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Cui LY, Liu BY, Li HM, Zhu YX, Zhou YH, Su C, Tian YP, Xu HT, Liu D, Li XP, Ma Y, Jiang GS, Liu H, Yang SH, Lan TM, Xu YC. A simple and effective method to enrich endogenous DNA from mammalian faeces. Mol Ecol Resour 2024; 24:e13939. [PMID: 38372463 DOI: 10.1111/1755-0998.13939] [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: 11/01/2023] [Revised: 02/06/2024] [Accepted: 02/09/2024] [Indexed: 02/20/2024]
Abstract
Utilization of faeces has long been a popular approach for genetic and ecological studies of wildlife. However, the success of molecular marker genotyping and genome resequencing is often unpredictable due to insufficient enrichment of endogenous DNA in the total faecal DNA that is dominated by bacterial DNA. Here, we report a simple and cheap method named PEERS to predominantly lyse animal cells over bacteria by using sodium dodecyl sulphate so as to discharge endogenous DNA into liquid phase before bacterial DNA. By brief centrifugation, total DNA with enriched endogenous fraction can be extracted from the supernatant using routine methods. Our assessments showed that the endogenous DNA extracted by PEERS was significantly enriched for various types of faeces from different species, preservation time and conditions. It significantly improves the genotyping correctness and efficiency of genome resequencing with the total additional cost of $ 0.1 and a short incubation step to treat a faecal sample. We also provide methods to assess the enrichment efficiency of mitochondrial and nuclear DNA and models to predict the usability of faecal DNA for genotyping of short tandem repeat, single-nucleotide polymorphism and whole-genome resequencing.
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Affiliation(s)
- Liang Yu Cui
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin, China
| | - Bo Yang Liu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin, China
| | - Hai Meng Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yi Xin Zhu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yong Heng Zhou
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin, China
| | - Chang Su
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin, China
| | - Yin Ping Tian
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin, China
| | - Hai Tao Xu
- Heilongjiang Siberian Tiger Park, Harbin, China
| | - Dan Liu
- Heilongjiang Siberian Tiger Park, Harbin, China
| | - Xiao Ping Li
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
| | - Yue Ma
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
| | - Guang Shun Jiang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
- National Forestry and Grassland Administration Feline Research Center, Harbin, China
| | - Huan Liu
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
| | - Shu Hui Yang
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
| | - Tian Ming Lan
- State Key Laboratory of Agricultural Genomics, BGI-Shenzhen, Shenzhen, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
| | - Yan Chun Xu
- College of Wildlife and Protected Area, Northeast Forestry University, Harbin, China
- National Forestry and Grassland Administration Research Center of Engineering Technology for Wildlife Conservation and Utilization, Harbin, China
- BGI Life Science Joint Research Center, Northeast Forestry University, Harbin, China
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Lin X, Feng M, Li Y, Liu Y, Wang M, Li Y, Yang T, Zhao C. Study on the origin of the Baise horse based on whole- genome resequencing. Anim Genet 2024. [PMID: 38584302 DOI: 10.1111/age.13424] [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: 09/09/2023] [Revised: 03/09/2024] [Accepted: 03/20/2024] [Indexed: 04/09/2024]
Abstract
The Baise horse, an indigenous horse breed mainly distributed in the Baise region of Guangxi province in southwest China, has a long history as draft animal. However, there is a lack of research regarding the origin and ancestral composition of the Baise horse. In this study, whole-genome resequencing data from 236 horses of seven Chinese indigenous horse breeds, five foreign horse breeds, and four Przewalski's horses were used to investigate the relationships between the Baise horse and other horse breeds. The results showed that foreign horse breeds had no significant impact on the formation of the Baise horse. The two southwestern horse populations, the Debao pony and the Jinjiang horse, exhibit the closest genetic affinity with the Baise horse. This is consistent with their adjacent geographical distribution. Analysis of the migration route revealed a gene flow from the Chakouyi horse into the Baise horse. In summary, our results confirm that the formation of the Baise horse did not involve participation from foreign breeds. Geographical distance emerges as a crucial factor in determining the genetic relationships with the Baise horse. Gene flows of indigenous horse breeds along ancient routes of trade activities had played a role in the formation of the Baise horse.
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Affiliation(s)
- Xiaoran Lin
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- Beijing General Station of Animal Husbandry, Beijing, China
| | - Mo Feng
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ying Li
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yu Liu
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Min Wang
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yuanyuan Li
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Tao Yang
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Chunjiang Zhao
- Equine Center, China Agricultural University, Beijing, China
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- National Engineering Laboratory for Animal Breeding, Beijing, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Beijing, China
- Beijing Key Laboratory of Animal Genetic Improvement, Beijing, China
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Jeffery NW, Vercaemer B, Stanley RRE, Kess T, Dufresne F, Noisette F, O'Connor MI, Wong MC. Variation in genomic vulnerability to climate change across temperate populations of eelgrass ( Zostera marina). Evol Appl 2024; 17:e13671. [PMID: 38650965 PMCID: PMC11033490 DOI: 10.1111/eva.13671] [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: 01/20/2023] [Revised: 02/05/2024] [Accepted: 02/07/2024] [Indexed: 04/25/2024] Open
Abstract
A global decline in seagrass populations has led to renewed calls for their conservation as important providers of biogenic and foraging habitat, shoreline stabilization and carbon storage. Eelgrass (Zostera marina) occupies the largest geographic range among seagrass species spanning a commensurately broad spectrum of environmental conditions. In Canada, eelgrass is managed as a single phylogroup despite occurring across three oceans and a range of ocean temperatures and salinity gradients. Previous research has focused on applying relatively few markers to reveal population structure of eelgrass, whereas a whole-genome approach is warranted to investigate cryptic structure among populations inhabiting different ocean basins and localized environmental conditions. We used a pooled whole-genome re-sequencing approach to characterize population structure, gene flow and environmental associations of 23 eelgrass populations ranging from the Northeast United States to Atlantic, subarctic and Pacific Canada. We identified over 500,000 SNPs, which when mapped to a chromosome-level genome assembly revealed six broad clades of eelgrass across the study area, with pairwise F ST ranging from 0 among neighbouring populations to 0.54 between Pacific and Atlantic coasts. Genetic diversity was highest in the Pacific and lowest in the subarctic, consistent with colonization of the Arctic and Atlantic oceans from the Pacific less than 300 kya. Using redundancy analyses and two climate change projection scenarios, we found that subarctic populations are predicted to be potentially more vulnerable to climate change through genomic offset predictions. Conservation planning in Canada should thus ensure that representative populations from each identified clade are included within a national network so that latent genetic diversity is protected, and gene flow is maintained. Northern populations, in particular, may require additional mitigation measures given their potential susceptibility to a rapidly changing climate.
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Affiliation(s)
- Nicholas W. Jeffery
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Benedikte Vercaemer
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Ryan R. E. Stanley
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
| | - Tony Kess
- Fisheries and Oceans Canada, Northwest Atlantic Fisheries CentreSt. John'sNewfoundland and LabradorCanada
| | - France Dufresne
- Département de BiologieUniversité du Québec à RimouskiRimouskiQuebecCanada
| | - Fanny Noisette
- Institut des Sciences de la mer, Université du Québec à RimouskiRimouskiQuebecCanada
| | - Mary I. O'Connor
- Department of Zoology and Biodiversity Research CentreUniversity of British ColumbiaVancouverBritish ColumbiaCanada
| | - Melisa C. Wong
- Fisheries and Oceans CanadaBedford Institute of OceanographyDartmouthNova ScotiaCanada
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Estravis Barcala M, van der Valk T, Chen Z, Funda T, Chaudhary R, Klingberg A, Fundova I, Suontama M, Hallingbäck H, Bernhardsson C, Nystedt B, Ingvarsson PK, Sherwood E, Street N, Gyllensten U, Nilsson O, Wu HX. Whole- genome resequencing facilitates the development of a 50K single nucleotide polymorphism genotyping array for Scots pine (Pinus sylvestris L.) and its transferability to other pine species. Plant J 2024; 117:944-955. [PMID: 37947292 DOI: 10.1111/tpj.16535] [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] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/12/2023]
Abstract
Scots pine (Pinus sylvestris L.) is one of the most widespread and economically important conifer species in the world. Applications like genomic selection and association studies, which could help accelerate breeding cycles, are challenging in Scots pine because of its large and repetitive genome. For this reason, genotyping tools for conifer species, and in particular for Scots pine, are commonly based on transcribed regions of the genome. In this article, we present the Axiom Psyl50K array, the first single nucleotide polymorphism (SNP) genotyping array for Scots pine based on whole-genome resequencing, that represents both genic and intergenic regions. This array was designed following a two-step procedure: first, 192 trees were sequenced, and a 430K SNP screening array was constructed. Then, 480 samples, including haploid megagametophytes, full-sib family trios, breeding population, and range-wide individuals from across Eurasia were genotyped with the screening array. The best 50K SNPs were selected based on quality, replicability, distribution across the draft genome assembly, balance between genic and intergenic regions, and genotype-environment and genotype-phenotype associations. Of the final 49 877 probes tiled in the array, 20 372 (40.84%) occur inside gene models, while the rest lie in intergenic regions. We also show that the Psyl50K array can yield enough high-confidence SNPs for genetic studies in pine species from North America and Eurasia. This new genotyping tool will be a valuable resource for high-throughput fundamental and applied research of Scots pine and other pine species.
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Affiliation(s)
- Maximiliano Estravis Barcala
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Tom van der Valk
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Zhiqiang Chen
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Tomas Funda
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Rajiv Chaudhary
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Adam Klingberg
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, Umeå, Sweden
- Skogforsk, Sävar, Uppsala, Sweden
| | - Irena Fundova
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, Umeå, Sweden
| | | | | | - Carolina Bernhardsson
- Department of Organismal Biology, Human Evolution, Uppsala University, Uppsala, Sweden
- Department of Plant Biology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Björn Nystedt
- Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Pär K Ingvarsson
- Department of Plant Biology, Linnean Centre for Plant Biology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ellen Sherwood
- Department of Biochemistry and Biophysics, Science for Life Laboratory, Stockholm University, Stockholm, Sweden
- Department of Gene Technology, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Nathaniel Street
- Department of Plant Physiology, Umeå Plant Science Centre (UPSC), Umeå University, Umeå, Sweden
| | - Ulf Gyllensten
- Department of Immunology, Genetics, and Pathology, Biomedical Center, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ove Nilsson
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, Umeå, Sweden
| | - Harry X Wu
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre (UPSC), Swedish University of Agricultural Sciences, Umeå, Sweden
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Zhang S, Song F, Wang J, Li X, Zhang Y, Zhou W, Xu L. Gut microbiota facilitate adaptation of invasive moths to new host plants. ISME J 2024; 18:wrae031. [PMID: 38423525 PMCID: PMC10980833 DOI: 10.1093/ismejo/wrae031] [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] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/23/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Gut microbiota are important in the adaptation of phytophagous insects to their plant hosts. However, the interaction between gut microbiomes and pioneering populations of invasive insects during their adaptation to new hosts, particularly in the initial phases of invasion, has been less studied. We studied the contribution of the gut microbiome to host adaptation in the globally recognized invasive pest, Hyphantria cunea, as it expands its range into southern China. The southern population of H. cunea shows effective adaptation to Metasequoia glyptostroboides and exhibits greater larval survival on Metasequoia than the original population. Genome resequencing revealed no significant differences in functions related to host adaptation between the two populations. The compatibility between southern H. cunea populations and M. glyptostroboides revealed a correlation between the abundance of several gut bacteria genera (Bacteroides, Blautia, and Coprococcus) and H. cunea survival. Transplanting the larval gut microbiome from southern to northern populations enhanced the adaptability of the latter to the previously unsuitable plant M. glyptostroboides. This research provides evidence that the gut microbiome of pioneering populations can enhance the compatibility of invasive pests to new hosts and enable more rapid adaptation to new habitats.
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Affiliation(s)
- Shouke Zhang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Feng Song
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Jie Wang
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Hangzhou 311300, China
| | - Xiayu Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yuxin Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Wenwu Zhou
- Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests & Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Insect Science, Zhejiang University, Hangzhou 310058, China
| | - Letian Xu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan 430062, China
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Zeng Z, Gu J, Lin S, Li Q, Wang W, Guo Y. Molecular basis of the phenotypic variants arising from a Pseudoalteromonas lipolytica mutator. Microb Genom 2023; 9:001118. [PMID: 37850970 PMCID: PMC10634453 DOI: 10.1099/mgen.0.001118] [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: 06/29/2023] [Accepted: 10/04/2023] [Indexed: 10/19/2023] Open
Abstract
Bacterial deficiencies in the DNA repair system can produce mutator strains that promote adaptive microevolution. However, the role of mutator strains in marine Pseudoalteromonas, capable of generating various gain-of-function genetic variants within biofilms, remains largely unknown. In this study, inactivation of mutS in Pseudoalteromonas lipolytica conferred an approximately 100-fold increased resistance to various antibiotics, including ciprofloxacin, rifampicin and aminoglycoside. Furthermore, the mutator of P. lipolytica generated variants that displayed enhanced biofilm formation but reduced swimming motility, indicating a high phenotypic diversity within the ΔmutS population. Additionally, we observed a significant production rate of approximately 50 % for the translucent variants, which play important roles in biofilm formation, when the ΔmutS strain was cultured on agar plates or under shaking conditions. Using whole-genome deep-sequencing combined with genetic manipulation, we demonstrated that point mutations in AT00_17115 within the capsular biosynthesis cluster were responsible for the generation of translucent variants in the ΔmutS subpopulation, while mutations in flagellar genes fliI and flgP led to a decrease in swimming motility. Collectively, this study reveals a specific mutator-driven evolution in P. lipolytica, characterized by substantial genetic and phenotypic diversification, thereby offering a reservoir of genetic attributes associated with microbial fitness.
