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Li S, Wang J, Wang K, Chen J, Wang K, Du L, Ni Z, Lin Z, Ye X. Development of PCR markers specific to Dasypyrum villosum genome based on transcriptome data and their application in breeding Triticum aestivum-D. villosum#4 alien chromosome lines. BMC Genomics 2019; 20:289. [PMID: 30987602 PMCID: PMC6466811 DOI: 10.1186/s12864-019-5630-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 03/20/2019] [Indexed: 11/10/2022] Open
Abstract
Background Dasypyrum villosum is an important wild species of wheat (Triticum aestivum L.) and harbors many desirable genes that can be used to improve various traits of wheat. Compared with other D. villosum accessions, D. villosum#4 still remains less studied. In particular, chromosomes of D. villosum#4 except 6V#4 have not been introduced into wheat by addition or substitution and translocation, which is an essential step to identify and apply the alien desired genes. RNA-seq technology can generate large amounts of transcriptome sequences and accelerate the development of chromosome-specific molecular markers and assisted selection of alien chromosome line. Results We obtained the transcriptome of D. villosum#4 via a high-throughput sequencing technique, and then developed 76 markers specific to each chromosome arm of D. villosum#4 based on the bioinformatic analysis of the transcriptome data. The D. villosum#4 sequences containing the specific DNA markers were expected to be involved in different genes, among which most had functions in metabolic processes. Consequently, we mapped these newly developed molecular markers to the homologous chromosome of barley and obtained the chromosome localization of these markers on barley genome. Then we analyzed the collinearity of these markers among D. villosum, wheat, and barley. In succession, we identified six types of T. aestivum-D. villosum#4 alien chromosome lines which had one or more than one D. villosum#4 chromosome in the cross and backcross BC3F5 populations between T. durum–D. villosum#4 amphidiploid TH3 and wheat cv. Wan7107 by employing the selected specific markers, some of which were further confirmed to be translocation or addition lines by genomic in situ hybridization (GISH). Conclusion Seventy-six PCR markers specific to chromosomes of D. villosum#4 based on transcriptome data were developed in the current study and their collinearity among D. villosum, wheat, and barley were carried out. Six types of Triticum aestivum-D. villosum#4 alien chromosome lines were identified by using 12 developed markers and some of which were further confirmed by GISH. These novel T. aestivum-D. villosum#4 chromosome lines have great potential to be used for the introduction of desirable genes from D. villosum#4 into wheat by chromosomal translocation to breed new wheat varieties. Electronic supplementary material The online version of this article (10.1186/s12864-019-5630-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shijin Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.,College of Agronomy and Biotechnology/State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, 100193, China
| | - Jing Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Kunyang Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jingnan Chen
- School of Plant Science and Technology, Beijing University of Agriculture, Beijing, 102206, China
| | - Ke Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lipu Du
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Zhongfu Ni
- College of Agronomy and Biotechnology/State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), Key Laboratory of Crop Genetic Improvement (Beijing Municipality), China Agricultural University, Beijing, 100193, China.
| | - Zhishan Lin
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. .,National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Xingguo Ye
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China. .,National Key Facility of Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Książczyk T, Zwierzykowska E, Molik K, Taciak M, Krajewski P, Zwierzykowski Z. Genome-dependent chromosome dynamics in three successive generations of the allotetraploid Festuca pratensis × Lolium perenne hybrid. PROTOPLASMA 2015; 252:985-996. [PMID: 25480732 PMCID: PMC4491343 DOI: 10.1007/s00709-014-0734-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2014] [Accepted: 11/17/2014] [Indexed: 06/04/2023]
Abstract
We focus on the identification of complete and recombined ribosomal DNA-bearing chromosomes, and the dynamics of chromosomal number and position of ribosomal DNA (rDNA) loci in the F2-F4 generations derived from the F1 hybrid of Festuca pratensis Huds. (2n = 4x = 28) × Lolium perenne L. (2n = 4x = 28). Lolium genomic DNA and rRNA genes were mapped by means of genomic and fluorescence in situ hybridization (GISH and FISH). The results revealed that plants of the three generations share various rDNA loci profiles with chromosome structural changes, possibly as a result of chromosomal inter- and intra-rearrangements. We observed an asymmetrical variation in the number of recombinant arms with and without rDNA loci between parental genomes. The Lolium genome was more affected by rearrangements in arms with rDNA loci, while Festuca was more affected in arms without them. Statistically significant differences between L. perenne and F. pratensis genomes concerned the number of recombined chromosomes without rDNA, and the number of recombined rDNA-bearing chromosomal arms of marked chromosomes, showing a tendency of F. pratensis genome-like chromosomes to be less stable, compared with L. perenne. We postulate a novel genome-dependent range and type of chromosome variation in plants of the F2-F4 generations derived from F. pratensis × L. perenne hybrid.
