[go: up one dir, main page]
More Web Proxy on the site http://driver.im/ Skip to main content
Springer Nature Link
Log in

A high-density genetic linkage map of bronze loquat based on SSR and RAPD markers

  • Original Article
  • Published:
Tree Genetics & Genomes Aims and scope Submit manuscript

Abstract

We constructed a high-density genetic linkage map of bronze loquat (Eriobotrya deflexa) by using a three-way cross of loquat (Eriobotrya japonica) × (loquat × bronze loquat) and simple sequence repeat (SSR) and random amplified polymorphic DNA (RAPD) markers. The positions of the SSR loci used in this study were previously identified on reference maps of pears (Pyrus spp.) and apples (Malus spp.). The map of bronze loquat (‘Taiwan loquat No. 1’) consisted of 308 loci including 167 SSRs (8 loquat, 57 pear, and 102 apple SSRs), 140 RAPDs, and the loquat canker resistance gene Pse-a on 19 linkage groups covering a genetic distance of 1036 cM. Almost all loquat linkage groups were aligned to the pear consensus map by using at least two pear or apple SSRs, suggesting that positions and linkages of SSR loci were well conserved between loquat and pear and between loquat and apple. The constructed map may be used to determine the location of genes and quantitative trait loci of interest and to analyze genome synteny in the tribe Pyreae, subfamily Spiraeoideae of the family Rosaceae.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
£29.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price includes VAT (United Kingdom)

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1

Similar content being viewed by others

References

  • Antanaviciute L, Fernández-Fernández F, Jansen J, Banchi E, Evans KM, Viola R, Velasco R, Dunwell JM, Troggio M, Sargent DJ (2012) Development of a dense SNP-based linkage map of an apple rootstock progeny using the Malus Infinium whole genome genotyping array. BMC Genet 13:203

    Article  CAS  Google Scholar 

  • Caballero P, Fernandez MA (2003) Loquat, production and market. In: Llacer G, Badenes ML (eds) First international symposium on loquat. CIHEAM, Zaragoza, pp. 11–20

    Google Scholar 

  • Campbell CS, Evans RC, Morgan DR, Dickinson TA, Arsenault MP (2007) Phylogeny of subtribe (formerly the Maloideae, Rosaceae): limited resolution of a complex evolutionary history. Plant Syst Evol 266:119–145

    Article  CAS  Google Scholar 

  • Celton JM, Tustin DS, Chagné D, Gardiner SE (2009) Construction of a dense genetic linkage map for apple rootstocks using SSRs developed from Malus ESTs and Pyrus genomic sequences. Tree Genet Genomes 5:93–107

    Article  Google Scholar 

  • Chagné D, Crowhurst RN, Troggio M, Davey MW, Gilmore B, Lawley C, Vanderzande S, Hellens RP, Kumar S, Cestaro A, Velasco R, Main D, Rees JD, Iezzoni A, Mockler T, Wilhelm L, Van de Weg E, Gardiner SE, Bassil N, Peace C (2012) Genome-wide SNP detection, validation, and development of an 8K SNP array for apple. PLoS One 7:e31745

    Article  PubMed  PubMed Central  Google Scholar 

  • Dickson EE, Arumuganathan K, Kresovich S, Doyle JJ (1992) Nuclear DNA content variation within the Rosaceae. Am J Bot 79:1081–1086

    Article  Google Scholar 

  • Doyle JJ, Doyle JL (1987) A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull 19:11–15

    Google Scholar 

  • Evans RC, Campbell CS (2002) The origin of the apple subfamily (Maloideae; Rosaceae) is clarified by DNA sequence data from duplicated GBSSI genes. Am J Bot 89:1478–1484

    Article  CAS  PubMed  Google Scholar 

  • Fernandez-Fernandez F, Harvey NG, James CM (2006) Isolation and characterization of polymorphic microsatellite markers from European pear (Pyrus communis L.). Mol Ecol Notes 6:1039–1041

    Article  CAS  Google Scholar 

  • Fernandez-Fernandez F, Evans KM, Clarke JB, Govan CL, James CM, Maric S, Tobutt KR (2008) Development of an STS map of an interspecific progeny of Malus. Tree Genet Genomes 4:469–479