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Affiliation(s)
- Zhenshun Zeng
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, PR China
| | - Jiayu Gu
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Shituan Lin
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Qian Li
- Key Laboratory for Water Quality and Conservation of the Pearl River Delta, Ministry of Education, School of Environmental Science and Engineering, Guangzhou University, Guangzhou, PR China
| | - Weiquan Wang
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Yuexue Guo
- Key Laboratory of Tropical Marine Bio-Resources and Ecology, Guangdong Key Laboratory of Marine Materia Medica, RNAM Center for Marine Microbiology, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
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Sun Z, Lu Z, Xiao T, Chen Y, Fu P, Lu K, Gui F. Genome-Wide Scanning Loci and Differentially Expressed Gene Analysis Unveils the Molecular Mechanism of Chlorantraniliprole Resistance in Spodoptera frugiperda. J Agric Food Chem 2023; 71:14092-14107. [PMID: 37699662 DOI: 10.1021/acs.jafc.3c04228] [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] [Indexed: 09/14/2023]
Abstract
Chlorantraniliprole has been widely used to controlSpodoptera frugiperda, but it has led to the development of chlorantraniliprole resistance. Multiomics analysis of strains with two extreme traits helps to elucidate the complex mechanisms involved. Herein, following genome resequencing and application of the Euclidean distance algorithm, 550 genes within a 16.20-Mb-linked region were identified from chlorantraniliprole-resistant (Ch-R) and chlorantraniliprole-susceptible (Ch-Sus) strains. Using transcriptome sequencing, 2066 differentially expressed genes were identified between Ch-R and Ch-Sus strains. Through association analysis, three glutathione S-transferase family genes and four trehalose transporter genes were selected for functional verification. Notably, SfGSTD1 had the strongest binding ability with chlorantraniliprole and is responsible for chlorantraniliprole tolerance. The Ch-R strain also increased the intracellular trehalose content by upregulating the transcription of SfTret1, thereby contributing to chlorantraniliprole resistance. These findings provide a new perspective to reveal the mechanism of resistance of agricultural pests to insecticides.
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Affiliation(s)
- Zhongxiang Sun
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Zhihui Lu
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Tianxiang Xiao
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Yaping Chen
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Pengfei Fu
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
| | - Kai Lu
- Anhui Province Key Laboratory of Crop Integrated Pest Management, Anhui Province Engineering Laboratory for Green Pesticide Development and Application, School of Plant Protection, Anhui Agricultural University, Hefei 230036, China
| | - Furong Gui
- State Key Laboratory of Conservation and Utilization of Biological Resources of Yunnan, College of Plant Protection, Yunnan Agricultural University, Kunming 650201, China
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8
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Masonick P, Meyer A, Hulsey CD. A kiss of deep homology: partial convergence in the genomic basis of hypertrophied lips in cichlid fish and human cleft lip. Genome Biol Evol 2023; 15:7151268. [PMID: 37140021 DOI: 10.1093/gbe/evad072] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 04/06/2023] [Accepted: 04/24/2023] [Indexed: 05/05/2023] Open
Abstract
The genomic loci generating both adaptive and maladaptive variation could be surprisingly predictable in deeply homologous vertebrate structures like lips. Variation in highly conserved vertebrate traits such as jaws and teeth in organisms as evolutionarily disparate as teleost fishes and mammals are known to be structured by the same genes. Likewise, hypertrophied lips that have evolved repeatedly in Neotropical and African cichlid fish lineages could share unexpectedly similar genetic bases themselves and even provide surprising insight into the loci underlying human craniofacial anomalies. To isolate the genomic regions underlying adaptive divergence in hypertrophied lips, we first employed genome wide associations (GWA) in several species of African cichlids from Lake Malawi. Then, we tested if these GWA regions were shared through hybridization with another Lake Malawi cichlid lineage that has evolved hypertrophied lips seemingly in parallel. Overall, introgression among hypertrophied lip lineages appeared limited. Among our Malawi GWA regions, one contained the gene kcnj16 that has been implicated in the convergently evolved hypertrophied lips in Central American Midas cichlids that diverged from the Malawi radiation over 50 million years ago. The Malawi hypertrophied lip GWA regions also contained several additional genes that cause human lip-associated birth defects. Cichlid fishes are becoming prominent examples of replicated genomic architecture underlying trait convergence and are increasingly providing insight into human craniofacial anomalies such as cleft lip.
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Affiliation(s)
- Paul Masonick
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - Axel Meyer
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
| | - C Darrin Hulsey
- Department of Biology, University of Konstanz, Universitätsstraße 10, 78464 Konstanz, Germany
- School of Biology and Environmental Science, University College Dublin, Belfield, Dublin 4, Ireland
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9
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Yang W, Han H, Guo B, Qi K, Zhang J, Zhou S, Yang X, Li X, Lu Y, Liu W, Liu X, Li L. The Genomic Variation and Differentially Expressed Genes on the 6P Chromosomes in Wheat- Agropyron cristatum Addition Lines 5113 and II-30-5 Confer Different Desirable Traits. Int J Mol Sci 2023; 24:ijms24087056. [PMID: 37108219 PMCID: PMC10139034 DOI: 10.3390/ijms24087056] [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: 03/04/2023] [Revised: 03/29/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Wild relatives of wheat are essential gene pools for broadening the genetic basis of wheat. Chromosome rearrangements and genomic variation in alien chromosomes are widespread. Knowledge of the genetic variation between alien homologous chromosomes is valuable for discovering and utilizing alien genes. In this study, we found that 5113 and II-30-5, two wheat-A. cristatum 6P addition lines, exhibited considerable differences in heading date, grain number per spike, and grain weight. Genome resequencing and transcriptome analysis revealed significant differences in the 6P chromosomes of the two addition lines, including 143,511 single-nucleotide polymorphisms, 62,103 insertion/deletion polymorphisms, and 757 differentially expressed genes. Intriguingly, genomic variations were mainly distributed in the middle of the chromosome arms and the proximal centromere region. GO and KEGG analyses of the variant genes and differentially expressed genes showed the enrichment of genes involved in the circadian rhythm, carbon metabolism, carbon fixation, and lipid metabolism, suggesting that the differential genes on the 6P chromosome are closely related to the phenotypic differences. For example, the photosynthesis-related genes PsbA, PsbT, and YCF48 were upregulated in II-30-5 compared with 5113. ACS and FabG are related to carbon fixation and fatty acid biosynthesis, respectively, and both carried modification variations and were upregulated in 5113 relative to II-30-5. Therefore, this study provides important guidance for cloning desirable genes from alien homologous chromosomes and for their effective utilization in wheat improvement.
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Affiliation(s)
- Wenjing Yang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiming Han
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Baojin Guo
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Kai Qi
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Jinpeng Zhang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Shenghui Zhou
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xinming Yang
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiuquan Li
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yuqing Lu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Weihua Liu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xu Liu
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Lihui Li
- Key Laboratory of Grain Crop Genetic Resources Evaluation and Utilization, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
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10
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Tao X, Kong FJ, Liang Y, Yang XM, Yang YK, Zhong ZJ, Wang Y, Hu ZH, Chen XH, Gong JJ, Pang JH, Zhu KP, Wang Y, Liao K, Lv XB, He ZP, Gu YR. Screening of candidate genes related to differences in growth and development between Chinese indigenous and Western pig breeds. Physiol Genomics 2023; 55:147-153. [PMID: 36847439 DOI: 10.1152/physiolgenomics.00157.2022] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
Neijiang (NJ) and Yacha (YC) are two indigenous pig breeds in the Sichuan basin of China, displaying higher resistance to diseases, lower lean ratio, and slower growth rate than the commercial Western pig breed Yorkshire (YS). The molecular mechanisms underlying the differences in growth and development between these pig breeds are still unknown. In the present study, five pigs from NJ, YC, and YS breeds were subjected to the whole genome resequencing, and then the differential single-nucleotide polymorphisms (SNPs) were screened using a 10-kb window sliding in 1-kb step using the Fst method. Finally, 48,924, 48,543, and 46,228 nonsynonymous single-nucleotide polymorphism loci (nsSNPs) were identified between NJ and YS, NJ and YC, and YC and YS, which highly or moderately affected 2,490, 800, and 444 genes, respectively. Moreover, three nsSNPs were detected in the genes of acetyl-CoA acetyltransferase 1 (ACAT1) insulin-like growth factor 2 receptor (IGF2R), insulin-like growth factor 2 and mRNA-binding protein 3 (IGF2BP3), which potentially affected the transformation of acetyl-CoA to acetoacetyl-CoA and the normal functions of the insulin signaling pathways. Moreover, serous determinations revealed significantly lower acetyl-CoA content in YC than in YS, supporting that ACAT1 might be a reason explaining the differences in growth and development between YC and YS breeds. Contents of phosphatidylcholine (PC) and phosphatidic acid (PA) significantly differed between the pig breeds, suggesting that glycerophospholipid metabolism might be another reason for the differences between Chinese and Western pig breeds. Overall, these results might contribute basic information to understand the genetic differences determining the phenotypical traits in pigs.
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Affiliation(s)
- Xuan Tao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Fan-Jing Kong
- Luzhou Modern Agriculture Development Promotion Center, Luzhou, China
| | - Yan Liang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Xue-Mei Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Yue-Kui Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Zhi-Jun Zhong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Yan Wang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Zi-Hui Hu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Xiao-Hui Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Jian-Jun Gong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | | | - Kang-Ping Zhu
- Sichuan Dekon Livestock Foodstuff Group, Zigong, China
| | - Yong Wang
- Luzhou Agricultural and Rural Bureau, Luzhou, China
| | - Kun Liao
- Tongjiang County Animal Husbandry Station, Bazhong, China
| | - Xue-Bin Lv
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Zhi-Ping He
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
| | - Yi-Ren Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, China
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11
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Qin SY, Zuo ZY, Guo C, Du XY, Liu SY, Yu XQ, Xiang XG, Rong J, Liu B, Liu ZF, Ma PF, Li DZ. Phylogenomic insights into the origin and evolutionary history of evergreen broadleaved forests in East Asia under Cenozoic climate change. Mol Ecol 2023; 32:2850-2868. [PMID: 36847615 DOI: 10.1111/mec.16904] [Citation(s) in RCA: 2] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 02/09/2023] [Accepted: 02/23/2023] [Indexed: 03/01/2023]
Abstract
The evergreen versus deciduous leaf habit is an important functional trait for adaptation of forest trees and has been hypothesized to be related to the evolutionary processes of the component species under paleoclimatic change, and potentially reflected in the dynamic history of evergreen broadleaved forests (EBLFs) in East Asia. However, knowledge about the shift of evergreen versus deciduous leaf with the impact of paleoclimatic change using genomic data remains rare. Here, we focus on the Litsea complex (Lauraceae), a key lineage with dominant species of EBLFs, to gain insights into how evergreen versus deciduous trait shifted, providing insights into the origin and historical dynamics of EBLFs in East Asia under Cenozoic climate change. We reconstructed a robust phylogeny of the Litsea complex using genome-wide single-nucleotide variants (SNVs) with eight clades resolved. Fossil-calibrated analyses, diversification rate shifts, ancestral habit, ecological niche modelling and climate niche reconstruction were employed to estimate its origin and diversification pattern. Taking into account studies on other plant lineages dominating EBLFs of East Asia, it was revealed that the prototype of EBLFs in East Asia probably emerged in the Early Eocene (55-50 million years ago [Ma]), facilitated by the greenhouse warming. As a response to the cooling and drying climate in the Middle to Late Eocene (48-38 Ma), deciduous habits were evolved in the dominant lineages of the EBLFs in East Asia. Up to the Early Miocene (23 Ma), the prevailing of East Asian monsoon increased the extreme seasonal precipitation and accelerated the emergence of evergreen habits of the dominant lineages, and ultimately shaped the vegetation resembling that of today.
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Affiliation(s)
- Sheng-Yuan Qin
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Zheng-Yu Zuo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Cen Guo
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xin-Yu Du
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Shui-Yin Liu
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiang-Qin Yu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Xiao-Guo Xiang
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Centre for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Jun Rong
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Centre for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Bing Liu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China.,Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Zhi-Fang Liu
- Key Laboratory of Chemical Biology of Ministry of Education, School of Pharmaceutical Sciences, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Peng-Fei Ma
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - De-Zhu Li
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China.,University of Chinese Academy of Sciences, Beijing, China.,CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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12
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Dossou SSK, Song S, Liu A, Li D, Zhou R, Berhe M, Zhang Y, Sheng C, Wang Z, You J, Wang L. Resequencing of 410 Sesame Accessions Identifies SINST1 as the Major Underlying Gene for Lignans Variation. Int J Mol Sci 2023; 24:ijms24021055. [PMID: 36674569 PMCID: PMC9860558 DOI: 10.3390/ijms24021055] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Sesame is a promising oilseed crop that produces specific lignans of clinical importance. Hence, a molecular description of the regulatory mechanisms of lignan biosynthesis is essential for crop improvement. Here, we resequence 410 sesame accessions and identify 5.38 and 1.16 million SNPs (single nucleotide polymorphisms) and InDels, respectively. Population genomic analyses reveal that sesame has evolved a geographic pattern categorized into northern (NC), middle (MC), and southern (SC) groups, with potential origin in the southern region and subsequent introduction to the other regions. Selective sweeps analysis uncovers 120 and 75 significant selected genomic regions in MC and NC groups, respectively. By screening these genomic regions, we unveiled 184 common genes positively selected in these subpopulations for exploitation in sesame improvement. Genome-wide association study identifies 17 and 72 SNP loci for sesamin and sesamolin variation, respectively, and 11 candidate causative genes. The major pleiotropic SNPC/A locus for lignans variation is located in the exon of the gene SiNST1. Further analyses revealed that this locus was positively selected in higher lignan content sesame accessions, and the "C" allele is favorable for a higher accumulation of lignans. Overexpression of SiNST1C in sesame hairy roots significantly up-regulated the expression of SiMYB58, SiMYB209, SiMYB134, SiMYB276, and most of the monolignol biosynthetic genes. Consequently, the lignans content was significantly increased, and the lignin content was slightly increased. Our findings provide insights into lignans and lignin regulation in sesame and will facilitate molecular breeding of elite varieties and marker-traits association studies.
