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Wu T, Yang S, Fang J, Ye Y, Zhang Y, Gao J, Leng J, Zhang Z, Tang K, Bhat JA, Feng X. MutL homolog 1 participates in interference-sensitive meiotic crossover formation in soybean. PLANT PHYSIOLOGY 2024; 195:2579-2595. [PMID: 38492234 PMCID: PMC11288737 DOI: 10.1093/plphys/kiae165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 02/07/2024] [Accepted: 02/15/2024] [Indexed: 03/18/2024]
Abstract
MutL homolog 1 (MLH1), a member of the MutL homolog family, is required for normal recombination in most organisms. However, its role in soybean (Glycine max) remains unclear to date. Here, we characterized the Glycine max female and male sterility 1 (Gmfms1) mutation that reduces pollen grain viability and increases embryo sac abortion in soybean. Map-based cloning revealed that the causal gene of Gmfms1 is Glycine max MutL homolog 1 (GmMLH1), and CRISPR/Cas9 knockout approach further validated that disruption of GmMLH1 confers the female-male sterility phenotype in soybean. Loss of GmMLH1 function disrupted bivalent formation, leading to univalent mis-segregation during meiosis and ultimately to female-male sterility. The Gmmlh1 mutant showed about a 78.16% decrease in meiotic crossover frequency compared to the wild type. The residual chiasmata followed a Poisson distribution, suggesting that interference-sensitive crossover formation was affected in the Gmmlh1 mutant. Furthermore, GmMLH1 could interact with GmMLH3A and GmMLH3B both in vivo and in vitro. Overall, our work demonstrates that GmMLH1 participates in interference-sensitive crossover formation in soybean, and provides additional information about the conserved functions of MLH1 across plant species.
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Affiliation(s)
- Tao Wu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Suxin Yang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Junling Fang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- College of Life Science, Jilin Agricultural University, Changchun 130118, China
| | - Yongheng Ye
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yaohua Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Jinshan Gao
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Jiantian Leng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | - Zhirui Zhang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kuanqiang Tang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
| | | | - Xianzhong Feng
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China
- Zhejiang Lab, Hangzhou 311121, China
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2
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Garg V, Bohra A, Mascher M, Spannagl M, Xu X, Bevan MW, Bennetzen JL, Varshney RK. Unlocking plant genetics with telomere-to-telomere genome assemblies. Nat Genet 2024:10.1038/s41588-024-01830-7. [PMID: 39048791 DOI: 10.1038/s41588-024-01830-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 06/12/2024] [Indexed: 07/27/2024]
Abstract
Contiguous genome sequence assemblies will help us to realize the full potential of crop translational genomics. Recent advances in sequencing technologies, especially long-read sequencing strategies, have made it possible to construct gapless telomere-to-telomere (T2T) assemblies, thus offering novel insights into genome organization and function. Plant genomes pose unique challenges, such as a continuum of ancient to recent polyploidy and abundant highly similar and long repetitive elements. Owing to progress in sequencing approaches, for most crop plants, chromosome-scale reference genome assemblies are available, but T2T assembly construction remains challenging. Here we describe methods for haplotype-resolved, gapless T2T assembly construction in plants, including various crop species. We outline the impact of T2T assemblies in elucidating the roles of repetitive elements in gene regulation, as well as in pangenomics, functional genomics, genome-assisted breeding and targeted genome manipulation. In conjunction with sequence-enriched germplasm repositories, T2T assemblies thus hold great promise for basic and applied plant sciences.
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Affiliation(s)
- Vanika Garg
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Abhishek Bohra
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
- ICAR-Indian Institute of Pulses Research, Kanpur, India
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Seeland, Germany
| | - Manuel Spannagl
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
- Plant Genome and Systems Biology, German Research Center for Environmental Health, Helmholtz Zentrum München, Neuherberg, Germany
| | - Xun Xu
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia
- BGI-Shenzhen, Shenzhen, China
| | | | | | - Rajeev K Varshney
- WA State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Food Futures Institute, Murdoch University, Murdoch, Western Australia, Australia.
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3
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Lukjanová E, Řepková J. Chromosome and Genome Diversity in the Genus Trifolium (Fabaceae). PLANTS (BASEL, SWITZERLAND) 2021; 10:2518. [PMID: 34834880 PMCID: PMC8621578 DOI: 10.3390/plants10112518] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/11/2021] [Accepted: 11/16/2021] [Indexed: 06/13/2023]
Abstract
Trifolium L. is an economically important genus that is characterized by variable karyotypes relating to its ploidy level and basic chromosome numbers. The advent of genomic resources combined with molecular cytogenetics provides an opportunity to develop our understanding of plant genomes in general. Here, we summarize the current state of knowledge on Trifolium genomes and chromosomes and review methodologies using molecular markers that have contributed to Trifolium research. We discuss possible future applications of cytogenetic methods in research on the Trifolium genome and chromosomes.
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Affiliation(s)
| | - Jana Řepková
- Department of Experimental Biology, Faculty of Sciences, Masaryk University, 611 37 Brno, Czech Republic;
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4
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Wang W, Chen L, Wang X, Duan J, Flynn RD, Wang Y, Clark CB, Sun L, Zhang D, Wang DR, Kessler SA, Ma J. A transposon-mediated reciprocal translocation promotes environmental adaptation but compromises domesticability of wild soybeans. THE NEW PHYTOLOGIST 2021; 232:1765-1777. [PMID: 34363228 DOI: 10.1111/nph.17671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Large structural variations frequently occur in higher plants; however, the impact of such variations on plant diversification, adaptation and domestication remains elusive. Here, we mapped and characterised a reciprocal chromosomal translocation in soybeans and assessed its effects on diversification and adaptation of wild (Glycine soja) and semiwild (Glycine gracilis) soybeans, and domestication of cultivated soybean (Glycine max), by tracing the distribution of the translocation in the USDA Soybean Germplasm Collection and population genetics analysis. We demonstrate that the translocation occurred through CACTA transposon-mediated chromosomal breakage in wild soybean c. 0.34 Ma and is responsible for semisterility in translocation heterozygotes and reduces their reproductive fitness. The translocation has differentiated Continental (i.e. China and Russia) populations from Maritime (i.e. Korea and Japan) populations of G. soja and predominately adapted to cold and dry climates. Further analysis revealed that the divergence of G. max from G. soja predates the translocation event and that G. gracilis is an evolutionary intermediate between G. soja and G. max. Our results highlight the effects of a chromosome rearrangement on the processes leading to plant divergence and adaptation, and provides evidence that suggests G. gracilis, rather than G. soja, as the ancestor of cultivated soybean.
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Affiliation(s)
- Weidong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Liyang Chen
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Xutong Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Jingbo Duan
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Rachel D Flynn
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
| | - Ying Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
- College of Plant Science, Jilin University, Changchun, Jilin, 130062, China
| | - Chancelor B Clark
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Lianjun Sun
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100083, China
| | - Dajian Zhang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
- College of Agronomy, Shandong Agricultural University, Tai'an, Shandong, 271018, China
| | - Diane R Wang
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Sharon A Kessler
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN, 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
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5
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Kim MS, Lee T, Baek J, Kim JH, Kim C, Jeong SC. Genome assembly of the popular Korean soybean cultivar Hwangkeum. G3 (BETHESDA, MD.) 2021; 11:jkab272. [PMID: 34568925 PMCID: PMC8496230 DOI: 10.1093/g3journal/jkab272] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/18/2021] [Accepted: 07/27/2021] [Indexed: 01/01/2023]
Abstract
Massive resequencing efforts have been undertaken to catalog allelic variants in major crop species including soybean, but the scope of the information for genetic variation often depends on short sequence reads mapped to the extant reference genome. Additional de novo assembled genome sequences provide a unique opportunity to explore a dispensable genome fraction in the pan-genome of a species. Here, we report the de novo assembly and annotation of Hwangkeum, a popular soybean cultivar in Korea. The assembly was constructed using PromethION nanopore sequencing data and two genetic maps and was then error-corrected using Illumina short-reads and PacBio SMRT reads. The 933.12 Mb assembly was annotated as containing 79,870 transcripts for 58,550 genes using RNA-Seq data and the public soybean annotation set. Comparison of the Hwangkeum assembly with the Williams 82 soybean reference genome sequence (Wm82.a2.v1) revealed 1.8 million single-nucleotide polymorphisms, 0.5 million indels, and 25 thousand putative structural variants. However, there was no natural megabase-scale chromosomal rearrangement. Incidentally, by adding two novel subfamilies, we found that soybean contains four clearly separated subfamilies of centromeric satellite repeats. Analyses of satellite repeats and gene content suggested that the Hwangkeum assembly is a high-quality assembly. This was further supported by comparison of the marker arrangement of anthocyanin biosynthesis genes and of gene arrangement at the Rsv3 locus. Therefore, the results indicate that the de novo assembly of Hwangkeum is a valuable additional reference genome resource for characterizing traits for the improvement of this important crop species.
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Affiliation(s)
- Myung-Shin Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
- Plant Immunity Research Center, Interdisciplinary Program in Agricultural Genomics, College of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Taeyoung Lee
- Bioinformatics Institute, Macrogen Inc., Seoul 08511, Republic of Korea
| | - Jeonghun Baek
- Bioinformatics Institute, Macrogen Inc., Seoul 08511, Republic of Korea
| | - Ji Hong Kim
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, Chungbuk 28116, Republic of Korea
| | - Changhoon Kim
- Bioinformatics Institute, Macrogen Inc., Seoul 08511, 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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6
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Kwiatek MT, Drozdowska Z, Kurasiak-Popowska D, Noweiska A, Nawracała J. Cytomolecular analysis of mutants, breeding lines, and varieties of camelina (Camelina sativa L. Crantz). J Appl Genet 2021; 62:199-205. [PMID: 33409934 DOI: 10.1007/s13353-020-00600-5] [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: 09/18/2020] [Revised: 11/21/2020] [Accepted: 11/26/2020] [Indexed: 10/22/2022]
Abstract
Camelina sativa L. Crantz (Brassicaceae family), known as camelina, has gained new attention as a re-emerging oil seed crop. With a unique seed oil profile, with the majority of the fatty acids consisting of linolenic (C18:3), oleic (C18:1), linoleic (C18:2), and eicosenoic (C20:1), camelina oil is reported to be useful as a food oil and biofuel. However, there are still many unknown factors about the structure and genetic variability of this crop. Chromosomal localization of ribosomal DNA was performed using fluorescence in situ hybridization (FISH) with 5S rDNA and 25S rDNA sequences as molecular probes on mitotic chromosomes of enzymatically digested root-tip meristematic cells. Here, we present for the first time a comparative analysis of selected genotypes (cultivars, breeding lines and mutants) of C. sativa with the use of cytogenetic techniques. The main aim of the study was to determine the intraspecific and interspecific polymorphisms in the structure of chromosomes of selected accessions using conserved 5S and 25S rDNA repetitive sequences as molecular probes. The results were compared with C. microcarpa (closely related to C. sativa) rDNA gene loci distribution. The presence of minor rDNA sites was discussed and compared with other Brassicaceae species. In addition, demonstration karyograms of C. sativa and C. microcarpa mapped with rDNA probes were prepared based on the cv. "Przybrodzka" and GE2011-02 genotype, respectively. The use of 5S and 25S rDNA probes provided an insight on the genome structure of C. sativa at the cytogenetic level and can help to understand the genome organization of this crop. The putative role of cytogenetic markers in phylogenetic analyses of camelina was discussed, as well.
