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Zhou A, Ding Y, Zhang X, Zhou Y, Liu Y, Li T, Xiao L. Whole-genome resequencing reveals new mutations in candidate genes for Beichuan-white goat prolificacya. Anim Biotechnol 2024; 35:2258166. [PMID: 37729465 DOI: 10.1080/10495398.2023.2258166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]
Abstract
In this study, we evaluated the copy number variation in the genomes of two groups of Beichuan-white goat populations with large differences in litter size by FST method, and identified 1739 genes and 485 missense mutations in the genes subject to positive selection. Through functional enrichment, ITGAV, LRP4, CDH23, TPRN, RYR2 and CELSR1 genes, involved in embryonic morphogenesis, were essential for litter size trait, which received intensive attention. In addition, some mutation sites of these genes have been proposed (ITGAV: c.38C > T; TPRN: c.133A > T, c.1192A > G, c.1250A > C; CELSR1: c.7640T > C), whose allele frequencies were significantly changed in the high fecundity goat group. Besides, we found that new mutations at these sites altered the hydrophilicity and 3D structure of the protein. Candidate genes related to litter size in this study and their missense mutation sites were identified. These candidate genes are helpful to understand the genetic mechanism of fecundity in Beichuan white goat, and have important significance for future goat breeding.
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Affiliation(s)
- Aimin Zhou
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, P. R. China
| | - Yi Ding
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan, P. R. China
| | - Xiaohui Zhang
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| | - Yugang Zhou
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| | - Yadong Liu
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| | - Tingjian Li
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
| | - Long Xiao
- Animal Husbandry Research Institute, Mianyang Academy of Agricultural Sciences, Mianyang, P. R. China
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Wu SX, Zeng QF, Han WT, Wang MY, Ding H, Teng MX, Wang MY, Li PY, Gao X, Bao ZM, Wang B, Hu JJ. Deciphering the population structure and genetic basis of growth traits from whole-genome resequencing of the leopard coral grouper ( Plectropomus leopardus). Zool Res 2024; 45:329-340. [PMID: 38485503 PMCID: PMC11017084 DOI: 10.24272/j.issn.2095-8137.2023.270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/10/2023] [Indexed: 03/19/2024] Open
Abstract
The leopard coral grouper ( Plectropomus leopardus) is a species of significant economic importance. Although artificial cultivation of P. leopardus has thrived in recent decades, the advancement of selective breeding has been hindered by the lack of comprehensive population genomic data. In this study, we identified over 8.73 million single nucleotide polymorphisms (SNPs) through whole-genome resequencing of 326 individuals spanning six distinct groups. Furthermore, we categorized 226 individuals with high-coverage sequencing depth (≥14×) into eight clusters based on their genetic profiles and phylogenetic relationships. Notably, four of these clusters exhibited pronounced genetic differentiation compared with the other populations. To identify potentially advantageous loci for P. leopardus, we examined genomic regions exhibiting selective sweeps by analyzing the nucleotide diversity ( θπ) and fixation index ( F ST) in these four clusters. Using these high-coverage resequencing data, we successfully constructed the first haplotype reference panel specific to P. leopardus. This achievement holds promise for enabling high-quality, cost-effective imputation methods. Additionally, we combined low-coverage sequencing data with imputation techniques for a genome-wide association study, aiming to identify candidate SNP loci and genes associated with growth traits. A significant concentration of these genes was observed on chromosome 17, which is primarily involved in skeletal muscle and embryonic development and cell proliferation. Notably, our detailed investigation of growth-related SNPs across the eight clusters revealed that cluster 5 harbored the most promising candidate SNPs, showing potential for genetic selective breeding efforts. These findings provide a robust toolkit and valuable insights into the management of germplasm resources and genome-driven breeding initiatives targeting P. leopardus.
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Affiliation(s)
- Shao-Xuan Wu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
| | - Qi-Fan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
- Hainan Seed Industry Laboratory, Sanya, Hainan 572025, China
| | - Wen-Tao Han
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
| | - Meng-Ya Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
| | - Hui Ding
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
| | - Ming-Xuan Teng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
| | - Ming-Yi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
| | - Pei-Yu Li
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
| | - Xin Gao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
| | - Zhen-Min Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
- Hainan Seed Industry Laboratory, Sanya, Hainan 572025, China
- Southern Marine Science and Engineer Guangdong Laboratory, Guangzhou, Guangdong 511458, China
| | - Bo Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
- Hainan Seed Industry Laboratory, Sanya, Hainan 572025, China. E-mail:
| | - Jing-Jie Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences/Key Laboratory of Tropical Aquatic Germplasm of Hainan Province, Sanya Oceanographic Institution, Ocean University of China, Qingdao, Shandong/Sanya, Hainan 266100/572025, China
- Hainan Seed Industry Laboratory, Sanya, Hainan 572025, China
- Southern Marine Science and Engineer Guangdong Laboratory, Guangzhou, Guangdong 511458, China. E-mail:
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Zhou Z, Li Y, Shen Y, Zang X, Wang Q, Liu X, Wang Z. Integration of transcriptome and whole-genome re-sequencing analyses reveal growth-related candidate genes in Procambarus clarkii. Comp Biochem Physiol Part D Genomics Proteomics 2024; 49:101198. [PMID: 38306949 DOI: 10.1016/j.cbd.2024.101198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 01/15/2024] [Accepted: 01/27/2024] [Indexed: 02/04/2024]
Abstract
Growth is a crucial economic trait of all aquaculture species. It is important to explore the molecular regulation on growth, which could help improve the growth rate of species. Mining the growth-related genes is the foundation for revealing its molecular regulation on growth. Presently, the molecular regulation of growth in Procambarus clarkii is not clear, and the study on exploring growth-related genes is limited. In this study, RNA-Seq was used to compare gene expression profiles of the individuals with different growth rates involved in four groups including Big Male (BM), Big Female (BF), Small male (SM), and Small Female (SF) from one P. clarkii family, and the analyses were performed in combination with sex. Meanwhile, whole-genome resequencing data was used to get growth-specific SNP (Single Nucleotide Polymorphism)/InDel (Insertion/Deletion) sites information. Totally, we identified 16,127 genes, of which 9065 were successfully annotated in the GO database. Among these, 1328 DEGs were identified in BM vs. SM, with 357 up-regulated and 971 down-regulated. Additionally, 3507 DEGs were identified in BF vs. SF, with 241 up-regulated and 3266 down-regulated. 96 DEGs were up-regulated and 820 DEGs were down-regulated in Growth-related Group. The expression levels of nine DEGs were validated by RT-qPCR to verify the analysis results of sequencing. 684,040 growth-related SNPs and 182,050 growth-related InDels were obtained after screened. These findings provide candidate growth-related genes and growth-specific SNP/InDel sites for regulation of growth traits in P. clarkii, and new insight into the molecular regulation of P. clarkii growth.
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Affiliation(s)
- Zihao Zhou
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Yanhe Li
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yudong Shen
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaolei Zang
- Animal Husbandry and Fisheries Research Center, Guangdong Haid Group Co., Ltd., Guangzhou 511400, China.
| | - Qishuai Wang
- College of Fisheries, Key Lab of Freshwater Animal Breeding, Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China.
| | - Xiaolong Liu
- Animal Husbandry and Fisheries Research Center, Guangdong Haid Group Co., Ltd., Guangzhou 511400, China.
| | - Zhengkai Wang
- Animal Husbandry and Fisheries Research Center, Guangdong Haid Group Co., Ltd., Guangzhou 511400, China.
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Chen W, Xiang D, Gao S, Zhu S, Wu Z, Li Y, Li J. Whole-genome resequencing confirms the genetic effects of dams on an endangered fish Hemibagrus guttatus (Siluriformes: Bagridae): A case study in a tributary of the Pearl River. Gene 2024; 895:148000. [PMID: 37979951 DOI: 10.1016/j.gene.2023.148000] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/31/2023] [Accepted: 11/08/2023] [Indexed: 11/20/2023]
Abstract
Dam construction in riverine ecosystems has fragmented natural aquatic habitats and has altered environmental conditions. As a result, damming has been demonstrated to threaten aquatic biodiversity by reducing species distribution ranges and hindering gene exchange, leading to the inability to adapt to environmental changes. Knowledge of the contemporary genetic diversity and genetic structure of fish populations that are separated by dams is vital to developing effective conservation strategies, particularly for endangered fish species. We chose the Lianjiang River, a tributary of the Pearl River, as a case study to assess the effects of dams on the genetic diversity and genetic structure of an endangered fish species, Hemibagrus guttatus, using whole-genome resequencing data from 63 fish samples. The results indicated low levels of genetic diversity, high levels of inbreeding and decreasing trend of effective population size in fragmented H. guttatus populations. In addition, there were significant genetic structure and genetic differentiation among populations, suggesting that the dams might have affected H. guttatus populations. Our findings may benefit management and conservation practices for this endangered species that is currently suffering from the effects of dam construction.
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Affiliation(s)
- Weitao Chen
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China; Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
| | - Denggao Xiang
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Shang Gao
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Shuli Zhu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China; Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
| | - Zhi Wu
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China; Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
| | - Yuefei Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China; Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China
| | - Jie Li
- Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China; Key Laboratory of Aquatic Animal Immune Technology of Guangdong Province, Guangzhou 510380, China; Guangzhou Scientific Observing and Experimental Station of National Fisheries Resources and Environment, Guangzhou 510380, China.
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Li L, Quan J, Liu H, Yu H, Chen H, Xia C, Zhao S, Gao C. Identification of the genetic characteristics of copy number variations in experimental specific pathogen-free ducks using whole-genome resequencing. BMC Genomics 2024; 25:17. [PMID: 38166615 PMCID: PMC10759622 DOI: 10.1186/s12864-023-09928-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Specific pathogen-free ducks are a valuable laboratory resource for waterfowl disease research and poultry vaccine development. High throughput sequencing allows the systematic identification of structural variants in genomes. Copy number variation (CNV) can explain the variation of important duck genetic traits. Herein, the genome-wide CNVs of the three experimental duck species in China (Jinding ducks (JD), Shaoxing ducks (SX), and Fujian Shanma ducks (SM)) were characterized using resequencing to determine their genetic characteristics and selection signatures. RESULTS We obtained 4,810 CNV regions (CNVRs) by merging 73,012 CNVs, covering 4.2% of the duck genome. Functional analysis revealed that the shared CNVR-harbored genes were significantly enriched for 31 gene ontology terms and 16 Kyoto Encyclopedia of Genes and Genomes pathways (e.g., olfactory transduction and immune system). Based on the genome-wide fixation index for each CNVR, growth (SPAG17 and PTH1R), disease resistance (CATHL3 and DMBT1), and thermoregulation (TRPC4 and SLIT3) candidate genes were identified in strongly selected signatures specific to JD, SM, and SX, respectively. CONCLUSIONS In conclusion, we investigated the genome-wide distribution of experimental duck CNVs, providing a reference to establish the genetic basis of different phenotypic traits, thus contributing to the management of experimental animal genetic resources.