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Affiliation(s)
- Senouwa Segla Koffi Dossou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Laboratory of Plant Physiology and Biotechnologies, Faculty of Sciences, University of Lomé, Lomé 01BP 1515, Togo
| | - Shengnan Song
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Aili Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Donghua Li
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Rong Zhou
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Muez Berhe
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yanxin Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Chen Sheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Zhijian Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Jun You
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Correspondence: (J.Y.); (L.W.); Tel.: +86-18607147952 (J.Y.); +86-15926338805 (L.W.)
| | - Linhai Wang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan 430062, China
- Correspondence: (J.Y.); (L.W.); Tel.: +86-18607147952 (J.Y.); +86-15926338805 (L.W.)
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13
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Wang Y, Chen G, Zeng F, Han Z, Qiu CW, Zeng M, Yang Z, Xu F, Wu D, Deng F, Xu S, Chater C, Korol A, Shabala S, Wu F, Franks P, Nevo E, Chen ZH. Molecular evidence for adaptive evolution of drought tolerance in wild cereals. New Phytol 2023; 237:497-514. [PMID: 36266957 DOI: 10.1111/nph.18560] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [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: 08/08/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
The considerable drought tolerance of wild cereal crop progenitors has diminished during domestication in the pursuit of higher productivity. Regaining this trait in cereal crops is essential for global food security but requires novel genetic insight. Here, we assessed the molecular evidence for natural variation of drought tolerance in wild barley (Hordeum spontaneum), wild emmer wheat (Triticum dicoccoides), and Brachypodium species collected from dry and moist habitats at Evolution Canyon, Israel (ECI). We report that prevailing moist vs dry conditions have differentially shaped the stomatal and photosynthetic traits of these wild cereals in their respective habitats. We present the genomic and transcriptomic evidence accounting for differences, including co-expression gene modules, correlated with physiological traits, and selective sweeps, driven by the xeric site conditions on the African Slope (AS) at ECI. Co-expression gene module 'circadian rhythm' was linked to significant drought-induced delay in flowering time in Brachypodium stacei genotypes. African Slope-specific differentially expressed genes are important in barley drought tolerance, verified by silencing Disease-Related Nonspecific Lipid Transfer 1 (DRN1), Nonphotochemical Quenching 4 (NPQ4), and Brassinosteroid-Responsive Ring-H1 (BRH1). Our results provide new genetic information for the breeding of resilient wheat and barley in a changing global climate with increasingly frequent drought events.
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Affiliation(s)
- Yuanyuan Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Hubei Insect Resources Utilization and Sustainable Pest Management Key Laboratory, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Guang Chen
- Central Laboratory, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Fanrong Zeng
- Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Zhigang Han
- State Key Laboratory of Subtropical Silviculture, Zhejiang A&F University, Lin'an, Hangzhou, 311300, China
| | - Cheng-Wei Qiu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Meng Zeng
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Zujun Yang
- School of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, Sichuan, 611731, China
| | - Fei Xu
- Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Dezhi Wu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Fenglin Deng
- Central Laboratory, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Shengchun Xu
- Collaborative Innovation Centre for Grain Industry, College of Agriculture, Yangtze University, Jingzhou, 434025, China
| | - Caspar Chater
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Mount Carmel, 34988384, Haifa, Israel
| | - Sergey Shabala
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, TAS, 7004, Australia
- School of Biological Science, University of Western Australia, Crawley, WA, 6009, Australia
| | - Feibo Wu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Peter Franks
- School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Eviatar Nevo
- Institute of Evolution, University of Haifa, Mount Carmel, 34988384, Haifa, Israel
| | - Zhong-Hua Chen
- School of Science, Western Sydney University, Penrith, NSW, 2751, Australia
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, NSW, 2751, Australia
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14
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Del Giudice L, Bazakos C, Vassiliou MF. Study of genetic variation and its association with tensile strength among bamboo species through whole genome resequencing. Front Plant Sci 2022; 13:935751. [PMID: 35968086 PMCID: PMC9365670 DOI: 10.3389/fpls.2022.935751] [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] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/05/2022] [Indexed: 06/15/2023]
Abstract
Moso bamboo (Phyllostachys edulis) is a versatile plant species that is widely used as a construction material by many low-income countries due to the lack of major construction materials such as steel and reinforced concrete. It is also widely used in China. Bamboo is an economically sustainable material that behaves exceptionally in natural disasters such as earthquakes and it can offer viable solutions for contemporary engineering challenges. Despite bamboo's potential in the engineering sector, biological features such as its long generation time, its large genome size, and its polyploidy are constraining factors for genetic and genomic studies that potentially can assist the breeding efforts. This study re-sequenced 8 Phyllostachys species and 18 natural accessions of Ph. edulis, generating a large set of functionally annotated molecular markers (Single Nucleotide Polymorphisms (SNPs) and InDels) providing key genomic resource information. Moreover, all this genomic information was used to carry out a preliminary genome-wide association analysis and several candidate genes were identified to be correlated with a mechanical property that is of high interest to structural engineers: its tensile strength normal to its fibers (i.e., splitting).
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Affiliation(s)
- Lorenzo Del Giudice
- Chair of Seismic Design and Analysis, Institute of Structural Engineering, ETH Zurich, Zurich, Switzerland
| | - Christos Bazakos
- Chair of Seismic Design and Analysis, Institute of Structural Engineering, ETH Zurich, Zurich, Switzerland
- Institute of Plant Breeding and Genetic Resources, ELGO-Dimitra, Thessaloniki, Greece
- Joint Laboratory of Horticulture, ELGO-Dimitra, Thessaloniki, Greece
- Department of Comparative Development and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Michalis F. Vassiliou
- Chair of Seismic Design and Analysis, Institute of Structural Engineering, ETH Zurich, Zurich, Switzerland
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15
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Virrueta Herrera S, Johnson KP, Sweet AD, Ylinen E, Kunnasranta M, Nyman T. High levels of inbreeding with spatial and host-associated structure in lice of an endangered freshwater seal. Mol Ecol 2022; 31:4593-4606. [PMID: 35726520 PMCID: PMC9544963 DOI: 10.1111/mec.16569] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 05/12/2022] [Accepted: 05/20/2022] [Indexed: 02/02/2023]
Abstract
Host-specialist parasites of endangered large vertebrates are in many cases more endangered than their hosts. In particular, low host population densities and reduced among-host transmission rates are expected to lead to inbreeding within parasite infrapopulations living on single host individuals. Furthermore, spatial population structures of directly-transmitted parasites should be concordant with those of their hosts. Using population genomic approaches, we investigated inbreeding and population structure in a host-specialist seal louse (Echinophthirius horridus) infesting the Saimaa ringed seal (Phoca hispida saimensis), which is endemic to Lake Saimaa in Finland, and is one of the most endangered pinnipeds in the world. We conducted genome resequencing of pairs of lice collected from 18 individual Saimaa ringed seals throughout the Lake Saimaa complex. Our analyses showed high genetic similarity and inbreeding between lice inhabiting the same individual seal host, indicating low among-host transmission rates. Across the lake, genetic differentiation among individual lice was correlated with their geographic distance, and assignment analyses revealed a marked break in the genetic variation of the lice in the middle of the lake, indicating substantial population structure. These findings indicate that movements of Saimaa ringed seals across the main breeding areas of the fragmented Lake Saimaa complex may in fact be more restricted than suggested by previous population-genetic analyses of the seals themselves.
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Affiliation(s)
- Stephany Virrueta Herrera
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, Illinois, USA.,Program in Ecology, Evolution, and Conservation, University of Illinois, Urbana, Illinois, USA
| | - Kevin P Johnson
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois, Champaign, Illinois, USA
| | - Andrew D Sweet
- Department of Biological Sciences, Arkansas State University, Jonesboro, Arkansas, USA
| | - Eeva Ylinen
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland
| | - Mervi Kunnasranta
- Department of Environmental and Biological Sciences, University of Eastern Finland, Joensuu, Finland.,Natural Resources Institute Finland, Joensuu, Finland
| | - Tommi Nyman
- Department of Ecosystems in the Barents Region, Svanhovd Research Station, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
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16
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Kong W, Deng X, Yang J, Zhang C, Sun T, Ji W, Zhong H, Fu X, Li Y. High-resolution bin-based linkage mapping uncovers the genetic architecture and heterosis-related loci of plant height in indica-japonica derived populations. Plant J 2022; 110:814-827. [PMID: 35165965 DOI: 10.1111/tpj.15705] [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] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 02/05/2022] [Accepted: 02/10/2022] [Indexed: 06/14/2023]
Abstract
Plant height (PH) is an important trait affecting the plant architecture, seed yield, and harvest index. However, the molecular mechanisms underlying PH heterosis remain unclear. In addition, useful PH-related genes must be urgently identified to facilitate ideal plant architecture breeding in rice (Oryza sativa L.). In the present study, to explore rice quantitative trait loci (QTLs) and heterosis-related loci of PH in rice, we developed a high-generation (>F15 ) population of 272 recombinant inbred lines (RIL) from a cross of two elite varieties, Luohui 9 (indica/xian) × RPY geng (japonica/geng), and two testcross hybrid populations derived from the crosses of RILs and two cytoplasmic male sterile lines (YTA [indica] and Z7A [japonica]). Using deep resequencing data, a high-density genetic map containing 4758 bin markers was constructed, with a total map distance of 2356.41 cM. Finally, 31 PH-related QTLs for different PH component lengths or tiller numbers across five seasons were identified. Two major environment-specific PH QTLs were stably detected in Hainan (qPH-3.1) or Hubei (qPH-5.1), which have undergone significant functional alterations in rice with changes in geographical environment. Based on comparative genomics, gene function annotation, homolog identification, and existing literature (pioneering studies), candidate genes for multiple QTLs were fine-mapped, and the candidate genes qPH-3.1 and qPH-5.1 for PH were further validated using CRISPR-Cas9 gene editing. Specifically, qPH-3.1 was characterized as a pleiotropic gene, and the qPH-3.1 knockout line showed reduced PH, delayed heading, a decreased seed setting rate, and increased tiller numbers. Importantly, 10 PH heterosis-related QTLs were identified in the testcross populations, and a better-parent heterosis locus (qBPH-5.2) completely covered qPH-5.1. Furthermore, the cross results of fixed-genotype RILs verified the dominant effects of qPH-3.1 and qPH-5.1. Together, these findings further our understanding of the genetic mechanisms of PH and offer multiple highly reliable gene targets for breeding rice varieties with ideal architecture and high yield potential in the immediate future.
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Affiliation(s)
- Weilong Kong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
| | - Xiaoxiao Deng
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jing Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Chenhao Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Tong Sun
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Wenjie Ji
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Hua Zhong
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Xiaopeng Fu
- Key Laboratory of Horticultural Plant Biology, Ministry of Education, College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yangsheng Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, 430072, China
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17
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Han W, Zhao J, Deng X, Gu A, Li D, Wang Y, Lu X, Zu Q, Chen Q, Chen Q, Zhang J, Qu Y. Quantitative Trait Locus Mapping and Identification of Candidate Genes for Resistance to Fusarium Wilt Race 7 Using a Resequencing-Based High Density Genetic Bin Map in a Recombinant Inbred Line Population of Gossypium barbadense. Front Plant Sci 2022; 13:815643. [PMID: 35371113 PMCID: PMC8965654 DOI: 10.3389/fpls.2022.815643] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 01/10/2022] [Indexed: 05/16/2023]
Abstract
Fusarium wilt caused by Fusarium oxysporum f. sp. vasinfectum (FOV) is one of the most destructive diseases in cotton (Gossypium spp.) production, and use of resistant cultivars is the most cost-effective method managing the disease. To understand the genetic basis of cotton resistance to FOV race 7 (FOV7), this study evaluated a recombinant inbred line (RIL) population of 110 lines of G. barbadense from a cross between susceptible Xinhai 14 and resistant 06-146 in eight tests and constructed a high-density genetic linkage map with resequencing-based 933,845 single-nucleotide polymorphism (SNP) markers covering a total genetic distance of 2483.17 cM. Nine quantitative trait loci (QTLs) for FOV7 resistance were identified, including qFOV7-D03-1 on chromosome D03 in two tests. Through a comparative analysis of gene expression and DNA sequence for predicted genes within the QTL region between the two parents and selected lines inoculated with FOV7, GB_D03G0217 encoding for a calmodulin (CaM)-like (CML) protein was identified as a candidate gene. A further analysis confirmed that the expression of GB_D03G0217 was suppressed, leading to increased disease severity in plants of the resistant parent with virus induced gene silencing (VIGS).