    Article  Google Scholar 

  • Fukuda S, Nishitani C, Hiehata N, Tominaga Y, Nesumi H, Yamamoto T (2013) Genetic diversity of loquat accessions in Japan as assessed by SSR markers. J Jpn Soc Hortic Sci 82:131–137

    Article  Google Scholar 

  • Fukuda S, Ishimoto K, Sato S, Terakami S, Yamamoto T, Hiehata N (2014) Genetic mapping of the loquat canker resistance locus in bronze loquat (Eriobotrya deflexa). Tree Genet Genomes 10:875–883

    Article  Google Scholar 

  • Gisbert AD, Lopez-Capuz I, Soriano JM, Llacer G, Romero C, Badenes ML (2009a) Development of microsatellite markers from loquat, Eriobotrya japonica (Thunb.) Lindl. Mol Ecol Res 9:803–805

    Article  CAS  Google Scholar 

  • Gisbert AD, Martınez-Calvo J, Llacer G, Badenes ML, Romero C (2009b) Development of two loquat [Eriobotrya japonica (Thunb.) Lindl.] linkage maps based on AFLPs and SSR markers from different Rosaceae species. Mol Breed 23:523–538

    Article  CAS  Google Scholar 

  • Gisbert AD, Romero C, Martınez-Calvo J, Leida C, Llacer G, Badenes ML (2009c) Genetic diversity evaluation of a loquat (Eriobotrya japonica (Thunb) Lindl) germplasm collection by SSRs and S-allele fragments. Euphytica 168:121–134

    Article  CAS  Google Scholar 

  • Guilford P, Prakash S, Zhu JM, Rikkerink E, Gardiner S, Bassett H, Forster R (1997) Microsatellites in Malus × domestica (apple): abundance, polymorphism and cultivar identification. Theor Appl Genet 94:249–254

    Article  CAS  Google Scholar 

  • He Q, Li XW, Lian GL, Guo QG, Yuan WM, Zhou GZ, Chen KS, van de Weg E, Gao ZS (2011) Genetic diversity and identity of Chinese loquat cultivars/accessions (Eriobotrya japonica) using apple SSR markers. Plant Mol Biol Report 29:197–208

    Article  Google Scholar 

  • Inoue E, Matsuki Y, Anzai H, Evans K (2007) Isolation and characterization of microsatellite markers in Japanese pear (Pyrus pyrifolia Nakai). Mol Ecol Notes 7:445–447

    Article  CAS  Google Scholar 

  • Ishimoto K, Fukuda S, Nakayama H, Hiehata N (2014) Identification of new self-incompatibility alleles (S-RNases) and molecular S-genotyping of genetic resources in loquat [Eriobotrya japonica (Thunb.) Lindl.]. Hort Res (Japan) 13:11–17

    Article  CAS  Google Scholar 

  • Kovanda M (1965) On the generic concepts in the Maloideae. Preslia (Praha) 37:27–34

    Google Scholar 

  • Liebhard R, Gianfranceschi L, Koller B, Ryder CD, Tarchini R, van de Weg E, Gessler C (2002) Development and characterization of 140 new microsatellites in apple (Malus × domestica Borkh.) genome. Mol Breed 10:217–241

    Article  CAS  Google Scholar 

  • Liebhard R, Koller B, Gianfranceschi L, Gessler C (2003) Creating a saturated reference map for the apple (Malus × domestica Borkh.) genome. Theor Appl Genet 106:1497–1508

    CAS  PubMed  Google Scholar 

  • Lin S, Sharpe RH, Janick J (1999) Loquat: botany and horticulture. Hortic Rev 23:233–276

    Google Scholar 

  • Luby JJ, Shaw DV (2001) Does marker-assisted selection make dollars and sense in a fruit breeding program? Hortscience 36:872–879

    Google Scholar 

  • Moriya S, Iwanami H, Kotoda N, Haji T, Okada K, Terakami S, Mimida N, Yamamoto T, Abe K (2012) Aligned genetic linkage maps of apple rootstock cultivar ‘JM7’ and Malus sieboldii ‘Sanashi 63’ constructed with novel EST-SSRs. Tree Genet Genomes 8:709–723

