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Chen A, Zhao X, Wen J, Zhao X, Wang G, Zhang X, Ren X, Zhang Y, Cheng X, Yu X, Mei X, Wang H, Guo M, Jiang X, Wei G, Wang X, Jiang R, Guo X, Ning Z, Qu L. Genetic parameter estimation and molecular foundation of chicken beak shape. Poult Sci 2024; 103:103666. [PMID: 38703454 PMCID: PMC11087718 DOI: 10.1016/j.psj.2024.103666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 03/02/2024] [Accepted: 03/12/2024] [Indexed: 05/06/2024] Open
Abstract
The bird beak is mainly functioned as feeding and attacking, and its shape has extremely important significance for survival and reproduction. In chickens, since beak shape could lead to some disadvantages including pecking and waste of feed, it is important to understand the inheritance of chicken beak shape. In the present study, we firstly established 4 indicators to describe the chicken beak shapes, including upper beak length (UL), lower beak length (LL), distance between upper and lower beak tips (DB) and upper beak curvature (BC). And then, we measured the 4 beak shape indicators as well as some production traits including body weight (BW), shank length (SL), egg weight (EW), eggshell strength (ES) of a layer breed, Rhode Island Red (RIR), in order to estimate genetic parameters of chicken beak shape. The heritabilities of UL and LL were 0.41 and 0.37, and the heritabilities of DB and BC were 0.22 and 0.21, indicating that beak shape was a highly or mediumly heritable. There were significant positive genetic and phenotypic correlations among UL, LL, and DB. And UL was positively correlated with body weight (BW18) and shank length (SL18) at 18 weeks of age in genetics, and DB was positively correlated with BC in terms of genetics and phenotype. We also found that layers of chicken cages played a role on beak shape, which could be attributed to the difference of lightness in different cage layers. By a genome-wide association study (GWAS) for the chicken UL, we identified 9 significant candidate genes associated with UL in RIR. For the variants with low minor allele frequencies (MAF <0.01) and outside of high linkage disequilibrium (LD) regions, we also conducted rare variant association studies (RVA) and GWAS to find the association between genotype and phenotype. We also analyzed transcriptomic data from multiple tissues of chicken embryos and revealed that all of the 9 genes were highly expressed in beak of chicken embryos, indicating their potential function for beak development. Our results provided the genetic foundation of chicken beak shape, which could help chicken breeding on beak related traits.
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Affiliation(s)
- Anqi Chen
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaoyu Zhao
- Xingrui Agricultural Stock Breeding, Baoding 072550, Hebei Province, China
| | - Junhui Wen
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing 100097, China
| | - Xiurong Zhao
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gang Wang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xinye Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xufang Ren
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yalan Zhang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xue Cheng
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaofan Yu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaohan Mei
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Huie Wang
- Xinjiang Production and Construction Corps, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar 843300, China
| | - Menghan Guo
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xiaoyu Jiang
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Guozhen Wei
- Qingliu Animal Husbandry, Veterinary and Aquatic Products Center, Sanming, China
| | - Xue Wang
- VVBK Animal Medical Diagnostic Technology (Beijing) Co., Ltd, Beijing, China
| | - Runshen Jiang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Xing Guo
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
| | - Zhonghua Ning
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lujiang Qu
- National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; Xinjiang Production and Construction Corps, Key Laboratory of Protection and Utilization of Biological Resources in Tarim Basin, Tarim University, Alar 843300, China.
