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Feng J, Zhu W, Shi H, Peng D, Zang L, Wang Y, ZhaXi L, BaiMa J, Amevor FK, Wang X, Ma X, Zhao X. Analysis of the Selection Signal of the Tibetan Black Chicken Genome Based on Whole-Genome Sequencing. Genes (Basel) 2023; 14:1672. [PMID: 37761812 PMCID: PMC10531317 DOI: 10.3390/genes14091672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND The Tibetan chicken has adapted well to high altitudes genetically after its long-term habitation in the plateau. In this study, we analyzed the selection signal of Tibetan black chickens (TBCs) and discovered genes associated with the characteristics of germplasm. METHODS Whole-genome sequencing (WGS) was used to identify the single-nucleotide polymorphism (SNP) markers and genetic structures in the genome of Tibetan black chickens. Further, we performed a comparative population genomics analysis between the genomic data obtained in this present study and the genomic data for five wild red jungle fowls (RJFs) accessed from the NCBI database (GenBank accession number PRJNA241474). Thereafter, the Fst and Pi selections were used to identify genes under positive selection in the Tibetan black chicken genome. RESULTS A total of 9,490,690 SNPs were identified in the Tibetan black chickens. In addition, the results from the gene ontology (GO) analysis showed that 732 genes of TBCs were enriched in a total of 210 GO terms with specific molecular functions such as regulation of cellular catabolic process, the MAPK signaling pathway, regulation of ion transport, growth, morphogenesis and lung alveolus development which may provide a better mechanism to facilitate oxygen transport and utilization in TBCs. Moreover, the results from the KEGG analysis showed that 732 genes of the TBCs were significantly enriched in the calcium signaling pathway, circadian entrainment (ADCY1, GNG7 and PER3), oxytocin signaling pathway and pathways of multiple neurodegeneration diseases. In addition, the CD86 antigen (CD86) was identified as a gene associated with the immune response in chickens. It was also revealed that genes such as TRIT1, HPCAL4, NT5C1A and HEYL were discovered under selection in Tibetan black chickens on chromosome 23. These genes may be related to the local adaptive characteristics of Tibetan black chickens, for instance, NT5C1A and HEYL may be involved in the high-altitude adaption of oxygen delivery in Tibetan black chickens. CONCLUSIONS In summary, we found that selection mainly affects the disease resistance and cold acclimatization of Tibetan black chickens. Hence, these results may provide important genetic information for the evolution and breeding of Tibetan black chickens.
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Affiliation(s)
- Jing Feng
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa 850009, China
| | - Wei Zhu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (W.Z.); (F.K.A.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Hairen Shi
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Da Peng
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
| | - Lei Zang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
| | - Yan Wang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
| | - Luobu ZhaXi
- Shannan Longzi County Agriculture and Animal Husbandry Comprehensive Service Center, Shannan 856600, China (J.B.)
| | - Jiancai BaiMa
- Shannan Longzi County Agriculture and Animal Husbandry Comprehensive Service Center, Shannan 856600, China (J.B.)
| | - Felix Kwame Amevor
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (W.Z.); (F.K.A.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoqi Wang
- Agriculture and Animal Husbandry Comprehensive Service Center of Lazi County, Shigatse 858100, China;
| | - Xueying Ma
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
| | - Xiaoling Zhao
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (W.Z.); (F.K.A.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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2
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Parida M, Gouda G, Chidambaranathan P, Umakanta N, Katara JL, Sai CB, Samantaray S, Patra BC, Mohapatra T. Mitochondrial markers differentiate two distinct phylogenetic groups in indigenous rice landraces of northeast India: an evolutionary insight. J Genet 2023. [DOI: 10.1007/s12041-023-01422-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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3
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Wang M, Chen J, Zhou F, Yuan J, Chen L, Wu R, Liu Y, Zhang Q. The ties of brotherhood between japonica and indica rice for regional adaptation. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1369-1379. [PMID: 34902099 DOI: 10.1007/s11427-021-2019-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Accepted: 10/20/2021] [Indexed: 06/14/2023]
Abstract
Selection of beneficial genomic variants was crucial for regional adaptation of crops during domestication, but the underlying genomic basis remains largely unexplored. Here we report a genome-wide selective-sweep analysis of 655 japonica and 1,205 indica accessions selected from 2,673 landraces through principal component analysis to identify 5,636 non-synonymous single nucleotide polymorphisms (SNPs) fixed in at least one subspecies. We classified these SNPs into three groups, jiS (japonica- and indica-selected), jS (japonica-selected only), and iS (indica-selected only), and documented evidence for selection acting on these groups, their relation to yield-related traits, such as heading date, and their practical value in cropping area prediction. We also demonstrated the role of a jiS-SNP-containing gene in temperature adaptability. Our study informs genes underpinning adaptation that may shape Green Super Rice and proposes a time-saving, cost-reducing selection strategy of genomic breeding, sweep-SNP-guided selection, for developing regionally-adapted heterosis.