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Affiliation(s)
- Tomasz Książczyk
- Department of Environmental Stress Biology, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland,
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Zhang J, Long H, Pan Z, Liang J, Yu S, Deng G, Yu M. Characterization of a genome-specific Gypsy-like retrotransposon sequence and development of a molecular marker specific for Dasypyrum villosum (L.). J Genet 2013; 92:103-8. [PMID: 23640412 DOI: 10.1007/s12041-013-0218-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jie Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, People's Republic of China
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Hu L, Huang X, Mao J, Wang C, Bao Z. Genomic characterization of interspecific hybrids between the scallops Argopecten purpuratus and A. irradians irradians. PLoS One 2013; 8:e62432. [PMID: 23620828 PMCID: PMC3631176 DOI: 10.1371/journal.pone.0062432] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Accepted: 03/21/2013] [Indexed: 11/19/2022] Open
Abstract
The Peruvian scallop (Argopecten purpuratus) has been introduced to China and has successfully been hybridized with the bay scallop (A. irradians irradians). The F1 hybrids of these two scallops exhibited a large increase in production traits and some other interesting new characteristics. To understand the genetic basis of this heterosis, nuclear gene and partial mtDNA sequences, and genomic in situ hybridization (GISH) were employed to analyze the genomic organization of the hybrids. Amplification of the ribosomal DNA internal transcribed spacer (ITS) showed that the parental ITS sequences were present in all the hybrid individuals, illustrating that the hybrid offspring inherited nuclear DNA from both parents. Sequence analyses of the ITS region further confirmed that the hybrids harbored alleles from their parents; some recombinant variants were also detected, which revealed some alterations in the nuclear genetic material of the hybrids. The analysis of mitochondrial 16S rDNA showed that the hybrids possessed sequences that were identical to the 16S rDNA of the female parents, proving a matrilineal inheritance of mitochondrial genes in scallops. In addition, GISH clearly discriminated between the parental chromosomes and indicated a combination of haploid genomes of duplex parents in the hybrids. The genetic analyses in our study illustrated that the F1 hybrids inherited nuclear material from both parents and cytoplasmic genetic material maternally, and some variations occurred in the genome, which might contribute to a further understanding of crossbreeding and heterosis in scallop species.
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Affiliation(s)
- Liping Hu
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Xiaoting Huang
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
- * E-mail:
| | - Junxia Mao
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
| | - Chunde Wang
- College of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, China
| | - Zhenmin Bao
- Key Laboratory of Marine Genetics and Breeding (MGB), Ministry of Education, College of Marine Life Sciences, Ocean University of China, Qingdao, China
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Caceres M, Pupilli F, Ceccarelli M, Vaccino P, Sarri V, De Pace C, Cionini P. Cryptic Introgression of Dasypyrum villosum Parental DNA in Wheat Lines Derived from Intergeneric Hybridization. Cytogenet Genome Res 2011; 136:75-81. [DOI: 10.1159/000334275] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2011] [Indexed: 11/19/2022] Open
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Książczyk T, Apolinarska B, Kulak-Książczyk S, Wiśniewska H, Stojałowski S, Łapiński M. Identification of the chromosome complement and the spontaneous 1R/1V translocations in allotetraploid Secale cereale × Dasypyrum villosum hybrids through cytogenetic approaches. J Appl Genet 2011; 52:305-11. [PMID: 21584731 PMCID: PMC3132420 DOI: 10.1007/s13353-011-0048-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 03/27/2011] [Accepted: 04/07/2011] [Indexed: 11/25/2022]
Abstract
Genome modifications that occur at the initial interspecific hybridization event are dynamic and can be consolidated during the process of stabilization in successive generations of allopolyploids. This study identifies the number and chromosomal location of ribosomal DNA (rDNA) sites between Secale cereale, Dasypyrum villosum, and their allotetraploid S. cereale × D. villosum hybrids. For the first time, we show the advantages of FISH to reveal chromosome rearrangements in the tetraploid Secale × Dasypyrum hybrids. Based on the specific hybridization patterns of ribosomal 5S, 35S DNA and rye species-specific pSc200 DNA probes, a set of genotypes with numerous Secale/Dasypyrum translocations of 1R/1V chromosomes were identified in successive generations of allotetraploid S. cereale × D. villosum hybrids. In addition we analyse rye chromosome pairs using FISH with chromosome-specific DNA sequences on S. cereale × D. villosum hybrids.