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Affiliation(s)
- Lanlan Li
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China
- College of Animal Science & Technology, Ningxia University, Yinchuan, 750021, P.R. China
| | - Jinqiang Quan
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China.
| | - Hongyi Liu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Haibo Yu
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Hongyan Chen
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Changyou Xia
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China
| | - Shengguo Zhao
- College of Animal Science & Technology, Gansu Agricultural University, Lanzhou, 730070, P.R. China
| | - Caixia Gao
- State Key Laboratory of Veterinary Biotechnology, Heilongjiang Provincial Key Laboratory of Laboratory Animal and Comparative Medicine, National Poultry Laboratory Animal Resource Center, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, 150069, P.R. China.
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Zhao K, Bai Y, Zhang Q, Zhao Z, Cao Y, Yang L, Wang N, Xu J, Wang B, Wu L, Gong X, Lin T, Wang Y, Wang W, Cai X, Yin Y, Xiong Z. Karyotyping of aneuploid and polyploid plants from low coverage whole-genome resequencing. BMC Plant Biol 2023; 23:630. [PMID: 38062348 PMCID: PMC10704825 DOI: 10.1186/s12870-023-04650-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/30/2023] [Indexed: 12/18/2023]
Abstract
BACKGROUND Karyotype, as a basic characteristic of species, provides valuable information for fundamental theoretical research and germplasm resource innovation. However, traditional karyotyping techniques, including fluorescence in situ hybridization (FISH), are challenging and low in efficiency, especially when karyotyping aneuploid and polyploid plants. The use of low coverage whole-genome resequencing (lcWGR) data for karyotyping was explored, but existing methods are complicated and require control samples. RESULTS In this study, a new protocol for molecular karyotype analysis was provided, which proved to be a simpler, faster, and more accurate method, requiring no control. Notably, our method not only provided the copy number of each chromosome of an individual but also an accurate evaluation of the genomic contribution from its parents. Moreover, we verified the method through FISH and published resequencing data. CONCLUSIONS This method is of great significance for species evolution analysis, chromosome engineering, crop improvement, and breeding.
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Affiliation(s)
- Kanglu Zhao
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yanbo Bai
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Qingyu Zhang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Zhen Zhao
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yao Cao
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Lu Yang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ni Wang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Junxiong Xu
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Bo Wang
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Lei Wu
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Xiufeng Gong
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Tuanrong Lin
- Institute of Ulanqab Agricultural and Forestry Sciences, Inner Mongolia, Ulanqab, 012000, China
| | - Yufeng Wang
- Institute of Ulanqab Agricultural and Forestry Sciences, Inner Mongolia, Ulanqab, 012000, China
| | - Wei Wang
- Institute of Ulanqab Agricultural and Forestry Sciences, Inner Mongolia, Ulanqab, 012000, China
| | - Xingkui Cai
- Key Laboratory of Horticultural Plant Biology, Key Laboratory of Potato Biology and Biotechnology, Ministry of Agriculture and Rural Affairs, College of Horticulture and Forestry Sciences, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yuhe Yin
- Institute of Ulanqab Agricultural and Forestry Sciences, Inner Mongolia, Ulanqab, 012000, China
| | - Zhiyong Xiong
- Key Laboratory of Herbage and Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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Li H, Chen Y. Whole-genome resequencing to explore genome‑wide single nucleotide polymorphisms and genes associated with avian leukosis virus subgroup J infection in chicken. 3 Biotech 2023; 13:417. [PMID: 38031589 PMCID: PMC10682322 DOI: 10.1007/s13205-023-03834-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Avian leukosis virus subgroup J (ALV-J) is an oncogenic virus that causes serious economic loss in the poultry industry. Currently, no effective vaccine or drug is available against this virus. Therefore, it is imperative to explore and understand the molecular regulatory mechanisms underlying ALV-J infection. In this study, blood samples from 21 ALV-J-infected and 22 ALV-J-uninfected (DZ) chickens (JZ) were analyzed by whole-genome resequencing (WGR). By combining the fixation index (FST) with the nucleotide diversity (π) ratio based on WGR data, 425 candidate genes were identified. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed the top 20 enriched pathways, among which 9 pathways were significantly associated with diseases, including endometrial cancer, Chagas disease, PD-L1 expression and PD-1 checkpoint pathway in cancer, colorectal cancer, endocrine resistance, fluid shear stress, atherosclerosis, basal cell carcinoma, non-small cell lung cancer, and melanoma. Fourteen single nucleotide polymorphisms related to twelve genes showed a notable difference between DZ and JZ group chickens. The genes included COMMD3, PPP1CB, VEGFA, GTF2H1, NOTCH2, ITPR1, FGFR4, GNAS, NECTIN1, WNT2B, PPP1CC, and MRC2. These findings may provide a valuable foundation for further exploration of the pathogenesis of ALV-J in chickens.
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Affiliation(s)
- Hongwei Li
- School of Life Science, Huizhou University, No. 46 Yanda Road, Huizhou, 516007 China
| | - Yuan Chen
- School of Life Science, Huizhou University, No. 46 Yanda Road, Huizhou, 516007 China
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Li D, Lin HY, Wang X, Bi B, Gao Y, Shao L, Zhang R, Liang Y, Xia Y, Zhao YP, Zhou X, Zhang L. Genome and whole-genome resequencing of Cinnamomum camphora elucidate its dominance in subtropical urban landscapes. BMC Biol 2023; 21:192. [PMID: 37697363 PMCID: PMC10496300 DOI: 10.1186/s12915-023-01692-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Accepted: 08/25/2023] [Indexed: 09/13/2023] Open
Abstract
BACKGROUND Lauraceae is well known for its significant phylogenetic position as well as important economic and ornamental value; however, most evergreen species in Lauraceae are restricted to tropical regions. In contrast, camphor tree (Cinnamomum camphora) is the most dominant evergreen broadleaved tree in subtropical urban landscapes. RESULTS Here, we present a high-quality reference genome of C. camphora and conduct comparative genomics between C. camphora and C. kanehirae. Our findings demonstrated the significance of key genes in circadian rhythms and phenylpropanoid metabolism in enhancing cold response, and terpene synthases (TPSs) improved defence response with tandem duplication and gene cluster formation in C. camphora. Additionally, the first comprehensive catalogue of C. camphora based on whole-genome resequencing of 75 accessions was constructed, which confirmed the crucial roles of the above pathways and revealed candidate genes under selection in more popular C. camphora, and indicated that enhancing environmental adaptation is the primary force driving C. camphora breeding and dominance. CONCLUSIONS These results decipher the dominance of C. camphora in subtropical urban landscapes and provide abundant genomic resources for enlarging the application scopes of evergreen broadleaved trees.
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Affiliation(s)
- Danqing Li
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Han-Yang Lin
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
- School of Advanced Study, Taizhou University, Taizhou, China
| | - Xiuyun Wang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Bo Bi
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- ZJU-Hangzhou Global Scientific and Technological Innovation Center, Hangzhou, China
| | - Yuan Gao
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Lingmei Shao
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Runlong Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuwei Liang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yiping Xia
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yun-Peng Zhao
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Xiaofan Zhou
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou, China
| | - Liangsheng Zhang
- Genomics and Genetic Engineering Laboratory of Ornamental Plants, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Hainan Institute of Zhejiang University, Sanya, China.
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Liu J, Xiao Y, Ren P, Zhang S, Liu Y, Zhu M. Integrating genomics and transcriptomics to identify candidate genes for high egg production in Wulong geese (Anser cygnoides orientalis). BMC Genomics 2023; 24:481. [PMID: 37620752 PMCID: PMC10464066 DOI: 10.1186/s12864-023-09603-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023] Open
Abstract
BACKGROUND Wulong geese (Anser cygnoides orientalis) are known for their excellent egg-laying performance. However, they show considerable population differences in egg-laying behavior. This study combined genome-wide selection signal analysis with transcriptome analysis (RNA-seq) to identify the genes related to high egg production in Wulong geese. RESULTS A total of 132 selected genomic regions were screened using genome-wide selection signal analysis, and 130 genes related to high egg production were annotated in these regions. These selected genes were enriched in pathways related to egg production, including oocyte meiosis, the estrogen signaling pathway, the oxytocin signaling pathway, and progesterone-mediated oocyte maturation. Furthermore, a total of 890 differentially expressed genes (DEGs), including 340 up-regulated and 550 down-regulated genes, were identified by RNA-seq. Two genes - GCG and FAP - were common to the list of selected genes and DEGs. A non-synonymous single nucleotide polymorphism was identified in an exon of FAP. CONCLUSIONS Based on genome-wide selection signal analysis and transcriptome data, GCG and FAP were identified as candidate genes associated with high egg production in Wulong geese. These findings could promote the breeding of Wulong geese with high egg production abilities and provide a theoretical basis for exploring the mechanisms of reproductive regulation in poultry.
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Affiliation(s)
- Jingjing Liu
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Yu Xiao
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Pengwei Ren
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Shuer Zhang
- Shandong Animal Husbandry General Station, Jinan, 250010, China
| | - Yang Liu
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng, 252000, China
| | - Mingxia Zhu
- College of Agronomy and Agricultural Engineering, Liaocheng University, Liaocheng, 252000, China.
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Zhu M, Yang Y, Yang H, Zhao Z, Zhang H, Blair HT, Zheng W, Wang M, Fang C, Yu Q, Zhou H, Qi H. Whole-genome resequencing of the native sheep provides insights into the microevolution and identifies genes associated with reproduction traits. BMC Genomics 2023; 24:392. [PMID: 37434152 DOI: 10.1186/s12864-023-09479-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/22/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND Sheep genomes undergo numerous genes losses, gains and mutation that generates genome variability among breeds of the same species after long time natural and artificial selection. However, the microevolution of native sheep in northwest China remains elusive. Our aim was to compare the genomes and relevant reproductive traits of four sheep breeds from different climatic environments, to unveil the selection challenges that this species cope with, and the microevolutionary differences in sheep genomes. Here, we resequenced the genomes of 4 representative sheep breeds in northwest China, including Kazakh sheep and Duolang sheep of native breeds, and Hu sheep and Suffolk sheep of exotic breeds with different reproductive characteristics. RESULTS We found that these four breeds had a similar expansion experience from ~ 10,000 to 1,000,000 years ago. In the past 10,000 years, the selection intensity of the four breeds was inconsistent, resulting in differences in reproductive traits. We explored the sheep variome and selection signatures by FST and θπ. The genomic regions containing genes associated with different reproductive traits that may be potential targets for breeding and selection were detected. Furthermore, non-synonymous mutations in a set of plausible candidate genes and significant differences in their allele frequency distributions across breeds with different reproductive characteristics were found. We identified PAK1, CYP19A1 and PER1 as a likely causal gene for seasonal reproduction in native sheep through qPCR, Western blot and ELISA analyses. Also, the haplotype frequencies of 3 tested gene regions related to reproduction were significantly different among four sheep breeds. CONCLUSIONS Our results provide insights into the microevolution of native sheep and valuable genomic information for identifying genes associated with important reproductive traits in sheep.
