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Wu J, Zhang M, Liu J, Huang Y, Xu L, Deng Z, Zhao X. Efficient Anchoring of Erianthus arundinaceus Chromatin Introgressed into Sugarcane by Specific Molecular Markers. Int J Mol Sci 2022; 23:ijms23169435. [PMID: 36012702 PMCID: PMC9408830 DOI: 10.3390/ijms23169435] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/18/2022] [Accepted: 08/18/2022] [Indexed: 11/24/2022] Open
Abstract
Erianthus arundinaceus is a valuable gene reservoir for sugarcane improvement. However, insufficient molecular markers for high-accuracy identification and tracking of the introgression status of E. arundinaceus chromatin impede sugarcane breeding. Fortunately, suppression subtractive hybridization (SSH) technology provides an excellent opportunity for the development of high-throughput E. arundinaceus-specific molecular markers at a reasonable cost. In this study, we constructed a SSH library of E. arundinaceus. In total, 288 clones of E. arundinaceus-specific repetitive sequences were screened out and their distribution patterns on chromosomes were characterized by fluorescence in situ hybridization (FISH). A subtelomeric repetitive sequence Ea086 and a diffusive repetitive sequence Ea009, plus 45S rDNA-bearing E. arundinaceus chromosome repetitive sequence EaITS were developed as E. arundinaceus-specific molecular markers, namely, Ea086-128, Ea009-257, and EaITS-278, covering all the E. arundinaceus chromosomes for high-accuracy identification of putative progeny. Both Ea086-128 and Ea009-257 were successfully applied to identify the authenticity of F1, BC1, BC2, BC3, and BC4 progeny between sugarcane and E. arundinaceus. In addition, EaITS-278 was a 45S rDNA-bearing E. arundinaceus chromosome-specific molecular marker for rapid tracking of the inherited status of this chromosome in a sugarcane background. Three BC3 progeny had apparently lost the 45S rDNA-bearing E. arundinaceus chromosome. We reported herein a highly effective and reliable SSH-based technology for discovery of high-throughput E. arundinaceus-specific sequences bearing high potential as molecular markers. Given its reliability and savings in time and efforts, the method is also suitable for development of species-specific molecular markers for other important wild relatives to accelerate introgression of wild relatives into sugarcane.
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Affiliation(s)
- Jiayun Wu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Guangdong Sugarcane Genetic Improvement Engineering Center, Institute of Nanfan and Seed Industry, Guangdong Academy of Sciences, Guangzhou 510316, China
| | - Mingxiao Zhang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiarui Liu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Yongji Huang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liangnian Xu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zuhu Deng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- State Key Laboratory for Protection and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (Z.D.); (X.Z.)
| | - Xinwang Zhao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- State Key Laboratory for Protection and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- Correspondence: (Z.D.); (X.Z.)
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Metcalfe CJ, Li J, Zheng B, Stiller J, Healey A, Piperidis N, Aitken KS. Isolation and sequencing of a single copy of an introgressed chromosome from a complex genome for gene and SNP identification. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:1279-1292. [PMID: 35275251 DOI: 10.1007/s00122-022-04030-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
This manuscript describes the identification, isolation and sequencing of a single chromosome containing high value resistance genes from a complex polyploid where sequencing the whole genome is too costly. The large complex genomes of many crops constrain the use of new technologies for genome-assisted selection and genetic improvement. One method to simplify a genome is to break it into individual chromosomes by flow cytometry; however, in many crop species most chromosomes cannot be isolated individually. Flow sorting of a single copy of a chromosome has been developed in wheat, and here we demonstrate its use to identify markers of interest in an Erianthus/Sacchurum hybrid. Erianthus/Saccharum hybrids are of interest because Erianthus is known to be highly resistant to soil borne diseases which cause extensive sugarcane yield losses in Australia. Sugarcane (Saccharum) cultivars are autopolyploids with a highly complex genome and over 100 chromosomes. Flow cytometry for sugarcane, as in most crops, does not resolve individual chromosomes to a karyotype peak for sorting. To isolate a single chromosome, we used genomic in situ hybridization (GISH) to identify the flow karyotype region containing the Erianthus chromosomes, flow sorted single chromosomes from this region, PCR screened for the Erianthus chromosomes and sequenced them. One Erianthus chromosome amplified and sequenced well, and from this data we could identify 57 resistant type genes and SNPs in nearly half of these genes. We developed KASP SNP assays and demonstrated that the identified SNP markers segregated as expected in a small introgression population. The pipeline we developed here to flow sort and sequence single chromosomes could be used in any crop with a large complex genome to rapidly discover and develop markers to important loci.
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Affiliation(s)
- Cushla J Metcalfe
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, 306 Carmody Rd, St. Lucia, QLD, 4067, Australia
| | - Jingchuan Li
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, 306 Carmody Rd, St. Lucia, QLD, 4067, Australia
| | - Bangyou Zheng
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, 306 Carmody Rd, St. Lucia, QLD, 4067, Australia
| | - Jiri Stiller
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, 306 Carmody Rd, St. Lucia, QLD, 4067, Australia
| | - Adam Healey
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35806, USA
| | | | - Karen S Aitken
- CSIRO Agriculture and Food, Queensland Biosciences Precinct, 306 Carmody Rd, St. Lucia, QLD, 4067, Australia.