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Affiliation(s)
- Wanli Han
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Jieyin Zhao
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Xiaojuan Deng
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Aixing Gu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Duolu Li
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Yuxiang Wang
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Xiaoshuang Lu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Qianli Zu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Qin Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Quanjia Chen
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
| | - Jinfa Zhang
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM, United States
| | - Yanying Qu
- Engineering Research Centre of Cotton, Ministry of Education/College of Agriculture, Xinjiang Agricultural University, Ürümqi, China
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18
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Chen S, Milne R, Zhou R, Meng K, Yin Q, Guo W, Ma Y, Mao K, Xu K, Kim YD, Do TV, Liao W, Fan Q. When tropical and subtropical congeners met: Multiple ancient hybridization events within Eriobotrya in the Yunnan-Guizhou Plateau, a tropical-subtropical transition area in China. Mol Ecol 2021; 31:1543-1561. [PMID: 34910340 DOI: 10.1111/mec.16325] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 01/09/2023]
Abstract
Global climate changes during the Miocene may have created ample opportunities for hybridization between members of tropical and subtropical biomes at the boundary between these zones. Yet, very few studies have explored this possibility. The Yunnan-Guizhou Plateau (YGP) in Southwest China is a biodiversity hotspot for vascular plants, located in a transitional area between the floristic regions of tropical Southeast Asia and subtropical East Asia. The genus Eriobotrya (Rosaceae) comprises both tropical and subtropical taxa, with 12 species recorded in the YGP, making it a suitable basis for testing the hypothesis of between-biome hybridization. Therefore, we surveyed the evolutionary history of Eriobotrya by examining three chloroplast regions and five nuclear genes for 817 individuals (47 populations) of 23 Eriobotrya species (including 19 populations of 12 species in the YGP), plus genome re-sequencing of 33 representative samples. We concluded that: (1) phylogenetic positions for 16 species exhibited strong cytonuclear conflicts, most probably due to ancient hybridization; (2) the YGP is a hotspot for hybridization, with 11 species showing clear evidence of chloroplast capture; and (3) Eriobotrya probably originated in tropical Asia during the Eocene. From the Miocene onwards, the intensification of the Eastern Asia monsoon and global cooling may have shifted the tropical-subtropical boundary and caused secondary contact between species, thus providing ample opportunity for hybridization and diversification of Eriobotrya, especially in the YGP. Our study highlights the significant role that paleoclimate changes probably played in driving hybridization and generating rich species diversity in climate transition zones.
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Affiliation(s)
- Sufang Chen
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Richard Milne
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, UK
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Kaikai Meng
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Qianyi Yin
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Wei Guo
- Department of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou, China
| | - Yongpeng Ma
- Kunming Botanical Garden, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Kangshan Mao
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, State Key Laboratory of Hydraulics and Mountain River Engineering, Sichuan University, Chengdu, China
| | - Kewang Xu
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Young-Dong Kim
- Department of Life Science, Multidisciplinary Genome Institute, Hallym University, Chuncheon City, South Korea
| | - Truong Van Do
- Vietnam National Museum of Nature, Vietnam Academy of Science & Technology, Hanoi, Vietnam.,Graduate University of Science and Technology, Vietnam Academy of Science & Technology, Hanoi, Vietnam
| | - Wenbo Liao
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Qiang Fan
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
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Yin X, Zhang Y, Chen Y, Wang J, Wang RRC, Fan C, Hu Z. Precise Characterization and Tracking of Stably Inherited Artificial Minichromosomes Made by Telomere-Mediated Chromosome Truncation in Brassica napus. Front Plant Sci 2021; 12:743792. [PMID: 34671377 PMCID: PMC8521072 DOI: 10.3389/fpls.2021.743792] [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] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 09/08/2021] [Indexed: 06/13/2023]
Abstract
Plant artificial minichromosomes are the next-generation technology for plant genetic engineering and represent an independent platform for expressing foreign genes and the tools for studying the structure and function of chromosomes. Minichromosomes have been successfully produced by telomere-mediated chromosome truncation in several plants. However, previous studies have primarily focused on the construction and rough characterization of minichromosomes, while the development of stably inherited minichromosomes and their precise characterization and tracking over different generations have rarely been demonstrated. In this study, a 0.35-kb direct repeat of the Arabidopsis telomeric sequence was transformed into Brassica napus to produce artificial minichromosomes, which were analyzed by multifluorescence in situ hybridization (multi-FISH), Southern hybridization, and primer extension telomere rapid amplification (PETRA). The stably inherited minichromosomes C2 and C4 were developed by crossing transgenic plants with wild-type plants and then selfing the hybrids. Notably, two truncation sites on chromosomes C2 and C4, respectively, were identified by resequencing; thus, the artificial minichromosomes were tracked over different generations with insertion site-specific PCR. This study provided two stably inherited minichromosomes in oilseed rape and describes approaches to precisely characterize the truncation position and track the minichromosomes in offspring through multi-FISH, genome resequencing, and insertion site-specific PCR.
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Affiliation(s)
- Xiangzhen Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Yingxin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Agriculture, Yangtze University, Jingzhou, China
| | - Yuhong Chen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Jingqiao Wang
- Institute of Economical Crops, Yunnan Agricultural Academy, Kunming, China
| | - Richard R.-C. Wang
- Forage and Range Research Laboratory, United States Department of Agriculture, Agricultural Research Service, Utah State University, Logan, UT, United States
| | - Chengming Fan
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Zanmin Hu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- College of Agriculture, University of Chinese Academy of Sciences, Beijing, China
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20
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Bernhardsson C, Zan Y, Chen Z, Ingvarsson PK, Wu HX. Development of a highly efficient 50K single nucleotide polymorphism genotyping array for the large and complex genome of Norway spruce (Picea abies L. Karst) by whole genome resequencing and its transferability to other spruce species. Mol Ecol Resour 2020; 21:880-896. [PMID: 33179386 PMCID: PMC7984398 DOI: 10.1111/1755-0998.13292] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/23/2020] [Accepted: 11/04/2020] [Indexed: 12/30/2022]
Abstract
Norway spruce (Picea abies L. Karst) is one of the most important forest tree species with significant economic and ecological impact in Europe. For decades, genomic and genetic studies on Norway spruce have been challenging due to the large and repetitive genome (19.6 Gb with more than 70% being repetitive). To accelerate genomic studies, including population genetics, genome‐wide association studies (GWAS) and genomic selection (GS), in Norway spruce and related species, we here report on the design and performance of a 50K single nucleotide polymorphism (SNP) genotyping array for Norway spruce. The array is developed based on whole genome resequencing (WGS), making it the first WGS‐based SNP array in any conifer species so far. After identifying SNPs using genome resequencing data from 29 trees collected in northern Europe, we adopted a two‐step approach to design the array. First, we built a 450K screening array and used this to genotype a population of 480 trees sampled from both natural and breeding populations across the Norway spruce distribution range. These samples were then used to select high‐confidence probes that were put on the final 50K array. The SNPs selected are distributed over 45,552 scaffolds from the P. abies version 1.0 genome assembly and target 19,954 unique gene models with an even coverage of the 12 linkage groups in Norway spruce. We show that the array has a 99.5% probe specificity, >98% Mendelian allelic inheritance concordance, an average sample call rate of 96.30% and an SNP call rate of 98.90% in family trios and haploid tissues. We also observed that 23,797 probes (50%) could be identified with high confidence in three other spruce species (white spruce [Picea glauca], black spruce [P. mariana] and Sitka spruce [P. sitchensis]). The high‐quality genotyping array will be a valuable resource for genetic and genomic studies in Norway spruce as well as in other conifer species of the same genus.
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Affiliation(s)
- Carolina Bernhardsson
- Department of Ecology and Environmental Science, Umeå University, Umeå, Sweden.,Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Yanjun Zan
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå, Sweden
| | - Zhiqiang Chen
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Science, Uppsala, Sweden
| | - Harry X Wu
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Science, Umeå, Sweden.,Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, China.,Black Mountain Laboratory, CSIRO National Research Collection Australia, Canberra, ACT, Australia
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21
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Liu Z, Zhu H, Zhou J, Jiang S, Wang Y, Kuang J, Ji Q, Peng J, Wang J, Gao L, Bai M, Jian J, Ke W. Resequencing of 296 cultivated and wild lotus accessions unravels its evolution and breeding history. Plant J 2020; 104:1673-1684. [PMID: 33073434 DOI: 10.1111/tpj.15029] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 04/19/2020] [Revised: 08/02/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
Lotus (family: Nelumbonaceae) are perennial aquatic plants that represent one of the most ancient basal dicots. In the present study, we resequenced 296 lotus accessions from various geographical locations and germplasms to explore their genomic diversity and population structure. This germplasm set consisted of four accessions of American wild lotus and 292 accessions of Asian lotus, which were divided into four subgroups: wild, rhizome, flower and seed. Total single nucleotide polymorphisms (SNPs) suggested that the wild lotus had the highest variant number (7 191 010). Population structure and genome diversity analysis indicated that the American wild lotus demonstrated a distant genetic relationship with the Asian lotus. Furthermore, the seed and rhizome lotus groups had not originated from a single source but rather had a more complex multisource origin. Besides that, the seed lotus showed higher genetic diversity, which might have been due to the gene flow from the flower lotus to seed lotus by artificial crossing, and the rhizome lotus showed a much lower genetic diversity than the other groups. The present study provides SNP markers for lotus genomic diversity analysis, which will be useful for guiding lotus breeding.
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Affiliation(s)
- Zhengwei Liu
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Honglian Zhu
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Juhong Zhou
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China
| | - Sanjie Jiang
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China
| | - Yun Wang
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Jing Kuang
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Qun Ji
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Jing Peng
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
| | - Jie Wang
- Genetic Engineering Research Center, School of Life Sciences, Chongqing University, Chongqing, 401331, People's Republic of China
- BGI-Agro Seed Service (Wuhan) Co Ltd, Wuhan, 430090, People's Republic of China
| | - Li Gao
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China
| | - Mingzhou Bai
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China
| | - Jianbo Jian
- BGI Genomics, BGI-Shenzhen, Shenzhen, Guangdong, 518083, People's Republic of China
| | - Weidong Ke
- Institute of Vegetable, Wuhan Academy of Agriculture Science, Hubei, 430065, People's Republic of China
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22
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Meng S, Xu Z, Xu P, Chen A, Guo Q, Zhao L, Chen X, Wen T, Zhang X, Zhang G, Ni W, Shen X. A complete set of monosomic alien addition lines developed from Gossypium anomalum in a Gossypium hirsutum background: genotypic and phenotypic characterization. Breed Sci 2020; 70:494-501. [PMID: 32968353 PMCID: PMC7495200 DOI: 10.1270/jsbbs.19146] [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] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 04/14/2020] [Indexed: 06/11/2023]
Abstract
Gossypium anomalum (B1B1) is a valuable wild resource for the genetic improvement of G. hirsutum (A1A1D1D1) in terms of fiber quality and disease and pest resistance, but the inherent difficulties in distant hybridization hinder its utilization in breeding programs. Monosomic alien addition lines (MAALs) are powerful tools for interspecific gene transfer. First, to access useful genes from G. anomalum, a fertile hexaploid from G. hirsutum × G. anomalum was obtained and then additional chromosomes were selected using SSR markers in successive backcrosses and self-crossing from BC2F1 to BC4F4. Finally, a complete set of 13 MAALs were developed. All the MAALs were confirmed by chromosome-specific anchored SSRs and genome-wide resequencing. The MAALs demonstrated abundant variation in morphological, agronomic, yield-related, and fiber quality traits. MAAL_3B had excellent fiber strength and fineness, indicating that the transmitted chromosome may carry desirable genes for the observed phenotypes. This complete set of MAALs will provide important genetic bridge material for the identification and introgression of favorable genes from G. anomalum and lay an important foundation for the genetic improvement of cotton.
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Affiliation(s)
- Shan Meng
- Key Laboratory for Cotton and Canola Research at the Lower Reach of the Yangtze River Plain, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing 210014, China
| | - Zhenzhen Xu
- Key Laboratory for Cotton and Canola Research at the Lower Reach of the Yangtze River Plain, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing 210014, China
| | - Peng Xu
- Key Laboratory for Cotton and Canola Research at the Lower Reach of the Yangtze River Plain, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing 210014, China
| | - Aimin Chen
- JOIN HOPE SEEDS Co., Ltd., Changji, Xinjiang 831100, China
| | - Qi Guo
- Key Laboratory for Cotton and Canola Research at the Lower Reach of the Yangtze River Plain, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing 210014, China
| | - Liang Zhao
- Key Laboratory for Cotton and Canola Research at the Lower Reach of the Yangtze River Plain, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing 210014, China
| | - Xianglong Chen
- Key Laboratory for Cotton and Canola Research at the Lower Reach of the Yangtze River Plain, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing 210014, China
| | - Tian Wen
- JOIN HOPE SEEDS Co., Ltd., Changji, Xinjiang 831100, China
| | - Xianggui Zhang
- Key Laboratory for Cotton and Canola Research at the Lower Reach of the Yangtze River Plain, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing 210014, China
| | - Guowei Zhang
- Key Laboratory for Cotton and Canola Research at the Lower Reach of the Yangtze River Plain, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing 210014, China
| | - Wanchao Ni
- Key Laboratory for Cotton and Canola Research at the Lower Reach of the Yangtze River Plain, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing 210014, China
| | - Xinlian Shen
- Key Laboratory for Cotton and Canola Research at the Lower Reach of the Yangtze River Plain, Ministry of Agriculture and Rural Affairs, Nanjing 210014, China
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing 210014, China
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23
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Nvsvrot T, Xia W, Xiao Z, Zhan C, Liu M, Yang X, Zhang Y, Wang N. Combining QTL Mapping with Genome Resequencing Identifies an Indel in an R Gene that is Associated with Variation in Leaf Rust Disease Resistance in Poplar. Phytopathology 2020; 110:900-906. [PMID: 31958037 DOI: 10.1094/phyto-10-19-0402-r] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Poplar trees (Populus spp.) are important and are widely grown worldwide. However, the extensive occurrence of leaf rust disease caused by Melampsora spp. seriously inhibits their growth and reduces their biomass. In our previous study, a high-quality genetic map was constructed for the poplar F1 population I-69 × XYY by using next-generation sequencing-based genotyping-by-sequencing. Here, we collected phenotypic data on leaf rust disease resistance on three different dates for all 300 progenies of the F1 population. Combining a high-quality genetic map and phenotypic data, we were able to detect 11 major quantitative trait loci (QTLs) for leaf rust disease resistance. Among these 11 QTLs, two pairs were detected on at least two dates. In the corresponding genomic sequence, we found that resistance (R) gene clusters were located in these two QTL regions. By using genome resequencing, PCR confirmation and statistical analysis, a 611-bp deletion within an R gene in one QTL region was found to be associated with variation in leaf rust disease resistance. A PCR-based examination of this 611-bp deletion was performed. This 611-bp deletion was also found to affect mRNA splicing and form a new protein with the loss of some key protein domains. Based on this study, we were able to determine the genetic architecture of variation in poplar leaf rust disease resistance, and the 611-bp deletion in the R gene could be used as a diagnostic marker for future poplar molecular breeding.
