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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (10 January 2022) | Viewed by 33004

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Prof. Dr. Lujiang Qu

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Department of Animal Genetics and Breeding, National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Yuanmingyuan West Road 2, Beijing 100193, China
Interests: evolution; animals; genetics; domestication
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Dear Colleagues,

Driven by ongoing updates in genomic technologies and the decreasing price of genome sequencing, research on poultry genetics has entered an unprecedented era. In the last twenty years, when genomic sequencing was extensively applied in the field of poultry genetics, more and more intensive reference genomes of poultry have been updated all the time. Evolutionary adaption and domestication on genomic levels of poultry were explained by various bioinformatic analyses. The genetic foundation of some simple traits including pigmentation-related phenotypes, combs and so on was completely determined, and some complex traits like production, reproduction, immunity, disease resistance and heat tolerance-related traits were also gradually unveiled. Importantly, knowing the genetic basement and molecular mechanisms of poultry phenotypes does not only help us to understand our closest birds, but also to develop poultry lines with more productive efficiency by using the related genetic variants on genomic levels. In this Special Issue, in order to help researchers and readers understand the recent application of genomic methods in poultry genetics, we invite a wide range of paper submissions on poultry genetics and genomics, including reviews, research papers and so on.

Prof. Dr. Lujiang Qu
Guest Editor

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Keywords

chicken
duck
goose
turkey
quail
pigeon
genetics
genomics
evolution
domestication

Published Papers (12 papers)

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Research

17 pages, 1265 KiB

Open AccessArticle

Characterization of Chicken α_2A-Adrenoceptor: Molecular Cloning, Functional Analysis, and Its Involvement in Ovarian Follicular Development

by Biying Jiang, Baolong Cao, Zhichun Zhou, Zejiao Li, Can Lv, Jiannan Zhang, Heyuan Zhang, Yajun Wang and Juan Li

Genes 2022, 13(7), 1113; https://doi.org/10.3390/genes13071113 - 21 Jun 2022

Cited by 5 | Viewed by 1986

Abstract

Adrenoceptors are suggested to mediate the functions of norepinephrine (NE) and epinephrine (EPI) in the central nervous system (CNS) and peripheral tissues in vertebrates. Compared to mammals, the functionality and expression of adrenoceptors have not been well characterized in birds. Here, we reported the structure, expression, and functionality of chicken functional α_2A-adrenoceptor, named ADRA2A. The cloned chicken ADRA2A cDNA is 1335 bp in length, encoding the receptor with 444 amino acids (a.a.), which shows high amino acid sequence identity (63.4%) with its corresponding ortholog in humans. Using cell-based luciferase reporter assays and Western blot, we demonstrated that the ADRA2A could be activated by both NE and EPI through multiple signaling pathways, including MAPK/ERK signaling cascade. In addition, the mRNA expression of ADRA2A is found to be expressed abundantly in adult chicken tissues including thyroid, lung, ovary and adipose from the reported RNA-Seq data sets. Moreover, the mRNA expression of ADRA2A is also found to be highly expressed in the granulosa cells of 6–8 mm and F5 chicken ovarian follicles, which thus supports that ADRA2A signaling may play a role in ovarian follicular growth and differentiation. Taken together, our data provide the first proof that the α_2A-adrenoceptor is functional in birds involving avian ovarian follicular development. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Genomics)

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21 pages, 3624 KiB

Open AccessArticle

Liver Transcriptome Response to Heat Stress in Beijing You Chickens and Guang Ming Broilers

by Astrid Lissette Barreto Sánchez, Qiao Wang, Mamadou Thiam, Zixuan Wang, Jin Zhang, Qi Zhang, Na Zhang, Qinghe Li, Jie Wen and Guiping Zhao