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Yu F, Chai J, Li X, Yu Z, Yang R, Ding X, Wang Q, Wu J, Yang X, Deng Z. Chromosomal Characterization of Tripidium arundinaceum Revealed by Oligo-FISH. Int J Mol Sci 2021; 22:ijms22168539. [PMID: 34445245 PMCID: PMC8395171 DOI: 10.3390/ijms22168539] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 08/06/2021] [Accepted: 08/07/2021] [Indexed: 11/29/2022] Open
Abstract
Sugarcane is of important economic value for producing sugar and bioethanol. Tripidium arundinaceum (old name: Erianthus arundinaceum) is an intergeneric wild species of sugarcane that has desirable resistance traits for improving sugarcane varieties. However, the scarcity of chromosome markers has hindered the cytogenetic study of T. arundinaceum. Here we applied maize chromosome painting probes (MCPs) to identify chromosomes in sorghum and T. arundinaceum using a repeated fluorescence in situ hybridization (FISH) system. Sequential FISH revealed that these MCPs can be used as reliable chromosome markers for T. arundinaceum, even though T. arundinaceum has diverged from maize over 18 MYs (million years). Using these MCPs, we identified T. arundinaceum chromosomes based on their sequence similarity compared to sorghum and labeled them 1 through 10. Then, the karyotype of T. arundinaceum was established by multiple oligo-FISH. Furthermore, FISH results revealed that 5S rDNA and 35S rDNA are localized on chromosomes 5 and 6, respectively, in T. arundinaceum. Altogether, these results represent an essential step for further cytogenetic research of T. arundinaceum in sugarcane breeding.
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Affiliation(s)
- Fan Yu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (F.Y.); (J.C.); (X.L.); (R.Y.); (X.D.); (Q.W.)
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jin Chai
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (F.Y.); (J.C.); (X.L.); (R.Y.); (X.D.); (Q.W.)
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xueting Li
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (F.Y.); (J.C.); (X.L.); (R.Y.); (X.D.); (Q.W.)
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Zehuai Yu
- State Key Laboratory for Protection and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China; (Z.Y.); (X.Y.)
| | - Ruiting Yang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (F.Y.); (J.C.); (X.L.); (R.Y.); (X.D.); (Q.W.)
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xueer Ding
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (F.Y.); (J.C.); (X.L.); (R.Y.); (X.D.); (Q.W.)
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Qiusong Wang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (F.Y.); (J.C.); (X.L.); (R.Y.); (X.D.); (Q.W.)
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jiayun Wu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (F.Y.); (J.C.); (X.L.); (R.Y.); (X.D.); (Q.W.)
- Institute of Nanfan & Seed Industry, Guangdong Academy of Sciences, Guangzhou 510316, China
- Correspondence: (J.W.); (Z.D.)
| | - Xiping Yang
- State Key Laboratory for Protection and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China; (Z.Y.); (X.Y.)
| | - Zuhu Deng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou 350002, China; (F.Y.); (J.C.); (X.L.); (R.Y.); (X.D.); (Q.W.)
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou 350002, China
- State Key Laboratory for Protection and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning 530004, China; (Z.Y.); (X.Y.)
- Correspondence: (J.W.); (Z.D.)
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Sobhakumari VP, Mohanraj K, Nair NV, Mahadevaswamy HK, Ram B. Cytogenetic and Molecular Approaches to Detect Alien Chromosome Introgression and Its Impact in Three Successive Generations of Erianthus procerus × Saccharum. CYTOLOGIA 2020. [DOI: 10.1508/cytologia.85.341] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | | | | | | | - Bakshi Ram
- Crop Improvement Division, ICAR-Sugarcane Breeding Institute
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Piperidis N. GISH: Resolving Interspecific and Intergeneric Hybrids. Methods Mol Biol 2020; 2222:381-394. [PMID: 33301103 DOI: 10.1007/978-1-0716-0997-2_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Genomic in situ hybridization (GISH) is an invaluable cytogenetic technique which enables the visualization of whole genomes in hybrids and polyploidy taxa. Total genomic DNA from one or two different species/genomes is used as a probe, labeled with a fluorochrome, and directly detected on mitotic chromosomes from root tip meristems. In sugarcane and sugarcane hybrids, we were able to characterize interspecific hybrids of two closely related species as well as intergeneric hybrids of two closely related genera.
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Genome-Wide Characterization of OFP Family Genes in Wheat ( Triticum aestivum L.) Reveals That TaOPF29a-A Promotes Drought Tolerance. BIOMED RESEARCH INTERNATIONAL 2020; 2020:9708324. [PMID: 33224986 DOI: 10.1155/2020/9708324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 09/15/2020] [Accepted: 09/22/2020] [Indexed: 12/21/2022]
Abstract
OVATE family proteins (OFPs) are plant-specific transcription factors that play important roles in plant development. Although common wheat (Triticum aestivum L.) is a major staple food worldwide, OFPs have not been systematically analyzed in this important crop. Here, we performed a genome-wide survey of OFP genes in wheat and identified 100 genes belonging to 34 homoeologous groups. Arabidopsis thaliana, rice (Oryza sativa), and wheat OFP genes were divided into four subgroups based on their phylogenetic relationships. Structural analysis indicated that only four TaOFPs contain introns. We mapped the TaOFP genes onto the wheat chromosomes and determined that TaOFP17 was duplicated in this crop. A survey of cis-acting elements along the promoter regions of TaOFP genes suggested that subfunctionalization of homoeologous genes might have occurred during evolution. The TaOFPs were highly expressed in wheat, with tissue- or organ-specific expression patterns. In addition, these genes were induced by various hormone and stress treatments. For instance, TaOPF29a-A was highly expressed in roots in response to drought stress. Wheat plants overexpressing TaOPF29a-A had longer roots and higher dry weights than nontransgenic plants under drought conditions, suggesting that this gene improves drought tolerance. Our findings provide a starting point for further functional analysis of this important transcription factor family and highlight the potential of using TaOPF29a-A to genetically engineer drought-tolerant crops.