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Cheng Y, Lei F. Avian lower beak is always overlooked: its coordinate role in shaping species-specific beak should not be underestimated. Integr Zool 2024; 19:339-342. [PMID: 37794566 DOI: 10.1111/1749-4877.12769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Affiliation(s)
- Yalin Cheng
- College of Life Science/Hebei Basic Science Center for Biotic Interactions, Institute of Life Science and Green Development, Hebei University, Baoding, China
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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Yu D, Li Z, Cao J, Wei G, Shen F. LSD1 knockdown confers protection against osteoclast formation by reducing histone 3 lysine 9 monomethylation and dimethylation in ITGB3 promoter. Acta Histochem 2023; 125:152073. [PMID: 37422927 DOI: 10.1016/j.acthis.2023.152073] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/09/2023] [Accepted: 06/25/2023] [Indexed: 07/11/2023]
Abstract
ITGB3, an osteoclast marker, is involved in osteoclast formation. Nevertheless, its related mechanism remains poorly characterized. Herein, this study examines the mechanisms affecting osteoclast formation with the involvement of ITGB3. Osteoclast formation was induced with macrophage colony-stimulating factor (M-CSF) and receptor activator of nuclear factor-kappa B ligand (RANKL), followed by measurement of the mRNA and protein expression of ITGB3 and LSD1. After gain- and loss-of-function assays, cell viability and the expression of osteoclast marker genes (NFATc1, ACP5, and CTSK) were assessed, and osteoclast formation was evaluated with TRAP staining. ChIP assays were used to examine histone 3 lysine 9 (H3K9) monomethylation (H3K9me1) and H3K9 dimethylation (H3K9me2) modifications and LSD1 protein enrichment in the ITGB3 promoter. During osteoclast formation, ITGB3 and LSD1 were gradually augmented. Knockdown of LSD1 or ITGB3 curbed cell viability, the expression of osteoclast marker genes, and osteoclast formation. Moreover, overexpression of ITGB3 nullified the suppressive impact of LSD1 knockdown on osteoclast formation. Mechanistically, LSD1 promoted ITGB3 expression by reducing H3K9 levels in the ITGB3 promoter. LSD1 enhanced ITGB3 expression by decreasing H3K9me1 and H3K9me2 levels in ITGB3 promoter to boost osteoclast formation.
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Affiliation(s)
- Dongping Yu
- Department of Orthopedics, the First Hospital of Nanchang, Nanchang, Jiangxi 330008, PR China
| | - Zhen Li
- Department of Pathology, the First Hospital of Changsha, Changsha, Hunan 410005, PR China
| | - Jie Cao
- Department of Digestive, the First Hospital of Nanchang, Nanchang, Jiangxi 330008, PR China
| | - Guowen Wei
- Department of Orthopedics, the First Hospital of Nanchang, Nanchang, Jiangxi 330008, PR China
| | - Feng Shen
- Department of Orthopedics, the First Hospital of Nanchang, Nanchang, Jiangxi 330008, PR China.
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Li J, Sun K, Dai W, Leng H, Feng J. Divergence in interspecific and intersubspecific gene expression between two closely related horseshoe bats ( Rhinolophus). J Mammal 2022. [DOI: 10.1093/jmammal/gyac103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Abstract
Closely related species have been used as representative systems to investigate the genetic mechanisms involved in the early stages of species differentiation. Previous studies have indicated that variation in gene expression might be a sensitive indicator of initial species divergence, although the role of expression divergence, and especially that associated with phenotypic variation remained relatively undefined. For three organs (cochlea, brain, and liver) from two closely related bat species (Rhinolophus siamensis and R. episcopus), the interspecific and intersubspecific gene expression profiles were compared using transcriptomics in this study. Striking organ specificity of expression was observed, and expression profiles exhibited similarities between cochlea and brain tissues. Numerous differentially expressed genes (DEGs) were identified for each organ in the interspecific comparison (cochlea/brain/liver: 1,069/647/692) and intersubspecific comparison (608/528/368). Functional enrichment analysis indicated vital variation in expression related to the immune system, ion activities, neuronal function, and multisensory system regulation in both comparisons. DEGs relevant to the variation in echolocation calls (RF) were found, and some of them were involved in the pivotal patterns of expression variation. The regulation of immune, ion channel, neural activity, and sophisticated sensory functions at the expression level might be key mechanisms in the early species divergence of bats, and the expression variation related to acoustical signal could have played a crucial part. This study expands our knowledge of gene expression and patterns of variation for three key organs to echolocation at both the interspecific and intersubspecific levels. Further, the framework described here provides insight into the genetic basis of phenotypic variation during the incipient stage of species differentiation.