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Affiliation(s)
- Michał T Kwiatek
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11Str., 60-632, Poznan, Poland.
| | - Zofia Drozdowska
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11Str., 60-632, Poznan, Poland
| | - Danuta Kurasiak-Popowska
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11Str., 60-632, Poznan, Poland
| | - Aleksandra Noweiska
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11Str., 60-632, Poznan, Poland
| | - Jerzy Nawracała
- Department of Genetics and Plant Breeding, Faculty of Agronomy and Bioengineering, Poznań University of Life Sciences, Dojazd 11Str., 60-632, Poznan, Poland
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7
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A universal chromosome identification system for maize and wild Zea species. Chromosome Res 2020; 28:183-194. [PMID: 32219602 DOI: 10.1007/s10577-020-09630-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/16/2020] [Accepted: 03/17/2020] [Indexed: 12/16/2022]
Abstract
Maize was one of the first eukaryotic species in which individual chromosomes can be identified cytologically, which made maize one of the oldest models for genetics and cytogenetics research. Nevertheless, consistent identification of all 10 chromosomes from different maize lines as well as from wild Zea species remains a challenge. We developed a new technique for maize chromosome identification based on fluorescence in situ hybridization (FISH). We developed two oligonucleotide-based probes that hybridize to 24 chromosomal regions. Individual maize chromosomes show distinct FISH signal patterns, which allow universal identification of all chromosomes from different Zea species. We developed karyotypes from three Zea mays subspecies and two additional wild Zea species based on individually identified chromosomes. A paracentric inversion was discovered on the long arm of chromosome 4 in Z. nicaraguensis and Z. luxurians based on modifications of the FISH signal patterns. Chromosomes from these two species also showed distinct distribution patterns of terminal knobs compared with other Zea species. These results support that Z. nicaraguensis and Z. luxurians are closely related species.
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8
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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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9
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Valliyodan B, Cannon SB, Bayer PE, Shu S, Brown AV, Ren L, Jenkins J, Chung CYL, Chan TF, Daum CG, Plott C, Hastie A, Baruch K, Barry KW, Huang W, Patil G, Varshney RK, Hu H, Batley J, Yuan Y, Song Q, Stupar RM, Goodstein DM, Stacey G, Lam HM, Jackson SA, Schmutz J, Grimwood J, Edwards D, Nguyen HT. Construction and comparison of three reference-quality genome assemblies for soybean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 100:1066-1082. [PMID: 31433882 DOI: 10.1111/tpj.14500] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 07/10/2019] [Accepted: 07/17/2019] [Indexed: 05/15/2023]
Abstract
We report reference-quality genome assemblies and annotations for two accessions of soybean (Glycine max) and for one accession of Glycine soja, the closest wild relative of G. max. The G. max assemblies provided are for widely used US cultivars: the northern line Williams 82 (Wm82) and the southern line Lee. The Wm82 assembly improves the prior published assembly, and the Lee and G. soja assemblies are new for these accessions. Comparisons among the three accessions show generally high structural conservation, but nucleotide difference of 1.7 single-nucleotide polymorphisms (snps) per kb between Wm82 and Lee, and 4.7 snps per kb between these lines and G. soja. snp distributions and comparisons with genotypes of the Lee and Wm82 parents highlight patterns of introgression and haplotype structure. Comparisons against the US germplasm collection show placement of the sequenced accessions relative to global soybean diversity. Analysis of a pan-gene collection shows generally high conservation, with variation occurring primarily in genomically clustered gene families. We found approximately 40-42 inversions per chromosome between either Lee or Wm82v4 and G. soja, and approximately 32 inversions per chromosome between Wm82 and Lee. We also investigated five domestication loci. For each locus, we found two different alleles with functional differences between G. soja and the two domesticated accessions. The genome assemblies for multiple cultivated accessions and for the closest wild ancestor of soybean provides a valuable set of resources for identifying causal variants that underlie traits for the domestication and improvement of soybean, serving as a basis for future research and crop improvement efforts for this important crop species.
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Affiliation(s)
- Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA
- Department of Agriculture and Environmental Sciences, Lincoln University, Jefferson City, 65101, MO, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Ames, 50011, IA, USA
| | - Philipp E Bayer
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Anne V Brown
- Corn Insects and Crop Genetics Research Unit, US Department of Agriculture-Agricultural Research Service, Ames, 50011, IA, USA
| | - Longhui Ren
- Interdepartmental Genetics Program, Iowa State University, Ames, 50011, IA, USA
| | - Jerry Jenkins
- Hudson-Alpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | - Claire Y-L Chung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Ting-Fung Chan
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Christopher G Daum
- Department of Energy Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Christopher Plott
- Hudson-Alpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | | | | | - Kerrie W Barry
- Department of Energy Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Wei Huang
- Department of Agronomy, Iowa State University, Ames, 50011, IA, USA
| | - Gunvant Patil
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA
| | - Rajeev K Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, 502 324, India
| | - Haifei Hu
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Jacqueline Batley
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Yuxuan Yuan
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Qijian Song
- Soybean Genomics and Improvement Lab, US Department of Agriculture - Agricultural Research Service, Beltsville, 20705, MD, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, 55108, MN, USA
| | - David M Goodstein
- Department of Energy Joint Genome Institute, Walnut Creek, 94598, CA, USA
| | - Gary Stacey
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA
| | - 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, Hong Kong Special Administrative Region, China
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, 30602, GA, USA
| | - Jeremy Schmutz
- Hudson-Alpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | - Jane Grimwood
- Hudson-Alpha Institute for Biotechnology, Huntsville, 35806, AL, USA
| | - David Edwards
- School of Biological Sciences, The University of Western Australia, Crawley, 6009, WA, Australia
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, 65211, MO, USA
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10
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Identification of P genome chromosomes in Agropyron cristatum and wheat-A. cristatum derivative lines by FISH. Sci Rep 2019; 9:9712. [PMID: 31273296 PMCID: PMC6609639 DOI: 10.1038/s41598-019-46197-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Accepted: 06/24/2019] [Indexed: 11/08/2022] Open
Abstract
Agropyron cristatum (L.) Gaertn. (P genome) is cultivated as pasture fodder and can provide many desirable genes for wheat improvement. With the development of genomics and fluorescence in situ hybridization (FISH) technology, probes for identifying plant chromosomes were also developed. However, there are few reports on A. cristatum chromosomes. Here, FISH with the repeated sequences pAcTRT1 and pAcpCR2 enabled the identification of all diploid A. cristatum chromosomes. An integrated idiogram of A. cristatum chromosomes was constructed based on the FISH patterns of five diploid A. cristatum individuals. Structural polymorphisms of homologous chromosomes were observed not only among different individuals but also within individuals. Moreover, seventeen wheat-A. cristatum introgression lines containing different P genome chromosomes were identified with pAcTRT1 and pAcpCR2 probes. The arrangement of chromosomes in diploid A. cristatum was determined by identifying correspondence between the P chromosomes in these genetically identified introgression lines and diploid A. cristatum chromosomes. The two probes were also effective for discriminating all chromosomes of tetraploid A. cristatum, and the differences between two tetraploid A. cristatum accessions were similar to the polymorphisms among individuals of diploid A. cristatum. Collectively, the results provide an effective means for chromosome identification and phylogenetic studies of P genome chromosomes.
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Schmidt T, Heitkam T, Liedtke S, Schubert V, Menzel G. Adding color to a century-old enigma: multi-color chromosome identification unravels the autotriploid nature of saffron (Crocus sativus) as a hybrid of wild Crocus cartwrightianus cytotypes. THE NEW PHYTOLOGIST 2019; 222:1965-1980. [PMID: 30690735 DOI: 10.1111/nph.15715] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Accepted: 01/20/2019] [Indexed: 05/25/2023]
Abstract
Saffron crocus (Crocus sativus) is the source of the most expensive spice of the world, produced from manually harvested stigmas, thus serving as a cash crop for rural communities. However, despite its economic importance, its genome and chromosomes are poorly studied. C. sativus is a sterile triploid species harboring eight chromosome triplets, and propagated only as a clonal lineage by corms. Saffron's evolutionary origin, parental species and allo- or autotriploidy has been a matter of discussion for almost a century. We performed a survey sequencing of the saffron genome and selected cytogenetic landmark sequences consisting of major tandem repeats, which we used as probes in comparative multicolor fluorescent in situ hybridization (FISH). We tagged 92 chromosomal positions and resolved the chromosomal composition of saffron triplets. By comparative FISH of six Crocus species from 11 accessions, we demonstrate that C. sativus is an autotriploid hybrid derived from heterogeneous Crocus cartwrightianus cytotypes. The FISH reference karyotype of saffron is crucial for integrating genome sequencing data with chromosomes and for investigating the relationship among Crocus species. We provide an evolutionary model of the saffron emergence; the knowledge of the parental origin offers a route towards the resynthesis of C. sativus from C. cartwrightianus to broaden saffron's gene pool.
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Affiliation(s)
- Thomas Schmidt
- Faculty of Biology, Technische Universität Dresden, Dresden, D-01062, Germany
| | - Tony Heitkam
- Faculty of Biology, Technische Universität Dresden, Dresden, D-01062, Germany
| | - Susan Liedtke
- Faculty of Biology, Technische Universität Dresden, Dresden, D-01062, Germany
| | - Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research, Corrensstr. 3, Seeland, D-06466, Germany
| | - Gerhard Menzel
- Faculty of Biology, Technische Universität Dresden, Dresden, D-01062, Germany
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Susek K, Bielski W, Czyż KB, Hasterok R, Jackson SA, Wolko B, Naganowska B. Impact of Chromosomal Rearrangements on the Interpretation of Lupin Karyotype Evolution. Genes (Basel) 2019; 10:genes10040259. [PMID: 30939837 PMCID: PMC6523792 DOI: 10.3390/genes10040259] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 03/27/2019] [Accepted: 03/27/2019] [Indexed: 02/06/2023] Open
Abstract
Plant genome evolution can be very complex and challenging to describe, even within a genus. Mechanisms that underlie genome variation are complex and can include whole-genome duplications, gene duplication and/or loss, and, importantly, multiple chromosomal rearrangements. Lupins (Lupinus) diverged from other legumes approximately 60 mya. In contrast to New World lupins, Old World lupins show high variability not only for chromosome numbers (2n = 32–52), but also for the basic chromosome number (x = 5–9, 13) and genome size. The evolutionary basis that underlies the karyotype evolution in lupins remains unknown, as it has so far been impossible to identify individual chromosomes. To shed light on chromosome changes and evolution, we used comparative chromosome mapping among 11 Old World lupins, with Lupinus angustifolius as the reference species. We applied set of L. angustifolius-derived bacterial artificial chromosome clones for fluorescence in situ hybridization. We demonstrate that chromosome variations in the species analyzed might have arisen from multiple changes in chromosome structure and number. We hypothesize about lupin karyotype evolution through polyploidy and subsequent aneuploidy. Additionally, we have established a cytogenomic map of L. angustifolius along with chromosome markers that can be used for related species to further improve comparative studies of crops and wild lupins.
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Affiliation(s)
- Karolina Susek
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland.
| | - Wojciech Bielski
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland.
| | - Katarzyna B Czyż
- Department of Biometry and Bioinformatics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland.
| | - Robert Hasterok
- Department of Plant Anatomy and Cytology, University of Silesia in Katowice, 40-032 Katowice, Poland.
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA 30602, USA.
| | - Bogdan Wolko
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland.
| | - Barbara Naganowska
- Department of Genomics, Institute of Plant Genetics, Polish Academy of Sciences, 60-479 Poznan, Poland.
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13
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Xie M, Chung CYL, Li MW, Wong FL, Wang X, Liu A, Wang Z, Leung AKY, Wong TH, Tong SW, Xiao Z, Fan K, Ng MS, Qi X, Yang L, Deng T, He L, Chen L, Fu A, Ding Q, He J, Chung G, Isobe S, Tanabata T, Valliyodan B, Nguyen HT, Cannon SB, Foyer CH, Chan TF, Lam HM. A reference-grade wild soybean genome. Nat Commun 2019; 10:1216. [PMID: 30872580 PMCID: PMC6418295 DOI: 10.1038/s41467-019-09142-9] [Citation(s) in RCA: 131] [Impact Index Per Article: 26.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/22/2019] [Indexed: 01/01/2023] Open
Abstract
Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 and 13 of some genotypes is shown to interfere with the assignment of QTLs. Third, we find a region containing copy number variations of the Kunitz trypsin inhibitor (KTI) genes. Such findings illustrate the power of this assembly in the analysis of large structural variations in soybean germplasm collections. The wild soybean genome assembly has wide applications in comparative genomic and evolutionary studies, as well as in crop breeding and improvement programs.