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Affiliation(s)
- Man Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jiehu Chen
- Science Corporation of Gene, Guangzhou, 510000, China
| | - Feng Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Jianming Yuan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Libin Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China
| | - Rongling Wu
- Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, 17033, USA.
| | - Yaoguang Liu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
- SCAU Main Campus Teaching & Research Base, Guangzhou, 510642, China.
| | - Qunyu Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China.
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642, China.
- SCAU Main Campus Teaching & Research Base, Guangzhou, 510642, China.
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4
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Zhang X, He Q, Zhang W, Shu F, Wang W, He Z, Xiong H, Peng J, Deng H. Genetic relationships and identification of core germplasm among rice photoperiod- and thermo-sensitive genic male sterile lines. BMC PLANT BIOLOGY 2021; 21:313. [PMID: 34215178 PMCID: PMC8252326 DOI: 10.1186/s12870-021-03062-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/20/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Harnessing heterosis is one of the major approaches to increase rice yield and has made a great contribution to food security. The identification and selection of outstanding parental genotypes especially among male sterile lines is a key step for exploiting heterosis. Two-line hybrid system is based on the discovery and application of photoperiod- and thermo-sensitive genic sensitive male sterile (PTGMS) materials. The development of wide-range of male sterile lines from a common gene pool leads to a narrower genetic diversity, which is vulnerable to biotic and abiotic stress. Hence, it is valuable to ascertain the genetic background of PTGMS lines and to understand their relationships in order to select and design a future breeding strategy. RESULTS A collection of 118 male sterile rice lines and 13 conventional breeding lines from the major rice growing regions of China was evaluated and screened against the photosensitive (pms3) and temperature sensitive male sterility (tms5) genes. The total gene pool was divided into four major populations as P1 possessing the pms3, P2 possessing tms5, P3 possessing both pms3 and tms5 genes, and P4 containing conventional breeding lines without any male sterility allele. The high genetic purity was revealed by homozygous alleles in all populations. The population admixture, principle components and the phylogenetic analysis revealed the close relations of P2 and P3 with P4. The population differentiation analysis showed that P1 has the highest differentiation coefficient. The lines from P1 were observed as the ancestors of other three populations in a phylogenetic tree, while the lines in P2 and P3 showed a close genetic relation with conventional lines. A core collection of top 10% lines with maximum within and among populations genetic diversity was constructed for future research and breeding efforts. CONCLUSION The low genetic diversity and close genetic relationship among PTGMS lines in P2, P3 and P4 populations suggest a selection sweep and they might result from a backcrossing with common ancestors including the pure lines of P1. The core collection from PTGMS panel updated with new diverse germplasm will serve best for further two-line hybrid breeding.
