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Siraree A, Banerjee N, Kumar S, Khan MS, Singh PK, Kumar S, Sharma S, Singh RK, Singh J. Agro-morphological description, genetic diversity and population structure of sugarcane varieties from sub-tropical India. 3 Biotech 2018; 8:469. [PMID: 30402371 DOI: 10.1007/s13205-018-1481-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 10/16/2018] [Indexed: 10/27/2022] Open
Abstract
Genetic diversity in 92 sugarcane varieties of sub-tropical India was assessed using 30 morphological descriptors and 643 simple sequence repeat (SSR) marker loci. Out of the 30 morphological descriptors, 14 were found polymorphic, and significant variability was recorded for plant height, cane diameter and number of millable canes. Grouping traits like plant growth habit, leaf blade curvature and leaf sheath adherence were found to be predominantly monomorphic. There were a few pairs of varieties (e.g., CoP 9702 and CoP 9302, CoP 9301 and CoSe 01424, UP 05 and Co 1336, CoS 96258 and CoH 110) that showed similar DUS profiles except differing for a few descriptors. The STRUCTURE profile suggest that all the 92 sugarcane varieties had admixtures and no sub-group had a pure unblemished structure profile. An average Nei's genetic distance of 0.49 was found to be a better measure of diversity, whereas, the average band informativeness (Ibav) value of all the 80 SSR primers was 0.434. Although, the mean Ibav values for EST-SSR and genomic-SSR primers were same (0.43), the range of Ibav of EST-SSR (0.04-0.85) was more compared to genomic-SSR (0.12-0.63) primers. The segregation of the varieties based on morphological traits was not in accordance with their geographical distribution or maturity groups, but principal component analysis was able to group the sugarcane varieties that had similar pedigree together. Results indicate that the SSRs have a potential use in the DNA fingerprinting of varieties to prevent any malpractice like unauthorised re-registration of a previously registered sugarcane variety under PPV&FR Act. The marker profiles could also be utilised for variety identification and release, since at present, it has been made mandatory to include it in addition to the morphological descriptors.
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Liu L, Chen W, Zheng X, Li J, Yan DT, Liu L, Liu X, Wang YL. Genetic diversity of Ulmus lamellosa by morphological traits and sequence-related amplified polymorphism (SRAP) markers. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.04.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Ferreira SS, Hotta CT, Poelking VGDC, Leite DCC, Buckeridge MS, Loureiro ME, Barbosa MHP, Carneiro MS, Souza GM. Co-expression network analysis reveals transcription factors associated to cell wall biosynthesis in sugarcane. PLANT MOLECULAR BIOLOGY 2016; 91:15-35. [PMID: 26820137 PMCID: PMC4837222 DOI: 10.1007/s11103-016-0434-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 01/07/2016] [Indexed: 05/18/2023]
Abstract
Sugarcane is a hybrid of Saccharum officinarum and Saccharum spontaneum, with minor contributions from other species in Saccharum and other genera. Understanding the molecular basis of cell wall metabolism in sugarcane may allow for rational changes in fiber quality and content when designing new energy crops. This work describes a comparative expression profiling of sugarcane ancestral genotypes: S. officinarum, S. spontaneum and S. robustum and a commercial hybrid: RB867515, linking gene expression to phenotypes to identify genes for sugarcane improvement. Oligoarray experiments of leaves, immature and intermediate internodes, detected 12,621 sense and 995 antisense transcripts. Amino acid metabolism was particularly evident among pathways showing natural antisense transcripts expression. For all tissues sampled, expression analysis revealed 831, 674 and 648 differentially expressed genes in S. officinarum, S. robustum and S. spontaneum, respectively, using RB867515 as reference. Expression of sugar transporters might explain sucrose differences among genotypes, but an unexpected differential expression of histones were also identified between high and low Brix° genotypes. Lignin biosynthetic genes and bioenergetics-related genes were up-regulated in the high lignin genotype, suggesting that these genes are important for S. spontaneum to allocate carbon to lignin, while S. officinarum allocates it to sucrose storage. Co-expression network analysis identified 18 transcription factors possibly related to cell wall biosynthesis while in silico analysis detected cis-elements involved in cell wall biosynthesis in their promoters. Our results provide information to elucidate regulatory networks underlying traits of interest that will allow the improvement of sugarcane for biofuel and chemicals production.