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Affiliation(s)
- Tashbek Nvsvrot
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China
| | - Wenxiu Xia
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Logistics Service Group, Wuhan University, Wuhan, 430070, China
| | - Zheng'ang Xiao
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chang Zhan
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Meifeng Liu
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xiaoqing Yang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Yan Zhang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
| | - Nian Wang
- College of Horticulture and Forestry Sciences, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Engineering Technology Research Center for Forestry Information, Huazhong Agricultural University, Wuhan, 430070, China
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24
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Shi T, Luo W, Li H, Huang X, Ni Z, Gao H, Iqbal S, Gao Z. Association between blooming time and climatic adaptation in Prunus mume. Ecol Evol 2020; 10:292-306. [PMID: 31988729 PMCID: PMC6972806 DOI: 10.1002/ece3.5894] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 11/13/2019] [Accepted: 11/14/2019] [Indexed: 12/16/2022] Open
Abstract
Prunus mume Sieb. et Zucc. is an important fruit crop of the subtropical region, originating in China. It blooms earlier than other deciduous fruit trees, but different regions have different blooming periods. The time of anthesis is related to the dormancy period, and a certain amount of chilling promotes bud break and blooming. To identify the relationship between blooming time and the climatic adaptation of P. mume cultivars in China, the nuclear and chloroplast genomes of 19 cultivars from the main cultivation areas of P. mume in China were resequenced. The average depth of coverage was 34X-76X, and a total of 388,134 single nucleotide polymorphisms were located within the coding regions of the gene (CDs). Additionally, the 19 cultivar accessions were divided into three groups based on their blooming time: early, mid, and late. Associated with the blooming time groups, 21 selective sweep regions were identified, which could provide evidence supporting the possible model of P. mume domestication originating due to natural selection. Furthermore, we identified a flowering gene, FRIGIDA-LIKE 3 (FRL3), seems to affect the blooming time and the climatic adaptation of P. mume cultivars. This study is a major step toward understanding the climatic adaptation of P. mume cultivars in China.
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Affiliation(s)
- Ting Shi
- Nanjing Agricultural UniversityNanjingChina
- Guangdong Provincial Key Laboratory for Plant EpigeneticsCollege of Life Sciences and OceanographyShenzhen UniversityShenzhenChina
| | - Wenjie Luo
- Nanjing Agricultural UniversityNanjingChina
| | - Hantao Li
- Nanjing Agricultural UniversityNanjingChina
| | - Xiao Huang
- Nanjing Agricultural UniversityNanjingChina
| | - Zhaojun Ni
- Nanjing Agricultural UniversityNanjingChina
| | - Haidong Gao
- Genepioneer Biotechnologies Co. LtdNanjingChina
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25
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Wu Z, Deng Z, Huang M, Hou Y, Zhang H, Chen H, Ren J. Whole- Genome Resequencing Identifies KIT New Alleles That Affect Coat Color Phenotypes in Pigs. Front Genet 2019; 10:218. [PMID: 30949195 PMCID: PMC6436083 DOI: 10.3389/fgene.2019.00218] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 11/15/2018] [Accepted: 02/27/2019] [Indexed: 12/13/2022] Open
Abstract
The Duroc × (Landrace × Large White) hybrid pig (DLY) is the most popular commercial pig used in the Chinese pig industry. DLY pigs are usually white but sometimes show colored phenotypes. Colored DLY pigs are not favored by slaughterhouses and retailers, thus causing certain economic losses to farmers in China. In this study, we first conducted a genome-wide association study and RNA sequencing to demonstrate that KIT variants are responsible for diversifying coat color phenotypes segregating in a DLY population. We then defined the precise sizes and locations of four duplications (DUP1-4), four candidate causative mutations at the KIT locus, in the pig reference genome using the whole-genome sequence data of representative colored individuals. The sequence data also enabled us to identify a list of new KIT alleles. By investigating the association between these new alleles and coat color phenotypes, we provide further evidence that DUP2 is another causative mutation for the solid white coat color in pigs. DUP1 (the KIT gene duplication), DUP2 and the splice mutation are all required for the manifestation of a solid white coat color. DUP4 had a more significant effect on the formation of the belt phenotype compared with DUP3. Given the necessity of DUP2 for the solid white coat color, we detected IN/IN homozygotes lacking DUP2 in Large White and Landrace pigs and found that French Landrace pigs had the highest frequency (8.98%) of IN/IN individuals. This study not only advances our understanding of the molecular mechanism of the color phenotype in pigs, but also establishes a simple and accurate method for the screening of KIT IN/IN homozygotes in Large White and Landrace that would cause colored DLY pigs.
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Affiliation(s)
- Zhongping Wu
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Zheng Deng
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Min Huang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Yong Hou
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Hui Zhang
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Hao Chen
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Jun Ren
- State Key Laboratory of Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
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Casola C. Resequencing of massive pine genomes helps to unlock the genetic underpinning of quantitative traits in conifer trees. New Phytol 2019; 221:1669-1671. [PMID: 30729581 DOI: 10.1111/nph.15655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Affiliation(s)
- Claudio Casola
- Department of Ecosystem Science and Management, Texas A&M University, 495 Horticulture Rd, College Station, TX, 77843-2138, USA
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27
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Wu D, Liang Z, Yan T, Xu Y, Xuan L, Tang J, Zhou G, Lohwasser U, Hua S, Wang H, Chen X, Wang Q, Zhu L, Maodzeka A, Hussain N, Li Z, Li X, Shamsi IH, Jilani G, Wu L, Zheng H, Zhang G, Chalhoub B, Shen L, Yu H, Jiang L. Whole- Genome Resequencing of a Worldwide Collection of Rapeseed Accessions Reveals the Genetic Basis of Ecotype Divergence. Mol Plant 2019; 12:30-43. [PMID: 30472326 DOI: 10.1016/j.molp.2018.11.007] [Citation(s) in RCA: 117] [Impact Index Per Article: 23.4] [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: 07/29/2018] [Revised: 11/17/2018] [Accepted: 11/18/2018] [Indexed: 05/18/2023]
Abstract
Rapeseed (Brassica napus), an important oilseed crop, has adapted to diverse climate zones and latitudes by forming three main ecotype groups, namely winter, semi-winter, and spring types. However, genetic variations underlying the divergence of these ecotypes are largely unknown. Here, we report the global pattern of genetic polymorphisms in rapeseed determined by resequencing a worldwide collection of 991 germplasm accessions. A total of 5.56 and 5.53 million single-nucleotide polymorphisms (SNPs) as well as 1.86 and 1.92 million InDels were identified by mapping reads to the reference genomes of "Darmor-bzh" and "Tapidor," respectively. We generated a map of allelic drift paths that shows splits and mixtures of the main populations, and revealed an asymmetric evolution of the two subgenomes of B. napus by calculating the genetic diversity and linkage disequilibrium parameters. Selective-sweep analysis revealed genetic changes in genes orthologous to those regulating various aspects of plant development and response to stresses. A genome-wide association study identified SNPs in the promoter regions of FLOWERING LOCUS T and FLOWERING LOCUS C orthologs that corresponded to the different rapeseed ecotype groups. Our study provides important insights into the genomic footprints of rapeseed evolution and flowering-time divergence among three ecotype groups, and will facilitate screening of molecular markers for accelerating rapeseed breeding.
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Affiliation(s)
- Dezhi Wu
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Zhe Liang
- Temasek Life Sciences Laboratory and Department of Biological Science, National University of Singapore, Singapore 117543, Singapore
| | - Tao Yan
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Ying Xu
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Lijie Xuan
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Juan Tang
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Gang Zhou
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Ulrike Lohwasser
- Department of Genebank, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466 Stadt Seeland, Germany
| | - Shuijin Hua
- Institute of Crop and Nuclear Agricultural Sciences, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Haoyi Wang
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Xiaoyang Chen
- Institute of Crop Science, Jinhua Academy of Agricultural Sciences, Jinhua 321017, China
| | - Qian Wang
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Le Zhu
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Antony Maodzeka
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Nazim Hussain
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Zhilan Li
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Xuming Li
- Biomarker Technologies Corporation, Beijing 101300, China
| | | | - Ghulam Jilani
- Office of Research, Innovation & Commercialization, PMAS-Arid Agricultural University Rawalpindi, 46300 Rawalpindi, Pakistan
| | - Linde Wu
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Hongkun Zheng
- Biomarker Technologies Corporation, Beijing 101300, China
| | - Guoping Zhang
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Boulos Chalhoub
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China
| | - Lisha Shen
- Temasek Life Sciences Laboratory and Department of Biological Science, National University of Singapore, Singapore 117543, Singapore.
| | - Hao Yu
- Temasek Life Sciences Laboratory and Department of Biological Science, National University of Singapore, Singapore 117543, Singapore.
| | - Lixi Jiang
- Institute of Crop Science, Zhejiang University, Hangzhou 310058, China.
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28
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Itoh H, Wada KC, Sakai H, Shibasaki K, Fukuoka S, Wu J, Yonemaru JI, Yano M, Izawa T. Genomic adaptation of flowering-time genes during the expansion of rice cultivation area. Plant J 2018. [PMID: 29570873 DOI: 10.1111/tpj] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The diversification of flowering time in response to natural environments is critical for the spread of crops to diverse geographic regions. In contrast with recent advances in understanding the molecular basis of photoperiodic flowering in rice (Oryza sativa), little is known about how flowering-time diversification is structured within rice subspecies. By analyzing genome sequencing data and a set of 429 chromosome segment substitution lines (CSSLs) originating from 10 diverse rice accessions with wide distributions, we revealed diverse effects of allelic variations for common flowering-time quantitative trait loci in the recipient's background. Although functional variations associated with a few loci corresponded to standing variations among subspecies, the identified functional nucleotide polymorphisms occurred recently after rice subgroup differentiation, indicating that the functional diversity of flowering-time gene sequences was not particularly associated with phylogenetic relationship between rice subspecies. Intensive analysis of the Hd1 genomic region identified the signature of an early introgression of the Hd1 with key mutation(s) in aus and temperate japonica accessions. Our data suggested that, after such key introgressions, new mutations were selected and accelerated the flowering-time diversity within subspecies during the expansion of rice cultivation area. This finding may imply that new genome-wide changes for flowering-time adaptation are one of the critical determinants for establishing genomic architecture of local rice subgroups. In-depth analyses of various rice genomes coupling with the genetically confirmed phenotypic changes in a large set of CSSLs enabled us to demonstrate how rice genome dynamics has coordinated with the adaptation of cultivated rice during the expansion of cultivation area.
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Affiliation(s)
- Hironori Itoh
- Functional Plant Research Unit, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
- National Agriculture and Food Research Organization, Institute of Crop Science, NARO (NICS), Kannondai 2-1-2, 305-8518, Tsukuba, Japan
| | - Kaede C Wada
- Functional Plant Research Unit, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
- Horticultural Research Institute, Ibaraki Agricultural Center, Ago 3165-1, 319-0292, Kasama, Japan
| | - Hiroaki Sakai
- Agrogenomics Research Center, NIAS, Kannondai 2-1-2, 305-8602, Tsukuba, Japan
- Advanced Analysis Center, NARO, Kannondai 2-1-2, 305-8602, Tsukuba, Japan
| | - Kyohei Shibasaki
- Functional Plant Research Unit, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, 230-0045, Yokohama, Japan
| | - Shuichi Fukuoka
- National Agriculture and Food Research Organization, Institute of Crop Science, NARO (NICS), Kannondai 2-1-2, 305-8518, Tsukuba, Japan
- Rice Applied Genomics Research Unit, NIAS, 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
| | - Jianzhong Wu
- Agrogenomics Research Center, NIAS, Kannondai 2-1-2, 305-8602, Tsukuba, Japan
- Advanced Analysis Center, NARO, Kannondai 2-1-2, 305-8602, Tsukuba, Japan
| | - Jun-Ichi Yonemaru
- National Agriculture and Food Research Organization, Institute of Crop Science, NARO (NICS), Kannondai 2-1-2, 305-8518, Tsukuba, Japan
- Rice Applied Genomics Research Unit, NIAS, 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
| | - Masahiro Yano
- National Agriculture and Food Research Organization, Institute of Crop Science, NARO (NICS), Kannondai 2-1-2, 305-8518, Tsukuba, Japan
- Rice Applied Genomics Research Unit, NIAS, 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
| | - Takeshi Izawa
- Functional Plant Research Unit, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
- Faculty of Agriculture, Laboratory of Plant Breeding and Genetics, University of Tokyo, Bunkyo-ku, Yayoi 1-1-1, 113-8657, Tokyo, Japan
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29
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Itoh H, Wada KC, Sakai H, Shibasaki K, Fukuoka S, Wu J, Yonemaru JI, Yano M, Izawa T. Genomic adaptation of flowering-time genes during the expansion of rice cultivation area. Plant J 2018; 94:895-909. [PMID: 29570873 DOI: 10.1111/tpj.13906] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 12/18/2017] [Revised: 03/02/2018] [Accepted: 03/09/2018] [Indexed: 05/04/2023]
Abstract
The diversification of flowering time in response to natural environments is critical for the spread of crops to diverse geographic regions. In contrast with recent advances in understanding the molecular basis of photoperiodic flowering in rice (Oryza sativa), little is known about how flowering-time diversification is structured within rice subspecies. By analyzing genome sequencing data and a set of 429 chromosome segment substitution lines (CSSLs) originating from 10 diverse rice accessions with wide distributions, we revealed diverse effects of allelic variations for common flowering-time quantitative trait loci in the recipient's background. Although functional variations associated with a few loci corresponded to standing variations among subspecies, the identified functional nucleotide polymorphisms occurred recently after rice subgroup differentiation, indicating that the functional diversity of flowering-time gene sequences was not particularly associated with phylogenetic relationship between rice subspecies. Intensive analysis of the Hd1 genomic region identified the signature of an early introgression of the Hd1 with key mutation(s) in aus and temperate japonica accessions. Our data suggested that, after such key introgressions, new mutations were selected and accelerated the flowering-time diversity within subspecies during the expansion of rice cultivation area. This finding may imply that new genome-wide changes for flowering-time adaptation are one of the critical determinants for establishing genomic architecture of local rice subgroups. In-depth analyses of various rice genomes coupling with the genetically confirmed phenotypic changes in a large set of CSSLs enabled us to demonstrate how rice genome dynamics has coordinated with the adaptation of cultivated rice during the expansion of cultivation area.