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Affiliation(s)
- Jun Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun 130117 , China
- Key Laboratory of Vegetation Ecology, Ministry of Education , Changchun 130024 , China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun 130117 , China
- Key Laboratory of Vegetation Ecology, Ministry of Education , Changchun 130024 , China
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun 130117 , China
- Key Laboratory of Vegetation Ecology, Ministry of Education , Changchun 130024 , China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun 130117 , China
- Key Laboratory of Vegetation Ecology, Ministry of Education , Changchun 130024 , China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University , Changchun 130117 , China
- College of Life Science, Jilin Agricultural University , Changchun 130118 , China
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Li J, Sun K, Dai W, Leng H, Li A, Feng J. Extensive Adaptive Variation in Gene Expression within and between Closely Related Horseshoe Bats (Chiroptera, Rhinolophus) Revealed by Three Organs. Animals (Basel) 2022; 12:ani12233432. [PMID: 36496954 PMCID: PMC9741297 DOI: 10.3390/ani12233432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/29/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022] Open
Abstract
In the process of species differentiation and adaption, the relative influence of natural selection on gene expression variation often remains unclear (especially its impact on phenotypic divergence). In this study, we used differentially expressed genes from brain, cochlea, and liver samples collected from two species of bats to determine the gene expression variation forced by natural selection when comparing at the interspecific (Rhinolophus siamensis and R. episcopus episcopus) and the intraspecific (R. e. episcopus and R. episcopus spp.) levels. In both cases, gene expression variation was extensively adaptive (>66.0%) and mainly governed by directional selection, followed by stabilizing selection, and finally balancing selection. The expression variation related to acoustic signals (resting frequency, RF) and body size (forearm length, FA) was also widely governed by natural selection (>69.1%). Different functional patterns of RF- or FA-related adaptive expression variation were found between the two comparisons, which manifested as abundant immune-related regulations between subspecies (indicating a relationship between immune response and phenotypic adaption). Our study verifies the extensive adaptive expression variation between both species and subspecies and provides insight into the effects of natural selection on species differentiation and adaptation as well as phenotypic divergence at the expression level.
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Affiliation(s)
- Jun Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Keping Sun
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
- Correspondence: (K.S.); (J.F.)
| | - Wentao Dai
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Haixia Leng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Aoqiang Li
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- Key Laboratory of Vegetation Ecology, Ministry of Education, Changchun 130024, China
| | - Jiang Feng
- Jilin Provincial Key Laboratory of Animal Resource Conservation and Utilization, Northeast Normal University, Changchun 130117, China
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
- Correspondence: (K.S.); (J.F.)
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Yu D, Li Z, Cao J, Shen F, Wei G. microRNA-25-3p suppresses osteogenic differentiation of BMSCs in patients with osteoporosis by targeting ITGB3. Acta Histochem 2022; 124:151926. [PMID: 35777302 DOI: 10.1016/j.acthis.2022.151926] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 06/10/2022] [Accepted: 06/13/2022] [Indexed: 11/01/2022]
Abstract
This study was conducted to investigate the impact of the microRNA (miR)-25-3p/ITGB3 axis on the osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs) from patients with osteoporosis (OP). BMSCs isolated from the bone marrow of healthy controls and OP patients were identified by flow cytometry, in which ITGB3 mRNA and miR-25-3p expression was detected by RT-qPCR and ITGB3, Runx2, OPN, ALP, and OSX protein expression by western blot. The binding between ITGB3 and miR-25-3p was assessed by dual-luciferase reporter gene and Ago2-RIP assays. BMSC osteogenic differentiation was observed by alizarin red staining and ALP activity. The differentiation of BMSCs to adipocytes and chondrocytes was measured by oil red O staining and alcian blue staining, respectively. BMSCs were successfully isolated from the bone marrow of healthy controls (normal-BMSCs) and OP patients (OP-BMSCs). ITGB3, Runx2, OPN, ALP, and OSX expression was poorer and miR-25-3p expression was higher in OP-BMSCs than in normal-BMSCs. Mechanistically, ITGB3 was negatively targeted by miR-25-3p. After osteogenic, adipogenic, and chondrogenic differentiation of BMSCs were successfully induced, adipogenic differentiation increased and osteogenic and chondrogenic differentiation decreased in OP-BMSCs compared with normal-BMSCs. Overexpression of ITGB3 facilitated mineralized nodule formation and elevated ALP activity and Runx2, OPN, and ALP expression in OP-BMSCs. miR-25-3p upregulation diminished mineralized nodule formation, ALP activity, and Runx2, OPN, and ALP expression in OP-BMSCs and normal-BMSCs, which was annulled by additional ITGB3 overexpression. miR-25-3p targets ITGB3, thereby suppressing osteogenic differentiation of BMSCs from OP patients.