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Affiliation(s)
- Min Xie
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Claire Yik-Lok Chung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Man-Wah Li
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Fuk-Ling Wong
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Xin Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Ailin Liu
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Zhili Wang
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Alden King-Yung Leung
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Tin-Hang Wong
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Suk-Wah Tong
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Zhixia Xiao
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Kejing Fan
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, 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, Hong Kong Special Administrative Region, China
| | - Xinpeng Qi
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Linfeng Yang
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Tianquan Deng
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Lijuan He
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Lu Chen
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, Guangdong, China
| | - Aisi Fu
- Wuhan Institute of Biotechnology, Wuhan, 430075, Hubei, China
| | - Qiong Ding
- Wuhan Institute of Biotechnology, Wuhan, 430075, Hubei, China
| | - Junxian He
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Gwangju, 550-749, Jeonnam, South Korea
| | - Sachiko Isobe
- Kazusa DNA Research Institute, Kazusa-Kamatari, Kisarazu, 292-0818, Chiba, Japan
| | - Takanari Tanabata
- Kazusa DNA Research Institute, Kazusa-Kamatari, Kisarazu, 292-0818, Chiba, Japan
| | - Babu Valliyodan
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri, 65211, USA
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, Missouri, 65211, USA
| | - Steven B Cannon
- Corn Insects and Crop Genetics Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Ames, Iowa, 50011-4014, USA
| | - Christine H Foyer
- Faculty of Biological Sciences, Centre for Plant Sciences, University of Leeds, Leeds, LS2 9JT, Yorkshire, UK
| | - Ting-Fung Chan
- Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong Special Administrative Region, China.
| | - 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, Hong Kong Special Administrative Region, China.
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15
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Gao H, Wang Y, Li W, Gu Y, Lai Y, Bi Y, He C. Transcriptomic comparison reveals genetic variation potentially underlying seed developmental evolution of soybeans. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:5089-5104. [PMID: 30113693 PMCID: PMC6184420 DOI: 10.1093/jxb/ery291] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2018] [Accepted: 07/31/2018] [Indexed: 05/22/2023]
Abstract
Soybean (Glycine max) was domesticated from its wild relative Glycine soja. However, the genetic variations underlying soybean domestication are not well known. Comparative transcriptomics revealed that a small portion of the orthologous genes might have been fast evolving. In contrast, three gene expression clusters were identified as divergent by their expression patterns, which occupied 37.44% of the total genes, hinting at an essential role for gene expression alteration in soybean domestication. Moreover, the most divergent stage in gene expression between wild and cultivated soybeans occurred during seed development around the cotyledon stage (15 d after fertilization, G15). A module in which the co-expressed genes were significantly down-regulated at G15 of wild soybeans was identified. The divergent clusters and modules included substantial differentially expressed genes (DEGs) between wild and cultivated soybeans related to cell division, storage compound accumulation, hormone response, and seed maturation processes. Chromosomal-linked DEGs, quantitative trait loci controlling seed weight and oil content, and selection sweeps revealed candidate DEGs at G15 in the fruit-related divergence of G. max and G. soja. Our work establishes a transcriptomic selection mechanism for altering gene expression during soybean domestication, thus shedding light on the molecular networks underlying soybean seed development and breeding strategy.
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Affiliation(s)
- Huihui Gao
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yan Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China
| | - Wei Li
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Yongzhe Gu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yongcai Lai
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Yingdong Bi
- Crop Tillage and Cultivation Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, Heilongjiang, China
| | - Chaoying He
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
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16
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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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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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18
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Findley SD, Birchler JA, Stacey G. Fluorescence In Situ Hybridization for Glycine max Metaphase Chromosomes. CURRENT PROTOCOLS IN PLANT BIOLOGY 2017; 2:89-107. [PMID: 31725974 DOI: 10.1002/cppb.20045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
This article presents protocols for fluorescence in situ hybridization (FISH) in the cultivated soybean, Glycine max. The protocols represent soybean-optimized versions developed for maize. We describe the use of two different probes types: genomic-repeat-based fluorescently-tagged oligonucleotides and bacterial artificial chromosomes (BACs). The two probe types can be used either individually or together, depending on the experimental questions. The article also includes starting points for executing FISH in additional legume species. © 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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Zhang L, Yang X, Tian L, Chen L, Yu W. Identification of peanut (Arachis hypogaea) chromosomes using a fluorescence in situ hybridization system reveals multiple hybridization events during tetraploid peanut formation. THE NEW PHYTOLOGIST 2016; 211:1424-39. [PMID: 27176118 DOI: 10.1111/nph.13999] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/31/2016] [Indexed: 05/17/2023]
Abstract
The cultivated peanut Arachis hypogaea (AABB) is thought to have originated from the hybridization of Arachis duranensis (AA) and Arachis ipaënsis (BB) followed by spontaneous chromosome doubling. In this study, we cloned and analyzed chromosome markers from cultivated peanut and its wild relatives. A fluorescence in situ hybridization (FISH)-based karyotyping cocktail was developed with which to study the karyotypes and chromosome evolution of peanut and its wild relatives. Karyotypes were constructed in cultivated peanut and its two putative progenitors using our FISH-based karyotyping system. Comparative karyotyping analysis revealed that chromosome organization was highly conserved in cultivated peanut and its two putative progenitors, especially in the B genome chromosomes. However, variations existed between A. duranensis and the A genome chromosomes in cultivated peanut, especially for the distribution of the interstitial telomere repeats (ITRs). A search of additional A. duranensis varieties from different geographic regions revealed both numeric and positional variations of ITRs, which were similar to the variations in tetraploid peanut varieties. The results provide evidence for the origin of cultivated peanut from the two diploid ancestors, and also suggest that multiple hybridization events of A. ipaënsis with different varieties of A. duranensis may have occurred during the origination of peanut.
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Affiliation(s)
- Laining Zhang
- School of Life Sciences, Institute of Plant Molecular Biology and Agricultural Biotechnology, State (China) Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Xiaoyu Yang
- School of Life Sciences, Institute of Plant Molecular Biology and Agricultural Biotechnology, State (China) Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA
| | - Lei Chen
- Shenzhen Research Institute, the Chinese University of Hong Kong, Shenzhen, 518000, China
| | - Weichang Yu
- Shenzhen Research Institute, the Chinese University of Hong Kong, Shenzhen, 518000, China
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20
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Dynamics of a Novel Highly Repetitive CACTA Family in Common Bean (Phaseolus vulgaris). G3-GENES GENOMES GENETICS 2016; 6:2091-101. [PMID: 27185400 PMCID: PMC4938662 DOI: 10.1534/g3.116.028761] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Transposons are ubiquitous genomic components that play pivotal roles in plant gene and genome evolution. We analyzed two genome sequences of common bean (Phaseolus vulgaris) and identified a new CACTA transposon family named pvCACTA1. The family is extremely abundant, as more than 12,000 pvCACTA1 elements were found. To our knowledge, this is the most abundant CACTA family reported thus far. The computational and fluorescence in situ hybridization (FISH) analyses indicated that the pvCACTA1 elements were concentrated in terminal regions of chromosomes and frequently generated AT-rich 3 bp target site duplications (TSD, WWW, W is A or T). Comparative analysis of the common bean genomes from two domesticated genetic pools revealed that new insertions or excisions of pvCACTA1 elements occurred after the divergence of the two common beans, and some of the polymorphic elements likely resulted in variation in gene sequences. pvCACTA1 elements were detected in related species but not outside the Phaseolus genus. We calculated the molecular evolutionary rate of pvCACTA1 transposons using orthologous elements that indicated that most transposition events likely occurred before the divergence of the two gene pools. These results reveal unique features and evolution of this new transposon family in the common bean genome.
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Wyrwa K, Książkiewicz M, Szczepaniak A, Susek K, Podkowiński J, Naganowska B. Integration of Lupinus angustifolius L. (narrow-leafed lupin) genome maps and comparative mapping within legumes. Chromosome Res 2016; 24:355-78. [PMID: 27168155 PMCID: PMC4969343 DOI: 10.1007/s10577-016-9526-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/14/2016] [Accepted: 04/24/2016] [Indexed: 11/30/2022]
Abstract
Narrow-leafed lupin (Lupinus angustifolius L.) has recently been considered a reference genome for the Lupinus genus. In the present work, genetic and cytogenetic maps of L. angustifolius were supplemented with 30 new molecular markers representing lupin genome regions, harboring genes involved in nitrogen fixation during the symbiotic interaction of legumes and soil bacteria (Rhizobiaceae). Our studies resulted in the precise localization of bacterial artificial chromosomes (BACs) carrying sequence variants for early nodulin 40, nodulin 26, nodulin 45, aspartate aminotransferase P2, asparagine synthetase, cytosolic glutamine synthetase, and phosphoenolpyruvate carboxylase. Together with previously mapped chromosomes, the integrated L. angustifolius map encompasses 73 chromosome markers, including 5S ribosomal DNA (rDNA) and 45S rDNA, and anchors 20 L. angustifolius linkage groups to corresponding chromosomes. Chromosomal identification using BAC fluorescence in situ hybridization identified two BAC clones as narrow-leafed lupin centromere-specific markers, which served as templates for preliminary studies of centromere composition within the genus. Bioinformatic analysis of these two BACs revealed that centromeric/pericentromeric regions of narrow-leafed lupin chromosomes consisted of simple sequence repeats ordered into tandem repeats containing the trinucleotide and pentanucleotide simple sequence repeats AGG and GATAC, structured into long arrays. Moreover, cross-genus microsynteny analysis revealed syntenic patterns of 31 single-locus BAC clones among several legume species. The gene and chromosome level findings provide evidence of ancient duplication events that must have occurred very early in the divergence of papilionoid lineages. This work provides a strong foundation for future comparative mapping among legumes and may facilitate understanding of mechanisms involved in shaping legume chromosomes.
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Affiliation(s)
- Katarzyna Wyrwa
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, Poznań, 60-479, Poland.
| | - Michał Książkiewicz
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, Poznań, 60-479, Poland
| | - Anna Szczepaniak
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, Poznań, 60-479, Poland
| | - Karolina Susek
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, Poznań, 60-479, Poland
| | - Jan Podkowiński
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Z. Noskowskiego 12/14, Poznań, 61-704, Poland
| | - Barbara Naganowska
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, Poznań, 60-479, Poland
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22
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Li KP, Wu YX, Zhao H, Wang Y, Lü XM, Wang JM, Xu Y, Li ZY, Han YH. Cytogenetic relationships among Citrullus species in comparison with some genera of the tribe Benincaseae (Cucurbitaceae) as inferred from rDNA distribution patterns. BMC Evol Biol 2016; 16:85. [PMID: 27090090 PMCID: PMC4835933 DOI: 10.1186/s12862-016-0656-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2016] [Accepted: 04/12/2016] [Indexed: 12/27/2022] Open
Abstract
Background Comparative mapping of 5S and 45S rDNA by fluorescent in situ hybridization (FISH) technique is an excellent tool to determine cytogenetic relationships among closely related species. Results In this study, the number and position of 5S and 45S rDNA loci in all Citrullus species and subspecies were determined. The cultivated watermelon (C. lanatus subsp. vulgaris), C. lanatus subsp. mucosospermus, C. colocynthis and C. naudinianus (or Acanthosicyos naudinianus) had two 45S rDNA loci and one 5S rDNA locus which was located syntenic to one of the 45S rDNA loci. C. ecirrhosus and C. lanatus subsp. lanatus had one 45S rDNA locus and two 5S rDNA loci, each located on a different chromosome. C. rehmii had one 5S and one 45S rDNA locus positioned on different chromosomes. The distribution of 5S and 45S rDNA in several species belonging to other genera in Benincaseae tribe was also investigated. The distribution pattern of rDNAs showed a great difference among these species. Conclusions The present study confirmed evolutionary closeness among cultivated watermelon (C. lanatus subsp. vulgaris), C. lanatus subsp. mucosospermus and C. colocynthis. Our result also supported that C. lanatus subsp. lanatus was not a wild form of the cultivated watermelon instead was a separate crop species. In addition, present cytogenetic analysis suggested that A. naudinianus was more closely related to Cucumis than to Citrullus or Acanthosicyos, but with a unique position and may be a link bridge between the Citrullus and the Cucumis.