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Affiliation(s)
- Hironori Itoh
- Functional Plant Research Unit, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
- National Agriculture and Food Research Organization, Institute of Crop Science, NARO (NICS), Kannondai 2-1-2, 305-8518, Tsukuba, Japan
| | - Kaede C Wada
- Functional Plant Research Unit, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
- Horticultural Research Institute, Ibaraki Agricultural Center, Ago 3165-1, 319-0292, Kasama, Japan
| | - Hiroaki Sakai
- Agrogenomics Research Center, NIAS, Kannondai 2-1-2, 305-8602, Tsukuba, Japan
- Advanced Analysis Center, NARO, Kannondai 2-1-2, 305-8602, Tsukuba, Japan
| | - Kyohei Shibasaki
- Functional Plant Research Unit, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
- RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro, Tsurumi, 230-0045, Yokohama, Japan
| | - Shuichi Fukuoka
- National Agriculture and Food Research Organization, Institute of Crop Science, NARO (NICS), Kannondai 2-1-2, 305-8518, Tsukuba, Japan
- Rice Applied Genomics Research Unit, NIAS, 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
| | - Jianzhong Wu
- Agrogenomics Research Center, NIAS, Kannondai 2-1-2, 305-8602, Tsukuba, Japan
- Advanced Analysis Center, NARO, Kannondai 2-1-2, 305-8602, Tsukuba, Japan
| | - Jun-Ichi Yonemaru
- National Agriculture and Food Research Organization, Institute of Crop Science, NARO (NICS), Kannondai 2-1-2, 305-8518, Tsukuba, Japan
- Rice Applied Genomics Research Unit, NIAS, 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
| | - Masahiro Yano
- National Agriculture and Food Research Organization, Institute of Crop Science, NARO (NICS), Kannondai 2-1-2, 305-8518, Tsukuba, Japan
- Rice Applied Genomics Research Unit, NIAS, 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
| | - Takeshi Izawa
- Functional Plant Research Unit, National Institute of Agrobiological Sciences (NIAS), 2-1-2 Kannondai, 305-8602, Tsukuba, Japan
- Faculty of Agriculture, Laboratory of Plant Breeding and Genetics, University of Tokyo, Bunkyo-ku, Yayoi 1-1-1, 113-8657, Tokyo, Japan
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30
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Tomatsu C, Uesaka K, Yamakawa H, Tsuchiya T, Ihara K, Fujita Y. In vivo transposon tagging in the nonheterocystous nitrogen-fixing cyanobacterium Leptolyngbya boryana. FEBS Lett 2018; 592:1634-1642. [PMID: 29723391 DOI: 10.1002/1873-3468.13079] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 02/01/2018] [Revised: 04/23/2018] [Accepted: 04/23/2018] [Indexed: 01/16/2023]
Abstract
Nitrogenase is an oxygen-vulnerable metalloenzyme that catalyzes nitrogen fixation. It largely remains unknown how nitrogenase coexists with oxygenic photosynthesis in nonheterocystous cyanobacteria, since there have been no appropriate model cyanobacteria so far. Here, we demonstrate in vivo transposon tagging in the nonheterocystous cyanobacterium Leptolyngbya boryana as a forward genetics approach. By conjugative transfer, a mini-Tn5-derived vector, pKUT-Tn5-Sm/Sp, was transferred from Escherichia coli to L. boryana cells. Of 1839 streptomycin-resistant colonies, we isolated three mutants showing aberrant diazotrophic growth. Genome resequencing identified the insertion sites of the transposon in the mutants. This in vivo transposon tagging mutagenesis of L. boryana provides a promising system to investigate molecular mechanisms to resolve the Oxygen Paradox between nitrogen fixation and oxygenic photosynthesis in cyanobacteria.
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Affiliation(s)
- Chie Tomatsu
- Graduate School of Bioagricultural Sciences, Nagoya University, Japan
| | | | - Hisanori Yamakawa
- Graduate School of Bioagricultural Sciences, Nagoya University, Japan
| | - Tohru Tsuchiya
- Graduate School of Global Environmental Studies, Kyoto University, Japan.,Graduate School of Human and Environmental Studies, Kyoto University, Japan
| | - Kunio Ihara
- Center for Gene Research, Nagoya University, Japan
| | - Yuichi Fujita
- Graduate School of Bioagricultural Sciences, Nagoya University, Japan
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31
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Wang X, Chen ZH, Yang C, Zhang X, Jin G, Chen G, Wang Y, Holford P, Nevo E, Zhang G, Dai F. Genomic adaptation to drought in wild barley is driven by edaphic natural selection at the Tabigha Evolution Slope. Proc Natl Acad Sci U S A 2018; 115:5223-8. [PMID: 29712833 DOI: 10.1073/pnas.1721749115] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [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] [Indexed: 02/02/2023] Open
Abstract
Ecological divergence at a microsite suggests adaptive evolution, and this study examined two abutting wild barley populations, each 100 m across, differentially adapted to drought tolerance on two contrasting soil types, Terra Rossa and basalt at the Tabigha Evolution Slope, Israel. We resequenced the genomes of seven and six wild barley genotypes inhabiting the Terra Rossa and basalt soils, respectively, and identified a total of 69,192,653 single-nucleotide variants (SNVs) and insertions/deletions in comparison with a reference barley genome. Comparative genomic analysis between these abutting wild barley populations involved 19,615,087 high-quality SNVs. The results revealed dramatically different selection sweep regions relevant to drought tolerance driven by edaphic natural selection within 2,577 selected genes in these regions, including key drought-responsive genes associated with ABA synthesis and degradation (such as Cytochrome P450 protein) and ABA receptor complex (such as PYL2, SNF1-related kinase). The genetic diversity of the wild barley population inhabiting Terra Rossa soil is much higher than that from the basalt soil. Additionally, we identified different sets of genes for drought adaptation in the wild barley populations from Terra Rossa soil and from wild barley populations from Evolution Canyon I at Mount Carmel. These genes are associated with abscisic acid signaling, signaling and metabolism of reactive oxygen species, detoxification and antioxidative systems, rapid osmotic adjustment, and deep root morphology. The unique mechanisms for drought adaptation of the wild barley from the Tabigha Evolution Slope may be useful for crop improvement, particularly for breeding of barley cultivars with high drought tolerance.
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Silva Ferreira D, Kevei Z, Kurowski T, de Noronha Fonseca ME, Mohareb F, Boiteux LS, Thompson AJ. BIFURCATE FLOWER TRUSS: a novel locus controlling inflorescence branching in tomato contains a defective MAP kinase gene. J Exp Bot 2018; 69:2581-2593. [PMID: 29509915 PMCID: PMC5920302 DOI: 10.1093/jxb/ery076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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: 05/29/2017] [Accepted: 02/21/2018] [Indexed: 06/08/2023]
Abstract
A mutant line, bifurcate flower truss (bif), was recovered from a tomato genetics programme. Plants from the control line produced a mean of 0.16 branches per truss, whereas the value for bif plants was 4.1. This increase in branching was accompanied by a 3.3-fold increase in flower number and showed a significant interaction with exposure to low temperature during truss development. The control line and bif genomes were resequenced and the bif gene was mapped to a 2.01 Mbp interval on chromosome 12; all coding region polymorphisms in the interval were surveyed, and five candidate genes displaying altered protein sequences were detected. One of these genes, SlMAPK1, encoding a mitogen-activated protein (MAP) kinase, contained a leucine to stop codon mutation predicted to disrupt kinase function. SlMAPK1 is an excellent candidate for bif because knock-out mutations of an Arabidopsis orthologue MPK6 were reported to have increased flower number. An introgression browser was used to demonstrate that the origin of the bif genomic DNA at the BIF locus was Solanum galapagense and that the SlMAPK1 null mutant is a naturally occurring allele widespread only on the Galápagos Islands. This work strongly implicates SlMAPK1 as part of the network of genes controlling inflorescence branching in tomato.
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Affiliation(s)
| | - Zoltan Kevei
- Cranfield Soil and Agrifood Institute, Cranfield University, Cranfield, UK
| | - Tomasz Kurowski
- Cranfield Soil and Agrifood Institute, Cranfield University, Cranfield, UK
| | | | - Fady Mohareb
- Cranfield Soil and Agrifood Institute, Cranfield University, Cranfield, UK
| | - Leonardo S Boiteux
- National Center for Vegetable Crops Research, CNPH—Embrapa Hortaliças, Brasília-DF, Brazil
| | - Andrew J Thompson
- Cranfield Soil and Agrifood Institute, Cranfield University, Cranfield, UK
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33
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Gao G, Nome T, Pearse DE, Moen T, Naish KA, Thorgaard GH, Lien S, Palti Y. A New Single Nucleotide Polymorphism Database for Rainbow Trout Generated Through Whole Genome Resequencing. Front Genet 2018; 9:147. [PMID: 29740479 PMCID: PMC5928233 DOI: 10.3389/fgene.2018.00147] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [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: 02/13/2018] [Accepted: 04/09/2018] [Indexed: 11/13/2022] Open
Abstract
Single-nucleotide polymorphisms (SNPs) are highly abundant markers, which are broadly distributed in animal genomes. For rainbow trout (Oncorhynchus mykiss), SNP discovery has been previously done through sequencing of restriction-site associated DNA (RAD) libraries, reduced representation libraries (RRL) and RNA sequencing. Recently we have performed high coverage whole genome resequencing with 61 unrelated samples, representing a wide range of rainbow trout and steelhead populations, with 49 new samples added to 12 aquaculture samples from AquaGen (Norway) that we previously used for SNP discovery. Of the 49 new samples, 11 were double-haploid lines from Washington State University (WSU) and 38 represented wild and hatchery populations from a wide range of geographic distribution and with divergent migratory phenotypes. We then mapped the sequences to the new rainbow trout reference genome assembly (GCA_002163495.1) which is based on the Swanson YY doubled haploid line. Variant calling was conducted with FreeBayes and SAMtools mpileup, followed by filtering of SNPs based on quality score, sequence complexity, read depth on the locus, and number of genotyped samples. Results from the two variant calling programs were compared and genotypes of the double haploid samples were used for detecting and filtering putative paralogous sequence variants (PSVs) and multi-sequence variants (MSVs). Overall, 30,302,087 SNPs were identified on the rainbow trout genome 29 chromosomes and 1,139,018 on unplaced scaffolds, with 4,042,723 SNPs having high minor allele frequency (MAF > 0.25). The average SNP density on the chromosomes was one SNP per 64 bp, or 15.6 SNPs per 1 kb. Results from the phylogenetic analysis that we conducted indicate that the SNP markers contain enough population-specific polymorphisms for recovering population relationships despite the small sample size used. Intra-Population polymorphism assessment revealed high level of polymorphism and heterozygosity within each population. We also provide functional annotation based on the genome position of each SNP and evaluate the use of clonal lines for filtering of PSVs and MSVs. These SNPs form a new database, which provides an important resource for a new high density SNP array design and for other SNP genotyping platforms used for genetic and genomics studies of this iconic salmonid fish species.
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Affiliation(s)
- Guangtu Gao
- National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, WV, United States
| | - Torfinn Nome
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre of Integrative Genetics, Norwegian University of Life Sciences, Ås, Norway
| | - Devon E Pearse
- Fisheries Ecology Division, Southwest Fisheries Science Center, National Marine Fisheries Service, Santa Cruz, CA, United States
| | | | - Kerry A Naish
- School of Aquatic and Fishery Sciences, University of Washington, Seattle, WA, United States
| | - Gary H Thorgaard
- School of Biological Sciences and Center for Reproductive Biology, Washington State University, Pullman, WA, United States
| | - Sigbjørn Lien
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Centre of Integrative Genetics, Norwegian University of Life Sciences, Ås, Norway
| | - Yniv Palti
- National Center for Cool and Cold Water Aquaculture, ARS-USDA, Kearneysville, WV, United States
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Liu J, Liu R, Wang J, Zhang Y, Xing S, Zheng M, Cui H, Li Q, Li P, Cui X, Li W, Zhao G, Wen J. Exploring Genomic Variants Related to Residual Feed Intake in Local and Commercial Chickens by Whole Genomic Resequencing. Genes (Basel) 2018; 9:genes9020057. [PMID: 29364149 PMCID: PMC5852553 DOI: 10.3390/genes9020057] [Citation(s) in RCA: 12] [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: 10/17/2017] [Revised: 12/20/2017] [Accepted: 01/02/2018] [Indexed: 02/01/2023] Open
Abstract
Improving feed efficiency is a major goal in poultry production to reduce production costs and increase profitability. The genomic variants and possible molecular mechanisms responsible for residual feed intake (RFI) in chickens, however, remain poorly understood. In this study, using both local and commercial breeds, genome re-sequencing of low RFI and high RFI chickens was performed to elucidate the genomic variants underlying RFI. Results showed that 8,505,214 and 8,479,041 single nucleotide polymorphisms (SNPs) were detected in low and high RFI Beijing-You chickens, respectively; 8,352,008 and 8,372,769 SNPs were detected in low- and high-RFI Cobb chickens, respectively. Through a series of filtering processes, 3746 candidate SNPs assigned to 1137 genes in Beijing-You chickens and 575 candidate SNPs (448 genes) in Cobb chickens were found. The validation of the selected 191 SNPs showed that 46 SNPs were significantly associated with the RFI in an independent population of 779 Cobb chickens, suggesting that the method of screening associated SNPs with whole genome sequencing (WGS) strategy was reasonable. Functions annotation of RFI-related genes indicated that genes in Beijing-You were enriched in lipid and carbohydrate metabolism, as well as the phosphatase and tensin homolog (PTEN) signaling pathway. In Cobb, however, RFI-related genes were enriched in the feed behavior process and cAMP responsive element binding protein (CREB) signaling pathway. For both breeds, organismal development physiological processes were enriched. Correspondingly, NOS1, PHKG1, NEU3 and PIP5K1B were differentially expressed in Beijing-You, while CDC42, CSK, PIK3R3, CAMK4 and PLCB4 were differentially expressed in Cobb, suggesting that these might be key genes that contribute to RFI. The results of the present study identified numerous novel SNPs for RFI, which provide candidate biomarkers for use in the genetic selection for RFI. The study has improved knowledge of the genomic variants and potential biological pathways underlying RFI in chickens.