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Affiliation(s)
- Dongping Yu
- Department of Orthopedics, the First Hospital of Nanchang, Nanchang, Jiangxi 330008, PR China
| | - Zhen Li
- Department of Pathology, the First Hospital of Changsha, Changsha, Hunan 410005, PR China.
| | - Jie Cao
- Department of Digestive, the First Hospital of Nanchang, Nanchang, Jiangxi 330008, PR China
| | - Feng Shen
- Department of Orthopedics, the First Hospital of Nanchang, Nanchang, Jiangxi 330008, PR China
| | - Guowen Wei
- Department of Orthopedics, the First Hospital of Nanchang, Nanchang, Jiangxi 330008, PR China
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Huang J, Wang C, Ouyang J, Tang H, Zheng S, Xiong Y, Gao Y, Wu Y, Wang L, Yan X, Chen H. Identification of Key Candidate Genes for Beak Length Phenotype by Whole-Genome Resequencing in Geese. Front Vet Sci 2022; 9:847481. [PMID: 35372529 PMCID: PMC8964941 DOI: 10.3389/fvets.2022.847481] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2022] [Accepted: 02/15/2022] [Indexed: 12/14/2022] Open
Abstract
The domestic goose is an important economic animal in agriculture and its beak, a trait with high heritability, plays an important role in promoting food intake and defending against attacks. In this study, we sequenced 772 420-day-old Xingguo gray geese (XGG) using a low-depth (~1 ×) whole-genome resequencing strategy. We detected 12,490,912 single nucleotide polymorphisms (SNPs) using the standard GATK and imputed with STITCH. We then performed a genome-wide association study on the beak length trait in XGG. The results indicated that 57 SNPs reached genome-wide significance levels for the beak length trait and were assigned to seven genes, including TAPT1, DHX15, CCDC149, LGI2, SEPSECS, ANAPC4, and Slc34a2. The different genotypes of the most significant SNP (top SNP), which was located upstream of LGI2 and explained 7.24% of the phenotypic variation in beak length, showed significant differences in beak length. Priority-based significance analysis concluded that CCDC149, LGI2, and SEPSECS genes in the most significant quantitative trait locus interval were the most plausible positional and functional candidate genes for beak length development in the XGG population. These findings not only enhance our understanding of the genetic mechanism of the beak length phenotype in geese, but also lay the foundation for further studies to facilitate the genetic selection of traits in geese.
