Abstract
Jute, including white and dark jute, is an agroeconomically important fiber crop worldwide. However, no practical information is available for expressed sequence tag-derived InDel (insertion and deletion) in jute to date. Previously, we de novo assembled 48,914 unigenes from white jute. In this study, 4815 InDels were called from these unigenes. The size <5 bp was the most abundant types (69.88%), and the AG-rich nucleotide InDels were the predominant. Subsequently, a sample of 173 InDels (TFCcID), located in genes encoding transcription factors, were selected to survey polymorphisms among 24 diverse accessions derived from a panel of 159 jute germplasm. Of these, 119(68.8%) successfully amplified and detected polymorphism, indicating that these InDels are of good quality. The 119 polymorphic InDels were successfully mapped to the existing contigs of jute variety CVL-1. Single marker analysis of these polymorphic TFCcIDs was conducted to associate specific markers to cellulose content of bast fiber. Five markers from TFCcIDs were identified to be significantly correlated to cellulose content of bast fiber. To our knowledge, it is the first successful development of InDel markers on a large scale in jute, which will accelerate related researches on genetic map construction and marker assisted selection of bast fiber quality.
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Acknowledgements
This work was supported by the National Natural Science Foundation of China (31771369), http://www.nsfc.gov.cn/; Foreign Cooperation Project of Science and Technology Department in Fujian, China (2015I0001), http://xmgl.fjkjt.gov.cn/; Distinguished Young Research Fund in Fujian Agriculture and Forestry University (xjq201401); National Agri-Industry Technology Research System for Crops of Bast and Leaf Fiber, China (nycytx-19-E06), http://119.253.58.231/; Experiment Station of Jute and Kenaf in Southeast China (Nongkejiaofa 2011); Construction of Germplasm Resources Platform of Bast Fiber Crops in Fujian, China (2010 N2002), http://xmgl.fjkjt.gov.cn/.
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Supervised and designed the experiments: L. Z. Performed the experiments: Z. G. and L. Z. Analyzed the data: Z. G. and L. Z. Contributed reagents/materials/analysis tools: Z. G., L. Z., and P. F. Developed the materials: P. F. and J.Q. Wrote the manuscript: L. Z. All authors reviewed the manuscript.
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Communicated by: Hongwei Cai
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Zhang, L., Gao, Z., Wan, X. et al. Development of Novel Small InDel Markers in Jute (Corchorus spp.). Tropical Plant Biol. 10, 169–176 (2017). https://doi.org/10.1007/s12042-017-9193-8
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DOI: https://doi.org/10.1007/s12042-017-9193-8