Construction of high-resolution genetic linkage map in pear pseudo-BC1 ((Pyrus pyrifolia × P. communis) × P. pyrifolia) using GBS-SNPs and SSRs

Abe K, Kotobuki K (1998) Inheritance of high resistance to Venturia nashicola Tanaka et Yamamoto in Japanese pear (Pyrus pyrifolia Nakai) and Chinese pear (P. ussuriensis Maxim.). J Jpn Soc Hortic Sci 67:677–680 Abe K, Kotobuki K, Saito T, Terai O (2000) Inheritance of resistance to pear scab from European pears to Asian pears. J Jpn Soc Hortic Sci 69:1–8 Ban SH, Choi C (2018) Development of an apple F1 segregating population genetic linkage map using genotyping-by-sequencing. Plant Breed Biotechnol 6:434–443 Bielenberg DG, Rauh B, Fan S, Gasic K, Abbott AG, Reighard GL, Okie WR, Wells CE (2015) Genotyping by sequencing for SNP-based linkage map construction and QTL analysis of chilling requirement and bloom date in peach [Prunus persica (L.) Batsch]. PLoS ONE 10:e0139406. https://doi.org/10.1371/journal.pone.0139406 Bouquet A (1986) Introduction dans l’espece Vitis vinifera L. d’un caractere de resistance àl’oidium (Uncinula necator Schw. Burr.) issu de l’espèce Muscadinia rotundifolia (Michx.) Small. Vignevini 13:141–146 Chen H, Song Y, Li LT, Khan A, Li XG, Korban SS, Wu J, Zhang SL (2015) Construction of a high-density simple sequence repeat consensus genetic map for pear (Pyrus spp.). Plant Mol Biol Rep 33:316–325 Chevreau E, Leuliette S, Gallet M (1997) Inheritance and linkage of isozyme loci in pear (Pyrus communis L.). Theor Appl Genet 94:498–506 Chung YS, Jun T, Kim C (2017) Digestion efficiency differences of restriction enzymes frequently used for genotyping-by-sequencing technology. Korean J Agric Sci 44:318–323 Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, Handsaker RE, Lunter G, Marth GT et al (2011) The variant call format and VCFtools. Bioinformatics 27:2156–2158 Dettori MT, Quarta R, Verde I (2001) A peach linkage map integrating RFLPs, SSRs, RAPDs, and morphological markers. Genome 44:783–790 Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379. https://doi.org/10.1371/journal.pone.0019379 Flachowsky H, Le Roux PM, Peil A, Patocchi A, Richter K, Hanke MV (2011) Application of a high-speed breeding technology to apple (Malus × domestica) based on transgenic early flowering plants and marker-assisted selection. New Phytol 192:364–377 Gardner KM, Brown P, Cooke TF, Cann S, Costa F, Bustamante C, Velasco R, Troggio M, Myles S (2014) Fast and cost-effective genetic mapping in apple using next-generation sequencing. G3-Genes Genomes Genet 4:1681–1686 Gonai T, Terakami S, Nishitani C, Yamamoto T, Kasumi M (2009) The validity of marker-assisted selection using DNA markers linked to a pear scab resistance gene (Vnk) in two populations. J Jpn Soc Hortic Sci 78:49–54 Grattapaglia D, Sederoff R (1994) Genetic linkage maps of Eucalyptus grandis and Eucalyptus urophylla using a pseudo-testcross: mapping strategy and RAPD markers. Genetics 137:1121–1137 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 Hamblin MT, Rabbi IY (2014) The effects of restriction-enzyme choice on properties of genotyping-by-sequencing libraries: a study in cassava (Manihot esculenta). Crop Sci 54:2603–2608 Han K, Lee HY, Ro NY, Hur OS, Lee JH, Kwon JK, Kang BC (2018) QTL mapping and GWAS reveal candidate genes controlling capsaicinoid content in Capsicum. Plant Biotechnol J 16:1546–1558 Han H, Oh Y, Kim K, Oh S, Cho S, Kim YK, Kim D (2019) Integrated genetic linkage maps for Korean pears (Pyrus hybrid) using GBS-based SNPs and SSRs. Hortic Environ Biotechnol 60:779–786 Huang N, Angeles ER, Domingo J, Magpantay G, Singh S, Zhang G, Kumaravadivel N, Bennett J, Khush GS (1997) Pyramiding of bacterial blight resistance genes in rice: marker-assisted selection using RFLP and PCR. Theor Appl Genet 95:313–320 Hwang K, Oh S, Kim K, Han H, Oh Y, Lim H, Kim YK, Kim D (2019) Genotyping-by-sequencing approaches using optimized two-enzyme