101
|
Genetic relationships and diversity analysis in Turkish laurel (Laurus nobilis L.) germplasm using ISSR and SCoT markers. Mol Biol Rep 2021; 48:4537-4547. [PMID: 34148209 DOI: 10.1007/s11033-021-06474-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/01/2021] [Indexed: 10/21/2022]
Abstract
Laurel (Laurus nobilis L.) has been used in the Mediterranean basin since ancient ages. Nowadays, Turkey, Mexico, Portugal, Italy, Spain, France, Algeria, and Morocco use aromatic leaves for commercial purposes, and Turkey is the largest exporter in the world. In this study, molecular characterization, and genetic relationships of 94 Turkish laurel genotypes were determined by ISSR and SCoT markers. The experiment was conducted with 16 ISSR and 10 SCoT markers. While 348 of 373 bands were polymorphic with a 93.3% polymorphism rate, Nei's genetic distances ranged between 0.17 and 0.70 with 0.39 mean in ISSR. In SCoT, 175 of 227 bands were polymorphic with 77.1% polymorphism rate, and Nei's genetic distances varied between 0.12 and 0.51. Sufficient genetic diversity determined with diversity parameters consisting of the average Shannon's information index (ISSR: 0.46, SCoT:0.35), the overall gene diversity (ISSR:0.19, SCoT:0.18), and the effective number of alleles (ISSR:1.52, SCoT:1.38). AMOVA (Analysis of molecular variance) revealed most of the variation was within genotypes (96%). Neighbor-joining algorithms, principal coordinate analysis (PCoA), and model-based structure resulted in harmony and clustered according to the geographical regions and provinces they collected. Genotypes were divided into two groups in ISSR and SCoT with UPGMA clustering resulting in a similar polymorphism distribution. The correlation coefficient (r) determined by marker systems' Nei's genetic distances was 0.25. The results of the study put forward resources for advanced breeding techniques, contribute to the preservation of genetic diversity, and management of genetic resources for the breeders.
Collapse
|
102
|
Genome-Wide Association Studies for Striga asiatica Resistance in Tropical Maize. Int J Genomics 2021; 2021:9979146. [PMID: 34239920 PMCID: PMC8238628 DOI: 10.1155/2021/9979146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 05/28/2021] [Accepted: 05/30/2021] [Indexed: 11/17/2022] Open
Abstract
Striga asiatica L. is a parasitic weed in cereal crops including maize leading to tremendous yield losses up to 100% under severe infestation. The available S. asiatica control methods include cultural control options such as uprooting and burning the Striga plants before they flower, field sanitation, crop rotation, intercropping, organic matter usage, improved fallows, and application of herbicides. Resource limitation among smallholder farmers renders almost all of the control methods impossible. Development and use of Striga resistant genotypes are seen as the most feasible management option. Marker identification formulates tools that are faster, cheaper, and easier to utilise in breeding for S. asiatica resistance which has low heritability. The objective of this study was to identify single nucleotide polymorphism (SNP) markers for Striga resistance using the genome-wide association study (GWAS). Genotyping by sequencing was done on tropical maize inbred lines followed by their evaluation for Striga resistance. Analysis of variance showed significant (p < 0.05) variation among evaluated genotypes for Striga resistance traits such as germination distance, germination percentage, haustoria root attachments, total Striga plants emerged, total biomass, and growth rate. There were also significant differences (p < 0.05) for cobs, leaves, stems, and roots weight. The broad sense heritability was fairly high (up to 61%) for most traits. The means for derived traits on stress tolerance indices were subjected to a t-test, and significant differences (p < 0.05) were found for leaves, stem, roots, shoots, and total biomass. The Manhattan plots from GWAS showed the presence of three SNP markers on chromosome numbers 5, 6, and 7 for total Striga plants emerged. The identified markers for resistance to S. asiatica should be validated and utilised to breed for Striga resistance in tropical maize.
Collapse
|
103
|
Song X, Yang Q, Bai Y, Gong K, Wu T, Yu T, Pei Q, Duan W, Huang Z, Wang Z, Liu Z, Kang X, Zhao W, Ma X. Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants. HORTICULTURE RESEARCH 2021; 8:122. [PMID: 34059664 PMCID: PMC8167114 DOI: 10.1038/s41438-021-00562-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 02/10/2021] [Accepted: 03/14/2021] [Indexed: 05/05/2023]
Abstract
Simple sequence repeats (SSRs) are one of the most important genetic markers and widely exist in most species. Here, we identified 249,822 SSRs from 3,951,919 genes in 112 plants. Then, we conducted a comprehensive analysis of these SSRs and constructed a plant SSR database (PSSRD). Interestingly, more SSRs were found in lower plants than in higher plants, showing that lower plants needed to adapt to early extreme environments. Four specific enriched functional terms in the lower plant Chlamydomonas reinhardtii were detected when it was compared with seven other higher plants. In addition, Guanylate_cyc existed in more genes of lower plants than of higher plants. In our PSSRD, we constructed an interactive plotting function in the chart interface, and users can easily view the detailed information of SSRs. All SSR information, including sequences, primers, and annotations, can be downloaded from our database. Moreover, we developed Web SSR Finder and Batch SSR Finder tools, which can be easily used for identifying SSRs. Our database was developed using PHP, HTML, JavaScript, and MySQL, which are freely available at http://www.pssrd.info/ . We conducted an analysis of the Myb gene families and flowering genes as two applications of the PSSRD. Further analysis indicated that whole-genome duplication and whole-genome triplication played a major role in the expansion of the Myb gene families. These SSR markers in our database will greatly facilitate comparative genomics and functional genomics studies in the future.
Collapse
Affiliation(s)
- Xiaoming Song
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China.
- School of Life Science and Technology and Center for Informational Biology, University of Electronic Science and Technology of China, 610054, Chengdu, China.
- Food Science and Technology Department, University of Nebraska-Lincoln, Lincoln, NE, 68588, USA.
| | - Qihang Yang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Yun Bai
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Ke Gong
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Tong Wu
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Tong Yu
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Qiaoying Pei
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Weike Duan
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, 223003, Huai'an, China
| | - Zhinan Huang
- College of Life Sciences and Food Engineering, Huaiyin Institute of Technology, 223003, Huai'an, China
| | - Zhiyuan Wang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Zhuo Liu
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Xi Kang
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Wei Zhao
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China
| | - Xiao Ma
- School of Life Sciences/Library, North China University of Science and Technology, Tangshan, Hebei, 063210, China.
| |
Collapse
|
104
|
Nadeem MA, Yeken MZ, Shahid MQ, Habyarimana E, Yılmaz H, Alsaleh A, Hatipoğlu R, Çilesiz Y, Khawar KM, Ludidi N, Ercişli S, Aasim M, Karaköy T, Baloch FS. Common bean as a potential crop for future food security: an overview of past, current and future contributions in genomics, transcriptomics, transgenics and proteomics. BIOTECHNOL BIOTEC EQ 2021. [DOI: 10.1080/13102818.2021.1920462] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Mehmet Zahit Yeken
- Department of Field Crops, Faculty of Agriculture, Bolu Abant İzzet Baysal University, Bolu, Turkey
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, South China Agricultural University, Guangzhou, PR China
| | | | - Hilal Yılmaz
- Department of Plant and Animal Production, Izmit Vocational School, Kocaeli University, Kocaeli, Turkey
| | - Ahmad Alsaleh
- Department of Food and Agriculture, Insitutue of Hemp Research, Yozgat Bozok University, 66200, Yozgat, Turkey
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agricultural, University of Cukurova, Adana, Turkey
| | - Yeter Çilesiz
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Khalid Mahmood Khawar
- Department of Field Crops, Faculty of Agriculture, Ankara University, Ankara, Turkey
| | - Ndiko Ludidi
- Department of Biotechnology and DSI-NRF Center of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Sezai Ercişli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| | - Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Turkey
| |
Collapse
|
105
|
Wesołowski W, Domnicz B, Augustynowicz J, Szklarczyk M. VCF2CAPS-A high-throughput CAPS marker design from VCF files and its test-use on a genotyping-by-sequencing (GBS) dataset. PLoS Comput Biol 2021; 17:e1008980. [PMID: 34014924 PMCID: PMC8186816 DOI: 10.1371/journal.pcbi.1008980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 06/08/2021] [Accepted: 04/18/2021] [Indexed: 11/21/2022] Open
Abstract
Next-generation sequencing (NGS) is a powerful tool for massive detection of DNA sequence variants such as single nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs) and insertions/deletions (indels). For routine screening of numerous samples, these variants are often converted into cleaved amplified polymorphic sequence (CAPS) markers which are based on the presence versus absence of restriction sites within PCR products. Current computational tools for SNP to CAPS conversion are limited and usually infeasible to use for large datasets as those generated with NGS. Moreover, there is no available tool for massive conversion of MNPs and indels into CAPS markers. Here, we present VCF2CAPS–a new software for identification of restriction endonucleases that recognize SNP/MNP/indel-containing sequences from NGS experiments. Additionally, the program contains filtration utilities not available in other SNP to CAPS converters–selection of markers with a single polymorphic cut site within a user-specified sequence length, and selection of markers that differentiate up to three user-defined groups of individuals from the analyzed population. Performance of VCF2CAPS was tested on a thoroughly analyzed dataset from a genotyping-by-sequencing (GBS) experiment. A selection of CAPS markers picked by the program was subjected to experimental verification. CAPS markers, also referred to as PCR-RFLPs, belong to basic tools exploited in plant, animal and human genetics. Our new software–VCF2CAPS–fills the gap in the current inventory of genetic software by high-throughput CAPS marker design from next-generation sequencing (NGS) data. The program should be of interest to geneticists involved in molecular diagnostics. In this paper we show a successful exemplary application of VCF2CAPS and we believe that its usefulness is guaranteed by the growing availability of NGS services.
Collapse
Affiliation(s)
- Wojciech Wesołowski
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Beata Domnicz
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Joanna Augustynowicz
- Department of Botany, Physiology and Plant Protection, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
| | - Marek Szklarczyk
- Department of Plant Biology and Biotechnology, Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Krakow, Poland
- * E-mail:
| |
Collapse
|
106
|
Yu GE, Shin Y, Subramaniyam S, Kang SH, Lee SM, Cho C, Lee SS, Kim CK. Machine learning, transcriptome, and genotyping chip analyses provide insights into SNP markers identifying flower color in Platycodon grandiflorus. Sci Rep 2021; 11:8019. [PMID: 33850210 PMCID: PMC8044237 DOI: 10.1038/s41598-021-87281-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 03/24/2021] [Indexed: 11/27/2022] Open
Abstract
Bellflower is an edible ornamental gardening plant in Asia. For predicting the flower color in bellflower plants, a transcriptome-wide approach based on machine learning, transcriptome, and genotyping chip analyses was used to identify SNP markers. Six machine learning methods were deployed to explore the classification potential of the selected SNPs as features in two datasets, namely training (60 RNA-Seq samples) and validation (480 Fluidigm chip samples). SNP selection was performed in sequential order. Firstly, 96 SNPs were selected from the transcriptome-wide SNPs using the principal compound analysis (PCA). Then, 9 among 96 SNPs were later identified using the Random forest based feature selection method from the Fluidigm chip dataset. Among six machines, the random forest (RF) model produced higher classification performance than the other models. The 9 SNP marker candidates selected for classifying the flower color classification were verified using the genomic DNA PCR with Sanger sequencing. Our results suggest that this methodology could be used for future selection of breeding traits even though the plant accessions are highly heterogeneous.