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Affiliation(s)
- Kun-Peng Li
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Yun-Xiang Wu
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Hong Zhao
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing, 100097, China
| | - Yan Wang
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Xing-Ming Lü
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China
| | - Ji-Ming Wang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009, China
| | - Yong Xu
- National Engineering Research Center for Vegetables, Beijing Academy of Agriculture and Forestry Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Beijing, 100097, China
| | - Zong-Yun Li
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China.
| | - Yong-Hua Han
- Institute of Integrative Plant Biology, School of Life Sciences, Jiangsu Normal University, Xuzhou, 221116, China.
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Fluorescence In Situ Hybridization (FISH)-Based Karyotyping Reveals Rapid Evolution of Centromeric and Subtelomeric Repeats in Common Bean (Phaseolus vulgaris) and Relatives. G3-GENES GENOMES GENETICS 2016; 6:1013-22. [PMID: 26865698 PMCID: PMC4825637 DOI: 10.1534/g3.115.024984] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Fluorescence in situ hybridization (FISH)-based karyotyping is a powerful cytogenetics tool to study chromosome organization, behavior, and chromosome evolution. Here, we developed a FISH-based karyotyping system using a probe mixture comprised of centromeric and subtelomeric satellite repeats, 5S rDNA, and chromosome-specific BAC clones in common bean, which enables one to unambiguously distinguish all 11 chromosome pairs. Furthermore, we applied the karyotyping system to several wild relatives and landraces of common bean from two distinct gene pools, as well as other related Phaseolus species, to investigate repeat evolution in the genus Phaseolus. Comparison of karyotype maps within common bean indicates that chromosomal distribution of the centromeric and subtelomeric satellite repeats is stable, whereas the copy number of the repeats was variable, indicating rapid amplification/reduction of the repeats in specific genomic regions. In Phaseolus species that diverged approximately 2–4 million yr ago, copy numbers of centromeric repeats were largely reduced or diverged, and chromosomal distributions have changed, suggesting rapid evolution of centromeric repeats. We also detected variation in the distribution pattern of subtelomeric repeats in Phaseolus species. The FISH-based karyotyping system revealed that satellite repeats are actively and rapidly evolving, forming genomic features unique to individual common bean accessions and Phaseolus species.
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24
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Gujaria-Verma N, Ramsay L, Sharpe AG, Sanderson LA, Debouck DG, Tar'an B, Bett KE. Gene-based SNP discovery in tepary bean (Phaseolus acutifolius) and common bean (P. vulgaris) for diversity analysis and comparative mapping. BMC Genomics 2016; 17:239. [PMID: 26979462 PMCID: PMC4793507 DOI: 10.1186/s12864-016-2499-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 02/18/2016] [Indexed: 11/10/2022] Open
Abstract
Background Common bean (Phaseolus vulgaris) is an important grain legume and there has been a recent resurgence in interest in its relative, tepary bean (P. acutifolius), owing to this species’ ability to better withstand abiotic stresses. Genomic resources are scarce for this minor crop species and a better knowledge of the genome-level relationship between these two species would facilitate improvement in both. High-throughput genotyping has facilitated large-scale single nucleotide polymorphism (SNP) identification leading to the development of molecular markers with associated sequence information that can be used to place them in the context of a full genome assembly. Results Transcript-based SNPs were identified from six common bean and two tepary bean accessions and a subset were used to generate a 768-SNP Illumina GoldenGate assay for each species. The tepary bean assay was used to assess diversity in wild and cultivated tepary bean and to generate the first gene-based map of the tepary bean genome. Genotypic analyses of the diversity panel showed a clear separation between domesticated and cultivated tepary beans, two distinct groups within the domesticated types, and P. parvifolius was confirmed to be distinct. The genetic map of tepary bean was compared to the common bean genome assembly to demonstrate high levels of collinearity between the two species with differences limited to a few intra-chromosomal rearrangements. Conclusions The development of the first set of genomic resources specifically for tepary bean has allowed for greater insight into the structure of this species and its relationship to its agriculturally more prominent relative, common bean. These resources will be helpful in the development of efficient breeding strategies for both species and will facilitate the introgression of agriculturally important traits from one crop into the other. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2499-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Neha Gujaria-Verma
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada
| | - Larissa Ramsay
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada
| | - Andrew G Sharpe
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK, S7N 0W9, Canada
| | - Lacey-Anne Sanderson
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada
| | - Daniel G Debouck
- Genetic Resources Program, International Center for Tropical Agriculture, Km 17 recta a Palmira, AA6713, Cali, Colombia
| | - Bunyamin Tar'an
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada
| | - Kirstin E Bett
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N 5A8, Canada.
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25
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Iwata-Otsubo A, Lin JY, Gill N, Jackson SA. Highly distinct chromosomal structures in cowpea (Vigna unguiculata), as revealed by molecular cytogenetic analysis. Chromosome Res 2016; 24:197-216. [PMID: 26758200 PMCID: PMC4856725 DOI: 10.1007/s10577-015-9515-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 12/21/2015] [Accepted: 12/23/2015] [Indexed: 11/19/2022]
Abstract
Cowpea (Vigna unguiculata (L.) Walp) is an important legume, particularly in developing countries. However, little is known about its genome or chromosome structure. We used molecular cytogenetics to characterize the structure of pachytene chromosomes to advance our knowledge of chromosome and genome organization of cowpea. Our data showed that cowpea has highly distinct chromosomal structures that are cytologically visible as brightly DAPI-stained heterochromatic regions. Analysis of the repetitive fraction of the cowpea genome present at centromeric and pericentromeric regions confirmed that two retrotransposons are major components of pericentromeric regions and that a 455-bp tandem repeat is found at seven out of 11 centromere pairs in cowpea. These repeats likely evolved after the divergence of cowpea from common bean and form chromosomal structure unique to cowpea. The integration of cowpea genetic and physical chromosome maps reveals potential regions of suppressed recombination due to condensed heterochromatin and a lack of pairing in a few chromosomal termini. This study provides fundamental knowledge on cowpea chromosome structure and molecular cytogenetics tools for further chromosome studies.
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Affiliation(s)
- Aiko Iwata-Otsubo
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.,Department of Biology, University of Pennsylvania, Philadelphia, 19104, PA, USA
| | - Jer-Young Lin
- Department of Agronomy, Purdue University, 170 S. University Street, West Lafayette, IN, USA.,Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA, 90095, USA
| | - Navdeep Gill
- Department of Agronomy, Purdue University, 170 S. University Street, West Lafayette, IN, USA.,Department of Botany, University of British Columbia, Vancouver, British Columbia, V6T 1Z4, Canada
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA, 30602, USA.
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26
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Kirov IV, Van Laere K, Van Roy N, Khrustaleva LI. Towards a FISH-based karyotype of Rosa L. (Rosaceae). COMPARATIVE CYTOGENETICS 2016; 10:543-554. [PMID: 28123677 PMCID: PMC5240508 DOI: 10.3897/compcytogen.v10i4.9536] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/08/2016] [Indexed: 05/18/2023]
Abstract
The genus Rosa Linnaeus, 1753 has important economic value in ornamental sector and many breeding activities are going on supported by molecular studies. However, the cytogenetic studies of rose species are scarce and mainly focused on chromosome counting and chromosome morphology-based karyotyping. Due to the small size of the chromosomes and a high frequency of polyploidy in the genus, karyotyping is very challenging for rose species and requires FISH-based cytogenetic markers to be applied. Therefore, in this work the aim is to establish a FISH-based karyotype for Rosa wichurana (Crépin, 1888), a rose species with several benefits for advanced molecular cytogenetic studies of genus Rosa (Kirov et al. 2015a). It is shown that FISH signals from 5S, 45S and an Arabidopsis-type telomeric repeat are distributed on five (1, 2, 4, 5 and 7) of seven chromosome pairs. In addition, it is demonstrated that the interstitial telomeric repeat sequences (ITR) are located in the centromeric regions of four chromosome pairs. Using low hybridization stringency for ITR visualization, we showed that the number of ITR signals increases four times (1-4 signals). This study is the first to propose a FISH-based Rosa wichurana karyotype for the reliable identification of chromosomes. The possible origin of Rosa wichurana ITR loci is discussed.
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Affiliation(s)
- Ilya V. Kirov
- Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str. 49, 127550, Moscow, Russia
- Department of Genetics and Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str. 3, 127550, Moscow, Russia
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 39, 9090, Melle, Belgium
| | - Katrijn Van Laere
- Institute for Agricultural and Fisheries Research (ILVO), Plant Sciences Unit, Applied Genetics and Breeding, Caritasstraat 39, 9090, Melle, Belgium
| | - Nadine Van Roy
- Center of Medical Genetics, Faculty of Medicine and Health Sciences, Ghent University, De Pintelaan 185, 9000, Ghent, Belgium
| | - Ludmila I. Khrustaleva
- Center of Molecular Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str. 49, 127550, Moscow, Russia
- Department of Genetics and Biotechnology, Russian State Agrarian University - Moscow Timiryazev Agricultural Academy, Timiryazevskay str. 3, 127550, Moscow, Russia
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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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28
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Chromosome-Specific Painting in Cucumis Species Using Bulked Oligonucleotides. Genetics 2015; 200:771-9. [PMID: 25971668 DOI: 10.1534/genetics.115.177642] [Citation(s) in RCA: 133] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 05/12/2015] [Indexed: 11/18/2022] Open
Abstract
Chromosome-specific painting is a powerful technique in molecular cytogenetic and genome research. We developed an oligonucleotide (oligo)-based chromosome painting technique in cucumber (Cucumis sativus) that will be applicable in any plant species with a sequenced genome. Oligos specific to a single chromosome of cucumber were identified using a newly developed bioinformatic pipeline and then massively synthesized de novo in parallel. The synthesized oligos were amplified and labeled with biotin or digoxigenin for use in fluorescence in situ hybridization (FISH). We developed three different probes with each containing 23,000-27,000 oligos. These probes spanned 8.3-17 Mb of DNA on targeted cucumber chromosomes and had the densities of 1.5-3.2 oligos per kilobases. These probes produced FISH signals on a single cucumber chromosome and were used to paint homeologous chromosomes in other Cucumis species diverged from cucumber for up to 12 million years. The bulked oligo probes allowed us to track a single chromosome in early stages during meiosis. We were able to precisely map the pairing between cucumber chromosome 7 and chromosome 1 of Cucumis hystrix in a F1 hybrid. These two homeologous chromosomes paired in 71% of prophase I cells but only 25% of metaphase I cells, which may provide an explanation of the higher recombination rates compared to the chiasma frequencies between homeologous chromosomes reported in plant hybrids.
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29
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Intra- and interchromosomal rearrangements between cowpea [Vigna unguiculata (L.) Walp.] and common bean (Phaseolus vulgaris L.) revealed by BAC-FISH. Chromosome Res 2015; 23:253-66. [PMID: 25634499 DOI: 10.1007/s10577-014-9464-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Revised: 12/22/2014] [Accepted: 12/26/2014] [Indexed: 12/22/2022]
Abstract
Cowpea (Vigna unguiculata) is an annual legume grown in tropical and subtropical regions, which is economically relevant due to high protein content in dried beans, green pods, and leaves. In this work, a comparative cytogenetic study between V. unguiculata and Phaseolus vulgaris (common bean) was conducted using BAC-FISH. Sequences previously mapped in P. vulgaris chromosomes (Pv) were used as probes in V. unguiculata chromosomes (Vu), contributing to the analysis of macrosynteny between both legumes. Thirty-seven clones from P. vulgaris 'BAT93' BAC library, corresponding to its 11 linkage groups, were hybridized in situ. Several chromosomal rearrangements were identified, such as translocations (between BACs from Pv1 and Pv8; Pv2 and Pv3; as well as Pv2 and Pv11), duplications (BAC from Pv3), as well as paracentric and pericentric inversions (BACs from Pv3, and Pv4, respectively). Two BACs (from Pv2 and Pv7), which hybridized at terminal regions in almost all P. vulgaris chromosomes, showed single-copy signal in Vu. Additionally, 17 BACs showed no signal in V. unguiculata chromosomes. The present results demonstrate the feasibility of using BAC libraries in comparative chromosomal mapping and karyotype evolution studies between Phaseolus and Vigna species, and revealed several macrosynteny and collinearity breaks among both legumes.