    Article  Google Scholar 

  • Nishitani C, Terakami S, Sawamura Y, Takada N, Yamamoto T (2009) Development of novel EST-SSR markers derived from Japanese pear (Pyrus pyrifolia). Breed Sci 59:391–400

    Article  CAS  Google Scholar 

  • Potter D, Eriksson T, Evans RC, Oh S, Smedmark JEE, Morgan DR, Kerr M, Robertson KR, Arsenault M, Dickinson TA, Campbell CS (2007) Phylogeny and classification of Rosaceae. Plant Syst Evol 266:5–43

    Article  Google Scholar 

  • Sax K (1931) The origins and relationships of the Pomoideae. J Arnold Arbor 12:3–22

    Google Scholar 

  • Sax K (1932) Chromosome relationships in the Pomoideae. J Arnold Arbor 13:363–367

    Google Scholar 

  • Silfverberg-Dilworth E, Matasci CL, van de Weg WE, van Kaauwen MPW, Walser M, Kodde LP, Soglio V, Gianfranceschi L, Durel CE, Costa F, Yamamoto T, Koller B, Gessler C, Patocchi A (2006) Microsatellite markers spanning the apple (Malus × domestica Borkh.) genome. Tree Genet Genomes 2:202–224

    Article  Google Scholar 

  • Soriano JM, Romero C, Vilanova S, Llacer G, Badenes ML (2005) Genetic diversity of loquat germplasm (Eriobotrya japonica (Thunb.) Lindl.) assessed by SSR markers. Genome 48:108–114

    Article  CAS  PubMed  Google Scholar 

  • Terakami S, Adachi Y, Iketani H, Sato Y, Sawamura Y, Takada N, Nishitani C, Yamamoto T (2007) Genetic mapping of genes for susceptibility to black spot disease in Japanese pears. Genome 50:735–741

    Article  CAS  PubMed  Google Scholar 

  • Terakami S, Kimura T, Nishitani C, Sawamura Y, Saito T, Hirabayashi T, Yamamoto T (2009) Genetic linkage map of the Japanese pear ‘Housui’ identifying three homozygous genomic regions. J Jpn Soc Hortic Sci 78:417–424

    Article  CAS  Google Scholar 

  • Van Ooijen JW (2006) JoinMap 4, software for the calculation of genetic linkage maps in experimental populations. Kyazma BV, Wageningen

    Google Scholar 

  • Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D, Salvi S, Pindo M, Baldi P, Castelletti S, Cavaiuolo M, Coppola G, Costa F, Cova V, Dal Ri A, Goremykin V, Komjanc M, Longhi S, Magnago P, Malacarne G, Malnoy M, Micheletti D, Moretto M, Perazzolli M, Si-Ammour A, Vezzulli S, Zini E, Eldredge G, Fitzgerald LM, Gutin N, Lanchbury J, Macalma T, Mitchell JT, Reid J, Wardell B, Kodira C, Chen Z, Desany B, Niazi F, Palmer M, Koepke T, Jiwan D, Schaeffer S, Krishnan V, Wu C, Chu VT, King ST, Vick J, Tao Q, Mraz A, Stormo A, Stormo K, Bogden R, Ederle D, Stella A, Vecchietti A, Kater MM, Masiero S, Lasserre P, Lespinasse Y, Allan AC, Bus V, Chagné D, Crowhurst RN, Gleave AP, Lavezzo E, Fawcett JA, Proost S, Rouzé P, Sterck L, Toppo S, Lazzari B, Hellens RP, Durel CE, Gutin A, Bumgarner RE, Gardiner SE, Skolnick M, Egholm M, Van de Peer Y, Salamini F, Viola R (2010) The genome of the domesticated apple (Malus × domestica Borkh.). Nat Genet 42:833–839

    Article  CAS  PubMed  Google Scholar 

  • Voorrips RE (2002) MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered 93:77–78

    Article  CAS  PubMed  Google Scholar 

  • Watanabe M, Yamamoto T, Ohara M, Nishitani C, Yahata S (2008) Cultivar differentiation identified by SSR markers and the application for polyploid loquat plants. J Jpn Soc Hortic Sci 77:388–394

