251
|
Ssamula A, Okiror A, Avrahami-Moyal L, Tam Y, Gal-On A, Gaba V, Mukasa SB, Wasswa P. In silico prediction and segregation analysis of putative virus defense genes based on SSR markers in sweet potato F1 progenies of cultivars 'New Kawogo' and 'Resisto'. AFRICAN JOURNAL OF BIOTECHNOLOGY 2019; 18:AJB-18-16-334. [PMID: 33281890 PMCID: PMC7672372 DOI: 10.5897/ajb2018/16724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 03/22/2019] [Indexed: 12/04/2022]
Abstract
In sweet potato, an anti-virus defense mechanism termed reversion has been postulated to lead to virus freedom from once infected plants. The objectives of this study were to identify anti-virus defense genes and evaluate their segregation in progenies. Reference genes from different plant species were used to assemble transcript sequences of each sweet potato defense gene in silico. Sequences were used for evaluate phylogenetic relationships with similar genes from different plant species, mining respective defense genes and thereafter developing simple sequence repeats (SSRs) for segregation analysis. Eight potential defense genes were identified: RNA dependent RNA polymerases 1, 2, 5, and 6; Argonaute 1, and Dicer-like 1, 2, and 4. Identified genes were differentially related to those of other plants and were observed on different chromosomes. The defense genes contained mono-, di-, tri-, tetra, penta-, and hexa-nucleotide repeat motifs. The SSR markers within progenies were segregated in disomic, co-segregation, nullisomic, monosomic, and trisomic modes. These findings indicate the possibility of deriving and utilizing SSRs using published genomic information. Furthermore, and given that the SSR markers were derived from known genes on defined chromosomes, this work will contribute to future molecular breeding and development of resistance gene analogs in this economically important crop.
Collapse
Affiliation(s)
- Alexander Ssamula
- Department of Agricultural Production, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Anthony Okiror
- Department of Agricultural Production, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Liat Avrahami-Moyal
- Department of Plant Pathology and Weed Research, Agricultural Research Organization-The Volcani Center, Rishon LeZion 7505101, Israel
| | - Yehudit Tam
- Department of Plant Pathology and Weed Research, Agricultural Research Organization-The Volcani Center, Rishon LeZion 7505101, Israel
| | - Amit Gal-On
- Department of Plant Pathology and Weed Research, Agricultural Research Organization-The Volcani Center, Rishon LeZion 7505101, Israel
| | - Victor Gaba
- Department of Plant Pathology and Weed Research, Agricultural Research Organization-The Volcani Center, Rishon LeZion 7505101, Israel
| | - Settumba B Mukasa
- Department of Agricultural Production, Makerere University, P. O. Box 7062, Kampala, Uganda
| | - Peter Wasswa
- Department of Agricultural Production, Makerere University, P. O. Box 7062, Kampala, Uganda
| |
Collapse
|
252
|
Yurkevich OY, Samatadze TE, Levinskikh MA, Zoshchuk SA, Signalova OB, Surzhikov SA, Sychev VN, Amosova AV, Muravenko OV. Molecular Cytogenetics of Pisum sativum L. Grown under Spaceflight-Related Stress. BIOMED RESEARCH INTERNATIONAL 2018; 2018:4549294. [PMID: 30627557 PMCID: PMC6304655 DOI: 10.1155/2018/4549294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Revised: 10/26/2018] [Accepted: 11/22/2018] [Indexed: 11/17/2022]
Abstract
The ontogenesis and reproduction of plants cultivated aboard a spacecraft occur inside the unique closed ecological system wherein plants are subjected to serious abiotic stresses. For the first time, a comparative molecular cytogenetic analysis of Pisum sativum L. (Fabaceae) grown on board the RS ISS during the Expedition-14 and Expedition-16 and also plants of their succeeding (F1 and F2) generations cultivated on Earth was performed in order to reveal possible structural chromosome changes in the pea genome. The karyotypes of these plants were studied by multicolour fluorescence in situ hybridization (FISH) with five different repeated DNA sequences (45S rDNA, 5S rDNA, PisTR-B/1, microsatellite motifs (AG)12, and (GAA)9) as probes. A chromosome aberration was revealed in one F1 plant. Significant changes in distribution of the examined repeated DNAs in karyotypes of the "space grown" pea plants as well as in F1 and F2 plants cultivated on Earth were not observed if compared with control plants. Additional oligo-(GAA)9 sites were detected on chromosomes 6 and 7 in karyotypes of F1 and F2 plants. The detected changes might be related to intraspecific genomic polymorphism or plant cell adaptive responses to spaceflight-related stress factors. Our findings suggest that, despite gradual total trace contamination of the atmosphere on board the ISS associated with the extension of the space station operating life, exposure to the space environment did not induce serious chromosome reorganizations in genomes of the "space grown" pea plants and generations of these plants cultivated on Earth.
Collapse
Affiliation(s)
- Olga Yu. Yurkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Tatiana E. Samatadze
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | | | - Svyatoslav A. Zoshchuk
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga B. Signalova
- Institute of Biomedical Problems, Russian Academy of Sciences, 123007 Moscow, Russia
| | - Sergei A. Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Vladimir N. Sychev
- Institute of Biomedical Problems, Russian Academy of Sciences, 123007 Moscow, Russia
| | - Alexandra V. Amosova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Olga V. Muravenko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| |
Collapse
|
253
|
De Novo Transcriptomic Analysis and Development of EST–SSRs for Styrax japonicus. FORESTS 2018. [DOI: 10.3390/f9120748] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Styrax japonicus sieb. et Zucc. is widely distributed in China with ornamental and medicinal values. However, the transcriptome of S. japonicus has not yet been reported. In this study, we carried out the first transcriptome analysis of S. japonicus and developed a set of expressed sequence tag–simple sequence repeats (EST–SSRs). We obtained 338,570,222 clean reads in total, of which the mean GC content was 41.58%. In total, 136,071 unigenes were obtained having an average length of 611 bp and 71,226 unigenes were favorably annotated in the database. In total, we identified 55,977 potential EST–SSRs from 38,611 unigenes, of which there was 1 SSR per 6.73 kb. The di-nucleotide repeats (40.40%) were the most identified SSRs. One set of 60 primer pairs was randomly selected, and the amplified products in S. japonicus were validated; 28 primer pairs successfully produced clear amplicons. A total of 21 (35%) polymorphic genic SSR markers were identified between two populations. In total, 15 alleles were detected and the average number was 6. The average of observed heterozygosity and expected heterozygosity was 0.614 and 0.552, respectively. The polymorphism information content (PIC) value fluctuated between 0.074 and 0.855, with a mean value of 0.504, which was also the middle level. This study provides useful information for diversity studies and resource assessments of S. japonicus.
