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García-Abolafio Y, Villanueva F, Urrutia M. Simple, fast and inexpensive hot sodium hydroxide and tris DNA extraction method for genotyping tomato and melon seeds. Biotechniques 2023; 75:245-249. [PMID: 37916446 DOI: 10.2144/btn-2023-0054] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
Seed commerce is a highly profitable global market. Most commercialized seeds are hybrid seeds originating from a controlled cross between two selected parental lines. The market value of hybrid seeds depends on their hybrid genetic purity. DNA molecular markers are a reliable and widespread tool to genotype plant materials; however, DNA extraction from seeds is challenging, often laborious and expensive. With the ultimate goal of creating a tomato and melon hybrid seeds purity test, various challenges arise. To overcome these problems and with the purpose of crude DNA extraction, a simple, fast, inexpensive and easily scalable adaptation of the hot sodium hydroxide and tris method coupled to a competitive allele-specific PCR genotyping method is proposed.
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Affiliation(s)
| | - Francisco Villanueva
- Huerta Valle Hibri2 S.L. Camino Remanente, Huerta Valle, Vélez-Málaga, Málaga, 29700, Spain
| | - María Urrutia
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora (IHSM. UMA-CSIC), Plant Breeding & Biotechnology, Consejo Superior de Investigaciones Científicas, Algarrobo-Costa, Málaga, 29750, Spain
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2
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Almeida Hummel Pimenta Santos ME, Rodrigues MS, Siqueira WJ, Mayo Marques MO, Costa Mondego JM. Comparative analysis indicates a simple protocol for DNA extraction of the aromatic plant Lippia alba. Anal Biochem 2023:115225. [PMID: 37364681 DOI: 10.1016/j.ab.2023.115225] [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: 03/28/2023] [Revised: 06/13/2023] [Accepted: 06/23/2023] [Indexed: 06/28/2023]
Abstract
An efficient method of genomic DNA extraction that provides high quality and yield is a crucial pre-requisite and limiting factor in plant genetic analysis. However, pure genomic DNA can be challenging to obtain from some plant species due to their sugar and secondary metabolite contents. Lippia alba is an important aromatic and medicinal plant, chemically characterized by the presence of tannins, flavonoids, anthocyanins, and essential oils, which interfere with the extraction of pure genomic DNA. In this scenario, optimizing the extraction methods and minimizing the effects of these compounds are necessary. This study compares six plant DNA extraction protocols based on the CTAB method. The quality and quantity of DNA samples obtained were determined by physical appearance by electrophoresis in agarose gels and spectrophotometry. The results highlight the difficulty in obtaining pure and clear bands for all tested methods, except for the polyvinylpyrrolidone (PVP)-based protocol created by our team, which was the better option for obtaining high-quality genomic DNA of L. alba. We conclude that adding PVP-40 into DNA extraction buffers can optimize the DNA extraction of L. alba and indicate this protocol for DNA extraction from other aromatic plants.
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Affiliation(s)
| | - Mariana Sanitá Rodrigues
- Center for Research and Development in Plant Genetic Resources, Agronomic Institute of Campinas, Campinas, SP, Brazil
| | - Walter José Siqueira
- Center for Research and Development in Plant Genetic Resources, Agronomic Institute of Campinas, Campinas, SP, Brazil
| | - Marcia Ortiz Mayo Marques
- Center for Research and Development in Plant Genetic Resources, Agronomic Institute of Campinas, Campinas, SP, Brazil
| | - Jorge Mauricio Costa Mondego
- Center for Research and Development in Plant Genetic Resources, Agronomic Institute of Campinas, Campinas, SP, Brazil.