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Yang S, Zeng K, Chen K, Wu J, Wang Q, Li X, Deng Z, Huang Y, Huang F, Chen R, Zhang M. Chromosome transmission in BC 4 progenies of intergeneric hybrids between Saccharum spp. and Erianthus arundinaceus (Retz.) Jeswiet. Sci Rep 2019; 9:2528. [PMID: 30792411 PMCID: PMC6385618 DOI: 10.1038/s41598-019-38710-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 01/07/2019] [Indexed: 12/15/2022] Open
Abstract
Intergeneric hybrids between Saccharum spp. and Erianthus arundinaceus and clones derived from these hybrids and backcrosses to Saccharum spp. were used to study the transmission of E. arundinaceus chromosomes by genomic in situ hybridization (GISH). True hybrid progenies were precisely identified using PCR with a primer pair, AGRP52/53. The results showed that AGRP52/53 was an E. arundinaceus-specific primer pair and could be used as molecular marker to assist breeding. EaHN92, a 364 bp E. arundinaceus-specific tandem repeat satellite DNA sequence, was cloned from the E. arundinaceus clone HN92-105 with AGRP52/53, and was localized on sub-telomeric regions of all E. arundinaceus chromosomes. YCE06-61, a BC3 progeny, had 7 E. arundinaceus chromosomes and its progenies had approximately 1-6 E. arundinaceus chromosomes. The number of E. arundinaceus chromosomes in true hybrids appeared as Gaussian distribution in 3 cross combinations. In addition, GISH detected intergeneric chromosome translocation in a few progenies. Hence, screening clones containing approximately 1-2 E. arundinaceus chromosomes without translocation could be used for sorting and sequencing E. arundinaceus chromosomes. This study provides a method for breeders to select true hybrid progenies between Saccharum spp. and E. arundinaceus, which will accelerate this intergeneric hybridization breeding.
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Affiliation(s)
- Shan Yang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.,Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Kai Zeng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ke Chen
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jiayun Wu
- Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute, Guangzhou, 510316, China
| | - Qinnan Wang
- Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute, Guangzhou, 510316, China
| | - Xueting Li
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Zuhu Deng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China.
| | - Yongji Huang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Fei Huang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Rukai Chen
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Muqing Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, 530004, China
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Pachakkil B, Terajima Y, Ohmido N, Ebina M, Irei S, Hayashi H, Takagi H. Cytogenetic and agronomic characterization of intergeneric hybrids between Saccharum spp. hybrid and Erianthus arundinaceus. Sci Rep 2019; 9:1748. [PMID: 30742000 PMCID: PMC6370852 DOI: 10.1038/s41598-018-38316-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 12/21/2018] [Indexed: 11/09/2022] Open
Abstract
In sugarcane (Saccharum spp. hybrid) breeding, introgression of useful genes via intergeneric hybridization is a powerful strategy for improving the crop productivity. Erianthus arundinaceus shows great potential in terms of useful traits; however, little is known about the cytogenetic and agronomic characteristics of intergeneric hybrids between these two species. Here, we examine the cytogenetic and agronomic characteristics, and relationships between the two in intergeneric F1 hybrids between modern sugarcane cultivar and E. arundinaceus identified by amplification of 5S rDNA markers and morphological characteristics. The nuclear DNA content of the hybrids varied from 6.07 to 8.94 pg/2C, with intra-clonal variation in DNA content and 5S rDNA sites. Genomic in situ hybridization revealed 53 to 82 chromosomes in the hybrids, with 53 to 56 derived from sugarcane and 1 to 29 from E. arundinaceus. There were significant positive correlations between the number of E. arundinaceus chromosomes and dry matter yield, millable stalk weight, single stalk weight, and stalk diameter, but not sucrose content, reducing sugar content, sucrose/reducing sugar ratio or fiber content. This detailed information on intergeneric F1 hybrids between modern sugarcane cultivar and E. arundinaceus will contribute to effective utilization of E. arundinaceus in sugarcane breeding.
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Affiliation(s)
- Babil Pachakkil
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences, Ishigaki, 907-0002, Japan.,Tokyo University of Agriculture, Tokyo, 156-8502, Japan
| | - Yoshifumi Terajima
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences, Ishigaki, 907-0002, Japan.