    Article  CAS  Google Scholar 

  • Yang XH, Glakpe K, Lin SQ, YL H, He YH, Nguyen TCN, Liu YX, GB H, Liu CM (2005) Taxa of plants of genus Eriobotrya around the world and native to Southeastern Asia. J Fruit Sci 22:55–59

    CAS  Google Scholar 

  • Yamamoto T, Kimura T, Shoda M, Ban Y, Hayashi T, Matsuta N (2002a) Development of microsatellite markers in the Japanese pear (Pyrus pyrifolia Nakai). Mol Ecol Notes 2:14–16

    Article  CAS  Google Scholar 

  • Yamamoto T, Kimura T, Shoda M, Imai T, Saito T, Sawamura Y, Kotobuki K, Hayashi T, Matsuta N (2002b) Genetic linkage maps constructed by using an interspecific cross between Japanese and European pears. Theor Appl Genet 106:9–18

    CAS  PubMed  Google Scholar 

  • Yamamoto T, Kimura T, Saito T, Kotobuki K, Matsuta N, Liebhard R, Gessler C, Van de Weg WE, Hayashi T (2004) Genetic linkage maps of Japanese and European pears aligned to the apple consensus map. Acta Hortic 663:51–56

    Article  CAS  Google Scholar 

  • Yamamoto T, Kimura T, Terakami S, Nishitani C, Sawamura Y, Saito T, Kotobuki K, Hayashi T (2007) Integrated reference genetic linkage maps of pear based on SSR and AFLP markers. Breed Sci 57:321–329

    Article  CAS  Google Scholar 

  • Yamamoto T, Terakami S, Moriya S, Hosaka F, Kurita K, Kanamori H, Katayose Y, Saito T, Nishitani C (2013) DNA markers developed from genome sequencing analysis in Japanese pear (Pyrus pyrifolia). Acta Hortic 976:477–483

    Article  Google Scholar 

  • Yamamoto T, Terakami S, Takada N, Nishio S, Onoue N, Nishitani C, Kunihisa M, Inoue E, Iwata H, Hayashi H, Itai A, Saito T (2014) Identification of QTLs controlling harvest time and fruit skin color in Japanese pear (Pyrus pyrifolia Nakai). Breed Sci 64:351–361

    Article  PubMed  PubMed Central  Google Scholar 

Download references

Acknowledgments

We thank Ms. R. Maemoto and S. Anzai for their technical help. This work was partially supported by a grant from the Ministry of Agriculture, Forestry and Fisheries of Japan (Development of mitigation and adaptation techniques to global warming in the sectors of agriculture, forestry, and fisheries, C-3-2060).

Author information

Author notes

  1. Shinji Fukuda

    Present address: Center for Education and Research in Agricultural Innovation, Saga University, Saga, 849-0903, Japan

  2. Naofumi Hiehata

    Present address: Ken’ou Development Bureau, Nagasaki Prefectural Government, Isahaya, Nagasaki, 854-0071, Japan

Authors and Affiliations

  1. Agriculture and Forestry Technical Development Center, Nagasaki Prefectural Government, Omura, Nagasaki, 856-0021, Japan

    Shinji Fukuda, Keiichiro Ishimoto & Naofumi Hiehata

  2. Kazusa DNA Research Institute, Kisarazu, Chiba, 292-0818, Japan

    Shusei Sato

  3. NARO Institute of Fruit Tree Science, Tsukuba, Ibaraki, 305-8605, Japan

    Shingo Terakami & Toshiya Yamamoto

Authors
  1. Shinji Fukuda
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Keiichiro Ishimoto
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Shusei Sato
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shingo Terakami
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Naofumi Hiehata
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Toshiya Yamamoto
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Toshiya Yamamoto.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Data archiving statement

A genetic linkage map of bronze loquat will be submitted to the genome database for Rosaceae (www.rosaceae.org) after the final acceptance.

Additional information

Communicated by Y. Tsumura

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Fukuda, S., Ishimoto, K., Sato, S. et al. A high-density genetic linkage map of bronze loquat based on SSR and RAPD markers. Tree Genetics & Genomes 12, 80 (2016). https://doi.org/10.1007/s11295-016-1040-9

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s11295-016-1040-9

Keywords

Search

Navigation