Genes 2022, 13(3), 416; https://doi.org/10.3390/genes13030416 - 25 Feb 2022

Cited by 10 | Viewed by 2592

Abstract

Heat stress is one of the most prevalent issues in poultry production that reduces performance, robustness, and economic gains. Previous studies have demonstrated that native chickens are more tolerant of heat than commercial breeds. However, the underlying mechanisms of the heat tolerance observed in native chicken breeds remain unelucidated. Therefore, we performed a phenotypical, physiological, liver transcriptome comparative analysis and WGCNA in response to heat stress in one native (Beijing You, BY) and one commercial (Guang Ming, GM) chicken breed. The objective of this study was to evaluate the heat tolerance and identify the potential driver and hub genes related to heat stress in these two genetically distinct chicken breeds. In brief, 80 BY and 60 GM, 21 days old chickens were submitted to a heat stress experiment for 5 days (33 °C, 8 h/day). Each breed was divided into experimental groups of control (Ctl) and heat stress (HS). The results showed that BY chickens were less affected by heat stress and displayed reduced DEGs than GM chickens, 365 DEGs and 382 DEGs, respectively. The transcriptome analysis showed that BY chickens exhibited enriched pathways related to metabolism activity, meanwhile GM chickens’ pathways were related to inflammatory reactions. CPT1A and ANGPTL4 for BY chickens, and HSP90B1 and HSPA5 for GM chickens were identified as potential candidate genes associated with HS. The WGCNA revealed TLR7, AR, BAG3 genes as hub genes, which could play an important role in HS. The results generated in this study provide valuable resources for studying liver transcriptome in response to heat stress in native and commercial chicken lines. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Genomics)

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7 pages, 4394 KiB

Open AccessCommunication

A Deletion Upstream of SOX10 Causes Light Yellow Plumage Colour in Chicken

by Tao Zhu, Mengchao Liu, Shan Peng, Xinye Zhang, Yu Chen, Xueze Lv, Weifang Yang, Kaiyang Li, Jianwei Zhang, Huie Wang, Haiying Li, Zhonghua Ning, Liang Wang and Lujiang Qu

Genes 2022, 13(2), 327; https://doi.org/10.3390/genes13020327 - 10 Feb 2022

Cited by 9 | Viewed by 2610

Abstract

Chicken plumage colour is a complex trait controlled by many genes. Herein, through Rhode Island Red (RIR) and White Leghorn (WL) F1 cross populations, the segregation of plumage color was observed in females, showing white in males, and dark red (DR) and light yellow (LY) in females. The white has been found to be caused by dominant white alleles (I) and the DR phenotype is attributed to a sex-linked recessive silver allele (

S * S

). LY is a derived feather colour phenotype and the genetic mechanism of this is unclear. In order to explore the genetic basis for LY, we randomly selected 40 DR and 39 LY chickens for paired-end sequencing. Through the use of association analysis, we found the LY phenotype is caused by a 7.6 kb non-coding deletion near the SOX10 gene. This mutation has been reported to be responsible for dark brown plumage in chicken, and subsequent diagnostic PCR tests showed that the length of the long-range non-coding deletion is 7.6 kb instead of 8.3 kb as previously reported. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Genomics)

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12 pages, 5225 KiB

Open AccessArticle

Identification of Candidate Genes for Meat Color of Chicken by Combing Selection Signature Analyses and Differentially Expressed Genes

by Jiahong Sun, Xiaodong Tan, Xinting Yang, Lu Bai, Fuli Kong, Guiping Zhao, Jie Wen and Ranran Liu