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Affiliation(s)
- Xianwen Zhang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
- Huazhi Biotech Co. Ltd, Changsha, 410125, China
| | - Qiang He
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Wuhan Zhang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Fu Shu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Weiping Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, 410128, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Zhizhou He
- Huazhi Biotech Co. Ltd, Changsha, 410125, China
| | - Hairong Xiong
- School of Chemistry and Materials Science, Hunan Agricultural University, Changsha, 410128, China
| | - Junhua Peng
- Huazhi Biotech Co. Ltd, Changsha, 410125, China
| | - Huafeng Deng
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
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5
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Qin C, Guo Y, Wu J, Wang L, Traw MB, Zhang Y. Comparative population genomic analysis provides insights into breeding of modern indica rice in China. Gene 2020; 768:145303. [PMID: 33181256 DOI: 10.1016/j.gene.2020.145303] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 09/26/2020] [Accepted: 11/04/2020] [Indexed: 11/17/2022]
Abstract
Comparative genomic analysis within Asian cultivated rice (Oryza sativa L.) populations has greatly enriched our knowledge regarding rice domestication and the divergence of the indica and japonica subspecies, while study on genomic regions associated with improvement within the indica subspecies is still limited. Here, through combined investigation of 2,429 indica cultivar genomes from public sequencing projects, we depict the improvement of modern indica rice in China. We identify three subgroups within indica populations: two geographically distinct, historical subgroups indica I (Ind_I) and indica III (Ind_III) and a modern subgroup indica II (Ind_II). The modern indica subgroup Ind_II shows admixture of the other two subgroups and enrichment of alleles that had been low-frequency in the other two subgroups. The Chinese indica cultivars exhibit a strong subgroup component change from Ind_I to Ind_II in the 1980s. Through haplotype-based comparative analysis, we detect 187 regions associated with separation of Ind_II compared to Ind_I or Ind_III. Within those regions we find strong representation of beneficial agricultural production-related alleles in Ind_II and a positive correlation between grain yield and number of differentiated haplotypes. Phenotypic features of long and slender grain, small tiller angle and decreased flowering time were detected for Ind_II. Through haplotype-based comparative analysis between rice subpopulations and subspecies, we find differentiated haplotypes not only from indica itself but also from japonica and aus, suggesting that introgression from other rice sub-populations has substantially contributed to modern indica rice breeds. These results help clarify the evolutionary landscape of modern indica rice in China and provide useful targets for future improvement.
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Affiliation(s)
- Chao Qin
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China
| | - Yanru Guo
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China
| | - Jianzhuang Wu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China
| | - Long Wang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China
| | - Milton Brian Traw
- State Key Laboratory for Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yanchun Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Science, Nanjing University, Nanjing 210023, China.
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6
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Nie X, Wen T, Shao P, Tang B, Nuriman‐guli A, Yu Y, Du X, You C, Lin Z. High-density genetic variation maps reveal the correlation between asymmetric interspecific introgressions and improvement of agronomic traits in Upland and Pima cotton varieties developed in Xinjiang, China. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:677-689. [PMID: 32246786 PMCID: PMC7496985 DOI: 10.1111/tpj.14760] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2019] [Revised: 03/11/2020] [Accepted: 03/23/2020] [Indexed: 05/11/2023]
Abstract
The two new world tetraploid cottons, Gossypium hirsutum and Gossypium barbadense, are cultivated worldwide and are characterised by a high yield and superior fibre quality, respectively. Historical genetic introgression has been reported between them; however, the existence of introgression and its genetic effects on agronomic traits remain unclear with regard to independent breeding of G. hirsutum (Upland cotton) and G. barbadense (Pima cotton) elite cultivars. We collected 159 G. hirsutum and 70 G. barbadense cultivars developed in Xinjiang, China, along with 30 semi-wild accessions of G. hirsutum, to perform interspecific introgression tests, intraspecific selection analyses and genome-wide association studies (GWAS) with fibre quality and yield component traits in multiple environments. In total, we identified seven interspecific introgression events and 52 selective sweep loci in G. hirsutum, as well as 17 interspecific introgression events and 19 selective sweep loci in G. barbadense. Correlation tests between agronomic traits and introgressions showed that introgression loci were mutually beneficial for the improvement of fibre quality and yield traits in both species. In addition, the phenotypic effects of four interspecific introgression events could be detected by intraspecific GWAS, with Gb_INT13 significantly improving fibre yield in G. barbadense. The present study describes the landscape of genetic introgression and selection between the two species, and highlights the genetic effects of introgression among populations, which can be used for future improvement of fibre yield and quality in G. barbadense and G. hirsutum, respectively.