Collapse
Affiliation(s)
- Go-Eun Yu
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, 54874, Korea
| | - Younhee Shin
- Research and Development Center, Insilicogen Inc., Yongin-si 16954, Gyeonggi-do, Republic of Korea
| | | | - Sang-Ho Kang
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, 54874, Korea
| | - Si-Myung Lee
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, 54874, Korea
| | - Chuloh Cho
- Crop Foundation Research Division, National Institute of Crop Science, RDA, Wanju, 55365, Korea
| | - Seung-Sik Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, 29 Geumgu-gil, Jeongeup, 56212, Korea.,Department of Radiation Science and Technology, University of Science and Technology, Daejeon, 34113, Korea
| | - Chang-Kug Kim
- Genomics Division, National Institute of Agricultural Sciences, Jeonju, 54874, Korea.
| |
Collapse
|
107
|
Gemmill CEC, Grierson ERP. Inter-Simple Sequence Repeats (ISSR), Microsatellite-Primed Genomic Profiling Using Universal Primers. Methods Mol Biol 2021; 2222:249-262. [PMID: 33301098 DOI: 10.1007/978-1-0716-0997-2_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Inter-simple sequence repeat (ISSR) markers are highly polymorphic, relatively easy to develop, and inexpensive compared to other methods and have numerous applications. Importantly, the same ISSR primers can potentially be used universally across plant phylogenetic diversity. The basic technique of ISSRs is flexible and can be modified with options for implementation for a broad range of projects and budgets. Ranked in increasing order of technical demand and costs, these are manual agarose and manual polyacrylamide with silver staining and automated using fluorescently labeled primers and capillary electrophoresis. Overall manual agarose-based ISSRs are a sound, safe, easy, and low-cost method for reliably inferring plant genetic diversity. Here, we provide detailed protocols to undertake this fingerprinting method and provide guidance to the literature for the many options available for this technique.
Collapse
|
108
|
Korotkov EV, Kamionskya AM, Korotkova MA. Detection of Highly Divergent Tandem Repeats in the Rice Genome. Genes (Basel) 2021; 12:genes12040473. [PMID: 33806152 PMCID: PMC8064497 DOI: 10.3390/genes12040473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 03/11/2021] [Accepted: 03/23/2021] [Indexed: 11/25/2022] Open
Abstract
Currently, there is a lack of bioinformatics approaches to identify highly divergent tandem repeats (TRs) in eukaryotic genomes. Here, we developed a new mathematical method to search for TRs, which uses a novel algorithm for constructing multiple alignments based on the generation of random position weight matrices (RPWMs), and applied it to detect TRs of 2 to 50 nucleotides long in the rice genome. The RPWM method could find highly divergent TRs in the presence of insertions or deletions. Comparison of the RPWM algorithm with the other methods of TR identification showed that RPWM could detect TRs in which the average number of base substitutions per nucleotide (x) was between 1.5 and 3.2, whereas T-REKS and TRF methods could not detect divergent TRs with x > 1.5. Applied to the search of TRs in the rice genome, the RPWM method revealed that TRs occupied 5% of the genome and that most of them were 2 and 3 bases long. Using RPWM, we also revealed the correlation of TRs with dispersed repeats and transposons, suggesting that some transposons originated from TRs. Thus, the novel RPWM algorithm is an effective tool to search for highly divergent TRs in the genomes.
Collapse
Affiliation(s)
- Eugene V Korotkov
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Bld.2, 33 Leninsky Ave., 119071 Moscow, Russia
- MEPhI (Moscow Engineering Physics Institute), National Research Nuclear University, 31 Kashirskoye Shosse, 115409 Moscow, Russia
| | - Anastasiya M Kamionskya
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences, Bld.2, 33 Leninsky Ave., 119071 Moscow, Russia
| | - Maria A Korotkova
- MEPhI (Moscow Engineering Physics Institute), National Research Nuclear University, 31 Kashirskoye Shosse, 115409 Moscow, Russia
| |
Collapse
|
109
|
Lafrance R, Villicaña C, Valdéz-Torres JB, Martínez-Montoya H, Castillo-Ruiz O, Alemán-Castillo SE, Esparza-Araiza MJ, León-Félix J. Optimization of PCR-based TYLCV molecular markers by response surface methodology. Gene 2021; 785:145606. [PMID: 33771604 DOI: 10.1016/j.gene.2021.145606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2020] [Revised: 02/24/2021] [Accepted: 03/17/2021] [Indexed: 11/27/2022]
Abstract
Tomato (Solanum lycopersicum L.) is one of the most economically important vegetables worldwide. However, its production is affected by the tomato yellow leaf curl virus (TYLCV), causing the greatest devastation in the crop. One strategy to cope with TYLCV implies the use of resistant varieties, whose development can be accelerated by molecular markers. The aim of this study was to optimize endpoint PCR protocols for the detection of the molecular markers TG178, TG105A and P6-25, linked to Ty-1, Ty-2 and Ty-3 resistance genes, respectively, through a response surface methodology (RSM) using a central composite design (CCD) for four factors (temperature of annealing (Ta), DNA amount, MgCl2 and primer concentrations). Applicability, the limit of detection and dynamic range were also analyzed. The optimized PCR conditions were: for TG178: Ta = 60 °C, 90 ng DNA, 3.36 mM MgCl2 and 0.13 µM primers; for TG105A: Ta = 54.4 °C, 10 ng DNA, 1.5 mM MgCl2 and 0.9 µM primers; for P6-25, Ta = 52.5 °C, 50 ng DNA, 2.5 mM MgCl2 and 0.5 µM primers. Dynamic ranges varied from 0.42 to 103.3 ng of DNA, while the limit of detection was 3.82, 0.42 and 11.47 ng of DNA for the TG178, TG105A and P6-25 molecular makers respectively and was 100% positive in replicates. CCD allowed the optimization of PCR protocols for molecular markers, which may further apply in identifying TYLCV resistant tomato lines.
Collapse
Affiliation(s)
- Richecarde Lafrance
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C., Culiacán, Sinaloa, Mexico; Unidad Académica Multidisciplinaria Reynosa-Aztlán, Universidad Autónoma de Tamaulipas, Reynosa, Tamaulipas, Mexico
| | - Claudia Villicaña
- CONACYT-Centro de Investigación en Alimentación y Desarrollo, A.C., Culiacán, Sinaloa, Mexico
| | | | - Humberto Martínez-Montoya
- Unidad Académica Multidisciplinaria Reynosa-Aztlán, Universidad Autónoma de Tamaulipas, Reynosa, Tamaulipas, Mexico
| | - Octelina Castillo-Ruiz
- Unidad Académica Multidisciplinaria Reynosa-Aztlán, Universidad Autónoma de Tamaulipas, Reynosa, Tamaulipas, Mexico
| | | | - Mayra Janeth Esparza-Araiza
- Centro de Innovación y Transferencia de Tecnología de Sinaloa- Fundacion Produce Sinaloa A.C. Aguaruto, Sinaloa, México
| | - Josefina León-Félix
- Centro de Investigación en Alimentación y Desarrollo (CIAD), A.C., Culiacán, Sinaloa, Mexico.
| |
Collapse
|
110
|
Manivannan A, Choi S, Jun TH, Yang EY, Kim JH, Lee ES, Lee HE, Kim DS, Ahn YK. Genotyping by Sequencing-Based Discovery of SNP Markers and Construction of Linkage Map from F 5 Population of Pepper with Contrasting Powdery Mildew Resistance Trait. BIOMED RESEARCH INTERNATIONAL 2021; 2021:6673010. [PMID: 33816626 PMCID: PMC7987414 DOI: 10.1155/2021/6673010] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/24/2021] [Accepted: 03/09/2021] [Indexed: 11/17/2022]
Abstract
Powdery mildew (PM) is a common fungal disease infecting pepper plants worldwide. Molecular breeding of pepper cultivars with powdery mildew resistance is desirable for the economic improvement of pepper cultivation. In the present study, 188 F5 population derived from AR1 (PM resistant) and TF68 (PM sensitive) parents were subjected to high-throughput genotyping by sequencing (GBS) for the identification of single nucleotide polymorphism (SNP) markers. Further, the identified SNP markers were utilized for the construction of genetic linkage map and QTL analysis. Overall read mapping percentage of 87.29% was achieved in this study with the total length of mapped region ranging from 2,956,730 to 25,537,525 bp. A total of 41,111 polymorphic SNPs were identified, and a final of 1,841 SNPs were filtered for the construction of a linkage map. A total of 12 linkage groups were constructed corresponding to each chromosome with 1,308 SNP markers with the map length of 2506.8 cM. Further, two QTLs such as Pm-2.1 and Pm-5.1 were identified in chromosomes 2 and 5, respectively, for the PM resistance. Overall, the outcomes of the present endeavor can be utilized for the marker-assisted selection of pepper with powdery mildew-resistant trait.
Collapse
Affiliation(s)
- Abinaya Manivannan
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju 55365, Republic of Korea
| | - Sena Choi
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju 55365, Republic of Korea
| | - Tae-Hwan Jun
- Department of Plant Bioscience, Pusan National University, Busan 46241, Republic of Korea
| | - Eun-Young Yang
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju 55365, Republic of Korea
| | - Jin-Hee Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju 55365, Republic of Korea
| | - Eun-Su Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju 55365, Republic of Korea
| | - Hye-Eun Lee
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju 55365, Republic of Korea
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Jeonju 55365, Republic of Korea
| | - Yul-Kyun Ahn
- Department of Vegetable Crops, Korea National College of Agriculture and Fisheries, Jeonju 54874, Republic of Korea
| |
Collapse
|
111
|
Abebrese SO, Amoah NKA, Dartey PKA, Bimpong IK, Akromah R, Gracen VE, Offei SK, Danquah EY. Mapping chromosomal regions associated with anther indehiscence with exerted stigmas in CRI-48 and Jasmine 85 cross of rice ( Oryza sativa L). Heliyon 2021; 7:e06483. [PMID: 33763616 PMCID: PMC7973294 DOI: 10.1016/j.heliyon.2021.e06483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/07/2020] [Accepted: 03/08/2021] [Indexed: 11/18/2022] Open
Abstract
Anther indehiscence in certain wide crosses combines male sterility with stigma exertion, a phenomenon that is desirable for hybrid rice seed production. This study sought to identify chromosomal region(s) that combine anther indehiscence with exerted stigmas. A mapping population consisting of 189 BC1F1 plants was derived from a cross between CRI-48 and Jasmine 85 and backcrossing the resulting F1 to Jasmine 85. Contrary to the three complementary genes mode of inheritance reported earlier, a single locus (AI6-1) was mapped on chromosome 6 at 27.4 cM for anther indehiscence with exerted stigmas through a mixed model-based composite interval mapping (MCIM). This locus was flanked by two single nucleotide polymorphism (SNP) markers, K_ID6002884 and K_ID6003341 within a range of 23.1-28.9 cM. The allele at the locus was contributed by the CRI-48 parent which has Oryza glaberrima ancestry. This locus is suggested to control anther indehiscence and stigma exertion through pleiotropic gene action or cluster of genes.
