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Genetic analysis of the sugarcane (Saccharum spp.) cultivar ‘LCP 85-384’. I. Linkage mapping using AFLP, SSR, and TRAP markers

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Abstract

Sugarcane hybrids are complex aneu-polyploids (2n = 100–130) derived from inter-specific hybridization between ancestral polyploid species, namely S. officinarum L. and S. spontaneum L. Efforts to understand the sugarcane genome have recently been enhanced through the use of new molecular marker technologies. A framework genetic linkage map of Louisiana’s popular cultivar LCP 85-384 was constructed using the selfed progeny and based on polymorphism derived from 64 AFLP, 19 SSR and 12 TRAP primer pairs. Of 1,111 polymorphic markers detected, 773 simplex (segregated in 3:1 ratio) and 182 duplex (segregate in 77:4 ratio) markers were used to construct the map using a LOD value of ≥4.0 and recombination threshold of 0.44. The genetic distances between pairs of markers linked in the coupling phase was computed using the Kosambi mapping function. Of the 955 markers, 718 simplex and 66 duplex markers were assigned to 108 co-segregation groups (CGs) with a cumulative map length of 5,617 cM and a density of 7.16 cM per marker. Fifty-five simplex and 116 duplex markers remained unlinked. With an estimated genome size of 12,313 cM for LCP 85-384, the map covered approximately 45.6% of the genome. Forty-four of the 108 CGs were assigned into 9 homo(eo)logous groups (HGs) based on information from locus-specific SSR and duplex markers, and repulsion phase linkages detected between CGs. Meiotic behavior of chromosomes in cytogenetic studies and repulsion phase linkage analysis between CGs in this study inferred the existence of strong preferential chromosome pairing behavior in LCP 85-384. This framework map marks an important beginning for future mapping of QTLs associated with important agronomic traits in the Louisiana sugarcane breeding programs.

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Acknowledgments

We thank Johan W. Van Ooijen for his kind assistance on how best to use the JoinMap 3.0 software in mapping a polyploid species. We also appreciate Anudeep Paturi, Lionel Lomax, and Jennifer Shaw for their immense help in this project. Financial support from the American Sugar Cane League of the USA, Inc., and the School of Plant, Environmental and Soil Sciences, Louisiana State University are gratefully acknowledged.

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  1. Suman Andru

    Present address: Pioneer Hi-Bred, 7250 NW 62nd Ave, PO Box 552, Johnston, IA, 50131-2935, USA

Authors and Affiliations

  1. School of Plant Environmental and Soil Sciences, Louisiana State University, Baton Rouge, LA, 70803, USA

    Suman Andru

  2. Sugarcane Research Laboratory, USDA-ARS, MSA, Houma, LA, 70360, USA

    Yong-Bao Pan

  3. Center for Agricultural Biotechnology, Kasetsart University, Kamphaengsaen Campus, NakornPathom, 73140, Thailand

    Songkran Thongthawee

  4. USDA-ARS, SPA, Dale Bumpers Small Farms Research Center, Booneville, AR, 72927, USA

    David M. Burner

  5. Sugar Research Station, Louisiana State University Agricultural Center, St Gabriel, LA, 70776, USA

    Collins A. Kimbeng

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  1. Suman Andru
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Correspondence to Collins A. Kimbeng.

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Andru, S., Pan, YB., Thongthawee, S. et al. Genetic analysis of the sugarcane (Saccharum spp.) cultivar ‘LCP 85-384’. I. Linkage mapping using AFLP, SSR, and TRAP markers. Theor Appl Genet 123, 77–93 (2011). https://doi.org/10.1007/s00122-011-1568-x

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