1
|
Meena MR, Mohanraj K, Kumar R, Kumar RA, Chhabra ML, Kulshreshtha N, Krishnappa G, Swamy HKM, Suganya A, Govindaraj P, Hemaprabha G. Deciphering Winter Sprouting Potential of Erianthus procerus Derived Sugarcane Hybrids under Subtropical Climates. PLANTS (BASEL, SWITZERLAND) 2024; 13:1023. [PMID: 38611552 PMCID: PMC11013679 DOI: 10.3390/plants13071023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/08/2024] [Accepted: 03/06/2024] [Indexed: 04/14/2024]
Abstract
Winter sprouting potential and red rot resistance are two key parameters for successful sugarcane breeding in the subtropics. However, the cultivated sugarcane hybrids had a narrow genetic base; hence, the present study was planned to evaluate the Erianthus procerus genome introgressed Saccharum hybrids for their ratooning potential under subtropical climates and red rot tolerance under tropical and subtropical climates. A set of 15 Erianthus procerus derived hybrids confirmed through the 5S rDNA marker, along with five check varieties, were evaluated for agro-morphological, quality, and physiological traits for two years (2018-2019 and 2019-2020) and winter sprouting potential for three years (2018-2019, 2019-2020, and 2020-2021). The experimental material was also tested against the most prevalent isolates of the red rot pathogen in tropical (Cf671 and Cf671 + Cf9401) and subtropical regions (Cf08 and Cf09). The E. procerus hybrid GU 12-19 had the highest winter sprouting potential, with a winter sprouting index (WSI) of 10.6, followed by GU 12-22 with a WSI of 8.5. The other top-performing hybrids were as follows: GU 12-21 and GU 12-29 with a WSI of 7.2 and 6.9, respectively. A set of nine E. procerus-derived hybrids, i.e., GU04 (28) EO-2, GU12-19, GU12-21, GU12-22, GU12-23, GU12-26, GU12-27, GU12-30, and GU12-31, were resistant to the most prevalent isolates of red rot in both tropical and subtropical conditions. The association analysis revealed significant correlations between the various traits, particularly the fibre content, with a maximum number of associations, which indicates its multifaceted impact on sugarcane characteristics. Principal component analysis (PCA) summarised the data, explaining 57.6% of the total variation for the measured traits and genotypes, providing valuable insights into the performance and characteristics of the Erianthus procerus derived hybrids under subtropical climates. The anthocyanin content of Erianthus procerus hybrids was better than the check varieties, ranging from 0.123 to 0.179 (2018-2019) and 0.111 to 0.172 (2019-2020); anthocyanin plays a vital role in mitigating cold injury, acting as an antioxidant in cool weather conditions, particularly in sugarcane. Seven hybrids recorded a more than 22% fibre threshold, indicating their industrial potential. These hybrids could serve as potential donors for cold tolerance and a high ratooning ability, along with red rot resistance, under subtropical climates.
Collapse
Affiliation(s)
- Mintu Ram Meena
- ICAR Sugarcane Breeding Institute, Regional Centre, Karnal 132011, India; (R.K.)
| | - K. Mohanraj
- ICAR Sugarcane Breeding Institute, Coimbatore 641007, India; (R.A.K.); (G.K.); (H.K.M.S.); (A.S.); (P.G.); (G.H.)
| | - Ravinder Kumar
- ICAR Sugarcane Breeding Institute, Regional Centre, Karnal 132011, India; (R.K.)
| | - Raja Arun Kumar
- ICAR Sugarcane Breeding Institute, Coimbatore 641007, India; (R.A.K.); (G.K.); (H.K.M.S.); (A.S.); (P.G.); (G.H.)
| | - Manohar Lal Chhabra
- ICAR Sugarcane Breeding Institute, Regional Centre, Karnal 132011, India; (R.K.)
| | | | - Gopalareddy Krishnappa
- ICAR Sugarcane Breeding Institute, Coimbatore 641007, India; (R.A.K.); (G.K.); (H.K.M.S.); (A.S.); (P.G.); (G.H.)
| | - H. K. Mahadeva Swamy
- ICAR Sugarcane Breeding Institute, Coimbatore 641007, India; (R.A.K.); (G.K.); (H.K.M.S.); (A.S.); (P.G.); (G.H.)
| | - A. Suganya
- ICAR Sugarcane Breeding Institute, Coimbatore 641007, India; (R.A.K.); (G.K.); (H.K.M.S.); (A.S.); (P.G.); (G.H.)
| | - Perumal Govindaraj
- ICAR Sugarcane Breeding Institute, Coimbatore 641007, India; (R.A.K.); (G.K.); (H.K.M.S.); (A.S.); (P.G.); (G.H.)
| | - Govind Hemaprabha
- ICAR Sugarcane Breeding Institute, Coimbatore 641007, India; (R.A.K.); (G.K.); (H.K.M.S.); (A.S.); (P.G.); (G.H.)
| |
Collapse
|
2
|
Wang Y, Li R, Chen B. Cytogenetic Characterization and Metabolomic Differences of Full-Sib Progenies of Saccharum spp. PLANTS (BASEL, SWITZERLAND) 2023; 12:810. [PMID: 36840158 PMCID: PMC9968213 DOI: 10.3390/plants12040810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 02/01/2023] [Accepted: 02/02/2023] [Indexed: 06/18/2023]
Abstract
Sugarcane smut is a worldwide fungal disease. Disease resistance breeding is the most economical and effective measure to prevent and control sugarcane smut. The cytogenetic characteristics and metabolomic differences of sugarcane F1s are closely related to disease resistance. Zhongzhe 1 and G160 sugarcane from the same parents (ROC25 and Yunzhe89-7) were used; the plants were grown in accordance with the barrel method. When the seedlings had 4-5 leaves, genomic in situ hybridization (GISH) was performed; digoxigenin (DIG)-labeled female parental (ROC25)DNA and biotin-labeled male parental (Yunzhe89-7) DNA were used as probes, and the karyotypes of two hybrids were analyzed. The new sugarcane smut-resistant variety (Zhongzhe 1) and the susceptible variety (G160) derived from the same parent were analyzed via gas chromatography-mass spectrometry technology (GC-MS) to compare the metabolomic differences between them. GISH analysis revealed that the chromosome ploidy number of Zhongzhe 1 sugarcane and G160 sugarcane were 114 and 110, respectively. However, the two contain different numbers of chromosomes from the female (ROC25) and male (Yunzhe89-7) parents. Moreover, 258 significantly changed metabolites were identified in smut-resistant Zhongzhe 1, as compared with the smut-susceptible G160 sugarcane: 56 flavonoids, 52 phenolic acids, 30 lipids, 26 organic acids, 26 amino acids and derivatives, 19 nucleotides and derivatives, 5 alkaloids, 9 terpenoids, and 35 others. Multivariate statistical analysis revealed a distinct difference in metabolic pathways between Zhongzhe 1 sugarcane and G160, and both of these varieties had unique functional metabolites. Differences in chromosome composition may constitute the genetic basis for the difference in resistance to smut disease between Zhongzhe 1 sugarcane and G160 sugarcane, and a high accumulation of flavonoids, lipids, terpenoids and tannins may constitute the basis of resistance to smut disease for the Zhongzhe 1 variety.
Collapse
Affiliation(s)
- Yi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
- College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Ru Li
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| | - Baoshan Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi University, Nanning 530004, China
| |
Collapse
|
3
|
Meng Z, Wang F, Xie Q, Li R, Shen H, Li H. Reconstruction of karyotypic evolution in Saccharum spontaneum species by comparative oligo-FISH mapping. BMC PLANT BIOLOGY 2022; 22:599. [PMID: 36539690 PMCID: PMC9764494 DOI: 10.1186/s12870-022-04008-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Karyotype dynamics driven by chromosomal rearrangements has long been considered as a fundamental question in the evolutionary genetics. Saccharum spontaneum, the most primitive and complex species in the genus Saccharum, has reportedly undergone at least two major chromosomal rearrangements, however, its karyotypic evolution remains unclear. RESULTS In this study, four representative accessions, i.e., hypothetical diploid sugarcane ancestor (sorghum, x = 10), Sa. spontaneum Np-X (x = 10, tetraploid), 2012-46 (x = 9, hexaploid) and AP85-441 (x = 8, tetraploid), were selected for karyotype evolution studies. A set of oligonucleotide (oligo)-based barcode probes was developed based on the sorghum genome, which allowed universal identification of all chromosomes from sorghum and Sa. spontaneum. By comparative FISH assays, we reconstructed the karyotype evolutionary history and discovered that although chromosomal rearrangements resulted in greater variation in relative lengths of some chromosomes, all chromosomes maintained a conserved metacentric structure. Additionally, we found that the barcode oligo probe was not applicable for chromosome identification in both Sa. robustum and Sa. officinarum species, suggesting that sorghum is more distantly related to Sa. robustum and Sa. officinarum compared with Sa. spontaneum species. CONCLUSIONS Our study demonstrated that the barcode oligo-FISH is an efficient tool for chromosome identification and karyotyping research, and expanded our understanding of the karyotypic and chromosomal evolution in the genus Saccharum.