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Tanaka K, Zhao C, Wang N, Kubota S, Kanehara M, Kamijo N, Ishikawa R, Tasaki H, Kanehara M, Liu B, Chen M, Nakamura SI, Udatsu T, Wang C. Classification of archaic rice grains excavated at the Mojiaoshan site within the Liangzhu site complex reveals an Indica and Japonica chloroplast complex. FOOD PRODUCTION, PROCESSING AND NUTRITION 2020. [DOI: 10.1186/s43014-020-00028-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
To understand rice types that were utilized during postdomestication and in the modern age and the potential of genetic research in aged rice materials, archaeogenetic analysis was conducted for two populations of archaic rice grains from the Mojiaoshan site during the Liangzhu Period in China (2940 to 2840 BC). Sequencing after the PCR amplification of three regions of the chloroplast genome and one region of the nuclear genome showed recovery rates that were comparable to those in previous studies except for one chloroplast genome region, suggesting that the materials used in this work were appropriate for recovering genetic information related to domestication traits by using advanced technology. Classification after sequencing in these regions proved the existence of Japonica and Indica chloroplasts in archaic grains from the west trench, which were subsequently classified into eight plastid groups (type I–VIII), and indicated that these rice grains derived from different maternal lineages were stored together in storage houses at the Mojiaohsan site. Among these plastid groups, type V exhibited the same sequences as two modern Indica accessions that are utilized in basic studies and rice breeding. It was inferred that part of the chloroplast genome of archaic rice has been preserved in modern genetic resources in these two modern Indica accessions, and the results indicated that rice related to their maternal ancestor was present at the Mojiaoshan site during the Liangzhu Period in China. The usefulness of archaeogenetic analysis can be demonstrated by our research data as well as previous studies, providing encouragement for the possibility that archaeogenetic analysis can be applied to older rice materials that were utilized in the rice-domesticated period.
Graphical abstract
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Data on genome resequencing of pigmented and non-pigmented Malaysian rice varieties. Data Brief 2020; 31:105806. [PMID: 32566707 PMCID: PMC7298397 DOI: 10.1016/j.dib.2020.105806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Revised: 04/20/2020] [Accepted: 05/22/2020] [Indexed: 11/23/2022] Open
Abstract
The genomics and genetic data of pigmented and non-pigmented Malaysian rice varieties are still limited. Hence, we performed the genome resequencing of two black rice varieties (Bali, Pulut Hitam 9), two red rice varieties (MRM16, MRQ100) and two white rice varieties (MR297 and MRQ76) using Illumina HiSeq 4000 platform with 30x sequencing coverage. We aimed to identify and annotate single nucleotide polymorphisms (SNPs) from the genome of these four pigmented and two non-pigmented rice varieties. The potential SNPs will be used in developing the functional SNP markers related to nutritional (i.e. antioxidant, folate, amylose) and quality (i.e. aromatic) traits. Raw data of the pigmented and non-pigmented rice varieties have been deposited into the European Nucleotide Archive (ENA) database with accession number PRJEB29070 and PRJEB32344, respectively.
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Muto C, Tanaka K, Tabuchi H, Kurauchi N, Sato YI, Ishikawa R. Genetic diversity of preserved rice seed samples from the Mikawa area, Japan, stored in the Meiji era. BREEDING SCIENCE 2020; 70:347-354. [PMID: 32714057 PMCID: PMC7372032 DOI: 10.1270/jsbbs.19143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Accepted: 02/03/2020] [Indexed: 05/23/2023]
Abstract
Preserved rice (Oryza sativa L.) seeds stored for nearly a century as an emergency food stocks from the Mikawa area were investigated for their genetic diversity. Morphologically, the seeds appeared to be typical Japonica. One chloroplast INDEL petN-trnC, two nuclear INDELs Acp1 and Cat1, and three SNP markers in Starch synthase IIa were amplified to characterize the molecular profile. The efficiency of amplification varied among the markers. Most of preserved seeds were classified as Japonica, but some were identified as Indica. The heterozygous genotypes detected suggested a high frequency of outcrossing at that time. On the other hand, 21 SSR markers showed quite a high degree of amplification efficiency. Principal coordinate analysis and STRUCTURE analysis based on the SSR polymorphisms proved that the preserved seeds contained alleles that were not detected among current landraces and breeding varieties, and there were the expected three subpopulations among 96 preserved seeds. These results indicated that these preserved seeds from Mikawa area in Meiji era had high genetic diversity and consisted of some subpopulations including Indica landraces with typical Japonica seed shape. These lines were considered to have been lost from current genetic resources.