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Determining the variation in premaxillary and dentary bone morphology that may underlie beak shape between two pure layer lines. Poult Sci 2021; 100:101500. [PMID: 34700097 PMCID: PMC8554249 DOI: 10.1016/j.psj.2021.101500] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/14/2021] [Accepted: 09/14/2021] [Indexed: 11/22/2022] Open
Abstract
Beak treatment is an effective method of reducing the damage inflicted by severe feather pecking (SFP) but there is significant pressure to eliminate these treatments and rely solely on alternative strategies. Substantial variation in beak shape exists within non-beak treated layer flocks and beak shape appears to be heritable. There is the potential to use this pre-existing variation and genetically select for hens whose beak shapes are less apt to cause damage during SFP. To do this, we must first understand the range of phenotypes that exist for both the external beak shape and the bones that provide its structure. The objective of this study was to determine the variation in premaxillary (within the top beak) and dentary (within the bottom beak) bone morphology that exists in 2 non-beak treated pure White Leghorn layer lines using geometric morphometrics to analyze radiographs. Lateral head radiographs were taken of 825 hens and the premaxillary and dentary bones were landmarked. Landmark coordinates were standardized by Procrustes superimposition and the covariation was analyzed by principal components analysis and multivariate regression using Geomorph (an R package). Three principal components (PCs) explained 85% of total premaxillary bone shape variation and showed that the shape ranged from long and narrow with pointed bone tips to short and wide with more curved tips. Two PCs explained 81% of total dentary bone shape variation. PC1 described the dentary bone length and width and PC2 explained the angle between the bone tip and its articular process. For both bones, shape was significantly associated with bone size and differed significantly between the two lines. Bone size accounted for 42% of the total shape variation for both bones. Together, the results showed a range of phenotypic variation in premaxillary and dentary bone shape, which in turn may influence beak shape. These bone phenotypes will guide further quantitative genetic and behavioral analyses that will help identify which beaks shapes cause the least damage when birds engage in SFP.
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Cheng Y, Miller MJ, Zhang D, Song G, Jia C, Qu Y, Lei F. Comparative Genomics Reveals Evolution of a Beak Morphology Locus in a High-Altitude Songbird. Mol Biol Evol 2020; 37:2983-2988. [PMID: 32592485 DOI: 10.1093/molbev/msaa157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The Ground Tit (Pseudopodoces humilis) has lived on the Qinghai-Tibet Plateau for ∼5.7 My and has the highest altitudinal distribution among all parids. This species has evolved an elongated beak in response to long-term selection imposed by ground-foraging and cavity-nesting habits, yet the genetic basis for beak elongation remains unknown. Here, we perform genome-wide analyses across 14 parid species and identify 25 highly divergent genomic regions that are significantly associated with beak length, finding seven candidate genes involved in bone morphogenesis and remolding. Neutrality tests indicate that a model allowing for a selective sweep in the highly conserved COL27A1 gene best explains variation in beak length. We also identify two nonsynonymous fixed mutations in the collagen domain that are predicted to be functionally deleterious yet may have facilitated beak elongation. Our study provides evidence of adaptive alleles in COL27A1 with major effects on beak elongation of Ps. humilis.
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Affiliation(s)
- Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Matthew J Miller
- Sam Noble Oklahoma Museum of Natural History and Department of Biology, University of Oklahoma, Norman, OK
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chenxi Jia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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The Genomic Landscape of Divergence Across the Speciation Continuum in Island-Colonising Silvereyes ( Zosterops lateralis). G3-GENES GENOMES GENETICS 2020; 10:3147-3163. [PMID: 32660974 PMCID: PMC7466963 DOI: 10.1534/g3.120.401352] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Inferring the evolutionary dynamics at play during the process of speciation by analyzing the genomic landscape of divergence is a major pursuit in population genomics. However, empirical assessments of genomic landscapes under varying evolutionary scenarios that are known a priori are few, thereby limiting our ability to achieve this goal. Here we combine RAD-sequencing and individual-based simulations to evaluate the genomic landscape of divergence in the silvereye (Zosterops lateralis). Using pairwise comparisons that differ in divergence timeframe and the presence or absence of gene flow, we document how genomic patterns accumulate along the speciation continuum. In contrast to previous predictions, our results provide limited support for the idea that divergence accumulates around loci under divergent selection or that genomic islands widen with time. While a small number of genomic islands were found in populations diverging with and without gene flow, in few cases were SNPs putatively under selection tightly associated with genomic islands. The transition from localized to genome-wide levels of divergence was captured using individual-based simulations that considered only neutral processes. Our results challenge the ubiquity of existing verbal models that explain the accumulation of genomic differences across the speciation continuum and instead support the idea that divergence both within and outside of genomic islands is important during the speciation process.