Collapse
Affiliation(s)
| | - Nana Kofi Abaka Amoah
- Africa Rice Centre, Headquarters, M'bé Research Station. 01 B.P 2551, Bouaké o1, Cote d’Ivoire
| | | | - Isaac Kofi Bimpong
- Africa Rice Centre, Headquarters, M'bé Research Station. 01 B.P 2551, Bouaké o1, Cote d’Ivoire
| | | | | | - Samuel Kwame Offei
- West Africa Centre for Crop Improvement, University of Ghana, Legon, Ghana
| | | |
Collapse
|
112
|
Badu-Apraku B, Garcia-Oliveira AL, Petroli CD, Hearne S, Adewale SA, Gedil M. Genetic diversity and population structure of early and extra-early maturing maize germplasm adapted to sub-Saharan Africa. BMC PLANT BIOLOGY 2021; 21:96. [PMID: 33596835 PMCID: PMC7888073 DOI: 10.1186/s12870-021-02829-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 01/07/2021] [Indexed: 05/25/2023]
Abstract
BACKGROUND Assessment and effective utilization of genetic diversity in breeding programs is crucial for sustainable genetic improvement and rapid adaptation to changing breeding objectives. During the past two decades, the commercialization of the early and extra-early maturing cultivars has contributed to rapid expansion of maize into different agro-ecologies of sub-Saharan Africa (SSA) where maize has become an important component of the agricultural economy and played a vital role in food and nutritional security. The present study aimed at understanding the population structure and genetic variability among 439 early and extra-early maize inbred lines developed from three narrow-based and twenty-seven broad-based populations by the International Iinstitute of Tropical Agriculture Maize Improvement Program (IITA-MIP). These inbreds were genotyped using 9642 DArTseq-based single nucleotide polymorphism (SNP) markers distributed uniformly throughout the maize genome. RESULTS About 40.8% SNP markers were found highly informative and exhibited polymorphic information content (PIC) greater than 0.25. The minor allele frequency and PIC ranged from 0.015 to 0.500 and 0.029 to 0.375, respectively. The STRUCTURE, neighbour-joining phylogenetic tree and principal coordinate analysis (PCoA) grouped the inbred lines into four major classes generally consistent with the selection history, ancestry and kernel colour of the inbreds but indicated a complex pattern of the genetic structure. The pattern of grouping of the lines based on the STRUCTURE analysis was in concordance with the results of the PCoA and suggested greater number of sub-populations (K = 10). Generally, the classification of the inbred lines into heterotic groups based on SNP markers was reasonably reliable and in agreement with defined heterotic groups of previously identified testers based on combining ability studies. CONCLUSIONS Complete understanding of potential heterotic groups would be difficult to portray by depending solely on molecular markers. Therefore, planned crosses involving representative testers from opposing heterotic groups would be required to refine the existing heterotic groups. It is anticipated that the present set of inbreds could contribute new beneficial alleles for population improvement, development of hybrids and lines with potential to strengthen future breeding programs. Results of this study would help breeders in formulating breeding strategies for genetic enhancement and sustainable maize production in SSA.
Collapse
Affiliation(s)
- Baffour Badu-Apraku
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, 200001 Nigeria
| | - Ana Luísa Garcia-Oliveira
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, 200001 Nigeria
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, 56237 Texcoco, Mexico
| | - César Daniel Petroli
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, 56237 Texcoco, Mexico
| | - Sarah Hearne
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, 56237 Texcoco, Mexico
| | - Samuel Adeyemi Adewale
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, 200001 Nigeria
| | - Melaku Gedil
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, 200001 Nigeria
| |
Collapse
|
113
|
In-Depth Genetic Diversity and Population Structure of Endangered Peruvian Amazon Rosewood Germplasm Using Genotyping by Sequencing (GBS) Technology. FORESTS 2021. [DOI: 10.3390/f12020197] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Research studies on conservative genetics of endangered plants are very important to establish the management plans for the conservation of biodiversity. Rosewood is an evergreen tree of the Amazon region and its essential oil has great acceptance in the medical and cosmetic industry. The present study aimed to explore the genetic diversity and population structure of 90 rosewood accessions collected from eight localities of Peruvian Amazon territory through DArTseq markers. A total of 7485 informative markers resulted from genotyping by sequencing (GBS) analysis were used for the molecular characterization of rosewood germplasm. Mean values of various calculated diversity parameters like observed number of alleles (1.962), the effective number of alleles (1.669), unbiased expected heterozygosity (0.411), and percent polymorphism (93.51%) over the entire germplasm showed the existence of a good level of genetic variations. Our results showed that the Mairiricay population was more diverse compared to the rest of the populations. Tamshiyacu-2 and Mairiricay-15 accessions were found genetically distinct accessions. The analysis of molecular variance (AMOVA) reflected maximum variations (75%) are due to differences within populations. The implemented clustering algorithms, i.e., STRUCTURE, neighbor-joining analysis and principal coordinate analysis (PCoA) separated the studied germplasm on the basis of their geographical locations. Diversity indices for STRUCTURE-based populations showed that subpopulation A is more diverse population than the rest of the populations, for such reason, individuals belonging to this subpopulation should be used for reintroduction or reinforcement plans of rosewood conservation. We envisage that molecular characterization of Peruvian rosewood germplasm with DArTseq markers will provide a platform for the conservation, management and restoration of endangered rosewood in upcoming years.
Collapse
|
114
|
Strategy of Salt Tolerance and Interactive Impact of Azotobacter chroococcum and/or Alcaligenes faecalis Inoculation on Canola ( Brassica napus L.) Plants Grown in Saline Soil. PLANTS 2021; 10:plants10010110. [PMID: 33430173 PMCID: PMC7825586 DOI: 10.3390/plants10010110] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 12/27/2020] [Accepted: 12/31/2020] [Indexed: 12/11/2022]
Abstract
A pot experiment was designed and performed in a completely randomized block design (CRBD) to determine the main effect of two plant growth-promoting rhizobacteria (PGPR) and their co-inoculation on growth criteria and physio-biochemical attributes of canola plants (Brassica napus L.) plant grown in saline soil. The results showed that inoculation with two PGPR (Azotobacter chroococcum and/or Alcaligenes faecalis) energized the growth parameters and photosynthetic pigments of stressed plants. Moreover, soluble sugars’ and proteins’ contents were boosted due to the treatments mentioned above. Proline, malondialdehyde (MDA), and hydrogen peroxide (H2O2) contents were markedly declined. At the same time, antioxidant enzymes, viz. superoxide dismutase (SOD), ascorbate peroxidase (APX), and peroxidase (POD), were augmented due to the inoculation with Azotobacter chroococcum and/or Alcaligenes faecalis. Regarding minerals’ uptake, there was a decline in sodium (Na) and an increase in nitrogen (N), potassium (K), calcium (Ca), and magnesium (Mg) uptake due to the application of either individual or co-inoculation with the mentioned bacterial isolates. This study showed that co-inoculation with Azotobacter chroococcum and Alcaligenes faecalis was the most effective treatment and could be considered a premium tool used in facing environmental problems, especially saline soils.
Collapse
|
115
|
Molecular breeding for rust resistance in wheat genotypes. Mol Biol Rep 2021; 48:731-742. [PMID: 33389532 DOI: 10.1007/s11033-020-06015-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 11/16/2020] [Indexed: 10/22/2022]
Abstract
Rusts are a group of major diseases that have an adverse effect on crop production. Those targeting wheat are found in three principal forms: leaf, stripe, and stem rust. Leaf rust causes foliar disease in wheat; in Egypt, this causes a significant annual yield loss. The deployment of resistant genotypes has proved to be a relatively economical and environmentally sustainable method of controlling the disease. Gene pyramiding can be performed using traditional breeding techniques. Additionally, pathotypes can be introduced to examine specific leaf rust genes, or the breeder may conduct more complex breeding methods. Indirect selection via DNA markers linked to resistance genes may facilitate the transfer of targeted genes, either individually or in combination, even in a disease-free environment. The use of selective crosses to counter virulent races of leaf, stripe, and stem rust has resulted in the transfer of several resistance genes into new wheat germplasm from cultivated or wild species. Quantitative trait locus (QTL) technology has been adopted in a wide variety of novel approaches and is becoming increasingly recognized in wheat breeding. Moreover, several researchers have reported the transference of leaf and stripe rust resistance genes into susceptible wheat cultivars.
Collapse
|
116
|
Abstract
Understanding biology and genetics at molecular level has become very important for dissection and manipulation of genome architecture for addressing evolutionary and taxonomic questions. Knowledge of genetic variation and genetic relationship among genotypes is an important consideration for classification, utilization of germplasm resources, and breeding. Molecular markers have contributed significantly in this respect and have been widely used in plant science in a number of ways, including genetic fingerprinting, diagnostics, identification of duplicates and selection of core collections, determination of genetic distances, genome analysis, development of molecular maps, and identification of markers associated with desirable breeding traits. The application of molecular markers largely depends on the type of markers employed, distribution of markers in the genome, type of loci they amplify, level of polymorphism, and reproducibility of products. Among many DNA markers available, random amplified polymorphic DNA (RAPD) is the simplest, is cost-effective, and can be performed in a moderate laboratory for most of its applications. In addition, RAPDs can touch much of the genome and has the advantage that no prior knowledge of the genome under research is necessary. The recent improvements in the RAPD technique like arbitrarily primed polymerase chain reaction (AP-PCR), sequence characterized amplified region (SCAR), DNA amplification fingerprinting (DAF), sequence-related amplified polymorphism (SRAP), cleaved amplified polymorphic sequences (CAPS), random amplified microsatellite polymorphism (RAMPO), and random amplified hybridization microsatellites (RAHM) can complement the shortcomings of RAPDs and have enhanced the utility of this simple technique for specific applications. Simple protocols for these techniques are presented along with the applications of RAPD in genetic diversity analysis, mapping, varietal identification, genetic fidelity testing, etc.
Collapse
|
117
|
Letting FK, Venkataramana PB, Ndakidemi PA. Breeding potential of lablab [ Lablab purpureus (L.) Sweet]: a review on characterization and bruchid studies towards improved production and utilization in Africa. GENETIC RESOURCES AND CROP EVOLUTION 2021; 68:3081-3101. [PMID: 34580565 PMCID: PMC8457029 DOI: 10.1007/s10722-021-01271-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 09/14/2021] [Indexed: 05/15/2023]
Abstract
Lablab (Lablab purpureus) [Lablab purpureus (L.) Sweet] is termed a lost, underutilized and neglected crop in Africa. Despite the multipurpose use, production, consumption and research are still limited. Wide genetic diversity of lablab germplasm exists in Africa. Diversity studies provide significant information for subsequent research programs and improvement. The advent of genotyping and sequencing technologies has enabled the identification of unique and agronomically important traits. Application of next-generation sequencing on lablab as a pioneer orphan crop is currently underway. This has enabled description of the whole genome, generation of reference genome and resequencing that provide information on variation within the entire genome. Information from these technological advances helps in identifying potential traits for biotic and abiotic stress for further breeding programs. Storage pests specifically bruchids (Callosobruchus spp.), are considered a major obstacle in lablab production. Screening of available genotypes for bruchid resistance and studies on the physical and biochemical factors that confer resistance in lablab is required. Applying advanced technologies provides precise and reliable identification of the novel markers responsible for bruchid resistance allowing for introgression of important genes to breeding programs. This review provides a detailed analysis on the characterization of lablab and the information on bruchid resistance vital for breeding farmer-preferred varieties that possess agronomically beneficial traits. Concerted efforts and research on this neglected crop will enhance its production, utilization and consumption.
Collapse
Affiliation(s)
- Fanuel K. Letting
- Department of Sustainable Agriculture, Biodiversity and Ecosystems Management, School of Life Science and Bio-Engineering, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
- Department of Seed, Crop and Horticultural Sciences, School of Agriculture and Biotechnology, University of Eldoret, Eldoret, Kenya
| | - Pavithravani B. Venkataramana
- Department of Sustainable Agriculture, Biodiversity and Ecosystems Management, School of Life Science and Bio-Engineering, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| | - Patrick A. Ndakidemi
- Department of Sustainable Agriculture, Biodiversity and Ecosystems Management, School of Life Science and Bio-Engineering, The Nelson Mandela African Institution of Science and Technology, Arusha, Tanzania
| |
Collapse
|
118
|
Kushanov FN, Turaev OS, Ernazarova DK, Gapparov BM, Oripova BB, Kudratova MK, Rafieva FU, Khalikov KK, Erjigitov DS, Khidirov MT, Kholova MD, Khusenov NN, Amanboyeva RS, Saha S, Yu JZ, Abdurakhmonov IY. Genetic Diversity, QTL Mapping, and Marker-Assisted Selection Technology in Cotton ( Gossypium spp.). FRONTIERS IN PLANT SCIENCE 2021; 12:779386. [PMID: 34975965 PMCID: PMC8716771 DOI: 10.3389/fpls.2021.779386] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2021] [Accepted: 11/23/2021] [Indexed: 02/05/2023]
Abstract
Cotton genetic resources contain diverse economically important traits that can be used widely in breeding approaches to create of high-yielding elite cultivars with superior fiber quality and adapted to biotic and abiotic stresses. Nevertheless, the creation of new cultivars using conventional breeding methods is limited by the cost and proved to be time consuming process, also requires a space to make field observations and measurements. Decoding genomes of cotton species greatly facilitated generating large-scale high-throughput DNA markers and identification of QTLs that allows confirmation of candidate genes, and use them in marker-assisted selection (MAS)-based breeding programs. With the advances of quantitative trait loci (QTL) mapping and genome-wide-association study approaches, DNA markers associated with valuable traits significantly accelerate breeding processes by replacing the selection with a phenotype to the selection at the DNA or gene level. In this review, we discuss the evolution and genetic diversity of cotton Gossypium genus, molecular markers and their types, genetic mapping and QTL analysis, application, and perspectives of MAS-based approaches in cotton breeding.