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Affiliation(s)
- Mengting Zhu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Yonglin Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Hua Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China.
| | - Zongsheng Zhao
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China.
| | - Hongmei Zhang
- First Affiliated Hospital, School of Medical College, Shihezi University, Shihezi, Xinjiang, China
| | - Hugh T Blair
- Institute Veterinary, Animal & Biomedical Sciences, Massey University, Auckland, Palmerston North, New Zealand
| | - Wei Zheng
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Mingyuan Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Chenhui Fang
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Qian Yu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, China
| | - Huaqian Zhou
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Hangdong Qi
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
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Sun CF, Zhang XH, Dong JJ, You XX, Tian YY, Gao FY, Zhang HT, Shi Q, Ye X, Shi Q, Ye X. Whole-genome resequencing reveals recent signatures of selection in five populations of largemouth bass ( Micropterus salmoides). Zool Res 2023; 44:78-89. [PMID: 36349358 PMCID: PMC9841193 DOI: 10.24272/j.issn.2095-8137.2022.274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Largemouth bass ( Micropterus salmoides) is an economically important fish species in North America, Europe, and China. Various genetic improvement programs and domestication processes have modified its genome sequence through selective pressure, leaving nucleotide signals that can be detected at the genomic level. In this study, we sequenced 149 largemouth bass fish, including protospecies (imported from the US) and improved breeds (four domestic breeding populations from China). We detected genomic regions harboring certain genes associated with improved traits, which may be useful molecular markers for practical domestication, breeding, and selection. Subsequent analyses of genetic diversity and population structure revealed that the improved breeds have undergone more rigorous genetic changes. Through selective signal analysis, we identified hundreds of putative selective sweep regions in each largemouth bass line. Interestingly, we predicted 103 putative candidate genes potentially subjected to selection, including several associated with growth (p sst1 and grb10), early development ( klf9, sp4, and sp8), and immune traits ( pkn2, sept2, bcl6, and ripk2). These candidate genes represent potential genomic landmarks that could be used to improve important traits of biological and commercial interest. In summary, this study provides a genome-wide map of genetic variations and selection footprints in largemouth bass, which may benefit genetic studies and accelerate genetic improvement of this economically important fish.
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Affiliation(s)
- Cheng-Fei Sun
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Xin-Hui Zhang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun-Jian Dong
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Xin-Xin You
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yuan-Yuan Tian
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Feng-Ying Gao
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - He-Tong Zhang
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China,College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China,E-mail:
| | - Xing Ye
- Key Laboratory of Tropical and Subtropical Fishery Resources Application and Cultivation, Ministry of Agriculture and Rural Affairs, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, Guangdong 510380, China,
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Yang Y, Qin B, Chen Q, Nie Q, Zhang J, Zhang L, Liu S. Construction of the first high-density SNP genetic map and identification of QTLs for the natural rubber content in Taraxacum kok-saghyz Rodin. BMC Genomics 2023; 24:13. [PMID: 36627555 PMCID: PMC9830913 DOI: 10.1186/s12864-022-09105-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/30/2022] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND Taraxacum kok-saghyz Rodin (TKS) is a promising commercial alternative natural rubber (NR) yielding plant. Cultivating TKS with a high NR content is an important breeding target, and developing molecular markers related to NR content can effectively accelerate the breeding process of TKS. RESULTS To construct a high-density SNP genetic map and uncover genomic regions related to the NR content in TKS, an F1 mapping population of TKS was constructed by crossing two parents (l66 and X51) with significant differences in NR contents. The NR content of the F1 plants ranged from 0.30 to 15.14% and was distributed normally with a coefficient of variation of 47.61%, indicating quantitative trait inheritance. Then, employing whole-genome resequencing (WGR), a TKS genetic linkage map of 12,680 bin markers comprising 322,439 SNPs was generated. Based on the genetic map and NR content of the F1 population, six quantitative trait loci (QTLs) for NR content with LOD > 4.0 were identified on LG01/Chr01 and LG06/Chr06. Of them, the 2.17 Mb genomic region between qHRC-C6-1 and qHRC-C6-2 on ChrA06, with 65.62% PVE in total, was the major QTL region. In addition, the six QTLs have significant additive genetic effects on NR content and could be used to develop markers for marker-assisted selection (MAS) in TKS with a high NR content. CONCLUSION This work constructed the first high-density TKS genetic map and identified the QTLs and genomic regions controlling the NR content, which provides useful information for fine mapping, map-based cloning, and MAS in TKS.
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Affiliation(s)
- Yushuang Yang
- grid.453499.60000 0000 9835 1415Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, 571101 Haikou, China
| | - Bi Qin
- grid.453499.60000 0000 9835 1415Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, 571101 Haikou, China
| | - Qiuhui Chen
- grid.453499.60000 0000 9835 1415Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, 571101 Haikou, China
| | - Qiuhai Nie
- Beijing Linglong Dandelion Technology and Development Ltd, 101102 Beijing, China
| | - Jichuan Zhang
- grid.48166.3d0000 0000 9931 8406College of Materials and Engineering, Beijing University of Chemical Technology, 100029 Beijing, China
| | - Liqun Zhang
- grid.48166.3d0000 0000 9931 8406College of Materials and Engineering, Beijing University of Chemical Technology, 100029 Beijing, China
| | - Shizhong Liu
- grid.453499.60000 0000 9835 1415Rubber Research Institute, Chinese Academy of Tropical Agricultural Science, 571101 Haikou, China
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Luo X, Li S, Liu Y, Ahmed Z, Wang F, Liu J, Zhang J, Chen N, Lei C, Huang B. Assessing the Role of Ancestral Fragments and Selection Signatures by Whole-Genome Scanning in Dehong Humped Cattle at the China-Myanmar Border. Biology (Basel) 2022; 11. [PMID: 36138810 DOI: 10.3390/biology11091331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Revised: 08/31/2022] [Accepted: 09/04/2022] [Indexed: 12/05/2022]
Abstract
Dehong humped cattle are precious livestock resources of Yunnan Province, China; they have typical zebu traits. Here, we investigated their genetic characteristics using whole-genome resequencing data of Dehong humped animals (n = 18). When comparing our data with the publicly-available data, we found that Dehong humped cattle have high nucleotide diversity. Based on clustering models in a population structure analysis, Dehong humped cattle had a mutual genome ancestor with Chinese and Indian indicine cattle. While using the RFMix method, it is speculated that the body sizes of Dehong humped cattle were influenced by the Chinese indicine segments and that the immune systems of Dehong humped cattle were affected by additional ancestral segments (Indian indicine). Furthermore, we explored the position selection regions harboring genes in the Dehong humped cattle, which were related to heat tolerance (FILIP1L, ABHD6) and immune responses (GZMM, PRKCZ, STOML2, LRBA, PIK3CD). Notably, missense mutations were detected in the candidate gene ABHD6 (c.870C>A p.Asp290Glu; c.987C>A p.Ser329Arg). The missense mutations may have implications for Dehong humped cattle adaptation to hot environments. This study provides valuable genomic resource data at the genome-wide level and paves the way for future genetic breeding work in the Dehong humped cattle.
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Zheng J, Zhao L, Zhao X, Gao T, Song N. High Genetic Connectivity Inferred from Whole-Genome Resequencing Provides Insight into the Phylogeographic Pattern of Larimichthys polyactis. Mar Biotechnol (NY) 2022; 24:671-680. [PMID: 35701688 DOI: 10.1007/s10126-022-10134-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 05/20/2022] [Indexed: 06/15/2023]
Abstract
Compared with terrestrial biota, marine fishes usually present lower genetic differentiation among different geographical populations because of high-level gene flow and lack of physical barriers. Understanding the genetic structure of marine fishes is essential for dividing management unit and making reasonable protection measures. The small yellow croaker (Larimichthys polyactis) belongs to the family Sciaenidae, which is an economic fish and widely distributed in the Western Pacific. To delineate genetic diversity and phylogeographic pattern, whole-genome resequencing was used to evaluate genetic connectivity, genetic diversity, and spatial pattern of L. polyactis for the first time. We obtained 6,645,711 high-quality single nucleotide polymorphisms (SNPs) markers from 40 L. polyactis individuals. The phylogenetic analysis, STRUCTURE, principal component analysis, and Fst results all indicated that no genetic structure consistent with the distribution pattern was found. This result revealed high genetic connectivity of L. polyactis in different sampling sites. High genetic diversity was also detected, indicating that there was sufficient evolutionary potential to maintain its effective population size. Besides, a similar result of high genetic connectivity and genetic diversity was also detected by mitochondria DNA marker. Our study demonstrated the persistence of high levels of genetic connectivity and a lack of population structure across L. polyactis in different sea areas. This study aimed to analyze the division of population structure and the reason for the decline and not exhaustion of L. polyactis resource on a genetic level.
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Affiliation(s)
- Jian Zheng
- Key Laboratory of Mariculture, Ministry of Education, (Ocean University of China), 266003, Qingdao, China
| | - Linlin Zhao
- First Institute of Oceanography, Ministry of Natural Resources, Qingdao, 266100, Shandong, China
| | - Xiang Zhao
- Key Laboratory of Mariculture, Ministry of Education, (Ocean University of China), 266003, Qingdao, China
| | - Tianxiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, 316022, China.
| | - Na Song
- Key Laboratory of Mariculture, Ministry of Education, (Ocean University of China), 266003, Qingdao, China.