Collapse
|
254
|
Du L, Zhang C, Liu Q, Zhang X, Yue B, Hancock J. Krait: an ultrafast tool for genome-wide survey of microsatellites and primer design. Bioinformatics 2018; 34:681-683. [PMID: 29048524 DOI: 10.1093/bioinformatics/btx665] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 10/17/2017] [Indexed: 12/16/2022] Open
Abstract
Summary Microsatellites are found to be related with various diseases and widely used in population genetics as genetic markers. However, it remains a challenge to identify microsatellite from large genome and screen microsatellites for primer design from a huge result dataset. Here, we present Krait, a robust and flexible tool for fast investigation of microsatellites in DNA sequences. Krait is designed to identify all types of perfect or imperfect microsatellites on a whole genomic sequence, and is also applicable to identification of compound microsatellites. Primer3 was seamlessly integrated into Krait so that users can design primer for microsatellite amplification in an efficient way. Additionally, Krait can export microsatellite results in FASTA or GFF3 format for further analysis and generate statistical report as well as plotting. Availability and implementation Krait is freely available at https://github.com/lmdu/krait under GPL2 License, implemented in C and Python, and supported on Windows, Linux and Mac operating systems. Contact chizhang_swmu@126.com. Supplementary information Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Lianming Du
- Institute for Advanced Study, Chengdu University, Chengdu, Sichuan 610106, China
| | - Chi Zhang
- Rehabilitation Medicine Department, The Affiliated Hospital of Southwest Medical University, Luzhou, Sichuan 646099, China
| | - Qin Liu
- College of Life Sciences and Food Engineering, Yibin University, Yibin, Sichuan 644000, China
| | - Xiuyue Zhang
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan 610065, China
| | - Bisong Yue
- Key Laboratory of Bio-Resources and Eco-Environment, Ministry of Education, College of Life Science, Sichuan University, Chengdu, Sichuan 610065, China
| | | |
Collapse
|
255
|
Pei J, Bao P, Chu M, Liang C, Ding X, Wang H, Wu X, Guo X, Yan P. Evaluation of 17 microsatellite markers for parentage testing and individual identification of domestic yak ( Bos grunniens). PeerJ 2018; 6:e5946. [PMID: 30473935 PMCID: PMC6237114 DOI: 10.7717/peerj.5946] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 10/17/2018] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Yak (Bos grunniens) is the most important domestic animal for people living at high altitudes. Yak ordinarily feed by grazing, and this behavior impacts the accuracy of the pedigree record because it is difficult to control mating in grazing yak. This study aimed to evaluate the pedigree system and individual identification in polled yak. METHODS A total of 71 microsatellite loci were selected from the literature, mostly from the studies on cattle. A total of 35 microsatellite loci generated excellent PCR results and were evaluated for the parentage testing and individual identification of 236 unrelated polled yaks. A total of 17 of these 35 microsatellite loci had polymorphic information content (PIC) values greater than 0.5, and these loci were in Hardy-Weinberg equilibrium without linkage disequilibrium. RESULTS Using multiplex PCR, capillary electrophoresis, and genotyping, very high exclusion probabilities were obtained for the combined core set of 17 loci. The exclusion probability (PE) for one candidate parent when the genotype of the other parent is not known was 0.99718116. PE for one candidate parent when the genotype of the other parent is known was 0.99997381. PE for a known candidate parent pair was 0.99999998. The combined PEI (PE for identity of two unrelated individuals) and PESI (PE for identity of two siblings) were >0.99999999 and 0.99999899, respectively. These findings indicated that the combination of 17 microsatellite markers could be useful for efficient and reliable parentage testing and individual identification in polled yak. DISCUSSION Many microsatellite loci have been investigated for cattle paternity testing. Nevertheless, these loci cannot be directly applied to yak identification because the two bovid species have different genomic sequences and organization. A total of 17 loci were selected from 71 microsatellite loci based on efficient amplification, unambiguous genotyping, and high PIC values for polled yaks, and were suitable for parentage analysis in polled yak populations.
Collapse
Affiliation(s)
- Jie Pei
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Pengjia Bao
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Min Chu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Chunnian Liang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Xuezhi Ding
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Hongbo Wang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Xiaoyun Wu
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Xian Guo
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, Gansu, China
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Lanzhou, Gansu, China
| |
Collapse
|
256
|
Lv J, Jiao W, Guo H, Liu P, Wang R, Zhang L, Zeng Q, Hu X, Bao Z, Wang S. HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay. Genome Res 2018; 28:1919-1930. [PMID: 30409770 PMCID: PMC6280760 DOI: 10.1101/gr.235820.118] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 10/25/2018] [Indexed: 01/03/2023]
Abstract
Targeted genotyping of transcriptome-scale genetic markers is highly attractive for genetic, ecological, and evolutionary studies, but achieving this goal in a cost-effective manner remains a major challenge, especially for laboratories working on nonmodel organisms. Here, we develop a high-throughput, sequencing-based GoldenGate approach (called HD-Marker), which addresses the array-related issues of original GoldenGate methodology and allows for highly multiplexed and flexible targeted genotyping of more than 12,000 loci in a single-tube assay (in contrast to fewer than 3100 in the original GoldenGate assay). We perform extensive analyses to demonstrate the power and performance of HD-Marker on various multiplex levels (296, 795, 1293, and 12,472 genic SNPs) across two sequencing platforms in two nonmodel species (the scallops Chlamys farreri and Patinopecten yessoensis), with extremely high capture rate (98%-99%) and genotyping accuracy (97%-99%). We also demonstrate the potential of HD-Marker for high-throughput targeted genotyping of alternative marker types (e.g., microsatellites and indels). With its remarkable cost-effectiveness (as low as $0.002 per genotype) and high flexibility in choice of multiplex levels and marker types, HD-Marker provides a highly attractive tool over array-based platforms for fulfilling genome/transcriptome-wide targeted genotyping applications, especially in nonmodel organisms.
Collapse
Affiliation(s)
- Jia Lv
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Wenqian Jiao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Haobing Guo
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Pingping Liu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Ruijia Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lingling Zhang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Qifan Zeng
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Xiaoli Hu
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Zhenmin Bao
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Fisheries Science and Food Production Processes, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| | - Shi Wang
- MOE Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China.,Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
| |
Collapse
|
257
|
Nichols J, Conroy GC, Kasinadhuni N, Lamont RW, Ogbourne SM. In silico detection of polymorphic microsatellites in the endangered Isis tamarind, Alectryon ramiflorus (Sapindaceae). APPLICATIONS IN PLANT SCIENCES 2018; 6:e01196. [PMID: 30473942 PMCID: PMC6240448 DOI: 10.1002/aps3.1196] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Accepted: 09/12/2018] [Indexed: 06/09/2023]
Abstract
PREMISE OF THE STUDY Alectryon ramiflorus (Sapindaceae) is an endangered rainforest tree known from only two populations. In this study, we identified polymorphic microsatellites, in silico, improving the effectiveness and efficiency of microsatellite development of nonmodel species. The development of genetic markers will support future conservation management of the species. METHODS AND RESULTS We used next-generation sequencing and bioinformatics to detect polymorphic microsatellites, in silico, reducing both the time and cost of marker development. A panel of 15 microsatellites, 12 of which were polymorphic, were subsequently characterized in 64 adult trees representing the entire species range. Mean observed heterozygosity and expected heterozygosity were 0.471 and 0.425, respectively. The polymorphism information content across loci ranged from 0.152 to 0.875. CONCLUSIONS The microsatellite markers developed in this study will be useful in gaining an understanding of A. ramiflorus' genetic diversity, level of inbreeding, and population structure and for guiding future restoration and management efforts.
Collapse
Affiliation(s)
- Joel Nichols
- GeneCology Research CentreFaculty of ScienceHealth, Engineering, and EducationUniversity of the Sunshine CoastMaroochydore DCQueensland4558Australia
| | - Gabriel C. Conroy
- GeneCology Research CentreFaculty of ScienceHealth, Engineering, and EducationUniversity of the Sunshine CoastMaroochydore DCQueensland4558Australia
| | - Naga Kasinadhuni
- Australian Genome Research FacilityLevel 5 Gehrmann LaboratoriesUniversity of QueenslandResearch RoadBrisbaneQueensland4072Australia
| | - Robert W. Lamont
- GeneCology Research CentreFaculty of ScienceHealth, Engineering, and EducationUniversity of the Sunshine CoastMaroochydore DCQueensland4558Australia
| | - Steven M. Ogbourne
- GeneCology Research CentreFaculty of ScienceHealth, Engineering, and EducationUniversity of the Sunshine CoastMaroochydore DCQueensland4558Australia
| |
Collapse
|
258
|
Singh AK, Chaurasia S, Kumar S, Singh R, Kumari J, Yadav MC, Singh N, Gaba S, Jacob SR. Identification, analysis and development of salt responsive candidate gene based SSR markers in wheat. BMC PLANT BIOLOGY 2018; 18:249. [PMID: 30342465 PMCID: PMC6195990 DOI: 10.1186/s12870-018-1476-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 10/09/2018] [Indexed: 05/31/2023]
Abstract
BACKGROUND Salinity severely limits wheat production in many parts of the world. Development of salt tolerant varieties represents the most practical option for enhancing wheat production from these areas. Application of marker assisted selection may assist in fast tracking development of salt tolerant wheat varieties. However, SSR markers available in the public domain are not specifically targeted to functional regions of wheat genome, therefore large numbers of these need to be analysed for identification of markers associated with traits of interest. With the availability of a fully annotated wheat genome assembly, it is possible to develop SSR markers specifically targeted to genic regions. We performed extensive analysis to identify candidate gene based SSRs and assessed their utility in characterizing molecular diversity in a panel of wheat genotypes. RESULTS Our analysis revealed, 161 SSR motifs in 94 salt tolerance candidate genes of wheat. These SSR motifs were nearly equally distributed on the three wheat sub-genomes; 29.8% in A, 35.7% in B and 34.4% in D sub-genome. The maximum number of SSR motifs was present in exons (31.1%) followed by promoters (29.8%), 5'UTRs (21.1%), introns (14.3%) and 3'UTRs (3.7%). Out of the 65 candidate gene based SSR markers selected for validation, 30 were found polymorphic based on initial screening and employed for characterizing genetic diversity in a panel of wheat genotypes including salt tolerant and susceptible lines. These markers generated an average of 2.83 alleles/locus. Phylogenetic analysis revealed four clusters. Salt susceptible genotypes were mainly represented in clusters I and III, whereas high and moderate salt tolerant genotypes were distributed in the remaining two clusters. Population structure analysis revealed two sub-populations, sub-population 1 contained the majority of salt tolerant whereas sub-population 2 contained majority of susceptible genotypes. Moreover, we observed reasonably higher transferability of SSR markers to related wheat species. CONCLUSION We have developed salt responsive gene based SSRs in wheat for the first time. These were highly useful in unravelling functional diversity among wheat genotypes with varying responses to salt stress. The identified gene based SSR markers will be valuable genomic resources for genetic/association mapping of salinity tolerance in wheat.