combinations in Asian pears (Pyrus spp.). Mol Breed 39:161. https://doi.org/10.1007/s11032-019-1071-7 Iketani H, Abe K, Yamamoto T, Kotobuki K, Sato Y, Saito T, Terai O, Matsuta N, Hayashi T (2001) Mapping of disease-related genes in Japanese pear using a molecular linkage map with RAPD markers. Breed Sci 51:179–184 Kim YK, Kang SS, Won KH, Shin IS, Cho KS, Ma KB, Kim MS, Choi JJ, Choi JH (2016) Breeding of the scab-resistant pear cultivar ‘Greensis’. Korean J Hortic Sci Technol 34:655–661 Kullan ARK, Van Dyk MM, Jones N, Kanzler A, Bayley A, Myburg AA (2012) High-density genetic linkage maps with over 2,400 sequence-anchored DArT markers for genetic dissection in an F2 pseudo-backcross Eucalyptus grandis × E. urophylla. Tree Genet Genomes 8:163–175 Kumar S, Kirk C, Deng CH, Wiedow C, Qin M, Espley R, Wu J, Brewer L (2019) Fine-mapping and validation of the genomic region underpinning pear red skin colour. Hortic Res 6:29. https://doi.org/10.1038/s41438-018-0112-4 Li H, Durbin R (2009) Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics 25:1754–1760 Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup (2009) The sequence alignment/map format and SAMtools. Bioinformatics 25:2078–2079 Li G, Wang Y, Chen MS, Edae E, Poland J, Akhunov E, Chao S, Bai G, Carver BF, Yan L (2015) Precisely mapping a major gene conferring resistance to Hassian fly in bread wheat using genotyping-by-sequencing. BMC Genom 16:108. https://doi.org/10.1186/s12864-015-1297-7 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.). Mol Breed 10:217–241 Liu N, Li M, Hu X, Ma Q, Mu Y, Tan Z, Xia Q, Zhang G, Nian H (2017) Construction of high-density genetic map and QTL mapping of yield-related and two quality traits in soybean RILs population by RAD-sequencing. BMC Genom 18:466. https://doi.org/10.1186/s12864-017-3854-8 Luby JJ, Shaw DV (2001) Does marker-assisted selection make dollars and sense in a fruit breeding program? HortScience 36:872–879 Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10–12 McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S et al (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303 Molnár S, Galbács Z, Halász G, Hoffmann S, Kiss E, Kozma P, Veres A, Galli Z, Szõke A, Heszky L (2007) Marker assisted selection (MAS) for powdery mildew resistance in a grapevine hybrid family. Vitis 46:212–213 Montoya C, Cochard B, Flori A, Cros D, Lopes R, Cuellar T, Espeout S, Syaputra I, Villeneuve P et al (2014) Genetic architecture of palm oil fatty acid composition in cultivated oil palm (Elaeis guineensis Jacq.) compared to its wild relative E. oleifera (H.B.K) cortés. PLoS ONE 9:e95412. https://doi.org/10.1371/journal.pone.0095412 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 Novaes E, Osorio L, Drost DR, Miles BL, Boaventura-Novaes CR, Benedict C (2009) Quantitative genetic analysis of biomass and wood chemistry of Populus under different nitrogen levels. New Phytol 182:878–890 Padmarasu S, Sargent DJ, Jaensch M, Kellerhals M, Tartarini S, Velasco R, Troggio M, Patocchi A (2014) Fine-mapping of the apple scab resistance locus Rvi12 (Vb) derived from ‘Hansen’s baccata #2’. Mol Breed 34:2119–2129 Pauquet J, Bouquet A, This P, Adam-Blondon AF (2001) Establishment of a local map of AFLP markers around the powdery mildew resistance gene Run1 in grapevine and assessment of their usefulness for marker assisted selection. Theor Appl Genet 103:1201–1210 Pieratoni L, Dondini L, Cho KH, Shin IS, Gennari F, Chiodini R, Tartarini S, Kang SJ, Sansavini S (2007) Pear scab resistance QTLs via a European pear (Pyrus communis). Tree Genet Genomes 3:311. https://doi.org/10.1007/s11295-006-0070-0 Poland JA, Brown PJ, Sorrells ME, Jannink JL (2012) Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS ONE 7:332253. https://doi.org/10.1371/journal.pone.0032253 Pootakham W, Sonthirod C, Naktang C, Jomchai N, Sangsrakru D, Tangphatsornruang S (2016) Effects of methylation-sensitive