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Identification of quantitative trait loci controlling sucrose content based on an enriched genetic linkage map of sugarcane (Saccharum spp. hybrids) cultivar ‘LCP 85-384’

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Abstract

Sucrose content is one of the most important traits considered in sugarcane breeding. Since sugarcane cultivars possess >100 chromosomes (2n = 100–130) and are genetically complex polyploid and aneuploids, identification of quantitative trait loci (QTLs) associated with sucrose content is considered the best option to improve sucrose content through molecular breeding. A preliminary genetic linkage map of Louisiana sugarcane cultivar ‘LCP 85-384’ from a previous study was enriched using 65 additional polymorphism simple-sequence-repeats (SSR) primer-pairs to identify more co-segregated and homologous groups (CGs and HGs) and QTLs controlling sucrose content. Eighty-four SSR primer-pairs produced 456 markers, of which 441 were polymorphic. Both simplex (993) and duplex (225) amplified fragment length polymorphism (AFLP) and target region amplification polymorphism (TRAP) markers reported previously were also included to construct the LCP 85-384 map. These simplex and duplex markers were assigned to 108 CGs successfully using JoinMap®. This map had a cumulative genome length of 7406.3 cM that included 675 AFLP (69.8 %), 90 TRAP (9.3 %), and 202 SSR (20.9 %) markers. The 202 SSR markers were assigned to 65 CGs and 8 HGs. Based on this map, 24 putative QTLs affecting sucrose content were identified. Five QTLs were unlinked and the other 19 QTLs were located on nine CGs within four HGs. Of these QTLs, 11 had an effect in both plant-cane (20.33 %) and first-stubble (25.68 %) crops. A higher efficiency of QTLs’ identification with AFLP, TRAP and SSR markers in such a genetically complex crop, proposes its wider utility in molecular breeding in sugarcane.

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Acknowledgments

AFLP and TRAP marker data were kindly provided by Collins Kimbeng and Suman Andru. This research was partially funded by grower/processor check-off funds administrated by the American Sugar Cane League of the USA., Inc., Thibodaux, Louisiana, USA. Greenhouse and field technical supports were provided by Jennifer Chiasson, Elta Duet, Brian Duet, Cory Landry, Lionel Lomax, Jeri Maggio, Norris Matherne, Eric Petrie, Clinton Randall, Randy Richard, David Verdun, and Kathy Warnke. SSR-PCR and ABI3730XL-based fragment analysis were conducted by Sheron Simpson at the USDA-ARS, MSA Genomics Laboratory directed by Brian Scheffler. Amaresh Chandra gratefully acknowledges Department of Biotechnology, Government of India for DBT-CREST Fellowship Award.

Authors’ contributions

YBP conceived, designed and directed the study. PL, YQ and YBP collected SSR marker data. PL analyzed the molecular and phenotypic data, constructed the genetic and QTL map, and drafted the manuscript. AC performed phenotypic data analysis, interpreted the data, and participated in manuscript preparation. PHC, MPG, CDD, TLT, WHW, and YBP conducted field trials and collected phenotypic data. PL, AC, YQ, MPG, and YBP participated in manuscript preparation. All authors have read and approved the final manuscript.

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    Authors and Affiliations

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

      Pingwu Liu, Amaresh Chandra, Michael P. Grisham, William H. White, Caleb D. Dalley, Thomas L. Tew & Yong-Bao Pan

    2. State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Collaborative Innovation Center of Sugar Industry in Guangxi, Guangxi University, Nanning, 530004, China

      Pingwu Liu

    3. ICAR-Indian Institute of Sugarcane Research, Lucknow, 226002, India

      Amaresh Chandra

    4. Key Lab of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China

      Youxiong Que & Ping-Hua Chen

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    Pingwu Liu and Amaresh Chandra have contributed equally to this work.

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    Liu, P., Chandra, A., Que, Y. et al. Identification of quantitative trait loci controlling sucrose content based on an enriched genetic linkage map of sugarcane (Saccharum spp. hybrids) cultivar ‘LCP 85-384’. Euphytica 207, 527–549 (2016). https://doi.org/10.1007/s10681-015-1538-5

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