Genes 2022, 13(2), 307; https://doi.org/10.3390/genes13020307 - 07 Feb 2022

Cited by 5 | Viewed by 1923

Abstract

Meat color, an important index of chicken quality, is highly related to heme pigment, glycolysis, and intramuscular fat metabolisms. The objective of this study is to obtain candidate genes associated with meat color in chickens based on the comparison of fast-growing, white-feathered chickens (Line B) and slow-growing, yellow-feathered chickens (Jingxing Yellow), which have significant differences in meat color. The differentially expressed genes (DEGs) between Line B and Jingxing Yellow were identified in beast muscle. The fixation index (F_ST) method was used to detect signatures of positive selection between the two breeds. Screening of 1109 genes by the F_ST and 1317 candidate DEGs identified by RNA-seq. After gene ontology analysis along with the Kyoto Encyclopedia of Genes and Genomes, 16 genes associated with glycolysis, fatty acid metabolism, protein metabolism, and heme content were identified as candidate genes that regulate the color of chicken breast meat, especially TBXAS1 (redness), GDPD5 (yellowness), SLC2A6 (lightness), and MMP27 (lightness). These findings should be helpful for further elucidating the molecular mechanisms and developing molecular markers to facilitate the selection of chicken meat color. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Genomics)

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11 pages, 2626 KiB

Open AccessArticle

The SLC27A1 Gene and Its Enriched PPAR Pathway Are Involved in the Regulation of Flavor Compound Hexanal Content in Chinese Native Chickens

by Yuxi Jin, Xiaoya Yuan, Wenjuan Zhao, Hua Li, Guiping Zhao and Jianfeng Liu

Genes 2022, 13(2), 192; https://doi.org/10.3390/genes13020192 - 22 Jan 2022

Cited by 2 | Viewed by 2680

Abstract

The role of hexanal in flavor as an indicator of the degree of oxidation of meat products is undeniable. However, the genes and pathways of hexanal formation have not been characterized in detail. In this study, we performed differential gene expression analysis and weighted gene co-expression network analysis (WGCNA) on groups of Tiannong partridge chickens with different relative hexanal content in order to find the genes involved in the formation of hexanal and the specific pathways of hexanal formation. Then we confirmed the relationship of these candidate genes with hexanal using Jingxing Yellow chicken and Wenchang chicken. In this study, WGCNA revealed a module of co-expressed genes that were highly associated with the volatile organic compound hexanal. We also compared transcriptome gene expression data of samples from chicken groups with high and low relative contents of hexanal and identified a total of 651 differentially expressed genes (DEGs). Among them, 356 genes were up regulated, and 295 genes were downregulated. The different biological functions associated with the DEGs, hub genes and hexanal were identified by functional analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations. Among all the hub genes in the significant module identified by WGCNA, more were enriched in the PPAR signaling pathway, the proteasome pathway, etc. Additionally, we found that DEGs and hub genes, including SLC27A1, ACOX3, NR4A1, VEGFA, JUN, EGR1, CACNB1, GADD45A and DUSP1, were co-enriched in the peroxisome proliferator-activated receptor (PPAR) signaling pathway, p53 signaling pathway and mitogen-activated protein kinases (MAPK) signaling pathway, etc. Transcriptome results of the Jingxing Yellow chicken population showed that the SLC27A1 gene was significantly associated with hexanal and enriched in the PPAR pathway. Our study provides a comprehensive insight into the key genes related to hexanal content, and can be further explored by functional and molecular studies. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Genomics)

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18 pages, 3594 KiB

Open AccessArticle

Understanding Transcriptomic and Serological Differences between Forced Molting and Natural Molting in Laying Hens

by Tongyu Zhang, Zhonghua Ning, Yu Chen, Junhui Wen, Yaxiong Jia, Liang Wang, Xueze Lv, Weifang Yang, Changqing Qu, Haiying Li, Huie Wang and Lujiang Qu

