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Albert PS, Birchler JA. Nitrous Oxide-Induced Metaphase Arrest: A Technique for Somatic Chromosome Analysis. Methods Mol Biol 2023; 2672:129-139. [PMID: 37335472 DOI: 10.1007/978-1-0716-3226-0_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
Abstract
Procedures to arrest metaphase chromosomes are used for determining chromosome numbers, chromosomal aberrations, and natural chromosome variation, as well as chromosome sorting. Here is described a technique of nitrous oxide gas treatment of freshly harvested root tips that is highly effective at producing an excellent mitotic index together with well-spread chromosomes. The details of the treatment and equipment used are provided. The metaphase spreads can be used directly for determining chromosome numbers or for in situ hybridization to reveal chromosomal features.
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Affiliation(s)
- Patrice S Albert
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA
| | - James A Birchler
- Division of Biological Sciences, University of Missouri, Columbia, MO, USA.
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2
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Lee K, Kim MS, Lee JS, Bae DN, Jeong N, Yang K, Lee JD, Park JH, Moon JK, Jeong SC. Chromosomal features revealed by comparison of genetic maps of Glycine max and Glycine soja. Genomics 2020; 112:1481-1489. [PMID: 31461668 DOI: 10.1016/j.ygeno.2019.08.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Revised: 08/08/2019] [Accepted: 08/24/2019] [Indexed: 11/18/2022]
Abstract
Recombination is a crucial component of evolution and breeding. New combinations of variation on chromosomes are shaped by recombination. Recombination is also involved in chromosomal rearrangements. However, recombination rates vary tremendously among chromosome segments. Genome-wide genetic maps are one of the best tools to study variation of recombination. Here, we describe high density genetic maps of Glycine max and Glycine soja constructed from four segregating populations. The maps were used to identify chromosomal rearrangements and find the highly predictable pattern of cross-overs on the broad scale in soybean. Markers on these genetic maps were used to evaluate assembly quality of the current soybean reference genome sequence. We find a strong inversion candidate larger than 3 Mb based on patterns of cross-overs. We also identify quantitative trait loci (QTL) that control number of cross-overs. This study provides fundamental insights relevant to practical strategy for breeding programs and for pan-genome researches.
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Affiliation(s)
- Kwanghee Lee
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
| | - Myung-Shin Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
| | - Ju Seok Lee
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
| | - Dong Nyuk Bae
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
| | - Namhee Jeong
- National Institute of Crop Science, Rural Development Administration, Wanju, Jeonbuk 55365, Republic of Korea
| | - Kiwoung Yang
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea; Present address, Geolim Pharmaceutical Co., Ltd, QB e centum, 2307, Centumjunggang-ro 90, Heaundae-gu, Busan, Republic of Korea
| | - Jeong-Dong Lee
- School of Applied Biosciences, Kyungpook National University, Daegu 41566, Republic of Korea
| | - Jung-Ho Park
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
| | - Jung-Kyung Moon
- Agricultural Genome Center, National Academy of Agricultural Sciences, Rural Development Administration, Jeonju, Jeonbuk 55365, Republic of Korea
| | - Soon-Chun Jeong
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea.
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Campbell BW, Hoyle JW, Bucciarelli B, Stec AO, Samac DA, Parrott WA, Stupar RM. Functional analysis and development of a CRISPR/Cas9 allelic series for a CPR5 ortholog necessary for proper growth of soybean trichomes. Sci Rep 2019; 9:14757. [PMID: 31611562 PMCID: PMC6791840 DOI: 10.1038/s41598-019-51240-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Accepted: 09/27/2019] [Indexed: 11/19/2022] Open
Abstract
Developments in genomic and genome editing technologies have facilitated the mapping, cloning, and validation of genetic variants underlying trait variation. This study combined bulked-segregant analysis, array comparative genomic hybridization, and CRISPR/Cas9 methodologies to identify a CPR5 ortholog essential for proper trichome growth in soybean (Glycine max). A fast neutron mutant line exhibited short trichomes with smaller trichome nuclei compared to its parent line. A fast neutron-induced deletion was identified within an interval on chromosome 6 that co-segregated with the trichome phenotype. The deletion encompassed six gene models including an ortholog of Arabidopsis thaliana CPR5. CRISPR/Cas9 was used to mutate the CPR5 ortholog, resulting in five plants harboring a total of four different putative knockout alleles and two in-frame alleles. Phenotypic analysis of the mutants validated the candidate gene, and included intermediate phenotypes that co-segregated with the in-frame alleles. These findings demonstrate that the CPR5 ortholog is essential for proper growth and development of soybean trichomes, similar to observations in A. thaliana. Furthermore, this work demonstrates the value of using CRISPR/Cas9 to generate an allelic series and intermediate phenotypes for functional analysis of candidate genes and/or the development of novel traits.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA.
