Abstract
Sugarcane (Saccharum spp) is an important crop for both sugar and biofuel production. However, the sugarcane breeding process has resulted in modern sugarcane cultivars with a narrow genetic basis. To broaden the genetic basis and promote international collaborations in sugarcane cultivar development, we documented the peidgrees of representative sugarcane culativars widely used in China and the United States of America (USA), recruited more than six thousand simple sequence repeat (SSR) markers for sugarcane, and assessed the genetic diversity and relationships beween representative sugarcane cultivars and their potential ancestry accessions. The SSR gentoyping results indicated that both the USA and Chiniese cultivars had low genetic diversity, specifically the Chinese cultivars. The USA sugarcane cultivars experienced high presure of selection for sugar content as they had the closest relationship with S. officinarum, followed by Chinese cultivars, S. robustum, and S. spontaneum. The sugarcane accessions assessed could be divided into five and four groups through cluster and principal component analysis, respectively. S. spontaneum as a potential ancestor contributing to the stress tolerance of sugarcane cultivars was grouped into distinct clusters, and S. officinarum was grouped with sugarcane cultivars in both countries. S. robustum did not seem to contribute to the sugarcane cultivar development in China, but may have contributed to the USA cultivar development. This study not only provided a collection of easy to use SSR markers, but also detailed genetic diversity and relationship among the cultivars in the two counties, which will be referable to promote international collaboration and broaden the genetic basis of sugarcane cultivars.
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References
Aitken KS, Jackson PA, McIntyre CL (2005) A combination of AFLP and SSR markers provides extensive map coverage and identification of homo (eo) logous linkage groups in a sugarcane cultivar. Theor Appl Genet 110:789–801
Aitken KS, Li J, Jackson P, Piperidis G, McIntyre CL (2006) AFLP analysis of genetic diversity within Saccharum officinarum and comparison with sugarcane cultivars. Aust J Agric Res 57:1167–1184
Alwala S, Suman A, Arro JA, Veremis JC, Kimbeng CA (2006) Target region amplification polymorphism (TRAP) for assessing genetic diversity in sugarcane germplasm collections. Crop Sci 46:448–455
Andru S (2009) Genetic linkage map of LCP 85-384, genetic diversity of a S. spontaneum collection and the contribution of S. spontaneum to Louisiana commercial germplasm. Dissertation, Louisiana State University
Backeljau T, De Bruyn L, De Wolf H, Jordaens K, Van Dongen S, Winnepennincks B (1996) Multiple UPGMA and neighbor-joining trees and the performance of some computer packages. Mol Biol Evol 13:309
Baucum LE, Rice RW, Schueneman TJ (2006) An overview of Florida sugarcane. University of Florida, Institute of Food and Agricultural Science Extension. Accessed 7 Dec 2017
Besse P, Taylor G, Carroll B, Berding N, Burner D1, McIntyre CL (1998) Assessing genetic diversity in a sugarcane germplasm collection using an automated AFLP analysis. Genetica 104:143–153
Bremer G (1962) Problems in breeding and cytology of sugar cane. Euphytica 11:65–80
Bull T, Glasziou K (1979) In: Lovett J, Lazenby A (eds) Australian field crops. Angus and Robertson Publishers, Sydney, pp 95–113
Chen H, Fan Y, Xiang-Yu J (2003) Phylogenetic relationships of Saccharum and related species inferred from sequence analysis of the nrDNA ITS region. Acta Agronomica Sinica 29(3):379–385
Chen P, Pan Y, Chen R, Xu L, Chen Y (2010) SSR marker-based analysis of genetic relatedness among sugarcane cultivars (Saccharum spp. hybrids) from breeding programs in China and other countries. Sugar Tech 11(4):347–354
Cordeiro G, Taylor G, Henry R (2000) Characterisation of microsatellite markers from sugarcane (Saccharum sp.), a highly polyploid species. Plant Sci 155(2):161–168
Cordeiro GM, Pan Y, Henry RJ (2003) Sugarcane microsatellites for the assessment of genetic diversity in sugarcane germplasm. Plant Sci 165:181–189
Cordeiro GM, Eliott F, McIntyre CL, Casu RE, Henry RJ (2006) Characterisation of single nucleotide polymorphisms in sugarcane ESTs. Theor Appl Genet 113:331–343
