- Genome-wide association studies detects candidate genes for wool traits by re-. - Background: The quality and yield of wool determine the economic value of the fine-wool sheep. - Therefore, discovering markers or genes relevant to wool traits is the cornerstone for the breeding of fine-wool sheep. - A genome-wide association study (GWAS) was performed to detect the candidate genes for the eight wool traits.. - And a total of 57 genome-wide significant SNPs and 30 candidate genes were detected for the desired wool traits. - Conclusion: This is the first GWAS on the wool traits by using re-sequencing data in Chinese fine-wool sheep. - Keywords: Fine-wool sheep, Re-sequencing, GWAS, Enrichment analyses, Wool traits. - The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. - Full list of author information is available at the end of the article. - In general, wool traits are affected by diverse genetic and environ- mental factors simultaneously, with moderate to low herit- ability [1]. - For a fine-wool sheep breeder, understanding the genetic background and detecting genetic markers as- sociated with wool traits can facilitate improved genetic selection for desirable traits to accelerate the genetic pro- gress. - These processes involve complex coordination among various genes and cell types, and occurs in the skin [9].. - Mutations in related genes and status changes in the cor- responding cells potentially affects the wool traits. - From the perspective of genetic control, the detection of candi- date genes associated with wool traits is particularly im- portant. - GWAS has been successfully implemented in mapping QTL for economically import- ant traits in the livestock breeding populations [13, 14].. - GWAS have been conducted to detect genetic variants for economic traits in sheep [15, 16], and several studies have reported the presence of candidate genes for wool traits in a variety of sheep breeds. - Moreover, genome-wide significant SNPs associ- ated with wool traits in Chinese Merino Sheep (JunKen type) and yearling wool traits in Chinese Merino sheep have been detected by using OvineSNP50k BeadChip [10, 17]. - In addition, single-trait GWAS, multi-trait GWAS, and identified putative QTL for wool traits have been conducted in both Merino and Merino crossbred sheep by using OvineHD BeadChip [18]. - However, genotype data of the above mentioned stud- ies were obtained based on the SNP array. - The currently available commercial SNP array such as the Illumina Ovine SNP50K BeadChip cannot cover all the SNPs in- volved in the fine-wool sheep genome. - With reference to the gen- etic background of Chinese fine-wool sheep breeds, the previous GWAS was mainly based on one breed, which inevitably affected the applicability of QTL for wool traits. - In this study, we utilized the re-sequencing data and wool phenotypic data of 460 sheep belonging to four different genetic backgrounds of fine-wool sheep breeds in China including Alpine Merino sheep (AMS), Chinese Merino sheep (CMS), Aohan fine-wool sheep (AHS) and Qinghai fine-wool sheep (QHS) to conduct GWAS aim- ing to explore the candidate genes and the common po- tential causal genetic variants involved in the development of wool traits in different breeds. - Moreover, we believe that the detected candidate genes will facilitate the comprehension of the development mechanisms of wool traits in the future.. - The descriptive statistics of eight phenotypic wool traits and the numbers of sheep are presented in Table 1 and Supplementary Table S1. - In fact, the genetic back- ground of the CMS, AHS, and AMS showed some. - The scatterplots of the first (1.30. - Table 1 Descriptive statistics for the wool traits evaluated. - Wool traits (unit) Mean ± SD Minimum Maximum No. - Genetic variance, residual variance, and the heritability of wool traits were estimated by the AI-REML using the genomic BLUP (gBLUP) for the data of four breeds. - The estimated genetic parameters of wool traits are shown in Table 2. - The estimated heritability of wool traits was 0.44–0.77. - Wool traits genome-wide association studies. - After gene annotation, 30 candidate genes were finally identified as being related to wool traits. - To evaluate the characteristics of the candidate genes in detail annotated by significant SNPs, we enriched these genes further. - We performed the enrichment analysis on these genes annotated at the SNP sites with p -value<2E- 06 (Supplementary Table S5) related to the above wool traits by GO and KEGG. - The p-value of the GO term associated with SL and GFW was approximately 0.05. - Among them, WDPCP and KANK1 were enriched in the regula- tion of cell polarity establishment. - PID1 was enriched in the negative regulation of insulin receptor signaling pathway (GO:0046627). - In terms of the wool stretch Table 2 Estimation of genetic parameters of eight wool traits. - Table 3 Significant SNPs associated with seven wool traits. - analysis revealed that the candidate genes were significantly enriched in the four pathways (Table 4). - Table 3 Significant SNPs associated with seven wool traits (Continued). - Generally, the development of wool traits involves a complex genetic mechanism. - performed in the ovine species to investigate wool traits [10, 18]. - However, these studies were based on SNP array, and may missed some key SNPs inevitably in- volved with wool traits. - 3 Manhattan plots and QQ plots of the a SL, b GFW and c CWR traits. - No points were detected in the SS traits. - detect candidate genes that influence eight beneficial wool traits. - The estimated heritability of the FD traits in this study was 0.64, which is relatively close to the previously reported values. - Notably, heritabil- ity of the GFW trait in our study was 0.77, which is much greater than that reported previously, such as for the Chinese