Variation in a Newly Identified Caprine KRTAP Gene Is Associated with Raw Cashmere Fiber Weight in Longdong Cashmere Goats.
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ABSTRACT:
SUBMITTER: Zhao M
PROVIDER: S-EPMC8143586 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:Keratin-associated proteins (KAPs) are a structural component of cashmere fibers and in part determine fiber attributes. The gene encoding the high-glycine/tyrosine KAP6-2 (called KRTAP6-2) has been described in sheep, but it has not been identified goats. In this study, a 252-bp open reading frame with similarity to ovine KRTAP6-2 was found on goat chromosome 1, with its upstream and downstream flanking sequences are closely related with ovine KRTAP6-2 but are clearly distinct from other ovine KRTAP6-n sequences. Polymerase chain reaction amplification followed by single strand conformation polymorphism analysis of this region revealed five distinct banding patterns representing five different sequences (A to E) in 230 Longdong cashmere goats. Eleven diallelic single nucleotide polymorphisms (SNPs), a three-nucleotide sequence variation, and a 12-bp insertion/deletion were found among these five sequences, with most SNPs being either outside the coding region or synonymous. The presence of variant D was found to be associated with decreased mean fiber diameter (MFD; present: 13.26 ± 0.07 µm; absent: 13.55 ± 0.04 µm; p < 0.001), suggesting that variation in KRTAP6-2 may affect fiber diameter and have value as a molecular marker for improving the cashmere fiber diameter trait.
| S-EPMC9404442 | biostudies-literature
Project description: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.
| S-EPMC7463587 | biostudies-literature
Project description: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.
| S-EPMC6357099 | biostudies-literature
Project description:Five keratin-associated protein 6 genes (KRTAP6) have been identified in sheep and variation in some KRTAP6 has been associated with wool fiber diameter-related traits, but none of these homologues have been identified in goats. In this study, we reported the identification of the sheep KRTAP6-5 homologue on goat chromosome 1 and polymerase chain reaction (PCR)-single strand conformation polymorphism analysis in 300 Longdong cashmere goats revealed the existence of 12 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 23 genotypes, which was the most polymorphism gene in KRTAPs that have been studied. Among these sequences, 15 nucleotide substitutions and a 24-bp insertion/detection were identified. Variation in goat KRTAP6-5 was associated with variation in mean-fiber diameter, suggesting that KRTAP6-5 is worthy of further study in the context of variation in cashmere traits.
| S-EPMC8442941 | biostudies-literature
Project description: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 (PCR) amplicons for the goat nucleotide sequences in 385 Longdong cashmere goats in China, five unique banding patterns were detected using single-stranded conformational polymorphism (SSCP). 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.
| S-EPMC7074440 | biostudies-literature
Project description: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.
| S-EPMC6852866 | biostudies-literature
Project description:Long non-coding RNAs (lncRNAs) are a kind of non-coding RNA being >200 nucleotides in length, and they are found to participate in hair follicle growth and development and wool fiber traits regulation. However, there are limited studies reporting the role of lncRNAs in cashmere fiber production in cashmere goats. In this study, Liaoning cashmere (LC) goats (n = 6) and Ziwuling black (ZB) goats (n = 6) with remarkable divergences in cashmere yield, cashmere fiber diameter, and cashmere color were selected for the construction of expression profiles of lncRNAs in skin tissue using RNA sequencing (RNA-seq). According to our previous report about the expression profiles of mRNAs originated from the same skin tissue as those used in the study, the cis and trans target genes of differentially expressed lncRNAs between the two caprine breeds were screened, resulting in a lncRNA-mRNA network. A total of 129 lncRNAs were differentially expressed in caprine skin tissue samples between LC goats and ZB goats. The presence of 2 cis target genes and 48 trans target genes for the differentially expressed lncRNAs resulted in 2 lncRNA-cis target gene pairs and 93 lncRNA-trans target gene pairs. The target genes concentrated on signaling pathways that were related to fiber follicle development, cashmere fiber diameter, and cashmere fiber color, including PPAR signaling pathway, metabolic pathways, fatty acid metabolism, fatty acid biosynthesis, tyrosine metabolism, and melanogenesis. A lncRNA-mRNA network revealed 22 lncRNA-trans target gene pairs for seven differentially expressed lncRNAs selected, of which 13 trans target genes contributed to regulation of cashmere fiber diameter, while nine trans target genes were responsible for cashmere fiber color. This study brings a clear explanation about the influences of lncRNAs over cashmere fiber traits in cashmere goats.