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Affiliation(s)
- Chiaki Muto
- Genetic Resources Center, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba, Ibaraki 305-8602, Japan
| | - Katsunori Tanaka
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
| | - Hiroaki Tabuchi
- Miyakonojo Research Station, Kyushu Okinawa Agricultural Research Center, National Agriculture and Food Research Organization (NARO), Yokoichi-cho 6651-2, Miyakonojo, Miyazaki 885-0091, Japan
| | - Nobuyuki Kurauchi
- Department of International Development Studies, College of Bioresource Sciences, Nihon University, Fujisawa, Kanagawa 252-0880, Japan
| | - Yo-Ichiro Sato
- Research Institute for Humanity and Nature (RIHN), 457-4 Motoyama, Kamigamo, Kita-ku, Kyoto 603-8047, Japan
| | - Ryuji Ishikawa
- Faculty of Agriculture and Life Science, Hirosaki University, 3 Bunkyo-cho, Hirosaki, Aomori 036-8561, Japan
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Kannangara S, Karunarathne S, Ranaweera L, Ananda K, Ranathunga D, Jayarathne H, Weebadde C, Sooriyapathirana S. Assessment of the applicability of wood anatomy and DNA barcoding to detect the timber adulterations in Sri Lanka. Sci Rep 2020; 10:4352. [PMID: 32152386 PMCID: PMC7062781 DOI: 10.1038/s41598-020-61415-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 02/19/2020] [Indexed: 11/22/2022] Open
Abstract
The wood adulteration is a common problem and under-studied aspect in the timber industry of Sri Lanka. Hence we conducted a survey to assess the status of timber adulteration and check the applicability of morphometric parameters and DNA barcoding to detect the adulterated timber sources. We interviewed the stakeholders of the timber industry to collect information regarding timber adulterations. We measured the morphometric parameters; wood density and sizes of the xylem elements of the standard and adulterant species. For DNA barcoding, DNA was extracted from the wood of the selected standard and adulterant species and subjected to PCR using the markers, matK-trnT and atpB-rbcL. The PCR products were subjected to DNA sequencing. According to the survey, 92.5% of patrons, 73.7% of manufacturers and 96.7% of carpenters said timber adulteration is taking place in the country. The respondents said that the standard timber species; Tectona grandis, Artocarpus heterophyllus, and Swietenia macrophylla, profoundly undergo adulteration in Sri Lanka. The morphometric parameters did not discriminate the adulterant species from the standard species. The DNA barcodes matK-trnT and atpB-rbcL provided unique polymorphic DNA sequences with specific lengths for each species permitting the precise establishment of species identity and enabling the accurate detection of timber adulterations.
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Affiliation(s)
- Sachithrani Kannangara
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, 20400, Peradeniya, Sri Lanka
| | - Sachinthani Karunarathne
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, 20400, Peradeniya, Sri Lanka
| | - Lahiru Ranaweera
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, 20400, Peradeniya, Sri Lanka
| | - Kalpani Ananda
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, 20400, Peradeniya, Sri Lanka
| | - Disnie Ranathunga
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, 20400, Peradeniya, Sri Lanka
| | - Hashan Jayarathne
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, 20400, Peradeniya, Sri Lanka
| | - Cholani Weebadde
- Department of Plant, Soil and Microbial Sciences, College of Agriculture and Natural Resources, Michigan State University, East Lansing, Michigan, USA
| | - Suneth Sooriyapathirana
- Department of Molecular Biology and Biotechnology, Faculty of Science, University of Peradeniya, 20400, Peradeniya, Sri Lanka.
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Discovery of Functional SNPs via Genome-Wide Exploration of Malaysian Pigmented Rice Varieties. Int J Genomics 2019; 2019:4168045. [PMID: 31687375 PMCID: PMC6811786 DOI: 10.1155/2019/4168045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 08/01/2019] [Accepted: 08/19/2019] [Indexed: 01/30/2023] Open
Abstract
Recently, rice breeding program has shown increased interests on the pigmented rice varieties due to their benefits to human health. However, the genetic variation of pigmented rice varieties is still scarce and remains unexplored. Hence, we performed genome-wide SNP analysis from the genome resequencing of four Malaysian pigmented rice varieties, representing two black and two red rice varieties. The genome of four pigmented varieties was mapped against Nipponbare reference genome sequences, and 1.9 million SNPs were discovered. Of these, 622 SNPs with polymorphic sites were identified in 258 protein-coding genes related to metabolism, stress response, and transporter. Comparative analysis of 622 SNPs with polymorphic sites against six rice SNP datasets from the Ensembl Plants variation database was performed, and 70 SNPs were identified as novel SNPs. Analysis of SNPs in the flavonoid biosynthetic genes revealed 40 nonsynonymous SNPs, which has potential as molecular markers for rice seed colour identification. The highlighted SNPs in this study show effort in producing valuable genomic resources for application in the rice breeding program, towards the genetic improvement of new and improved pigmented rice varieties.
