Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, Tao S, Korban SS, Wang H. The genome of the pear (Pyrus bretschneideri Rehd.). Genome Res. 2013;23(2):396–408.
Article
CAS
Google Scholar
Chagne D, Crowhurst RN, Pindo M, Thrimawithana A, Deng C, Ireland H, Fiers M, Dzierzon H, Cestaro A, Fontana P. The draft genome sequence of European pear (Pyrus communis L. 'Bartlett'). PLoS One. 2014;9(4):e92644.
Article
Google Scholar
Wu J, Li LT, Li M, Khan MA, Li XG, Chen H, Yin H, Zhang SL. High-density genetic linkage map construction and identification of fruit-related QTLs in pear using SNP and SSR markers. J Exp Bot. 2014;65(20):5771–81.
Article
CAS
Google Scholar
Xue H, Zhang P, Shi T, Yang J, Wang L, Wang S, Su Y, Zhang H, Qiao Y, Li X. Genome-wide characterization of simple sequence repeats in Pyrus bretschneideri and their application in an analysis of genetic diversity in pear. BMC Genomics. 2018;19(1):473.
Article
Google Scholar
Chen H, Song Y, Li L-T, Khan MA, Li X-G, Korban SS, Wu J, Zhang S-L. Construction of a high-density simple sequence repeat consensus genetic map for pear (Pyrus spp.). Plant Mol Biol Report. 2014;33(2):316–25.
Article
Google Scholar
Li L, Deng CH, Knabel M, Chagne D, Kumar S, Sun J, Zhang S, Wu J. Integrated high-density consensus genetic map of Pyrus and anchoring of the 'Bartlett' v1.0 (Pyrus communis) genome. DNA Res. 2017;24(3):289–301.
PubMed
PubMed Central
Google Scholar
Iketani H, Abe K, Yamamoto T, Kotobuki K, Sato Y, Saito T, Terai O, Matsuta N, Hayashi T. Mapping of disease-related genes in Japanese pear using a molecular linkage map with RAPD markers. Breed Sci. 2001;51(3):179–84.
Article
CAS
Google Scholar
Dondini L, Pierantoni L, Gaiotti F, Chiodini R, Tartarini S, Bazzi C, Sansavini S. Identifying QTLs for fire-blight resistance via a European pear (Pyrus communis L.) genetic linkage map. Mol Breed. 2004;14(4):407–18.
Article
CAS
Google Scholar
Le Roux P-MF, Christen D, Duffy B, Tartarini S, Dondini L, Yamamoto T, Nishitani C, Terakami S, Lespinasse Y, Kellerhals M. Redefinition of the map position and validation of a major quantitative trait locus for fire blight resistance of the pear cultivar ‘harrow sweet’ (Pyrus communis L.). Plant Breed 2012;131(5):656–664.
Sun W, Zhang Y, Zhang X, Le W, Zhang H. Construction of a genetic linkage map and QTL analysis for some growth traits in pear. J Plant Genet Resour. 2009;10(2):182–9.
CAS
Google Scholar
Dondini L, Pierantoni L, Ancarani V, D’Angelo M, Cho KH, Shin IS, Musacchi S, Kang SJ, Sansavini S. The inheritance of the red colour character in European pear (Pyrus communis) and its map position in the mutated cultivar ‘max red Bartlett. Plant Breed. 2008;127(5):524–6.
Article
Google Scholar
Yamamoto T, Terakami S, Takada N, Nishio S, Onoue N, Nishitani C, Kunihisa M, Inoue E, Iwata H, Hayashi T. Identification of QTLs controlling harvest time and fruit skin color in Japanese pear (Pyrus pyrifolia Nakai). Breed Sci. 2014;64(4):351–61.
Article
CAS
Google Scholar
Han M, LIu Y, Zheng X, Yang J, Wang L, Wang S, Li X, Teng Y. Construction of a genetic linkage map and QTL analysis for some fruit traits in pear [Chinese]. J Fruit Sci. 2010;27(4):496–503.
CAS
Google Scholar
Liu J, Cui H, Wang L, Wang X, Yang J, Zhang Z, Li X, Qiao Y. Analysis of pear fruit acid /low-acid trait by SSR marker [Chinese]. J Fruit Sci. 2011;28(3):389–93.
CAS
Google Scholar
Zhang R, Wu J, Li X, Yang J, Wang L, Wang S, Zhang S. Construction of AFLP genetic linkage map and analysis of QTLs related to fruit traits in pear [Chinese]. Acta Horticulturae Sinica. 2011;38(10):1991–8.
CAS
Google Scholar
Zhang R, Wu J, Li X, Khan MA, Chen H, Korban SS, Zhang S, An AFLP. SRAP, and SSR genetic linkage map and identification of QTLs for fruit traits in pear (Pyrus L.). Plant Mol Biol Report. 2012;31(3):678–87.
Article
Google Scholar
Kumar S, Kirk C, Deng C, Wiedow C, Knaebel M, Brewer L. Genotyping-by-sequencing of pear (Pyrus spp.) accessions unravels novel patterns of genetic diversity and selection footprints. Horticulture research. 2017;4:17015.