| S-EPMC9956036 | biostudies-literature
Project description:Objective: Body weight is an important economic trait for a goat, which greatly affects animal growth and survival. The purpose of this study was to identify genes associated with birth weight (BW), weaning weight (WW), and yearling weight (YW). Materials and Methods: In this study, a genome-wide association study (GWAS) of BW, WW, and YW was determined using the GGP_Goat_70K single-nucleotide polymorphism (SNP) chip in 1,920 Inner Mongolia cashmere goats. Results: We discovered that 21 SNPs were significantly associated with BW on the genome-wide levels. These SNPs were located in 10 genes, e.g., Mitogen-Activated Protein Kinase 3 (MAPK3), LIM domain binding 2 (LDB2), and low-density lipoprotein receptor-related protein 1B (LRP1B), which may be related to muscle growth and development in Inner Mongolia Cashmere goats. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that these genes were significantly enriched in the regulation of actin cytoskeleton and phospholipase D signaling pathway etc. Conclusion: In summary, this study will improve the marker-assisted breeding of Inner Mongolia cashmere goats and the molecular mechanisms of important economic traits.
| S-EPMC8673091 | biostudies-literature
Project description:BackgroundCashmere goats are a heterogeneous hairy mammal. The fineness of cashmere can affect its economic value. Therefore, in this study, we used transcriptome sequencing techniques to analyze the gene expression profiles of the skin tissues of cashmere goats with different cashmere fineness. The selected candidate genes were functionally verified with the secondary hair follicle hair papillary cells of cashmere goats.ResultsWe identified 479 DEGs, of which 238 mRNAs were up-regulated in the fine velvet group and 241 mRNA were down-regulated. Based on functional annotation and protein interaction network analysis, we found some genes that may affect the fineness of cashmere, including SOX18, SOX4, WNT5A, IGFBP4, KAP8, KRT36, and FA2H. Using qRT-PCR, Western blot, CCK-8 cell viability detection, EDU cell proliferation detection, and flow cytometry, we found that overexpression of the FA2H gene could promote the proliferation of secondary hair follicle DPCs in cashmere goats. At the same time, we proved that FA2H could regulate the expression levels of the FGF5 and BMP2 genes in DPCs.ConclusionThe results of this study provide a useful reference for the genetics and breeding of Jiangnan cashmere goats and goat genome annotation, and provide an experimental basis for improving cashmere quality of the cashmere goat.
| S-EPMC9306159 | biostudies-literature
Project description:This study aimed to conduct precise supplementation for pregnant cashmere goats under grazing based on the feeding standard. Eight Inner Mongolian pregnant cashmere goats of near-average body weight were selected at early gestation (44.41 ± 4.03 kg) and late gestation (46.54 ± 4.02 kg) to measure their nutrient intake. Then, two pregnant cashmere goat flocks, No. 10 (control group, on-farm supplement) and No. 11 (supplemented group, supplement based on standard), with the same goat herd structure and grassland type, were chosen to conduct the supplemental feeding experiment. The results showed that pregnant cashmere goats lacked daily the intake of dry matter, digestive energy, crude protein and most essential mineral elements under grazing. After supplemental feeding, the supplementation based on the feeding standard increased the cashmere length and cashmere length growth volume and decreased the cashmere fineness, with no statistical significance. The goat cashmere yield, goat weight after shearing, single and twin-birth kid weight and kids' mature secondary hair follicle density were significantly higher in the supplemented group (p < 0.05). In conclusion, supplementation in accordance with "Nutrient Requirements of Cashmere Goats" can enhance pregnant cashmere goats' fiber production, growth performance, fertility and kids' secondary hair follicles development, which is of great importance for the healthy and precise nutrition and management of cashmere goats.
| S-EPMC9913870 | biostudies-literature