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Affiliation(s)
- Xinhui Nie
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang BingtuanAgricultural CollegeShihezi UniversityShiheziXinjiang832000China
| | - Tianwang Wen
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070China
| | - Panxia Shao
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang BingtuanAgricultural CollegeShihezi UniversityShiheziXinjiang832000China
| | - Binghui Tang
- Cotton Research InstituteShihezi Academy of Agriculture ScienceShiheziXinjiang832000China
| | - Aini Nuriman‐guli
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang BingtuanAgricultural CollegeShihezi UniversityShiheziXinjiang832000China
| | - Yu Yu
- Cotton Research InstituteXinjiang Academy of Agriculture and Reclamation ScienceShiheziXinjiang832000China
| | - Xiongming Du
- State Key Laboratory of Cotton BiologyInstitute of Cotton ResearchChinese Academy of Agriculture ScienceAnyangHenan45500China
| | - Chunyuan You
- Cotton Research InstituteShihezi Academy of Agriculture ScienceShiheziXinjiang832000China
| | - Zhongxu Lin
- Key Laboratory of Oasis Ecology Agricultural of Xinjiang BingtuanAgricultural CollegeShihezi UniversityShiheziXinjiang832000China
- National Key Laboratory of Crop Genetic ImprovementCollege of Plant Science and TechnologyHuazhong Agricultural UniversityWuhanHubei430070China
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7
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Koropoulis A, Alachiotis N, Pavlidis P. Detecting Positive Selection in Populations Using Genetic Data. Methods Mol Biol 2020; 2090:87-123. [PMID: 31975165 DOI: 10.1007/978-1-0716-0199-0_5] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
High-throughput genomic sequencing allows to disentangle the evolutionary forces acting in populations. Among evolutionary forces, positive selection has received a lot of attention because it is related to the adaptation of populations in their environments, both biotic and abiotic. Positive selection, also known as Darwinian selection, occurs when an allele is favored by natural selection. The frequency of the favored allele increases in the population and, due to genetic hitchhiking, neighboring linked variation diminishes, creating so-called selective sweeps. Such a process leaves traces in genomes that can be detected in a future time point. Detecting traces of positive selection in genomes is achieved by searching for signatures introduced by selective sweeps, such as regions of reduced variation, a specific shift of the site frequency spectrum, and particular linkage disequilibrium (LD) patterns in the region. A variety of approaches can be used for detecting selective sweeps, ranging from simple implementations that compute summary statistics to more advanced statistical approaches, e.g., Bayesian approaches, maximum-likelihood-based methods, and machine learning methods. In this chapter, we discuss selective sweep detection methodologies on the basis of their capacity to analyze whole genomes or just subgenomic regions, and on the specific polymorphism patterns they exploit as selective sweep signatures. We also summarize the results of comparisons among five open-source software releases (SweeD, SweepFinder, SweepFinder2, OmegaPlus, and RAiSD) regarding sensitivity, specificity, and execution times. Furthermore, we test and discuss machine learning methods and present a thorough performance analysis. In equilibrium neutral models or mild bottlenecks, most methods are able to detect selective sweeps accurately. Methods and tools that rely on linkage disequilibrium (LD) rather than single SNPs exhibit higher true positive rates than the site frequency spectrum (SFS)-based methods under the model of a single sweep or recurrent hitchhiking. However, their false positive rate is elevated when a misspecified demographic model is used to build the distribution of the statistic under the null hypothesis. Both LD and SFS-based approaches suffer from decreased accuracy on localizing the true target of selection in bottleneck scenarios. Furthermore, we present an extensive analysis of the effects of gene flow on selective sweep detection, a problem that has been understudied in selective sweep literature.
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Affiliation(s)
- Angelos Koropoulis
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece
- Computer Science Department, University of Crete, Crete, Heraklion, Greece
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology Hellas, Heraklion, Greece.
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8
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Zhang X, Huang N, Mo L, Lv M, Gao Y, Wang J, Liu C, Yin S, Zhou J, Xiao N, Pan C, Xu Y, Dong G, Yang Z, Li A, Huang J, Wang Y, Yao Y. Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation. Int J Mol Sci 2019; 20:ijms20184358. [PMID: 31491955 PMCID: PMC6769861 DOI: 10.3390/ijms20184358] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 09/01/2019] [Accepted: 09/03/2019] [Indexed: 02/02/2023] Open
Abstract
Japonica and indica are two important subspecies in cultivated Asian rice. Irradiation is a classical approach to induce mutations and create novel germplasm. However, little is known about the differential response between japonica and indica rice after γ radiation. Here, we utilized the RNA sequencing and Weighted Gene Co-expression Network Analysis (WGCNA) to compare the transcriptome differences between japonica Nipponbare (NPB) and indica Yangdao6 (YD6) in response to irradiation. Japonica subspecies are more sensitive to irradiation than the indica subspecies. Indica showed a higher seedling survival rate than japonica. Irradiation caused more extensive DNA damage in shoots than in roots, and the severity was higher in NPB than in YD6. GO and KEGG pathway analyses indicate that the core genes related to DNA repair and replication and cell proliferation are similarly regulated between the varieties, however the universal stress responsive genes show contrasting differential response patterns in japonica and indica. WGCNA identifies 37 co-expressing gene modules and ten candidate hub genes for each module. This provides novel evidence indicating that certain peripheral pathways may dominate the molecular networks in irradiation survival and suggests more potential target genes in breeding for universal stress tolerance in rice.