| | - Nobuko Ohmido
- Graduate School of Human Development and Environment, Kobe University, Kobe, 657-8501, Japan
| | - Masumi Ebina
- Institute of Livestock and Grassland Science, National Agriculture and Food Research Organization, Nasushiobara, 329-2793, Japan
| | - Shin Irei
- Okinawa Prefectural Agricultural Research Center, Itoman, 901-0336, Japan
| | | | - Hiroko Takagi
- Tropical Agriculture Research Front, Japan International Research Center for Agricultural Sciences, Ishigaki, 907-0002, Japan
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Lloyd Evans D, Joshi SV, Wang J. Whole chloroplast genome and gene locus phylogenies reveal the taxonomic placement and relationship of Tripidium (Panicoideae: Andropogoneae) to sugarcane. BMC Evol Biol 2019; 19:33. [PMID: 30683070 PMCID: PMC6347779 DOI: 10.1186/s12862-019-1356-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 01/03/2019] [Indexed: 11/13/2022] Open
Abstract
Background For over 50 years, attempts have been made to introgress agronomically useful traits from Erianthus sect. Ripidium (Tripidium) species into sugarcane based on both genera being part of the ‘Saccharum Complex’, an interbreeding group of species believed to be involved in the origins of sugarcane. However, recent low copy number gene studies indicate that Tripidium and Saccharum are more divergent than previously thought. The extent of genus Tripidium has not been fully explored and many species that should be included in Tripidium are still classified as Saccharum. Moreover, Tripidium is currently defined as incertae sedis within the Andropogoneae, though it has been suggested that members of this genus are related to the Germainiinae. Results Eight newly-sequenced chloroplasts from potential Tripidium species were combined in a phylogenetic study with 46 members of the Panicoideae, including seven Saccharum accessions, two Miscanthidium and three Miscanthus species. A robust chloroplast phylogeny was generated and comparison with a gene locus phylogeny clearly places a monophyletic Tripidium clade outside the bounds of the Saccharinae. A key to the currently identified Tripidium species is presented. Conclusion For the first time, we have undertaken a large-scale whole plastid study of eight newly assembled Tripidium accessions and a gene locus study of five Tripidium accessions. Our findings show that Tripidium and Saccharum are 8 million years divergent, last sharing a common ancestor 12 million years ago. We demonstrate that four species should be removed from Saccharum/Erianthus and included in genus Tripidium. In a genome context, we show that Tripidium evolved from a common ancestor with and extended Germainiinae clade formed from Germainia, Eriochrysis, Apocopis, Pogonatherum and Imperata. We re-define the ‘Saccharum complex’ to a group of genera that can interbreed in the wild and extend the Saccharinae to include Sarga along with Sorghastrum, Microstegium vimineum and Polytrias (but excluding Sorghum). Monophyly of genus Tripidium is confirmed and the genus is expanded to include Tripidium arundinaceum, Tripidium procerum, Tripidium kanashiroi and Tripidium rufipilum. As a consequence, these species are excluded from genus Saccharum. Moreover, we demonstrate that genus Tripidium is distinct from the Germainiinae. Electronic supplementary material The online version of this article (10.1186/s12862-019-1356-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dyfed Lloyd Evans
- South African Sugarcane Research Institute, 170 Flanders Drive, Private Bag X02, Mount Edgecombe, Durban, 4300, South Africa. .,School of Life Sciences, College of Agriculture, Engineering and Science, University of Kwa-Zulu Natal, Private Bag X54001, Durban, 4000, South Africa. .,BeauSci Ltd., Waterbeach, Cambridge, CB25 9TL, UK.
| | - Shailesh V Joshi
- South African Sugarcane Research Institute, 170 Flanders Drive, Private Bag X02, Mount Edgecombe, Durban, 4300, South Africa.,School of Life Sciences, College of Agriculture, Engineering and Science, University of Kwa-Zulu Natal, Private Bag X54001, Durban, 4000, South Africa
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, USA.,Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, China.,Plant Molecular and Biology Program, Genetics Institute, University of Florida, Gainesville, FL, USA
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10
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Yu F, Huang Y, Luo L, Li X, Wu J, Chen R, Zhang M, Deng Z. An improved suppression subtractive hybridization technique to develop species-specific repetitive sequences from Erianthus arundinaceus (Saccharum complex). BMC PLANT BIOLOGY 2018; 18:269. [PMID: 30400857 PMCID: PMC6220460 DOI: 10.1186/s12870-018-1471-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 10/05/2018] [Indexed: 05/17/2023]
Abstract
BACKGROUND Sugarcane has recently attracted increased attention for its potential as a source of bioethanol and methane. However, a narrow genetic base has limited germplasm enhancement of sugarcane. Erianthus arundinaceus is an important wild genetic resource that has many excellent traits for improving cultivated sugarcane via wide hybridization. Species-specific repetitive sequences are useful for identifying genome components and investigating chromosome inheritance in noblization between sugarcane and E. arundinaceus. Here, suppression subtractive hybridization (SSH) targeting E. arundinaceus-specific repetitive sequences was performed. The five critical components of the SSH reaction system, including enzyme digestion of genomic DNA (gDNA), adapters, digested gDNA concentrations, primer concentrations, and LA Taq polymerase concentrations, were improved using a stepwise optimization method to establish a SSH system suitable for obtaining E. arundinaceus-specific gDNA fragments. RESULTS Specificity of up to 85.42% was confirmed for the SSH method as measured by reverse dot blot (RDB) of an E. arundinaceus subtractive library. Furthermore, various repetitive sequences were obtained from the E. arundinaceus subtractive library via fluorescence in situ hybridization (FISH), including subtelomeric and centromeric regions. EaCEN2-166F/R and EaSUB1-127F/R primers were then designed as species-specific markers to accurately validate E. arundinaceus authenticity. CONCLUSIONS This is the first report that E. arundinaceus-specific repetitive sequences were obtained via an improved SSH method. These results suggested that this novel SSH system could facilitate screening of species-specific repetitive sequences for species identification and provide a basis for development of similar applications for other plant species.