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Chen X, Guo HY, Zhang QY, Wang L, Guo R, Zhan YX, Lv P, Xu YP, Guo MB, Zhang Y, Zhang K, Liu YH, Yang M. Whole-genome resequencing of wild and cultivated cannabis reveals the genetic structure and adaptive selection of important traits. BMC Plant Biol 2022; 22:371. [PMID: 35883045 PMCID: PMC9327241 DOI: 10.1186/s12870-022-03744-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 06/27/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Cannabis is an important industrial crop species whose fibre, seeds, flowers and leaves are widely used by humans. The study of cannabinoids extracted from plants has been popular research topic in recent years. China is one of the origins of cannabis and one of the few countries with wild cannabis plants. However, the genetic structure of Chinese cannabis and the degree of adaptive selection remain unclear. RESULTS The main morphological characteristics of wild cannabis in China were assessed. Based on whole-genome resequencing SNPs, Chinese cannabis could be divided into five groups in terms of geographical source and ecotype: wild accessions growing in the northwestern region; wild accessions growing in the northeastern region; cultivated accessions grown for fibre in the northeastern region; cultivated accessions grown for seed in northwestern region, and cultivated accessions in southwestern region. We further identified genes related to flowering time, seed germination, seed size, embryogenesis, growth, and stress responses selected during the process of cannabis domestication. The expression of flowering-related genes under long-day (LD) and short-day (SD) conditions showed that Chinese cultivated cannabis is adapted to different photoperiods through the regulation of Flowering locus T-like (FT-like) expression. CONCLUSION This study clarifies the genetic structure of Chinese cannabis and offers valuable genomic resources for cannabis breeding.
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Affiliation(s)
- Xuan Chen
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Hong-Yan Guo
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Qing-Ying Zhang
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Lu Wang
- State Key Laboratory for Conservation, School of Life Sciences, Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650500 China
| | - Rong Guo
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Yi-Xun Zhan
- State Key Laboratory for Conservation, School of Life Sciences, Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650500 China
| | - Pin Lv
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Yan-Ping Xu
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Meng-Bi Guo
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Yuan Zhang
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Kun Zhang
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
| | - Yan-Hu Liu
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223 China
| | - Ming Yang
- Industrial Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, 650205 China
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Zhu Y, Lu N, Chen JY, He C, Huang Z, Lu Z. Deep whole-genome resequencing sheds light on the distribution and effect of amphioxus SNPs. BMC Genom Data 2022; 23:26. [PMID: 35395709 PMCID: PMC8994340 DOI: 10.1186/s12863-022-01038-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/13/2022] [Indexed: 02/11/2023] Open
Abstract
Background Amphioxus is a model organism for vertebrate evolutionary research. The significant contrast between morphological phenotypic similarity and high-level genetic polymorphism among amphioxus populations has aroused scientists' attention. Here we resequenced 21 amphioxus genomes to over 100X depth and mapped them to a haploid reference. Results More than 11.5 million common SNPs were detected in the amphioxus population, which mainly affect genes enriched in ion transport, signal transduction and cell adhesion, while protein structure analysis via AlphaFold2 revealed that these SNPs fail to bring effective structural variants. Conclusions Our work provides explanation for “amphioxus polymorphism paradox” in a micro view, and generates an enhanced genomic dataset for amphioxus research. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-022-01038-w.
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Affiliation(s)
- Yunchi Zhu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu, China
| | - Na Lu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu, China
| | - J-Y Chen
- Nanjing Institute of Paleontology and Geology, Nanjing, China
| | - Chunpeng He
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu, China.
| | - Zhen Huang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, College of Life Sciences, Fujian Normal University, Fuzhou, Fujian, China. .,Key Laboratory of Special Marine Bio-Resources Sustainable Utilization of Fujian Province, Fuzhou, Fujian, China.
| | - Zuhong Lu
- State Key Laboratory of Bioelectronics, Southeast University, Nanjing, Jiangsu, China.
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Zhang H, Jiang H, Hu Z, Song Q, An YQC. Development of a versatile resource for post-genomic research through consolidating and characterizing 1500 diverse wild and cultivated soybean genomes. BMC Genomics 2022; 23:250. [PMID: 35361112 PMCID: PMC8973893 DOI: 10.1186/s12864-022-08326-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2021] [Accepted: 01/20/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND With advances in next-generation sequencing technologies, an unprecedented amount of soybean accessions has been sequenced by many individual studies and made available as raw sequencing reads for post-genomic research. RESULTS To develop a consolidated and user-friendly genomic resource for post-genomic research, we consolidated the raw resequencing data of 1465 soybean genomes available in the public and 91 highly diverse wild soybean genomes newly sequenced. These altogether provided a collection of 1556 sequenced genomes of 1501 diverse accessions (1.5 K). The collection comprises of wild, landraces and elite cultivars of soybean that were grown in East Asia or major soybean cultivating areas around the world. Our extensive sequence analysis discovered 32 million single nucleotide polymorphisms (32mSNPs) and revealed a SNP density of 30 SNPs/kb and 12 non-synonymous SNPs/gene reflecting a high structural and functional genomic diversity of the new collection. Each SNP was annotated with 30 categories of structural and/or functional information. We further identified paired accessions between the 1.5 K and 20,087 (20 K) accessions in US collection as genomic "equivalent" accessions sharing the highest genomic identity for minimizing the barriers in soybean germplasm exchange between countries. We also exemplified the utility of 32mSNPs in enhancing post-genomics research through in-silico genotyping, high-resolution GWAS, discovering and/or characterizing genes and alleles/mutations, identifying germplasms containing beneficial alleles that are potentially experiencing artificial selection. CONCLUSION The comprehensive analysis of publicly available large-scale genome sequencing data of diverse cultivated accessions and the newly in-house sequenced wild accessions greatly increased the soybean genome-wide variation resolution. This could facilitate a variety of genetic and molecular-level analyses in soybean. The 32mSNPs and 1.5 K accessions with their comprehensive annotation have been made available at the SoyBase and Ag Data Commons. The dataset could further serve as a versatile and expandable core resource for exploring the exponentially increasing genome sequencing data for a variety of post-genomic research.
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Affiliation(s)
- Hengyou Zhang
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - He Jiang
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Zhenbin Hu
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA
| | - Qijian Song
- US Department of Agriculture, Agricultural Research Service, Soybean Genomics and Improvement Laboratory, Beltsville, MD 20705, USA
| | - Yong-Qiang Charles An
- Donald Danforth Plant Science Center, St Louis, MO 63132, USA.
- US Department of Agriculture, Agricultural Research Service, Midwest Area, Plant Genetics Research Unit, 975 N Warson Rd, St. Louis, MO 63132, USA.
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Cumer T, Machado AP, Dumont G, Bontzorlos V, Ceccherelli R, Charter M, Dichmann K, Kassinis N, Lourenço R, Manzia F, Martens HD, Prévost L, Rakovic M, Roque I, Siverio F, Roulin A, Goudet J. Landscape and climatic variations shaped secondary contacts amid barn owls of the Western Palearctic. Mol Biol Evol 2021; 39:6454100. [PMID: 34893883 PMCID: PMC8789042 DOI: 10.1093/molbev/msab343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
The combined actions of climatic variations and landscape barriers shape the history of natural populations. When organisms follow their shifting niches, obstacles in the landscape can lead to the splitting of populations, on which evolution will then act independently. When two such populations are reunited, secondary contact occurs in a broad range of admixture patterns, from narrow hybrid zones to the complete dissolution of lineages. A previous study suggested that barn owls colonized the Western Palearctic after the last glaciation in a ring-like fashion around the Mediterranean Sea, and conjectured an admixture zone in the Balkans. Here, we take advantage of whole-genome sequences of 94 individuals across the Western Palearctic to reveal the complex history of the species in the region using observational and modeling approaches. Even though our results confirm that two distinct lineages colonized the region, one in Europe and one in the Levant, they suggest that it predates the last glaciation and identify a secondary contact zone between the two in Anatolia. We also show that barn owls recolonized Europe after the glaciation from two distinct glacial refugia: a previously identified western one in Iberia and a new eastern one in Italy. Both glacial lineages now communicate via eastern Europe, in a wide and permeable contact zone. This complex history of populations enlightens the taxonomy of Tyto alba in the region, highlights the key role played by mountain ranges and large water bodies as barriers and illustrates the power of population genomics in uncovering intricate demographic patterns.
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Affiliation(s)
- Tristan Cumer
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ana Paula Machado
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Guillaume Dumont
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Vasileios Bontzorlos
- Green Fund, Kifisia, Athens, Greece.,"TYTO" - Organization for the Management and Conservation of Biodiversity in Agricultural Ecosystems, Larisa, Greece
| | | | - Motti Charter
- Shamir Research Institute, University of Haifa, Katzrin, Israel.,Department of Geography and Environmental Sciences, University of Haifa, Haifa, Israel
| | | | | | - Rui Lourenço
- MED Mediterranean Institute for Agriculture, Environment and Development, Laboratory of Ornithology, IIFA, University of Évora, Évora, Portugal
| | | | | | - Laure Prévost
- Association C.H.E.N.E, Centre d'Hébergement et d'Etude sur la Nature et l'Environnement, Allouville-Bellefosse, 76190, France
| | - Marko Rakovic
- Natural History Museum of Belgrade, Belgrade, Serbia
| | - Inês Roque
- MED Mediterranean Institute for Agriculture, Environment and Development, Laboratory of Ornithology, IIFA, University of Évora, Évora, Portugal
| | - Felipe Siverio
- Canary Islands' Ornithology and Natural History Group (GOHNIC), 38480 Buenavista del Norte, Tenerife, Canary Islands, Spain
| | - Alexandre Roulin
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
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Xu NY, Si W, Li M, Gong M, Larivière JM, Nanaei HA, Bian PP, Jiang Y, Zhao X. Genome-wide scan for selective footprints and genes related to cold tolerance in Chantecler chickens. Zool Res 2021; 42:710-720. [PMID: 34581031 PMCID: PMC8645888 DOI: 10.24272/j.issn.2095-8137.2021.189] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
The Chantecler chicken, a unique Canadian indigenous breed, is well adapted to extremely cold environments. However, its genetic characteristics have not been well studied. Here, we analyzed the whole genomes of 10 Chantecler chickens and 121 worldwide chickens, which indicated that Chantecler chickens were derived from commercial chickens and exhibit a high level of inbreeding. Based on a genome-wide scan, we identified two vital candidate regions containing ME3 and ZNF536, which are related to fat metabolism and nervous system in cold adaptation, respectively. We also found that the genetic mechanism of cold adaptation in Chantecler chickens differed from that of chickens from other cold regions, such as northern China. Our study indicated that specialized commercial chickens in the early 20th century contained sufficient genetic diversity to adapt to extreme cold environments over a very short time. These findings enrich our understanding of the adaptive potential of commercial species.