Collapse
Affiliation(s)
- Amit Kumar Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Shiksha Chaurasia
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Sundeep Kumar
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Jyoti Kumari
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Mahesh C. Yadav
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Nidhi Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| | - Sonam Gaba
- ICAR-Indian Agricultural Statistics Research Institute, Pusa, New Delhi, 110012 India
| | - Sherry Rachel Jacob
- Division of Germplasm Conservation, ICAR-National Bureau of Plant Genetic Resources, Pusa, New Delhi, 110012 India
| |
Collapse
|
259
|
Vázquez-Ovando A, Escalona-Buendía H, Ovando-Medina I, Salvador-Figueroa M. Association Between SSR Molecular Markers and Chemical and Sensory Traits of Cacao Samples Using Multiple Regression Analysis. Biochem Genet 2018; 57:301-322. [PMID: 30284127 DOI: 10.1007/s10528-018-9891-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 09/25/2018] [Indexed: 11/26/2022]
Abstract
The sensory properties of cacao beans are linked to the chemical composition of the seeds, and both characteristics are the partial results of its allelic composition. Therefore, it is useful to search for molecular markers associated with these traits. We perform multiple regression analysis to associate previously generated data of alleles generated with 12 SSR (of cultivated cacao trees) with data obtained from chemical and sensory characterization (of beans) of plants grown in the southern region from Mexico. When the association was significant, the mathematical models for predictive purposes were proposed. All phenotypic traits evaluated showed equations with setting values R2 > 0.5. All chemical characters tested have a significant association with at least two alleles (P < 0.05). In addition, the fat content was associated with six molecular markers (mTcCIR03209, mTcCIR12188, mTcCIR19286, mTcCIR07150, mTcCIR19310). The most common allele was mTcCIR12188, which was associated with the contents of eicosanoic acid, moisture, fat and total polyphenols content. The mTcCIR28362 allele is associated with sensory characters bitterness, musty odor, and roasted odor. These alleles could be useful as molecular markers of chemical and sensory characteristics of cacao samples.
Collapse
Affiliation(s)
- Alfredo Vázquez-Ovando
- Instituto de Biociencias, Universidad Autónoma de Chiapas. Boulevard Príncipe Akishino sin número, Colonia Solidaridad 2000, C.P. 30798, Tapachula, Chiapas, Mexico
| | - Héctor Escalona-Buendía
- Departamento de Biotecnología, Universidad Autónoma Metropolitana, Unidad Iztapalapa, 09340, Ciudad de México, Mexico
| | - Isidro Ovando-Medina
- Instituto de Biociencias, Universidad Autónoma de Chiapas. Boulevard Príncipe Akishino sin número, Colonia Solidaridad 2000, C.P. 30798, Tapachula, Chiapas, Mexico
| | - Miguel Salvador-Figueroa
- Instituto de Biociencias, Universidad Autónoma de Chiapas. Boulevard Príncipe Akishino sin número, Colonia Solidaridad 2000, C.P. 30798, Tapachula, Chiapas, Mexico.
| |
Collapse
|
260
|
Rao S, Sharda S, Oddi V, Nandineni MR. The Landscape of Repetitive Elements in the Refined Genome of Chilli Anthracnose Fungus Colletotrichum truncatum. Front Microbiol 2018; 9:2367. [PMID: 30337918 PMCID: PMC6180176 DOI: 10.3389/fmicb.2018.02367] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/14/2018] [Indexed: 12/15/2022] Open
Abstract
The ascomycete fungus Colletotrichum truncatum is a major phytopathogen with a broad host range which causes anthracnose disease of chilli. The genome sequencing of this fungus led to the discovery of functional categories of genes that may play important roles in fungal pathogenicity. However, the presence of gaps in C. truncatum draft assembly prevented the accurate prediction of repetitive elements, which are the key players to determine the genome architecture and drive evolution and host adaptation. We re-sequenced its genome using single-molecule real-time (SMRT) sequencing technology to obtain a refined assembly with lesser and smaller gaps and ambiguities. This enabled us to study its genome architecture by characterising the repetitive sequences like transposable elements (TEs) and simple sequence repeats (SSRs), which constituted 4.9 and 0.38% of the assembled genome, respectively. The comparative analysis among different Colletotrichum species revealed the extensive repeat rich regions, dominated by Gypsy superfamily of long terminal repeats (LTRs), and the differential composition of SSRs in their genomes. Our study revealed a recent burst of LTR amplification in C. truncatum, C. higginsianum, and C. scovillei. TEs in C. truncatum were significantly associated with secretome, effectors and genes in secondary metabolism clusters. Some of the TE families in C. truncatum showed cytosine to thymine transitions indicative of repeat-induced point mutation (RIP). C. orbiculare and C. graminicola showed strong signatures of RIP across their genomes and "two-speed" genomes with extensive AT-rich and gene-sparse regions. Comparative genomic analyses of Colletotrichum species provided an insight into the species-specific SSR profiles. The SSRs in the coding and non-coding regions of the genome revealed the composition of trinucleotide repeat motifs in exons with potential to alter the translated protein structure through amino acid repeats. This is the first genome-wide study of TEs and SSRs in C. truncatum and their comparative analysis with six other Colletotrichum species, which would serve as a useful resource for future research to get insights into the potential role of TEs in genome expansion and evolution of Colletotrichum fungi and for development of SSR-based molecular markers for population genomic studies.
Collapse
Affiliation(s)
- Soumya Rao
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Graduate Studies, Manipal Academy of Higher Education, Manipal, India
| | - Saphy Sharda
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Vineesha Oddi
- Laboratory of Cell Signalling, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| | - Madhusudan R. Nandineni
- Laboratory of Genomics and Profiling Applications, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
- Laboratory of DNA Fingerprinting Services, Centre for DNA Fingerprinting and Diagnostics, Hyderabad, India
| |
Collapse
|
261
|
Yasodha R, Vasudeva R, Balakrishnan S, Sakthi AR, Abel N, Binai N, Rajashekar B, Bachpai VKW, Pillai C, Dev SA. Draft genome of a high value tropical timber tree, Teak (Tectona grandis L. f): insights into SSR diversity, phylogeny and conservation. DNA Res 2018; 25:409-419. [PMID: 29800113 PMCID: PMC6105116 DOI: 10.1093/dnares/dsy013] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 04/19/2018] [Indexed: 12/31/2022] Open
Abstract
Teak (Tectona grandis L. f.) is one of the precious bench mark tropical hardwood having qualities of durability, strength and visual pleasantries. Natural teak populations harbour a variety of characteristics that determine their economic, ecological and environmental importance. Sequencing of whole nuclear genome of teak provides a platform for functional analyses and development of genomic tools in applied tree improvement. A draft genome of 317 Mb was assembled at 151× coverage and annotated 36, 172 protein-coding genes. Approximately about 11.18% of the genome was repetitive. Microsatellites or simple sequence repeats (SSRs) are undoubtedly the most informative markers in genotyping, genetics and applied breeding applications. We generated 182,712 SSRs at the whole genome level, of which, 170,574 perfect SSRs were found; 16,252 perfect SSRs showed in silico polymorphisms across six genotypes suggesting their promising use in genetic conservation and tree improvement programmes. Genomic SSR markers developed in this study have high potential in advancing conservation and management of teak genetic resources. Phylogenetic studies confirmed the taxonomic position of the genus Tectona within the family Lamiaceae. Interestingly, estimation of divergence time inferred that the Miocene origin of the Tectona genus to be around 21.4508 million years ago.