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Affiliation(s)
- Jie Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
| | - Ranran Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
| | - Jie Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
| | - Yonghong Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- College of Animal Science, Jilin University, Changchun 130062, China.
| | - Siyuan Xing
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
| | - Maiqing Zheng
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
| | - Huanxian Cui
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
| | - Qinghe Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
| | - Peng Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
| | - Xiaoyan Cui
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
| | - Wei Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
| | - Guiping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
| | - Jie Wen
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- State Key Laboratory of Animal Nutrition, Beijing 100193, China.
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Abstract
Large-scale initiatives aiming to recover the complete sequence of thousands of human genomes are currently being undertaken worldwide, concurring to the generation of a comprehensive catalog of human genetic variation. The ultimate and most ambitious goal of human population scale genomics is the characterization of the so-called human “variome,” through the identification of causal mutations or haplotypes. Several research institutions worldwide currently use genotyping assays based on Next-Generation Sequencing (NGS) for diagnostics and clinical screenings, and the widespread application of such technologies promises major revolutions in medical science. Bioinformatic analysis of human resequencing data is one of the main factors limiting the effectiveness and general applicability of NGS for clinical studies. The requirement for multiple tools, to be combined in dedicated protocols in order to accommodate different types of data (gene panels, exomes, or whole genomes) and the high variability of the data makes difficult the establishment of a ultimate strategy of general use. While there already exist several studies comparing sensitivity and accuracy of bioinformatic pipelines for the identification of single nucleotide variants from resequencing data, little is known about the impact of quality assessment and reads pre-processing strategies. In this work we discuss major strengths and limitations of the various genome resequencing protocols are currently used in molecular diagnostics and for the discovery of novel disease-causing mutations. By taking advantage of publicly available data we devise and suggest a series of best practices for the pre-processing of the data that consistently improve the outcome of genotyping with minimal impacts on computational costs.
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Affiliation(s)
- Matteo Chiara
- Dipartimento di Bioscienze, Università di MilanoMilan, Italy
| | - Giulio Pavesi
- Dipartimento di Bioscienze, Università di MilanoMilan, Italy
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Ruggiero RP, Bourgeois Y, Boissinot S. LINE Insertion Polymorphisms are Abundant but at Low Frequencies across Populations of Anolis carolinensis. Front Genet 2017; 8:44. [PMID: 28450881 PMCID: PMC5389967 DOI: 10.3389/fgene.2017.00044] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 12/23/2016] [Accepted: 03/29/2017] [Indexed: 12/30/2022] Open
Abstract
Vertebrate genomes differ considerably in size and structure. Among the features that show the most variation is the abundance of Long Interspersed Nuclear Elements (LINEs). Mammalian genomes contain 100,000s LINEs that belong to a single clade, L1, and in most species a single family is usually active at a time. In contrast, non-mammalian vertebrates (fish, amphibians and reptiles) contain multiple active families, belonging to several clades, but each of them is represented by a small number of recently inserted copies. It is unclear why vertebrate genomes harbor such drastic differences in LINE composition. To address this issue, we conducted whole genome resequencing to investigate the population genomics of LINEs across 13 genomes of the lizard Anolis carolinensis sampled from two geographically and genetically distinct populations in the Eastern Florida and the Gulf Atlantic regions of the United States. We used the Mobile Element Locator Tool to identify and genotype polymorphic insertions from five major clades of LINEs (CR1, L1, L2, RTE and R4) and the 41 subfamilies that constitute them. Across these groups we found large variation in the frequency of polymorphic insertions and the observed length distributions of these insertions, suggesting these groups vary in their activity and how frequently they successfully generate full-length, potentially active copies. Though we found an abundance of polymorphic insertions (over 45,000) most of these were observed at low frequencies and typically appeared as singletons. Site frequency spectra for most LINEs showed a significant shift toward low frequency alleles compared to the spectra observed for total genomic single nucleotide polymorphisms. Using Tajima's D, FST and the mean number of pairwise differences in LINE insertion polymorphisms, we found evidence that negative selection is acting on LINE families in a length-dependent manner, its effects being stronger in the larger Eastern Florida population. Our results suggest that a large effective population size and negative selection limit the expansion of polymorphic LINE insertions across these populations and that the probability of LINE polymorphisms reaching fixation is extremely low.
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Sedivy EJ, Wu F, Hanzawa Y. Soybean domestication: the origin, genetic architecture and molecular bases. New Phytol 2017; 214:539-553. [PMID: 28134435 DOI: 10.1111/nph.14418] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [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: 07/16/2016] [Accepted: 11/28/2016] [Indexed: 05/20/2023]
Abstract
Domestication provides an important model for the study of evolution, and information learned from domestication research aids in the continued improvement of crop species. Recent progress in de novo assembly and whole-genome resequencing of wild and cultivated soybean genomes, in addition to new archeological discoveries, sheds light on the origin of this important crop and provides a clearer view on the modes of artificial selection that drove soybean domestication and diversification. This novel genomic information enables the search for polymorphisms that underlie variation in agronomic traits and highlights genes that exhibit a signature of selection, leading to the identification of a number of candidate genes that may have played important roles in soybean domestication, diversification and improvement. These discoveries provide a novel point of comparison on the evolutionary bases of important agronomic traits among different crop species.
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Affiliation(s)
- Eric J Sedivy
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Faqiang Wu
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Yoshie Hanzawa
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
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Keung HY, Li TK, Sham LT, Cheung MK, Cheung PCK, Kwan HS. Mechanistic Study of Utilization of Water-Insoluble Saccharomyces cerevisiae Glucans by Bifidobacterium breve Strain JCM1192. Appl Environ Microbiol 2017; 83:e03442-16. [PMID: 28115383 DOI: 10.1128/AEM.03442-16] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 01/14/2017] [Indexed: 11/20/2022] Open
Abstract
Bifidobacteria exert beneficial effects on hosts and are extensively used as probiotics. However, due to the genetic inaccessibility of these bacteria, little is known about their mechanisms of carbohydrate utilization and regulation. Bifidobacterium breve strain JCM1192 can grow on water-insoluble yeast (Saccharomyces cerevisiae) cell wall glucans (YCWG), which were recently considered as potential prebiotics. According to the results of 1H nuclear magnetic resonance (NMR) spectrometry, the YCWG were composed of highly branched (1→3,1→6)-β-glucans and (1→4,1→6)-α-glucans. Although the YCWG were composed of 78.3% β-glucans and 21.7% α-glucans, only α-glucans were consumed by the B. breve strain. The ABC transporter (malEFG1) and pullulanase (aapA) genes were transcriptionally upregulated in the metabolism of insoluble yeast glucans, suggesting their potential involvement in the process. A nonsense mutation identified in the gene encoding an ABC transporter ATP-binding protein (MalK) led to growth failure of an ethyl methanesulfonate-generated mutant with yeast glucans. Coculture of the wild-type strain and the mutant showed that this protein was responsible for the import of yeast glucans or their breakdown products, rather than the export of α-glucan-catabolizing enzymes. Further characterization of the carbohydrate utilization of the mutant and three of its revertants indicated that this mutation was pleiotropic: the mutant could not grow with maltose, glycogen, dextrin, raffinose, cellobiose, melibiose, or turanose. We propose that insoluble yeast α-glucans are hydrolyzed by extracellular pullulanase into maltose and/or maltooligosaccharides, which are then transported into the cell by the ABC transport system composed of MalEFG1 and MalK. The mechanism elucidated here will facilitate the development of B. breve and water-insoluble yeast glucans as novel synbiotics.IMPORTANCE In general, Bifidobacterium strains are genetically intractable. Coupling classic forward genetics with next-generation sequencing, here we identified an ABC transporter ATP-binding protein (MalK) responsible for the import of insoluble yeast glucan breakdown products by B. breve JCM1192. We demonstrated the pleiotropic effects of the ABC transporter ATP-binding protein in maltose/maltooligosaccharide, raffinose, cellobiose, melibiose, and turanose transport. With the addition of transcriptional analysis, we propose that insoluble yeast glucans are broken down by extracellular pullulanase into maltose and/or maltooligosaccharides, which are then transported into the cell by the ABC transport system composed of MalEFG1 and MalK. The mechanism elucidated here will facilitate the development of B. breve and water-insoluble yeast glucans as novel synbiotics.
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Fu CY, Liu WG, Liu DL, Li JH, Zhu MS, Liao YL, Liu ZR, Zeng XQ, Wang F. Genome-wide DNA polymorphism in the indica rice varieties RGD-7S and Taifeng B as revealed by whole genome re-sequencing. Genome 2016; 59:197-207. [PMID: 26926666 DOI: 10.1139/gen-2015-0101] [Citation(s) in RCA: 12] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Next-generation sequencing technologies provide opportunities to further understand genetic variation, even within closely related cultivars. We performed whole genome resequencing of two elite indica rice varieties, RGD-7S and Taifeng B, whose F1 progeny showed hybrid weakness and hybrid vigor when grown in the early- and late-cropping seasons, respectively. Approximately 150 million 100-bp pair-end reads were generated, which covered ∼86% of the rice (Oryza sativa L. japonica 'Nipponbare') reference genome. A total of 2,758,740 polymorphic sites including 2,408,845 SNPs and 349,895 InDels were detected in RGD-7S and Taifeng B, respectively. Applying stringent parameters, we identified 961,791 SNPs and 46,640 InDels between RGD-7S and Taifeng B (RGD-7S/Taifeng B). The density of DNA polymorphisms was 256.8 SNPs and 12.5 InDels per 100 kb for RGD-7S/Taifeng B. Copy number variations (CNVs) were also investigated. In RGD-7S, 1989 of 2727 CNVs were overlapped in 218 genes, and 1231 of 2010 CNVs were annotated in 175 genes in Taifeng B. In addition, we verified a subset of InDels in the interval of hybrid weakness genes, Hw3 and Hw4, and obtained some polymorphic InDel markers, which will provide a sound foundation for cloning hybrid weakness genes. Analysis of genomic variations will also contribute to understanding the genetic basis of hybrid weakness and heterosis.
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Affiliation(s)
- Chong-Yun Fu
- a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.,b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China
| | - Wu-Ge Liu
- a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.,b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China
| | - Di-Lin Liu
- a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.,b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China
| | - Ji-Hua Li
- a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.,b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China
| | - Man-Shan Zhu
- a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.,b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China
| | - Yi-Long Liao
- a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.,b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China
| | - Zhen-Rong Liu
- a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.,b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China
| | - Xue-Qin Zeng
- a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.,b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China
| | - Feng Wang
- a Rice Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, P.R. China.,b Guangdong Provincial Key Laboratory of New Technology in Rice Breeding, Guangzhou 510640, P.R. China
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40
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Wall JD, Schlebusch SA, Alberts SC, Cox LA, Snyder-Mackler N, Nevonen K, Carbone L, Tung J. Genomewide ancestry and divergence patterns from low-coverage sequencing data reveal a complex history of admixture in wild baboons. Mol Ecol 2016; 25:3469-83. [PMID: 27145036 PMCID: PMC5306399 DOI: 10.1111/mec.13684] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [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: 02/21/2016] [Revised: 04/26/2016] [Accepted: 04/27/2016] [Indexed: 11/26/2022]
Abstract
Naturally occurring admixture has now been documented in every major primate lineage, suggesting its key role in primate evolutionary history. Active primate hybrid zones can provide valuable insight into this process. Here, we investigate the history of admixture in one of the best-studied natural primate hybrid zones, between yellow baboons (Papio cynocephalus) and anubis baboons (Papio anubis) in the Amboseli ecosystem of Kenya. We generated a new genome assembly for yellow baboon and low-coverage genomewide resequencing data from yellow baboons, anubis baboons and known hybrids (n = 44). Using a novel composite likelihood method for estimating local ancestry from low-coverage data, we found high levels of genetic diversity and genetic differentiation between the parent taxa, and excellent agreement between genome-scale ancestry estimates and a priori pedigree, life history and morphology-based estimates (r(2) = 0.899). However, even putatively unadmixed Amboseli yellow individuals carried a substantial proportion of anubis ancestry, presumably due to historical admixture. Further, the distribution of shared vs. fixed differences between a putatively unadmixed Amboseli yellow baboon and an unadmixed anubis baboon, both sequenced at high coverage, is inconsistent with simple isolation-migration or equilibrium migration models. Our findings suggest a complex process of intermittent contact that has occurred multiple times in baboon evolutionary history, despite no obvious fitness costs to hybrids or major geographic or behavioural barriers. In combination with the extensive phenotypic data available for baboon hybrids, our results provide valuable context for understanding the history of admixture in primates, including in our own lineage.
