| Literature DB >> 32823629 |
Mengli Zhao1,2, Huitong Zhou2,3, Yuzhu Luo1,2, Jiqing Wang1,2, Jiang Hu1,2, Xiu Liu1,2, Shaobin Li1,2, Zhiyun Hao1,2, Xiayang Jin1,2, Yize Song1,2, Xinmiao Wu1,2, Liyan Hu1,2, Jon G H Hickford2,3.
Abstract
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.Entities:
Keywords: KAP27-1 gene (KRTAP27-1); Longdong cashmere goats; mean fiber diameter; skin
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Year: 2020 PMID: 32823629 PMCID: PMC7463587 DOI: 10.3390/genes11080934
Source DB: PubMed Journal: Genes (Basel) ISSN: 2073-4425 Impact factor: 4.096
Figure 1KRTAPs identified on goat chromosome 1. Eleven identified KRTAPs and the newly identified KRTAP27-1 (boxed) are located on goat chromosome 1. Vertical bars and arrows represent KRTAPs and the direction of transcription, respectively, with the names of the genes being indicated below (i.e., 11-1 represents KRTAP11-1). The distances between these genes are approximate and refer to the caprine chromosome 1 sequence (NC_030808.1).
Figure 2Polymerase chain reaction–single-strand conformation polymorphism (PCR-SSCP) analysis of caprine KRTAP27-1. Three different banding patterns, representing three different variants (A–C), are shown in either homozygous or heterozygous forms.
Figure 3Alignment of the KRTAP27-1 variants identified in goats with the human KRTAP27-1 coding sequence. The prefixes “g” and “h” stand for goat and human sequences, respectively, and homology with caprine KRTAP27-1*A is indicated by dashes. Nucleotides in the coding region are shown in uppercase, while those in the noncoding region are in lowercase. The primer-binding regions are indicated with horizontal lines above the sequences, and the start codon (ATG) and stop codon (TAA and TGA) are shown in bold. Two single nucleotide polymorphisms (SNPs) identified in caprine KRTAP27-1 are indicated. A reverse complementary Chi sequence (CCACCAGC) and a Chi-like sequence (ACTGGTGG) are shaded. The numbering of the nucleotides and amino acids follows the Human Genome Variation Society (HGVS) nomenclature (http://varnomen.hgvs.org/). The GenBank Accession Numbers of these sequences are MN934937 (gKRTAP27-1*A), MN934938 (gKRTAP27-1*B), MN934939 (gKRTAP27-1*C) and AB096937 (hKRTAP27-1). The predicted caprine KRTAP27-1 sequence described in Caprine Genome Assembly sequence NC_030808.1 is identical to gKRTAP27-1*A and hence is not shown separately.
Figure 4Phylogenetic tree of HS-KAPs from goats, sheep and humans. The amino acid sequences of HS-KAPs from humans, sheep and goats were used to construct the tree. The sequences from goats are represented with a prefix “g”, while the sequences from humans and sheep are indicated with the prefixes “h” and “s”, respectively. The putative newly identified caprine KAP27-1 sequences are shown in a box. The numbers at the forks represented the bootstrap confidence values and only those equal to or higher than 60% are shown. The sequence of gKAP28-1 was sourced from Wang et al. [7], and the other KAP sequences were retrieved from GenBank with Accession Numbers: NM_001285774 (gKAP3-1), NM_001285767.1 (gKAP11-1), AY510115 (gKAP13-1), JX426138 (gKAP13-3), NM_001285771 (gKAP15-1), MG996011 (gKAP24-1), X01610 (sKAP1-1 and sKAP1-4), HQ897975 (sKAP1-2), NM_001159761 (sKAP1-3), P02443 (sKAP2-1), U60024 (sKAP2-3), M21099 (sKAP3-1), M21100 (sKAP3-2), M21103 (sKAP3-3), HQ595352 (sKAP11-1), JN377429 (sKAP13-3), MH742372 (sKAP15-1), JX112014 (sKAP24-1), KX644903 (sKAP26-1), MN053920 (sKAP28-1), NM_030967.2 (hKAP1-1), NM_030966.1 (hKAP1-3), NM_001257305.1 (hKAP1-4), NM_031957.1 (hKAP1-5), NM_001123387.1 (hKAP2-1), NM_033032.2 (hKAP2-2), NM_001165252.1 (hKAP2-3), NM_033184.3 (hKAP2-4), NM_031958.1 (hKAP3-1), NM_031959.2 (hKAP3-2), NM_033185.2 (hKAP3-3), NM_175858.2 (hKAP11-1), NM_181599.2 (hKAP13-1), NM_181621.3 (hKAP13-2), NM_181622.2 (hKAP13-3), NM_181600.1 (hKAP13-4), NM_181623.2 (hKAP15-1), NM_001146182.1 (hKAP16-1), NM_001085455.2 (hKAP24-1), NM_001128598.1 (hKAP25-1), NM_203405.1 (hKAP26-1) and AB096937.1 (hKAP27-1).
Figure 5Reverse-transcriptase polymerase chain reaction (RT-PCR) analysis of caprine KRTAP27-1 and ACTB in various tissues of Longdong cashmere goats. These tissues are (1) skin, (2) heart, (3) liver, (4) spleen, (5) lung, (6) kidney and (7) longissimus dorsi muscle. M: DNA marker (Direct-Load PCR Marker II, GenStar, Beijing, China).
Association of caprine KRTAP27-1 genotypes with cashmere fiber traits in Longdong cashmere goats (Mean ± SE) 1.
| Fiber Trait | Raw Mean ± SE | (Mean ± SE) 1 | |||
|---|---|---|---|---|---|
| Cashmere fiber yield (g) | 397.5 ± 3.18 | 420.4 ± 4.88 | 417.0 ± 5.75 | 412.3 ± 11.45 | 0.721 |
| Mean fiber diameter (μm) | 13.3 ± 0.03 |
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| Curly fiber length (cm) | 4.1 ± 0.03 | 4.4 ± 0.05 | 4.3 ± 0.06 | 4.2 ± 0.12 | 0.127 |
1 Estimated marginal means and standard errors (SE) of those means from general linear mixed-effects models. Means that do not share a superscript letter (a or b) within rows are significantly different at p < 0.05 and are shown in bold.