Collapse
Affiliation(s)
- Ramasamy Yasodha
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Ramesh Vasudeva
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur, Kerala, India
| | - Swathi Balakrishnan
- Department of Forest Biology and Tree Improvement, University of Agricultural Sciences, College of Forestry, Sirsi, Uttara Kannada, Karnataka, India
| | - Ambothi Rathnasamy Sakthi
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Nicodemus Abel
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Nagarajan Binai
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Balaji Rajashekar
- Genotypic Technology Private Limited, Bengaluru, Karnataka, India.,Institute of Computer Science, University of Tartu, Estonia
| | - Vijay Kumar Waman Bachpai
- Division of Plant Biotechnology, Institute of Forest Genetics and Tree Breeding, R.S. Puram, Coimbatore, Tamil Nadu, India
| | - Chandrasekhara Pillai
- Department of Forest Biology and Tree Improvement, University of Agricultural Sciences, College of Forestry, Sirsi, Uttara Kannada, Karnataka, India
| | - Suma Arun Dev
- Department of Forest Biology and Tree Improvement, University of Agricultural Sciences, College of Forestry, Sirsi, Uttara Kannada, Karnataka, India
| |
Collapse
|
262
|
Hirpara DG, Gajera HP. Molecular heterozygosity and genetic exploitations of Trichoderma inter-fusants enhancing tolerance to fungicides and mycoparasitism against Sclerotium rolfsii Sacc. INFECTION GENETICS AND EVOLUTION 2018; 66:26-36. [PMID: 30219319 DOI: 10.1016/j.meegid.2018.09.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2018] [Revised: 09/04/2018] [Accepted: 09/11/2018] [Indexed: 11/29/2022]
Abstract
Protoplast fusion is an imperative tool to develop Trichoderma inter-fusants having desire traits through genetic manipulation. Study designed to develop diverse Trichoderma fusants for fungicide tolerance (Mancozeb, Thiram, Tebuconazole, and Carbendazim) and enhanced mycoparasitic activity against Sclerotium rolfsii sacc. The mycoparasitic T. virens NBAII Tvs12 and fungicide tolerant T. koningii MTCC 796 were utilized for protoplast fusion. The derived inter-fusants were subjected to diploidization using d-camphor in minimal media followed by successive three sub culturing onto potato dextrose agar to obtain 36 stable fusants. The stable fusants were employed for conidial size, fungicide tolerance, mycoparasitism, gene specific SSR amplification and molecular heterozygosity analysis. The results explained that 22 homozygous mutants illustrated characteristic of either one parental strain and 14 heterozygous recombinants depicted traits of both parental strains. The antagonistic activity of fusants against S. rolfsii depicted highest growth inhibition (87.91%) by potent inter-fusant (Fu 21) with improved fungicide tolerance capacity. The molecular study revealed highest observed heterozygocity (0.544), coefficient of gene differentiation (0.526) and gene flow (0.387) by Fu 21 indicating better genetic exploitation of parental strains into that fusant with good genetic purity. Principal coordinate analysis of fusants and parental strains exhibited 65.07% total variation and confirmed the scattering pattern matched with UPGMA clustering pattern. The stable heterozygous Fu 21 derived from inter-fusion between Tvs 12 and MTCC 796 might be useful to practice eco-friendly bioformulation tolerance to fungicides for effective integrated stem rot disease management in groundnut.
Collapse
Affiliation(s)
- Darshna G Hirpara
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh 362 001, Gujarat, India
| | - H P Gajera
- Department of Biotechnology, College of Agriculture, Junagadh Agricultural University, Junagadh 362 001, Gujarat, India.
| |
Collapse
|
263
|
Hemocytes transcriptome profile of the Chinese mitten crab (Eriocheir sinensis). AQUACULTURE AND FISHERIES 2018. [DOI: 10.1016/j.aaf.2018.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
|
264
|
Munhoz CF, Costa ZP, Cauz-Santos LA, Reátegui ACE, Rodde N, Cauet S, Dornelas MC, Leroy P, Varani ADM, Bergès H, Vieira MLC. A gene-rich fraction analysis of the Passiflora edulis genome reveals highly conserved microsyntenic regions with two related Malpighiales species. Sci Rep 2018; 8:13024. [PMID: 30158558 PMCID: PMC6115403 DOI: 10.1038/s41598-018-31330-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Accepted: 08/14/2018] [Indexed: 12/22/2022] Open
Abstract
Passiflora edulis is the most widely cultivated species of passionflowers, cropped mainly for industrialized juice production and fresh fruit consumption. Despite its commercial importance, little is known about the genome structure of P. edulis. To fill in this gap in our knowledge, a genomic library was built, and now completely sequenced over 100 large-inserts. Sequencing data were assembled from long sequence reads, and structural sequence annotation resulted in the prediction of about 1,900 genes, providing data for subsequent functional analysis. The richness of repetitive elements was also evaluated. Microsyntenic regions of P. edulis common to Populus trichocarpa and Manihot esculenta, two related Malpighiales species with available fully sequenced genomes were examined. Overall, gene order was well conserved, with some disruptions of collinearity identified as rearrangements, such as inversion and translocation events. The microsynteny level observed between the P. edulis sequences and the compared genomes is surprising, given the long divergence time that separates them from the common ancestor. P. edulis gene-rich segments are more compact than those of the other two species, even though its genome is much larger. This study provides a first accurate gene set for P. edulis, opening the way for new studies on the evolutionary issues in Malpighiales genomes.
Collapse
Affiliation(s)
- Carla Freitas Munhoz
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Zirlane Portugal Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Luiz Augusto Cauz-Santos
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Alina Carmen Egoávil Reátegui
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Nathalie Rodde
- Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomique Végétales, 31326, Castanet-Tolosan, France
| | - Stéphane Cauet
- Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomique Végétales, 31326, Castanet-Tolosan, France
| | - Marcelo Carnier Dornelas
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, 13083-862, Campinas, Brazil
| | - Philippe Leroy
- INRA, UCA, UMR 1095, GDEC, 63000, Clermont-Ferrand, France
| | - Alessandro de Mello Varani
- Departamento de Tecnologia, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista, 14884-900, Jaboticabal, Brazil
| | - Hélène Bergès
- Institut National de la Recherche Agronomique (INRA), Centre National de Ressources Génomique Végétales, 31326, Castanet-Tolosan, France
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil.
| |
Collapse
|
265
|
Sundqvist L, Godhe A, Jonsson PR, Sefbom J. The anchoring effect-long-term dormancy and genetic population structure. ISME JOURNAL 2018; 12:2929-2941. [PMID: 30068937 DOI: 10.1038/s41396-018-0216-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 05/18/2018] [Accepted: 06/11/2018] [Indexed: 11/09/2022]
Abstract
Understanding the genetic structure of populations is key to revealing past and present demographic and evolutionary processes in a species. In the past decade high genetic differentiation has been observed in many microbial species challenging the previous view of cosmopolitan distribution. Populations have displayed high genetic differentiation, even at small spatial scales, despite apparent high dispersal. Numerous species of microalgae have a life-history strategy that includes a long-term resting stage, which can accumulate in sediments and serve as refuge during adverse conditions. It is presently unclear how these seed banks affect the genetic structure of populations in aquatic environments. Here we provide a conceptual framework, using a simple model, to show that long-term resting stages have an anchoring effect on populations leading to increased genetic diversity and population differentiation in the presence of gene flow. The outcome that species with resting stages have a higher degree of genetic differentiation compared to species without, is supported by empirical data obtained from a systematic literature review. With this work we propose that seed banks in aquatic microalgae play an important role in the contradicting patterns of gene flow, and ultimately the adaptive potential and population dynamics in species with long-term resting stages.
Collapse
Affiliation(s)
- Lisa Sundqvist
- Department of Marine Sciences, University of Gothenburg, Box 461, Göteborg, SE, 40530, Sweden
| | - Anna Godhe
- Department of Marine Sciences, University of Gothenburg, Box 461, Göteborg, SE, 40530, Sweden
| | - Per R Jonsson
- Department of Marine Sciences - Tjärnö, University of Gothenburg, Strömstad, SE, 45296, Sweden
| | - Josefin Sefbom
- Department of Marine Sciences, University of Gothenburg, Box 461, Göteborg, SE, 40530, Sweden. .,Department of Biology, Laboratory of Protistology and Aquatic Ecology, Ghent University, Krijgslaan 281-S8, Gent, B-9000, Belgium.
| |
Collapse
|
266
|
Ricciardi F, Del Cueto J, Bardaro N, Mazzeo R, Ricciardi L, Dicenta F, Sánchez-Pérez R, Pavan S, Lotti C. Synteny-Based Development of CAPS Markers Linked to the Sweet kernel LOCUS, Controlling Amygdalin Accumulation in Almond (Prunus dulcis (Mill.) D.A.Webb). Genes (Basel) 2018; 9:genes9080385. [PMID: 30065184 PMCID: PMC6115797 DOI: 10.3390/genes9080385] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/20/2018] [Accepted: 07/24/2018] [Indexed: 11/19/2022] Open
Abstract
The bitterness and toxicity of wild-type seeds of Prunoideae is due to the cyanogenic glucoside amygdalin. In cultivated almond (Prunus dulcis (Mill.) D.A. Webb), a dominant mutation at the Sk locus prevents amygdalin accumulation and thus results in edible sweet kernels. Here, we exploited sequence similarity and synteny between the genomes of almond and peach (Prunus persica (L.) Batsch) to identify cleaved amplified polymorphic sequence (CAPS) molecular markers linked to the Sk locus. A segregant F1 population was used to map these markers on the Sk genomic region, together with Sk-linked simple sequence repeat (SSR) markers previously described. Molecular fingerprinting of a cultivar collection indicated the possibility to use CAPS polymorphisms identified in this study in breeding programs arising from different parental combinations. Overall, we highlight a set of codominant markers useful for early selection of sweet kernel genotypes, an aspect of primary importance in almond breeding. In addition, by showing collinearity between the physical map of peach and the genetic map of almond with respect to the Sk genomic region, we provide valuable information for further marker development and Sk positional cloning.