Collapse
Affiliation(s)
- Zhuang Meng
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Fei Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Quanliang Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Rong Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Haitao Shen
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Hongbin Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| |
Collapse
|
4
|
Ling K, Yi-ning D, Majeed A, Zi-jiang Y, Jun-wen C, Li-lian H, Xian-hong W, Lu-feng L, Zhen-feng Q, Dan Z, Shu-jie G, Rong X, Lin-yan X, Fu X, Yang D, Fu-sheng L. Evaluation of genome size and phylogenetic relationships of the Saccharum complex species. 3 Biotech 2022; 12:327. [PMID: 36276474 PMCID: PMC9582063 DOI: 10.1007/s13205-022-03338-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 08/16/2022] [Indexed: 11/29/2022] Open
Abstract
"Saccharum complex" is a hypothetical group of species, which is supposed to be involved in the origin of modern sugarcane, and displays large genomes and complex chromosomal alterations. The utilization of restricted parents in breeding programs of modern cultivated sugarcane has resulted in a genetic blockage, which controlled its improvement because of the limited genetic diversity. The use of wild relatives is an effective way to broaden the genetic composition of cultivated sugarcane. Due to the infrequent characterization of genomes, the potential of wild relatives is diffused in improving the cultivated sugarcane. To characterize the genomes of the wild relatives, the genome size and phylogenetic relationships among eight species, including Saccharum spontaneum, Erianthus arundinaceus, E. fulvus, E. rockii, Narenga porphyrocoma, Miscanthus floridulus, Eulalia quadrinervis, and M. sinensis were evaluated based on flow cytometry, genome surveys, K-mer analysis, chloroplast genome sequencing, and whole-genome SNPs analysis. We observed highly heterozygous genomes of S. spontaneum, E. rockii, and E. arundinaceus and the highly repetitive genome of E. fulvus. The genomes of Eulalia quadrinervis, N. porphyrocoma, M. sinensis, and M. floridulus were highly complex. Phylogenetic results of the two approaches were dissimilar, however, both indicate E. fulvus displayed closer relationships to Miscanthus and Saccharum than other species of Saccharum complex. Eulalia quadrinervis was more closely related to M. floridulus than M. sinensis; E. arundinaceus differ significantly from Miscanthus, Narenga, and Saccharum, but was relatively close to Erianthus. We proved the point of E. rockii and E. fulvus should not be classified as one genus, and E. fulvus should be classified as the Saccharum genus. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03338-5.
Collapse
Affiliation(s)
- Kui Ling
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
- Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, 518067 China
| | - Di Yi-ning
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - Aasim Majeed
- School of Agricultural Biotechnology, Punjab Agriculture University, Ludhiana, 141004 India
| | - Yang Zi-jiang
- Applied Genomics Technology Laboratory, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Chen Jun-wen
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - He Li-lian
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Wang Xian-hong
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - Liu Lu-feng
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Qian Zhen-feng
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - Zeng Dan
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Gu Shu-jie
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - Xu Rong
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Xie Lin-yan
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
| | - Xu Fu
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Dong Yang
- Applied Genomics Technology Laboratory, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| | - Li Fu-sheng
- The Key Laboratory for Crop Production and Intelligent Agriculture of Yunnan Province, Kunming, 650201 Yunnan China
- Sugarcane Research Institute, Yunnan Agricultural University, Kunming, 650201 Yunnan China
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, 650201 Yunnan China
| |
Collapse
|
5
|
Comparative Analysis of Chloroplast Genome in Saccharum spp. and Related Members of ‘Saccharum Complex’. Int J Mol Sci 2022; 23:ijms23147661. [PMID: 35887005 PMCID: PMC9315705 DOI: 10.3390/ijms23147661] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 07/05/2022] [Accepted: 07/05/2022] [Indexed: 02/04/2023] Open
Abstract
High ploids of the sugarcane nuclear genome limit its genomic studies, whereas its chloroplast genome is small and conserved, which is suitable for phylogenetic studies and molecular marker development. Here, we applied whole genome sequencing technology to sequence and assemble chloroplast genomes of eight species of the ‘Saccharum Complex’, and elucidated their sequence variations. In total, 19 accessions were sequenced, and 23 chloroplast genomes were assembled, including 6 species of Saccharum (among them, S. robustum, S. sinense, and S. barberi firstly reported in this study) and 2 sugarcane relative species, Tripidium arundinaceum and Narenga porphyrocoma. The plastid phylogenetic signal demonstrated that S. officinarum and S. robustum shared a common ancestor, and that the cytoplasmic origins of S. sinense and S. barberi were much more ancient than the S. offcinarum/S. robustum linage. Overall, 14 markers were developed, including 9 InDel markers for distinguishing Saccharum from its relative species, 4 dCAPS markers for distinguishing S. officinarum from S. robustum, and 1 dCAPS marker for distinguishing S. sinense and S. barberi from other species. The results obtained from our studies will contribute to the understanding of the classification and plastome evolution of Saccharinae, and the molecular markers developed have demonstrated their highly discriminatory power in Saccharum and relative species.
Collapse
|
6
|
Repetitive Sequence Barcode Probe for Karyotype Analysis in Tripidium arundinaceum. Int J Mol Sci 2022; 23:ijms23126726. [PMID: 35743180 PMCID: PMC9224303 DOI: 10.3390/ijms23126726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 11/17/2022] Open
Abstract
The barcode probe is a convenient and efficient tool for molecular cytogenetics. Tripidium arundinaceum, as a polyploid wild allied genus of Saccharum, is a useful genetic resource that confers biotic and abiotic stress resistance for sugarcane breeding. Unfortunately, the basic cytogenetic information is still unclear due to the complex genome. We constructed the Cot-20 library for screening moderately and highly repetitive sequences from T. arundinaceum, and the chromosomal distribution of these repetitive sequences was explored. We used the barcode of repetitive sequence probes to distinguish the ten chromosome types of T. arundinaceum by fluorescence in situ hybridization (FISH) with Ea-0907, Ea-0098, and 45S rDNA. Furthermore, the distinction among homology chromosomes based on repetitive sequences was constructed in T. arundinaceum by the repeated FISH using the barcode probes including Ea-0663, Ea-0267, EaCent, 5S rDNA, Ea-0265, Ea-0070, and 45S rDNA. We combined these probes to distinguish 37 different chromosome types, suggesting that the repetitive sequences may have different distributions on homologous chromosomes of T. arundinaceum. In summary, this method provide a basis for the development of similar applications for cytogenetic analysis in other species.
Collapse
|
7
|
Meng Z, Wang Q, Khurshid H, Raza G, Han J, Wang B, Wang K. Chromosome Painting Provides Insights Into the Genome Structure and Evolution of Sugarcane. FRONTIERS IN PLANT SCIENCE 2021; 12:731664. [PMID: 34512706 PMCID: PMC8429501 DOI: 10.3389/fpls.2021.731664] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 08/10/2021] [Indexed: 06/13/2023]
Abstract
The genus Saccharum is composed of species with high polyploidy and highly varied chromosome numbers, laying a challenge for uncovering its genomic structure and evolution. We developed a chromosome 2 painting (CP2) probe by designing oligonucleotides covering chromosome 2 of Saccharum spontaneum (2n = 8x = 64). Fluorescence in situ hybridization (FISH) using this CP2 probe revealed six types of ploidies from twenty S. spontaneum clones, including 6x, 8x, 10x, 11x, 12x, and 13x clones. The finding of S. spontaneum clones with uneven of ploid suggested that certain S. spontaneum clones come from hybridization. It renews our knowledge that S. spontaneum is derived from autopolyploidization. Combined with a S. spontaneum-specific probe, chromosome 2-derived chromosome or fragments from either S. spontaneum or Saccharum officinarum can be identified in sugarcane modern cultivars. We revealed unexpected high level of interspecific recombination from introgressive S. spontaneum chromosomes (>50.0%) in cultivars ROC22 and ZZ1, indicating frequent chromosome exchange in cultivars. Intriguingly, we observed interspecific recombination recurring among either homoeologous or non-homoeologous chromosomes in sugarcane cultivars. These results demonstrated that chromosome painting FISH is a powerful tool in the genome dissection of sugarcane and provide new insights into the genome structure and evolution of the complex genus Saccharum.
Collapse
Affiliation(s)
- Zhuang Meng
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops (MOE), Fujian Agriculture and Forestry University, Fuzhou, China
| | - Qinnan Wang
- Institute of Bioengineering, Guangdong Academy of Sciences, Guangzhou, China
| | - Haris Khurshid
- Oilseeds Research Program, National Agricultural Research Centre, Islamabad, Pakistan
| | - Ghulam Raza
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong, China
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong, China
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong, China
- Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops (MOE), Fujian Agriculture and Forestry University, Fuzhou, China
| |
Collapse
|
8
|
Li X, Huang F, Chai J, Wang Q, Yu F, Huang Y, Wu J, Wang Q, Xu L, Zhang M, Deng Z. Chromosome behavior during meiosis in pollen mother cells from Saccharum officinarum × Erianthus arundinaceus F 1 hybrids. BMC PLANT BIOLOGY 2021; 21:139. [PMID: 33726673 PMCID: PMC7968283 DOI: 10.1186/s12870-021-02911-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 03/03/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND In recent years, sugarcane has attracted increasing attention as an energy crop. Wild resources are widely used to improve the narrow genetic base of sugarcane. However, the infertility of F1 hybrids between Saccharum officinarum (S. officinarum) and Erianthus arundinaceus (E. arundinaceus) has hindered sugarcane breeding efforts. To discover the cause of this infertility, we studied the hybridization process from a cytological perspective. RESULTS We examined the meiotic process of pollen mother cells (PMCs) in three F1 hybrids between S. officinarum and E. arundinaceus. Cytological analysis showed that the male parents, Hainan 92-77 and Hainan 92-105, had normal meiosis. However, the meiosis process in F1 hybrids showed various abnormal phenomena, including lagging chromosomes, micronuclei, uneven segregation, chromosome bridges, and inability to form cell plates. Genomic in situ hybridization (GISH) showed unequal chromatin distribution during cell division. Interestingly, 96.70% of lagging chromosomes were from E. arundinaceus. Furthermore, fluorescence in situ hybridization (FISH) was performed using 45S rDNA and 5S rDNA as probes. Either 45S rDNA or 5S rDNA sites were lost during abnormal meiosis, and results of unequal chromosomal separation were also clearly observed in tetrads. CONCLUSIONS Using cytogenetic analysis, a large number of meiotic abnormalities were observed in F1. GISH further confirmed that 96.70% of the lagging chromosomes were from E. arundinaceus. Chromosome loss was found by further investigation of repeat sequences. Our findings provide insight into sugarcane chromosome inheritance to aid innovation and utilization in sugarcane germplasm resources.
Collapse
Affiliation(s)
- Xueting Li
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Fei Huang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jin Chai
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Qiusong Wang
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - 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
| | - Jiayun Wu
- Guangdong Key Laboratory of Sugarcane Improvement and Biorefinery, Guangdong Provincial Bioengineering Institute, Guangzhou, China
| | - Qinnan Wang
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Liangnian Xu
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, 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.
- Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, 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.
| |
Collapse
|
9
|
Ma P, Zhang X, Chen L, Zhao Q, Zhang Q, Hua X, Wang Z, Tang H, Yu Q, Zhang M, Ming R, Zhang J. Comparative analysis of sucrose phosphate synthase (SPS) gene family between Saccharum officinarum and Saccharum spontaneum. BMC PLANT BIOLOGY 2020; 20:422. [PMID: 32928111 PMCID: PMC7488781 DOI: 10.1186/s12870-020-02599-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 08/13/2020] [Indexed: 05/19/2023]
Abstract
BACKGROUND Sucrose phosphate synthase (SPS) genes play vital roles in sucrose production across various plant species. Modern sugarcane cultivar is derived from the hybridization between the high sugar content species Saccharum officinarum and the high stress tolerance species Saccharum spontaneum, generating one of the most complex genomes among all crops. The genomics of sugarcane SPS remains under-studied despite its profound impact on sugar yield. RESULTS In the present study, 8 and 6 gene sequences for SPS were identified from the BAC libraries of S. officinarum and S. spontaneum, respectively. Phylogenetic analysis showed that SPSD was newly evolved in the lineage of Poaceae species with recently duplicated genes emerging from the SPSA clade. Molecular evolution analysis based on Ka/Ks ratios suggested that polyploidy reduced the selection pressure of SPS genes in Saccharum species. To explore the potential gene functions, the SPS expression patterns were analyzed based on RNA-seq and proteome dataset, and the sugar content was detected using metabolomics analysis. All the SPS members presented the trend of increasing expression in the sink-source transition along the developmental gradient of leaves, suggesting that the SPSs are involved in the photosynthesis in both Saccharum species as their function in dicots. Moreover, SPSs showed the higher expression in S. spontaneum and presented expressional preference between stem (SPSA) and leaf (SPSB) tissue, speculating they might be involved in the differentia of carbohydrate metabolism in these two Saccharum species, which required further verification from experiments. CONCLUSIONS SPSA and SPSB genes presented relatively high expression and differential expression patterns between the two Saccharum species, indicating these two SPSs are important in the formation of regulatory networks and sucrose traits in the two Saccharum species. SPSB was suggested to be a major contributor to the sugar accumulation because it presented the highest expressional level and its expression positively correlated with sugar content. The recently duplicated SPSD2 presented divergent expression levels between the two Saccharum species and the relative protein content levels were highest in stem, supporting the neofunctionalization of the SPSD subfamily in Saccharum.
Collapse
Affiliation(s)
- Panpan Ma
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xingtan Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lanping Chen
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qian Zhao
- Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qing Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xiuting Hua
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Zhengchao Wang
- College of Life Sciences, Fujian Normal University, Fuzhou, 350007 China
| | - Haibao Tang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Qingyi Yu
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Texas A&M AgriLife Research, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, TX 75252 USA
| | - Muqing Zhang
- Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning, Guangxi China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Crop Science, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Guangxi Key Lab of Sugarcane Biology, Guangxi University, Nanning, Guangxi China
| |
Collapse
|
10
|
Piperidis N, D'Hont A. Sugarcane genome architecture decrypted with chromosome-specific oligo probes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:2039-2051. [PMID: 32537783 DOI: 10.1111/tpj.14881] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/28/2020] [Accepted: 06/02/2020] [Indexed: 05/04/2023]
Abstract
Sugarcane (Saccharum spp.) is probably the crop with the most complex genome. Modern cultivars (2n = 100-120) are highly polyploids and aneuploids derived from interspecific hybridization between Saccharum officinarum (2n = 80) and Saccharum spontaneum (2n = 40-128). Chromosome-specific oligonucleotide probes were used in combination with genomic in situ hybridization to analyze the genome architecture of modern cultivars and representatives of their parental species. The results validated a basic chromosome number of x = 10 for S. officinarum. In S. spontaneum, rearrangements occurred from a basic chromosome of x = 10, probably in the Northern part of India, in two steps leading to x = 9 and then x = 8. Each step involved three chromosomes that were rearranged into two. Further polyploidization led to the wide geographical extension of clones with x = 8. We showed that the S. spontaneum contribution to modern cultivars originated from cytotypes with x = 8 and varied in proportion between cultivars (13-20%). Modern cultivars had mainly 12 copies for each of the first four basic chromosomes, and a more variable number for those basic chromosomes whose structure differs between the two parental species. One-four of these copies corresponded to entire S. spontaneum chromosomes or interspecific recombinant chromosomes. In addition, a few inter-chromosome translocations were revealed. The new information and cytogenetic tools described in this study substantially improve our understanding of the extreme level of complexity of modern sugarcane cultivar genomes.
Collapse
Affiliation(s)
- Nathalie Piperidis
- SRA, Sugar Research Australia, 26135 Peak Downs Highway, Te Kowai, Qld, 4741, Australia
| | - Angélique D'Hont
- CIRAD, UMR AGAP, Montpellier, F-34398, France
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro, Montpellier, 34060, France
| |
Collapse
|
11
|
An enriched sugarcane diversity panel for utilization in genetic improvement of sugarcane. Sci Rep 2020; 10:13390. [PMID: 32770152 PMCID: PMC7414218 DOI: 10.1038/s41598-020-70292-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Accepted: 07/27/2020] [Indexed: 11/23/2022] Open
Abstract
Sugarcane crop is important for both sugar and biofuels. A world collection of sugarcane and related grasses (WCSRG) maintained at Miami, FL contains > 1,200 non-redundant clones of different species and genera within the Saccharum complex. However, linkage of undesirable alleles with useful genes in wild species has hindered its efficient utilization in sugarcane breeding. A core collection developed previously with smaller number of clones representing WCSRG did not take into account > 120 wild/exotic clones maintained at the USDA-ARS Sugarcane Research Unit in Houma, Louisiana. Moreover, the genome complexity and sub-tropical to temperate growing climate of Louisiana warrant a region-specific core collection that can be used for base-broadening breeding aimed at efficient introgression of desirable alleles. Genetic diversity of 1,485 clones within WCSRG and Louisiana (commercials, wild/exotic) using 423 SSR alleles showed an average gene diversity (h) at 0.208 among all species groups where Erianthus-like Saccharum species (ELSS), Miscanthus spp., and S. spontaneum each formed a distinct cluster, Saccharum robustum, S. officinarum, hybrid cultivars, and S. edule grouped together in a major cluster, and Saccharum sinense and S. barberi formed distinct grouping. A 309-clone diversity panel (SDP1) was developed that captured the genetic diversity based on the combination of maximum length subtree and manual selection to maximize representation of Louisiana clones and minimize import of clones from Miami. SDP1 shared 324 alleles out of the 423 alleles in the entire population of 1,485 clones and captured the genetic diversity of the entire collection with an average gene diversity (h) at 0.163. The variation within (11–17%) and among (83–89%) the populations in SDP1 were comparable with the entire population of 1,485 clones (9–15% and 85–91%, respectively). The breadth of the genetic variation of SDP1 was exemplified by the intra- and inter-specific diversity of a 190-clone mini-core collection with markers derived from known cold-responsive genes. SDP1 will facilitate genome-wide association studies for identification of trait-specific markers for use in marker-assisted breeding in Louisiana and elsewhere.
Collapse
|
12
|
Peter SC, Murugan N, Mohanan MV, Sasikumar SPT, Selvarajan D, Jayanarayanan AN, Shivalingamurthy SG, Chennappa M, Ramanathan V, Govindakurup H, Ram B, Chinnaswamy A. Isolation, characterization and expression analysis of stress responsive plant nuclear transcriptional factor subunit ( NF-YB2) from commercial Saccharum hybrid and wild relative Erianthus arundinaceus. 3 Biotech 2020; 10:304. [PMID: 32566442 DOI: 10.1007/s13205-020-02295-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 06/07/2020] [Indexed: 12/26/2022] Open
Abstract
Plant nuclear factor (NF-Y) is a transcription activating factor, consisting of three subunits, and plays a key regulatory role in many stress-responsive mechanisms including drought and salinity stresses. NF-Ys function both as complex and individual subunits. Considering the importance of sugarcane as a commercial crop with high socio-economic importance and the crop being affected mostly by water deficit stress and salinity stress causing significant yield loss, nuclear transcriptional factor NF-YB2 was focused in this study. Plant nuclear factor subunit B2 from Erianthus arundinaceus (EaNF-YB2), a wild relative of sugarcane which is known for its drought and salinity stress tolerance, and commercial Saccharum hybrid Co 86032 (ShNF-YB2) was isolated and characterized. Both EaNF-YB2 and ShNF-YB2 genes are 543 bp long that encodes for a polypeptide of 180 amino acid residues. Comparison of EaNF-YB2 and ShNF-YB2 gene sequences revealed nucleotide substitutions at nine positions corresponding to three synonymous and six nonsynonymous amino acid substitutions that resulted in variations in physiochemical properties. However, multiple sequence alignment (MSA) of NF-YB2 proteins showed conservation of functionally important amino acid residues. In silico analysis revealed NF-YB2 to be a hydrophilic and intracellular protein, and EaNF-YB2 is thermally more stable than that of ShNF-YB2. Phylogenetic analysis suggested the lower rate of evolution of NF-YB2. Subcellular localization in sugarcane callus revealed NF-YB2 localization at nucleus that further evidenced it to be a transcription activation factor. Comparative RT-qPCR experiments showed a significantly higher level of NF-YB2 expression in E. arundinaceus when compared to that in the commercial Saccharum hybrid Co 86032 under drought and salinity stresses. Hence, EaNF-YB2 could be an ideal candidate gene, and its overexpression in sugarcane through genetic engineering approach might enhance tolerance to drought and salinity stresses.