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Affiliation(s)
- Fan Yu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Yongji Huang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Ling Luo
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Xueting Li
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Jiayun Wu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangdong Provincial Bioengineering Institute, Guangzhou, China
| | - Rukai Chen
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Muqing Zhang
- State Key Laboratory for protection and utilization of subtropical agro-bioresources, Guangxi University, Nanning, 530004 China
| | - Zuhu Deng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- State Key Laboratory for protection and utilization of subtropical agro-bioresources, Guangxi University, Nanning, 530004 China
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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11
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Yu F, Wang P, Li X, Huang Y, Wang Q, Luo L, Jing Y, Liu X, Deng Z, Wu J, Yang Y, Chen R, Zhang M, Xu L. Characterization of chromosome composition of sugarcane in nobilization by using genomic in situ hybridization. Mol Cytogenet 2018; 11:35. [PMID: 29977338 PMCID: PMC5992832 DOI: 10.1186/s13039-018-0387-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 05/24/2018] [Indexed: 11/29/2022] Open
Abstract
Background Interspecific hybridization is an effective strategy for germplasm innovation in sugarcane. Nobilization refers to the breeding theory of development and utilization of wild germplasm. Saccharum spontaneum is the main donor of resistance and adaptive genes in the nobilization breeding process. Chromosome transfer in sugarcane is complicated; thus, research of different inheritance patterns can provide guidance for optimal sugarcane breeding. Results Through chromosome counting and genomic in situ hybridization, we found that six clones with 80 chromosomes were typical S. officinarum and four other clones with more than 80 chromosomes were interspecific hybrids between S. officinarum and S. spontaneum. These data support the classical view that S. officinarum is characterized by 2n = 80. In addition, genomic in situ hybridization showed that five F1 clones were products of a 2n + n transmission and one F1 clone was the product of an n + n transmission in clear pedigree noble hybrids between S. officinarum and S. spontaneum. Interestingly, Yacheng 75–408 and Yacheng 75–409 were the sibling lines of the F1 progeny from the same parents but with different genetic transmissions. Conclusions This is the first clear evidence of Loethers, Crystallina, Luohanzhe, Vietnam Niuzhe, and Nanjian Guozhe were typical S. officinarum by GISH. Furthermore, for the first time, we identified the chromosome transmission of six F1 hybrids between S. officinarum and S. spontaneum. These findings may provide a theoretical basis for germplasm innovation in sugarcane breeding and guidance for further sugarcane nobilization. Electronic supplementary material The online version of this article (10.1186/s13039-018-0387-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Fan Yu
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ping Wang
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xueting Li
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yongji Huang
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinnan Wang
- 2Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Ling Luo
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanfen Jing
- Sugarcane Research Institute of Yunnan Agriculture Science Academy, Kaiyuan, China
| | - Xinlong Liu
- Sugarcane Research Institute of Yunnan Agriculture Science Academy, Kaiyuan, China
| | - Zuhu Deng
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China.,4Guangxi Collaborative Innovation Center of Sugar Industries, Guangxi University, Nanning, China
| | - Jiayun Wu
- 2Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Yongqing Yang
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Rukai Chen
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Muqing Zhang
- 4Guangxi Collaborative Innovation Center of Sugar Industries, Guangxi University, Nanning, China
| | - Liangnian Xu
- 1National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
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12
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Huang Y, Luo L, Hu X, Yu F, Yang Y, Deng Z, Wu J, Chen R, Zhang M. Characterization, Genomic Organization, Abundance, and Chromosomal Distribution of Ty1-copia Retrotransposons in Erianthus arundinaceus. FRONTIERS IN PLANT SCIENCE 2017; 8:924. [PMID: 28638390 PMCID: PMC5461294 DOI: 10.3389/fpls.2017.00924] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/17/2017] [Indexed: 06/16/2023]
Abstract
Erianthus arundinaceus is an important wild species of the genus Saccharum with many valuable traits. However, the composition and structure of its genome are largely unknown, which have hindered its utilization in sugarcane breeding and evolutionary research. Retrotransposons constitute an appreciable fraction of plant genomes and may have played a significant role in the evolution and sequence organization of genomes. In the current study, we investigate the phylogenetic diversity and genomic abundance of Ty1-copia retrotransposons for the first time and inspect their chromosomal distribution patterns in E. arundinaceus. In total, 70 Ty1-copia reverse transcriptase (RT) sequences with significant levels of heterogeneity were obtained. The phylogenetic analysis revealed these Ty1-copia retrotransposons were classified into four distinct evolutionary lineages (Tork/TAR, Tork/Angela, Retrofit/Ale, and Sire/Maximus). Dot-blot analysis showed estimated the total copy number of Ty1-copia retrotransposons to be about 4.5 × 103 in the E. arundinaceus genome, indicating they were a significant component. Fluorescence in situ hybridization revealed that Ty1-copia retrotransposons from the four lineages had strikingly similar patterns of chromosomal enrichment, being exclusively enriched in the subterminal heterochromatic regions of most E. arundinaceus chromosomes. This is the first clear evidence of the presence of Ty1-copia retrotransposons in the subterminal heterochromatin of E. arundinaceus. Altogether, these results promote the understanding of the diversification of Ty1-copia retrotransposons and shed light on their chromosomal distribution patterns in E. arundinaceus.