Collapse
Affiliation(s)
- Francesca Ricciardi
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, via Napoli 25, I-71100 Foggia, Italy.
| | - Jorge Del Cueto
- Agroscope Forschungszentrum Conthey, Route des Eterpys 18, 1964 Conthey, Switzerland.
- Department of Plant Breeding, CEBAS-CSIC, 30100 Espinardo, Murcia, Spain.
| | - Nicoletta Bardaro
- Department of Soil, Plant and Food Science, University of Bari "Aldo Moro", Via Amendola 165/A, I-70126 Bari, Italy.
| | - Rosa Mazzeo
- Department of Soil, Plant and Food Science, University of Bari "Aldo Moro", Via Amendola 165/A, I-70126 Bari, Italy.
| | - Luigi Ricciardi
- Department of Soil, Plant and Food Science, University of Bari "Aldo Moro", Via Amendola 165/A, I-70126 Bari, Italy.
| | - Federico Dicenta
- Department of Plant Breeding, CEBAS-CSIC, 30100 Espinardo, Murcia, Spain.
| | - Raquel Sánchez-Pérez
- Department of Plant Breeding, CEBAS-CSIC, 30100 Espinardo, Murcia, Spain.
- Plant Biochemistry Laboratory, Faculty of Science, University of Copenhagen, DK-1871 Copenhagen C, Denmark.
- VILLUM Research Center for Plant Plasticity, DK-1871 Frederiksberg C, Denmark.
| | - Stefano Pavan
- Department of Soil, Plant and Food Science, University of Bari "Aldo Moro", Via Amendola 165/A, I-70126 Bari, Italy.
- Institute of Biomedical Technologies, National Research Council (CNR), Via Amendola 122/D, I-70126 Bari, Italy.
| | - Concetta Lotti
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, via Napoli 25, I-71100 Foggia, Italy.
| |
Collapse
|
267
|
Transcriptome Analysis of Bael (Aegle marmelos (L.) Corr.) a Member of Family Rutaceae. FORESTS 2018. [DOI: 10.3390/f9080450] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Aegle marmelos (L.) Corr. is a medicinally and horticulturally important tree member of the family Rutaceae. It is native to India, where it is also known as Bael. Despite its importance, the genomic resources of this plant are scarce. This study presented the first-ever report of expressed transcripts in the leaves of Aegle marmelos. A total of 133,616 contigs were assembled to 46,335 unigenes with minimum and maximum lengths of 201 bp and 14,853 bp, respectively. There were 7002 transcription factors and 94,479 simple sequence repeat (SSR) markers. The A. marmelos transcripts were also annotated based on information from other members of Rutaceae; namely Citrus clementina and Citrus sinensis. A total of 482 transcripts were annotated as cytochrome p450s (CYPs), and 314 transcripts were annotated as glucosyltransferases (GTs). In the A. marmelos leaves, the monoterpenoid biosynthesis pathway was predominant. This study provides an important genomic resource along with useful information about A. marmelos.
Collapse
|
268
|
Yang SY, Fong WL, Chow WS, Hsu CM, Chan CLC, Keshavmurthy S, Chen CA. Development of Novel Polymorphic Microsatellite Markers in Catch Bowl Coral, Isopora palifera (Scleractinia; Acroporidae) Using Next-generation Sequencing. Zool Stud 2018; 57:e32. [PMID: 31966272 PMCID: PMC6517735 DOI: 10.6620/zs.2018.57-32] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 05/21/2018] [Indexed: 11/18/2022]
Abstract
Sung-Yin Yang, Wai-Ling Fong, Wenhua Savanna Chow, Chia-Min Hsu, Chia-Ling Carynn Chan, Shashank Keshavmurthy, and Chaolun Allen Chen (2018) Catch bowl coral, Isopora palifera, is a shallow- water scleractinian species distributed in the Indo-West Pacific region, and has been studied for its reproduction, symbiont diversity, and population genetics. In order to develop microsatellite markers to reveal the genetic connectivity of I. palifera in the Kenting reefs, southern Taiwan, we applied a stepwise approach including Illumina sequencing, primer screening, and validation. DNA sequences of each 6,363,035 read pairs were assembled with high coverage and sequencing depth, and 1,173,835 potential SSRs were identified. A set of 60,986 primers were designed and tested, and six novel microsatellite markers with three type motifs, including 3 di- and 3 tetra- repeats, were successfully isolated. The ranges in number of alleles per locus and observed and expected heterozygosities were 3-5, 0.444-0.538, and 0.375-0.565, respectively. Application of these loci to the genetic diversity of an I. palifera population that experienced bleaching events in the Kenting reef between 1998 and 2015 showed a signature admixture of three clusters without temporal variation. These loci are useful for studying population genetics in the genus Isopora. Our results suggest that next-generation sequencing technology is convenient and cost-effective and can be utilized to isolate microsatellites in other reef-building corals.
Collapse
Affiliation(s)
- Sung-Yin Yang
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan. E-mail: (Yang); (Fong); (Chow); (Hsu); (CC Chan)
| | - Wai-Ling Fong
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan. E-mail: (Yang); (Fong); (Chow); (Hsu); (CC Chan)
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
| | - Wenhua Savanna Chow
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan. E-mail: (Yang); (Fong); (Chow); (Hsu); (CC Chan)
- Department of Life Science, National Taiwan Normal University, Taipei, 106, Taiwan
- Taiwan International Graduate Program (TIGP)-Biodiversity, Academia Sinica, Nankang, Taipei 115, Taiwan
| | - Chia-Min Hsu
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan. E-mail: (Yang); (Fong); (Chow); (Hsu); (CC Chan)
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
| | - Chia-Ling Carynn Chan
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan. E-mail: (Yang); (Fong); (Chow); (Hsu); (CC Chan)
| | - Shashank Keshavmurthy
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan. E-mail: (Yang); (Fong); (Chow); (Hsu); (CC Chan)
| | - Chaolun Allen Chen
- Biodiversity Research Center, Academia Sinica, Nankang, Taipei 115, Taiwan. E-mail: (Yang); (Fong); (Chow); (Hsu); (CC Chan)
- Institute of Oceanography, National Taiwan University, Taipei 106, Taiwan
- Department of Life Science, National Taiwan Normal University, Taipei, 106, Taiwan
- Taiwan International Graduate Program (TIGP)-Biodiversity, Academia Sinica, Nankang, Taipei 115, Taiwan
| |
Collapse
|
269
|
Dequigiovanni G, Ramos SLF, Alves-Pereira A, Fabri EG, Picanço-Rodrigues D, Clement CR, Gepts P, Veasey EA. Highly structured genetic diversity of Bixa orellana var. urucurana, the wild ancestor of annatto, in Brazilian Amazonia. PLoS One 2018; 13:e0198593. [PMID: 29874280 PMCID: PMC5991381 DOI: 10.1371/journal.pone.0198593] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 05/22/2018] [Indexed: 01/19/2023] Open
Abstract
Annatto (Bixa orellana L.) is a tropical American crop, commercially valuable due to its application in the food and cosmetics industries as a natural dye. The wild ancestor of cultivated annatto is B. orellana var. urucurana. Although never cultivated, this variety occurs in open forests and anthropogenic landscapes, and is always associated with riparian environments. In this study, we evaluated the genetic diversity and structure of B. orellana var. urucurana populations in Brazilian Amazonia using 16 microsatellite loci. We used Ecological Niche Modeling (ENM) to characterize the potential geographical range of this variety in northern South America. We analyzed 170 samples from 10 municipalities in the states of Rondônia, Pará and Roraima. A total of 194 alleles was observed, with an average of 12.1 alleles per locus. Higher levels of expected (HE) than observed (HO) heterozygosities were found for all populations. Bayesian analysis, Neighbor-Joining dendrograms and PCAs suggest the existence of three strongly structured groups of populations. A strong and positive correlation between genetic and geographic distances was found, suggesting that genetic differentiation might be caused by geographic isolation. From species distribution modelling, we detected that South Rondônia, Madre di Dios River basin, Llanos de Mojos, Llanos de Orinoco and eastern Ecuador are highly suitable areas for wild annatto to occur, providing additional targets for future exploration and conservation. Climatic adaptation analyses revealed strong differentiation among populations, suggesting that precipitation plays a key role in wild annatto’s current and potential distribution patterns.