Creste S, Accoroni KA, Pinto LR, Vencovsky R, Gimenes MA, Xavier MA, Landell MG (2010) Genetic variability among sugarcane genotypes based on polymorphisms in sucrose metabolism and drought tolerance genes. Euphytica 172:435–446
Dahlquist E (2013) Biomass as energy source: resources, systems and applications. CRC Press, London
Daniels J, Smith P, Paton N (1975) The origin of sugarcanes and centres of genetic diversity in Saccharum. South East Asian Plant Genetic Resources.Proceeding:20–22
Daugrois J, Grivet L, Roques D, Hoarau J, Lombard H, Glaszmann J, D’Hont A (1996) A putative major gene for rust resistance linked with a RFLP marker in sugarcane cultivar ‘R570’. Theor Appl Genet 92:1059–1064
Deren CW (1995) Genetic base of US mainland sugarcane. Crop Sci 35:1195–1199
D’Hont A, Lu YH, Feldmann P, Glaszmann J (1993) Cytoplasmic diversity in sugar cane revealed by heterologous probes. Sugar Cane (UK)
D’Hont A, Lu Y, Leon DG, Grivet L, Feldmann P, Lanaud C, Glaszmann JC (1994) A molecular approach to unraveling the genetics of sugarcane, a complex polyploid of the Andropogoneae tribe. Genome 37:222–230
D’Hont A, Grivet L, Feldmann P, Glaszmann JC, Rao S, Berding N (1996) Characterisation of the double genome structure of modern sugarcane cultivars (Saccharum spp.) by molecular cytogenetics. Mol Gen Genet MGG 250:405–413
D’Hont A, Ison D, Alix K, Roux C, Glaszmann JC (1998) Determination of basic chromosome numbers in the genus Saccharum by physical mapping of ribosomal RNA genes. Genome 41:221–225
FAO (2014) FAOSTAT, FAO Statistical Databases. Available at: http://faostat3.fao.org/. Accessed 07 Jun 2016
Fountain J, Qin H, Chen C, Dang P, Wang ML, Guo B (2011) A note on development of a low-cost and high-throughput SSR-based genotyping method in peanut (Arachis hypogaea L.). Peanut Sci 38:122–127
Glaszmann J, Lu YH, Lanaud C (1990) Variation of nuclear ribosomal DNA in sugarcane. J Genet Breed 44:191–197
Grivet L, D’Hont A, Roques D, Feldmann P, Lanaud C, Glaszmann JC (1996) RFLP mapping in cultivated sugarcane (Saccharum spp.): genome organization in a highly polyploid and aneuploid interspecific hybrid. Genetics 142:987–1000
Irvine JE (1999) Saccharum species as horticultural classes. Theor Appl Genet 98:186–194
James B, Chen C, Rudolph A, Swaminathan K, Murray J, Na J, Spence A, Smith B, Hudson M, Moose S (2012) Development of microsatellite markers in autopolyploid sugarcane and comparative analysis of conserved microsatellites in sorghum and sugarcane. Mol Breed 30(2):661–669
Langmead B, Trapnell C, Pop M, Salzberg SL (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25
Lao F, Liu R, He H, Deng H, Chen Z, Chen J, Fu C, Zhang C, Yang Y (2008) AFLP analysis of genetic diversity in series sugarcane parents developed at HSBS. Mol Plant Breed 6:517–522 (in Chinese)
Liu K, Muse SV (2005) PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics 21:2128–2129
Liu R, Lao F, Deng H (2011) AFLP analysis of genetic diversity in YT series sugarcane varieties. Guangdong Agri Sci 8:47
Lu YH, D’Hont A, Walker D, Rao PS, Feldmann P, Glaszmann J (1994) Relationships among ancestral species of sugarcane revealed with RFLP using single copy maize nuclear probes. Euphytica 78:7–18
Luo J, Deng ZH, Que YX, Yuan ZN, Chen RK (2012) Productivity and stability of sugarcane varieties in the 7th round national regional trial of China. Chin J Appl Environ Biol 18:734–739
Madan VK, Bikash M, Ansari MI, Anjani S, Soni N, Solomon S, Agnihotri VP (2000) RAPD-PCR analysis of molecular variability in the red rot pathogen (Colletotrichum falcatum) of sugarcane. Sugar Cane International:5–8
Mudge J, Andersen WR, Kehrer RL, Fairbanks DJ (1996) A RAPD genetic map of Saccharum officinarum. Crop Sci 36:1362–1366
Nair NV, Nair S, Sreenivasan TV, Mohan M (1999) Analysis of genetic diversity and phylogeny in Saccharum and related genera using RAPD markers. Genet Resour Crop Evol 46:73–79
Nayak SN, Song J, Villa A, Pathak B, Ayala-Silva T, Yang X, Todd J, Glynn NC, Kuhn DN, Glaz B (2014) Promoting utilization of Saccharum spp. genetic resources through genetic diversity analysis and core collection construction. PLoS ONE 9:e110856
