Skin transcriptome profiles associated with black- and white-coated regions in Boer and Macheng black crossbred goats

Xiong, Qi; Tao, Hu; Zhang, Nian; Zhang, Liqing; Wang, Guiqiang; Li, Xiaofeng; Suo, Xiaojun; Zhang, Na; Liu, Yang; Chen, Mingxin

doi:10.1016/j.ygeno.2019.10.019

Cited by 11 publications

(6 citation statements)

References 44 publications

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“…The result of alignment with reference genome showed that over 80% of the identified genes for the nine libraries could be mapped to the goat reference genome, the lowest mapping rate was 83.76%. In previous studies on mammary glands and on goat skin, the mapping haves have been no more than 80%, which indicated that the sequencing quality was high (Xiong et al, 2020;Lin et al, 2015).…”

Section: Discussionmentioning

confidence: 98%

Transcriptome analysis reveals potential immune function-related regulatory genes/pathways of female Lubo goat submandibular glands at different developmental stages

Wang

Chao

et al. 2020

PeerJ

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Background The submandibular glands, as major salivary glands, participate in rumen digestion in goats. Sialic acid, lysozyme, immunoglobulin A (IgA), lactoferrin and other biologically active substances secreted in the submandibular glands were reported in succession, which suggests that the submandibular gland may have immune functions in addition to participating in digestion. The aim of this study was to map the expression profile of differentially expressed genes (DEGs) at three different stages by transcriptome sequencing, screen immune-related genes and pathways by bioinformatics methods, and predict the immune function of submandibular glands at different developmental stages. Methods Nine submandibular gland tissue samples were collected from groups of 1-month-old kids, 12-month-old adolescent goats and 24-month-old adult goats (3 samples from each group), and high-throughput transcriptome sequencing was conducted on these samples. The DEGs among the three stages were screened and analysed. Key genes and signalling pathways were selected via protein-protein interaction (PPI) network analysis. Results The results revealed 2,706, 2,525 and 52 DEGs between 1-month-old and 12-month-old goats, between 1-month-old and 24-month-old goats, and between 12-month-old and 24-month-old goats, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses indicated that most of the DEGs were enriched in immune- related GO terms and pathways. Based on functional enrichment analysis and network analysis, 10 genes (PTPRC, CD28, SELL, LCP2, MYC, LCK, ZAP70, ITGB2, SYK and CCR7), two signalling pathways (the T cell receptor signalling pathway and the NF-κβ signalling pathway) and eight GO terms (T cell receptor signalling pathway, neutrophil mediated immunity, B cell mediated immunity, regulation of alpha-beta T cell activation, positive regulation of T cell proliferation, regulation of leukocyte differentiation, positive regulation of antigen receptor-mediated signalling pathway, positive regulation of lymphocyte proliferation) that may play key roles in the immune functions of the goat submandibular glands at different developmental stages were identified. Moreover, we found that eight antibacterial peptide-encoding genes were downregulated in the tuberculosis and salivary secretion pathways, while all immunoglobulins were upregulated in 10 immune system pathways. These findings indicate that the submandibular glands may be important immunological organs during the growth process of goats and that the immune function of these glands gradually weakens with age up to 12 months but remains relatively stable after 12 months of age. Overall, this study will improve our understanding of transcriptional regulation related to goat submandibular gland immune function.

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Section: Discussionmentioning

confidence: 98%

Transcriptome analysis reveals potential immune function-related regulatory genes/pathways of female Lubo goat submandibular glands at different developmental stages

Wang

Chao

et al. 2020

PeerJ

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“…The results of the analysis on the transcriptome level revealed that the expression of the tyrosinase gene family (TYR, TYRP1, TYRP2/DCT) which are key factors involved in the melanin synthesis in the melanosome was much lower in the albino-type than in the wildtype. The aforementioned expression patterns have been reported in research not only on Osteichthyes such as the catfish, tilapia, carp and sturgeon but also on vertebrate animals including the chicken and goat (Jiang et al, 2014;Zou et al, 2015;Zhu et al, 2016;Yu F. et al, 2018;Bhat et al, 2019;Gong et al, 2019;Xiong et al, 2020). TYR is known to be involved in melanin synthesis and a key enzyme in the hydroxylation of tyrosine to DOPA (3,4-dihydroxyphenylalanine) and the oxidation of DOPA to dopaquinone (del Marmol and Beermann, 1996).…”

Section: Discussionmentioning

confidence: 89%

Comprehensive RNA-seq Analysis to Evaluate the Pigmentation-Related Genes Involved in Albinism of Cichlid Fish, Aulonocara baenschi

Lee

2020

Front. Mar. Sci.