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Affiliation(s)
- Tomasz Książczyk
- Laboratory of Cytogenetics and Molecular Biology, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, Poznan, Poland.
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Szakács É, Molnár-Láng M. Molecular cytogenetic evaluation of chromosome instability inTriticum aestivum—Secale cereale disomic addition lines. J Appl Genet 2010; 51:149-52. [DOI: 10.1007/bf03195723] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Cao Y, Bie T, Wang X, Chen P. Induction and transmission of wheat-Haynaldia villosa chromosomal translocations. J Genet Genomics 2009; 36:313-20. [DOI: 10.1016/s1673-8527(08)60120-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2008] [Revised: 03/26/2009] [Accepted: 03/27/2009] [Indexed: 10/20/2022]
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Yuan WY, Tomita M. Centromeric distribution of 350-family inDasypyrum villosumand its application to identifyingDasypyrumchromatin in the wheat genome. Hereditas 2009; 146:58-66. [DOI: 10.1111/j.1601-5223.2009.02110.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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Natali L, Ceccarelli M, Giordani T, Sarri V, Zuccolo A, Jurman I, Morgante M, Cavallini A, Cionini PG. Phylogenetic relationships between annual and perennial species of Helianthus: evolution of a tandem repeated DNA sequence and cytological hybridization experiments. Genome 2008; 51:1047-53. [PMID: 19088818 DOI: 10.1139/g08-089] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The amplification and chromosomal localization of tandem repeated DNA sequences from Helianthus annuus (clone HAG004N15) and the physical organization of ribosomal DNA were studied in annual and perennial species of Helianthus. HAG004N15-related sequences, which did not show amplification in other Asteraceae except for Viguiera multiflora, were redundant in all the Helianthus species tested, but their frequency was significantly higher in perennials than in annuals. These sequences were located at the ends and intercalary regions of all chromosome pairs of annual species. A similar pattern was found in the perennials, but a metacentric pair in their complement was not labelled. Ribosomal cistrons were carried on two chromosome pairs in perennials and on three pairs in annuals except for H. annuus, where rDNA loci were on four pairs. No difference was observed between cultivated H. annuus and its wild accessions in the hybridization pattern of the HAG004N15 and ribosomal probes. These findings support the hypothesis that the separation between annual and perennial Helianthus species occurred through interspecific hybridization involving at least one different parent. However, GISH in H. annuus using genomic DNA from the perennial Helianthus giganteus as blocking DNA failed to reveal different genomic assets in annual and perennial species.
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Affiliation(s)
- L Natali
- Dipartimento di Biologia delle Piante Agrarie, Sezione di Genetica, Universita di Pisa, Via del Borghetto 80, 56124 Pisa, Italy
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Zhou JP, Yang ZJ, Li GR, Liu C, Ren ZL. Discrimination of repetitive sequences polymorphism in Secale cereale by genomic in situ hybridization-banding. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2008; 50:452-6. [PMID: 18713379 DOI: 10.1111/j.1744-7909.2008.00644.x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Genomic in situ hybridization banding (GISH-banding), a technique slightly modified from conventional GISH, was used to probe the Chinese native rye (Secale cereale L.) DNA, and enabled us to visualize the individual rye chromosomes and create a universal reference karyotype of the S. cereale chromosome 1R to 7R. The GISH-banding approach used in the present study was able to discriminate S. cereale chromosomes or segments in the wheat (Triticum aestivum L.) background, including the Triticale, wheat-rye addition and translocation lines. Moreover, the GISH-banding pattern of S. cereale subsp. Afghanicum chromosomes was consistent with that of Chinese native rye cv. Jingzhou rye; whereas the GISH-banding pattern of Secale vavilovii was different from that of S. cereale, indicating that GISH-banding can be used to study evolutionary polymorphism in species or subspecies of Secale. In addition, the production and application of GISH-banding to the study of adenine-thymine-riched heterochromatin is discussed.
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Affiliation(s)
- Jian-Ping Zhou
- Shcool of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu 610054, China
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