| | - Jacob W Hoyle
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
| | - Bruna Bucciarelli
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
- USDA-ARS-Plant Science Research Unit, St. Paul, MN, USA
| | - Adrian O Stec
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | - Deborah A Samac
- USDA-ARS-Plant Science Research Unit, St. Paul, MN, USA
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, USA
| | - Wayne A Parrott
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA.
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Watanabe S, Shimizu T, Machita K, Tsubokura Y, Xia Z, Yamada T, Hajika M, Ishimoto M, Katayose Y, Harada K, Kaga A. Development of a high-density linkage map and chromosome segment substitution lines for Japanese soybean cultivar Enrei. DNA Res 2018; 25:123-136. [PMID: 29186379 PMCID: PMC5909467 DOI: 10.1093/dnares/dsx043] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 09/28/2017] [Indexed: 01/20/2023] Open
Abstract
Using progeny of a cross between Japanese soybean Enrei and Chinese soybean Peking, we developed a high-density linkage map and chromosomal segment substitution lines (CSSLs). The map consists of 2,177 markers with polymorphism information for 32 accessions and provides a detailed genetic framework for these markers. The marker order on the linkage map revealed close agreement with that on the chromosome-scale assembly, Wm82.a2.v1. The differences, especially on Chr. 5 and Chr. 11, in the present map provides information to identify regions in the genome assembly where additional information is required to resolve marker order and assign remaining scaffolds. To cover the entire soybean genome, we used 999 BC3F2 backcross plants and selected 103 CSSLs carrying chromosomal segments from Peking in the genetic background of Enrei. Using these low-genetic-complexity resources, we dissected variation in traits related to flowering, maturity and yield into approximately 50 reproducible quantitative trait loci (QTLs) and evaluated QTLs with small genetic effects as single genetic factors in a uniform genetic background. CSSLs developed in this study may be good starting material for removing the unfavourable characteristics of Peking during pre-breeding and for isolation of genes conferring disease and stress resistance that have not yet been characterized.
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Affiliation(s)
- Satoshi Watanabe
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602, Japan
| | - Takehiko Shimizu
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602, Japan
| | - Kayo Machita
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602, Japan
| | - Yasutaka Tsubokura
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602, Japan
| | - Zhengjun Xia
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602, Japan
| | - Tetsuya Yamada
- Soybean Breeding Unit, Institute of Crop Science, NARO, Tsukuba, Ibaraki 305-8517, Japan
| | - Makita Hajika
- Soybean Breeding Unit, Institute of Crop Science, NARO, Tsukuba, Ibaraki 305-8517, Japan
| | - Masao Ishimoto
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602, Japan
| | - Yuichi Katayose
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602, Japan
| | - Kyuya Harada
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602, Japan
| | - Akito Kaga
- Soybean Applied Genomics Research Unit, National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602, Japan
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Dobbels AA, Michno JM, Campbell BW, Virdi KS, Stec AO, Muehlbauer GJ, Naeve SL, Stupar RM. An Induced Chromosomal Translocation in Soybean Disrupts a KASI Ortholog and Is Associated with a High-Sucrose and Low-Oil Seed Phenotype. G3 (BETHESDA, MD.) 2017; 7:1215-1223. [PMID: 28235823 PMCID: PMC5386870 DOI: 10.1534/g3.116.038596] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 02/11/2017] [Indexed: 12/15/2022]
Abstract
Mutagenesis is a useful tool in many crop species to induce heritable genetic variability for trait improvement and gene discovery. In this study, forward screening of a soybean fast neutron (FN) mutant population identified an individual that produced seed with nearly twice the amount of sucrose (8.1% on dry matter basis) and less than half the amount of oil (8.5% on dry matter basis) as compared to wild type. Bulked segregant analysis (BSA), comparative genomic hybridization, and genome resequencing were used to associate the seed composition phenotype with a reciprocal translocation between chromosomes 8 and 13. In a backcross population, the translocation perfectly cosegregated with the seed composition phenotype and exhibited non-Mendelian segregation patterns. We hypothesize that the translocation is responsible for the altered seed composition by disrupting a β-ketoacyl-[acyl carrier protein] synthase 1 (KASI) ortholog. KASI is a core fatty acid synthesis enzyme that is involved in the conversion of sucrose into oil in developing seeds. This finding may lead to new research directions for developing soybean cultivars with modified carbohydrate and oil seed composition.