Collapse
Affiliation(s)
- Gabriel Dequigiovanni
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brasil
| | | | - Alessandro Alves-Pereira
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brasil
| | - Eliane Gomes Fabri
- Centro de Horticultura, Instituto Agronômico de Campinas, Campinas, São Paulo, Brasil
| | - Doriane Picanço-Rodrigues
- Instituto de Ciências Biológicas, Universidade Federal do Amazonas (ICB-UFAM), Manaus, Amazonas, Brasil
| | | | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, California, United States of America
| | - Elizabeth Ann Veasey
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz”, Universidade de São Paulo (ESALQ-USP), Piracicaba, São Paulo, Brasil
- * E-mail:
| |
Collapse
|
270
|
Manechini JRV, da Costa JB, Pereira BT, Carlini-Garcia LA, Xavier MA, Landell MGDA, Pinto LR. Unraveling the genetic structure of Brazilian commercial sugarcane cultivars through microsatellite markers. PLoS One 2018; 13:e0195623. [PMID: 29684082 PMCID: PMC5912765 DOI: 10.1371/journal.pone.0195623] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2017] [Accepted: 03/26/2018] [Indexed: 01/20/2023] Open
Abstract
The Brazilian sugarcane industry plays an important role in the worldwide supply of sugar and ethanol. Investigation into the genetic structure of current commercial cultivars and comparisons to the main ancestor species allow sugarcane breeding programs to better manage crosses and germplasm banks as well as to promote its rational use. In the present study, the genetic structure of a group of Brazilian cultivars currently grown by commercial producers was assessed through microsatellite markers and contrasted with a group of basic germplasm mainly composed of Saccharum officinarum and S. spontaneum accessions. A total of 285 alleles was obtained by a set of 12 SSRs primer pairs that taken together were able to efficiently distinguish and capture the genetic variability of sugarcane commercial cultivars and basic germplasm accessions allowing its application in a fast and cost-effective way for routine cultivar identification and management of sugarcane germplasm banks. Allelic distribution revealed that 97.6% of the cultivar alleles were found in the basic germplasm while 42% of the basic germplasm alleles were absent in cultivars. Of the absent alleles, 3% was exclusive to S. officinarum, 33% to S. spontaneum and 19% to other species/exotic hybrids. We found strong genetic differentiation between the Brazilian commercial cultivars and the two main species (S. officinarum: Φ^ST = 0.211 and S. spontaneum: Φ^ST = 0.216, P<0.001), and significant contribution of the latter in the genetic variability of commercial cultivars. Average dissimilarity within cultivars was 1.2 and 1.4 times lower than that within S. officinarum and S. spontaneum. Genetic divergence found between cultivars and S. spontaneum accessions has practical applications for energy cane breeding programs as the choice of more divergent parents will maximize the frequency of transgressive individuals in the progeny.
Collapse
Affiliation(s)
- João Ricardo Vieira Manechini
- Departamento de Genética e Melhoramento de Plantas, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, SP, Brasil
- Centro de Cana, Instituto Agronômico de Campinas (IAC), Ribeirão Preto, SP, Brasil
| | | | | | | | | | | | - Luciana Rossini Pinto
- Departamento de Genética e Melhoramento de Plantas, Faculdade de Ciências Agrárias e Veterinárias (FCAV), Universidade Estadual Paulista “Júlio de Mesquita Filho”, Jaboticabal, SP, Brasil
- Centro de Cana, Instituto Agronômico de Campinas (IAC), Ribeirão Preto, SP, Brasil
- * E-mail:
| |
Collapse
|
271
|
Singh RS, Kesari R, Kumar U, Jha VK, Kumar A, Kumar T, Pal AK, Singh PK. Candidate genes of flavonoid biosynthesis in Selaginella bryopteris (L.) Baker identified by RNA-Seq. Funct Integr Genomics 2018; 18:505-517. [PMID: 29666977 DOI: 10.1007/s10142-018-0603-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 02/16/2018] [Accepted: 03/18/2018] [Indexed: 12/13/2022]
Abstract
In the present study, de novo transcriptome analysis of Selaginella bryopteris in frond and root was performed to understand the regulation of flavonoid (FL) biosynthesis. High-quality data of 5.84 and 5.86 Gb was generated for frond and root, respectively, that assembled into 94,713 and 81,567 transcripts. A total of 87,471 and 73,395 unigenes were obtained from frond and root, respectively. A total of 41,267 and 31,048 CDS of frond and root, respectively, were annotated by BLASTX, which showed maximum hits against S. moellendorffii. Out of 11,285 differentially expressed genes, a total of 5639 genes were found to be down-regulated and 5628 genes up-regulated in frond as compared to those in root. In silico analysis of expression of genes in frond as compared to that in root was done for those related to phenylpropanoid (PP)/FL biosynthesis along with transcription factors (TFs) after DESeq and MapMan-based information. Results showed that genes of PP/FL biosynthesis pathway namely SbCHS, SbCHI, SbF3H, SbF3'H, SbDFR, SbUF3GT, SbCCOAMT, and SbCATOMT and TFs (SbMYB1, SbMYB2, SbMYB3, SbBHLH1, and SbWD40-5) were up-regulated in frond in comparison to those in root. Further, this in silico expression data was validated by RT-PCR analysis which showed predominant expression of most of these genes in frond and indicated their importance in the biosynthesis of flavonoids in S. bryopteris. A total of 9074 simple sequence repeats (SSRs) were also identified for frond and 3811 SSRs for root; these can be used for experimental validation.
Collapse
Affiliation(s)
- Ravi S Singh
- Department of Plant Breeding and Genetics, Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar, 813210, India.
| | - Ravi Kesari
- Department of Plant Breeding and Genetics, Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar, 813210, India
| | - Ujjwal Kumar
- Department of Plant Breeding and Genetics, Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar, 813210, India
| | - Vikash Kumar Jha
- Department of Plant Breeding and Genetics, Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar, 813210, India
| | - Anjani Kumar
- Department of Plant Breeding and Genetics, Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar, 813210, India
| | - Tribhuwan Kumar
- Department of Plant Breeding and Genetics, Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar, 813210, India
| | - Awadhesh K Pal
- Department of Plant Breeding and Genetics, Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar, 813210, India
| | - Prabhash K Singh
- Department of Plant Breeding and Genetics, Bihar Agricultural College, Bihar Agricultural University, Sabour, Bhagalpur, Bihar, 813210, India
| |
Collapse
|
272
|
Brettanomyces bruxellensis population survey reveals a diploid-triploid complex structured according to substrate of isolation and geographical distribution. Sci Rep 2018. [PMID: 29515178 PMCID: PMC5841430 DOI: 10.1038/s41598-018-22580-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Brettanomyces bruxellensis is a unicellular fungus of increasing industrial and scientific interest over the past 15 years. Previous studies revealed high genotypic diversity amongst B. bruxellensis strains as well as strain-dependent phenotypic characteristics. Genomic assemblies revealed that some strains harbour triploid genomes and based upon prior genotyping it was inferred that a triploid population was widely dispersed across Australian wine regions. We performed an intraspecific diversity genotypic survey of 1488 B. bruxellensis isolates from 29 countries, 5 continents and 9 different fermentation niches. Using microsatellite analysis in combination with different statistical approaches, we demonstrate that the studied population is structured according to ploidy level, substrate of isolation and geographical origin of the strains, underlying the relative importance of each factor. We found that geographical origin has a different contribution to the population structure according to the substrate of origin, suggesting an anthropic influence on the spatial biodiversity of this microorganism of industrial interest. The observed clustering was correlated to variable stress response, as strains from different groups displayed variation in tolerance to the wine preservative sulfur dioxide (SO2). The potential contribution of the triploid state for adaptation to industrial fermentations and dissemination of the species B. bruxellensis is discussed.