Collapse
Affiliation(s)
- Fakhriddin N. Kushanov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
- *Correspondence: Fakhriddin N. Kushanov, ;
| | - Ozod S. Turaev
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Dilrabo K. Ernazarova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Bunyod M. Gapparov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Barno B. Oripova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Mukhlisa K. Kudratova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Feruza U. Rafieva
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Kuvandik K. Khalikov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Doston Sh. Erjigitov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Mukhammad T. Khidirov
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Madina D. Kholova
- Institute of Genetics and Plant Experimental Biology, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Naim N. Khusenov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| | - Roza S. Amanboyeva
- Department of Biology, National University of Uzbekistan, Tashkent, Uzbekistan
| | - Sukumar Saha
- Crop Science Research Laboratory, USDA-ARS, Washington, DC, United States
| | - John Z. Yu
- Southern Plains Agricultural Research Center, USDA-ARS, Washington, DC, United States
| | - Ibrokhim Y. Abdurakhmonov
- Center of Genomics and Bioinformatics, Academy of Sciences of the Republic of Uzbekistan, Tashkent, Uzbekistan
| |
Collapse
|
119
|
Arsenijević D, Blagojević S, Planojević N, Nikezić A, Vidanović D, Milosavljević N, Marković S. DNA-based molecular identification of Urnula mediterranea (Ascomycota, Pezizales) collected in Central Serbia. KRAGUJEVAC JOURNAL OF SCIENCE 2021. [DOI: 10.5937/kgjsci2143053a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022] Open
Abstract
Molecular systematics is a branch of systematics that analyzes genetic markers for the classification of organisms. Genetic markers include target sequences of molecules DNA, RNA, and amino acids. The most often used genetic markers are DNA markers, localized on DNA molecules. The study aim was DNA-based molecular identification of species Urnula mediterranea (M. Carbone, Agnello & Baglivo) M. Carbone, Agnello & P. Alvarado (2013), by using molecular systematics methods. This species was recently discovered for the first time in Central Serbia and determined only based on morphological characteristics. For the first time, U. mediterranea sampled in Serbia, was identified with DNA molecular markers. Extraction of DNA molecules was performed from the fruiting body of U. mediterranea. ITS region and the part of the gene for 28S rRNA were amplified and sequenced by the Sanger method. Comparing the analyzed sequences with the sequences from the database, a match of 99.72% was found for the ITS region and 100% for the part of the gene for 28S rRNA. By molecular identification, it has been established that the sample belongs to the species U. mediterranea. Both analyzed DNA sequences of U. mediterranea were deposited into the NCBI database.
Collapse
|
120
|
Tsanova T, Stefanova L, Topalova L, Atanasov A, Pantchev I. DNA-free gene editing in plants: a brief overview. BIOTECHNOL BIOTEC EQ 2020. [DOI: 10.1080/13102818.2020.1858159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
Affiliation(s)
- Tsveta Tsanova
- Department of Biochemistry, Faculty of Biology, Sofia University, Sofia, Bulgaria
| | - Lidia Stefanova
- Department of Biochemistry, Faculty of Biology, Sofia University, Sofia, Bulgaria
| | - Lora Topalova
- Department of Biochemistry, Faculty of Biology, Sofia University, Sofia, Bulgaria
| | | | - Ivelin Pantchev
- Department of Biochemistry, Faculty of Biology, Sofia University, Sofia, Bulgaria
- Joint Genomic Center Ltd, Sofia, Bulgaria
| |
Collapse
|
121
|
Kpatènon MJ, Salako KV, Santoni S, Zekraoui L, Latreille M, Tollon-Cordet C, Mariac C, Jaligot E, Beulé T, Adéoti K. Transferability, development of simple sequence repeat (SSR) markers and application to the analysis of genetic diversity and population structure of the African fan palm (Borassus aethiopum Mart.) in Benin. BMC Genet 2020; 21:145. [PMID: 33272218 PMCID: PMC7713368 DOI: 10.1186/s12863-020-00955-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 11/17/2020] [Indexed: 02/08/2023] Open
Abstract
Background In Sub-Saharan Africa, Borassus aethiopum Mart. (African fan palm) is an important non-timber forest product-providing palm that faces multiple anthropogenic threats to its genetic diversity. However, this species is so far under-studied, which prevents its sustainable development as a resource. The present work is a first attempt at characterizing the genetic diversity and population structure of B. aethiopum across nine collection sites spanning the three climatic regions of Benin, West Africa, through the use of microsatellite markers. Results During a first phase we relied on the reported transferability of primers developed in other palm species. We find that, in disagreement with previously published results, only 22.5% of the markers tested enable amplification of B. aethiopum DNA and polymorphism detection is very low. In a second phase, we generated a B. aethiopum-specific genomic dataset through high-throughput sequencing and used it for the de novo detection of microsatellite loci. Among the primer pairs targeting these, 11 detected polymorphisms and were further used for analyzing genetic diversity. Across the nine sites, expected heterozygosity (He) ranges from 0.263 to 0.451 with an overall average of 0.354, showing a low genetic diversity. Analysis of molecular variance (AMOVA) shows that within-site variation accounts for 53% of the genetic variation. Accordingly, the low number of migrants and positive values of the fixation index (F) in sites from both the Central (Sudano-Guinean) and the Southern (Guinean) climatic regions suggest limited gene flow between sites. The global correlation between genetic and geographic distances is weak; however, our clustering analyses indicate that B. aethiopum palms from Savè (Center) are genetically more similar to those from the North than to samples from other Central sites. Conclusions In the light of our results, we discuss the use of inter-species transfer vs. de novo development of microsatellite markers in genetic diversity analyses targeting under-studied species, and suggest future applications for our molecular resources. We propose that, while prominent short-range pollen and seed dispersal in Benin explain most of our results, gene flux between the Central and Northern regions, as a result of animal and/or human migrations, might underlie the Savè discrepancy. Supplementary Information The online version contains supplementary material available at 10.1186/s12863-020-00955-y.
Collapse
Affiliation(s)
- Mariano Joly Kpatènon
- Laboratoire de Microbiologie et de Technologie Alimentaire (LAMITA), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.,Biodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.,DIADE, Univ Montpellier, IRD, Montpellier, France
| | - Kolawolé Valère Salako
- Biodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.,Laboratoire de Biomathématiques et d'Estimations Forestières (LABEF), Faculté des Sciences Agronomiques, Université d'Abomey-Calavi, Cotonou, Bénin
| | - Sylvain Santoni
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | - Muriel Latreille
- AGAP, Univ Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | | | | | - Estelle Jaligot
- DIADE, Univ Montpellier, IRD, Montpellier, France.,CIRAD, UMR DIADE, Montpellier, France
| | - Thierry Beulé
- DIADE, Univ Montpellier, IRD, Montpellier, France.,CIRAD, UMR DIADE, Montpellier, France
| | - Kifouli Adéoti
- Laboratoire de Microbiologie et de Technologie Alimentaire (LAMITA), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin. .,Biodiversité et Ecologie des Plantes (BDEP), Faculté des Sciences et Techniques, Université d'Abomey-Calavi, Cotonou, Bénin.
| |
Collapse
|
122
|
Hernández-Piedra G, Ruiz-Carrera V, Sánchez AJ, Azpeitia-Morales A, Calva-Calva G. Induction of Hairy Roots on Somatic Embryos of Rhizoclones from Typha domingensis Seedlings. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9121679. [PMID: 33271755 PMCID: PMC7760117 DOI: 10.3390/plants9121679] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 05/29/2023]
Abstract
A protocol for the induction of hairy roots on somatic embryos of rhizoclones from Typha domingensis seedlings grown in hydroponic rhizotron systems was established for the first time. Rhizogenesis was induced through the agrotransformation of somatic embryos in oblong and scutellar states of development using the K599, LBA9402, and A4 strains of Agrobacterium rhizogenes. The transfection to the embryos was performed by cocultivation of rhizoclones on a Murashige and Skoog mineral medium at 50% strength (MS0.5), in the dark, at 28 ± 2 °C for 72 h. In contrast to nontransformed embryos that did not exhibit any root tissue, transformed embryos presented hairy roots that varied in number, length, and density depending on the bacterial strain, and K599 was the most effective strain. After analysis via optical microscopy, the transformed embryos were collected and transferred to fresh culture media supplemented with 400 mg mL-1 cefotaxime and 10 mg L-1 ascorbic acid. The efficiency of transformation and survival of the oblong and scutellar embryos were similar among the three bacterial strains. The results show that agrotransformation of somatic embryos of rhizoclones from T. domingensis is a novel and viable strategy for the generation of genetic transformants of Typha that have potential applications in bioremediation technologies.
Collapse
Affiliation(s)
- Guadalupe Hernández-Piedra
- Programa de Doctorado en Ecología y Manejo de Sistemas Tropicales, Universidad Juárez Autónoma de Tabasco, Carretera Villahermosa-Cárdenas Km. 0.5 S/N Entronque a Bosques de Saloya, Villahermosa 86150, Tabasco, Mexico
| | - Violeta Ruiz-Carrera
- Diagnóstico y Manejo de Humedales Tropicales, Universidad Juárez Autónoma de Tabasco, Carretera Villahermosa-Cárdenas Km. 0.5 S/N Entronque a Bosques de Saloya, Villahermosa 86150, Tabasco, Mexico;
| | - Alberto J. Sánchez
- Diagnóstico y Manejo de Humedales Tropicales, Universidad Juárez Autónoma de Tabasco, Carretera Villahermosa-Cárdenas Km. 0.5 S/N Entronque a Bosques de Saloya, Villahermosa 86150, Tabasco, Mexico;
| | - Alfonso Azpeitia-Morales
- Campo Experimental Huimanguillo, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias, Huimanguillo, Km. 1 Carretera Huimanguillo-Cárdenas, Huimanguillo 86400, Tabasco, Mexico;
| | - Graciano Calva-Calva
- Biotecnología y Bioingeniería, Centro de Investigación y de Estudios Avanzados del IPN, Avenida Instituto Politécnico Nacional 2508, Colonia San Pedro Zacatenco, Ciudad de México 07360, Mexico;
| |
Collapse
|
123
|
Yang T, Miller M, Forgacs D, Derr J, Stothard P. Development of SNP-Based Genomic Tools for the Canadian Bison Industry: Parentage Verification and Subspecies Composition. Front Genet 2020; 11:585999. [PMID: 33329724 PMCID: PMC7714993 DOI: 10.3389/fgene.2020.585999] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/28/2020] [Indexed: 11/30/2022] Open
Abstract
Genomic technologies have been increasingly applied in livestock production due to their utility in production management and animal genetic improvement. The current project aimed to develop genomic resources for the Canadian bison industry, specifically a parentage verification tool and a subspecies composition tool. Both products stand to help with building and maintaining purebred and crossbred bison populations, and in turn bison conservation and production. The development of this genomic toolkit proceeded in two stages. In the single-nucleotide polymorphism (SNP) discovery and selection stage, raw sequence information from 41 bison samples was analyzed, and approximately 52.5 million candidate biallelic SNPs were discovered from 21 samples with high sequence quality. A set of 19,954 SNPs (2,928 for parentage verification and 17,026 for subspecies composition) were then selected for inclusion on an Axiom myDesign custom array. In the refinement and validation stage, 480 bison were genotyped using the custom SNP panel, and the resulting genotypes were analyzed to further filter SNPs and assess tool performance. In various tests using real and simulated genotypes, the two genomic tools showed excellent performance for their respective tasks. Final SNP sets consisting of 191 SNPs for parentage and 17,018 SNPs for subspecies composition are described. As the first SNP-based genomic toolkit designed for the Canadian bison industry, our results may provide a new opportunity in improving the competitiveness and profitability of the industry in a sustainable manner.