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Affiliation(s)
- Xiaoxiang Zhang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225007, China
| | - Niansheng Huang
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225007, China
| | - Lanjing Mo
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Minjia Lv
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yingbo Gao
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Junpeng Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Chang Liu
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Shuangyi Yin
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Juan Zhou
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Ning Xiao
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225007, China
| | - Cunhong Pan
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225007, China
| | - Yabin Xu
- Yangzhou Irradiation Center, Yangzhou 225007, China
| | - Guichun Dong
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Zefeng Yang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Aihong Li
- Lixiahe Agricultural Research Institute of Jiangsu Province, Yangzhou 225007, China
| | - Jianye Huang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China
| | - Yulong Wang
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
| | - Youli Yao
- Jiangsu Key Laboratory of Crop Genetics and Physiology/Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou 225009, China.
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9
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Chen X, Tian X, Xue L, Zhang X, Yang S, Traw MB, Huang J. CRISPR-Based Assessment of Gene Specialization in the Gibberellin Metabolic Pathway in Rice. PLANT PHYSIOLOGY 2019; 180:2091-2105. [PMID: 31160507 PMCID: PMC6670093 DOI: 10.1104/pp.19.00328] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/22/2019] [Indexed: 05/21/2023]
Abstract
Gibberellin (GA) functions as an essential natural regulator of growth and development in plants. For each step of the GA metabolic pathway, different copy numbers can be found in different species, as is the case with the 13 genes across four enzymatic steps in rice (Oryza sativa). A common view is that such gene duplication creates homologs that buffer organisms against loss-of-function (LOF) mutations. Therefore, knockouts of any single homolog might be expected to have little effect. To test this question, we generated clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) knockouts for these homologs and measured effects on growth and reproduction. Surprisingly, we report here that there is consistently one or more essential gene at each enzymatic step, for which LOF mutation induces death or sterility-suggesting that the GA pathway does not have a redundancy route and that each gene family is essential for GA metabolism. In most of these genes from the same gene family, we observed defects in plant height and infertility, suggesting that the duplicated members retain functions related to GA synthesis or degradation. We identified both subfunctionalization of the three recently diversified homologs OsKO1, OsKO2, and OsKO5 and neofunctionalization in OsKO3 and OsKO4 Thus, although the function of each step is conserved, the evolution of duplicates in that step is diversified. Interestingly, the CRISPR/Cas9 lines at the SD1 locus were typically sterile, whereas the natural sd1 mutants, related to the "Green Revolution" in rice, show normal setting rates. Collectively, our results identify candidates for control of GA production and provide insight into the evolution of four critical gene families in plants.
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Affiliation(s)
- Xiao Chen
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xuejian Tian
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Lan Xue
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - M Brian Traw
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Ju Huang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
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Jiang M, Hu H, Kai J, Traw MB, Yang S, Zhang X. Different knockout genotypes of OsIAA23 in rice using CRISPR/Cas9 generating different phenotypes. PLANT MOLECULAR BIOLOGY 2019; 100:467-479. [PMID: 31004275 PMCID: PMC6586719 DOI: 10.1007/s11103-019-00871-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 04/11/2019] [Indexed: 05/07/2023]
Abstract
We have isolated several Osiaa23 rice mutants with different knockout genotypes, resulting in different phenotypes, which suggested that different genetic backgrounds or mutation types influence gene function. The Auxin/Indole-3-Acetic Acid (Aux/IAA) gene family performs critical roles in auxin signal transduction in plants. In rice, the gene OsIAA23 (Os06t0597000) is known to affect development of roots and shoots, but previous knockouts in OsIAA23 have been sterile and difficult for research continuously. Here, we isolate new Osiaa23 mutants using the CRISPR/Cas9 system in japonica (Wuyunjing24) and indica (Kasalath) rice, with extensive genome re-sequencing to confirm the absence of off-target effects. In Kasalath, mutants with a 13-amino acid deletion showed profoundly greater dwarfing, lateral root developmental disorder, and fertility deficiency, relative to mutants with a single amino acid deletion, demonstrating that those 13 amino acids in Kasalath are essential to gene function. In Wuyunjing24, we predicted that mutants with a single base-pair frameshift insertion would experience premature termination and strong phenotypic defects, but instead these lines exhibited negligible phenotypic difference and normal fertility. Through RNA-seq, we show here that new mosaic transcripts of OsIAA23 were produced de novo, which circumvented the premature termination and thereby preserved the wild-type phenotype. This finding is a notable demonstration in plants that mutants can mask loss of function CRISPR/Cas9 editing of the target gene through de novo changes in alternative splicing.