Collapse
Affiliation(s)
- Swathik Clarancia Peter
- Division of Crop Improvement, ICAR Sugarcane Breeding Institute, Tamil Nadu, Coimbatore, 641007 India
| | - Naveenarani Murugan
- Division of Crop Improvement, ICAR Sugarcane Breeding Institute, Tamil Nadu, Coimbatore, 641007 India
| | | | | | - Dharshini Selvarajan
- Division of Crop Improvement, ICAR Sugarcane Breeding Institute, Tamil Nadu, Coimbatore, 641007 India
| | | | | | - Mahadevaiah Chennappa
- Division of Crop Improvement, ICAR Sugarcane Breeding Institute, Tamil Nadu, Coimbatore, 641007 India
| | - Valarmathi Ramanathan
- Division of Crop Improvement, ICAR Sugarcane Breeding Institute, Tamil Nadu, Coimbatore, 641007 India
| | - Hemaprabha Govindakurup
- Division of Crop Improvement, ICAR Sugarcane Breeding Institute, Tamil Nadu, Coimbatore, 641007 India
| | - Bakshi Ram
- Division of Crop Improvement, ICAR Sugarcane Breeding Institute, Tamil Nadu, Coimbatore, 641007 India
| | - Appunu Chinnaswamy
- Division of Crop Improvement, ICAR Sugarcane Breeding Institute, Tamil Nadu, Coimbatore, 641007 India
| |
Collapse
|
13
|
Manimekalai R, Suresh G, Govinda Kurup H, Athiappan S, Kandalam M. Role of NGS and SNP genotyping methods in sugarcane improvement programs. Crit Rev Biotechnol 2020; 40:865-880. [PMID: 32508157 DOI: 10.1080/07388551.2020.1765730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Sugarcane (Saccharum spp.) is one of the most economically significant crops because of its high sucrose content and it is a promising biomass feedstock for biofuel production. Sugarcane genome sequencing and analysis is a difficult task due to its heterozygosity and polyploidy. Long sequence read technologies, PacBio Single-Molecule Real-Time (SMRT) sequencing, the Illumina TruSeq, and the Oxford Nanopore sequencing could solve the problem of genome assembly. On the applications side, next generation sequencing (NGS) technologies played a major role in the discovery of single nucleotide polymorphism (SNP) and the development of low to high throughput genotyping platforms. The two mainstream high throughput genotyping platforms are the SNP microarray and genotyping by sequencing (GBS). This paper reviews the NGS in sugarcane genomics, genotyping methodologies, and the choice of these methods. Array-based SNP genotyping is robust, provides consistent SNPs, and relatively easier downstream data analysis. The GBS method identifies large scale SNPs across the germplasm. A combination of targeted GBS and array-based genotyping methods should be used to increase the accuracy of genomic selection and marker-assisted breeding.
Collapse
Affiliation(s)
- Ramaswamy Manimekalai
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Gayathri Suresh
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Hemaprabha Govinda Kurup
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Selvi Athiappan
- Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India
| | - Mallikarjuna Kandalam
- Business Development, Asia Pacific Japan region, Thermo Fisher Scientific, Waltham, MA, USA
| |
Collapse
|
14
|
Konan NO, Mergeai G. Relationship between meiotic behaviour and fertility in backcross-1 derivatives of the [( Gossypium hirsutum × G. thurberi) 2 × G. longicalyx] trispecies hybrid. COMPARATIVE CYTOGENETICS 2020; 14:75-95. [PMID: 32047586 PMCID: PMC7000483 DOI: 10.3897/compcytogen.v14i1.47231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Accepted: 01/04/2020] [Indexed: 06/10/2023]
Abstract
Wild cotton species are an important source of desirable genes for genetic improvement of cultivated cotton Gossypium hirsutum Linnaeus, 1763. For the success of such an improvement, chromosome pairings and recombinations in hybrids are fundamental. The wild African species G. longicalyx Hutchinson & Lee, 1958 could be used as donor of the desirable trait of fiber fineness. Twelve BC1 plants obtained from the backcrossing of [(G. hirsutum × G. thurberi Todaro, 1877)2 × G. longicalyx] (AhDhD1F1, 2n = 4x = 52) trispecies hybrid (HTL) by G. hirsutum (cv. C2) (AhAhDhDh, 2n = 4x = 52) were investigated for meiotic behaviour and plant fertility. Their chromosome associations varied as follows: (2.5 to 11.5) I + (17 to 22) II + (0.31 to 1.93) III + (0.09 to 1.93) IV + (0 to 0.07) V + (0 to 0.14) VI. Their pollen fertility ranged from 4.67 to 32.10 %. Only four BC1 plants produced a few seeds through self-pollination. The remaining BC1 were totally self-sterile and usually presented the highest number of univalents. All BC1 materials produced BC2 seeds (0.44 to 6.50 seeds per backcross) with the number of seeds negatively correlated with the number of univalents (R2 = 0.45, P < 0.05). Most BC1 plants gave significantly finer fiber compared to the cultivated G. hirsutum. SSR markers showed a segregation of wild alleles among the backcross derivatives and Genomic in situ hybridization (GISH) revealed presence of entire chromosomes of G. longicalyx as well as recombinant chromosomes in the backcross derivatives. The significance and details of these results are presented and the prospects of successfully exploiting these plant materials are discussed.
Collapse
Affiliation(s)
- N’guessan Olivier Konan
- Gembloux Agro-Bio Tech, Liège University, Tropical agriculture Unit, 2 passage des Déportés, B-5030 Gembloux, BelgiumLiège UniversityGemblouxBelgium
- Jean Lorougnon Guédé University, Agroforestry Unit, BP 150, Cote D’ivoireJean Lorougnon Guédé UniversityDaloaCote d'Ivoire
| | - Guy Mergeai
- Gembloux Agro-Bio Tech, Liège University, Tropical agriculture Unit, 2 passage des Déportés, B-5030 Gembloux, BelgiumLiège UniversityGemblouxBelgium
| |
Collapse
|
15
|
Species-specific abundant retrotransposons elucidate the genomic composition of modern sugarcane cultivars. Chromosoma 2019; 129:45-55. [PMID: 31848693 DOI: 10.1007/s00412-019-00729-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 11/29/2019] [Accepted: 12/04/2019] [Indexed: 10/25/2022]
Abstract
Modern sugarcane cultivars are highly polyploid and derived from the hybridization of Saccharum officinarum and S. spontaneum, thus leading to singularly complex genomes. The complex genome has hindered the study of genomic structures. Here, we adopted a computational strategy to isolate highly repetitive and abundant sequences in either S. officinarum or S. spontaneum and isolated four S. spontaneum-enriched retrotransposons. Fluorescence in situ hybridization (FISH) assays with these repetitive DNA sequences generated whole-genome painting signals for S. spontaneum but not for S. officinarum. We demonstrated that these repetitive sequence-based probes distinguish the parental S. spontaneum genome in hybrids derived from crosses between it and S. officinarum. A cytological analysis of 14 modern sugarcane cultivars revealed that the percentages of chromosomes with introgressive S. spontaneum fragments ranged from 11.9 to 40.9% and substantially exceeded those determined for previously investigated cultivars (5-13%). The comparatively higher percentages of introgressive S. spontaneum fragments detected in the aforementioned cultivars indicate frequent recombination between parental genomes. Here, we present the application of our strategy to isolate species-specific cytological markers. This information may help to elucidate complex plant genomic structures and trace their evolutionary histories.
Collapse
|
16
|
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.
Collapse
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
| |
Collapse
|
17
|
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.
Collapse
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
| |
Collapse
|
18
|
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.
Collapse
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
| |
Collapse
|
19
|
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.
Collapse
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
| |
Collapse
|
20
|
Hu M, Yu H, Li Y, Li A, Cai Q, Liu P, Tu Y, Wang Y, Hu R, Hao B, Peng L, Xia T. Distinct polymer extraction and cellulose DP reduction for complete cellulose hydrolysis under mild chemical pretreatments in sugarcane. Carbohydr Polym 2018; 202:434-443. [PMID: 30287020 DOI: 10.1016/j.carbpol.2018.08.039] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/27/2018] [Accepted: 08/10/2018] [Indexed: 10/28/2022]
Abstract
In this study, liquid hot water (LHW) and chemical (H2SO4, NaOH, CaO) pretreatments were performed in Saccharum species including sugarcane bagasse. In comparison, the LHW and CaO pretreatments significantly enhanced biomass enzymatic hydrolysis, leading to much high bioethanol yield obtained at 19% (% dry matter) with an almost complete hexoses-ethanol conversion in the desirable So5 bagasse sample. Despite the LHW and CaO are distinctive for extracting hemicellulose and lignin, both pretreatments largely reduced cellulose degree of polymerization for enhanced lignocellulose enzymatic saccharification. Further chemical analysis indicated that the pretreated So5 sample had much lower cellulose crystalline index, hemicellulosic Xyl/Ara and lignin S/H ratio than those of other biomass samples, which explained that the So5 had the highest bioethanol yield among Saccharum species. Therefore, a mechanism model was proposed to elucidate how mild pretreatments could enhance biomass enzymatic saccharification for a high bioethanol production in the desirable sugarcane bagasse.
Collapse
Affiliation(s)
- Meng Hu
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Hua Yu
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yu Li
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; Guangdong Provincial Bioengineering Institute (Guangzhou Sugarcane Industry Research Institute), Guangzhou 510316, China.
| | - Ao Li
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Qiuming Cai
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Peng Liu
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yuanyuan Tu
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Yanting Wang
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Ruofei Hu
- College of Food Science and Technology, Hubei University of Arts and Science, Xiangyang City, Hubei Province 441053, China.
| | - Bo Hao
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Liangcai Peng
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Tao Xia
- Biomass and Bioenergy Research Centre, Huazhong Agricultural University, Wuhan 430070, China; College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| |
Collapse
|
21
|
Singh R, Jones T, Wai CM, Jifon J, Nagai C, Ming R, Yu Q. Transcriptomic analysis of transgressive segregants revealed the central role of photosynthetic capacity and efficiency in biomass accumulation in sugarcane. Sci Rep 2018. [PMID: 29535363 PMCID: PMC5849761 DOI: 10.1038/s41598-018-22798-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Sugarcane is among the most efficient crops in converting solar energy into chemical energy. However, due to its complex genome structure and inheritance, the genetic and molecular basis of biomass yield in sugarcane is still largely unknown. We created an F2 segregating population by crossing S. officinarum and S. spontaneum and evaluated the biomass yield of the F2 individuals. The F2 individuals exhibited clear transgressive segregation in biomass yield. We sequenced transcriptomes of source and sink tissues from 12 selected extreme segregants to explore the molecular basis of high biomass yield for future breeding of high-yielding energy canes. Among the 103,664 assembled unigenes, 10,115 and 728 showed significant differential expression patterns between the two extreme segregating groups in the top visible dewlap leaf and the 9th culm internode, respectively. The most enriched functional categories were photosynthesis and fermentation in the high-biomass and the low-biomass groups, respectively. Our results revealed that high-biomass yield was mainly determined by assimilation of carbon in source tissues. The high-level expression of fermentative genes in the low-biomass group was likely induced by their low-energy status. Group-specific expression alleles which can be applied in the development of new high-yielding energy cane varieties via molecular breeding were identified.