Collapse
|
273
|
Taheri S, Lee Abdullah T, Yusop MR, Hanafi MM, Sahebi M, Azizi P, Shamshiri RR. Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants. Molecules 2018; 23:E399. [PMID: 29438290 PMCID: PMC6017569 DOI: 10.3390/molecules23020399] [Citation(s) in RCA: 83] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Revised: 01/11/2018] [Accepted: 01/13/2018] [Indexed: 11/17/2022] Open
Abstract
Microsatellites, or simple sequence repeats (SSRs), are one of the most informative and multi-purpose genetic markers exploited in plant functional genomics. However, the discovery of SSRs and development using traditional methods are laborious, time-consuming, and costly. Recently, the availability of high-throughput sequencing technologies has enabled researchers to identify a substantial number of microsatellites at less cost and effort than traditional approaches. Illumina is a noteworthy transcriptome sequencing technology that is currently used in SSR marker development. Although 454 pyrosequencing datasets can be used for SSR development, this type of sequencing is no longer supported. This review aims to present an overview of the next generation sequencing, with a focus on the efficient use of de novo transcriptome sequencing (RNA-Seq) and related tools for mining and development of microsatellites in plants.
Collapse
Affiliation(s)
- Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Thohirah Lee Abdullah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohd Rafii Yusop
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mohamed Musa Hanafi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Laboratory of Plantation Science and Technology, Institute of Plantation Studies, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
- Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Parisa Azizi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Redmond Ramin Shamshiri
- Smart Farming Technology Research Center, Department of Biological and Agricultural Engineering, Faculty of Engineering, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| |
Collapse
|
274
|
Engelbrecht J, Duong TA, Berg NVD. New microsatellite markers for population studies of Phytophthora cinnamomi, an important global pathogen. Sci Rep 2017; 7:17631. [PMID: 29247246 PMCID: PMC5732169 DOI: 10.1038/s41598-017-17799-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 11/29/2017] [Indexed: 01/31/2023] Open
Abstract
Phytophthora cinnamomi is the causal agent of root rot, canker and dieback of thousands of plant species around the globe. This oomycete not only causes severe economic losses but also threatens natural ecosystems. In South Africa, P. cinnamomi affects eucalyptus, avocado, macadamia and indigenous fynbos. Despite being one of the most important plant pathogens with a global distribution, little information is available regarding origin, invasion history and population biology. This is partly due to the limited number of molecular markers available for studying P. cinnamomi. Using available genome sequences for three isolates of P. cinnamomi, sixteen polymorphic microsatellite markers were developed as a set of multiplexable markers for both PCR and Gene Scan assays. The application of these markers on P. cinnamomi populations from avocado production areas in South Africa revealed that they were all polymorphic in these populations. The markers developed in this study represent a valuable resource for studying the population biology and movement of P. cinnamomi and will aid in the understanding of the origin and invasion history of this important species.
Collapse
Affiliation(s)
- J Engelbrecht
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa.
| | - T A Duong
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| | - N V D Berg
- Department of Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, 0002, South Africa
| |
Collapse
|
275
|
Li J, Luo Y, Xu L. Development of microsatellite markers for Cypripedium tibeticum (Orchidaceae) and their applicability to two related species. APPLICATIONS IN PLANT SCIENCES 2017; 5:apps1700084. [PMID: 29299395 PMCID: PMC5749819 DOI: 10.3732/apps.1700084] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2017] [Accepted: 10/18/2017] [Indexed: 05/28/2023]
Abstract
PREMISE OF THE STUDY To investigate genetic diversity and structure, microsatellite markers were developed and characterized for Cypripedium tibeticum, an endangered orchid species, and their utility tested in two relatives: C. flavum and C. bardolphianum. METHODS AND RESULTS Candidate microsatellite loci were isolated based on next-generation sequencing. We identified 20 polymorphic loci with di- or trinucleotide repeats in three populations of C. tibeticum. Genotyping results showed the total number of alleles per locus varied from two to 21, and the observed and expected heterozygosity ranged from 0.261 to 0.967 and 0.441 to 0.960, respectively. Cross-species amplification showed most of the markers were applicable to C. flavum and C. bardolphianum. CONCLUSIONS The 20 polymorphic microsatellite markers developed in this study are useful tools for studying the conservation genetics and phylogeography of C. tibeticum and its related species.
Collapse
Affiliation(s)
- Jing Li
- School of Biological and Environmental Engineering, Xi’an University, No. 1 Keji Six Road, Xi’an 710065, Shaanxi Province, People’s Republic of China
| | - Yibo Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, People’s Republic of China
| | - Lingling Xu
- School of Biological and Environmental Engineering, Xi’an University, No. 1 Keji Six Road, Xi’an 710065, Shaanxi Province, People’s Republic of China
| |
Collapse
|
276
|
Jaiswal S, Sheoran S, Arora V, Angadi UB, Iquebal MA, Raghav N, Aneja B, Kumar D, Singh R, Sharma P, Singh GP, Rai A, Tiwari R, Kumar D. Putative Microsatellite DNA Marker-Based Wheat Genomic Resource for Varietal Improvement and Management. FRONTIERS IN PLANT SCIENCE 2017; 8:2009. [PMID: 29234333 PMCID: PMC5712362 DOI: 10.3389/fpls.2017.02009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 11/10/2017] [Indexed: 05/29/2023]
Abstract
Wheat fulfills 20% of global caloric requirement. World needs 60% more wheat for 9 billion population by 2050 but climate change with increasing temperature is projected to affect wheat productivity adversely. Trait improvement and management of wheat germplasm requires genomic resource. Simple Sequence Repeats (SSRs) being highly polymorphic and ubiquitously distributed in the genome, can be a marker of choice but there is no structured marker database with options to generate primer pairs for genotyping on desired chromosome/physical location. Previously associated markers with different wheat trait are also not available in any database. Limitations of in vitro SSR discovery can be overcome by genome-wide in silico mining of SSR. Triticum aestivum SSR database (TaSSRDb) is an integrated online database with three-tier architecture, developed using PHP and MySQL and accessible at http://webtom.cabgrid.res.in/wheatssr/. For genotyping, Primer3 standalone code computes primers on user request. Chromosome-wise SSR calling for all the three sub genomes along with choice of motif types is provided in addition to the primer generation for desired marker. We report here a database of highest number of SSRs (476,169) from complex, hexaploid wheat genome (~17 GB) along with previously reported 268 SSR markers associated with 11 traits. Highest (116.93 SSRs/Mb) and lowest (74.57 SSRs/Mb) SSR densities were found on 2D and 3A chromosome, respectively. To obtain homozygous locus, e-PCR was done. Such 30 loci were randomly selected for PCR validation in panel of 18 wheat Advance Varietal Trial (AVT) lines. TaSSRDb can be a valuable genomic resource tool for linkage mapping, gene/QTL (Quantitative trait locus) discovery, diversity analysis, traceability and variety identification. Varietal specific profiling and differentiation can supplement DUS (Distinctiveness, Uniformity, and Stability) testing, EDV (Essentially Derived Variety)/IV (Initial Variety) disputes, seed purity and hybrid wheat testing. All these are required in germplasm management as well as also in the endeavor of wheat productivity.
