C/T transition at position 436 in exon 1 of the GREM1 gene leads to synonymous substitution of amino acids, and T/C transition at position 690 in the coding region of the GREM2 gene leads to a non-synonymous substitution of amino acids (valine acid 114-to-alanine acid). Association analysis established that at the age of 43, 57 and 66 wks, hen-house egg production (HHEP) was more highly significantly associated (P<0.05) with the AA genotype in the GREM1 gene. In the GREM2 gene, the TC genotype was remarkably linked with higher HHEP at the age of 30, 57 and 66 wks. Our results provide evidence that the GREM1 and GREM2 genes have potential effects on HHEP in chickens. SNPs determined in this work may be utilised as favourable potential DNA markers for improving of egg-laying performance traits.

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