Linkage mapping of quantitative trait loci for fiber yield and its related traits in the population derived from cultivated ramie and wild B. nivea var. tenacissima

Gorshkova, T. et al. Plant Fiber Formation: State of the Art, Recent and Expected Progress, and Open Questions. Critical Reviews in Plant Sciences 31, 201–228 (2012).

Liao, L. et al. The domestication and dispersal of the cultivated ramie (Boehmeria nivea (L.) Gaud. in Freyc.) determined by nuclear SSR marker analysis. Genet. Resour. Crop Evol. 61, 55–67 (2014).

Aldaba, V. C. The structure and development of the cell wall in plants I. Bast fibers of Boehmeria and Linum. Amer. J. Bot. 14, 16–22 (1927).

Chen, J., Liu, F., Tang, Y., Yuan, Y. & Guo, Q. Transcriptome sequencing and profiling of expressed genes in phloem and xylem of ramie (Boehmeria nivea L. Gaud). PLoS ONE 9(10), e110623 (2014).

Chen, J. et al. Transcriptome profiling using pyrosequencing shows genes associated with bast fiber development in ramie (Boehmeria nivea L.). BMC Genomics 15, 919 (2014).

Liu, C. et al. QTL analysis of four main stem bark traits using a GBS-SNP-based high-density genetic map in ramie. Scientific Reports 7, 13458 (2017).

Liu, T., Zhu, S., Tang, Q. & Tang, S. QTL mapping for fiber yield-related traits by constructing the first genetic linkage map in ramie (Boehmeria nivea L. Gaud). Mol. Breeding 34, 883–892 (2014).

Liu, T., Tang, S., Zhu, S., Tang, Q. & Zheng, X. Transcriptome comparison reveals the patterns of selection in domesticated and wild ramie (Boehmeria nivea L. Gaud). Plant Mol. Biol. 86, 85–92 (2014).

Jiang, Y. & Jie, Y. Advances in research on the genetic relationships of Boehmeria in China. J. Plant Genet. Res. 6, 114–118 (2005).

Wu, Z. Y., Raven, P. H., Hong, D. Y. Flora of China. Volume 5: ulmaceae through Basellaceae. Science Press, Beijing (2003).

Liu, T. et al. Comparison of quantitative trait loci for 1,000-grain weight and spikelets per panicle across three connected rice populations. Euphytica 175, 383–394 (2010).

Liu, T. et al. Comparison of quantitative trait loci for rice yield, panicle length and spikelet density across three connected populations. J. Genet. 90, 377–382 (2011).

Zhong, R. & Ye, Z. Secondary cell walls: biosynthesis, patterned deposition and transcriptional regulation. Plant Cell Physiol. 56(2), 195–214 (2015).

Zhong, R. & Ye, Z. IFL1, a gene regulating interfascicular fiber differentiation in Arabidopsis, encodes a homeodomain-leucine zipper protein. Plant Cell 11, 2139–2152 (1999).

Ranocha, P. et al. Arabidopsis WAT1 is a vacuolar auxin transport facilitator required for auxin homoeostasis. Nat. Commun. 4, 2625 (2013).

Zhang, H., Scheirer, D. C., Fowle, W. H. & Goodman, H. M. Expression of antisense or sense RNA of an ankyrin repeat-containing gene blocks chloroplast differentiation in Arabidopsis. Plant Cell 4, 1575–1588 (1992).

Qi, J. et al. A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity. Nat. Genet. 45, 1510–1515 (2013).

Mao, D. et al. Multiple cold resistance loci confer the high cold tolerance adaptation of Dongxiang wild rice (Oryza rufipogon) to its high-latitude habitat. Theor. Appl. Genet. 128, 1359–1371 (2015).

Lin, T. et al. Genomic analyses provide insights into the history of tomato breeding. Nat. Genet. 46, 1220–1226 (2014).

Luan, M. et al. Draft genome sequence of ramie, Boehmerianivea (L.) Gaudich. Mol. Ecol. Resour. 18, 639–645 (2018).

Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).

Kosambi, D. D. The estimation of map distance from recombination values. Ann Eugenics 12, 172–175 (1943).

Li, H. et al. and 1000 Genome Project Data Processing Subgroup. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).

Zhang, Z., Wei, T., Zhong, Y., Li, X. & Huang, J. Construction of a high-density genetic map of Ziziphus jujube Mill. using genotyping by sequencing technology. Tree Genetics & Genomes 12, 76 (2016).

Zhou, Z. et al. Genetic dissection of maize plant architecture with an ultra-high density bin map based on recombinant inbred lines. BMC Genomics 17, 178 (2016).

van Ooijen, J. W. Multi point maximum likelihood mapping in a full sib family of an out breeding species. Genet. Res. (Camb) 93, 343–349 (2011).

Rastas, P. Lep-MAP3: robust linkage mapping even for low-coverage whole genome sequencing data. Bioinformatics 33, 3726–3732 (2017).

Voorrips, R. MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered. 93, 77–8 (2002).

Wang, S., Basten, C., Zeng, Z. Windows QTL Cartographer 2.5. Department of Statistics, North Carolina State University, Raleigh, NC (2012).

Wen, Y. et al. An efficient multi-locus mixed model framework for the detection of small and linked QTLs in F2. Briefings in Bioinformatics, https://doi.org/10.1093/bib/bby058 (2018)

Wang, S. et al. Mapping small-effect and linked quantitative trait loci for complex traits in backcross or DH populations via a multi-locus GWAS methodology. Sci. Rep. 6, 29951 (2016).

Liu, T. et al. Comparison of quantitative trait loci for 1,000-grain weight and spikelets per panicle across three connected rice populations. Euphytica 175, 383–394 (2010).