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Książkiewicz M, Zielezinski A, Wyrwa K, Szczepaniak A, Rychel S, Karlowski W, Wolko B, Naganowska B. Remnants of the Legume Ancestral Genome Preserved in Gene-Rich Regions: Insights from Lupinus angustifolius Physical, Genetic, and Comparative Mapping. PLANT MOLECULAR BIOLOGY REPORTER 2015; 33:84-101. [PMID: 25620837 PMCID: PMC4295026 DOI: 10.1007/s11105-014-0730-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The narrow-leafed lupin (Lupinus angustifolius) was recently considered as a legume reference species. Genetic resources have been developed, including a draft genome sequence, linkage maps, nuclear DNA libraries, and cytogenetic chromosome-specific landmarks. Here, we used a complex approach, involving DNA fingerprinting, sequencing, genetic mapping, and molecular cytogenetics, to localize and analyze L. angustifolius gene-rich regions (GRRs). A L. angustifolius genomic bacterial artificial chromosome (BAC) library was screened with short sequence repeat (SSR)-based probes. Selected BACs were fingerprinted and assembled into contigs. BAC-end sequence (BES) annotation allowed us to choose clones for sequencing, targeting GRRs. Additionally, BESs were aligned to the scaffolds of the genome sequence. The genetic map was supplemented with 35 BES-derived markers, distributed in 14 linkage groups and tagging 37 scaffolds. The identified GRRs had an average gene density of 19.6 genes/100 kb and physical-to-genetic distance ratios of 11 to 109 kb/cM. Physical and genetic mapping was supported by multi-BAC-fluorescence in situ hybridization (FISH), and five new linkage groups were assigned to the chromosomes. Syntenic links to the genome sequences of five legume species (Medicago truncatula, Glycine max, Lotus japonicus, Phaseolus vulgaris, and Cajanus cajan) were identified. The comparative mapping of the two largest lupin GRRs provides novel evidence for ancient duplications in all of the studied species. These regions are conserved among representatives of the main clades of Papilionoideae. Furthermore, despite the complex evolution of legumes, some segments of the nuclear genome were not substantially modified and retained their quasi-ancestral structures. Cytogenetic markers anchored in these regions constitute a platform for heterologous mapping of legume genomes.
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Affiliation(s)
- Michał Książkiewicz
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
| | - Andrzej Zielezinski
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Katarzyna Wyrwa
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
| | - Anna Szczepaniak
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
| | - Sandra Rychel
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
| | - Wojciech Karlowski
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Bogdan Wolko
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
| | - Barbara Naganowska
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
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31
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Imran MK, Sultana SS, Alam SS. Differential Chromosome Banding and RAPD Analysis in Three Varieties of Glycine max (L.) Merr. CYTOLOGIA 2015. [DOI: 10.1508/cytologia.80.447] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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32
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Chang S, Thurber CS, Brown PJ, Hartman GL, Lambert KN, Domier LL. Comparative mapping of the wild perennial Glycine latifolia and soybean (G. max) reveals extensive chromosome rearrangements in the genus Glycine. PLoS One 2014; 9:e99427. [PMID: 24937645 PMCID: PMC4061007 DOI: 10.1371/journal.pone.0099427] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/14/2014] [Indexed: 12/22/2022] Open
Abstract
Soybean (Glycine max L. Mer.), like many cultivated crops, has a relatively narrow genetic base and lacks diversity for some economically important traits. Glycine latifolia (Benth.) Newell & Hymowitz, one of the 26 perennial wild Glycine species related to soybean in the subgenus Glycine Willd., shows high levels of resistance to multiple soybean pathogens and pests including Alfalfa mosaic virus, Heterodera glycines Ichinohe and Sclerotinia sclerotiorum (Lib.) de Bary. However, limited information is available on the genomes of these perennial Glycine species. To generate molecular resources for gene mapping and identification, high-density linkage maps were constructed for G. latifolia using single nucleotide polymorphism (SNP) markers generated by genotyping by sequencing and evaluated in an F2 population and confirmed in an F5 population. In each population, greater than 2,300 SNP markers were selected for analysis and segregated to form 20 large linkage groups. Marker orders were similar in the F2 and F5 populations. The relationships between G. latifolia linkage groups and G. max and common bean (Phaseolus vulgaris L.) chromosomes were examined by aligning SNP-containing sequences from G. latifolia to the genome sequences of G. max and P. vulgaris. Twelve of the 20 G. latifolia linkage groups were nearly collinear with G. max chromosomes. The remaining eight G. latifolia linkage groups appeared to be products of multiple interchromosomal translocations relative to G. max. Large syntenic blocks also were observed between G. latifolia and P. vulgaris. These experiments are the first to compare genome organizations among annual and perennial Glycine species and common bean. The development of molecular resources for species closely related to G. max provides information into the evolution of genomes within the genus Glycine and tools to identify genes within perennial wild relatives of cultivated soybean that could be beneficial to soybean production.
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Affiliation(s)
- Sungyul Chang
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Carrie S. Thurber
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Patrick J. Brown
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Glen L. Hartman
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
- United States Department of Agriculture, Agricultural Research Service, Urbana, Illinois, United States of America
| | - Kris N. Lambert
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Leslie L. Domier
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
- United States Department of Agriculture, Agricultural Research Service, Urbana, Illinois, United States of America
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33
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Wang L, Cao C, Ma Q, Zeng Q, Wang H, Cheng Z, Zhu G, Qi J, Ma H, Nian H, Wang Y. RNA-seq analyses of multiple meristems of soybean: novel and alternative transcripts, evolutionary and functional implications. BMC PLANT BIOLOGY 2014; 14:169. [PMID: 24939556 PMCID: PMC4070088 DOI: 10.1186/1471-2229-14-169] [Citation(s) in RCA: 193] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Accepted: 06/05/2014] [Indexed: 05/21/2023]
Abstract
BACKGROUND Soybean is one of the most important crops, providing large amounts of dietary proteins and edible oil, and is also an excellent model for studying evolution of duplicated genes. However, relative to the model plants Arabidopsis and rice, the present knowledge about soybean transcriptome is quite limited. RESULTS In this study, we employed RNA-seq to investigate transcriptomes of 11 soybean tissues, for genome-wide discovery of truly expressed genes, and novel and alternative transcripts, as well as analyses of conservation and divergence of duplicated genes and their functional implications. We detected a total of 54,132 high-confidence expressed genes, and identified 6,718 novel transcriptional regions with a mean length of 372 bp. We also provided strong evidence for alternative splicing (AS) events for ~15.9% of the genes with two or more exons. Among them, 1,834 genes exhibited stage-dependent AS, and 202 genes had tissue-biased exon-skipping events. We further defined the conservation and divergence in expression patterns between duplicated gene pairs from recent whole genome duplications (WGDs); differentially expressed genes, tissue preferentially expressed genes, transcription factors and specific gene family members were identified for shoot apical meristem and flower development. CONCLUSIONS Our results significantly improved soybean gene annotation, and also provide valuable resources for functional genomics and studies of the evolution of duplicated genes from WGDs in soybean.
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Affiliation(s)
- Lei Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China
| | - Chenlong Cao
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China
| | - Qibin Ma
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, 510642 Guangzhou, China
- Guangdong Sub-Center of National Soybean Improvement Center, South China Agricultural University, 510642 Guangzhou, China
| | - Qiaoying Zeng
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, 510642 Guangzhou, China
- Guangdong Sub-Center of National Soybean Improvement Center, South China Agricultural University, 510642 Guangzhou, China
| | - Haifeng Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China
- Institute of Biomedical Sciences, Fudan University, 200032 Shanghai, China
| | - Zhihao Cheng
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China
| | - Genfeng Zhu
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China
- Institute of Biomedical Sciences, Fudan University, 200032 Shanghai, China
| | - Ji Qi
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China
- Institute of Biomedical Sciences, Fudan University, 200032 Shanghai, China
| | - Hong Ma
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China
- Institute of Biomedical Sciences, Fudan University, 200032 Shanghai, China
- Institute of Biodiversity Sciences, Fudan University, 200433 Shanghai, China
| | - Hai Nian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Agriculture, South China Agricultural University, 510642 Guangzhou, China
- Guangdong Sub-Center of National Soybean Improvement Center, South China Agricultural University, 510642 Guangzhou, China
| | - Yingxiang Wang
- State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, Institute of Plant Biology, Center of Evolutionary Biology, School of Life Sciences, Fudan University, 200433 Shanghai, China
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Kirov I, Divashuk M, Van Laere K, Soloviev A, Khrustaleva L. An easy "SteamDrop" method for high quality plant chromosome preparation. Mol Cytogenet 2014; 7:21. [PMID: 24602284 PMCID: PMC3995958 DOI: 10.1186/1755-8166-7-21] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 02/26/2014] [Indexed: 12/01/2022] Open
Abstract
Background The chromosome preparation is a crucial step for obtaining satisfactory results in molecular cytogenetic researches. The preparation of plant chromosomes for molecular cytogenetic purposes remains a challenge for some species. In contrast to human chromosome preparation, the processes occurring during plant chromosome preparation and causing chromosome spreading are still poorly understood. Results We studied the dynamics of plant chromosome spreading after dropping cell suspension on slides. We showed that steam stimulates cytoplasm hydrolysis and rapid chromosome spreading and that chromosomes stretch during this chromosome spreading. Based on these observations, we developed a novel method, named “SteamDrop”, for the preparation of well-spread mitotic and pachytene chromosomes and successfully used it for 28 plant species with large and small chromosomes. We applied cell suspensions in ethanol instead of the commonly used ethanol/acetic acid fixative. Mitotic and meiotic chromosomes prepared via “SteamDrop” were used in fluorescent in situ hybridization (FISH) experiments with repetitive and unique DNA probes. Long storage of cell suspensions in ethanol did not impair the quality of chromosome preparations. Conclusion The SteamDrop procedure provides a robust and routine method for high quality plant chromosome preparations. The method can be applied for metaphase as well as pachytene chromosome preparation in wide range of species. The chromosomes prepared by SteamDrop are well suitable for repetitive and unique DNA visualization.
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Affiliation(s)
| | | | | | | | - Ludmila Khrustaleva
- Department of Genetics and Biotechnology, Russian State Agrarian University-MTAA, Timiryazevskay str, 49, 127550 Moscow, Russia.
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Iwata A, Tek AL, Richard MMS, Abernathy B, Fonsêca A, Schmutz J, Chen NWG, Thareau V, Magdelenat G, Li Y, Murata M, Pedrosa-Harand A, Geffroy V, Nagaki K, Jackson SA. Identification and characterization of functional centromeres of the common bean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:47-60. [PMID: 23795942 DOI: 10.1111/tpj.12269] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2013] [Revised: 06/15/2013] [Accepted: 06/20/2013] [Indexed: 05/07/2023]
Abstract
In higher eukaryotes, centromeres are typically composed of megabase-sized arrays of satellite repeats that evolve rapidly and homogenize within a species' genome. Despite the importance of centromeres, our knowledge is limited to a few model species. We conducted a comprehensive analysis of common bean (Phaseolus vulgaris) centromeric satellite DNA using genomic data, fluorescence in situ hybridization (FISH), immunofluorescence and chromatin immunoprecipitation (ChIP). Two unrelated centromere-specific satellite repeats, CentPv1 and CentPv2, and the common bean centromere-specific histone H3 (PvCENH3) were identified. FISH showed that CentPv1 and CentPv2 are predominantly located at subsets of eight and three centromeres, respectively. Immunofluorescence- and ChIP-based assays demonstrated the functional significance of CentPv1 and CentPv2 at centromeres. Genomic analysis revealed several interesting features of CentPv1 and CentPv2: (i) CentPv1 is organized into an higher-order repeat structure, named Nazca, of 528 bp, whereas CentPv2 is composed of tandemly organized monomers; (ii) CentPv1 and CentPv2 have undergone chromosome-specific homogenization; and (iii) CentPv1 and CentPv2 are not likely to be commingled in the genome. These findings suggest that two distinct sets of centromere sequences have evolved independently within the common bean genome, and provide insight into centromere satellite evolution.