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The Nkhomo-benga peacock, Aulonocara baenschi is a species inhabiting Lake Malawi and its population has decreased by over 70% over the past 10 years. Since 2018, the species has been included in the IUCN Red list and its status has been set to the critically endangered (CR) level. And the fish is known to have rare but naturally occurring albino strain. Despite that, little has been done to develop its genetic resources such as sequence-based data and expression patterns of genes. Accordingly, this study performed high-throughput sequencing on the caudal fin of the two different-colored A. baenschi in order to identify their pigment-related genes and analyze the expression patterns of the genes on the transcriptome level. Through the Illumina sequencing platform, we obtained 77,035,702 and 88,689,756 reads from the caudal fin of the wildtype and the albino-type, respectively. In addition to that, using de novo assembly and various annotation databases, a total of 141,116 contigs, including 129,369 unigenes were obtained. In the comparative analysis of differentially expressed genes between the wild-type and the albino-type in terms of melanogenesis, the tyrosinase gene family involved in melanin synthesis tended to be less expressed in the albino-type than the wild-type. However, the expression of the critical proteins involved in the pigment synthesis of xanthophore was higher in the albino-type than in the wild-type. In addition, the yellow-orange pigment was more apparently expressed in the caudal fin of the albino-type than of the wild-type. This indicates that the external characteristics of the fish were in accordance with the analysis results on the transcriptome level. The results of this study will be the foundation of research on expression characteristics and gene networking analysis of the pigmentation-related genes of fish.

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“…Coat colour is one of the most important qualitative traits to distinguish between farm animals 40 . In the present study, IMCG and F 1 were light coat colour, while DBG had dark coat colour.…”

Section: Discussionmentioning

confidence: 99%

“…Also, the variability in the morphological characteristics may reflect an adaptability advantage to different ecological systems under which goats are raised including vegetation features pertaining to those zones 42 . Worth mentioning, the pigmentation of the coat colour is genetically regulated by several genes that control the packaging of pigment granules, the amount, pigment-cell number, and type, also, the transfer of pigments to surrounding-cells 40 .…”

Section: Discussionmentioning

confidence: 99%

Assessment of hair and cashmere properties and their genetic background of several goat breeds in Southwest China

Saleh

Rashad

Hassanine

et al. 2022

Sci Rep

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The aim of this study was to determine the properties and quality characteristics of hair and cashmere fibres of three goat breeds raised in Southwest China, namely; Dazu black goat (DBG, n = 203; ♂99, ♀104), Inner Mongolia cashmere goat (IMCG, n = 65; 21♂, 44♀) and their first cross (F1, n = 79; 39♂, 40♀). Totals of 5219, 2130 and 2981 fibre samples, from the three breeds respectively, were taken prior to shearing at 32.5 ± 01.25 months of age from four body sites; shoulder, side-portion, abdomen and leg. Breed effect was significant (P < 0.01) for most hair and cashmere properties. IMCG and F1 hair lengths were longer (P < 0.001) with less variable lengths than DBG. Shoulder hair diameters of the three breeds were not different (P > 0.05) but biggest of the side-portion and abdomen sites of DBG were bigger (P > 0.01), however, the biggest (P < 0.001) hair diameter was recorded for the leg site of F1 and the smallest (P > 0.01) for IMCG. IMCG recorded the longest value for cashmere lengths followed by DBG, while F1 recorded the lowest (P = 0.001), whilst F1 recorded the biggest (P = 0.001) diameter whereas no differences existed between parents' breeds. The cortical cell lengths of IMCG and DBG were 94.57 and 86.85 μm without significant difference detected between breeds. Differences between hair length and diameter for body sites of the studied goat breeds were significant (P < 0.01) but between whiteness, cashmere diameter and diameter of cortical cells were not. Sex had no significant effect on all hair/cashmere properties. Quality characteristics of cashmere fibres from IMCG and F1 were better (P < 0.001) than from DBG. Leg hair diameter, curl recovery rate and cashmere diameter were superior in the crossbred F1 compared to pure breed parents, and DBG was superior to IMCG for fibre elasticity and intensity traits. FGF-5 gene was detected as a candidate gene for hair and cashmere traits in IMCG breed. Whilst, KIT gene was found to be associated with coat colour in the studied breeds. Extra investigations to examine more cashmere goat breeds and crosses are needed to discover genetic variability in cashmere production locally and worldwide.

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Skin transcriptome profiles associated with black- and white-coated regions in Boer and Macheng black crossbred goats

Cited by 11 publications

References 44 publications

Transcriptome analysis reveals potential immune function-related regulatory genes/pathways of female Lubo goat submandibular glands at different developmental stages

Transcriptome analysis reveals potential immune function-related regulatory genes/pathways of female Lubo goat submandibular glands at different developmental stages

Comprehensive RNA-seq Analysis to Evaluate the Pigmentation-Related Genes Involved in Albinism of Cichlid Fish, Aulonocara baenschi

Assessment of hair and cashmere properties and their genetic background of several goat breeds in Southwest China

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