Collapse
Affiliation(s)
- Tianfu Yang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | | | - David Forgacs
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - James Derr
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|
124
|
Cibecchini G, Cecere P, Tumino G, Morcia C, Ghizzoni R, Carnevali P, Terzi V, Pompa PP. A Fast, Naked-Eye Assay for Varietal Traceability in the Durum Wheat Production Chain. Foods 2020; 9:foods9111691. [PMID: 33228015 PMCID: PMC7699333 DOI: 10.3390/foods9111691] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Revised: 11/05/2020] [Accepted: 11/13/2020] [Indexed: 01/08/2023] Open
Abstract
The development of a colorimetric mono-varietal discriminating assay, aimed at improving traceability and quality control checks of durum wheat products, is described. A single nucleotide polymorphism (SNP) was identified as a reliable marker for wheat varietal discrimination, and a rapid test for easy and clear identification of specific wheat varieties was developed. Notably, an approach based on the loop-mediated isothermal amplification reaction (LAMP) as an SNP discrimination tool, in combination with naked-eye visualization of the results, was designed and optimized. Our assay was proven to be effective in the detection of adulterated food products, including both substitution and mixing with different crop varieties.
Collapse
Affiliation(s)
- Giulia Cibecchini
- Istituto Italiano di Tecnologia, Nanobiointeractions & Nanodiagnostics, Via Morego 30, 16163 Genova, Italy; (G.C.); (P.C.)
- Department of Chemistry and Industrial Chemistry, University of Genova, Via Dodecaneso 31, 16146 Genova, Italy
| | - Paola Cecere
- Istituto Italiano di Tecnologia, Nanobiointeractions & Nanodiagnostics, Via Morego 30, 16163 Genova, Italy; (G.C.); (P.C.)
| | - Giorgio Tumino
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via San Protaso 302, 29017 Fiorenzuola d’Arda PC, Italy; (G.T.); (C.M.); (R.G.)
| | - Caterina Morcia
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via San Protaso 302, 29017 Fiorenzuola d’Arda PC, Italy; (G.T.); (C.M.); (R.G.)
| | - Roberta Ghizzoni
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via San Protaso 302, 29017 Fiorenzuola d’Arda PC, Italy; (G.T.); (C.M.); (R.G.)
| | | | - Valeria Terzi
- Council for Agricultural Research and Economics, Research Centre for Genomics and Bioinformatics, Via San Protaso 302, 29017 Fiorenzuola d’Arda PC, Italy; (G.T.); (C.M.); (R.G.)
- Correspondence: (V.T.); (P.P.P.)
| | - Pier Paolo Pompa
- Istituto Italiano di Tecnologia, Nanobiointeractions & Nanodiagnostics, Via Morego 30, 16163 Genova, Italy; (G.C.); (P.C.)
- Correspondence: (V.T.); (P.P.P.)
| |
Collapse
|
125
|
Yang R, Fan B, Wang S, Li L, Li Y, Li S, Zheng Y, Fu L, Lin CT. Electrochemical Voltammogram Recording for Identifying Varieties of Ornamental Plants. MICROMACHINES 2020; 11:E967. [PMID: 33138269 PMCID: PMC7693950 DOI: 10.3390/mi11110967] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Revised: 10/24/2020] [Accepted: 10/25/2020] [Indexed: 02/07/2023]
Abstract
An electrochemical voltammogram recording method for plant variety identification is proposed. Electrochemical voltammograms of Vistula, Andromeda, Danuta, Armandii 'Apple Blossom,' Proteus, Hagley Hybrid, Violet Elizabeth, Kiri Te Kanawa, Regina, and Veronica's Choice were recorded using leaf extracts with two solvents under buffer solutions. The voltametric data recorded under different conditions were derived as scatter plots, 2D density patterns, and hot maps for variety identification. In addition, the voltametric data were further used for genetic relationship studies. The dendrogram deduced from the voltammograms was used as evidence for relationship study. The dendrogram deduced from voltametric data suggested the Andromeda, Danuta, Proteus, Regina, and Hagley Hybrid were closely related, while Violet Elizabeth and Veronica's Choice were closely related. In addition, Vistula and Armandii 'Apple Blossom' could be considered outliers among the varieties.
Collapse
Affiliation(s)
- Rutong Yang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (R.Y.); (S.W.); (L.L.); (S.L.); (Y.Z.)
| | - Boyuan Fan
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, China;
| | - Shu’an Wang
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (R.Y.); (S.W.); (L.L.); (S.L.); (Y.Z.)
| | - Linfang Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (R.Y.); (S.W.); (L.L.); (S.L.); (Y.Z.)
| | - Ya Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (R.Y.); (S.W.); (L.L.); (S.L.); (Y.Z.)
| | - Sumei Li
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (R.Y.); (S.W.); (L.L.); (S.L.); (Y.Z.)
| | - Yuhong Zheng
- Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China; (R.Y.); (S.W.); (L.L.); (S.L.); (Y.Z.)
| | - Li Fu
- College of Materials and Environmental Engineering, Hangzhou Dianzi University, Hangzhou 310018, China;
| | - Cheng-Te Lin
- Key Laboratory of Marine Materials and Related Technologies, Zhejiang Key Laboratory of Marine Materials and Protective Technologies, Ningbo Institute of Materials Technology and Engineering (NIMTE), Chinese Academy of Sciences, Ningbo 315201, China;
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
126
|
Raw transcriptomics data to gene specific SSRs: a validated free bioinformatics workflow for biologists. Sci Rep 2020; 10:18236. [PMID: 33106560 PMCID: PMC7588437 DOI: 10.1038/s41598-020-75270-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2019] [Accepted: 09/21/2020] [Indexed: 02/07/2023] Open
Abstract
Recent advances in next-generation sequencing technologies have paved the path for a considerable amount of sequencing data at a relatively low cost. This has revolutionized the genomics and transcriptomics studies. However, different challenges are now created in handling such data with available bioinformatics platforms both in assembly and downstream analysis performed in order to infer correct biological meaning. Though there are a handful of commercial software and tools for some of the procedures, cost of such tools has made them prohibitive for most research laboratories. While individual open-source or free software tools are available for most of the bioinformatics applications, those components usually operate standalone and are not combined for a user-friendly workflow. Therefore, beginners in bioinformatics might find analysis procedures starting from raw sequence data too complicated and time-consuming with the associated learning-curve. Here, we outline a procedure for de novo transcriptome assembly and Simple Sequence Repeats (SSR) primer design solely based on tools that are available online for free use. For validation of the developed workflow, we used Illumina HiSeq reads of different tissue samples of Santalum album (sandalwood), generated from a previous transcriptomics project. A portion of the designed primers were tested in the lab with relevant samples and all of them successfully amplified the targeted regions. The presented bioinformatics workflow can accurately assemble quality transcriptomes and develop gene specific SSRs. Beginner biologists and researchers in bioinformatics can easily utilize this workflow for research purposes.
Collapse
|
127
|
Neik TX, Amas J, Barbetti M, Edwards D, Batley J. Understanding Host-Pathogen Interactions in Brassica napus in the Omics Era. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1336. [PMID: 33050509 PMCID: PMC7599536 DOI: 10.3390/plants9101336] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/02/2020] [Accepted: 10/06/2020] [Indexed: 12/12/2022]
Abstract
Brassica napus (canola/oilseed rape/rapeseed) is an economically important crop, mostly found in temperate and sub-tropical regions, that is cultivated widely for its edible oil. Major diseases of Brassica crops such as Blackleg, Clubroot, Sclerotinia Stem Rot, Downy Mildew, Alternaria Leaf Spot and White Rust have caused significant yield and economic losses in rapeseed-producing countries worldwide, exacerbated by global climate change, and, if not remedied effectively, will threaten global food security. To gain further insights into the host-pathogen interactions in relation to Brassica diseases, it is critical that we review current knowledge in this area and discuss how omics technologies can offer promising results and help to push boundaries in our understanding of the resistance mechanisms. Omics technologies, such as genomics, proteomics, transcriptomics and metabolomics approaches, allow us to understand the host and pathogen, as well as the interaction between the two species at a deeper level. With these integrated data in multi-omics and systems biology, we are able to breed high-quality disease-resistant Brassica crops in a more holistic, targeted and accurate way.
Collapse
Affiliation(s)
- Ting Xiang Neik
- Sunway College Kuala Lumpur, Bandar Sunway 47500, Selangor, Malaysia;
| | - Junrey Amas
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
| | - Martin Barbetti
- School of Agriculture and Environment and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia;
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
| | - Jacqueline Batley
- School of Biological Sciences and Institute of Agriculture, The University of Western Australia, Perth 6009, Australia; (J.A.); (D.E.)
| |
Collapse
|
128
|
El Zayat MAS, Ali MES, Amar MH. A systematic revision of Capparaceae and Cleomaceae in Egypt: an evaluation of the generic delimitations of Capparis and Cleome using ecological and genetic diversity. J Genet Eng Biotechnol 2020; 18:58. [PMID: 33025275 PMCID: PMC7538494 DOI: 10.1186/s43141-020-00069-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 09/02/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND The Capparaceae family is commonly recognized as a caper, while Cleomaceae represents one of small flowering family within the order Brassicales. Earlier, Cleomaceae was included in the family Capparaceae; then, it was moved to a distinct family after DNA evidence. Variation in habits and a bewildering array of floral and fruit forms contributed to making Capparaceae a "trash-basket" family in which many unrelated plants were placed. Indeed, family Capparaceae and Cleomaceae are in clear need of more detailed systematic revision. RESULTS Here, in the present study, the morphological characteristics and the ecological distribution as well as the genetic diversity analysis among the twelve species of both Capparaceae and Cleomaceae have been determined. The genetic analysis has been checked using 15 ISSR, 30 SRAP, and 18 ISTR to assess the systematic knots between the two families. In order to detect the molecular phylogeny, a comparative analysis of the three markers was performed based on the exposure of discriminating capacity, efficiency, and phylogenetic heatmap. Our results indicated that there is a morphological and ecological variation between the two families. Moreover, the molecular analysis confirmed that ISTR followed by SRAP markers has superior discriminating capacity for describing the genetic diversity and is able to simultaneously distinguish many polymorphic markers per reaction. Indeed, both the PCA and HCA data have drawn a successful annotation relationship in Capparaceae and Cleome species to evaluate whether the specific group sort individual or overlap groups. CONCLUSION The outcomes of the morphological and ecological characterization along with the genetic diversity indicated an insight solution thorny interspecies in Cleome and Gynandropsis genera as a distinct family (Cleomaceae) and the other genera (Capparis, Cadaba, Boscia, and Maerua) as Capparaceae. Finally, we recommended further studies to elucidate the systematic position of Dipterygium glaucum.
Collapse
|
129
|
|
130
|
Anteyi WO, Rasche F. Population genetic structure and marker-trait associations in East and West African Striga hermonthica with varying phenotypic response to Fusarium oxysporum f. sp. strigae isolates Foxy-2 and FK3. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:391-402. [PMID: 32654253 DOI: 10.1111/tpj.14930] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 06/11/2020] [Accepted: 07/03/2020] [Indexed: 06/11/2023]
Abstract
To examine the genetic basis for the variable susceptibility of Striga hermonthica from differing zones of sub-Saharan Africa to Fusarium oxysporum f. sp. strigae (Fos) isolates Foxy-2 and FK3, 10 S. hermonthica populations from Eastern and Western Africa were phenotyped for their susceptibility response to Foxy-2 and FK3, and then genotyped with 22 simple sequence repeat (SSR) markers. There is low genetic differentiation between East African and West African S. hermonthica populations (i.e. the proportion of the total genetic variance contained in the subpopulation relative to the total genetic variance, FST = 0.012, P < 0.05), but intermediate genetic differentiation (FST = 0.143, P < 0.01) underlies the S. hermonthica groups that are differentiated by their phenotypic responses to Fos isolates. An expressed sequence tag SSR (EST-SSR) marker Y53 (P < 0.01) and a genomic SSR marker E1009 (P < 0.05) were associated with the S. hermonthica class susceptible to Foxy-2 and FK3 (group A). A divergent S. hermonthica class, consisting of groups with intermediate susceptibility to Foxy-2 (group B) and susceptibility to either FK3 (group C) or Foxy-2 (group D), showed no marker-trait association, instead demonstrated linkage disequilibrium decay. Owing to point substitutions and insertion-deletion mutations, the unique, protein-coding nucleotide sequence at the E1009 locus in group A was partly dissimilar to group B, but was totally distinct from groups C and D. These findings implied that the inconsistent effectiveness of a Fos isolate is better explained by genomic variation in S. hermonthica, rather than by S. hermonthica sampling zones.
