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

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.

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

Animals ◽

10.3390/ani9010015 ◽

2019 ◽

Vol 9 (1) ◽

pp. 15 ◽

Cited By ~ 5

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.

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

Genes ◽

10.3390/genes11020148 ◽

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.

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

Genes ◽

10.3390/genes11080934 ◽

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.

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

Genes ◽

10.3390/genes11020121 ◽

2020 ◽

Vol 11 (2) ◽

pp. 121 ◽

Cited By ~ 1

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.

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Use of Single-Strand Conformation Polymorphism Analysis To Examine the Variability of the rpoSSequence in Environmental Isolates of Salmonellae

Applied and Environmental Microbiology ◽

10.1128/aem.65.8.3582-3587.1999 ◽

1999 ◽

Vol 65 (8) ◽

pp. 3582-3587 ◽

Cited By ~ 12

Author(s):

Suzanne J. Jordan ◽

Christine E. R. Dodd ◽

Gordon S. A. B. Stewart

Keyword(s):

Single Strand Conformation Polymorphism ◽

Single Strand ◽

Polymorphism Analysis ◽

Coding Region ◽

Environmental Isolates ◽

Probability Of Survival ◽

Base Level ◽

Analysis Technique ◽

Conformation Polymorphism Analysis ◽

Conformation Polymorphism

ABSTRACT The natural environment places its resident microflora under stress, which may often result in adaptation by the microflora in order to increase the probability of survival. One such mechanism that has been postulated involves rpoS, which encodes a sigma factor that is known to enhance survival upon exposure to stress. The present work aimed to examine the genetic variability of rpoS in a selection of Salmonella enterica subspecies environmental isolates with an automated single-strand conformation polymorphism analysis technique. The results indicated that sequence variation does occur and that these changes are mainly located in two areas: at the center and near the end of the coding region. The variability was generally at the single-base level, although one strain (S. arizonae) did demonstrate significant differences in nucleotide sequence.

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