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Sadier A, Santana SE, Sears KE. The role of core and variable Gene Regulatory Network modules in tooth development and evolution. Integr Comp Biol 2020; 63:icaa116. [PMID: 32761089 DOI: 10.1093/icb/icaa116] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 07/15/2020] [Accepted: 07/27/2020] [Indexed: 02/28/2024] Open
Abstract
Among the developmental processes that have been proposed to influence the direction of evolution, the modular organization of developmental gene regulatory networks (GRNs) has shown particular promise. In theory, GRNs have core modules comprised of essential, conserved circuits of genes, and sub-modules of downstream, secondary circuits of genes that are more susceptible to variation. While this idea has received considerable interest as of late, the field of evo-devo lacks the experimental systems needed to rigorously evaluate this hypothesis. Here, we introduce an experimental system, the vertebrate tooth, that has great potential as a model for testing this hypothesis. Tooth development and its associated GRN have been well studied and modeled in both model and non-model organisms. We propose that the existence of modules within the tooth GRN explains both the conservation of developmental mechanisms and the extraordinary diversity of teeth among vertebrates. Based on experimental data, we hypothesize that there is a conserved core module of genes that is absolutely necessary to ensure tooth or cusp initiation and development. In regard to tooth shape variation between species, we suggest that more relaxed sub-modules activated at later steps of tooth development, e.g., during the morphogenesis of the tooth and its cusps, control the different axes of tooth morphological variation.
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Affiliation(s)
- Alexa Sadier
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, California
| | - Sharlene E Santana
- Department of Biology and Burke Museum of Natural History and Culture, University of Washington, Seattle, Washington
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, University of California at Los Angeles, Los Angeles, California
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12
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Qu Y, Chen C, Xiong Y, She H, Zhang YE, Cheng Y, DuBay S, Li D, Ericson PGP, Hao Y, Wang H, Zhao H, Song G, Zhang H, Yang T, Zhang C, Liang L, Wu T, Zhao J, Gao Q, Zhai W, Lei F. Rapid phenotypic evolution with shallow genomic differentiation during early stages of high elevation adaptation in Eurasian Tree Sparrows. Natl Sci Rev 2019; 7:113-127. [PMID: 34692022 PMCID: PMC8289047 DOI: 10.1093/nsr/nwz138] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Revised: 08/31/2019] [Accepted: 09/01/2019] [Indexed: 02/06/2023] Open
Abstract
Abstract
Known as the ‘third polar region’, the Qinghai-Tibet Plateau represents one of the harshest highland environments in the world and yet a number of organisms thrive there. Previous studies of birds, animals and humans have focused on well-differentiated populations in later stages of phenotypic divergence. The adaptive processes during the initial phase of highland adaptation remain poorly understood. We studied a human commensal, the Eurasian Tree Sparrow, which has followed human agriculture to the Qinghai-Tibet Plateau. Despite strong phenotypic differentiation at multiple levels, in particular in muscle-related phenotypes, highland and lowland populations show shallow genomic divergence and the colonization event occurred within the past few thousand years. In a one-month acclimation experiment investigating phenotypic plasticity, we exposed adult lowland tree sparrows to a hypoxic environment and did not observe muscle changes. Through population genetic analyses, we identified a signature of polygenic adaptation, whereby shifts in allele frequencies are spread across multiple loci, many of which are associated with muscle-related processes. Our results reveal a case of positive selection in which polygenic adaptation appears to drive rapid phenotypic evolution, shedding light on early stages of adaptive evolution to a novel environment.