superfine merino sheep the heritability of the. - The wool traits values are generally affected by sex [28].. - this find- ing agrees with the genome-wide selection signatures for wool traits among Merino and Merino-derived sheep breeds [31]. - More interestingly, three SNPs lying in the genomic regions, including three candidate genes ( UBE2E3 , TNFSF4, and RHPN2. - In our study, the mitotic activity of germ cells in the hair folli- cles were found to affect the cell content of wool fibers, which resulted in the development of a variety of fiber diameter. - RHPN2 is involved in the Rho pathway [38]. - In addition, a previous study has shown that RHPN2 was upregulated in the production of hair follicle stem cells in mice [40].. - Although these sites were not located in the known QTL, three candidate genes (namely, NLGN1 , GEM , and NF2 ) were related to cell. - For the SE trait, the function of the candidate gene VAV3 is a guanine nucleotide exchange factor. - A previ- ously published research reported VAV3 only in the bulge outer root sheath (ORS) via gene expression pro- filing [46]. - This process may re- duce the toughness of the wool fiber, making it easily breakable.. - Based on extensive search and literature review, we be- lieve that this is the first GWAS research for wool traits in multiple Chinese fine-wool sheep breeds via re- sequencing data. - The disagreement in our results relative to that in previous studies can be possibly attributed to the difference in the breed and the density and quantity of SNPs used in the analysis. - These newly detected candi- date genes may be involved in the formation of wool traits, warranting further research of the biological func- tion of these genes.. - GWAS was con- ducted for eight wool traits by using the EMMAX model. - A total of 57 genome-wide significant SNPs were detected in associated with the selected wool traits.. - Most of the significant GO and KEGG pathways were found to be related to keratin and cell proliferation as well as to differentiation. - Wool traits were sampled from 460 sheep (adults aged. - The wool samples were collected from the posterior edge of the sheep’s scapula, slightly above the midline of the sheep’s body. - The samples were dispatched to the Na- tional Animal and Rural Ministry of Animal and Fur Quality Supervision and Inspection Center (Lanzhou, China), where the following seven wool traits were. - 2) The N content in single-ended access reads exceed- ing 10% of the read length was set as the standard for deleting paired reads;. - 3) When the number of low-quality (≤5) bases con- tained in the single-ended sequencing read exceeded 50% of the length of the read length, the paired reads were removed.. - The SNP at the k position of the individual i is repre- sented by [0,1,2]. - To test the significance level of the Eigen vectors, we used the Tracey-Widom method.. - Estimation of variance components and heritabilities In this study, the variance components and heritability were estimated using the Average Information Restricted Maximum likelihood algorithm (AI-REML) [59] in the. - In this study, the wool traits were processed in the EMMA. - β is a q × 1 vector representing coefficients of the fixed effects. - Identification of candidate genes and enrichment analysis Based on the results of LD attenuation distance analysis, the biochemical function of the related genes within 50- K base pairs upstream and downstream of the physical position of the significant SNP locus were examined.. - Summary of the statistics of 8 wool traits of 4 fine-wool sheep breeds.. - 460 phenotype data of wool traits.. - SNP density across the genome for data of the four fine-wool sheep breeds.. - The LD decay of the four fine-wool sheep breeds.. - AHS: Aohan fine-wool sheep. - QHS: Qinghai fine-wool sheep. - HZ and TG analyzed the content of the data. - TW, FL,YZ and FH contributed to the management of the phenotype data of wool traits. - The funding bodies played no role in the design of the study, the collection, analyses, or interpretation of data and in writing of the manuscript.. - The phenotype data of wool traits is provided in Additional file 6 (Table S6).. - Ethical permission to collect blood samples from sheep for genetic studies was approved by the Animal Management and Ethics Committee of the Lanzhou Institute of Husbandry and Pharmaceutical Sciences (Permit No.SYXK-2016-0039). - This procedure was approved by the Ethics Committee of the Lanzhou Institute of Husbandry and Pharmaceutical Sciences.. - Fraser AS, Short BF: The biology of the fleece. - Mitotic activity in cells of the wool follicle bulb. - Biology of the wool follicle: an excursion into a unique tissue interaction system waiting to be re-discovered. - Book of Abstracts of the Meeting of the European Federation of Animal Science. - Bolormaa S, Swan AA, Brown DJ, Hatcher S, Moghaddar N, van der Werf JH, Goddard ME, Daetwyler HD: Multiple-trait QTL mapping and genomic prediction for wool traits in sheep. - Estimation of (co) variance components and genetic parameters for growth and wool traits of Chinese superfine merino sheep with the use of a multi- trait animal model. - The difference analysis of wool traits among strains in Chinese Merino (Xinjiang type). - A combined multi-cohort approach reveals novel and known genome-wide selection signatures for wool traits in Merino and Merino-derived sheep breeds. - Regulation of proliferation, survival and apoptosis by members of the TNF superfamily. - Chromosomal organization and transcriptional regulation of human GEM and localization of the human and mouse GEM loci encoding an inducible Ras-like protein. - The dioxin receptor regulates the constitutive expression of the vav3 proto-oncogene and modulates cell shape and adhesion
Xem thử không khả dụng, vui lòng xem tại trang nguồn hoặc xem
Tóm tắt