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Affiliation(s)
- Yongji Huang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Ling Luo
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Xuguang Hu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Fan Yu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Yongqing Yang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Zuhu Deng
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry UniversityFuzhou, China
- Guangxi Collaborative Innovation Center of Sugar Industries, Guangxi UniversityNanning, China
| | - Jiayun Wu
- Guangdong Key Laboratory of Sugarcane Improvement and BiorefineryGuangzhou, China
- Guangdong Provincial Bioengineering Institute, Guangzhou Sugarcane Industry Research InstituteGuangzhou, China
| | - Rukai Chen
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry UniversityFuzhou, China
| | - Muqing Zhang
- Guangxi Collaborative Innovation Center of Sugar Industries, Guangxi UniversityNanning, China
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13
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Zhang J, Yan J, Shen X, Chang D, Bai S, Zhang Y, Zhang J. How genetic variation is affected by geographic environments and ploidy level in Erianthus arundinaceus? PLoS One 2017; 12:e0178451. [PMID: 28557997 PMCID: PMC5448781 DOI: 10.1371/journal.pone.0178451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Accepted: 05/12/2017] [Indexed: 11/18/2022] Open
Abstract
Erianthus arundinaceus is not only a candidate plant for sugarcane breeding programs, but also a potential bioenergy grass. Genetic variation that is affected by geographic environments and ploidy level is very important for the utilization of Erianthus arundinaceus. In this study, effects of geographic environments and ploidy level on genetic variation were studied through analyzing the genetic diversity, genetic similarity and cluster analysis of 46 E. arundinaceus materials from natural habitats in China by using 7 ISSRs and 15 SSRs. Results showed that: 1) Seven ISSRs generated total 66 bands, of which 77% were polymorphic bands, the Nei's genetic similarity coefficient of tested materials ranged from 0.642 to 0.904 with an average value of 0.765. Fifteen SSRs generated 138 bands, of which 81% were polymorphic bands, the Nei's genetic similarity coefficient of tested materials ranged from 0.634 to 0.963 with an average value of 0.802. The results indicated great genetic diversity existed in the tested materials. 2)The tested materials were clustered into 3 groups and 7 subgroups, which demonstrated a strong geographic effect on variation of the local E. arundinaceus, and weak relationship was found between genetic distance and geographic distance. Five tetraploid materials were not clustered together, and were clustered together with materials from similar geographical location. 3) The genetic variation and cluster results were affected by geographic landforms and environments, the gene flow was blocked by Ocean and mountains, and promoted by river. The effect of ploidy level on genetic variation was little.
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Affiliation(s)
- Jianbo Zhang
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Jiajun Yan
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Xiaoyun Shen
- State Engineerting Technology Institute for Karst Desertification Control, Guizhou Normal University, Guiyang, China
- School of Life Science and Engineering, Southwest Universtiy of Science and Technology, Mianyang, China
- Foreign capital project management center, Guizhou proverty alleviation and development office, Guiyang, China
| | - Dan Chang
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
- * E-mail:
| | - Yu Zhang
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Jin Zhang
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
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14
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Complete Chloroplast Genomes of Erianthus arundinaceus and Miscanthus sinensis: Comparative Genomics and Evolution of the Saccharum Complex. PLoS One 2017; 12:e0169992. [PMID: 28125648 PMCID: PMC5268433 DOI: 10.1371/journal.pone.0169992] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 12/27/2016] [Indexed: 11/19/2022] Open
Abstract
The genera Erianthus and Miscanthus, both members of the Saccharum complex, are of interest as potential resources for sugarcane improvement and as bioenergy crops. Recent studies have mainly focused on the conservation and use of wild accessions of these genera as breeding materials. However, the sequence data are limited, which hampers the studies of phylogenetic relationships, population structure, and evolution of these grasses. Here, we determined the complete chloroplast genome sequences of Erianthus arundinaceus and Miscanthus sinensis by using 454 GS FLX pyrosequencing and Sanger sequencing. Alignment of the E. arundinaceus and M. sinensis chloroplast genome sequences with the known sequence of Saccharum officinarum demonstrated a high degree of conservation in gene content and order. Using the data sets of 76 chloroplast protein-coding genes, we performed phylogenetic analysis in 40 taxa including E. arundinaceus and M. sinensis. Our results show that S. officinarum is more closely related to M. sinensis than to E. arundinaceus. We estimated that E. arundinaceus diverged from the subtribe Sorghinae before the divergence of Sorghum bicolor and the common ancestor of S. officinarum and M. sinensis. This is the first report of the phylogenetic and evolutionary relationships inferred from maternally inherited variation in the Saccharum complex. Our study provides an important framework for understanding the phylogenetic relatedness of the economically important genera Erianthus, Miscanthus, and Saccharum.
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15
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Yan J, Zhang J, Sun K, Chang D, Bai S, Shen Y, Huang L, Zhang J, Zhang Y, Dong Y. Ploidy Level and DNA Content of Erianthus arundinaceus as Determined by Flow Cytometry and the Association with Biological Characteristics. PLoS One 2016; 11:e0151948. [PMID: 27010798 PMCID: PMC4806844 DOI: 10.1371/journal.pone.0151948] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 03/07/2016] [Indexed: 11/18/2022] Open
Abstract
Erianthus arundinaceus is not only an important germplasm resource for sugarcane breeding but also a potential bioenergy plant. Making clear the distribution of the chromosome ploidy of wild E. arundinaceus in china is the premise of the research and utilization of this species. Therefore, the objectives of this study were to determine the ploidy level and DNA content of the 55 E. arundinaceus accessions using flow cytometry and to identify the correlation between ploidy and phenotypic traits. Among the 55 accessions, four tetraploids and 51 hexaploids were identified. The four tetraploids originated from Mengma Yunnan, Shuangjiang Yunnan, Gaozhou Guangdong and Chengle Sichuan. The mean DNA content was 4.82 pg/2C for the tetraploid and 7.30 pg/2C for the hexaploid plants. The ploidy was negatively correlated with cellulose content and positively correlated (P<0.05) with plant height, stem diameter, leaf width, dry weight per plant, fresh weight per plant and hemicellulose content. However, ploidy was not correlated with leaf length, tiller number and the ratio of dry weight and fresh weight. This study will be useful for revealing the distribution of the ploidy of wild E. arundinaceus in Chin, traits markers analysis, and utilization of this species, such as cultivar improvement and sugarcane breeding in the future.