Collapse
Affiliation(s)
- Ratnesh Singh
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA
| | - Tyler Jones
- Hawaii Agriculture Research Center, Kunia, HI, 96759, USA
| | - Ching Man Wai
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - John Jifon
- Texas A&M AgriLife Research Center at Weslaco, Texas A&M University System, Weslaco, TX, 78596, USA
| | - Chifumi Nagai
- Hawaii Agriculture Research Center, Kunia, HI, 96759, USA
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.,Center for Genomics and Biotechnology, Fujian Provincial Key laboratory of Haixia applied plant systems biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China
| | - Qingyi Yu
- Texas A&M AgriLife Research Center at Dallas, Texas A&M University System, Dallas, TX, 75252, USA. .,Center for Genomics and Biotechnology, Fujian Provincial Key laboratory of Haixia applied plant systems biology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, Fujian Province, China. .,Department of Plant Pathology & Microbiology, Texas A&M University, College Station, TX, 77843, USA.
| |
Collapse
|
22
|
Thirugnanasambandam PP, Hoang NV, Henry RJ. The Challenge of Analyzing the Sugarcane Genome. FRONTIERS IN PLANT SCIENCE 2018; 9:616. [PMID: 29868072 PMCID: PMC5961476 DOI: 10.3389/fpls.2018.00616] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/18/2018] [Indexed: 05/04/2023]
Abstract
Reference genome sequences have become key platforms for genetics and breeding of the major crop species. Sugarcane is probably the largest crop produced in the world (in weight of crop harvested) but lacks a reference genome sequence. Sugarcane has one of the most complex genomes in crop plants due to the extreme level of polyploidy. The genome of modern sugarcane hybrids includes sub-genomes from two progenitors Saccharum officinarum and S. spontaneum with some chromosomes resulting from recombination between these sub-genomes. Advancing DNA sequencing technologies and strategies for genome assembly are making the sugarcane genome more tractable. Advances in long read sequencing have allowed the generation of a more complete set of sugarcane gene transcripts. This is supporting transcript profiling in genetic research. The progenitor genomes are being sequenced. A monoploid coverage of the hybrid genome has been obtained by sequencing BAC clones that cover the gene space of the closely related sorghum genome. The complete polyploid genome is now being sequenced and assembled. The emerging genome will allow comparison of related genomes and increase understanding of the functioning of this polyploidy system. Sugarcane breeding for traditional sugar and new energy and biomaterial uses will be enhanced by the availability of these genomic resources.
Collapse
Affiliation(s)
- Prathima P. Thirugnanasambandam
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
- ICAR - Sugarcane Breeding Institute, Coimbatore, India
- *Correspondence: Prathima P. Thirugnanasambandam,
| | - Nam V. Hoang
- College of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Robert J. Henry
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD, Australia
| |
Collapse
|
23
|
Dong G, Shen J, Zhang Q, Wang J, Yu Q, Ming R, Wang K, Zhang J. Development and Applications of Chromosome-Specific Cytogenetic BAC-FISH Probes in S. spontaneum. FRONTIERS IN PLANT SCIENCE 2018; 9:218. [PMID: 29535742 PMCID: PMC5834487 DOI: 10.3389/fpls.2018.00218] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Saccharum spontaneum is a major Saccharum species that contributed to the origin of modern sugarcane cultivars, and due to a high degree of polyploidy is considered to be a plant species with one of the most complex genetics. Fluorescence in situ hybridization (FISH) is a powerful and widely used tool in genome studies. Here, we demonstrated that FISH based on bacterial artificial chromosome (BAC) clones can be used as a specific cytological marker to identify S. spontaneum individual chromosomes and study the relationship between S. spontaneum and other related species. We screened low-copy BACs as probes from the sequences of a high coverage of S. spontaneum BAC library based on BLAST search of the sorghum genome. In total, we isolated 49 positive BAC clones, and identified 27 BAC clones that can give specific signals on the S. spontaneum chromosomes. Of the 27 BAC probes, 18 were confirmed to be able to discriminate the eight basic chromosomes of S. spontaneum. Moreover, BAC-24, BAC-66, BAC-78, BAC-69, BAC-71, BAC-73, and BAC-77 probes were used to construct physical maps of chromosome 1 and chromosome 2 of S. spontaneum, which indicated synteny in Sb01 between S. spontaneum and sorghum. Furthermore, we found that BAC-14 and BAC-19 probes, corresponding to the sorghum chromosomes 2 and 8, respectively, localized to different arms of the same S. spontaneum chromosome, suggesting that there was an inter-chromosomal rearrangement event between S. spontaneum and sorghum. Our study provides the first set of chromosome-specific cytogenetic markers in Saccharum and is critical for future advances in cytogenetics and genome sequencing studies in Saccharum.
Collapse
Affiliation(s)
- Guangrui Dong
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jiao Shen
- College of Life Sciences, Fujian Normal University, Fuzhou, China
| | - Qing Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jianping Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Qingyi Yu
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Ray Ming
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Texas A&M AgriLife Research Center, Department of Plant Pathology and Microbiology, Texas A&M University System, Dallas, TX, United States
| | - Kai Wang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jisen Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
- College of Life Sciences, Fujian Normal University, Fuzhou, China
- *Correspondence: Jisen Zhang,
| |
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
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.
Collapse
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
| |
Collapse
|
26
|
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.
Collapse
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
| |
Collapse
|
27
|
Nayak SN, Song J, Villa A, Pathak B, Ayala-Silva T, Yang X, Todd J, Glynn NC, Kuhn DN, Glaz B, Gilbert RA, Comstock JC, Wang J. Promoting utilization of Saccharum spp. genetic resources through genetic diversity analysis and core collection construction. PLoS One 2014; 9:e110856. [PMID: 25333358 PMCID: PMC4205016 DOI: 10.1371/journal.pone.0110856] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2014] [Accepted: 09/25/2014] [Indexed: 12/22/2022] Open
Abstract
Sugarcane (Saccharum spp.) and other members of Saccharum spp. are attractive biofuel feedstocks. One of the two World Collections of Sugarcane and Related Grasses (WCSRG) is in Miami, FL. This WCSRG has 1002 accessions, presumably with valuable alleles for biomass, other important agronomic traits, and stress resistance. However, the WCSRG has not been fully exploited by breeders due to its lack of characterization and unmanageable population. In order to optimize the use of this genetic resource, we aim to 1) genotypically evaluate all the 1002 accessions to understand its genetic diversity and population structure and 2) form a core collection, which captures most of the genetic diversity in the WCSRG. We screened 36 microsatellite markers on 1002 genotypes and recorded 209 alleles. Genetic diversity of the WCSRG ranged from 0 to 0.5 with an average of 0.304. The population structure analysis and principal coordinate analysis revealed three clusters with all S. spontaneum in one cluster, S. officinarum and S. hybrids in the second cluster and mostly non-Saccharum spp. in the third cluster. A core collection of 300 accessions was identified which captured the maximum genetic diversity of the entire WCSRG which can be further exploited for sugarcane and energy cane breeding. Sugarcane and energy cane breeders can effectively utilize this core collection for cultivar improvement. Further, the core collection can provide resources for forming an association panel to evaluate the traits of agronomic and commercial importance.
Collapse
Affiliation(s)
- Spurthi N. Nayak
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - Jian Song
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
- College of Life Sciences, Dezhou University, Dezhou, Shandong, China
| | - Andrea Villa
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - Bhuvan Pathak
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - Tomas Ayala-Silva
- Subtropical Horticulture Research Station, USDA-ARS, Miami, Florida, United States of America
| | - Xiping Yang
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - James Todd
- Everglades Research and Education Center, University of Florida, Belle Glade, Florida, United States of America
| | - Neil C. Glynn
- Sugarcane Field Station, USDA-ARS, Canal Point, Florida, United States of America
| | - David N. Kuhn
- Subtropical Horticulture Research Station, USDA-ARS, Miami, Florida, United States of America
| | - Barry Glaz
- Sugarcane Field Station, USDA-ARS, Canal Point, Florida, United States of America
| | - Robert A. Gilbert
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
| | - Jack C. Comstock
- Sugarcane Field Station, USDA-ARS, Canal Point, Florida, United States of America
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, Florida, United States of America
- Genetics Institute, Plant Molecular and Biology Program, University of Florida, Gainesville, Florida, United States of America
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
| |
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Besse P, McIntyre CL, Burner DM, Almeida CG. Using genomic slot blot hybridization to assess intergeneric Saccharum x Erianthus hybrids (Andropogoneae - Saccharinae). Genome 2012; 40:428-32. [PMID: 18464838 DOI: 10.1139/g97-057] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The use of genomic slot blot hybridization enabled the differentiation of hybrids from selfs in Saccharum x Erianthus intergeneric crosses in which Saccharum was used as the female parent. Based on the genomic in situ hybridization technique, slot blots of DNA from the parents and the progeny were blocked with the Saccharum parent DNA and hybridized with the labelled male Erianthus genomic DNA. This technique allowed a rapid screening for hybrids and was sensitive enough to detect a 1/20 dilution of Erianthus in Saccharum DNA, which should enable the detection of most partial hybrids. The genomic slot blot hybridization technique was shown to be potentially useful for assessing crosses involving Saccharum species with either Old World Erianthus section Ripidium or North American Erianthus (= Saccharum) species. The effectiveness of the technique was assessed on 144 progeny of a Saccharum officinarum x Erianthus arundinaceus cross, revealing that 43% of the progeny were selfs. The importance of this test as a tool to support intergeneric breeding programs is discussed.