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Affiliation(s)
- Jeffrey D Wall
- Institute for Human Genetics, University of California-San Francisco, Box 0794, San Francisco, CA 94143, USA
| | - Stephen A Schlebusch
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch 7700, Cape Town, South Africa
| | - Susan C Alberts
- Department of Evolutionary Anthropology, Duke University, Box 90383, Durham, NC 27708, USA
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
- Institute of Primate Research, National Museums of Kenya, P. O. Box 24481, Karen 00502, Nairobi, Kenya
| | - Laura A Cox
- Department of Genetics and Southwest National Primate Research Center, Texas Biomedical Research Institute, Box 760549, San Antonio, TX 78245, USA
| | - Noah Snyder-Mackler
- Department of Evolutionary Anthropology, Duke University, Box 90383, Durham, NC 27708, USA
| | - Kimberly Nevonen
- Division of Neuroscience, Primate Genetics Section, Oregon National Primate Research Center, 505 NW 185 Ave, Beaverton, OR 97006, USA
- Behavioral Neuroscience Department, Oregon Health Sciences University, 3181 SW, Sam Jackson Park Road, Portland, OR 97239, USA
| | - Lucia Carbone
- Division of Neuroscience, Primate Genetics Section, Oregon National Primate Research Center, 505 NW 185 Ave, Beaverton, OR 97006, USA
- Behavioral Neuroscience Department, Oregon Health Sciences University, 3181 SW, Sam Jackson Park Road, Portland, OR 97239, USA
| | - Jenny Tung
- Department of Evolutionary Anthropology, Duke University, Box 90383, Durham, NC 27708, USA
- Department of Biology, Duke University, Box 90338, Durham, NC 27708, USA
- Institute of Primate Research, National Museums of Kenya, P. O. Box 24481, Karen 00502, Nairobi, Kenya
- Duke University Population Research Institute, Duke University, Box 90420, Durham, NC 27708, USA
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Liu Y, Yan L, Li Z, Huang WF, Pokhrel S, Liu X, Su S. Larva-mediated chalkbrood resistance-associated single nucleotide polymorphism markers in the honey bee Apis mellifera. Insect Mol Biol 2016; 25:239-250. [PMID: 26991518 DOI: 10.1111/imb.12216] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Chalkbrood is a disease affecting honey bees that seriously impairs brood growth and productivity of diseased colonies. Although honey bees can develop chalkbrood resistance naturally, the details underlying the mechanisms of resistance are not fully understood, and no easy method is currently available for selecting and breeding resistant bees. Finding the genes involved in the development of resistance and identifying single nucleotide polymorphisms (SNPs) that can be used as molecular markers of resistance is therefore a high priority. We conducted genome resequencing to compare resistant (Res) and susceptible (Sus) larvae that were selected following in vitro chalkbrood inoculation. Twelve genomic libraries, including 14.4 Gb of sequence data, were analysed using SNP-finding algorithms. Unique SNPs derived from chromosomes 2 and 11 were analysed in this study. SNPs from resistant individuals were confirmed by PCR and Sanger sequencing using in vitro reared larvae and resistant colonies. We found strong support for an association between the C allele at SNP C2587245T and chalkbrood resistance. SNP C2587245T may be useful as a genetic marker for the selection of chalkbrood resistance and high royal jelly production honey bee lines, thereby helping to minimize the negative effects of chalkbrood on managed honey bees.
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Affiliation(s)
- Y Liu
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - L Yan
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Z Li
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - W-F Huang
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, China
- Illinois Natural History Survey, Prairie Research Institute, University of Illinois at Urbana-Champaign, Illinois, USA
| | - S Pokhrel
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - X Liu
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, China
| | - S Su
- College of Bee Science, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Animal Sciences, Zhejiang University, Hangzhou, China
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Zhang JZ, Liu SR, Hu CG. Identifying the genome-wide genetic variation between precocious trifoliate orange and its wild type and developing new markers for genetics research. DNA Res 2016; 23:403-14. [PMID: 27106267 PMCID: PMC4991830 DOI: 10.1093/dnares/dsw017] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 12/13/2015] [Accepted: 03/21/2016] [Indexed: 01/01/2023] Open
Abstract
To increase our understanding of the genes involved in flowering in citrus, we performed genome resequencing of an early flowering trifoliate orange mutant (Poncirus trifoliata L. Raf.) and its wild type. At the genome level, 3,932,628 single nucleotide polymorphisms (SNPs), 1,293,383 insertion/deletion polymorphisms (InDels), and 52,135 structural variations were identified between the mutant and its wild type based on the citrus reference genome. Based on integrative analysis of resequencing and transcriptome analysis, 233,998 SNPs and 75,836 InDels were also identified between the mutant and its wild type at the transcriptional level. Also, 272 citrus homologous flowering-time transcripts containing genetic variation were also identified. Gene Ontology and Kyoto Encyclopaedia of Genes and Genomes annotation revealed that the transcripts containing the mutant- and the wild-type-specific InDel were involved in diverse biological processes and molecular function. Among these transcripts, there were 131 transcripts that were expressed differently in the two genotypes. When 268 selected InDels were tested on 32 genotypes of the three genera of Rutaceae for the genetic diversity assessment, these InDel-based markers showed high transferability. This work provides important information that will allow a better understanding of the citrus genome and that will be helpful for dissecting the genetic basis of important traits in citrus.
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Affiliation(s)
- Jin-Zhi Zhang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Sheng-Rui Liu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Chun-Gen Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), College of Horticulture and Forestry Science, Huazhong Agricultural University, Wuhan 430070, China
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43
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Snyder-Mackler N, Majoros WH, Yuan ML, Shaver AO, Gordon JB, Kopp GH, Schlebusch SA, Wall JD, Alberts SC, Mukherjee S, Zhou X, Tung J. Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples. Genetics 2016; 203:699-714. [PMID: 27098910 DOI: 10.1534/genetics.116.187492] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [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: 01/25/2016] [Accepted: 04/18/2016] [Indexed: 12/31/2022] Open
Abstract
Research on the genetics of natural populations was revolutionized in the 1990s by methods for genotyping noninvasively collected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomics era. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA from noninvasively collected samples, coupled with a novel computational approach to reconstruct pedigree links from the resulting low-coverage data. We validated both methods using fecal samples from 62 wild baboons, including 48 from an independently constructed extended pedigree. We enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA and reconstructed near-perfect pedigree relationships even with extremely low-coverage sequencing. We anticipate that these methods will be broadly applicable to the many research systems for which only noninvasive samples are available. The lab protocol and software (“WHODAD”) are freely available at www.tung-lab.org/protocols-and-software.html and www.xzlab.org/software.html, respectively.
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Atwell S, Corwin JA, Soltis NE, Subedy A, Denby KJ, Kliebenstein DJ. Whole genome resequencing of Botrytis cinerea isolates identifies high levels of standing diversity. Front Microbiol 2015; 6:996. [PMID: 26441923 PMCID: PMC4585241 DOI: 10.3389/fmicb.2015.00996] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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: 05/20/2015] [Accepted: 09/07/2015] [Indexed: 01/15/2023] Open
Abstract
How standing genetic variation within a pathogen contributes to diversity in host/pathogen interactions is poorly understood, partly because most studied pathogens are host-specific, clonally reproducing organisms which complicates genetic analysis. In contrast, Botrytis cinerea is a sexually reproducing, true haploid ascomycete that can infect a wide range of diverse plant hosts. While previous work had shown significant genomic variation between two isolates, we proceeded to assess the level and frequency of standing variation in a population of B. cinerea. To begin measuring standing genetic variation in B. cinerea, we re-sequenced the genomes of 13 different isolates and aligned them to the previously sequenced T4 reference genome. In addition one of these isolates was resequenced from four independently repeated cultures. A high level of genetic diversity was found within the 13 isolates. Within this variation, we could identify clusters of genes with major effect polymorphisms, i.e., polymorphisms that lead to a predicted functional knockout, that surrounded genes involved in controlling vegetative incompatibility. The genotype at these loci was able to partially predict the interaction of these isolates in vegetative fusion assays showing that these loci control vegetative incompatibility. This suggests that the vegetative incompatibility loci within B. cinerea are associated with regions of increased genetic diversity. The genome re-sequencing of four clones from the one isolate (Grape) that had been independently propagated over 10 years showed no detectable spontaneous mutation. This suggests that B. cinerea does not display an elevated spontaneous mutation rate. Future work will allow us to test if, and how, this diversity may be contributing to the pathogen's broad host range.
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Affiliation(s)
- Susanna Atwell
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Jason A. Corwin
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Nicole E. Soltis
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Anushryia Subedy
- Department of Plant Sciences, University of California, DavisDavis, CA, USA
| | - Katherine J. Denby
- School of Life Sciences and Warwick Systems Biology Centre, University of WarwickCoventry, UK
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Deatherage DE, Traverse CC, Wolf LN, Barrick JE. Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq. Front Genet 2015; 5:468. [PMID: 25653667 PMCID: PMC4301190 DOI: 10.3389/fgene.2014.00468] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [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: 11/10/2014] [Accepted: 12/18/2014] [Indexed: 12/20/2022] Open
Abstract
New mutations leading to structural variation (SV) in genomes—in the form of mobile element insertions, large deletions, gene duplications, and other chromosomal rearrangements—can play a key role in microbial evolution. Yet, SV is considerably more difficult to predict from short-read genome resequencing data than single-nucleotide substitutions and indels (SN), so it is not yet routinely identified in studies that profile population-level genetic diversity over time in evolution experiments. We implemented an algorithm for detecting polymorphic SV as part of the breseq computational pipeline. This procedure examines split-read alignments, in which the two ends of a single sequencing read match disjoint locations in the reference genome, in order to detect structural variants and estimate their frequencies within a sample. We tested our algorithm using simulated Escherichia coli data and then applied it to 500- and 1000-generation population samples from the Lenski E. coli long-term evolution experiment (LTEE). Knowledge of genes that are targets of selection in the LTEE and mutations present in previously analyzed clonal isolates allowed us to evaluate the accuracy of our procedure. Overall, SV accounted for ~25% of the genetic diversity found in these samples. By profiling rare SV, we were able to identify many cases where alternative mutations in key genes transiently competed within a single population. We also found, unexpectedly, that mutations in two genes that rose to prominence at these early time points always went extinct in the long term. Because it is not limited by the base-calling error rate of the sequencing technology, our approach for identifying rare SV in whole-population samples may have a lower detection limit than similar predictions of SNs in these data sets. We anticipate that this functionality of breseq will be useful for providing a more complete picture of genome dynamics during evolution experiments with haploid microorganisms.
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Affiliation(s)
- Daniel E Deatherage
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin Austin, TX, USA
| | - Charles C Traverse
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin Austin, TX, USA
| | - Lindsey N Wolf
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin Austin, TX, USA
| | - Jeffrey E Barrick
- Department of Molecular Biosciences, Center for Systems and Synthetic Biology, Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, The University of Texas at Austin Austin, TX, USA
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Fischer MC, Rellstab C, Tedder A, Zoller S, Gugerli F, Shimizu KK, Holderegger R, Widmer A. Population genomic footprints of selection and associations with climate in natural populations of Arabidopsis halleri from the Alps. Mol Ecol 2013; 22:5594-607. [PMID: 24102711 PMCID: PMC4274019 DOI: 10.1111/mec.12521] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [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: 02/29/2012] [Revised: 09/02/2013] [Accepted: 09/09/2013] [Indexed: 12/27/2022]
Abstract
Natural genetic variation is essential for the adaptation of organisms to their local environment and to changing environmental conditions. Here, we examine genomewide patterns of nucleotide variation in natural populations of the outcrossing herb Arabidopsis halleri and associations with climatic variation among populations in the Alps. Using a pooled population sequencing (Pool-Seq) approach, we discovered more than two million SNPs in five natural populations and identified highly differentiated genomic regions and SNPs using FST -based analyses. We tested only the most strongly differentiated SNPs for associations with a nonredundant set of environmental factors using partial Mantel tests to identify topo-climatic factors that may underlie the observed footprints of selection. Possible functions of genes showing signatures of selection were identified by Gene Ontology analysis. We found 175 genes to be highly associated with one or more of the five tested topo-climatic factors. Of these, 23.4% had unknown functions. Genetic variation in four candidate genes was strongly associated with site water balance and solar radiation, and functional annotations were congruent with these environmental factors. Our results provide a genomewide perspective on the distribution of adaptive genetic variation in natural plant populations from a highly diverse and heterogeneous alpine environment.
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Affiliation(s)
- Martin C Fischer
- ETH Zürich, Institute of Integrative BiologyUniversitätstrasse 16, 8092, Zürich, Switzerland
| | - Christian Rellstab
- WSL Swiss Federal Research InstituteZürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Andrew Tedder
- Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of ZurichWinterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Stefan Zoller
- ETH Zürich, Genetic Diversity CentreUniversitätstrasse 16, 8092, Zürich, Switzerland
| | - Felix Gugerli
- WSL Swiss Federal Research InstituteZürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Kentaro K Shimizu
- Institute of Evolutionary Biology and Environmental Studies and Institute of Plant Biology, University of ZurichWinterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Rolf Holderegger
- ETH Zürich, Institute of Integrative BiologyUniversitätstrasse 16, 8092, Zürich, Switzerland
- WSL Swiss Federal Research InstituteZürcherstrasse 111, 8903, Birmensdorf, Switzerland
| | - Alex Widmer
- ETH Zürich, Institute of Integrative BiologyUniversitätstrasse 16, 8092, Zürich, Switzerland
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Abstract
CRISPR-Cas is an efficient method for genome editing in organisms from bacteria to human cells. We describe a transgene-free method for CRISPR-Cas-mediated cleavage in nematodes, enabling RNA-homology-targeted deletions that cause loss of gene function; analysis of whole-genome sequencing indicates that the nuclease activity is highly specific.
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