High-density genetic map of Populus deltoides constructed by using specific length amplified fragment sequencing
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Populus deltoides is an important industrial tree species widely planted in many areas of the world, and de novo genome sequencing of this plant has been carried out by several research groups. A dense genetic map associating genome sequences is highly desirable for reconstructing the chromosome pseudomolecules using the obtained sequence scaffold assemblies. For this purpose, an intraspecific full-sib F1 mapping pedigree was established by using the sequenced P. deltoides as the maternal parent. With this mapping pedigree, we constructed a high-density genetic map using 92 randomly selected progenies. Single nucleotide polymorphism (SNP) markers were discovered by using specific length amplified fragment sequencing (SLAF-seq). In total, 487,038 SLAFs were generated, of which 179,360 were polymorphic. A high-density genetic map was built using HighMap software, which included 11,680 Mendelian segregation markers distributing in 2851 marker bins. The established map consisted of 19 linkage groups (LGs) that equaled to the 19 haploid chromosomes in poplar genome, and spanned a total genetic length of 3494.66 cM, with an average distance of 1.23 cM per marker bin. The map presented here will be useful for anchoring the genome sequence assemblies along chromosomes, and for many other aspects of genetic studies on P. deltoides and the closely related species.
KeywordsPopulus deltoides Specific length amplified fragment sequencing Single nucleotide polymorphism Linkage map
Data archiving statement
The raw data of SLAF-seq have been submitted to NCBI SRA database under the BioProject ID number PRJNA432808.
The work is supported by the National Key Research and Development Plan of China (2016YFD0600101) and the National Natural Science Foundation of China (31500533 and 31570662). It was also made possible by research funded by the Doctorate Fellowship Foundation and the PAPD (Priority Academic Program Development) program at Nanjing Forestry University and the Doctorate Fellowship Foundation of Nanjing Forestry University.
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