Collapse
|
30
|
Cheavegatti-Gianotto A, de Abreu HMC, Arruda P, Bespalhok Filho JC, Burnquist WL, Creste S, di Ciero L, Ferro JA, de Oliveira Figueira AV, de Sousa Filgueiras T, Grossi-de-Sá MDF, Guzzo EC, Hoffmann HP, de Andrade Landell MG, Macedo N, Matsuoka S, de Castro Reinach F, Romano E, da Silva WJ, de Castro Silva Filho M, César Ulian E. Sugarcane (Saccharum X officinarum): A Reference Study for the Regulation of Genetically Modified Cultivars in Brazil. TROPICAL PLANT BIOLOGY 2011; 4:62-89. [PMID: 21614128 PMCID: PMC3075403 DOI: 10.1007/s12042-011-9068-3] [Citation(s) in RCA: 93] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2010] [Accepted: 01/13/2011] [Indexed: 05/07/2023]
Abstract
Global interest in sugarcane has increased significantly in recent years due to its economic impact on sustainable energy production. Sugarcane breeding and better agronomic practices have contributed to a huge increase in sugarcane yield in the last 30 years. Additional increases in sugarcane yield are expected to result from the use of biotechnology tools in the near future. Genetically modified (GM) sugarcane that incorporates genes to increase resistance to biotic and abiotic stresses could play a major role in achieving this goal. However, to bring GM sugarcane to the market, it is necessary to follow a regulatory process that will evaluate the environmental and health impacts of this crop. The regulatory review process is usually accomplished through a comparison of the biology and composition of the GM cultivar and a non-GM counterpart. This review intends to provide information on non-GM sugarcane biology, genetics, breeding, agronomic management, processing, products and byproducts, as well as the current technologies used to develop GM sugarcane, with the aim of assisting regulators in the decision-making process regarding the commercial release of GM sugarcane cultivars.
Collapse
Affiliation(s)
| | | | - Paulo Arruda
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, 13083-875 Campinas, São Paulo Brasil
| | | | | | - Silvana Creste
- IAC/APTA - Centro de Cana, Instituto Agronômico de Campinas, Rodovia Antonio Duarte Nogueira, Km 321, CP 206, 14032-800 Ribeirão Preto, São Paulo Brazil
| | - Luciana di Ciero
- Amyris Crystalsev Biocombustíveis Ltda., Rua James Clerk Maxwell, 315, 13069-380 Campinas, São Paulo Brasil
| | - Jesus Aparecido Ferro
- Campus de Jaboticabal, Departamento de Tecnologia, Universidade Estadual Paulista, 14884-900 Jaboticabal, SP Brasil
| | | | | | - Mária de Fátima Grossi-de-Sá
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estação Biológica, Av. W5 Norte, 70770-900, CP 02372 Brasília, Distrito Federal Brasil
| | - Elio Cesar Guzzo
- Embrapa Tabuleiros Costeiros, Unidade de Execucao de Pesquisa, BR 104 Norte, Km 85, 57061-970, CP 2013 Maceió, Alagoas Brasil
| | - Hermann Paulo Hoffmann
- Campus de Araras, Universidade Federal de São Carlos, Rodovia Anhanguera, Km 174, CP 153, 13600-970 Araras, São Paulo Brasil
| | - Marcos Guimarães de Andrade Landell
- IAC/APTA - Centro de Cana, Instituto Agronômico de Campinas, Rodovia Antonio Duarte Nogueira, Km 321, CP 206, 14032-800 Ribeirão Preto, São Paulo Brazil
| | - Newton Macedo
- Araujo & Macedo Ltda., Rua Oswaldo Cruz, 205, Jardim Santa Cruz, 13601-252 Araras, São Paulo Brasil
| | - Sizuo Matsuoka
- CanaVialis/Alellyx S.A., Rua James Clerk Maxwell, 320, 13069-380 Campinas, São Paulo Brasil
| | | | - Eduardo Romano
- Embrapa Recursos Genéticos e Biotecnologia, Empresa Brasileira de Agropecuária, Av. W5 Norte, 70770-900, CP 02372 Brasília, Distrito Federal Brasil
| | - William José da Silva
- Dow Agroscience, Rodovia Anhanguera, Km 344, Jardinópolis, 14680-000 São Paulo, Brasil
| | - Márcio de Castro Silva Filho
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Avenida Pádua Dias, 11, CP 83, 13400-970 Piracicaba, São Paulo Brasil
| | - Eugenio César Ulian
- CanaVialis/Alellyx S.A., Rua James Clerk Maxwell, 320, 13069-380 Campinas, São Paulo Brasil
| |
Collapse
|
31
|
Piperidis N, Chen JW, Deng HH, Wang LP, Jackson P, Piperidis G. GISH characterization of Erianthus arundinaceus chromosomes in three generations of sugarcane intergeneric hybrids. Genome 2010; 53:331-6. [PMID: 20616864 DOI: 10.1139/g10-010] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Within Erianthus, a genus close to Saccharum, the species E. arundinaceus has the potential to contribute valuable traits to sugarcane, including adaptation to biotic and abiotic stresses and ratooning ability. Sugarcane breeders have tried for a long time to use Erianthus species in their breeding programs but until recently were constrained by a lack of fertile Saccharum x Erianthus hybrids. We report here for the first time the chromosome composition of fertile Saccharum officinarum x E. arundinaceus F1, BC1 (F1 x sugarcane cultivar), and BC2 (BC1 x sugarcane cultivar) hybrids. The F1 and BC2 resulted from n + n chromosome transmission, while the BC1 resulted from 2n + n transmission. In the BC1 clones, the number of E. arundinaceus chromosomes ranged from 21 to 30, and in the BC2 clones, the number ranged from 14 to 15, revealing cases of chromosome loss. No recombination events between Saccharum and Erianthus chromosomes were observed in either the BC1 or BC2 clones. The implications of these results for introgression of genes from E. arundinaceus in sugarcane breeding programs are discussed. We propose a strategy to identify the agronomic value of chromosomes from E. arundinaceus and to conduct targeted breeding based on this information.
Collapse
Affiliation(s)
- Nathalie Piperidis
- BSES Limited, Mackay, Peak Downs Highway, Te Kowai, Queensland 4741, Australia.
| | | | | | | | | | | |
Collapse
|
32
|
Piperidis G, Piperidis N, D'Hont A. Molecular cytogenetic investigation of chromosome composition and transmission in sugarcane. Mol Genet Genomics 2010; 284:65-73. [PMID: 20532565 DOI: 10.1007/s00438-010-0546-3] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2009] [Accepted: 05/18/2010] [Indexed: 11/28/2022]
Abstract
Modern sugarcane cultivars (Saccharum spp., 2n = 100-120) are complex polyploids derived from interspecific hybridization performed a century ago between the sugar-producing species S. officinarum L. and the wild species S. spontaneum L. Using genomic in situ hybridization, we revealed that between 15 and 27.5% of the genome of modern cultivars is derived from S. spontaneum, including 10-23% of entire chromosomes from this wild species and 8-13% chromosomes derived from interspecific recombination. We confirmed the occurrence of 2n + n transmission in crosses and first backcrosses between these two species and demonstrated that this also can occur in crosses between S. officinarum and modern cultivars. We analysed five S. officinarum clones with more than 80 chromosomes and demonstrated that they were derived from interspecific hybridization supporting the classical view that this species is characterized by 2n = 80. We also illustrated the complementarities between molecular cytogenetics and genetic mapping approaches for analysing complex genomes.
Collapse
|
33
|
Nawaz S, Khan FA, Tabasum S, Iqbal MZ, Saeed A. Genetic studies of "noble cane" for identification and exploitation of genetic markers. GENETICS AND MOLECULAR RESEARCH 2010; 9:1011-22. [PMID: 20533196 DOI: 10.4238/vol9-2gmr795] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Forty genotypes (clones) of sugarcane, including elite lines, commercial cultivars of Saccharum officinarum and clones of S. barberi were fingerprinted with 50 SSR markers using a PCR-based marker assay. Nei's genetic distances for SSR data were determined and relationships between accessions were portrayed graphically in the form of a dendrogram. Genetic distance values ranging from 0.60 to 1.11 were observed among the 40 sugarcane accessions. The shortest genetic distance of 0.60 was seen between genotypes US-804 and US-130. These two genotypes differed from each other only in 10 bands, with 20 primers. The most dissimilar of the accessions were CP-77-400 and US-133, with a genetic distance of 1.11. SSR fingerprints can help sugarcane breeders to clarify the genetic pedigree of commercial sugarcane varieties and evaluate the efficiency of breeding methods.
Collapse
Affiliation(s)
- S Nawaz
- CABB, University of Agriculture, Faisalabad, Pakistan
| | | | | | | | | |
Collapse
|
34
|
Wang J, Roe B, Macmil S, Yu Q, Murray JE, Tang H, Chen C, Najar F, Wiley G, Bowers J, Van Sluys MA, Rokhsar DS, Hudson ME, Moose SP, Paterson AH, Ming R. Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. BMC Genomics 2010; 11:261. [PMID: 20416060 PMCID: PMC2882929 DOI: 10.1186/1471-2164-11-261] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2009] [Accepted: 04/23/2010] [Indexed: 11/17/2022] Open
Abstract
Background Sugarcane (Saccharum spp.) has become an increasingly important crop for its leading role in biofuel production. The high sugar content species S. officinarum is an octoploid without known diploid or tetraploid progenitors. Commercial sugarcane cultivars are hybrids between S. officinarum and wild species S. spontaneum with ploidy at ~12×. The complex autopolyploid sugarcane genome has not been characterized at the DNA sequence level. Results The microsynteny between sugarcane and sorghum was assessed by comparing 454 pyrosequences of 20 sugarcane bacterial artificial chromosomes (BACs) with sorghum sequences. These 20 BACs were selected by hybridization of 1961 single copy sorghum overgo probes to the sugarcane BAC library with one sugarcane BAC corresponding to each of the 20 sorghum chromosome arms. The genic regions of the sugarcane BACs shared an average of 95.2% sequence identity with sorghum, and the sorghum genome was used as a template to order sequence contigs covering 78.2% of the 20 BAC sequences. About 53.1% of the sugarcane BAC sequences are aligned with sorghum sequence. The unaligned regions contain non-coding and repetitive sequences. Within the aligned sequences, 209 genes were annotated in sugarcane and 202 in sorghum. Seventeen genes appeared to be sugarcane-specific and all validated by sugarcane ESTs, while 12 appeared sorghum-specific but only one validated by sorghum ESTs. Twelve of the 17 sugarcane-specific genes have no match in the non-redundant protein database in GenBank, perhaps encoding proteins for sugarcane-specific processes. The sorghum orthologous regions appeared to have expanded relative to sugarcane, mostly by the increase of retrotransposons. Conclusions The sugarcane and sorghum genomes are mostly collinear in the genic regions, and the sorghum genome can be used as a template for assembling much of the genic DNA of the autopolyploid sugarcane genome. The comparable gene density between sugarcane BACs and corresponding sorghum sequences defied the notion that polyploidy species might have faster pace of gene loss due to the redundancy of multiple alleles at each locus.