Collapse
Affiliation(s)
- Williams Oyifioda Anteyi
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, 70593, Germany
| | - Frank Rasche
- Institute of Agricultural Sciences in the Tropics (Hans-Ruthenberg-Institute), University of Hohenheim, Stuttgart, 70593, Germany
| |
Collapse
|
131
|
Saidi A, Hajibarat Z. Application of Next Generation Sequencing, GWAS, RNA seq, WGRS, for genetic improvement of potato (Solanum tuberosum L.) under drought stress. BIOCATALYSIS AND AGRICULTURAL BIOTECHNOLOGY 2020. [DOI: 10.1016/j.bcab.2020.101801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
|
132
|
Ton LB, Neik TX, Batley J. The Use of Genetic and Gene Technologies in Shaping Modern Rapeseed Cultivars ( Brassica napus L.). Genes (Basel) 2020; 11:E1161. [PMID: 33008008 PMCID: PMC7600269 DOI: 10.3390/genes11101161] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 09/27/2020] [Accepted: 09/27/2020] [Indexed: 12/20/2022] Open
Abstract
Since their domestication, Brassica oilseed species have undergone progressive transformation allied with the development of breeding and molecular technologies. The canola (Brassica napus) crop has rapidly expanded globally in the last 30 years with intensive innovations in canola varieties, providing for a wider range of markets apart from the food industry. The breeding efforts of B. napus, the main source of canola oil and canola meal, have been mainly focused on improving seed yield, oil quality, and meal quality along with disease resistance, abiotic stress tolerance, and herbicide resistance. The revolution in genetics and gene technologies, including genetic mapping, molecular markers, genomic tools, and gene technology, especially gene editing tools, has allowed an understanding of the complex genetic makeup and gene functions in the major bioprocesses of the Brassicales, especially Brassica oil crops. Here, we provide an overview on the contributions of these technologies in improving the major traits of B. napus and discuss their potential use to accomplish new improvement targets.
Collapse
Affiliation(s)
- Linh Bao Ton
- School of Biological Science, The University of Western Australia, Perth, WA 6009, Australia;
| | - Ting Xiang Neik
- Sunway College Kuala Lumpur, No. 2, Jalan Universiti, Bandar Sunway, Selangor 47500, Malaysia;
| | - Jacqueline Batley
- School of Biological Science, The University of Western Australia, Perth, WA 6009, Australia;
| |
Collapse
|
133
|
Vu NTT, Zenger KR, Guppy JL, Sellars MJ, Silva CNS, Kjeldsen SR, Jerry DR. Fine-scale population structure and evidence for local adaptation in Australian giant black tiger shrimp (Penaeus monodon) using SNP analysis. BMC Genomics 2020; 21:669. [PMID: 32993495 PMCID: PMC7526253 DOI: 10.1186/s12864-020-07084-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 09/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Restrictions to gene flow, genetic drift, and divergent selection associated with different environments are significant drivers of genetic differentiation. The black tiger shrimp (Penaeus monodon), is widely distributed throughout the Indian and Pacific Oceans including along the western, northern and eastern coastline of Australia, where it is an important aquaculture and fishery species. Understanding the genetic structure and the influence of environmental factors leading to adaptive differences among populations of this species is important for farm genetic improvement programs and sustainable fisheries management. RESULTS Based on 278 individuals obtained from seven geographically disparate Australian locations, 10,624 high-quality SNP loci were used to characterize genetic diversity, population structure, genetic connectivity, and adaptive divergence. Significant population structure and differentiation were revealed among wild populations (average FST = 0.001-0.107; p < 0.05). Eighty-nine putatively outlier SNPs were identified to be potentially associated with environmental variables by using both population differentiation (BayeScan and PCAdapt) and environmental association (redundancy analysis and latent factor mixed model) analysis methods. Clear population structure with similar spatial patterns were observed in both neutral and outlier markers with three genetically distinct groups identified (north Queensland, Northern Territory, and Western Australia). Redundancy, partial redundancy, and multiple regression on distance matrices analyses revealed that both geographical distance and environmental factors interact to generate the structure observed across Australian P. monodon populations. CONCLUSION This study provides new insights on genetic population structure of Australian P. monodon in the face of environmental changes, which can be used to advance sustainable fisheries management and aquaculture breeding programs.
Collapse
Affiliation(s)
- Nga T T Vu
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia. .,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.
| | - Kyall R Zenger
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Jarrod L Guppy
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Melony J Sellars
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia.,CSIRO Agriculture & Food, Integrated Sustainable Aquaculture Production Program, Queensland Bioscience Precinct, St Lucia, 4067, Australia.,Present address: Genics Pty Ltd, Level 5, Gehrmann Building. 60 Research Road, St Lucia, QLD, 4067, Australia
| | - Catarina N S Silva
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Shannon R Kjeldsen
- Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia
| | - Dean R Jerry
- Australian Research Council Industrial Transformation Research Hub for Advanced Prawn Breeding, James Cook University, Townsville, QLD, 4811, Australia.,Centre for Sustainable Tropical Fisheries and Aquaculture, College of Science and Engineering, James Cook University, Townsville, QLD, 4811, Australia.,Tropical Futures Institute, James Cook University, Singapore, Singapore
| |
Collapse
|
134
|
Ku YS, Contador CA, Ng MS, Yu J, Chung G, Lam HM. The Effects of Domestication on Secondary Metabolite Composition in Legumes. Front Genet 2020; 11:581357. [PMID: 33193705 PMCID: PMC7530298 DOI: 10.3389/fgene.2020.581357] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 08/31/2020] [Indexed: 12/13/2022] Open
Abstract
Legumes are rich in secondary metabolites, such as polyphenols, alkaloids, and saponins, which are important defense compounds to protect the plant against herbivores and pathogens, and act as signaling molecules between the plant and its biotic environment. Legume-sourced secondary metabolites are well known for their potential benefits to human health as pharmaceuticals and nutraceuticals. During domestication, the color, smell, and taste of crop plants have been the focus of artificial selection by breeders. Since these agronomic traits are regulated by secondary metabolites, the basis behind the genomic evolution was the selection of the secondary metabolite composition. In this review, we will discuss the classification, occurrence, and health benefits of secondary metabolites in legumes. The differences in their profiles between wild legumes and their cultivated counterparts will be investigated to trace the possible effects of domestication on secondary metabolite compositions, and the advantages and drawbacks of such modifications. The changes in secondary metabolite contents will also be discussed at the genetic level to examine the genes responsible for determining the secondary metabolite composition that might have been lost due to domestication. Understanding these genes would enable breeding programs and metabolic engineering to produce legume varieties with favorable secondary metabolite profiles for facilitating adaptations to a changing climate, promoting beneficial interactions with biotic factors, and enhancing health-beneficial secondary metabolite contents for human consumption.
Collapse
Affiliation(s)
- Yee-Shan Ku
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Carolina A. Contador
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Ming-Sin Ng
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| | - Jeongjun Yu
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Yeosu, South Korea
| | - Hon-Ming Lam
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, China
| |
Collapse
|
135
|
Stanley A, Menkir A, Paterne A, Ifie B, Tongoona P, Unachukwu N, Meseka S, Mengesha W, Gedil M. Genetic Diversity and Population Structure of Maize Inbred Lines with Varying Levels of Resistance to Striga Hermonthica Using Agronomic Trait-Based and SNP Markers. PLANTS (BASEL, SWITZERLAND) 2020; 9:E1223. [PMID: 32957613 PMCID: PMC7570130 DOI: 10.3390/plants9091223] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 11/17/2022]
Abstract
Striga hermonthica is a serious biotic stress limiting maize production in sub-Saharan Africa. The limited information on the patterns of genetic diversity among maize inbred lines derived from source germplasm with mixed genetic backgrounds limits the development of inbred lines, hybrids, and synthetics with durable resistance to S. hermonthica. This study was conducted to assess the level of genetic diversity in a panel of 150 diverse maize inbred lines using agronomic and molecular data and also to infer the population structure among the inbred lines. Ten Striga-resistance-related traits were used for the phenotypic characterization, and 16,735 high-quality single-nucleotide polymorphisms (SNPs), identified by genotyping-by-sequencing (GBS), were used for molecular diversity. The phenotypic and molecular hierarchical cluster analyses grouped the inbred lines into five clusters, respectively. However, the grouping patterns between the phenotypic and molecular hierarchical cluster analyses were inconsistent due to non-overlapping information between the phenotypic and molecular data. The correlation between the phenotypic and molecular diversity matrices was very low (0.001), which is in agreement with the inconsistencies observed between the clusters formed by the phenotypic and molecular diversity analyses. The joint phenotypic and genotypic diversity matrices grouped the inbred lines into three groups based on their reaction patterns to S. hermonthica, and this was able to exploit a broad estimate of the actual diversity among the inbred lines. The joint analysis shows an invaluable insight for measuring genetic diversity in the evaluated materials. The result indicates that wide genetic variability exists among the inbred lines and that the joint diversity analysis can be utilized to reliably assign the inbred lines into heterotic groups and also to enhance the level of resistance to Striga in new maize varieties.
Collapse
Affiliation(s)
- Adekemi Stanley
- West Africa Centre for Crop Improvement University of Ghana, Legon PMB 30, Ghana; (A.S.); (B.I.); (P.T.)
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria; (A.P.); (N.U.); (S.M.); (W.M.); (M.G.)
| | - Abebe Menkir
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria; (A.P.); (N.U.); (S.M.); (W.M.); (M.G.)
| | - Agre Paterne
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria; (A.P.); (N.U.); (S.M.); (W.M.); (M.G.)
| | - Beatrice Ifie
- West Africa Centre for Crop Improvement University of Ghana, Legon PMB 30, Ghana; (A.S.); (B.I.); (P.T.)
| | - Pangirayi Tongoona
- West Africa Centre for Crop Improvement University of Ghana, Legon PMB 30, Ghana; (A.S.); (B.I.); (P.T.)
| | - Nnanna Unachukwu
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria; (A.P.); (N.U.); (S.M.); (W.M.); (M.G.)
| | - Silvestro Meseka
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria; (A.P.); (N.U.); (S.M.); (W.M.); (M.G.)
| | - Wende Mengesha
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria; (A.P.); (N.U.); (S.M.); (W.M.); (M.G.)
| | - Melaku Gedil
- International Institute of Tropical Agriculture (IITA), Ibadan 200001, Nigeria; (A.P.); (N.U.); (S.M.); (W.M.); (M.G.)
| |
Collapse
|
136
|
Zhang J, Yan J, Huang S, Pan G, Chang L, Li J, Zhang C, Tang H, Chen A, Peng D, Biswas A, Zhang C, Zhao L, Li D. Genetic Diversity and Population Structure of Cannabis Based on the Genome-Wide Development of Simple Sequence Repeat Markers. Front Genet 2020; 11:958. [PMID: 33061939 PMCID: PMC7518120 DOI: 10.3389/fgene.2020.00958] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Accepted: 07/30/2020] [Indexed: 12/20/2022] Open
Abstract
Cannabis has been used as a source of nutrition, medicine, and fiber. However, lack of genomic simple sequence repeat (SSR) markers had limited the genetic research on Cannabis species. In the present study, 92,409 motifs were identified, and 63,707 complementary SSR primer pairs were developed. The most abundant SSR motifs had six repeat units (36.60%). The most abundant type of motif was dinucleotides (70.90%), followed by trinucleotides, tetranucleotides, and pentanucleotides. We randomly selected 80 pairs of genomic SSR markers, of which 69 (86.25%) were amplified successfully; 59 (73.75%) of these were polymorphic. Genetic diversity and population structure were estimated using the 59 (72 loci) validated polymorphic SSRs and three phenotypic markers. Three hundred ten alleles were identified, and the major allele frequency ranged from 0.26 to 0.85 (average: 0.56), Nei’s genetic diversity ranged from 0.28 to 0.82 (average: 0.56), and the expected heterozygosity ranged from 0.28 to 0.81 (average: 0.56). The polymorphism information content ranged from 0.25 to 0.79 (average: 0.50), the observed number of alleles ranged from 2 to 8 (average: 4.13), and the effective number of alleles ranged from 0.28 to 0.81 (average: 0.5). The Cannabis population did not show mutation-drift equilibrium following analysis via the infinite allele model. A cluster analysis was performed using the unweighted pair group method using arithmetic means based on genetic distances. Population structure analysis was used to divide the germplasms into two subgroups. These results provide guidance for the molecular breeding and further investigation of Cannabis.