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Affiliation(s)
- Aiko Iwata
- Center for Applied Genetic Technologies and Institute for Plant Breeding Genetics, and Genomics, University of Georgia, Athens, GA, 30602, USA
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Begum R, Zakrzewski F, Menzel G, Weber B, Alam SS, Schmidt T. Comparative molecular cytogenetic analyses of a major tandemly repeated DNA family and retrotransposon sequences in cultivated jute Corchorus species (Malvaceae). ANNALS OF BOTANY 2013; 112:123-34. [PMID: 23666888 PMCID: PMC3690992 DOI: 10.1093/aob/mct103] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS The cultivated jute species Corchorus olitorius and Corchorus capsularis are important fibre crops. The analysis of repetitive DNA sequences, comprising a major part of plant genomes, has not been carried out in jute but is useful to investigate the long-range organization of chromosomes. The aim of this study was the identification of repetitive DNA sequences to facilitate comparative molecular and cytogenetic studies of two jute cultivars and to develop a fluorescent in situ hybridization (FISH) karyotype for chromosome identification. METHODS A plasmid library was generated from C. olitorius and C. capsularis with genomic restriction fragments of 100-500 bp, which was complemented by targeted cloning of satellite DNA by PCR. The diversity of the repetitive DNA families was analysed comparatively. The genomic abundance and chromosomal localization of different repeat classes were investigated by Southern analysis and FISH, respectively. The cytosine methylation of satellite arrays was studied by immunolabelling. KEY RESULTS Major satellite repeats and retrotransposons have been identified from C. olitorius and C. capsularis. The satellite family CoSat I forms two undermethylated species-specific subfamilies, while the long terminal repeat (LTR) retrotransposons CoRetro I and CoRetro II show similarity to the Metaviridea of plant retroelements. FISH karyotypes were developed by multicolour FISH using these repetitive DNA sequences in combination with 5S and 18S-5·8S-25S rRNA genes which enable the unequivocal chromosome discrimination in both jute species. CONCLUSIONS The analysis of the structure and diversity of the repeated DNA is crucial for genome sequence annotation. The reference karyotypes will be useful for breeding of jute and provide the basis for karyotyping homeologous chromosomes of wild jute species to reveal the genetic and evolutionary relationship between cultivated and wild Corchorus species.
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Affiliation(s)
- Rabeya Begum
- Department of Botany, University of Dhaka, Dhaka 1000, Bangladesh
| | - Falk Zakrzewski
- Institute of Botany, Technische Universität Dresden, D-01062 Dresden, Germany
| | - Gerhard Menzel
- Institute of Botany, Technische Universität Dresden, D-01062 Dresden, Germany
| | - Beatrice Weber
- Institute of Botany, Technische Universität Dresden, D-01062 Dresden, Germany
| | | | - Thomas Schmidt
- Institute of Botany, Technische Universität Dresden, D-01062 Dresden, Germany
- For correspondence. E-mail
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Motamayor JC, Mockaitis K, Schmutz J, Haiminen N, III DL, Cornejo O, Findley SD, Zheng P, Utro F, Royaert S, Saski C, Jenkins J, Podicheti R, Zhao M, Scheffler BE, Stack JC, Feltus FA, Mustiga GM, Amores F, Phillips W, Marelli JP, May GD, Shapiro H, Ma J, Bustamante CD, Schnell RJ, Main D, Gilbert D, Parida L, Kuhn DN. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color. Genome Biol 2013; 14:r53. [PMID: 23731509 PMCID: PMC4053823 DOI: 10.1186/gb-2013-14-6-r53] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 04/09/2013] [Accepted: 06/03/2013] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type. The availability of its genome sequence and methods for identifying genes responsible for important cacao traits will aid cacao researchers and breeders. RESULTS We describe the sequencing and assembly of the genome of Theobroma cacao L. cultivar Matina 1-6. The genome of the Matina 1-6 cultivar is 445 Mbp, which is significantly larger than a sequenced Criollo cultivar, and more typical of other cultivars. The chromosome-scale assembly, version 1.1, contains 711 scaffolds covering 346.0 Mbp, with a contig N50 of 84.4 kbp, a scaffold N50 of 34.4 Mbp, and an evidence-based gene set of 29,408 loci. Version 1.1 has 10x the scaffold N50 and 4x the contig N50 as Criollo, and includes 111 Mb more anchored sequence. The version 1.1 assembly has 4.4% gap sequence, while Criollo has 10.9%. Through a combination of haplotype, association mapping and gene expression analyses, we leverage this robust reference genome to identify a promising candidate gene responsible for pod color variation. We demonstrate that green/red pod color in cacao is likely regulated by the R2R3 MYB transcription factor TcMYB113, homologs of which determine pigmentation in Rosaceae, Solanaceae, and Brassicaceae. One SNP within the target site for a highly conserved trans-acting siRNA in dicots, found within TcMYB113, seems to affect transcript levels of this gene and therefore pod color variation. CONCLUSIONS We report a high-quality sequence and annotation of Theobroma cacao L. and demonstrate its utility in identifying candidate genes regulating traits.
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Affiliation(s)
| | - Keithanne Mockaitis
- Department of Biology, and Center for Genomics and Bioinformatics, Indiana University, 915 E. Third St, Bloomington, IN, 47405, USA
| | - Jeremy Schmutz
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, AL, 35806, USA
| | - Niina Haiminen
- IBM T J Watson Research, Yorktown Heights, NY, 10598, USA
| | - Donald Livingstone III
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
- United States Department of Agriculture-Agriculture Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Rd, Miami, FL, 33158, USA
| | - Omar Cornejo
- Department of Genetics, Stanford University, 300 Pasteur Dr, Stanford, CA, 94305, USA
| | - Seth D Findley
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
| | - Ping Zheng
- Department of Horticulture, Washington State University, Johnson Hall, Pullman, WA, 99164, USA
| | - Filippo Utro
- IBM T J Watson Research, Yorktown Heights, NY, 10598, USA
| | - Stefan Royaert
- United States Department of Agriculture-Agriculture Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Rd, Miami, FL, 33158, USA
| | - Christopher Saski
- Clemson University Genomics Institute, 105 Collings Street, Clemson, SC, 29634, USA
| | - Jerry Jenkins
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
- HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, AL, 35806, USA
| | - Ram Podicheti
- Center for Genomics and Bioinformatics and School of Informatics and Computing, Indiana University, 919 E 10th St, Bloomington, IN, 47408, USA
| | - Meixia Zhao
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Brian E Scheffler
- United States Department of Agriculture-Agriculture Research Service, Genomics and Bioinformatics Research Unit, 141 Experiment Station Road, Stoneville, MS, 38776, USA
| | - Joseph C Stack
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
| | - Frank A Feltus
- Clemson University Genomics Institute, 105 Collings Street, Clemson, SC, 29634, USA
| | | | - Freddy Amores
- Estación Experimental Tropical Pichilingue, Instituto Nacional Autónomo de Investigaciones Agropecuarias (INIAP), Código Postal 24, Km 5 vía Quevedo - El Empalme, Quevedo, Ecuador
| | - Wilbert Phillips
- Programa de Mejoramiento de Cacao, CATIE 7170, Turrialba, Costa Rica
| | | | - Gregory D May
- National Center for Genome Resources, 2935 Rodeo Park Drive E, Santa Fe, NM, 87505, USA
| | - Howard Shapiro
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
| | - Jianxin Ma
- Department of Agronomy, Purdue University, West Lafayette, IN, 47907, USA
| | - Carlos D Bustamante
- Department of Genetics, Stanford University, 300 Pasteur Dr, Stanford, CA, 94305, USA
| | - Raymond J Schnell
- Mars, Incorporated, 6885 Elm Street, McLean, VA, 22101, USA
- United States Department of Agriculture-Agriculture Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Rd, Miami, FL, 33158, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Johnson Hall, Pullman, WA, 99164, USA
| | - Don Gilbert
- Department of Biology, and Center for Genomics and Bioinformatics, Indiana University, 915 E. Third St, Bloomington, IN, 47405, USA
| | - Laxmi Parida
- IBM T J Watson Research, Yorktown Heights, NY, 10598, USA
| | - David N Kuhn
- United States Department of Agriculture-Agriculture Research Service, Subtropical Horticulture Research Station, 13601 Old Cutler Rd, Miami, FL, 33158, USA
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Lou Q, He Y, Cheng C, Zhang Z, Li J, Huang S, Chen J. Integration of high-resolution physical and genetic map reveals differential recombination frequency between chromosomes and the genome assembling quality in cucumber. PLoS One 2013; 8:e62676. [PMID: 23671621 PMCID: PMC3646037 DOI: 10.1371/journal.pone.0062676] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2013] [Accepted: 03/24/2013] [Indexed: 01/22/2023] Open
Abstract
Cucumber is an important model crop and the first species sequenced in Cucurbitaceae family. Compared to the fast increasing genetic and genomics resources, the molecular cytogenetic researches in cucumber are still very limited, which results in directly the shortage of relation between plenty of physical sequences or genetic data and chromosome structure. We mapped twenty-three fosmids anchored by SSR markers from LG-3, the longest linkage group, and LG-4, the shortest linkage group on pachytene chromosomes 3 and 4, using uorescence in situ hybridization (FISH). Integrated molecular cytogenetic maps of chromosomes 3 and 4 were constructed. Except for three SSR markers located on heterochromatin region, the cytological order of markers was concordant with those on the linkage maps. Distinct structural differences between chromosomes 3 and 4 were revealed by the high resolution pachytene chromosomes. The extreme difference of genetic length between LG-3 and LG-4 was mainly attributed to the difference of overall recombination frequency. The significant differentiation of heterochromatin contents in chromosomes 3 and 4 might have a direct correlation with recombination frequency. Meanwhile, the uneven distribution of recombination frequency along chromosome 4 was observed, and recombination frequency of the long arm was nearly 3.5 times higher than that of the short arm. The severe suppression of recombination was exhibited in centromeric and heterochromatin domains of chromosome 4. Whereas a close correlation between the gene density and recombination frequency was observed in chromosome 4, no significant correlation was observed between them along chromosome 3. The comparison between cytogenetic and sequence maps revealed a large gap on the pericentromeric heterochromatin region of sequence map of chromosome 4. These results showed that integrated molecular cytogenetic maps can provide important information for the study of genetic and genomics in cucumber.
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Affiliation(s)
- Qunfeng Lou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Yuhua He
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Chunyan Cheng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Zhonghua Zhang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ji Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Sanwen Huang
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinfeng Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
- * E-mail:
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Wolny E, Fidyk W, Hasterok R. Karyotyping of Brachypodium pinnatum (2n = 18) chromosomes using cross-species BAC-FISH. Genome 2013; 56:239-43. [PMID: 23706077 DOI: 10.1139/gen-2013-0012] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Identification of individual chromosomes in a complement is usually a difficult task in the case of most plant species, especially for those with small, numerous, and morphologically uniform chromosomes. In this paper, we demonstrate that the landmarks produced by cross-species fluorescence in situ hybridisation (FISH) of Brachypodium distachyon derived bacterial artificial chromosome (BAC) clones can be used for discrimination of Brachypodium pinnatum (2n = 18) chromosomes. Selected sets of clones were hybridised in several sequential experiments performed on exactly the same chromosome spreads, using reprobing of cytological preparations. Analysis of the morphometric features of B. pinnatum chromosomes was performed to establish their total length, the position of centromeres, and the position of BAC-based landmarks in relation to the centromere, thereby enabling their effective karyotyping, which is a prerequisite for more complex study of the grass genome structure and evolution at the cytomolecular level.