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Affiliation(s)
- Jiajun Yan
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Jianbo Zhang
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Kaiyan Sun
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
- Department of Grassland Science, Animal Science and Technology College, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Dan Chang
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
- Department of Grassland Science, Animal Science and Technology College,Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Yixin Shen
- Department of Grassland Science, Animal Science and Technology College, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Linkai Huang
- Department of Grassland Science, Animal Science and Technology College,Sichuan Agricultural University, Ya’an, Sichuan, China
| | - Jin Zhang
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Yu Zhang
- Sichuan Academy of Grassland Sciences, Chengdu, Sichuan, China
| | - Yanhai Dong
- Department of Grassland Science, Animal Science and Technology College,Sichuan Agricultural University, Ya’an, Sichuan, China
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16
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Huang Y, Wu J, Wang P, Lin Y, Fu C, Deng Z, Wang Q, Li Q, Chen R, Zhang M. Characterization of Chromosome Inheritance of the Intergeneric BC2 and BC3 Progeny between Saccharum spp. and Erianthus arundinaceus. PLoS One 2015. [PMID: 26196281 PMCID: PMC4510360 DOI: 10.1371/journal.pone.0133722] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Erianthus arundinaceus (E. arundinaceus) has many desirable agronomic traits for sugarcane improvement, such as high biomass, vigor, rationing ability, tolerance to drought, and water logging, as well as resistance to pests and disease. To investigate the introgression of the E. arundinaceus genome into sugarcane in the higher generations, intergeneric BC2 and BC3 progeny generated between Saccharum spp. and E. arundinaceus were studied using the genomic in situ hybridization (GISH) technique. The results showed that the BC2 and BC3 generations resulted from n + n chromosome transmission. Furthermore, chromosome translocation occurred at terminal fragments from the E. arundinaceus chromosome in some progeny of Saccharum spp. and E. arundinaceus. Notably, the translocated chromosomes could be stably transmitted to their progeny. This study illustrates the characterization of chromosome inheritance of the intergeneric BC2 and BC3 progeny between Saccharum spp. and E. arundinaceus. This work could provide more useful molecular cytogenetic information for the germplasm resources of E. arundinaceus, and may promote further understanding of the germplasm resources of E. arundinaceus for sugarcane breeders to accelerate its progress in sugarcane commercial breeding.
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Affiliation(s)
- Yongji Huang
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiayun Wu
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Ping Wang
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanquan Lin
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cheng Fu
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Zuhu Deng
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Guangxi Collaborative Center for Sugarcane & Cane Sugar Industries, Guangxi, China
- * E-mail:
| | - Qinnan Wang
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Qiwei Li
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Rukai Chen
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Muqing Zhang
- Guangxi Collaborative Center for Sugarcane & Cane Sugar Industries, Guangxi, China
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17
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Chen JW, Lao FY, Chen XW, Deng HH, Liu R, He HY, Fu C, Chen YS, Liu FY, Li QW, Jackson P, Aitken K. DNA Marker Transmission and Linkage Analysis in Populations Derived from a Sugarcane (Saccharum spp.) x Erianthus arundinaceus Hybrid. PLoS One 2015; 10:e0128865. [PMID: 26053338 PMCID: PMC4459986 DOI: 10.1371/journal.pone.0128865] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Accepted: 05/02/2015] [Indexed: 11/26/2022] Open
Abstract
Introgression of Erianthus arundinaceus has been the focus of several sugarcane breeding programs in the world, because the species has desirable traits such as high biomass production, vigour, ratooning ability and good resistance to environmental stresses and disease. In this study four genetic maps were constructed for two intergeneric populations. The first population (BC1) was generated from a cross between an Erianthus/Saccharum hybrid YC96-40 and a commercial sugarcane variety CP84-1198. The second population (BC2) was generated from a cross between YCE01-116, a progeny of the BC1 cross and NJ57-416, a commercial sugarcane cultivar. Markers across both populations were generated using 35 AFLP and 23 SSR primer pairs. A total of 756 and 728 polymorphic markers were scored in the BC1 and BC2 populations, respectively. In the BC1 population, a higher proportion of markers was derived from the Erianthus ancestor than those from the Saccharum ancestor Badila. In the BC2 population, both the number and proportion of markers derived from Erianthus were approximately half of those in the BC1 population. Linkage analysis led to the construction of 38, 57, 36 and 47 linkage groups (LGs) for YC96-40, CP84-1198, YCE01-116, and NJ57-416, encompassing 116, 174, 97 and 159 markers (including single dose, double dose and bi-parental markers), respectively. These LGs could be further placed into four, five, five and six homology groups (HGs), respectively, based on information from multi-allelic SSR markers and repulsion phase linkages detected between LGs. Analysis of repulsion phase linkage indicated that Erianthus behaved like a true autopolyploid.