Genes 2022, 13(1), 89; https://doi.org/10.3390/genes13010089 - 29 Dec 2021

Cited by 8 | Viewed by 3077

Abstract

Molting is natural adaptation to climate change in all birds, including chickens. Forced molting (FM) can rejuvenate and reactivate the reproductive potential of aged hens, but the effect of natural molting (NM) on older chickens is not clear. To explore why FM has a dramatically different effect on chickens compared with NM, the transcriptome analyses of the hypothalamus and ovary in forced molted and natural molted hens at two periods with feathers fallen and regrown were performed. Additionally, each experimental chicken was tested for serological indices. The results of serological indices showed that growth hormone, thyroid stimulating hormone, and thyroxine levels were significantly higher (p < 0.05) in forced molted hens than in natural molted hens, and calcitonin concentrations were lower in the forced molted than in the natural molted hens. Furthermore, the transcriptomic analysis revealed a large number of genes related to disease resistance and anti-aging in the two different FM and NM periods. These regulatory genes and serological indices promote reproductive function during FM. This study systematically revealed the transcriptomic and serological differences between FM and NM, which could broaden our understanding of aging, rejuvenation, egg production, and welfare issues related to FM in chickens. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Genomics)

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19 pages, 889 KiB

Open AccessArticle

Metformin Affects the Transcriptomic Profile of Chicken Ovarian Cancer Cells

by Lalitha Gopalan, Aswathy Sebastian, Craig A. Praul, Istvan Albert and Ramesh Ramachandran

Genes 2022, 13(1), 30; https://doi.org/10.3390/genes13010030 - 23 Dec 2021

Cited by 2 | Viewed by 4119

Abstract

Ovarian cancer is the most lethal gynecological malignancy in women. Metformin intake is associated with a reduced incidence of ovarian cancer and increased overall survival rate. We determined the effect of metformin on sphere formation, extracellular matrix invasion, and transcriptome profile of ovarian cancer cells (COVCAR) isolated from ascites of chickens that naturally developed ovarian cancer. We found that metformin treatment significantly decreased sphere formation and invasiveness of COVCAR cells. RNA-Seq data analysis revealed 0, 4, 365 differentially expressed genes in cells treated with 0.5, 1, 2 mM metformin, respectively compared to controls. Transcriptomic and ingenuity pathway analysis (IPA) revealed significant downregulation of MMP7, AICDA, GDPD2, APOC3, APOA1 and predicted inhibition of upstream regulators NFKB, STAT3, TP53 that are involved in epithelial–mesenchymal transition, DNA repair, and lipid metabolism. The analysis revealed significant upregulation of RASD2, IHH, CRABP-1 and predicted activation of upstream regulators VEGF and E2F1 that are associated with angiogenesis and cell cycle. Causal network analysis revealed novel pathways suggesting predicted inhibition of ovarian cancer through master regulator ASCL1 and dataset genes DCX, SEMA6B, HEY2, and KCNIP2. In summary, advanced pathway analysis in IPA revealed novel target genes, upstream regulators, and pathways affected by metformin treatment of COVCAR cells. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Genomics)

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15 pages, 2521 KiB

Open AccessArticle

Large-Scale Whole Genome Sequencing Study Reveals Genetic Architecture and Key Variants for Breast Muscle Weight in Native Chickens

by Xiaodong Tan, Lu Liu, Xiaojing Liu, Huanxian Cui, Ranran Liu, Guiping Zhao and Jie Wen

Genes 2022, 13(1), 3; https://doi.org/10.3390/genes13010003 - 21 Dec 2021

Cited by 11 | Viewed by 3008

Abstract

Breast muscle weight (BrW) is one of the most important economic traits in chicken, and directional breeding for that results in both phenotypic and genetic changes. The Jingxing yellow chicken, including an original (without human-driven selection) line and a selected line (based on selection for increased intramuscular fat content), were used to dissect the genetic architecture and key variants associated with BrW. We detected 1069 high-impact single nucleotide polymorphisms (SNPs) with high conserved score and significant frequency difference between two lines. Based on the annotation result, the ECM-receptor interaction and fatty acid biosynthesis were enriched, and muscle-related genes, including MYOD1, were detected. By performing genome-wide association study for the BrW trait, we defined a major haplotype and two conserved SNPs that affected BrW. By integrated genomic and transcriptomic analysis, IGF2BP1 was identified as the crucial gene associated with BrW. In conclusion, these results offer a new insight into chicken directional selection and provide target genetic markers by which to improve chicken BrW. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Genomics)