Collapse
Affiliation(s)
- Jianping Wang
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Lalitha R, Premachandran MN. Meiotic Abnormalities in Intergeneric Hybrids between Saccharum spontaneumand Erianthus arundinaceus (Gramineae). CYTOLOGIA 2007. [DOI: 10.1508/cytologia.72.337] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
36
|
D'Hont A. Unraveling the genome structure of polyploids using FISH and GISH; examples of sugarcane and banana. Cytogenet Genome Res 2005; 109:27-33. [PMID: 15753555 DOI: 10.1159/000082378] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2003] [Accepted: 07/26/2004] [Indexed: 11/19/2022] Open
Abstract
We review here the progress that has been achieved using molecular cytogenetics to analyze the genome structure of sugarcane (Saccharum spp) and banana (Musa spp), two crops that are polyploid, of interspecific origin and with chromosomes not distinguishable by their gross morphology. In Saccharum, molecular cytogenetics enabled us to determine the basic chromosome number of two species, Saccharum officinarum and S. spontaneum, involved in the origin of modern cultivars, to quantify the proportion of chromosomes of these species in the genome of modern cultivars, to assess the extent of interspecific chromosome recombination and to clarify the origin of the related species S. barberi. These techniques are also used to monitor introgression with related genera. In Musa, GISH enabled us to differentiate the four genomes involved in banana cultivars and allowed us to determine the genome constitution of several cultivars. FISH was used to analyze the distribution of repeated sequences along the genome.
Collapse
Affiliation(s)
- A D'Hont
- CIRAD, UMR1096, Montpellier, France.
| |
Collapse
|
37
|
Nakayama S. Species-specific accumulation of interspersed sequences in genus Saccharum. Genes Genet Syst 2005; 79:361-5. [PMID: 15729004 DOI: 10.1266/ggs.79.361] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The genus Saccharum consists of two wild and four cultivated species. Novel interspersed sequences were isolated from cultivated sugar cane S. officinarum. These sequences were accumulated in all four cultivated species and their wild ancestral species S. robustum, but were not detected in the other wild species S. spontaneum and the relative Erianthus arundinaceus. The species-specific accumulation of interspersed sequences would correlate to the domestication of sugar canes.
Collapse
Affiliation(s)
- Shigeki Nakayama
- National Institute of Agrobiological Sciences (NIAS), Tsukuba, Ibaraki 305-8602, Japan.
| |
Collapse
|
38
|
Abstract
The finding that even the smallest of plant genomes has incurred multiple genome-wide chromatin duplication events, some of which may predate the origins of the angiosperms and therefore shape all of flowering plant biology, adds new importance to the molecular analysis of polyploidization/diploidization cycles and their phenotypic consequences. Early clues as to the possible phenotypic consequences of polyploidy derive from recent QTL mapping efforts in a number of diverse crop plants of recent and well-defined polyploid origins. A small sampling examples of the role(s) of polyploidy in conferring crop adaptation from human needs include examples of (1) dosage effects of multiple alleles in autopolyploids, and (2) 'intergenomic heterosis' conferring novel traits or transgressive levels of existing traits, associated with merging divergent genomes in a common allopolyploid nucleus. A particularly interesting manifestation of #2 is the evolution of complementary alleles at corresponding ('homoeologous') loci in divergent polyploid taxa derived from a common ancestor. Burgeoning genomic data for both botanical models and major crops offer new avenues for investigation of the molecular and phenotypic consequences of polyploidy, promising new insights into the role of this important process in the evolution of botanical diversity.
Collapse
Affiliation(s)
- Andrew H Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA.
| |
Collapse
|
39
|
Besse P, DaSilva D, Humeau L, Govinden-Soulange J, Gurib-Fakim A, Kodja H. A genetic diversity study of endangered Psiadia species endemic from Mauritius Island using PCR markers. BIOCHEM SYST ECOL 2003. [DOI: 10.1016/s0305-1978(03)00131-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
40
|
D'Hont A, Paulet F, Glaszmann JC. Oligoclonal interspecific origin of 'North Indian' and 'Chinese' sugarcanes. Chromosome Res 2002; 10:253-62. [PMID: 12067214 DOI: 10.1023/a:1015204424287] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Sugarcanes consist of several groups of complex polyploid forms. The origin of 'North Indian' and 'Chinese' sugarcanes (referred to as S. barberi and S. sinense) was investigated using genomic in-situ hybridization (GISH), detection of species-specific repeated sequences and RFLP. GISH proved their interspecific hybrid origin. Together with the distribution of species-specific repeated sequences and earlier RFLP data, the results show that both taxa are derived from interspecific hybridization between S. officinarum and S. spontaneum and that no other genus has been directly involved. RFLP indicates that the clones are clustered into a few groups, each derived from a single interspecific hybrid that has subsequently undergone a few somatic mutations. These groups correspond quite well with those already defined based on morphological characters and chromosome numbers. However, the calculated genetic similarities do not support the existence of two distinct taxa. The 'North Indian' and 'Chinese' sugarcanes represent a set of horticultural groups rather than established species.
Collapse
Affiliation(s)
- Angélique D'Hont
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), Montpellier, France.
| | | | | |
Collapse
|
41
|
Grivet L, Arruda P. Sugarcane genomics: depicting the complex genome of an important tropical crop. CURRENT OPINION IN PLANT BIOLOGY 2002; 5:122-7. [PMID: 11856607 DOI: 10.1016/s1369-5266(02)00234-0] [Citation(s) in RCA: 117] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In the past few years, approaches such as molecular cytogenetics and the use of molecular markers have permitted significant advances in the establishment of the evolutionary origin and genome structure of sugarcane, an important polyploid crop. The availability of new resources, such as a bacterial artificial chromosome library and a huge collection of expressed sequence tags, has opened the gateway to promising functional analyses on a genomic scale.
Collapse
Affiliation(s)
- Laurent Grivet
- Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas, Campinas, SP, Brazil
| | | |
Collapse
|
42
|
Ming R, Liu SC, Moore PH, Irvine JE, Paterson AH. QTL analysis in a complex autopolyploid: genetic control of sugar content in sugarcane. Genome Res 2001; 11:2075-84. [PMID: 11731498 PMCID: PMC311218 DOI: 10.1101/gr.198801] [Citation(s) in RCA: 125] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
QTL mapping in autopolyploids is complicated by the possibility of segregation for three or more alleles at a locus and by a lack of preferential pairing, however the subset of polymorphic alleles that show simplex segregation ratios can be used to locate QTLs. In autopolyploid Saccharum, 36 significant associations between variation in sugar content and unlinked loci detected by 31 different probes were found in two interspecific F(1) populations. Most QTL alleles showed phenotypic effects consistent with the parental phenotypes, but occasional transgressive QTLs revealed opportunities to purge unfavorable alleles from cultivars or introgress valuable alleles from exotics. Several QTLs on homologous chromosomes appeared to correspond to one another-multiple doses of favorable 'alleles' at such chromosomal region(s) yielded diminishing returns-such negative epistasis may contribute to phenotypic buffering. Fewer sugar content QTLs were discovered from the highest-sugar genotype than from lower-sugar genotypes, perhaps suggesting that many favorable alleles have been fixed by prior selection, i.e. that the genes for which allelic variants (QTLs) persist in improved sugarcanes may be a biased subset of the population of genes controlling sugar content. Comparison of these data to mutations and QTLs previously mapped in maize hinted that seed and biomass crops may share a partly-overlapping basis for genetic variation in carbohydrate deposition. However, many QTLs do not correspond to known candidate genes, suggesting that other approaches will be necessary to isolate the genetic determinants of high sugar content of vegetative tissues.
Collapse
Affiliation(s)
- R Ming
- Plant Genome Mapping Laboratory, Department of Soil and Crop Sciences, Texas A&M University, College Station, Texas 77843, USA
| | | | | | | | | |
Collapse
|
43
|
Cordeiro GM, Casu R, McIntyre CL, Manners JM, Henry RJ. Microsatellite markers from sugarcane (Saccharum spp.) ESTs cross transferable to erianthus and sorghum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2001; 160:1115-1123. [PMID: 11337068 DOI: 10.1016/s0168-9452(01)00365-x] [Citation(s) in RCA: 186] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Analysis of a sugarcane (Saccharum spp.) EST (expressed sequence tag) library of 8678 sequences revealed approximately 250 microsatellite or simple sequence repeats (SSRs) sequences. A diversity of dinucleotide and trinucleotide SSR repeat motifs were present although most were of the (CGG)(n) trinucleotide motif. Primer sets were designed for 35 sequences and tested on five sugarcane genotypes. Twenty-one primer pairs produced a PCR product and 17 pairs were polymorphic. Primer pairs that produced polymorphisms were mainly located in the coding sequence with only a single pair located within the 5' untranslated region. No primer pairs producing a polymorphic product were found in the 3' untranslated region. The level of polymorphism (PIC value) in cultivars detected by these SSRs was low in sugarcane (0.23). However, a subset of these markers showed a significantly higher level of polymorphism when applied to progenitor and related genera (Erianthus sp. and Sorghum sp.). By contrast, SSRs isolated from sugarcane genomic libraries amplify more readily, show high levels of polymorphism within sugarcane with a higher PIC value (0.72) but do not transfer to related species or genera well.