Palhares A, Rodrigues-Morais T, Van Sluys M, Domingues D, Maccheroni W, Jordão H, Souza A, Marconi T, Mollinari M, Gazaffi R (2012) A novel linkage map of sugarcane with evidence for clustering of retrotransposon-based markers. BMC Genet 13(1):51
Pan Y (2006) Highly polymorphic microsatellite DNA markers for sugarcane germplasm evaluation and variety identity testing. Sugar Tech 8(4):246–256
Pan Y, Cordeiro GM, Richard EP, Henry RJ (2003) Molecular genotyping of sugarcane clones with microsatellite DNA markers. Maydica 48:319–329
Parida S, Pandit A, Gaikwad K, Sharma T, Srivastava P, Singh N, Mohapatra T (2010) Functionally relevant microsatellites in sugarcane unigenes. Bmc Plant Biol 10(4):1–19
Parker M (2011) The sugar barons: family, corruption, empire and war. Hutchinson, London
Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Haberer G, Hellsten U, Mitros T, Poliakov A (2009) The Sorghum bicolor genome and the diversification of grasses. Nature 457:551–556
Peakall R, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Res 6:288–295
Peakall R, Smouse PE (2012) GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research—an update. Bioinformatics 28:2537–2539
Pinto LR, Oliveira KM, Ulian EC, Garcia AAF, De Souza AP (2004) Survey in the sugarcane expressed sequence tag database (SUCEST) for simple sequence repeats. Genome 47:795–804
Que Y, Chen T, Xu L, Chen R (2009) Genetic diversity among key sugarcane clones revealed by TRAP markers. J Agri Biotechnol 17:496–503
Rohlf FJ (2002) NTSYS-pc: numerical taxonomy system ver. 2.1. Setauket, NY: Exeter Publishing Ltd, Chennai
Singh RK, Mishra SK, Singh SP, Mishra N, Sharma ML (2010) Evaluation of microsatellite markers for genetic diversity analysis among sugarcane species and commercial hybrids. Aust J Crop Sci 4(2):116–125
Sreenivasan TV, Ahloowalia BS (1987) Cytogenetics. In: Heinz DJ (ed) Sugarcane improvement through breeding. Elsevier, Amsterdam, pp 211–253
Stevenson GC (1965) Genetics and breeding of sugar cane. Longmans, London
Tai P, Miller JD (2001) A core collection for L. from the World Collection of Sugarcane. Crop Sci 41:879–885
Todd J, Wang J, Glaz B, Sood S, Ayala-Silva T, Nayak SN, Glynn NC, Gutierrez OA, Kuhn DN, Tahir M (2014) Phenotypic characterization of the Miami World Collection of sugarcane (Saccharum spp.) and related grasses for selecting a representative core. Genet Resour Crop Evol 61:1581–1596
Todd J, Glaz B, Burner D, Kimbeng C (2015) Historical use of cultivars as parents in Florida and Louisiana sugarcane breeding programs. International scholarly research notices
Walsh J (1981) Genetic vulnerability down on the farm. Science 214(4517):161
Wang J, Roe B, Macmil S, Yu Q, Murray JE, Tang H, Chen C, Najar F, Wiley G, Bowers J (2010) Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. BMC Genom 11:261
Wen M, Li Q, Yang J, Liu F, Wu W, Wu J, Pan F (2014) Pedigree analysis for Yuetang series of sugarcane varieties and utilization of core germplasm collection in recent years. Chin J Trop Crops 35:239–245
Yang C, Yang L, Li Y (2014) Origins and evolution of sugarcane. J South Agri 45(10):1744–1750
You Q, Xu L, Zheng Y, Que Y (2013) Genetic diversity analysis of sugarcane parents in Chinese breeding programmes using gSSR markers. The Scientific World Journal 2013
Acknowledgements
This work was supported by Center for Plant Genomics and Biotechnology of Fujian, Agriculture and Forestry University, Fuzhou, China. Authors are grateful to the sugarcane germplasms nursery (Yunnan, China) and the Sugarcane Research Institute (Fujian Agriculture and Forestry University, Fuzhou), China for providing some of the plant materials. Authors are grateful to Erik Hanson at University of Florida for review this manuscript. We are also very thankful to Dr. Per McCord at USDA-ARS Sugarcane Field Station for reviewing this manuscript and providing some plant materials.
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Liu, H., Yang, X., You, Q. et al. Pedigree, marker recruitment, and genetic diversity of modern sugarcane cultivars in China and the United States. Euphytica 214, 48 (2018). https://doi.org/10.1007/s10681-018-2127-1
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DOI: https://doi.org/10.1007/s10681-018-2127-1