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Affiliation(s)
- Elzbieta Wolny
- Department of Plant Anatomy and Cytology, Faculty of Biology and Environmental Protection, University of Silesia, Jagiellonska 28, 40-032 Katowice, Poland
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40
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Lee WK, Kim N, Kim J, Moon JK, Jeong N, Choi IY, Kim SC, Chung WH, Kim HS, Lee SH, Jeong SC. Dynamic genetic features of chromosomes revealed by comparison of soybean genetic and sequence-based physical maps. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1103-19. [PMID: 23306355 DOI: 10.1007/s00122-012-2039-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2012] [Accepted: 12/21/2012] [Indexed: 05/02/2023]
Abstract
Despite the intensive soybean [Glycine max (L.) Merrill] genome studies, the high chromosome number (20) of the soybean plant relative to many other major crops has hindered the development of a high-resolution genomewide genetic map derived from a single population. Here, we report such a map, which was constructed in an F15 population derived from a cross between G. max and G. soja lines using indel polymorphisms detected via a G. soja genome resequencing. By targeting novel indel markers to marker-poor regions, all marker intervals were reduced to under 6 cM on a genome scale. Comparison of the Williams 82 soybean reference genome sequence and our genetic map indicated that marker orders of 26 regions were discrepant with each other. In addition, our comparison showed seven misplaced and two absent markers in the current Williams 82 assembly and six markers placed on the scaffolds that were not incorporated into the pseudomolecules. Then, we showed that, by determining the missing sequences located at the presumed beginning points of the five major discordant segments, these observed discordant regions are mostly errors in the Williams 82 assembly. Distributions of the recombination rates along the chromosomes were similar to those of other organisms. Genotyping of indel markers and genome resequencing of the two parental lines suggested that some marker-poor chromosomal regions may represent introgression regions, which appear to be prevalent in soybean. Given the even and dense distribution of markers, our genetic map can serve as a bridge between genomics research and breeding programs.
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Affiliation(s)
- Woo Kyu Lee
- Bio-Evaluation Center, Korea Research Institute of Bioscience and Biotechnology, Cheongwon, Chungbuk 363-883, Republic of Korea
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Książkiewicz M, Wyrwa K, Szczepaniak A, Rychel S, Majcherkiewicz K, Przysiecka Ł, Karlowski W, Wolko B, Naganowska B. Comparative genomics of Lupinus angustifolius gene-rich regions: BAC library exploration, genetic mapping and cytogenetics. BMC Genomics 2013; 14:79. [PMID: 23379841 PMCID: PMC3618312 DOI: 10.1186/1471-2164-14-79] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Accepted: 02/01/2013] [Indexed: 01/06/2023] Open
Abstract
Background The narrow-leafed lupin, Lupinus angustifolius L., is a grain legume species with a relatively compact genome. The species has 2n = 40 chromosomes and its genome size is 960 Mbp/1C. During the last decade, L. angustifolius genomic studies have achieved several milestones, such as molecular-marker development, linkage maps, and bacterial artificial chromosome (BAC) libraries. Here, these resources were integratively used to identify and sequence two gene-rich regions (GRRs) of the genome. Results The genome was screened with a probe representing the sequence of a microsatellite fragment length polymorphism (MFLP) marker linked to Phomopsis stem blight resistance. BAC clones selected by hybridization were subjected to restriction fingerprinting and contig assembly, and 232 BAC-ends were sequenced and annotated. BAC fluorescence in situ hybridization (BAC-FISH) identified eight single-locus clones. Based on physical mapping, cytogenetic localization, and BAC-end annotation, five clones were chosen for sequencing. Within the sequences of clones that hybridized in FISH to a single-locus, two large GRRs were identified. The GRRs showed strong and conserved synteny to Glycine max duplicated genome regions, illustrated by both identical gene order and parallel orientation. In contrast, in the clones with dispersed FISH signals, more than one-third of sequences were transposable elements. Sequenced, single-locus clones were used to develop 12 genetic markers, increasing the number of L. angustifolius chromosomes linked to appropriate linkage groups by five pairs. Conclusions In general, probes originating from MFLP sequences can assist genome screening and gene discovery. However, such probes are not useful for positional cloning, because they tend to hybridize to numerous loci. GRRs identified in L. angustifolius contained a low number of interspersed repeats and had a high level of synteny to the genome of the model legume G. max. Our results showed that not only was the gene nucleotide sequence conserved between soybean and lupin GRRs, but the order and orientation of particular genes in syntenic blocks was homologous, as well. These findings will be valuable to the forthcoming sequencing of the lupin genome.
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Affiliation(s)
- Michał Książkiewicz
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland.
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Paesold S, Borchardt D, Schmidt T, Dechyeva D. A sugar beet (Beta vulgaris L.) reference FISH karyotype for chromosome and chromosome-arm identification, integration of genetic linkage groups and analysis of major repeat family distribution. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 72:600-11. [PMID: 22775355 DOI: 10.1111/j.1365-313x.2012.05102.x] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
We developed a reference karyotype for B. vulgaris which is applicable to all beet cultivars and provides a consistent numbering of chromosomes and genetic linkage groups. Linkage groups of sugar beet were assigned to physical chromosome arms by FISH (fluorescent in situ hybridization) using a set of 18 genetically anchored BAC (bacterial artificial chromosome) markers. Genetic maps of sugar beet were correlated to chromosome arms, and North-South orientation of linkage groups was established. The FISH karyotype provides a technical platform for genome studies and can be applied for numbering and identification of chromosomes in related wild beet species. The discrimination of all nine chromosomes by BAC probes enabled the study of chromosome-specific distribution of the major repetitive components of sugar beet genome comprising pericentromeric, intercalary and subtelomeric satellites and 18S-5.8S-25S and 5S rRNA gene arrays. We developed a multicolor FISH procedure allowing the identification of all nine sugar beet chromosome pairs in a single hybridization using a pool of satellite DNA probes. Fiber-FISH was applied to analyse five chromosome arms in which the furthermost genetic marker of the linkage group was mapped adjacently to terminal repetitive sequences on pachytene chromosomes. Only on two arms telomere arrays and the markers are physically linked, hence these linkage groups can be considered as terminally closed making the further identification of distal informative markers difficult. The results support genetic mapping by marker localization, the anchoring of contigs and scaffolds for the annotation of the sugar beet genome sequence and the analysis of the chromosomal distribution patterns of major families of repetitive DNA.
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MESH Headings
- Beta vulgaris/genetics
- Chromosomes, Artificial, Bacterial/genetics
- Chromosomes, Plant/genetics
- DNA Probes/genetics
- DNA, Plant/analysis
- DNA, Plant/genetics
- DNA, Satellite/analysis
- DNA, Satellite/genetics
- Genetic Linkage
- Genetic Markers
- Genome, Plant
- In Situ Hybridization, Fluorescence/methods
- Karyotype
- Pachytene Stage
- Physical Chromosome Mapping/methods
- RNA, Ribosomal/analysis
- RNA, Ribosomal/genetics
- RNA, Ribosomal, 18S/analysis
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 5.8S/analysis
- RNA, Ribosomal, 5.8S/genetics
- Reference Standards
- Tandem Repeat Sequences
- Telomere/genetics
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Affiliation(s)
- Susanne Paesold
- Institute of Botany, Dresden University of Technology, Zellescher Weg 20b, 01217 Dresden, Germany
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Yang L, Koo DH, Li Y, Zhang X, Luan F, Havey MJ, Jiang J, Weng Y. Chromosome rearrangements during domestication of cucumber as revealed by high-density genetic mapping and draft genome assembly. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:895-906. [PMID: 22487099 DOI: 10.1111/j.1365-313x.2012.05017.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Cucumber, Cucumis sativus L. is the only taxon with 2n = 2x = 14 chromosomes in the genus Cucumis. It consists of two cross-compatible botanical varieties: the cultivated C. sativus var. sativus and the wild C. sativus var. hardwickii. There is no consensus on the evolutionary relationship between the two taxa. Whole-genome sequencing of the cucumber genome provides a new opportunity to advance our understanding of chromosome evolution and the domestication history of cucumber. In this study, a high-density genetic map for cultivated cucumber was developed that contained 735 marker loci in seven linkage groups spanning 707.8 cM. Integration of genetic and physical maps resulted in a chromosome-level draft genome assembly comprising 193 Mbp, or 53% of the 367 Mbp cucumber genome. Strategically selected markers from the genetic map and draft genome assembly were employed to screen for fosmid clones for use as probes in comparative fluorescence in situ hybridization analysis of pachytene chromosomes to investigate genetic differentiation between wild and cultivated cucumbers. Significant differences in the amount and distribution of heterochromatins, as well as chromosomal rearrangements, were uncovered between the two taxa. In particular, six inversions, five paracentric and one pericentric, were revealed in chromosomes 4, 5 and 7. Comparison of the order of fosmid loci on chromosome 7 of cultivated and wild cucumbers, and the syntenic melon chromosome I suggested that the paracentric inversion in this chromosome occurred during domestication of cucumber. The results support the sub-species status of these two cucumber taxa, and suggest that C. sativus var. hardwickii is the progenitor of cultivated cucumber.
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Affiliation(s)
- Luming Yang
- Horticulture Department, University of Wisconsin, Madison, WI 53706, USA
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Young HA, Sarath G, Tobias CM. Karyotype variation is indicative of subgenomic and ecotypic differentiation in switchgrass. BMC PLANT BIOLOGY 2012; 12:117. [PMID: 22834676 PMCID: PMC3492167 DOI: 10.1186/1471-2229-12-117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Accepted: 07/11/2012] [Indexed: 05/07/2023]
Abstract
BACKGROUND Karyotypes can provide information about taxonomic relationships, genetic aberrations, and the evolutionary origins of species. However, differentiation of the tiny chromosomes of switchgrass (Panicum virgatum L.) and creation of a standard karyotype for this bioenergy crop has not been accomplished due to lack of distinguishing features and polyploidy. RESULTS A cytogenetic study was conducted on a dihaploid individual (2n = 2X = 18) of switchgrass to establish a chromosome karyotype. Size differences, condensation patterns, and arm-length ratios were used as identifying features and fluorescence in-situ hybridization (FISH) assigned 5S and 45S rDNA loci to chromosomes 7 and 2 respectively. Both a maize CentC and a native switchgrass centromeric repeat (PviCentC) that shared 73% sequence identity demonstrated a strong signal on chromosome 3. However, only the PviCentC probe labeled the centromeres of all chromosomes. Unexpected PviCentC and 5S rDNA hybidization patterns were consistent with severe reduction or total deletion of these repeats in one subgenome. These patterns were maintained in tetraploid and octoploid individuals. The 45S rDNA repeat produced the expected number of loci in dihaploid, tetraploid and octoploid individuals. Differences observed at the 5S rDNA loci between the upland and lowland ecotypes of switchgrass provided a basis for distinguishing these subpopulations. CONCLUSION Collectively, these results provide a quantitative karyotype of switchgrass chromosomes. FISH analyses indicate genetic divergence between subgenomes and allow for the classification of switchgrass plants belonging to divergent genetic pools. Furthermore, the karyotype structure and cytogenetic analysis of switchgrass provides a framework for future genetic and genomic studies.
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Affiliation(s)
- Hugh A Young
- Genomics and Gene Discovery Research Unit, USDA-Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
| | - Gautam Sarath
- USDA Central-East Regional Biomass Center, 137 Keim Hall, East Campus, UNL, Lincoln, NE, 68583, USA
| | - Christian M Tobias
- Genomics and Gene Discovery Research Unit, USDA-Agricultural Research Service, Western Regional Research Center, 800 Buchanan Street, Albany, CA, 94710, USA
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Chan C, Qi X, Li MW, Wong FL, Lam HM. Recent developments of genomic research in soybean. J Genet Genomics 2012; 39:317-24. [PMID: 22835978 DOI: 10.1016/j.jgg.2012.02.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2011] [Revised: 02/03/2012] [Accepted: 02/04/2012] [Indexed: 10/28/2022]
Abstract
Soybean is an important cash crop with unique and important traits such as the high seed protein and oil contents, and the ability to perform symbiotic nitrogen fixation. A reference genome of cultivated soybeans was established in 2010, followed by whole-genome re-sequencing of wild and cultivated soybean accessions. These efforts revealed unique features of the soybean genome and helped to understand its evolution. Mapping of variations between wild and cultivated soybean genomes were performed. These genomic variations may be related to the process of domestication and human selection. Wild soybean germplasms exhibited high genomic diversity and hence may be an important source of novel genes/alleles. Accumulation of genomic data will help to refine genetic maps and expedite the identification of functional genes. In this review, we summarize the major findings from the whole-genome sequencing projects and discuss the possible impacts on soybean researches and breeding programs. Some emerging areas such as transcriptomic and epigenomic studies will be introduced. In addition, we also tabulated some useful bioinformatics tools that will help the mining of the soybean genomic data.
