Construction of a linkage map based on retrotransposon insertion polymorphisms in sweetpotato via high-throughput sequencing

Sweetpotato (Ipomoea batatas L.) is an outcrossing hexaploid species with a large number of chromosomes (2n = 6x = 90). Although sweetpotato is one of the world’s most important crops, genetic analysis of the species has been hindered by its genetic complexity combined with the lack of a whole genome sequence. In the present study, we constructed a genetic linkage map based on retrotransposon insertion polymorphisms using a mapping population derived from a cross between ‘Purple Sweet Lord’ (PSL) and ‘90IDN-47’ cultivars. High-throughput sequencing and subsequent data analyses identified many Rtsp-1 retrotransposon insertion sites, and their allele dosages (simplex, duplex, triplex, or double-simplex) were determined based on segregation ratios in the mapping population. Using a pseudo-testcross strategy, 43 and 47 linkage groups were generated for PSL and 90IDN-47, respectively. Interestingly, most of these insertions (~90%) were present in a simplex manner, indicating their utility for linkage map construction in polyploid species. Additionally, our approach led to savings of time and labor for genotyping. Although the number of markers herein was insufficient for map-based cloning, our trial analysis exhibited the utility of retrotransposon-based markers for linkage map construction in sweetpotato.

[1]  A. Flavell,et al.  Ty1-copia retrotransposon-based SSAP marker development in cashew (Anacardium occidentale L.) , 2005, Theoretical and Applied Genetics.

[2]  Jinfeng Chen,et al.  Ty1-copia retrotransposon-based SSAP marker development and its potential in the genetic study of cucurbits. , 2007, Genome.

[3]  M. Grandbastien,et al.  Mobilization of retrotransposons in synthetic allotetraploid tobacco. , 2010, The New phytologist.

[4]  M. L. Magoon,et al.  Cytological evidence on the origin of sweet potato , 2004, Theoretical and Applied Genetics.

[5]  J. V. Moran,et al.  Dynamic interactions between transposable elements and their hosts , 2011, Nature Reviews Genetics.

[6]  A. Flavell,et al.  The application of LTR retrotransposons as molecular markers in plants. , 2012, Methods in molecular biology.

[7]  H. Zhai,et al.  Construction of Molecular Linkage Maps Using SRAP Markers in Sweetpotato , 2010 .

[8]  Cédric Feschotte,et al.  Plant transposable elements: where genetics meets genomics , 2002, Nature Reviews Genetics.

[9]  K. Ikeo,et al.  Efficient screening of long terminal repeat retrotransposons that show high insertion polymorphism via high-throughput sequencing of the primer binding site. , 2014, Genome.

[10]  S. Sinha,et al.  Taxonomic Significance of Karyomorphology in Ipomoea spp. , 1992 .

[11]  A. Dmitriev,et al.  The FaRE1 LTR-retrotransposon Based SSAP Markers Reveal Genetic Polymorphism of Strawberry (Fragaria x ananassa) Cultivars , 2012 .

[12]  M. Tanaka,et al.  Isolation of an active element from a high-copy-number family of retrotransposons in the sweetpotato genome , 2004, Molecular Genetics and Genomics.

[13]  W. J. Kent,et al.  BLAT--the BLAST-like alignment tool. , 2002, Genome research.

[14]  R. Kalendar.  The use of retrotransposon-based molecular markers to analyze genetic diversity , 2011 .

[15]  R. Sederoff,et al.  Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. , 1994, Genetics.

[16]  I. Shiotani,et al.  Genomic Structure of the Sweet Potato and Hexaploids in Ipomoea trifida (H.B.K.) DON. , 1989 .

[17]  K. McLean,et al.  Genetic distribution of Bare–1-like retrotransposable elements in the barley genome revealed by sequence-specific amplification polymorphisms (S-SAP) , 1997, Molecular and General Genetics MGG.

[18]  A. Flavell,et al.  Analysis of plant diversity with retrotransposon-based molecular markers , 2011, Heredity.

[19]  H. Hirochika,et al.  Applications of retrotransposons as genetic tools in plant biology. , 2001, Trends in plant science.

[20]  J. Valkonen,et al.  Advances in plant gene-targeted and functional markers: a review , 2013, Plant Methods.

[21]  Rodrigo Lopez,et al.  Clustal W and Clustal X version 2.0 , 2007, Bioinform..

[22]  M. Pavelek,et al.  Genetic diversity of cultivated flax (Linum usitatissimum L.) germplasm assessed by retrotransposon-based markers , 2011, Theoretical and Applied Genetics.

[23]  L. Shuzhen,et al.  Establishment of molecular linkage maps using SRAP markers in sweet potato. , 2010 .

[24]  M. Tahara,et al.  Characterization of a novel retrotransposon TriRe‒1 using nullisomic-tetrasomic lines of hexaploid wheat , 2014 .

[25]  N. Goncharov,et al.  Molecular markers based on LTR retrotransposons BARE-1 and Jeli uncover different strata of evolutionary relationships in diploid wheats , 2010, Molecular Genetics and Genomics.

[26]  A. Kriegner,et al.  A genetic linkage map of sweetpotato [Ipomoea batatas (L.) Lam.] based on AFLP markers , 2003, Molecular Breeding.

[27]  L. Brodsky,et al.  Transposable elements in a marginal plant population: temporal fluctuations provide new insights into genome evolution of wild diploid wheat , 2010, Mobile DNA.

[28]  A. Schulman,et al.  IRAP and REMAP: two new retrotransposon-based DNA fingerprinting techniques , 1999, Theoretical and Applied Genetics.

[29]  Kittipat Ukoskit,et al.  Autopolyploidy versus Allopolyploidy and Low-density Randomly Amplified Polymorphic DNA Linkage Maps of Sweetpotato , 1997 .

[30]  A. Jones.  Theoretical Segregation Ratios of Qualitatively Inherited Characters for Hexaploid Sweetpotato (Ipomoea batatas L.) , 1967 .

[31]  Y. Ting,et al.  MEIOTIC STUDIES IN THE SWEET POTATO (Ipomoea batatas Lam.) , 1953 .

[32]  J. C. Cervantes-Flores,et al.  Development of a genetic linkage map and identification of homologous linkage groups in sweetpotato using multiple-dose AFLP markers , 2008, Molecular Breeding.

[33]  M. Tahara,et al.  Efficient DNA Fingerprinting Based on the Targeted Sequencing of Active Retrotransposon Insertion Sites Using a Bench-Top High-Throughput Sequencing Platform , 2014, DNA research : an international journal for rapid publication of reports on genes and genomes.

[34]  A. Schulman,et al.  TRIM retrotransposons occur in apple and are polymorphic between varieties but not sports , 2006, Theoretical and Applied Genetics.

[35]  A genetic linkage map based on AFLP and SSR markers and mapping of QTL for dry-matter content in sweetpotato , 2013, Molecular Breeding.

[36]  Retrotransposon Insertional Polymorphism in Iranian Bread Wheat Cultivars and Breeding Lines Revealed by IRAP and REMAP Markers , 2013, Biochemical Genetics.