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Affiliation(s)
- Yanhua Qu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Chunhai Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Ying Xiong
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shane DuBay
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL 60637, USA
- Life Sciences Section, Integrative Research Center, Field Museum of Natural History, Chicago, IL 60605, USA
| | - Dongming Li
- Key Laboratory of Animal Physiology, Biochemistry and Molecular Biology of Hebei Province, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Per G P Ericson
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-104 05 Stockholm, Sweden
| | - Yan Hao
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongyuan Wang
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Hongfeng Zhao
- College of Life Sciences, Shaanxi Normal University, Xi'an 710119, China
| | - Gang Song
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Hailin Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Ting Yang
- China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Chi Zhang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Liping Liang
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Tianyu Wu
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Jinyang Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Qiang Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen 518084, China
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
- Human Genetics, Genome Institute of Singapore, Agency for Science, Technology, and Research, Singapore 138672, Singapore
| | - Fumin Lei
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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13
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Chen X, Yang Y, Chang T, Xu B, Wei H. Comparative Transcriptome Analysis of Unusual Localized Skin Laxity in Sika Deer ( Cervus nippon). DNA Cell Biol 2019; 38:670-677. [PMID: 31188027 DOI: 10.1089/dna.2019.4730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Cutis laxa represents a heterogeneous group of rare, inherited, or acquired connective tissue disorders with the common feature of loose and redundant skin with decreased elasticity. The skin of affected deer showed abnormal collagen fiber morphology. To identify the differentially expressed genes of the unusual localized skin laxity in sika deer, we performed transcriptome analysis in the affected and control sika deer. The transcriptome analysis showed 700 genes with significant differential expression in the affected skin as compared with normal skin. Pathway analysis revealed an enrichment of genes involved in tumor necrosis factor signaling, the extracellular matrix-receptor interaction, platelet activation, and Huntington's disease. A gene network was constructed, and the hub nodes such as PTGS2, THBS1, COL1A1, FOS, and NOS3 were found through PPI network analysis, which may contributed to the unusual localized skin laxity in sika deer. Abnormal expression patterns of genes during the development of the affected sika deer were successfully uncovered in the present study, which provides a reference for revealing the related mechanism underlying cutis laxa in sika deer and human beings.
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Affiliation(s)
- Xiumin Chen
- 1 Institute of Special Animals and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Yifeng Yang
- 1 Institute of Special Animals and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China.,2 Key Laboratory of Molecular Biology in Special Economic Animals, Changchun, China
| | - Tong Chang
- 1 Institute of Special Animals and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China
| | - Baozeng Xu
- 1 Institute of Special Animals and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China.,2 Key Laboratory of Molecular Biology in Special Economic Animals, Changchun, China
| | - Haijun Wei
- 1 Institute of Special Animals and Plant Sciences, Chinese Academy of Agricultural Sciences, Changchun, China.,2 Key Laboratory of Molecular Biology in Special Economic Animals, Changchun, China
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Schneider RA. Neural crest and the origin of species-specific pattern. Genesis 2018; 56:e23219. [PMID: 30134069 PMCID: PMC6108449 DOI: 10.1002/dvg.23219] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 05/15/2018] [Accepted: 05/16/2018] [Indexed: 12/20/2022]
Abstract
For well over half of the 150 years since the discovery of the neural crest, the special ability of these cells to function as a source of species-specific pattern has been clearly recognized. Initially, this observation arose in association with chimeric transplant experiments among differentially pigmented amphibians, where the neural crest origin for melanocytes had been duly noted. Shortly thereafter, the role of cranial neural crest cells in transmitting species-specific information on size and shape to the pharyngeal arch skeleton as well as in regulating the timing of its differentiation became readily apparent. Since then, what has emerged is a deeper understanding of how the neural crest accomplishes such a presumably difficult mission, and this includes a more complete picture of the molecular and cellular programs whereby neural crest shapes the face of each species. This review covers studies on a broad range of vertebrates and describes neural-crest-mediated mechanisms that endow the craniofacial complex with species-specific pattern. A major focus is on experiments in quail and duck embryos that reveal a hierarchy of cell-autonomous and non-autonomous signaling interactions through which neural crest generates species-specific pattern in the craniofacial integument, skeleton, and musculature. By controlling size and shape throughout the development of these systems, the neural crest underlies the structural and functional integration of the craniofacial complex during evolution.
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Affiliation(s)
- Richard A. Schneider
- Department of Orthopedic SurgeryUniversity of California at San Francisco, 513 Parnassus AvenueS‐1161San Francisco, California
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