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Affiliation(s)
- Ching Chan
- State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
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Belarmino LC, da S Oliveira AR, Brasileiro-Vidal AC, de A Bortoleti KC, Bezerra-Neto JP, Abdelnoor RV, Benko-Iseppon AM. Mining plant genome browsers as a means for efficient connection of physical, genetic and cytogenetic mapping: An example using soybean. Genet Mol Biol 2012; 35:335-47. [PMID: 22802719 PMCID: PMC3392886 DOI: 10.1590/s1415-47572012000200015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Physical maps are important tools to uncover general chromosome structure as well as to compare different plant lineages and species, helping to elucidate genome structure, evolution and possibilities regarding synteny and colinearity. The increasing production of sequence data has opened an opportunity to link information from mapping studies to the underlying sequences. Genome browsers are invaluable platforms that provide access to these sequences, including tools for genome analysis, allowing the integration of multivariate information, and thus aiding to explain the emergence of complex genomes. The present work presents a tutorial regarding the use of genome browsers to develop targeted physical mapping, providing also a general overview and examples about the possibilities regarding the use of Fluorescent In Situ Hybridization (FISH) using bacterial artificial chromosomes (BAC), simple sequence repeats (SSR) and rDNA probes, highlighting the potential of such studies for map integration and comparative genetics. As a case study, the available genome of soybean was accessed to show how the physical and in silico distribution of such sequences may be compared at different levels. Such evaluations may also be complemented by the identification of sequences beyond the detection level of cytological methods, here using members of the aquaporin gene family as an example. The proposed approach highlights the complementation power of the combination of molecular cytogenetics and computational approaches for the anchoring of coding or repetitive sequences in plant genomes using available genome browsers, helping in the determination of sequence location, arrangement and number of repeats, and also filling gaps found in computational pseudochromosome assemblies.
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Affiliation(s)
- Luis C Belarmino
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Universidade Federal de Pernambuco, Recife, PE, Brazil
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Integration of the Draft Sequence and Physical Map as a Framework for Genomic Research in Soybean (Glycine max (L.) Merr.) and Wild Soybean (Glycine soja Sieb. and Zucc.). G3-GENES GENOMES GENETICS 2012; 2:321-9. [PMID: 22413085 PMCID: PMC3291501 DOI: 10.1534/g3.111.001834] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2011] [Accepted: 12/21/2011] [Indexed: 11/21/2022]
Abstract
Soybean is a model for the legume research community because of its importance as a crop, densely populated genetic maps, and the availability of a genome sequence. Even though a whole-genome shotgun sequence and bacterial artificial chromosome (BAC) libraries are available, a high-resolution, chromosome-based physical map linked to the sequence assemblies is still needed for whole-genome alignments and to facilitate map-based gene cloning. Three independent G. max BAC libraries combined with genetic and gene-based markers were used to construct a minimum tiling path (MTP) of BAC clones. A total of 107,214 clones were assembled into 1355 FPC (FingerPrinted Contigs) contigs, incorporating 4628 markers and aligned to the G. max reference genome sequence using BAC end-sequence information. Four different MTPs were made for G. max that covered from 92.6% to 95.0% of the soybean draft genome sequence (gmax1.01). Because our purpose was to pick the most reliable and complete MTP, and not the MTP with the minimal number of clones, the FPC map and draft sequence were integrated and clones with unpaired BES were added to build a high-quality physical map with the fewest gaps possible (http://soybase.org). A physical map was also constructed for the undomesticated ancestor (G. soja) of soybean to explore genome variation between G. max and G. soja. 66,028 G. soja clones were assembled into 1053 FPC contigs covering approximately 547 Mbp of the G. max genome sequence. These physical maps for G. max and its undomesticated ancestor, G. soja, will serve as a framework for ordering sequence fragments, comparative genomics, cloning genes, and evolutionary analyses of legume genomes.
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Ribeiro T, dos Santos KGB, Fonsêca A, Pedrosa-Harand A. Isolation and characterization of a new repetitive DNA family recently amplified in the Mesoamerican gene pool of the common bean (Phaseolus vulgaris L., Fabaceae). Genetica 2011; 139:1135-42. [PMID: 22086374 DOI: 10.1007/s10709-011-9615-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Accepted: 11/07/2011] [Indexed: 12/21/2022]
Abstract
The common bean (Phaseolus vulgaris) is one of the most important crop plants. About 50% of its genome is composed of repetitive sequences, but only a little fraction was isolated and characterized so far. In this paper, a new repetitive DNA family from the species, named PvMeso, was isolated and characterized in both gene pools of P. vulgaris (Andean and Mesoamerican) and related species. Two fragments, 1.7 and 2.3 kb long, were cloned from BAC 255F18, which has previously shown a repetitive pattern. The subclone PvMeso-31 showed a terminal block in chromosome 7. This subclone contains a 1,705 bp long, AT-rich repeat with small internal repeats and shares a 1.2 kb region with PvMeso-47, derived from the 2.3 kb fragment. The presence of this repetitive block was restricted to Mesoamerican accessions of the common bean. In P. acutifolius, P. leptostachyus and Andean P. vulgaris, only a faint, 2.3 kb fragment was visualized in Southern experiments. Moreover, in Mesoamerican accessions, two other fragments (1.7 kb and 3.4 kb) were strongly labelled as well. Taken together, our results indicate that PvMeso is a recently emerged, repeat family initially duplicated in chromosome 11, on ancestral Mesoamerican accession, and later amplified in chromosome 7, after the split of the two major gene pools of the common bean.
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Affiliation(s)
- Tiago Ribeiro
- Department of Botany, Laboratory of Plant Cytogenetics, Federal University of Pernambuco, Recife, PE 50670-420, Brazil
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Findley SD, Pappas AL, Cui Y, Birchler JA, Palmer RG, Stacey G. Fluorescence in situ hybridization-based karyotyping of soybean translocation lines. G3 (BETHESDA, MD.) 2011; 1:117-29. [PMID: 22384324 PMCID: PMC3276125 DOI: 10.1534/g3.111.000034] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Accepted: 05/07/2011] [Indexed: 01/06/2023]
Abstract
Soybean (Glycine max [L.] Merr.) is a major crop species and, therefore, a major target of genomic and genetic research. However, in contrast to other plant species, relatively few chromosomal aberrations have been identified and characterized in soybean. This is due in part to the difficulty of cytogenetic analysis of its small, morphologically homogeneous chromosomes. The recent development of a fluorescence in situ hybridization -based karyotyping system for soybean has enabled our characterization of most of the chromosomal translocation lines identified to date. Utilizing genetic data from existing translocation studies in soybean, we identified the chromosomes and approximate breakpoints involved in five translocation lines.
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Indrasumunar A, Searle I, Lin MH, Kereszt A, Men A, Carroll BJ, Gresshoff PM. Nodulation factor receptor kinase 1α controls nodule organ number in soybean (Glycine max L. Merr). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 65:39-50. [PMID: 21175888 DOI: 10.1111/j.1365-313x.2010.04398.x] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Two allelic non-nodulating mutants, nod49 and rj1, were characterized using map-based cloning and candidate gene approaches, and genetic complementation. From our results we propose two highly related lipo-oligochitin LysM-type receptor kinase genes (GmNFR1α and GmNFR1β) as putative Nod factor receptor components in soybean. Both mutants contained frameshift mutations in GmNFR1α that would yield protein truncations. Both mutants contained a seemingly functional GmNFR1β homeologue, characterized by a 374-bp deletion in intron 6 and 20-100 times lower transcript levels than GmNFR1α, yet both mutants were unable to form nodules. Mutations in GmNFR1β within other genotypes had no defects in nodulation, showing that GmNFR1β was redundant. Transgenic overexpression of GmNFR1α, but not of GmNFR1β, increased nodule number per plant, plant nitrogen content and the ability to form nodules with restrictive, ultra-low Bradyrhizobium japonicum titres in transgenic roots of both nod49 and rj1. GmNFR1α overexpressing roots also formed nodules in nodulation-restrictive acid soil (pH 4.7). Our results show that: (i) NFR1α expression controls nodule number in soybean, and (ii) acid soil tolerance for nodulation and suppression of nodulation deficiency at low titre can be achieved by overexpression of GmNFR1α.
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Affiliation(s)
- Arief Indrasumunar
- ARC Centre of Excellence for Integrative Legume Research, The University of Queensland, Brisbane St Lucia, QLD 4072, AustraliaIndonesian Centre for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor 16111, IndonesiaSchool of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane St Lucia, QLD 4072, AustraliaSchool of Biochemistry and Molecular Biology, ANU, Canberra ACT 2601, AustraliaInstitute for Plant Genomics, Human Biotechnology and Bioenergy, Szeged, HungaryAustralian Genome Research Facility, Brisbane, Australia
| | - Iain Searle
- ARC Centre of Excellence for Integrative Legume Research, The University of Queensland, Brisbane St Lucia, QLD 4072, AustraliaIndonesian Centre for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor 16111, IndonesiaSchool of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane St Lucia, QLD 4072, AustraliaSchool of Biochemistry and Molecular Biology, ANU, Canberra ACT 2601, AustraliaInstitute for Plant Genomics, Human Biotechnology and Bioenergy, Szeged, HungaryAustralian Genome Research Facility, Brisbane, Australia
| | - Meng-Han Lin
- ARC Centre of Excellence for Integrative Legume Research, The University of Queensland, Brisbane St Lucia, QLD 4072, AustraliaIndonesian Centre for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor 16111, IndonesiaSchool of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane St Lucia, QLD 4072, AustraliaSchool of Biochemistry and Molecular Biology, ANU, Canberra ACT 2601, AustraliaInstitute for Plant Genomics, Human Biotechnology and Bioenergy, Szeged, HungaryAustralian Genome Research Facility, Brisbane, Australia
| | - Attila Kereszt
- ARC Centre of Excellence for Integrative Legume Research, The University of Queensland, Brisbane St Lucia, QLD 4072, AustraliaIndonesian Centre for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor 16111, IndonesiaSchool of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane St Lucia, QLD 4072, AustraliaSchool of Biochemistry and Molecular Biology, ANU, Canberra ACT 2601, AustraliaInstitute for Plant Genomics, Human Biotechnology and Bioenergy, Szeged, HungaryAustralian Genome Research Facility, Brisbane, Australia
| | - Artem Men
- ARC Centre of Excellence for Integrative Legume Research, The University of Queensland, Brisbane St Lucia, QLD 4072, AustraliaIndonesian Centre for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor 16111, IndonesiaSchool of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane St Lucia, QLD 4072, AustraliaSchool of Biochemistry and Molecular Biology, ANU, Canberra ACT 2601, AustraliaInstitute for Plant Genomics, Human Biotechnology and Bioenergy, Szeged, HungaryAustralian Genome Research Facility, Brisbane, Australia
| | - Bernard J Carroll
- ARC Centre of Excellence for Integrative Legume Research, The University of Queensland, Brisbane St Lucia, QLD 4072, AustraliaIndonesian Centre for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor 16111, IndonesiaSchool of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane St Lucia, QLD 4072, AustraliaSchool of Biochemistry and Molecular Biology, ANU, Canberra ACT 2601, AustraliaInstitute for Plant Genomics, Human Biotechnology and Bioenergy, Szeged, HungaryAustralian Genome Research Facility, Brisbane, Australia
| | - Peter M Gresshoff
- ARC Centre of Excellence for Integrative Legume Research, The University of Queensland, Brisbane St Lucia, QLD 4072, AustraliaIndonesian Centre for Agricultural Biotechnology and Genetic Resources Research and Development, Bogor 16111, IndonesiaSchool of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane St Lucia, QLD 4072, AustraliaSchool of Biochemistry and Molecular Biology, ANU, Canberra ACT 2601, AustraliaInstitute for Plant Genomics, Human Biotechnology and Bioenergy, Szeged, HungaryAustralian Genome Research Facility, Brisbane, Australia
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