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Tree Genetics & Genomes

, 14:79 | Cite as

High-density genetic map of Populus deltoides constructed by using specific length amplified fragment sequencing

  • Lecheng Fang
  • Hailin Liu
  • Suyun Wei
  • Ken Keefover-Ring
  • Tongming Yin
Original Article
  • 90 Downloads
Part of the following topical collections:
  1. Genome Biology

Abstract

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.

Keywords

Populus deltoides Specific length amplified fragment sequencing Single nucleotide polymorphism Linkage map 

Notes

Data archiving statement

The raw data of SLAF-seq have been submitted to NCBI SRA database under the BioProject ID number PRJNA432808.

Funding information

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.

Supplementary material

11295_2018_1290_MOESM1_ESM.pdf (21.5 mb)
Supplementary Figure S1 Genetic map of Populus deltoides. (PDF 21984 kb)
11295_2018_1290_MOESM2_ESM.pdf (6.9 mb)
Supplementary Figure S2 Haplotype map for each LG by each individual. Different individuals in rows were spaced by blank line, markers on the right were listed coordinate to the order in the linkage map. The swift of green and blue colors indicates the recombination events. The grey color represents missing marker. (PDF 7068 kb)
11295_2018_1290_MOESM3_ESM.pdf (12.2 mb)
Supplementary Figure S3 Heat map of each LG by pair-wise markers. Each cell represents the recombination rate of pair-wise markers. Yellow color indicates strong linkage, and changes of colors from yellow to purple indicating weaker linkage. (PDF 12537 kb)
11295_2018_1290_MOESM4_ESM.xlsx (3.8 mb)
Supplementary Table S1 The genotypes of the mapped SLAF markers. Note: ab×cd means both alleles are heterozygous in each parent, and 4 alleles are observed. Genotypes of ac, ad, bc, and bd are produced in the progeny; ef×eg means both alleles are heterozygous in each parent, and the alternate parents share the common “e” alleles. Genotypes of ef, eg, ee, fg are produced in the progeny; hk×hk means the alternate parents have the same heterozygous genotype, and both the “h” and “k” are intercross alleles; nn×np means the maternal parent are homozygous, and the paternal parent are heterozygous. Only the “p” allele from the paternal parent segregates in the progeny, and genotypes of nn, np are produced in the offsprings; lm×ll means the paternal parent are homozygous, and the maternal parent are heterozygous. Only the “m” allele from the maternal parent segregates in the progeny, and genotypes of ll, lm are produced in the offsprings. (XLSX 3870 kb)
11295_2018_1290_MOESM5_ESM.xlsx (263 kb)
Supplementary Table S2 The map text file for each linkage group of the consensus map. (XLSX 262 kb)
11295_2018_1290_MOESM6_ESM.xlsx (17.5 mb)
Supplementary Table S3 The sequence of each mapped SLAF marker. (XLSX 17894 kb)
11295_2018_1290_MOESM7_ESM.xlsx (12 kb)
Supplementary Table S4 Basic information for the sex-specific maps. (XLSX 12 kb)
11295_2018_1290_MOESM8_ESM.xlsx (430 kb)
Supplementary Table S5 The detail information of BLAST alignment between the genetic markers of P. deltoides and the genome sequence of P. trichocarpa. (XLSX 430 kb)

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Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2018

Authors and Affiliations

  • Lecheng Fang
    • 1
  • Hailin Liu
    • 1
  • Suyun Wei
    • 1
  • Ken Keefover-Ring
    • 2
  • Tongming Yin
    • 1
  1. 1.The Southern Modern Forestry Collaborative Innovation Center, College of ForestryNanjing Forestry UniversityNanjingChina
  2. 2.Departments of Botany and GeographyUniversity of Wisconsin – MadisonMadisonUSA

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