Collapse
Affiliation(s)
- Jiangjiang Zhang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Jiangtao Yan
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Siqi Huang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Gen Pan
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Li Chang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Jianjun Li
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Chao Zhang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Huijuan Tang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Anguo Chen
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Dingxiang Peng
- MOA Key Laboratory of Crop Ecophysiology and Farming System in the Middle Reaches of the Yangtze River, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Ashok Biswas
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China
| | - Cuiping Zhang
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Lining Zhao
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| | - Defang Li
- Research Team of Genetic Modification of Annual Bast Fiber Crops, Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, China.,Key Laboratory of Biological and Processing for Bast Fiber Crops, Ministry of Agriculture, Changsha, China
| |
Collapse
|
137
|
Application of Pedimap: a pedigree visualization tool to facilitate the decisioning of rice breeding in Sri Lanka. Sci Rep 2020; 10:14255. [PMID: 32868819 PMCID: PMC7459290 DOI: 10.1038/s41598-020-71260-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 07/21/2020] [Indexed: 11/09/2022] Open
Abstract
The development of rice cultivars with desirable traits is essential. The decision-making is a crucial step in rice breeding programs. Breeders can make efficient and pragmatic decisions if an organized pedigree visualization platform is available for the accessions and cultivars in rice breeding germplasm. In the present study, the available data of all the rice varieties released by Rice Research and Development Institute, Sri Lanka, and the related landraces and genotypes were arranged in Pedimap, a pedigree visualization tool. Pedimap can showcase pedigree relationships, phenotypic, and molecular data. The identity by descent probabilities were calculated using FlexQTL software and included in the Pedimap database. The parentage selection based on the variations of phenotypic traits, selection of marker alleles for molecular breeding, and detection of the founders of genetic effects can be swiftly conducted using Pedimap. However, the power of harnessing the value of Pedimap for making breeding decisions relies on the availability of data for the traits, markers, and genomic sequences. Thus, it is imperative to characterize the breeding germplasms using standard phenomic and genomic characterization procedures such as the assessment of before organized into Pedimap. Thereby, the worldwide breeding programs can benefit from each other to produce improved varieties to meet global challenges.
Collapse
|
138
|
Labate JA, Glaubitz JC, Havey MJ. Genotyping by sequencing for SNP marker development in onion. Genome 2020; 63:607-613. [PMID: 32853533 DOI: 10.1139/gen-2020-0011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Onion (Allium cepa) is not highly tractable for development of molecular markers due to its large (16 gigabases per 1C) nuclear genome. Single nucleotide polymorphisms (SNPs) are useful for genetic characterization and marker-aided selection of onion because of codominance and common occurrence in elite germplasm. We completed genotyping by sequencing (GBS) to identify SNPs in onion using 46 F2 plants, parents of the F2 plants (Ailsa Craig 43 and Brigham Yellow Globe 15-23), two doubled haploid (DH) lines (DH2107 and DH2110), and plants from 94 accessions in the USDA National Plant Germplasm System (NPGS). SNPs were called using the TASSEL 3.0 Universal Network Enabled Analysis (UNEAK) bioinformatics pipeline. Sequences from the F2 and DH plants were used to construct a pseudo-reference genome against which genotypes from all accessions were scored. Quality filters were used to identify a set of 284 high quality SNPs, which were placed onto an existing genetic map for the F2 family. Accessions showed a moderate level of diversity (mean He = 0.341) and evidence of inbreeding (mean F = 0.592). GBS is promising for SNP discovery in onion, although lack of a reference genome required extensive custom scripts for bioinformatics analyses to identify high quality markers.
Collapse
Affiliation(s)
- Joanne A Labate
- Plant Genetic Resources Unit, United States Department of Agriculture, Agricultural Research Service, 630 W. North St., Geneva, NY 14456, USA
| | - Jeffrey C Glaubitz
- Institute of Biotechnology, 526 Campus Rd., Cornell University, Ithaca, NY 14853, USA
| | - Michael J Havey
- Vegetable Crop Research Unit, United States Department of Agriculture, Agricultural Research Service, 1575 Linden Drive, Madison, WI 53706, USA
| |
Collapse
|
139
|
Gene Pyramiding for Sustainable Crop Improvement against Biotic and Abiotic Stresses. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10091255] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Sustainable agricultural production is endangered by several ecological factors, such as drought, extreme temperatures, excessive salts, parasitic ailments, and insect pest infestation. These challenging environmental factors may have adverse effects on future agriculture production in many countries. In modern agriculture, conventional crop-breeding techniques alone are inadequate for achieving the increasing population’s food demand on a sustainable basis. The advancement of molecular genetics and related technologies are promising tools for the selection of new crop species. Gene pyramiding through marker-assisted selection (MAS) and other techniques have accelerated the development of durable resistant/tolerant lines with high accuracy in the shortest period of time for agricultural sustainability. Gene stacking has not been fully utilized for biotic stress resistance development and quality improvement in most of the major cultivated crops. This review emphasizes on gene pyramiding techniques that are being successfully deployed in modern agriculture for improving crop tolerance to biotic and abiotic stresses for sustainable crop improvement.
Collapse
|
140
|
Enciso-Rodríguez FE, Osorio-Guarín JA, Garzón-Martínez GA, Delgadillo-Duran P, Barrero LS. Optimization of the genotyping-by-sequencing SNP calling for diversity analysis in cape gooseberry (Physalis peruviana L.) and related taxa. PLoS One 2020; 15:e0238383. [PMID: 32845934 PMCID: PMC7449456 DOI: 10.1371/journal.pone.0238383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/14/2020] [Indexed: 12/03/2022] Open
Abstract
A robust Genotyping-By-Sequencing (GBS) pipeline platform was examined to provide accurate discovery of Single Nucleotide Polymorphisms (SNPs) in a cape gooseberry (Physalis peruviana L.) and related taxa germplasm collection. A total of 176 accessions representing, wild, weedy, and commercial cultivars as well as related taxa from the Colombian germplasm bank and other world repositories were screened using GBS. The pipeline parameters mnLCov of 0.5 and a mnScov of 0.7, tomato and potato genomes, and cape gooseberry transcriptome for read alignments, were selected to better assess diversity and population structure in cape gooseberry and related taxa. A total of 7,425 SNPs, derived from P. peruviana common tags (unique 64 bp sequences shared between selected species), were used. Within P. peruviana, five subpopulations with a high genetic diversity and allele fixation (HE: 0.35 to 0.36 and FIS: -0.11 to -0.01, respectively) were detected. Conversely, low genetic differentiation (FST: 0.01 to 0.05) was also observed, indicating a high gene flow among subpopulations. These results contribute to the establishment of adequate conservation and breeding strategies for Cape gooseberry and closely related Physalis species.
Collapse
Affiliation(s)
- Felix E. Enciso-Rodríguez
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria–Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Jaime A. Osorio-Guarín
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria–Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Gina A. Garzón-Martínez
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria–Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Paola Delgadillo-Duran
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria–Agrosavia, Mosquera, Cundinamarca, Colombia
| | - Luz Stella Barrero
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria–Agrosavia, Mosquera, Cundinamarca, Colombia
- * E-mail:
| |
Collapse
|
141
|
Lee SI, Park JW, Kwon SJ, Jo YD, Hong MJ, Kim JB, Choi HI. Epigenetic Variation Induced by Gamma Rays, DNA Methyltransferase Inhibitors, and Their Combination in Rice. PLANTS 2020; 9:plants9091088. [PMID: 32847097 PMCID: PMC7570246 DOI: 10.3390/plants9091088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/16/2020] [Accepted: 08/19/2020] [Indexed: 02/07/2023]
Abstract
DNA methylation plays important roles in the regulation of gene expression and maintenance of genome stability in many organisms, including plants. In this study, we treated rice with gamma rays (GRs) and DNA methyltransferase inhibitors (DNMTis) to induce variations in DNA methylation and evaluated epigenetic diversity using methylation-sensitive amplified polymorphism (MSAP) and transposon methylation display (TMD) marker systems. Comparative and integrated analyses of the data revealed that both GRs and DNMTis alone have epimutagenic effects and that combined treatment enhanced these effects. Calculation of methylation rates based on band scoring suggested that both GRs and DNMTis induce epigenetic diversity by demethylation in a dose-dependent manner, and combined treatment can induce variations more synergistically. The difference in the changes in full and hemi-methylation rates between MSAP and TMD is presumed to be caused by the different genomic contexts of the loci amplified in the two marker systems. Principal coordinate, phylogenic, and population structure analyses commonly yielded two clusters of individuals divided by DNMTi treatment. The clustering pattern was more apparent in TMD, indicating that DNMTis have a stronger effect on hypermethylated repetitive regions. These findings provide a foundation for understanding epigenetic variations induced by GRs and DNMTis and for epigenetic mutation breeding.
Collapse
|
142
|
Comparative assessment of genetic diversity matrices and clustering methods in white Guinea yam (Dioscorea rotundata) based on morphological and molecular markers. Sci Rep 2020; 10:13191. [PMID: 32764649 PMCID: PMC7413250 DOI: 10.1038/s41598-020-69925-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Accepted: 07/16/2020] [Indexed: 11/11/2022] Open
Abstract
Understanding the diversity and genetic relationships among and within crop germplasm is invaluable for genetic improvement. This study assessed genetic diversity in a panel of 173 D. rotundata accessions using joint analysis for 23 morphological traits and 136,429 SNP markers from the whole-genome resequencing platform. Various diversity matrices and clustering methods were evaluated for a comprehensive characterization of genetic diversity in white Guinea yam from West Africa at phenotypic and molecular levels. The translation of the different diversity matrices from the phenotypic and genomic information into distinct groups varied with the hierarchal clustering methods used. Gower distance matrix based on phenotypic data and identity by state (IBS) distance matrix based on SNP data with the UPGMA clustering method found the best fit to dissect the genetic relationship in current set materials. However, the grouping pattern was inconsistent (r = − 0.05) between the morphological and molecular distance matrices due to the non-overlapping information between the two data types. Joint analysis for the phenotypic and molecular information maximized a comprehensive estimate of the actual diversity in the evaluated materials. The results from our study provide valuable insights for measuring quantitative genetic variability for breeding and genetic studies in yam and other root and tuber crops.
Collapse
|
143
|
Wang J, Long X, Chern M, Chen X. Understanding the molecular mechanisms of trade-offs between plant growth and immunity. SCIENCE CHINA-LIFE SCIENCES 2020; 64:234-241. [PMID: 32710363 DOI: 10.1007/s11427-020-1719-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Accepted: 05/05/2020] [Indexed: 12/24/2022]
Abstract
Trade-offs between plant growth and immunity are a well-known phenomenon in plants that are meant to ensure the best use of limited resources. Recently, many advances have been achieved on molecular regulations of the trade-offs between plant growth and immunity. Here, we provide an overview on molecular understanding of these trade-offs including those regulated at the transcriptional level or post-transcriptional level by transcriptional factors, microRNAs, and post-translational modifications of proteins, respectively The understanding on the molecular regulation of these trade-offs will provide new strategies to breed crops with high yield and enhanced resistance to disease.