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Affiliation(s)
- Nai-Yi Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Wei Si
- Department of Animal Science, McGill University, Montreal, Quebec H9X3V9, Canada
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Mian Gong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Jean-Marc Larivière
- Institut de technologie agroalimentaire du Québec, La Pocatière, Québec G0R1Z0, Canada
| | - Hojjat Asadollahpour Nanaei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Pei-Pei Bian
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China. E-mail:
| | - Xin Zhao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A & F University, Yangling, Shaanxi 712100, China. E-mail:.,Department of Animal Science, McGill University, Montreal, Quebec H9X3V9, Canada
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20
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Han ZQ, Guo XY, Liu Q, Liu SS, Zhang ZX, Xiao SJ, Gao TX. Whole-genome resequencing of Japanese whiting ( Sillago japonica) provide insights into local adaptations. Zool Res 2021; 42:548-561. [PMID: 34327887 PMCID: PMC8455465 DOI: 10.24272/j.issn.2095-8137.2021.116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
The genetic adaptations of various organisms to heterogeneous environments in the northwestern Pacific remain poorly understood. Heterogeneous genomic divergence among populations may reflect environmental selection. Advancing our understanding of the mechanisms by which organisms adapt to different temperatures in response to climate change and predicting the adaptive potential and ecological consequences of anthropogenic global warming are critical. We sequenced the whole genomes of Japanese whiting ( Sillago japonica) specimens collected from different latitudinal locations along the coastal waters of China and Japan to detect possible thermal adaptations. Using population genomics, a total of 5.48 million single nucleotide polymorphisms (SNPs) from five populations revealed a complete genetic break between the Chinese and Japanese groups, which was attributed to both geographic distance and local adaptation. The shared natural selection genes between two isolated populations (i.e., Zhoushan and Ise Bay/Tokyo Bay) indicated possible parallel evolution at the genetic level induced by temperature. These genes also indicated that the process of temperature selection on isolated populations is repeatable. Moreover, we observed natural candidate genes related to membrane fluidity, possibly underlying adaptation to cold environmental stress. These findings advance our understanding of the genetic mechanisms underlying the rapid adaptations of fish species. Species distribution projection models suggested that the Chinese and Japanese groups may have different responses to future climate change, with the former expanding and the latter contracting. The findings of this study enhance our understanding of genetic differentiation and adaptation to changing environments.
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Affiliation(s)
- Zhi-Qiang Han
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316002, China
| | - Xin-Yu Guo
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Qun Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Shan-Shan Liu
- BGI-Qingdao, BGI-Shenzhen, Qingdao, Shandong 266555, China
| | - Zhi-Xin Zhang
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, Konan, Minato, Tokyo 108-8477, Japan
| | - Shi-Jun Xiao
- Institute of Fisheries Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850000, China. E-mail:
| | - Tian-Xiang Gao
- Fishery College, Zhejiang Ocean University, Zhoushan, Zhejiang 316002, China. E-mail:
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Abstract
OBJECTIVES Pistacia genus belongs to the flowering plants in the cashew family and contains at least 11 species. The whole-genome resequencing data of different species from Pistacia genus are described herein. The data reported here will be useful for better understand the adaptive evolution, demographic history, genetic diversity, population structure, and domestication of pistachio. DATA DESCRIPTION Genomic DNA was isolated from fresh leaves and used to construct libraries with insert size of 350 bp. Sequence libraries were made and sequenced on the Illumina Hiseq 4000 platform to produce 150 bp paired-end reads. A total number of 4,851,118,730 billion reads (ranging from 33,305,900 to 34,990,618 reads per sample) were created across all samples. We produced a total of 727.67 Gbp data which have been deposited in the Genome Sequence Archive (GSA) database with the Accession of CRA000978. All of the data are also available as the sequence read archive (SRA) format in the National Center for Biotechnology Information (NCBI) with identifier of SRP189222, mirroring our deposited data in GSA.
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Affiliation(s)
- Ali Tajabadi
- Pistachio Research Center, Horticultural Sciences Research Institute, Agricultural Research, Education and Extension Organization (AREEO), Rafsanjan, Iran
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran. .,State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.
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22
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Shen J, Yu J, Dai X, Li M, Wang G, Chen N, Chen H, Lei C, Dang R. Genomic analyses reveal distinct genetic architectures and selective pressures in Chinese donkeys. J Genet Genomics 2021; 48:737-745. [PMID: 34373218 DOI: 10.1016/j.jgg.2021.05.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 05/09/2021] [Accepted: 05/10/2021] [Indexed: 12/28/2022]
Abstract
Donkey (Equus asinus) is an important livestock animal in China because of its draft and medicinal value. After a long period of natural and artificial selection, the variety and phenotype of donkeys have become abundant. We clarified the genetic and demographic characteristics of Chinese domestic donkeys and the selection pressures by analyzing 78 whole genomes from 12 breeds. According to population structure, most Chinese domestic donkeys showed a dominant ancestral type. However, the Chinese donkeys still represented a significant geographical distribution trend. In the selective sweep, gene annotation, functional enrichment, and differential expression analyses between large and small donkey groups, we identified selective signals, including NCAPG and LCORL, which are related to rapid growth and large body size. Our findings elucidate the evolutionary history and formation of different donkey breeds and provide theoretical insights into the genetic mechanism underlying breed characteristics and molecular breeding programs of donkey clades.
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Affiliation(s)
- Jiafei Shen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mei Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gang Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China.
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Wang W, Zou J, White PJ, Ding G, Li Y, Xu F, Shi L. Identification of QTLs associated with potassium use efficiency and underlying candidate genes by whole-genome resequencing of two parental lines in Brassica napus. Genomics 2021; 113:755-768. [PMID: 33516850 DOI: 10.1016/j.ygeno.2021.01.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 10/20/2020] [Accepted: 01/26/2021] [Indexed: 10/22/2022]
Abstract
Breeding crops that acquire and/or utilize potassium (K) more effectively could reduce the use of K fertilizers. Sixteen traits affecting K use efficiency (KUE) at the seedling stage were investigated in a B. napus double haploid population grown at an optimal K supply (OK) and a low K supply (LK) in a hydroponic culture system. In total, 50 and 62 QTLs associated with these traits were identified at OK and LK, respectively. A total of 25 orthologues of 23 Arabidopsis genes regulating K transport were identified in the confidence intervals of nine QTLs impacting shoot dry weight at LK, and 22 of these showed variations in coding sequences and/or exhibited significant differences in mRNA abundances in roots at LK between the two parental lines. This study provided insights to the genetic basis of KUE in B. napus, which will accelerate the breeding of K-efficient rapeseed cultivars by marker-assisted selection.
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Affiliation(s)
- Wei Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinsong Zou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Philip J White
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; The James Hutton Institute, Invergowrie, Dundee DD2 5DA, UK; Distinguished Scientist Fellowship Program, King Saud University, Riyadh 11451, Saudi Arabia
| | - Guangda Ding
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Yalin Li
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangsen Xu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China
| | - Lei Shi
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Microelement Research Centre, Key Laboratory of Arable Land Conservation (Middle and Lower Reaches of Yangtze River), Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan 430070, China.
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24
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Yuan C, Lu Z, Guo T, Yue Y, Wang X, Wang T, Zhang Y, Hou F, Niu C, Sun X, Zhao H, Zhu S, Liu J, Yang B. A global analysis of CNVs in Chinese indigenous fine-wool sheep populations using whole-genome resequencing. BMC Genomics 2021; 22:78. [PMID: 33485316 PMCID: PMC7825165 DOI: 10.1186/s12864-021-07387-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 01/13/2021] [Indexed: 12/13/2022] Open
Abstract
Background Copy number variation (CNV) is an important source of genetic variation that has a significant influence on phenotypic diversity, economically important traits and the evolution of livestock species. In this study, the genome-wide CNV distribution characteristics of 32 fine-wool sheep from three breeds were analyzed using resequencing. Results A total of 1,747,604 CNVs were detected in this study, and 7228 CNV regions (CNVR) were obtained after merging overlapping CNVs; these regions accounted for 2.17% of the sheep reference genome. The average length of the CNVRs was 4307.17 bp. “Deletion” events took place more frequently than “duplication” or “both” events. The CNVRs obtained overlapped with previously reported sheep CNVRs to variable extents (4.39–55.46%). Functional enrichment analysis showed that the CNVR-harboring genes were mainly involved in sensory perception systems, nutrient metabolism processes, and growth and development processes. Furthermore, 1855 of the CNVRs were associated with 166 quantitative trait loci (QTL), including milk QTLs, carcass QTLs, and health-related QTLs, among others. In addition, the 32 fine-wool sheep were divided into horned and polled groups to analyze for the selective sweep of CNVRs, and it was found that the relaxin family peptide receptor 2 (RXFP2) gene was strongly influenced by selection. Conclusions In summary, we constructed a genomic CNV map for Chinese indigenous fine-wool sheep using resequencing, thereby providing a valuable genetic variation resource for sheep genome research, which will contribute to the study of complex traits in sheep. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07387-7.
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Affiliation(s)
- Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Xijun Wang
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, 734031, China
| | - Tianxiang Wang
- Gansu Provincial Sheep Breeding Technology Extension Station, Sunan, 734031, China
| | - Yajun Zhang
- Xinjiang Gongnaisi Breeding Sheep Farm, Xinyuan, 835808, China
| | - Fujun Hou
- Aohan Banner Breeding Sheep Farm, Chifeng, 024300, China
| | - Chune Niu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Xiaopin Sun
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Hongchang Zhao
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Shaohua Zhu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China.
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Sheep Breeding Engineering Technology Research Center, Lanzhou, 730050, China.
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Chen Q, Huang Y, Wang Z, Teng S, Hanif Q, Lei C, Sun J. Whole-genome resequencing reveals diversity and selective signals in Longlin goat. Gene 2020; 771:145371. [PMID: 33346103 DOI: 10.1016/j.gene.2020.145371] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 12/03/2020] [Accepted: 12/11/2020] [Indexed: 11/30/2022]
Abstract
The Longlin goat is one of the most valuable livestock species in Guangxi Autonomous Region of China, but its genomic diversity and selective signals are not clearly elucidated. Here we compared 20 genomes of Longlin goat to 66 genomes of other seven goat breeds worldwide to analyze patterns of Longlin goat genetic variation. We found the lowest linkage disequilibrium at the large distances between SNPs associated with the highest effective population size in the recent generations ago in Longlin goat. The eight goat breeds could be divided into Euro-African and East Asian goat population. Interestingly, like East Asian taurine, the same two migration phases might have occurred in the history of East Asian goat. More importantly, we identified selective signals implicated in immune resistance to disease, especially for skin disease, in Longlin goat. Our findings will not only help understand the evolutionary history and breed characteristic but can provide valuable resources for conservation of germplasm resources and implementation of crossbreeding programs.