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14 pages, 1566 KiB

Open AccessArticle

Analysis of Serum Biochemical Indexes, Egg Quality, and Liver Transcriptome in Laying Hens Fed Diets Supplemented with Gynostemma pentaphyllum Powder

by Tao Li, Shuya Zhang, Jiqiao Zhang, Yiping Song, Xiuyu Bao, Fengwen Xu and Jianqin Zhang

Genes 2021, 12(12), 1942; https://doi.org/10.3390/genes12121942 - 30 Nov 2021

Cited by 4 | Viewed by 2501

Abstract

Gynostemma pentaphyllum (GP), known as “southern ginseng”, can reduce the blood pressure and blood lipid levels. In this study, 300 layer chicks of one day old were divided randomly into three groups (control group (base diet), high addition group (base diet with 1% GP), and low addition group (base diet with 0.5% GP)). After 29 weeks, the growth performance, egg quality, and serum index were determined. Additionally, liver mRNA was identified using RNA-seq to investigate the molecular mechanisms. The results indicated that the serum total cholesterol and triglycerides decreased significantly in the GP addition group. The addition of GP increased the egg weight, Haugh unit and redness (a*) of the egg yolk color, and reduced the yolk cholesterol concentration. Moreover, 95 differentially expressed genes (DEGs) were screened between the control and GP addition group. GO and the KEGG analysis showed that the PPAR pathway was significantly enriched. Five fatty acid metabolism-related genes (FABP3, CYP7A1, ANKRD22, SCD1, and PCK1) were validated by qRT-PCR analysis, which confirmed the tendency of the expression. These DEGs in the PPAR pathway may be the key factors of GP affecting fatty acid metabolism. These results may provide a theoretical basis for further research and new insights into GP as a feed additive. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Genomics)

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17 pages, 8727 KiB

Open AccessArticle

Integrated Analysis Reveals a lncRNA–miRNA–mRNA Network Associated with Pigeon Skeletal Muscle Development

by Tao Zhang, Can Chen, Shushu Han, Lan Chen, Hao Ding, Yueyue Lin, Genxi Zhang, Kaizhou Xie, Jinyu Wang and Guojun Dai

Genes 2021, 12(11), 1787; https://doi.org/10.3390/genes12111787 - 11 Nov 2021

Cited by 4 | Viewed by 2401

Abstract

Growing evidence has demonstrated the emerging role of long non-coding RNA as competitive endogenous RNA (ceRNA) in regulating skeletal muscle development. However, the mechanism of ceRNA regulated by lncRNA in pigeon skeletal muscle development remains unclear. To reveal the function and regulatory mechanisms of lncRNA, we first analyzed the expression profiles of lncRNA, microRNA (miRNA), and mRNA during the development of pigeon skeletal muscle using high-throughput sequencing. We then constructed a lncRNA–miRNA–mRNA ceRNA network based on differentially expressed (DE) lncRNAs, miRNAs, and mRNAs according to the ceRNA hypothesis. Functional enrichment and short time-series expression miner (STEM) analysis were performed to explore the function of the ceRNA network. Hub lncRNA–miRNA–mRNA interactions were identified by connectivity degree and validated using dual-luciferase activity assay. The results showed that a total of 1625 DE lncRNAs, 11,311 DE mRNAs, and 573 DE miRNAs were identified. A ceRNA network containing 9120 lncRNA–miRNA–mRNA interactions was constructed. STEM analysis indicated that the function of the lncRNA-associated ceRNA network might be developmental specific. Functional enrichment analysis identified potential pathways regulating pigeon skeletal muscle development, such as cell cycle and MAPK signaling. Based on the connectivity degree, lncRNAs TCONS_00066712, TCONS_00026594, TCONS_00001557, TCONS_00001553, and TCONS_00003307 were identified as hub genes in the ceRNA network. lncRNA TCONS_00026594 might regulate the FSHD region gene 1 (FRG1)/ SRC proto-oncogene, non-receptor tyrosine kinase (SRC) by sponge adsorption of cli-miR-1a-3p to affect the development of pigeon skeletal muscle. Our findings provide a data basis for in-depth elucidation of the lncRNA-associated ceRNA mechanism underlying pigeon skeletal muscle development. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Genomics)