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Affiliation(s)
- Austin A Dobbels
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Jean-Michel Michno
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Kamaldeep S Virdi
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Adrian O Stec
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota 55108
| | - Seth L Naeve
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota 55108
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Findley SD, Birchler JA, Stacey G. Metaphase Chromosome Preparation from Soybean (Glycine max) Root Tips. ACTA ACUST UNITED AC 2017; 2:78-88. [PMID: 31725978 DOI: 10.1002/cppb.20046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This unit presents a highly reliable protocol to produce and screen metaphase chromosome spreads from root tip cell suspensions of soybean (Glycine max), or other legumes. The procedures represent soybean-optimized versions of protocols developed for maize. The use of pressurized nitrous oxide to reliably generate metaphase-arrested chromosomes is crucial to overcoming one of the challenges of working with tiny and numerous soybean chromosomes. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Seth D Findley
- University of Missouri, Division of Plant Sciences, Columbia, Missouri
| | - James A Birchler
- University of Missouri, Division of Biological Sciences, Columbia, Missouri
| | - Gary Stacey
- University of Missouri, Division of Plant Sciences, Columbia, Missouri
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Campbell BW, Stupar RM. Soybean (Glycine max) Mutant and Germplasm Resources: Current Status and Future Prospects. ACTA ACUST UNITED AC 2016; 1:307-327. [PMID: 30775866 DOI: 10.1002/cppb.20015] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Genetic bottlenecks during domestication and modern breeding limited the genetic diversity of soybean (Glycine max (L.) Merr.). Therefore, expanding and diversifying soybean genetic resources is a major priority for the research community. These resources, consisting of natural and induced genetic variants, are valuable tools for improving soybean and furthering soybean biological knowledge. During the twentieth century, researchers gathered a wealth of genetic variation in the forms of landraces, Glycine soja accessions, Glycine tertiary germplasm, and the U.S. Department of Agriculture (USDA) Type and Isoline Collections. During the twenty-first century, soybean researchers have added several new genetic and genomic resources. These include the reference genome sequence, genotype data for the USDA soybean germplasm collection, next-generation mapping populations, new irradiation and transposon-based mutagenesis populations, and designer nuclease platforms for genome engineering. This paper briefly surveys the publicly accessible soybean genetic resources currently available or in development and provides recommendations for developing such genetic resources in the future. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- Benjamin W Campbell
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota
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Chen H, Chung MC, Tsai YC, Wei FJ, Hsieh JS, Hsing YIC. Distribution of new satellites and simple sequence repeats in annual and perennial Glycine species. BOTANICAL STUDIES 2015; 56:22. [PMID: 28510831 PMCID: PMC5430363 DOI: 10.1186/s40529-015-0103-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2015] [Accepted: 08/17/2015] [Indexed: 06/07/2023]
Abstract
The repeat sequences occupied more than 50 % of soybean genome. In order to understand where these repeat sequences distributed in soybean genome and its related Glycine species, we examined three new repeat sequences-soybean repeat sequence (SBRS1, SBRS2 and SBRS3), some nonspecific repeat sequences and 45S rDNA on several Glycine species, including annual and perennial accessions in this study. In the annual species, G. soja, signals for SBRS1 and ATT repeat can be found on each chromosome in GG genome, but those for SBRS2 and SBRS3 were located at three specific loci. In perennial Glycine species, these three SBR repeat frequently co-localized with 45S rDNA, two major 45S rDNA loci were found in all tetraploid species. However, an extra minor locus was found in one accession of the G. pescadrensis (Tab074), but not in another accession (Tab004). We demonstrate that some repetitive sequences are present in all Glycine species used in the study, but the abundancy is different in annual or perennial species. We suggest this study may provide additional information in investigations of the phylogeny in the Glycine species.
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Affiliation(s)
- Hsuan Chen
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 Taiwan
- Department of Agronomy, National Taiwan University, Taipei, 106 Taiwan
| | - Mei-Chu Chung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Yuan-Ching Tsai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Fu-Jin Wei
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 Taiwan
| | - Jaw-Shu Hsieh
- Department of Agronomy, National Taiwan University, Taipei, 106 Taiwan
| | - Yue-Ie C. Hsing
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, 115 Taiwan
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