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Affiliation(s)
- Qiuming Chen
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China; Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yingfei Huang
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China
| | - Zihao Wang
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China
| | - Shaohua Teng
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China
| | - Quratulain Hanif
- Computational Biology Laboratory, Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad 577, Pakistan; Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad 45650, Pakistan
| | - Chuzhao Lei
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China
| | - Junli Sun
- Guangxi Key Laboratory of Livestock Genetic Improvement, Animal Husbandry Research Institute of Guangxi Zhuang Autonomous Region, Nanning 530001, China.
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Amiri Ghanatsaman Z, Wang GD, Asadi Fozi M, Zhang YP, Esmailizadeh A. Genome resequencing data for Iranian local dogs and wolves. BMC Res Notes 2020; 13:436. [PMID: 32938490 PMCID: PMC7493879 DOI: 10.1186/s13104-020-05271-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/04/2020] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE The data provided herein represent the whole-genome resequencing data related to three wolves and three Iranian local dogs. The understanding of genome evolution during animal domestication is an interesting subject in genome biology. Dog is an excellent model for understanding of domestication due to its considerable variety of behavioral and physical traits. The Zagros area of current day Iran has been identified as one of the initial centers of animal domestication. The availability of the complete genome sequences of Iranian local canids can be a valuable resource for researchers to address questions and testing hypotheses on the dog domestication process. DATA DESCRIPTION We collected blood samples from six Iranian local canids including two hunting dogs (Saluki breed), a mastiff dog (Qahderijani ecotype) and three wolves. We extracted genomic DNA from blood samples. Sequence data were produced using the Illumina HiSeq 2500 system. All sequence data are available in the National Genomics Data Center (NGDC), Genome Sequence Archive (GSA) database under the accession of CRA001324 and the National Center for Biotechnology Information (NCBI) under the accession of PRJNA639312. The short-read sequences with the mean depth of 16X were aligned to the dog reference genome (CanFam3.1) and achieved 99% coverage of the reference assembly. The obtained information from this experiment will be useful in evolutionary biology.
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Affiliation(s)
- Zeinab Amiri Ghanatsaman
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
- Young Researchers Society, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China
| | - Masood Asadi Fozi
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran
| | - Ya-Ping Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650091, China
| | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran.
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, No. 32 Jiaochang Donglu, Kunming, 650223, Yunnan, China.
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Huang J, Sun W, Seong KM, Mittapalli O, Ojo J, Coates B, Paige KN, Clark JM, Pittendrigh BR. Dietary antioxidant vitamin C influences the evolutionary path of insecticide resistance in Drosophila melanogaster. Pestic Biochem Physiol 2020; 168:104631. [PMID: 32711765 DOI: 10.1016/j.pestbp.2020.104631] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 06/03/2020] [Accepted: 06/09/2020] [Indexed: 06/11/2023]
Abstract
Herbivorous insects encounter a variety of toxic environmental substances ranging from ingested plant defensive compounds to human-introduced insecticidal agents. Dietary antioxidants are known to reduce the negative physiological impacts of toxins in mammalian systems through amelioration of reactive oxygen-related cellular damage. The analogous impacts to insects caused by multigenerational exposure to pesticides and the effects on adaptive responses within insect populations, however, are currently unknown. To address these research gaps, we used Drosophila as a model system to explore adaptive phenotypic responses to acute dichlorodiphenyltrichloroethane (DDT) exposure in the presence of the dietary antioxidant vitamin C and to examine the structural genomic consequences of this exposure. DDT resistance increased significantly among four replicates exposed to a low concentration of DDT for 10 generations. In contrast, dietary intake of vitamin C significantly reduced DDT resistance after mutigenerational exposure to the same concentration of DDT. As to the genomic consequences, no significant differences were predicted in overall nucleotide substitution rates across the genome between any of the treatments. Despite this, replicates exposed to a low concentration of DDT without vitamin C showed the highest number of synonymous and non-synonymous variants (3196 in total), followed by the DDT plus vitamin C (1174 in total), and vitamin C alone (728 in total) treatments. This study demonstrates the potential role of diet (specifically, antioxidant intake) on adaptive genome responses, and thus on the evolution of pesticide resistance within insect populations.
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Affiliation(s)
- Jingfei Huang
- College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China.
| | - Weilin Sun
- Department of Entomology, Michigan State University, East Lansing, MI, USA
| | - Keon Mook Seong
- Department of Applied Biology, College of Ecology and Environment, Kyungpook National University, Sangju, Republic of Korea
| | | | - James Ojo
- Department of Crop Production, Kwara State University, Malete, Ilorin, Nigeria
| | - Brad Coates
- USDA-ARS, Corn Insects & Crop Genetics Research Unit, Ames, IA, USA
| | - Ken N Paige
- Department of Evolution, Ecology & Behavior, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - John M Clark
- Department of Veterinary & Animal Science, University of Massachusetts, Amherst, MA, USA
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Fang J, Wood AM, Chen Y, Yue J, Ming R. Genomic variation between PRSV resistant transgenic SunUp and its progenitor cultivar Sunset. BMC Genomics 2020; 21:398. [PMID: 32532215 PMCID: PMC7291442 DOI: 10.1186/s12864-020-06804-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 06/05/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND The safety of genetically transformed plants remains a subject of scrutiny. Genomic variants in PRSV resistant transgenic papaya will provide evidence to rationally address such concerns. RESULTS In this study, a total of more than 74 million Illumina reads for progenitor 'Sunset' were mapped onto transgenic papaya 'SunUp' reference genome. 310,364 single nucleotide polymorphisms (SNPs) and 34,071 small Inserts/deletions (InDels) were detected between 'Sunset' and 'SunUp'. Those variations have an uneven distribution across nine chromosomes in papaya. Only 0.27% of mutations were predicted to be high-impact mutations. ATP-related categories were highly enriched among these high-impact genes. The SNP mutation rate was about 8.4 × 10- 4 per site, comparable with the rate induced by spontaneous mutation over numerous generations. The transition-to-transversion ratio was 1.439 and the predominant mutations were C/G to T/A transitions. A total of 3430 nuclear plastid DNA (NUPT) and 2764 nuclear mitochondrial DNA (NUMT) junction sites have been found in 'SunUp', which is proportionally higher than the predicted total NUPT and NUMT junction sites in 'Sunset' (3346 and 2745, respectively). Among all nuclear organelle DNA (norgDNA) junction sites, 96% of junction sites were shared by 'SunUp' and 'Sunset'. The average identity between 'SunUp' specific norgDNA and corresponding organelle genomes was higher than that of norgDNA shared by 'SunUp' and 'Sunset'. Six 'SunUp' organelle-like borders of transgenic insertions were nearly identical to corresponding sequences in organelle genomes (98.18 ~ 100%). None of the paired-end spans of mapped 'Sunset' reads were elongated by any 'SunUp' transformation plasmid derived inserts. Significant amounts of DNA were transferred from organelles to the nuclear genome during bombardment, including the six flanking sequences of the three transgenic insertions. CONCLUSIONS Comparative whole-genome analyses between 'SunUp' and 'Sunset' provide a reliable estimate of genome-wide variations and evidence of organelle-to-nucleus transfer of DNA associated with biolistic transformation.
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Affiliation(s)
- Jingping Fang
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China.,Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, 350117, Fujian, China.,FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Andrew Michael Wood
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Youqiang Chen
- The Public Service Platform for Industrialization Development Technology of Marine Biological Medicine and Product of State Oceanic Administration, Key Laboratory of Developmental and Neural Biology, College of Life Sciences, Fujian Normal University, Fuzhou, 350117, Fujian, China.,Center of Engineering Technology Research for Microalgae Germplasm Improvement of Fujian, Southern Institute of Oceanography, Fujian Normal University, Fuzhou, 350117, Fujian, China
| | - Jingjing Yue
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China. .,Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Li Y, Zhu FL, Zheng XW, Hu ML, Dong C, Diao Y, Wang YW, Xie KQ, Hu ZL. Comparative population genomics reveals genetic divergence and selection in lotus, Nelumbo nucifera. BMC Genomics 2020; 21:146. [PMID: 32046648 PMCID: PMC7014656 DOI: 10.1186/s12864-019-6376-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Accepted: 12/08/2019] [Indexed: 12/26/2022] Open
Abstract
Background Lotus (Nelumbo nucifera) is an aquatic plant with important agronomic, horticulture, art and religion values. It was the basal eudicot species occupying a critical phylogenetic position in flowering plants. After the domestication for thousands of years, lotus has differentiated into three cultivated types -flower lotus, seed lotus and rhizome lotus. Although the phenotypic and genetic differentiations based on molecular markers have been reported, the variation on whole-genome level among the different lotus types is still ambiguous. Results In order to reveal the evolution and domestication characteristics of lotus, a total of 69 lotus accessions were selected, including 45 cultivated accessions, 22 wild sacred lotus accessions, and 2 wild American lotus accessions. With Illumina technology, the genomes of these lotus accessions were resequenced to > 13× raw data coverage. On the basis of these genomic data, 25 million single-nucleotide polymorphisms (SNPs) were identified in lotus. Population analysis showed that the rhizome and seed lotus were monophyletic and genetically homogeneous, whereas the flower lotus was biphyletic and genetically heterogeneous. Using population SNP data, we identified 1214 selected regions in seed lotus, 95 in rhizome lotus, and 37 in flower lotus. Some of the genes in these regions contributed to the essential domestication traits of lotus. The selected genes of seed lotus mainly affected lotus seed weight, size and nutritional quality. While the selected genes were responsible for insect resistance, antibacterial immunity and freezing and heat stress resistance in flower lotus, and improved the size of rhizome in rhizome lotus, respectively. Conclusions The genome differentiation and a set of domestication genes were identified from three types of cultivated lotus- flower lotus, seed lotus and rhizome lotus, respectively. Among cultivated lotus, flower lotus showed the greatest variation. The domestication genes may show agronomic importance via enhancing insect resistance, improving seed weight and size, or regulating lotus rhizome size. The domestication history of lotus enhances our knowledge of perennial aquatic crop evolution, and the obtained dataset provides a basis for future genomics-enabled breeding.