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17 pages, 1623 KiB

Open AccessArticle

Transcriptomic Analysis of Laying Hens Revealed the Role of Aging-Related Genes during Forced Molting

by Tongyu Zhang, Yu Chen, Junhui Wen, Yaxiong Jia, Liang Wang, Xueze Lv, Weifang Yang, Changqing Qu, Haiying Li, Huie Wang, Lujiang Qu and Zhonghua Ning

Genes 2021, 12(11), 1767; https://doi.org/10.3390/genes12111767 - 07 Nov 2021

Cited by 10 | Viewed by 2932

Abstract

Molting in birds provides us with an ideal genetic model for understanding aging and rejuvenation since birds present younger characteristics for reproduction and appearance after molting. Forced molting (FM) by fasting in chickens causes aging of their reproductive system and then promotes cell redevelopment by providing water and feed again. To reveal the genetic mechanism of rejuvenation, we detected blood hormone indexes and gene expression levels in the hypothalamus and ovary of hens from five different periods during FM. Three hormones were identified as participating in FM. Furthermore, the variation trends of gene expression levels in the hypothalamus and ovary at five different stages were found to be basically similar using transcriptome analysis. Among them, 45 genes were found to regulate cell aging during fasting stress and 12 genes were found to promote cell development during the recovery period in the hypothalamus. In addition, five hub genes (INO80D, HELZ, AGO4, ROCK2, and RFX7) were identified by WGCNA. FM can restart the reproductive function of aged hens by regulating expression levels of genes associated with aging and development. Our study not only enriches the theoretical basis of FM but also provides insights for the study of antiaging in humans and the conception mechanism in elderly women. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Genomics)

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11 pages, 1011 KiB

Open AccessArticle

miR-301a-5p Regulates TGFB2 during Chicken Spermatogenesis

by Qixin Guo, Yong Jiang, Hao Bai, Guohong Chen and Guobin Chang

Genes 2021, 12(11), 1695; https://doi.org/10.3390/genes12111695 - 25 Oct 2021

Cited by 6 | Viewed by 1941

Abstract

The process of spermatogenesis is complex and systemic, requiring the cooperation of many regulators. However, little is known about how micro RNAs (miRNAs) regulate spermatogenesis in poultry. In this study, we investigated key miRNAs and their target genes that are involved in spermatogenesis in chickens. Next-generation sequencing was conducted to determine miRNA expression profiles in five cell types: primordial germ cells (PGCs), spermatogonial stem cells (SSCs), spermatogonia (Spa), and chicken sperm. Next, we analyzed and identified several key miRNAs that regulate spermatogenesis in the four germline cell miRNA profiles. Among the enriched miRNAs, miRNA-301a-5p was the key miRNA in PGCs, SSCs, and Spa. Through reverse transcription quantitative PCR (RT-qPCR), dual-luciferase, and miRNA salience, we confirmed that miR-301a-5p binds to transforming growth factor-beta 2 (TGFβ2) and is involved in the transforming growth factor-beta (TGF-β) signaling pathway and germ cell development. To the best of our knowledge, this is the first demonstration of miR-301a-5p involvement in spermatogenesis by direct binding to TGFβ2, a key gene in the TGF-β signaling pathway. This finding contributes to the insights into the molecular mechanism through which miRNAs regulate germline cell differentiation and spermatogenesis in chickens. Full article

(This article belongs to the Special Issue Advances in Poultry Genetics and Genomics)

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