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Affiliation(s)
| | | | - Viviane Guzzo de Carli Poelking
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa, Brazil
- Universidade Federal do Recôncavo da Bahia, Cruz das Almas, Brazil
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Fan XR, Ren XR, Liu YL, Chen YY. Genetic structure of wild rice Zizania latifolia and the implications for its management in the Sanjiang Plain, Northeast China. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2015.11.017] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Luan MB, Zou ZZ, Zhu JJ, Wang XF, Xu Y, Sun ZM, Chen JH. Genetic diversity assessment using simple sequence repeats (SSR) and sequence-related amplified polymorphism (SRAP) markers in ramie. BIOTECHNOL BIOTEC EQ 2015. [DOI: 10.1080/13102818.2015.1026843] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Zhang J, Yan J, Zhang Y, Ma X, Bai S, Wu Y, Dao Z, Li D, Zhang C, Zhang Y, You M, Yang F, Zhang J. Molecular insights of genetic variation in Erianthus arundinaceus populations native to China. PLoS One 2013; 8:e80388. [PMID: 24282538 PMCID: PMC3840007 DOI: 10.1371/journal.pone.0080388] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2013] [Accepted: 10/02/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND E. arundinaceus (Retz.) Jeswiet is a warm-season, tall-growing perennial species native to much southern portion in China. The grass has been extensively used in sugarcane breeding and is recently targeted as a bioenergy feedstock crop. However, information on the genetic structure of the Chinese wild germplasm is limited. Knowledge of genetic variation within and among populations is essential for breeding new cultivars in the species. The major objective of this study was to quantify the magnitude of genetic variation among and within natural populations in China. METHODOLOGY/PRINCIPAL FINDINGS In this experiment, we analyzed genetic variation of 164 individuals of 18 populations collected from natural habitats in six Chinese provinces using 20 sequence-related amplified polymorphism (SRAP) primer pairs generating 277 polymorphic bands. Among and within the populations, the percentage of polymorphic bands (PPB) was 80.00% and 27.07%, genetic diversity (HE ) was 0.245 and 0.099, effective number of alleles (NE ) was 1.350 and 1.170, and Shannon's information index (I) was 0.340 and 0.147, respectively. The populations were clustered into six groups exhibiting a high level of genetic differentiation, which was highly associated with geographic origins of respective germplasm populations, but was not significantly associated with geographic distances between the populations. CONCLUSIONS/SIGNIFICANCE This is the first report indicating that large genetic variation exists in the Chinese E. arundinaceus germplasm based on the SRAP molecular marker analysis of native populations. The genetic structure of populations in the species has been substantially affected by geographic landforms and environments. The diverse collection will be highly valuable in genetic improvement in the species per se and likely in sugarcane.
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Affiliation(s)
- Jianbo Zhang
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya'an, Sichuan, China
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
- Guizhou Grassland Science Institute, Guiyang, Guizhou, China
| | - Jiajun Yan
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Yunwei Zhang
- Grassland Institute, China Agricultural University, Beijing, China
| | - Xiao Ma
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya'an, Sichuan, China
| | - Shiqie Bai
- Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Ya'an, Sichuan, China
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Yanqi Wu
- Plant and Soil Sciences Department, Oklahoma State University, Stillwater, Oklahoma, United States of America
| | - Zhixue Dao
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Daxu Li
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Changbing Zhang
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Yu Zhang
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Minghong You
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
| | - Fuyu Yang
- Grassland Institute, China Agricultural University, Beijing, China
| | - Jin Zhang
- Sichuan Academy of Grassland Science, Chengdu, Sichuan, China
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Genetic diversity analysis of sugarcane parents in Chinese breeding programmes using gSSR markers. ScientificWorldJournal 2013; 2013:613062. [PMID: 23990759 PMCID: PMC3749591 DOI: 10.1155/2013/613062] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2013] [Accepted: 07/09/2013] [Indexed: 11/21/2022] Open
Abstract
Sugarcane is the most important sugar and bioenergy crop in the world. The selection and combination of parents for crossing rely on an understanding of their genetic structures and molecular diversity. In the present study, 115 sugarcane genotypes used for parental crossing were genotyped based on five genomic simple sequence repeat marker (gSSR) loci and 88 polymorphic alleles of loci (100%) as detected by capillary electrophoresis. The values of genetic diversity parameters across the populations indicate that the genetic variation intrapopulation (90.5%) was much larger than that of interpopulation (9.5%). Cluster analysis revealed that there were three groups termed as groups I, II, and III within the 115 genotypes. The genotypes released by each breeding programme showed closer genetic relationships, except the YC series released by Hainan sugarcane breeding station. Using principle component analysis (PCA), the first and second principal components accounted for a cumulative 76% of the total variances, in which 43% were for common parents and 33% were for new parents, respectively. The knowledge obtained in this study should be useful to future breeding programs for increasing genetic diversity of sugarcane varieties and cultivars to meet the demand of sugarcane cultivation for sugar and bioenergy use.
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