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Affiliation(s)
- Ye Li
- State Key Laboratory of Hybrid Rice, Lotus Engineering Research Center of Hubei Province, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China
| | - Feng-Lin Zhu
- State Key Laboratory of Hybrid Rice, Lotus Engineering Research Center of Hubei Province, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China
| | - Xing-Wen Zheng
- State Key Laboratory of Hybrid Rice, Lotus Engineering Research Center of Hubei Province, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.,Guangchang Research School of White Lotus, Guangchang, 344900, People's Republic of China
| | - Man-Li Hu
- State Key Laboratory of Hybrid Rice, Lotus Engineering Research Center of Hubei Province, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China
| | - Chen Dong
- State Key Laboratory of Hybrid Rice, Lotus Engineering Research Center of Hubei Province, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China
| | - Ying Diao
- College of Landscape Architecture and Life Science / Institute of Special Plants, Chongqing University of Arts and Sciences, Chongqing, 402160, People's Republic of China
| | - You-Wei Wang
- Institute of Traditional Chinese Medicine and Natural Products, School of Pharmaceutical Sciences, Wuhan University, Wuhan, 430071, People's Republic of China
| | - Ke-Qiang Xie
- Guangchang Research School of White Lotus, Guangchang, 344900, People's Republic of China.
| | - Zhong-Li Hu
- State Key Laboratory of Hybrid Rice, Lotus Engineering Research Center of Hubei Province, College of Life Sciences, Wuhan University, Wuhan, 430072, People's Republic of China.
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He Y, Hu D, You J, Wu D, Cui Y, Dong H, Li J, Qian W. Genome-wide association study and protein network analysis for understanding candidate genes involved in root development at the rapeseed seedling stage. Plant Physiol Biochem 2019; 137:42-52. [PMID: 30738216 DOI: 10.1016/j.plaphy.2019.01.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 01/20/2019] [Accepted: 01/26/2019] [Indexed: 05/23/2023]
Abstract
Root system is essential for plants to absorb water and nutrients. The root related traits are complex quantitative traits and regulated by genetic control. Here, we used two association mapping panels to perform a genome-wide association study (GWAS) on seven root related traits in Brassica napus at the seedling stage and obtained 27 SNP loci significantly associated with the phenotypes. We further conducted a genome-wide LD block analysis of the candidate peak regions and obtained 295 candidate genes with high association peaks across seven phenotypes in LD region. In addition, a protein interaction network using the candidate genes identified here was constructed, and 113 genes were associated. Seven genes, BnaA03g47330D, BnaC09g16810D, BnaA06g22840D, BnaA03g28390D, BnaA08g19920D, BnaA03g28930D and BnaA03g11440D were in a large cluster, and may play important roles in interacting with other related genes. Our data may provide resources for molecular breeding and functional analysis of root growth and development in rapeseed.
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Affiliation(s)
- Yajun He
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Dingxue Hu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Jingcan You
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Daoming Wu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Hongli Dong
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, 400716, China.
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Li X, Ye J, Han X, Qiao R, Li X, Lv G, Wang K. Whole-genome sequencing identifies potential candidate genes for reproductive traits in pigs. Genomics 2019; 112:199-206. [PMID: 30707936 DOI: 10.1016/j.ygeno.2019.01.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2018] [Revised: 01/05/2019] [Accepted: 01/22/2019] [Indexed: 11/24/2022]
Abstract
Reproductive performance is a complex quantitative trait, that is determined by multiple genes, regulatory pathways and environmental factors. A list of major genes with large effect have been detected, although multiple QTLs are identified. To identify candidate genes for pig prolificacy, whole genome variants from five high- and five low-prolificacy Yorkshire sows were collected using whole-genome resequencing. A total of 13,955,609 SNPs and 2,666,366 indels were detected across the genome. Common differential SNPs and indels were identified between the two groups of sows. Genes encoding components of the TGF-beta signaling pathway were enriched with the variations, including BMP5, BMP6, BMP7, ACVR1, INHBA, ZFYVE9, TGFBR2, DCN, ID4, BAMBI, and ACVR2A. Several differential variants within these genes related to reproductive traits were identified to be associated with litter size. A comparison of selective regions and published QTL data suggests that NEDD9, SLC39A11, SNCA, and UNC5D are candidate genes for reproduction traits.
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Affiliation(s)
- Xinjian Li
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Jianwei Ye
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Xuelei Han
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Ruimin Qiao
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Xiuling Li
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Gang Lv
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China
| | - Kejun Wang
- College of Animal Sciences and Veterinary Medicine, Henan Agricultural University, Zhengzhou, Henan, People's Republic of China.
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Obala J, Saxena RK, Singh VK, Kumar CVS, Saxena KB, Tongoona P, Sibiya J, Varshney RK. Development of sequence-based markers for seed protein content in pigeonpea. Mol Genet Genomics 2018; 294:57-68. [PMID: 30173295 DOI: 10.1007/s00438-018-1484-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 08/22/2018] [Indexed: 12/30/2022]
Abstract
Pigeonpea is an important source of dietary protein to over a billion people globally, but genetic enhancement of seed protein content (SPC) in the crop has received limited attention for a long time. Use of genomics-assisted breeding would facilitate accelerating genetic gain for SPC. However, neither genetic markers nor genes associated with this important trait have been identified in this crop. Therefore, the present study exploited whole genome re-sequencing (WGRS) data of four pigeonpea genotypes (~ 12X coverage) to identify sequence-based markers and associated candidate genes for SPC. By combining a common variant filtering strategy on available WGRS data with knowledge of gene functions in relation to SPC, 108 sequence variants from 57 genes were identified. These genes were assigned to 19 GO molecular function categories with 56% belonging to only two categories. Furthermore, Sanger sequencing confirmed presence of 75.4% of the variants in 37 genes. Out of 30 sequence variants converted into CAPS/dCAPS markers, 17 showed high level of polymorphism between low and high SPC genotypes. Assay of 16 of the polymorphic CAPS/dCAPS markers on an F2 population of the cross ICP 5529 (high SPC) × ICP 11605 (low SPC), resulted in four of the CAPS/dCAPS markers significantly (P < 0.05) co-segregated with SPC. In summary, four markers derived from mutations in four genes will be useful for enhancing/regulating SPC in pigeonpea crop improvement programs.
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Affiliation(s)
- Jimmy Obala
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Rachit K Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Vikas K Singh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - C V Sameer Kumar
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - K B Saxena
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India
| | - Pangirayi Tongoona
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Julia Sibiya
- University of KwaZulu-Natal, African Center for Crop Improvement, Scottsville, Pietermaritzburg, 3209, South Africa
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324, India.
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He Q, Cao C, Hui W, Yu J, Zhang H, Zhang W. Genomic resequencing combined with quantitative proteomic analyses elucidate the survival mechanisms of Lactobacillus plantarum P-8 in a long-term glucose-limited experiment. J Proteomics 2018; 176:37-45. [PMID: 29414317 DOI: 10.1016/j.jprot.2018.01.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Revised: 01/09/2018] [Accepted: 01/19/2018] [Indexed: 12/20/2022]
Abstract
Lactobacillus plantarum, commonly isolated from plant material, is widely used to produce various types of fermented foods. However, nutrient-limiting conditions are often encountered during industrial applications. The present study aimed to investigate the response of L. plantarum P-8 to glucose-limited conditions in a long-term experiment. Genotypic and proteomic changes in L. plantarum P-8 were monitored over 3 years in glucose-limited and glucose-normal media using whole-genome resequencing and tandem mass tag-based quantitative proteomic analysis. Results showed that L. plantarum employed numerous survival mechanisms, including alteration of the cell envelope, activation of the PTS system, accumulation and consumption of amino acids, increase in the metabolism of carbohydrates (via glycolysis, citric acid cycle, and pyruvate metabolism), and increase in the production of ATP in response to glucose starvation. This study demonstrates the feasibility of experimental evolution of L. plantarum P-8, while whole-genome resequencing of adapted isolates provided clues toward bacterial functions involved and a deeper mechanistic understanding of the adaptive response of L. plantarum to glucose-limited conditions. SIGNIFICANCE We have conducted a 3-year experiment monitoring genotypic and proteomic changes in Lactobacillus plantarum P-8 in glucose-limited and glucose-normal media. Whole-genome resequencing and tandem mass tag-based quantitative proteomics were performed for analyzing genomic evolution of L. plantarum P-8 in glucose-limited and glucose-normal conditions. In addition, differential expressed proteins in all generations between these two conditions were identified and functions of these proteins specific to L group were predicted. L. plantarum employed numerous survival mechanisms, including alteration of the cell envelope, activation of the PTS system, accumulation and consumption of amino acids, increase in the metabolism of carbohydrates (glycolysis, citric acid cycle, and pyruvate metabolism), and increase in the production of ATP in response to glucose starvation.
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Affiliation(s)
- Qiuwen He
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Chenxia Cao
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Wenyan Hui
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Jie Yu
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Heping Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China
| | - Wenyi Zhang
- Key Laboratory of Dairy Biotechnology and Engineering, Ministry of Education, Key Laboratory of Dairy Products Processing, Ministry of Agriculture, Inner Mongolia Agricultural University, Huhhot 010018, China.
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Reilly MC, Kim J, Lynn J, Simmons BA, Gladden JM, Magnuson JK, Baker SE. Forward genetics screen coupled with whole-genome resequencing identifies novel gene targets for improving heterologous enzyme production in Aspergillus niger. Appl Microbiol Biotechnol 2018; 102:1797-1807. [PMID: 29305699 PMCID: PMC5794824 DOI: 10.1007/s00253-017-8717-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 12/11/2017] [Accepted: 12/12/2017] [Indexed: 12/12/2022]
Abstract
Plant biomass, once reduced to its composite sugars, can be converted to fuel substitutes. One means of overcoming the recalcitrance of lignocellulose is pretreatment followed by enzymatic hydrolysis. However, currently available commercial enzyme cocktails are inhibited in the presence of residual pretreatment chemicals. Recent studies have identified a number of cellulolytic enzymes from bacteria that are tolerant to pretreatment chemicals such as ionic liquids. The challenge now is generation of these enzymes in copious amounts, an arena where fungal organisms such as Aspergillus niger have proven efficient. Fungal host strains still need to be engineered to increase production titers of heterologous protein over native enzymes, which has been a difficult task. Here, we developed a forward genetics screen coupled with whole-genome resequencing to identify specific lesions responsible for a protein hyper-production phenotype in A. niger. This strategy successfully identified novel targets, including a low-affinity glucose transporter, MstC, whose deletion significantly improved secretion of recombinant proteins driven by a glucoamylase promoter.
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Affiliation(s)
- Morgann C Reilly
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Joonhoon Kim
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Jed Lynn
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Naval Medical Research Unit Dayton, Wright-Patterson Air Force Base, Dayton, OH, 45433, USA
| | - Blake A Simmons
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - John M Gladden
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Biomass Science and Conversion Technologies Department, Sandia National Laboratories, Livermore, CA, 94551, USA
| | - Jon K Magnuson
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA.,Chemical and Biological Processes Development Group, Pacific Northwest National Laboratory, Richland, WA, 99352, USA
| | - Scott E Baker
- Joint BioEnergy Institute, Emeryville, CA, 94608, USA. .,Biosystems Design and Simulation Group, Environmental Molecular Sciences Division, Pacific Northwest National Laboratory, Richland, WA, 99352, USA.