Collapse
Affiliation(s)
- G M. Cordeiro
- Centre for Plant Conservation Genetics, Southern Cross University, P.O. Box 157, NSW 2480, Lismore, Australia
| | | | | | | | | |
Collapse
|
44
|
Yan H, Liu G, Cheng Z, Min S, Zhu L. Characterization of euploid backcross progenies derived from interspecific hybrids between Oryza sativa and O. eichingeri by restriction fragment length polymorphism (RFLP) analysis and genomic in situ hybridization (GISH). Genome 2001. [DOI: 10.1139/g00-086] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Restriction fragment length polymorphism (RFLP) analysis and GISH (genomic in situ hybridization) were performed on euploid plants derived from crosses between Oryza sativa (2n = 24, AA) and two brown planthopper-resistant accessions of O. eichingeri (2n = 24, CC). After screening with 164 RFLP markers, 60 of the 67 euploid plants were identified as introgression lines, each carrying 16 small O. eichingeri segments integrated on chromosomes 1, 2, 6, or 10. In the somatic chromosome preparations of F1 hybrid, O. eichingeri chromosomes, fluorescing greenish-yellow in the sequential GISH, appeared to be longer and to contain more heterochromatin than O. sativa ones, and this karyotypic polymorphism can be used to detect some introgressed O. eichingeri segments in euploid plants. In addition, GISH identification presented direct evidence for the transfer of small segments from O. eichingeri to O. sativa chromosome(s) which were subsequently recognized according to their condensation pattern, arm ratio, and chromosome length. The present results would contribute to the molecular mapping and selection of O. eichingeri - derived brown planthopper-resistant gene and positive yield QTLs.Key words: Oryza sativa, Oryza eichingeri, introgression lines, RFLP, genomic in situ hybridization (GISH).
Collapse
|
45
|
Piperidis G, Christopher MJ, Carroll BJ, Berding N, D'Hont A. Molecular contribution to selection of intergeneric hybrids between sugarcane and the wild species Erianthus arundinaceus. Genome 2000. [DOI: 10.1139/g00-059] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Erianthus arundinaceus has great potential as a germplasm source for better ratoonability, vigour, tolerance to environmental stresses, and disease resistance in sugarcane. Many unsuccessful attempts have been made to introduce these characters into modern sugarcane cultivars. We report on significant progress made since molecular tools were implemented. Sequence-tagged PCR, revealing size variation in the 5S rDNA cluster, was performed on intact leaf tissue to identify genuine hybrids six weeks after germination. This early screening of seedlings avoids the loss of genuine hybrids due to competition with selfed progeny. Of 96 crosses made involving female Saccharum officinarum or sugarcane cultivars (Saccharum spp.) and male E. arundinaceus, 26 were fertile producing 1328 seedlings. Thirty-seven genuine hybrids were unequivocally identified but only 19 have survived. Genuine hybrids were produced from only three crosses, all involving S. officinarum as the female parent. Chromosome elimination was observed in all seven hybrids analyzed using genomic in situ hybridization (GISH). Very little cross-hybridization was observed between the genomes of the two species after GISH, confirming recent molecular studies which showed that E. arundinaceus is quite distant from the genus Saccharum. The major limitation in the introgression of E. arundinaceus resides now in the apparent sterility of the hybrids.Key words: sugarcane, Erianthus, intergeneric hybrid, genomic in situ hybridization, 5S rDNA, sequence-tagged PCR.
Collapse
|
46
|
Ming R, Liu SC, Lin YR, da Silva J, Wilson W, Braga D, van Deynze A, Wenslaff TF, Wu KK, Moore PH, Burnquist W, Sorrells ME, Irvine JE, Paterson AH. Detailed alignment of saccharum and sorghum chromosomes: comparative organization of closely related diploid and polyploid genomes. Genetics 1998; 150:1663-82. [PMID: 9832541 PMCID: PMC1460436 DOI: 10.1093/genetics/150.4.1663] [Citation(s) in RCA: 199] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The complex polyploid genomes of three Saccharum species have been aligned with the compact diploid genome of Sorghum (2n = 2x = 20). A set of 428 DNA probes from different Poaceae (grasses) detected 2460 loci in F1 progeny of the crosses Saccharum officinarum Green German x S. spontaneum IND 81-146, and S. spontaneum PIN 84-1 x S. officinarum Muntok Java. Thirty-one DNA probes detected 226 loci in S. officinarum LA Purple x S. robustum Molokai 5829. Genetic maps of the six Saccharum genotypes, including up to 72 linkage groups, were assembled into "homologous groups" based on parallel arrangements of duplicated loci. About 84% of the loci mapped by 242 common probes were homologous between Saccharum and Sorghum. Only one interchromosomal and two intrachromosomal rearrangements differentiated both S. officinarum and S. spontaneum from Sorghum, but 11 additional cases of chromosome structural polymorphism were found within Saccharum. Diploidization was advanced in S. robustum, incipient in S. officinarum, and absent in S. spontaneum, consistent with biogeographic data suggesting that S. robustum is the ancestor of S. officinarum, but raising new questions about the antiquity of S. spontaneum. The densely mapped Sorghum genome will be a valuable tool in ongoing molecular analysis of the complex Saccharum genome.
Collapse
Affiliation(s)
- R Ming
- Plant Genome Mapping Laboratory, Department of Soil and Crop Science, Texas A&M University, College Station, Texas 77843, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
47
|
Nagaki K, Tsujimoto H, Sasakuma T. A novel repetitive sequence of sugar cane, SCEN family, locating on centromeric regions. Chromosome Res 1998; 6:295-302. [PMID: 9688519 DOI: 10.1023/a:1009270824142] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Tandem repetitive sequences consisting of 140-bp repetitive units were cloned from sugar cane genomic DNA and designated the SCEN family. In situ hybridization revealed that they were located on the centromeric region of almost all of the chromosomes of sugar cane. The 140-bp sequence included three CENP-B box-like sequences. Phylogenetic analysis of the members of the SCEN family revealed that the sequences had 75% homology with each other, on average, and that the sequences could not be further classified into smaller subfamilies. The copy number of the sequence was estimated to be 2.6 x 10(5) per haploid sugar cane genome and, therefore, 4.6 x 10(3) or 630 kb per chromosome on average.
Collapse
Affiliation(s)
- K Nagaki
- Kihara Institute Biological Research, Yokohama City University, Yokohama, Japan.
| | | | | |
Collapse
|
48
|
|
49
|
Guimarães CT, Sills GR, Sobral BW. Comparative mapping of Andropogoneae: Saccharum L. (sugarcane) and its relation to sorghum and maize. Proc Natl Acad Sci U S A 1997; 94:14261-6. [PMID: 9405600 PMCID: PMC24932 DOI: 10.1073/pnas.94.26.14261] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Comparative genetic maps of Papuan Saccharum officinarum L. (2n = 80) and S. robustum (2n = 80) were constructed by using single-dose DNA markers (SDMs). SDM-framework maps of S. officinarum and S. robustum were compared with genetic maps of sorghum and maize by way of anchor restriction fragment length polymorphism probes. The resulting comparisons showed striking colinearity between the sorghum and Saccharum genomes. There were no differences in marker order between S. officinarum and sorghum. Furthermore, there were no alterations in SDM order between S. officinarum and S. robustum. The S. officinarum and S. robustum maps also were compared with the map of the polysomic octoploid S. spontaneum 'SES 208' (2n = 64, x = 8), thus permitting relations to homology groups ("chromosomes") of S. spontaneum to be studied. Investigation of transmission genetics in S. officinarum and S. robustum confirmed preliminary results that showed incomplete polysomy in these species. Because of incomplete polysomy, multiple-dose markers could not be mapped for lack of a genetic model for their segregation. To coalesce S. officinarum and S. robustum linkage groups into homology groups (composed of homologous pairing partners), they were compared with sorghum (2n = 20), which functioned as a synthetic diploid. Groupings suggested by comparative mapping were found to be highly concordant with groupings based on highly polymorphic restriction fragment length polymorphism probes detecting multiple SDMs. The resulting comparative maps serve as bridges to allow information from one Andropogoneae to be used by another, for breeding, ecology, evolution, and molecular biology.
Collapse
Affiliation(s)
- C T Guimarães
- Genetica Americas, 11099 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | | | | |
Collapse
|
50
|
D'Hont A, Grivet L, Feldmann P, Rao S, Berding N, Glaszmann JC. Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics. MOLECULAR & GENERAL GENETICS : MGG 1996; 250:405-13. [PMID: 8602157 DOI: 10.1007/bf02174028] [Citation(s) in RCA: 134] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Cultivated sugarcane clones (Saccharum spp., 2n=100 to 130) are derived from complex interspecific hybridizations between the species S. officinarum and S. spontaneum. Using comparative genomic DNA in situ hybridization, we demonstrated that it is possible to distinguish the chromosomes contributed by these two species in an interspecific F1 hybrid and a cultivated clone, R570. In the interspecific F1 studied, we observed n + n transmission of the parental chromosomes instead of the peculiar 2n + n transmission usually described in such crosses. Among the chromosomes of cultivar R570 (2n = 107-115) about 10% were identified as originating from S. spontaneum and about 10% were identified as recombinant chromosomes between the two species S. officinarum and S. spontaneum. This demonstrated for the first time the occurrence of recombination between the chromosomes of these two species. The rDNA sites were located by in situ hybridization in these two species and the cultivar R570. This supported different basic chromosome numbers and chromosome structural differences between the two species and provided a first bridge between physical and genetical mapping in sugarcane.
Collapse
Affiliation(s)
- A D'Hont
- CIRAD, Centre de Recherches de Montpellier, Montpellier, France
| | | | | | | | | | | |
Collapse
|