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Affiliation(s)
- Mengmeng Jiang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Huaying Hu
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Jing Kai
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Milton Brian Traw
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China
| | - Sihai Yang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
| | - Xiaohui Zhang
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, 210023, China.
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Ndjiondjop MN, Alachiotis N, Pavlidis P, Goungoulou A, Kpeki SB, Zhao D, Semagn K. Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2019; 132:1145-1158. [PMID: 30578434 PMCID: PMC6449321 DOI: 10.1007/s00122-018-3268-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 12/11/2018] [Indexed: 05/20/2023]
Abstract
The extent of molecular diversity parameters across three rice species was compared using large germplasm collection genotyped with genomewide SNPs and SNPs that fell within selective sweep regions. Previous studies conducted on limited number of accessions have reported very low genetic variation in African rice (Oryza glaberrima Steud.) as compared to its wild progenitor (O. barthii A. Chev.) and to Asian rice (O. sativa L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and O. barthii (115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of O. barthii, respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1-32.1 and 16.3-37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10-4, which is not only 20-fold smaller than the value estimated from all genomewide SNPs (π = 1.6 × 10-2), but also accounted for just 4.1%, 0.9% and 2.1% of that of O. barthii, lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use.
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Affiliation(s)
- Marie Noelle Ndjiondjop
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
| | - Nikolaos Alachiotis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas, Nikolaou Plastira 100, 70013, Heraklion, Crete, Greece
| | - Alphonse Goungoulou
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Sèdjro Bienvenu Kpeki
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Dule Zhao
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire
| | - Kassa Semagn
- M'bé Research Station, Africa Rice Center (AfricaRice), 01 B.P. 2551, Bouaké 01, Côte d'Ivoire.
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Zhang Y, Li S, Xue S, Yang S, Huang J, Wang L. Phylogenetic and CRISPR/Cas9 Studies in Deciphering the Evolutionary Trajectory and Phenotypic Impacts of Rice ERECTA Genes. FRONTIERS IN PLANT SCIENCE 2018; 9:473. [PMID: 29692796 PMCID: PMC5902711 DOI: 10.3389/fpls.2018.00473] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Accepted: 03/26/2018] [Indexed: 05/03/2023]
Abstract
The ERECTA family genes (ERfs) have been found to play diverse functions in Arabidopsis, including controlling cell proliferation and cell growth, regulating stomata patterning, and responding to various stresses. This wide range of functions has rendered them as a potential candidate for crop improvement. However, information on their functional roles, particularly their morphological impact, in crop genomes, such as rice, is limited. Here, through evolutionary prediction, we first depict the evolutionary trajectory of the ER family, and show that the ER family is actually highly conserved across different species, suggesting that most of their functions may also be observed in other plant species. We then take advantage of the CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats-associated nuclease 9) system to assess their morphological impact on one of the most important crops, rice. Loss-of-function mutants of OsER1 and OsER2 display shortened plant stature and reduced panicle size, suggesting they possibly also functioned in regulating cell proliferation and cell growth in rice. In addition to functions similar to that in Arabidopsis, we also find clues that rice ERfs may play unique functional roles. The OsER2 displayed more severe phenotypic changes than OsER1, indicating putative differentiation in their functions. The OsERL might be of essential in its function, and the proper function of all three rice ER genes might be dependent of their genetic background. Future investigations relating to these functions are key to exploiting ERfs in crop development.
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Affiliation(s)
| | | | | | | | - Ju Huang
- *Correspondence: Ju Huang, Long Wang,
| | - Long Wang
- *Correspondence: Ju Huang, Long Wang,
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