Collapse
Affiliation(s)
- Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sonia Sheoran
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Vasu Arora
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ulavappa B. Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir A. Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Nishu Raghav
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Bharti Aneja
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Deepender Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Rajender Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Pradeep Sharma
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - G. P. Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| |
Collapse
|
277
|
Pedersen NC, Shope B, Liu H. An autosomal recessive mutation in SCL24A4 causing enamel hypoplasia in Samoyed and its relationship to breed-wide genetic diversity. Canine Genet Epidemiol 2017; 4:11. [PMID: 29201383 PMCID: PMC5699110 DOI: 10.1186/s40575-017-0049-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 09/17/2017] [Indexed: 01/29/2023] Open
Abstract
Background Pure breeding of dogs has led to over 700 heritable disorders, of which almost 300 are Mendelian in nature. Seventy percent of the characterized mutations have an autosomal recessive mode of inheritance, indicative of positive selection during bouts of inbreeding primarily for new desired conformational traits. Samoyed suffer from several common complex genetic disorders, but up to this time only two X-linked and one autosomal dominant disorder have been identified. Previous studies based on pedigrees and SNP arrays have concluded that Samoyed breeders have done a good job in maintaining genetic diversity and avoiding excessive inbreeding. This may explain why autosomal recessive disorders have not occurred to the extent observed in many other breeds. However, an enamel hypoplasia analogous to a form of autosomal recessive amelogenesis imperfecta (ARAI) in humans has been recently characterized in Samoyed, although the causative mutation appears to have existed for three or more decades. The rise of such a mutation indicates that bouts of inbreeding for desired conformational traits are still occurring despite an old and well-defined breed standard. Therefore, the present study has two objectives: 1) measure genetic diversity in the breed using DNA and short tandem repeats (STR), and 2) identify the exact mutation responsible for enamel hypoplasia in the breed, possible explanations for its recent spread, and the effect of eliminating the mutation on existing genetic diversity. Results The recent discovery of an autosomal recessive amelogenesis imperfecta (ARAI) in Samoyed provides an opportunity to study the mutation as well as genetic factors that favored its occurrence and subsequent spread. The first step in the study was to use 33 short tandem repeat (STR) loci on 25/38 autosomes and seven STRs across the dog leukocyte antigen (DLA) class I and II regions on CFA12 to determine the DNA-based genetic profile of 182 individuals from North America, Europe and Australia. Samoyed from the three continents constituted a single breed with only slight genetic differences. Breed-wide genetic diversity was low, most likely from a small founder population and subsequent artificial genetic bottlenecks. Two alleles at each autosome locus occurred in 70–95% of the dogs and 54% of alleles were homozygous. The number of DLA class I and II haplotypes was also low and three class I and two class II haplotypes occurred in 80–90% of individuals. Therefore, most Samoyed belong to two lines, with most dogs possessing a minority of existing genetic diversity and a minority of dogs containing a majority of diversity. Although contemporary Samoyed lack genetic diversity, the bulk of parents are as unrelated as possible with smaller subpopulations either more inbred or outbred than the total population. A familial disorder manifested by hypocalcification of enamel has been recently identified. A genome wide association study (GWAS) on seven affected and five unrelated healthy dogs pointed to a region of extended homozygosity on Canis familiaris autosome 8 (CFA8). The region contained a gene in the solute carrier 24 family (SCL24A4) that encodes a protein involved in potassium dependent sodium/calcium exchange and transport. Mutations in this gene were recently found to cause a similar type of enamel hypoplasia in people. Sequencing of this candidate gene revealed a 21 bp duplication in exon 17. A test for the duplication was in concordance with the disease phenotype. The exact incidence of affected dogs is unknown, but 12% of the 168 healthy dogs tested were heterozygous for the mutation. This population was biased toward close relatives, so a liberal estimate of the incidence of affected dogs in the breed would be around 3.6/1000. Theoretical calculations based on the comparison of the whole population with a population devoid of carriers indicated that eliminating the trait would not affect existing genetic diversity at this time. Conclusions The contemporary Samoyed, like many other breeds, has retained only a small portion of the genetic diversity that exists among all dogs. This limited genetic diversity along with positive genetic selection for desirable traits has led to at least three simple non-recessive genetic disorders and a low incidence of complex genetic traits such as autoimmune disease and hip dysplasia. Unlike many other pure breeds, the Samoyed has been spared the spate of deleterious autosomal recessive traits that have plagued many other pure breeds. However, ARAI due to a mutation in the SCL24A4 gene has apparently existed in the breed for several decades but is being increasingly diagnosed. The increase in diseased dogs is most likely due to a period of intensified positive selection for some desired conformational trait. A genetic test has been developed for identifying the mutation carriers which will enable the breeders to eliminate enamel hypoplasia in Samoyed by selective breeding and it appears that this mutation can be eliminated now without loss of genetic diversity.
Collapse
Affiliation(s)
- Niels C Pedersen
- Center for Companion Animal Health, University of California, One Shields Avenue, Davis, CA 95616 USA
| | - Bonnie Shope
- Veterinary Dental Services, LLC, 530 Massachusetts Ave, Boxborough, MA 01719 USA
| | - Hongwei Liu
- Department of Veterinary Pathology, Microbiology and Immunology, University of California, One Shields Avenue, Davis, CA 65616 USA
| |
Collapse
|
278
|
Genetics and epigenetics in the pathogenesis of primary biliary cholangitis. Clin J Gastroenterol 2017; 11:11-18. [PMID: 29159718 DOI: 10.1007/s12328-017-0799-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 11/05/2017] [Indexed: 02/07/2023]
Abstract
Primary biliary cholangitis (PBC) is a chronic, slowly progressive cholestatic autoimmune liver disease predominantly afflicting women. PBC is characterized by the presence of disease-specific antimitochondrial antibodies and the histological destruction of intrahepatic bile ducts, which eventually lead to cirrhosis and hepatic failure. Fortunately, ursodeoxycholic acid therapy has improved the outcome of the vast majority of PBC cases. Although the etiology of PBC has not yet been elucidated, human leukocyte antigen (HLA) class II alleles have been consistently associated with disease onset for decades. PBC patients may also have genetically determined risk factors in non-HLA regions. Meanwhile, exposure to environmental factors, such as infectious diseases and harmful chemicals, can produce epigenetic alterations in some individuals and subsequent PBC onset. In this review, we describe the influence of HLA alleles and other gene polymorphisms on PBC along with the results of genome-wide association studies on this disease and its future prospects in terms of epigenetics.
Collapse
|
279
|
da Costa ZP, Munhoz CDF, Vieira MLC. Report on the development of putative functional SSR and SNP markers in passion fruits. BMC Res Notes 2017; 10:445. [PMID: 28874179 PMCID: PMC5585897 DOI: 10.1186/s13104-017-2771-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 08/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Passionflowers Passiflora edulis and Passiflora alata are diploid, outcrossing and understudied fruit bearing species. In Brazil, passion fruit cultivation began relatively recently and has earned the country an outstanding position as the world's top producer of passion fruit. The fruit's main economic value lies in the production of juice, an essential exotic ingredient in juice blends. Currently, crop improvement strategies, including those for underexploited tropical species, tend to incorporate molecular genetic approaches. In this study, we examined a set of P. edulis transcripts expressed in response to infection by Xanthomonas axonopodis, (the passion fruit's main bacterial pathogen that attacks the vines), aiming at the development of putative functional markers, i.e. SSRs (simple sequence repeats) and SNPs (single nucleotide polymorphisms). RESULTS A total of 210 microsatellites were found in 998 sequences, and trinucleotide repeats were found to be the most frequent (31.4%). Of the sequences selected for designing primers, 80.9% could be used to develop SSR markers, and 60.6% SNP markers for P. alata. SNPs were all biallelic and found within 15 gene fragments of P. alata. Overall, gene fragments generated 10,003 bp. SNP frequency was estimated as one SNP every 294 bp. Polymorphism rates revealed by SSR and SNP loci were 29.4 and 53.6%, respectively. CONCLUSIONS Passiflora edulis transcripts were useful for the development of putative functional markers for P. alata, suggesting a certain level of sequence conservation between these cultivated species. The markers developed herein could be used for genetic mapping purposes and also in diversity studies.
Collapse
Affiliation(s)
- Zirlane Portugal da Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Carla de Freitas Munhoz
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil.
| |
Collapse
|
280
|
The Complete Chloroplast Genome Sequences of Fritillaria ussuriensis Maxim. and Fritillaria cirrhosa D. Don, and Comparative Analysis with Other Fritillaria Species. Molecules 2017; 22:molecules22060982. [PMID: 28608849 PMCID: PMC6152782 DOI: 10.3390/molecules22060982] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Revised: 06/02/2017] [Accepted: 06/10/2017] [Indexed: 11/17/2022] Open
Abstract
The genus Fritillaria belongs to the widely distributed Liliaceae. The bulbs of Fritillaria, F. ussuriensis and F. cirrhosa are valuable herbaceous medicinal ingredients. However, they are still used indiscriminately in herbal medicine. Identification and molecular phylogenic analysis of Fritillaria species are therefore required. Here, we report the complete chloroplast (CP) genome sequences of F. ussuriensis and F. cirrhosa. The two Fritillaria CP genomes were 151,524 and 151,083 bp in length, respectively, and each included a pair of inverted repeated regions (52,678 and 52,156 bp) that was separated by a large single copy region (81,732 and 81,390 bp), and a small single copy region (17,114 and 17,537 bp). A total of 111 genes in F. ussuriensis and 112 in F. cirrhosa comprised 77 protein-coding regions in F. ussuriensis and 78 in F. cirrhosa, 30 transfer RNA (tRNA) genes, and four ribosomal RNA (rRNA) genes. The gene order, content, and orientation of the two Fritillaria CP genomes exhibited the general structure of flowering plants, and were similar to those of other Fritillaria species. Comparison of the six Fritillaria species’ CP genomes indicated seven highly divergent regions in intergenic spacers and in the matK, rpoC1, rpoC2, ycf1, ycf2, ndhD, and ndhF coding regions. We established the position of the six species through phylogenic analysis. The complete chloroplast genome sequences of the two Fritillaria species and a comparison study are useful genomic information for identifying and for studying the phylogenetic relationship among Fritillaria species within the Liliaceae.
Collapse
|