enzymes on the enrichment of genic SNPs and the degree of genome complexity reduction in a two-enzyme genotyping-by-sequencing (GBS) approach: a case study in oil palm (Elaeis guineensis). Mol Breed 36:154. https://doi.org/10.1007/s11032-016-0572-x Rabbi I, Hamblin M, Gedil M, Kulakow P, Ferguson M, Ikpan AS, Ly D, Jannink JL (2014) Genetic mapping using genotyping-by-sequencing in the clonally propagated cassava. Crop Sci 54:1384–1396 Rikkerink EHA, Oraguzie NC, Gardiner SE (2007) Prospects of association mapping in perennial horticultural crops. In: Orguzie NC, Rikkerink EHA, Gardiner SE, De Silva HN (eds) association mapping in plant. Springer, New York, pp 264–269 Rubtsov GA (1944) Geographical distribution of the genus Pyrus and trends and factors in its evolution. Am Nat 78:358–366 Schröder S, Mamidi S, Lee R, McKain MR, McClean PE, Osorno JM (2016) Optimization of genotyping by sequencing (GBS) data in common bean (Phaseolus vulgaris L.). Mol Breed 36:6. https://doi.org/10.1007/s11032-015-0431-1 Silfverberg-Dilworth E, Matasci CL, Van de Weg WE, Van Kaauwen MPW, Walser M, Kodde LP, Songlio V, Gianfranceschi L, Eurel CE et al (2006) Microsatellite markers spanning the apple (Malus × domestica Borkh.) genome. Tree Genet Genomes 2:202–224 Soufflet-Freslon V, Gianfranceschi L, Patocchi A, Eurel CE (2008) Inheritance studies of apple scab resistance and identification of Rvi14, a new major gene that acts together with other broad-spectrum QTL. Genome 51:657–667 Sun W, Zhang Y, Le W, Zhang H (2009) Construction of a genetic linkage map and QTL analysis for some leaf traits in pear (Pyrus L.). Front Agric China 3:67–74 Terakami S, Shoda M, Adachi Y, Gonai T, Kasumi M, Sawamura Y, Iketani H, Kotobuki K, Patocchi A et al (2006) Genetic mapping of the pear scab resistance gene Vnk of Japanese pear cultivar Kinchaku. Theor Appl Genet 113:743–752 Terakami S, Nishitani C, Kunihisa M, Shirasawa K, Sato S, Tabata S, Kurita K, Kanamori H, Katayose Y et al (2014) Transcriptome-based single nucleotide polymorphism markers for genome mapping in Japanese pear (Pyrus pyrifolia Nakai). Tree Genet Genomes 10:853–863 Wu S, Yang J, Huang Y, Li Y, Yin T, Wullschleger SD, Tuskan GA, Wu R (2010) An improved approach for mapping quantitative trait loci in a pseudo-testcross: revisiting a poplar mapping study. Bioinform Biol Insights 4:1–8 Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Awais Khan M, Tao S, Korban SS et al (2013) The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res 23:396–408 Wu J, Lu LT, Li M, Khan MA, Li XG, Chen H, Yin H, Zhang SL (2014) High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers. J Exp Bot 65:5771–5781 Xue H, Wang S, Yao JL, Deng CH, Wang L, Su Y, Zhang H, Zhou H, Sun M et al (2018) Chromosome level high-density integrated genetic maps improve the Pyrus bretschneideri ‘DangshanSuli’ v1.0 genome. BMC Genom 19:833. https://doi.org/10.1186/s12864-018-5224-6 Yamamoto T, Kimura T, Shoda M, Imai T, Saito T, Sawamura Y, Kotobuki K, Hayashi T, Matsuta N (2002a) Genetic linkage maps constructed by using an interspecific cross between Japanese and European pears. Theor Appl Genet 106:9–18 Yamamoto T, Kimura T, Sawamura Y, Manabe T, Kotobuki K, Hayashi T, Ban Y, Matsuta N (2002b) Simple sequence repeats for genetic analysis in pear. Euphytica 124:129–137 Yamamoto T, Kimura T, Shoda M, Ban Y, Hayashi T, Matsuta N (2002c) Development of microsatellite markers in the Japanese pear (Pyrus pyrifolia Nakai). Mol Ecol Notes 2:14–16 Zhang RP, Wu J, Li XG, Khan MA, Chen H, Korban SS, Zhang SL (2013) An AFLP, SRAP, and SSR genetic linkage map and identification of QTLs for fruit traits in pear (Pyrus L.). Plant Mol Biol Rep 31:678–687 Zhou G, Jian J, Wang P, Li C, Tao Y, Li X, Yang H (2018) Construction of an ultra-high density consensus genetic map, and enhancement of the physical map from genome sequencing in Lupinus angustifolius. Theor Appl Genet 131:209–223