Collapse
Affiliation(s)
- Jing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China (in preparation), Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, 611130, China
| | - Xiaoyu Long
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China (in preparation), Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, 611130, China
| | - Mawsheng Chern
- Department of Plant Pathology and the Genome Center, University of California, Davis, California, 95616, USA
| | - Xuewei Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China (in preparation), Rice Research Institute, Sichuan Agricultural University at Wenjiang, Chengdu, 611130, China.
| |
Collapse
|
144
|
Wang Y, Shahid MQ, Ghouri F, Baloch FS. De Novo Assembly and Annotation of the Juvenile Tuber Transcriptome of a Gastrodia elata Hybrid by RNA Sequencing: Detection of SSR Markers. Biochem Genet 2020; 58:914-934. [DOI: 10.1007/s10528-020-09983-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Accepted: 06/25/2020] [Indexed: 02/08/2023]
|
145
|
Salgotra RK, Stewart CN. Functional Markers for Precision Plant Breeding. Int J Mol Sci 2020; 21:E4792. [PMID: 32640763 PMCID: PMC7370099 DOI: 10.3390/ijms21134792] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/19/2020] [Accepted: 07/02/2020] [Indexed: 01/24/2023] Open
Abstract
Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals.
Collapse
Affiliation(s)
- Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu 190008, India
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
| |
Collapse
|
146
|
Lin S, Medina CA, Boge B, Hu J, Fransen S, Norberg S, Yu LX. Identification of genetic loci associated with forage quality in response to water deficit in autotetraploid alfalfa (Medicago sativa L.). BMC PLANT BIOLOGY 2020; 20:303. [PMID: 32611315 PMCID: PMC7328273 DOI: 10.1186/s12870-020-02520-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 06/24/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Alfalfa has been cultivated in many regions around the world as an important forage crop due to its nutritive value to livestock and ability to adapt to various environments. However, the genetic basis by which plasticity of quality-relevant traits influence alfalfa adaption to different water conditions remain largely unknown. RESULTS In the present study, 198 accessions of alfalfa of the core collection for drought tolerance were evaluated for 26 forage quality traits in a field trial under an imposed deficit irrigation gradient. Regression analysis between quality traits and water stress revealed that values of fiber-related traits were negatively correlated with values of energy-related traits as water deficit increased. More than one hundred significant markers associated with forage quality under different water treatments were identified using genome-wide association studies with genotyping by sequencing. Among them, 131 markers associated with multiple traits in all the water deficit treatments. Most of the associated markers were dependent to the levels of water deficit, suggesting genetic controls for forage quality traits were dependent to the stress treatment. Twenty-four loci associated with forage quality were annotated to functional genes that may play roles in cell development or in response to water stress. CONCLUSIONS This study addressed the genetic base of phenotypic variation of forage quality traits under water deficit. The SNP markers identified in this study will be useful in marker-assisted selection for the genetic improvement of alfalfa with enhanced drought tolerance while maintaining forage quality.
Collapse
Affiliation(s)
- Sen Lin
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, 24106 N Bunn Road, Prosser, WA, 99350, USA
| | - Cesar Augusto Medina
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, 24106 N Bunn Road, Prosser, WA, 99350, USA
| | - Bill Boge
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, 24106 N Bunn Road, Prosser, WA, 99350, USA
| | - Jinguo Hu
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, 24106 N Bunn Road, Prosser, WA, 99350, USA
| | - Steven Fransen
- Irrigated Agriculture Extension and Research Center, Washington State University, 24106 N Bunn Road, Prosser, Washington, USA
| | - Steven Norberg
- Washington State University Franklin County Extension Office, 404 West Clark Street, Pasco, Washington, USA
| | - Long-Xi Yu
- United States Department of Agriculture-Agricultural Research Service, Plant Germplasm Introduction and Testing Research, 24106 N Bunn Road, Prosser, WA, 99350, USA.
| |
Collapse
|
147
|
Teshome GE, Mekbib Y, Hu G, Li ZZ, Chen J. Comparative analyses of 32 complete plastomes of Tef ( Eragrostis tef ) accessions from Ethiopia: phylogenetic relationships and mutational hotspots. PeerJ 2020; 8:e9314. [PMID: 32596045 PMCID: PMC7307559 DOI: 10.7717/peerj.9314] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/17/2020] [Indexed: 12/31/2022] Open
Abstract
Eragrostis tef is an important cereal crop in Ethiopia with excellent storage properties, high–quality food, and the unique ability to thrive in extreme environmental conditions. However, the application of advanced molecular tools for breeding and conservation of these species is extremely limited. Therefore, developing chloroplast genome resources and high-resolution molecular markers are valuable to E. tef population and biogeographic studies. In the current study, we assembled and compared the complete plastomes of 32 E. tef accessions. The size of the plastomes ranged from 134,349 to 134,437 bp with similar GC content (∼38.3%). Genomes annotations revealed 112 individual genes, including 77 protein-coding, 31 tRNA, and 4 rRNA genes. Comparison of E. tef plastomes revealed a low degree of intraspecific sequence variations and no structural differentiations. Furthermore, we found 34 polymorphic sites (13 cpSSRs, 12 InDels, and 9 SNPs) that can be used as valuable DNA barcodes. Among them, the majority (88%) of the polymorphic sites were identified in the noncoding genomic regions. Nonsynonymous (ka) and synonymous (ks) substitution analysis showed that all PCGs were under purifying selection (ka/ks <1). The phylogenetic analyses of the whole plastomes and polymorphic region sequences were able to distinguish the accession from the southern population, indicating its potential to be used as a super-barcode. In conclusion, the newly generated plastomes and polymorphic markers developed here could be a useful genomic resource in molecular breeding, population genetics and the biogeographical study of E. tef.
Collapse
Affiliation(s)
- Girma Eshetu Teshome
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, Hubei, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yeshitila Mekbib
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, Hubei, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guangwan Hu
- Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, Hubei, China
| | - Zhi-Zhong Li
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jinming Chen
- CAS Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei, China.,Center of Conservation Biology, Core Botanical Gardens, Chinese Academy of Sciences, Wuhan, Hubei, China
| |
Collapse
|
148
|
Contreras R, van den Brink L, Burgos B, González M, Gacitúa S. Genetic Characterization of an Endangered Chilean Endemic Species, Prosopis burkartii Muñoz, Reveals its Hybrids Parentage. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9060744. [PMID: 32545703 PMCID: PMC7355918 DOI: 10.3390/plants9060744] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 05/31/2020] [Accepted: 06/11/2020] [Indexed: 05/25/2023]
Abstract
The hybridization of Prosopis burkartii, a critically endangered endemic species, and the identification of its paternal species has not been genetically studied before. In this study we aimed to genetically confirm the origin of this species. To resolve the parental status of P. burkartii, inter-simple sequence repeat (ISSR), simple sequence repeats (SSR) and intron trnL molecular markers were used, and compared with Chilean species from the Algarobia and Strombocarpa sections. Out of seven ISSRs, a total of 70 polymorphic bands were produced in four species of the Strombocarpa section. An Multi-dimensional scaling (MDS) and Bayasian (STRUCTURE) analysis showed signs of introgression of genetic material in P. burkartii. Unweighted pair group method with arithmetic average (UPGMA) cluster analysis showed three clusters, and placed the P. burkartii cluster nested within the P. tamarugo group. Sequencing of the trnL intron showed a fragment of 535 bp and 529 bp in the species of the Algarobia and Strombocarpa sections, respectively. Using maximum parsimony (MP) and maximum likelihood (ML) trees with the trnL intron, revealed four clusters. A species-specific diagnostic method was performed, using the trnL intron Single Nucleotide Polymorphism (SNP). This method identified if individuals of P. burkartii inherited their maternal DNA from P. tamarugo or from P. strombulifera. We deduced that P. tamarugo and P. strombulifera are involved in the formation of P. burkartii.
Collapse
Affiliation(s)
- Roberto Contreras
- Centro Regional de Investigación y Desarrollo Sustentable de Atacama (CRIDESAT), Universidad de Atacama, Av. Copayapu 485, 1530000 Copiapó, Chile
| | - Liesbeth van den Brink
- Department of Evolution and Ecology, Plant Ecology Group, Universität Tübingen, 72076 Tübingen, Germany;
| | - Boris Burgos
- Corporación Nacional Forestal (CONAF), Región de Atacama, Juan Martínez 55, 1530000 Copiapó, Chile;
| | - Marlene González
- Instituto Nacional Forestal (INFOR), Sede Metropolitana y Sede Diaguita, 1760000 Diaguitas, Chile; (M.G.); (S.G.)
| | - Sandra Gacitúa
- Instituto Nacional Forestal (INFOR), Sede Metropolitana y Sede Diaguita, 1760000 Diaguitas, Chile; (M.G.); (S.G.)
| |
Collapse
|
149
|
Wang Y, Nie F, Shahid MQ, Baloch FS. Molecular footprints of selection effects and whole genome duplication (WGD) events in three blueberry species: detected by transcriptome dataset. BMC PLANT BIOLOGY 2020; 20:250. [PMID: 32493212 PMCID: PMC7268529 DOI: 10.1186/s12870-020-02461-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Accepted: 05/24/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Both selection effects and whole genome duplication played very important roles in plant speciation and evolution, and to decipher the corresponding molecular footprint has always been a central task of geneticists. Vaccinium is species rich genus that comprised of about 450 species, and blueberry is one of the most important species of Vaccinium genus, which is gaining popularity because of high healthful value. In this article, we aimed to decipher the molecular footprints of natural selection on the single copy genes and WGD events occur in the evolutionary history of blueberry species. RESULTS We identified 30,143, 29,922 and 28,891 putative protein coding sequences from 45,535, 42,914 and 43,630 unigenes assembled from the leaves' transcriptome assembly of 19 rabbiteye (T1), 13 southern highbush (T2) and 22 northern highbush (T3) blueberry cultivars. A total of 17, 21 and 27 single copy orthologs were found to undergone positive selection in T1 versus T2, T1 versus T3, and T2 versus T3, respectively, and these orthologs were enriched in metabolic pathways including "Terpenoid backbone biosynthesis", "Valine, leucine and isoleucine biosynthesis", "Butanoate metabolism", "C5-Branched dibasic acid metabolism" "Pantothenate and CoA biosynthesis". We also detected significant molecular footprints of a recent (about 9.04 MYA), medium (about 43.44 MYA) and an ancient (about 116.39 MYA) WGD events that occurred in the evolutionary history of three blueberry species. CONCLUSION Some important functional genes revealed positive selection effect in blueberry. At least three rounds of WGD events were detected in the evolutionary history of blueberry species. Our work provides insights about the genetic mechanism of adaptive evolution in blueberry and species radiation of Vaccinium in short geological scale time.
Collapse
Affiliation(s)
- Yunsheng Wang
- College of Health and Life Science, Kaili University, Kaili City, 556011 Guizhou Province China
| | - Fei Nie
- Biological institute of Guizhou Province, Guiyang City, 556000 Guizhou Province China
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Provincial Key Laboratory of Plant Molecular Breeding, South China Agricultural University, Guangzhou, 510642 China
- College of Agriculture, South China Agricultural University, Guangzhou, 510642 Guangdong Province China
| | - Faheem Shehzad Baloch
- Department of Field Crops, Faculty of Agricultural and Natural Sciences, Abant İzzet Baysal University, Bolu, Turkey
| |
Collapse
|
150
|
Genetic relationship and nuclear dna content variation in Tef [Eragrostis tef (Zucc.) Trotter] accessions. Mol Biol Rep 2020; 47:4455-4463. [DOI: 10.1007/s11033-020-05537-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 05/15/2020] [Indexed: 10/24/2022]
|