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Affiliation(s)
- Jian-wen Chen
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Fang-ye Lao
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Xi-wen Chen
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Hai-hua Deng
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Rui Liu
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Hui-yi He
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Cheng Fu
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Yong-sheng Chen
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Fu-ye Liu
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
| | - Qi-wei Li
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangzhou Sugarcane Industry Research Institute, Guangzhou, China
- * E-mail: (PJ); (Q-wL)
| | - Phillip Jackson
- CSIRO Agriculture, Queensland Bioscience Precinct, Brisbane, Qld, Australia
- * E-mail: (PJ); (Q-wL)
| | - Karen Aitken
- CSIRO Agriculture, Queensland Bioscience Precinct, Brisbane, Qld, Australia
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18
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Wu J, Huang Y, Lin Y, Fu C, Liu S, Deng Z, Li Q, Huang Z, Chen R, Zhang M. Unexpected inheritance pattern of Erianthus arundinaceus chromosomes in the intergeneric progeny between Saccharum spp. and Erianthus arundinaceus. PLoS One 2014; 9:e110390. [PMID: 25310831 PMCID: PMC4195721 DOI: 10.1371/journal.pone.0110390] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Accepted: 09/12/2014] [Indexed: 01/28/2023] Open
Abstract
Erianthus arundinaceus is a valuable source of agronomic traits for sugarcane improvement such as ratoonability, biomass, vigor, tolerance to drought and water logging, as well as resistance to pests and disease. To investigate the introgression of the E. arundinaceus genome into sugarcane, five intergeneric F1 hybrids between S. officinarum and E. arundinaceus and 13 of their BC1 progeny were studied using the genomic in situ hybridization (GISH) technique. In doing so, we assessed the chromosome composition and chromosome transmission in these plants. All F1 hybrids were aneuploidy, containing either 28 or 29 E. arundinaceus chromosomes. The number of E. arundinaceus chromosomes in nine of the BC1 progeny was less than or equal to 29. Unexpectedly, the number of E. arundinaceus chromosomes in the other four BC1 progeny was above 29, which was more than in their F1 female parents. This is the first cytogenetic evidence for an unexpected inheritance pattern of E. arundinaceus chromosomes in sugarcane. We pointed to several mechanisms that may be involved in generating more than 2n gametes in the BC1 progeny. Furthermore, the implication of these results for sugarcane breeding programs was discussed.
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Affiliation(s)
- Jiayun Wu
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- Guangzhou Research Institute for Sugarcane Industry, Guangzhou, China
| | - Yongji Huang
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanquan Lin
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Cheng Fu
- Guangzhou Research Institute for Sugarcane Industry, Guangzhou, China
| | - Shaomou Liu
- Guangzhou Research Institute for Sugarcane Industry, Guangzhou, China
| | - Zuhu Deng
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qiwei Li
- Guangzhou Research Institute for Sugarcane Industry, Guangzhou, China
| | - Zhongxing Huang
- Guangzhou Research Institute for Sugarcane Industry, Guangzhou, China
| | - Rukai Chen
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Muqing Zhang
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- State Key lab for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
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19
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Abstract
Genomic in situ hybridization (GISH) is an invaluable cytogenetic technique which enables the visualization of whole genomes in hybrids and polyploidy taxa. Total genomic DNA from one or two different species/genome is used as a probe, labeled with a fluorochrome and directly detected on mitotic chromosomes from root-tip meristems. In sugarcane we were able to characterize interspecific hybrids of two closely related species as well as intergeneric hybrids of two closely related genera.
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20
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Zhang J, Yan J, Zhang Y, Ma X, Bai S, Wu Y, Dao Z, Li D, Zhang C, Zhang Y, You M, Yang F, Zhang J. Molecular insights of genetic variation in Erianthus arundinaceus populations native to China. PLoS One 2013; 8:e80388. [PMID: 24282538 PMCID: PMC3840007 DOI: 10.1371/journal.pone.0080388] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 10/02/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND E. arundinaceus (Retz.) Jeswiet is a warm-season, tall-growing perennial species native to much southern portion in China. The grass has been extensively used in sugarcane breeding and is recently targeted as a bioenergy feedstock crop. However, information on the genetic structure of the Chinese wild germplasm is limited. Knowledge of genetic variation within and among populations is essential for breeding new cultivars in the species. The major objective of this study was to quantify the magnitude of genetic variation among and within natural populations in China. METHODOLOGY/PRINCIPAL FINDINGS In this experiment, we analyzed genetic variation of 164 individuals of 18 populations collected from natural habitats in six Chinese provinces using 20 sequence-related amplified polymorphism (SRAP) primer pairs generating 277 polymorphic bands. Among and within the populations, the percentage of polymorphic bands (PPB) was 80.00% and 27.07%, genetic diversity (HE ) was 0.245 and 0.099, effective number of alleles (NE ) was 1.350 and 1.170, and Shannon's information index (I) was 0.340 and 0.147, respectively. The populations were clustered into six groups exhibiting a high level of genetic differentiation, which was highly associated with geographic origins of respective germplasm populations, but was not significantly associated with geographic distances between the populations. CONCLUSIONS/SIGNIFICANCE This is the first report indicating that large genetic variation exists in the Chinese E. arundinaceus germplasm based on the SRAP molecular marker analysis of native populations. The genetic structure of populations in the species has been substantially affected by geographic landforms and environments. The diverse collection will be highly valuable in genetic improvement in the species per se and likely in sugarcane.
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Affiliation(s)
- Jianbo Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya'an, Sichuan, China
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
- Guizhou Grassland Science Institute, Guiyang, Guizhou, China
| | - Jiajun Yan
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Yunwei Zhang
- Grassland Institute, China Agricultural University, Beijing, China
| | - Xiao Ma
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Shiqie Bai
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya'an, Sichuan, China
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Yanqi Wu
- Plant and Soil Sciences Department, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Zhixue Dao
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Daxu Li
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Changbing Zhang
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Yu Zhang
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Minghong You
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Fuyu Yang
- Grassland Institute, China Agricultural University, Beijing, China
| | - Jin Zhang
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
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