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Arbelaez JD, Tandayu E, Reveche MY, Jarana A, van Rogen P, Sandager L, Stolt P, Ng E, Varshney RK, Kretzschmar T, Cobb J. Methodology: ssb- MASS: a single seed-based sampling strategy for marker-assisted selection in rice. PLANT METHODS 2019; 15:78. [PMID: 31367224 PMCID: PMC6652012 DOI: 10.1186/s13007-019-0464-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Integrated breeding approaches such as combining marker-assisted selection and rapid line fixation through single-seed-descent, can effectively increase the frequency of desirable alleles in a breeding program and increase the rate of genetic gain for quantitative traits by shortening the breeding cycle. However, with most genotyping being outsourced to 3rd party service providers' nowadays, sampling has become the bottleneck for many breeding programs. While seed-chipping as prevailed as an automatable seed sampling protocol in many species, the symmetry of rice seeds makes this solution as laborious and costly as sampling leaf tissue. The aim of this study is to develop, validate and deploy a single seed sampling strategy for marker-assisted selection of fixed lines in rice that is more efficient, cost-effective and convenient compared to leaf-based sampling protocols without compromising the accuracy of the marker-assisted selection results. RESULTS Evaluations replicated across accessions and markers showed that a single rice seed is sufficient to generate enough DNA (7-8 ng/μL) to run at least ten PCR trait-markers suitable for marker-assisted selection strategies in rice. The DNA quantity and quality extracted from single seeds from fixed lines (F6) with different physical and/or chemical properties were not significantly different. Nor were there significant differences between single seeds collected 15 days after panicle initiation compared to those harvested at maturity. A large-scale comparison between single seed and leaf-based methodologies showed not only high levels of genotypic concordance between both protocols (~ 99%) but also higher SNP call rates in single seed (99.24% vs. 97.5% in leaf). A cost-benefit analysis showed that this single seed sampling strategy decreased the cost of sampling fourfold. An advantage of this approach is that desirable genotypes can be selected before investing in planting activities reducing the cost associated with field operations. CONCLUSION This study reports the development of a cost-effective and simple single seed genotyping strategy that facilitates the adoption and deployment of marker-assisted selection strategies in rice. This will allow breeders to increase the frequency of favorable alleles and combine rapid generation advancement techniques much more cost-effectively accelerating the process and efficiency of parental selection and varietal development.
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Affiliation(s)
- Juan David Arbelaez
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
| | - Erwin Tandayu
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
- Intertek - AgriTech, 2-230-53 Alnarp, Elevenborgsvägen Sweden
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana India
| | - Maria Ymber Reveche
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
| | - Annalhea Jarana
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
| | - Petra van Rogen
- Intertek - AgriTech, 2-230-53 Alnarp, Elevenborgsvägen Sweden
| | - Line Sandager
- Intertek - AgriTech, 2-230-53 Alnarp, Elevenborgsvägen Sweden
| | - Patrik Stolt
- Intertek - AgriTech, 2-230-53 Alnarp, Elevenborgsvägen Sweden
| | - Enghwa Ng
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana India
| | - Tobias Kretzschmar
- Southern Cross Plant Science, Southern Cross University, PO Box 157, Lismore, NSW 2480 Australia
| | - Joshua Cobb
- International Rice Research Institute, Metro Manila, DAPO Box 7777, Los Baños, 1301 Philippines
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Liang H, Deng Y, Wang C, Xu X. A high-throughput DNA extraction method from rice seeds. BIOTECHNOL BIOTEC EQ 2016. [DOI: 10.1080/13102818.2015.1088401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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