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Lian T, Li D, Tan X, Che T, Xu Z, Fan X, Wu N, Zhang L, Gaur U, Sun B, Yang M. Genetic diversity and natural selection in wild fruit flies revealed by whole-genome resequencing. Genomics 2017; 110:304-309. [PMID: 29247769 DOI: 10.1016/j.ygeno.2017.12.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 11/20/2017] [Accepted: 12/05/2017] [Indexed: 12/30/2022]
Abstract
We characterized 26 wild fruit flies comparative population genomics from six different altitude and latitude locations by whole genome resequencing. Genetic diversity was relatively higher in Ganzi and Chongqing populations. We also found 13 genes showing selection signature between different altitude flies and variants related to hypoxia and temperature stimulus, were preferentially selected during the flies evolution. One of the most striking selective sweeps found in all high altitude flies occurred in the region harboring Hsp70Aa and Hsp70Ab on chromosome 3R. Interestingly, these two genes are involved in GO terms including response to hypoxia, unfolded protein, temperature stimulus, heat, oxygen levels. Mutation in HPH gene, a candidate gene in the hypoxia inducible factor pathway, might contributes to hypoxic high-altitude adaptation. Intriguingly, some of the selected genes, primarily utilized in humans, were involved in the response to hypoxia, which could imply a conserved molecular mechanisms underlying high-altitude adaptation between insects and humans.
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Affiliation(s)
- Ting Lian
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Diyan Li
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
| | - Xinxin Tan
- Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China
| | - Tiandong Che
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongxian Xu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaolan Fan
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Nan Wu
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Long Zhang
- Institute of Ecology, China West Normal University, Nanchong 637009, China
| | - Uma Gaur
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Boyuan Sun
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Mingyao Yang
- Institute of Animal Genetics and Breeding, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China.
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Zhang X, Li R, Chen L, Niu S, Chen L, Gao J, Wen J, Yi B, Ma C, Tu J, Fu T, Shen J. Fine-mapping and candidate gene analysis of the Brassica juncea white-flowered mutant Bjpc2 using the whole-genome resequencing. Mol Genet Genomics 2018; 293:359-70. [PMID: 29119366 DOI: 10.1007/s00438-017-1390-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/31/2017] [Indexed: 12/27/2022]
Abstract
Flower color in Brassica spp. is an important trait and considered a major visual signal for insect-pollinated plants. In previous study, we isolated and identified two genes (BjPC1 and BjPC2) that control the flower color in B. juncea, and mapped BjPC1 to a 0.13-cM region. In this study, we report the fine-mapping and candidate analysis of BjPC2. We conducted whole-genome resequencing, using bulked segregant analysis (BSA) to determine the BjPC2 candidate intervals. Crossing, allelism testing, and repeated full-sib mating were used to generate XG3, a near isogenic line (NIL) population that segregated on the BjPC2 locus. Through a genome-wide comparison of single nucleotide polymorphism (SNP) profiles between the yellow- and white-flowered bulks, a candidate interval for BjPC2 was identified on chromosome B04 (2.45 Mb). The BjPC2 linkage map was constructed with the newly developed simple sequence repeat (SSR) markers in the candidate interval to narrow the candidate BjPC2 region to 31-kb. Expression profiling and RNA-seq analysis partially confirmed that the AtPES2 homolog, BjuB027334 is the most promising candidate gene for BjPC2. Furthermore, analyses with high pressure liquid chromatography and transmission electron microscopy demonstrated that BjPC2 might be important in xanthophyll esterification, a process that limits xanthophyll degradation and increases sequestration. Overall, we mapped the BjPC2 to a 31-kb region on the B04 in B. juncea and identified BjuB027334 as a valuable candidate gene. Our results provide a basis for understanding the molecular mechanisms underlying the white-flowered trait and for molecular marker-assisted selection of flower color in B. juncea breeding.
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Becker D, Minor KM, Letko A, Ekenstedt KJ, Jagannathan V, Leeb T, Shelton GD, Mickelson JR, Drögemüller C. A GJA9 frameshift variant is associated with polyneuropathy in Leonberger dogs. BMC Genomics 2017; 18:662. [PMID: 28841859 PMCID: PMC5574090 DOI: 10.1186/s12864-017-4081-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/21/2017] [Indexed: 01/15/2023] Open
Abstract
Background Many inherited polyneuropathies (PN) observed in dogs have clinical similarities to the genetically heterogeneous group of Charcot-Marie-Tooth (CMT) peripheral neuropathies in humans. The canine disorders collectively show a variable expression of progressive clinical signs and ages of onset, and different breed prevalences. Previously in the Leonberger breed, a variant highly associated with a juvenile-onset PN was identified in the canine orthologue of a CMT-associated gene. As this deletion in ARHGEF10 (termed LPN1) does not explain all cases, PN in this breed may encompass variants in several genes with similar clinical and histopathological features. Results A genome-wide comparison of 173 k SNP genotypes of 176 cases, excluding dogs homozygous for the ARHGEF10 variant, and 138 controls, was carried out to detect further PN-associated variants. A single suggestive significant association signal on CFA15 was found. The genome of a PN-affected Leonberger homozygous for the associated haplotype was sequenced and variants in the 7.7 Mb sized critical interval were identified. These variants were filtered against a database of variants observed in 202 genomes of various dog breeds and 3 wolves, and 6 private variants in protein-coding genes, all in complete linkage disequilibrium, plus 92 non-coding variants were revealed. Five of the coding variants were predicted to have low or moderate effect on the encoded protein, whereas a 2 bp deletion in GJA9 results in a frameshift of high impact. GJA9 encodes connexin 59, a connexin gap junction family protein, and belongs to a group of CMT-associated genes that have emerged as important components of peripheral myelinated nerve fibers. The association between the GJA9 variant and PN was confirmed in an independent cohort of 296 cases and 312 controls. Population studies showed a dominant mode of inheritance, an average age of onset of approximately 6 years, and incomplete penetrance. Conclusions This GJA9 variant represents a highly probable candidate variant for another form of PN in Leonberger dogs, which we have designated LPN2, and a new candidate gene for CMT disease. To date, approximately every third PN-diagnosed Leonberger dog can be explained by the ARHGEF10 or GJA9 variants, and we assume that additional genetic heterogeneity in this condition exists in the breed. Electronic supplementary material The online version of this article (10.1186/s12864-017-4081-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Doreen Becker
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Katie M Minor
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Kari J Ekenstedt
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA.,Department of Basic Medical Sciences, College of Veterinary Medicine, Purdue University, West Lafayette, Indiana, 47907, USA
| | - Vidhya Jagannathan
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Tosso Leeb
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - G Diane Shelton
- Department of Pathology, School of Medicine, University of California, San Diego, La Jolla, California, 92093, USA
| | - James R Mickelson
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, 55108, USA
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland.
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Liu Z, Ji Z, Wang G, Chao T, Hou L, Wang J. Genome-wide analysis reveals signatures of selection for important traits in domestic sheep from different ecoregions. BMC Genomics 2016; 17:863. [PMID: 27809776 PMCID: PMC5094087 DOI: 10.1186/s12864-016-3212-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2016] [Accepted: 10/25/2016] [Indexed: 12/22/2022] Open
Abstract
Background Throughout a long period of adaptation and selection, sheep have thrived in a diverse range of ecological environments. Mongolian sheep is the common ancestor of the Chinese short fat-tailed sheep. Migration to different ecoregions leads to changes in selection pressures and results in microevolution. Mongolian sheep and its subspecies differ in a number of important traits, especially reproductive traits. Genome-wide intraspecific variation is required to dissect the genetic basis of these traits. Results This research resequenced 3 short fat-tailed sheep breeds with a 43.2-fold coverage of the sheep genome. We report more than 17 million single nucleotide polymorphisms and 2.9 million indels and identify 143 genomic regions with reduced pooled heterozygosity or increased genetic distance to each other breed that represent likely targets for selection during the migration. These regions harbor genes related to developmental processes, cellular processes, multicellular organismal processes, biological regulation, metabolic processes, reproduction, localization, growth and various components of the stress responses. Furthermore, we examined the haplotype diversity of 3 genomic regions involved in reproduction and found significant differences in TSHR and PRL gene regions among 8 sheep breeds. Conclusions Our results provide useful genomic information for identifying genes or causal mutations associated with important economic traits in sheep and for understanding the genetic basis of adaptation to different ecological environments. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3212-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhaohua Liu
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Zhibin Ji
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Guizhi Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Tianle Chao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Lei Hou
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Jianmin Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Taian, Shandong, 271018, China.
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Kim TS, He Q, Kim KW, Yoon MY, Ra WH, Li FP, Tong W, Yu J, Oo WH, Choi B, Heo EB, Yun BK, Kwon SJ, Kwon SW, Cho YH, Lee CY, Park BS, Park YJ. Genome-wide resequencing of KRICE_CORE reveals their potential for future breeding, as well as functional and evolutionary studies in the post-genomic era. BMC Genomics 2016; 17:408. [PMID: 27229151 DOI: 10.1186/s12864-016-2734-y] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 05/12/2016] [Indexed: 11/10/2022] Open
Abstract
Background Rice germplasm collections continue to grow in number and size around the world. Since maintaining and screening such massive resources remains challenging, it is important to establish practical methods to manage them. A core collection, by definition, refers to a subset of the entire population that preserves the majority of genetic diversity, enhancing the efficiency of germplasm utilization. Results Here, we report whole-genome resequencing of the 137 rice mini core collection or Korean rice core set (KRICE_CORE) that represents 25,604 rice germplasms deposited in the Korean genebank of the Rural Development Administration (RDA). We implemented the Illumina HiSeq 2000 and 2500 platform to produce short reads and then assembled those with 9.8 depths using Nipponbare as a reference. Comparisons of the sequences with the reference genome yielded more than 15 million (M) single nucleotide polymorphisms (SNPs) and 1.3 M INDELs. Phylogenetic and population analyses using 2,046,529 high-quality SNPs successfully assigned rice accessions to the relevant rice subgroups, suggesting that these SNPs capture evolutionary signatures that have accumulated in rice subpopulations. Furthermore, genome-wide association studies (GWAS) for four exemplary agronomic traits in the KRIC_CORE manifest the utility of KRICE_CORE; that is, identifying previously defined genes or novel genetic factors that potentially regulate important phenotypes. Conclusion This study provides strong evidence that the size of KRICE_CORE is small but contains high genetic and functional diversity across the genome. Thus, our resequencing results will be useful for future breeding, as well as functional and evolutionary studies, in the post-genomic era. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2734-y) contains supplementary material, which is available to authorized users.
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