Article
Google Scholar
Yao G, Ming M, Allan AC, Gu C, Li L, Wu X, Wang R, Chang Y, Qi K, Zhang S. Map-based cloning of the pear gene MYB114 identifies an interaction with other transcription factors to coordinately regulate fruit anthocyanin biosynthesis. Plant J. 2017;92(3):437–51.
Article
CAS
Google Scholar
Kumar S, Chagne D, Bink MC, Volz RK, Whitworth C, Carlisle C. Genomic selection for fruit quality traits in apple (Malus x domestica Borkh.). PLoS One. 2012;7(5):e36674.
Article
CAS
Google Scholar
Montanari S, Saeed M, Knabel M, Kim Y, Troggio M, Malnoy M, Velasco R, Fontana P, Won K, Durel CE. Identification of Pyrus single nucleotide polymorphisms (SNPs) and evaluation for genetic mapping in European pear and interspecific Pyrus hybrids. PLoS One. 2013;8(10):e77022.
Article
CAS
Google Scholar
Xue H, Shi T, Wang F, Zhou H, Yang J, Wang L, Wang S, Su Y, Zhang Z, Qiao Y. Interval mapping for red/green skin color in Asian pears using a modified QTL-seq method. Hortic Res. 2017;4:17053.
Article
Google Scholar
Daccord N, Celton JM, Linsmith G, Becker C, Choisne N, Schijlen E, van de Geest H, Bianco L, Micheletti D, Velasco R. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nat Genet. 2017;49(7):1099–106.
Article
CAS
Google Scholar
Velasco R, Zharkikh A, Affourtit J, Dhingra A, Cestaro A, Kalyanaraman A, Fontana P, Bhatnagar SK, Troggio M, Pruss D. The genome of the domesticated apple (Malus x domestica Borkh.). Nat Genet. 2010;42(10):833–9.
Article
CAS
Google Scholar
Baird NA, Etter PD, Atwood TS, Currey MC, Shiver AL, Lewis ZA, Selker EU, Cresko WA, Johnson EA. Rapid SNP discovery and genetic mapping using sequenced RAD markers. PLoS One. 2008;3(10):e3376.
Article
Google Scholar
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES. Mitchell SE. A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS One. 2011;6(5):e19379.
Article
CAS
Google Scholar
Sun X, Liu D, Zhang X, Li W, Liu H, Hong W, Jiang C, Guan N, Ma C, Zeng H. SLAF-seq: an efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing. PLoS One. 2013;8(3):e58700.
Article
CAS
Google Scholar
Liu N, Li M, Hu X, Ma Q, Mu Y, Tan Z, Xia Q, Zhang G, Nian H. Construction of high-density genetic map and QTL mapping of yield-related and two quality traits in soybean RILs population by RAD-sequencing. BMC Genomics. 2017;18(1):466.
Article
Google Scholar
Yang Z, Chen Z, Peng Z, Yu Y, Liao M, Wei S. Development of a high-density linkage map and mapping of the three-pistil gene (Pis1) in wheat using GBS markers. BMC Genomics. 2017;18(1):567.
Article
Google Scholar
Zhang J, Zhang Q, Cheng T, Yang W, Pan H, Zhong J, Huang L, Liu E. High-density genetic map construction and identification of a locus controlling weeping trait in an ornamental woody plant (Prunus mume Sieb. Et Zucc). DNA Res. 2015;22(3):183–91.
Article
CAS
Google Scholar
Zhou G, Jian J, Wang P, Li C, Tao Y, Li X, Renshaw D, Clements J, Sweetingham M, Yang H. Construction of an ultra-high density consensus genetic map, and enhancement of the physical map from genome sequencing in Lupinus angustifolius. Theor Appl Genet. 2018;131(1):209–23.
Article
CAS
Google Scholar
Wang L, Li X, Wang L, Xue H, Wu J, Yin H, Zhang S. Construction of a high-density genetic linkage map in pear ( Pyrus communis × Pyrus pyrifolia Nakai) using SSRs and SNPs developed by SLAF-seq. Sci Hortic. 2017;218:198–204.
Article
CAS
Google Scholar
Wang L, Wang L, Xue H, Li X, Li J. Construction of SSR genetic linkage map and comparison on pears [Chinese]. Sci Agric Sin. 2016;49(12):2353–67.
CAS
Google Scholar
Lorieux M, Goffinet B, Perrier X, De Leon DG, Lanaud C. Maximum-likelihood models for mapping genetic markers showing segregation distortion. 1. Backcross populations. Theoret Appl Genet. 1995;90(1):73–80.
Article
CAS
Google Scholar
Lorieux M, Perrier X, Goffinet B, Lanaud C, De León DG. Maximum-likelihood models for mapping genetic markers showing segregation distortion. 2. F 2 populations. Theor Appl Genet. 1995;90(1):81–9.
Article
CAS
Google Scholar
Teng Y, Tanabe K, Tamura F, Itai A. Genetic relationships of Pyrus species and cultivars native to East Asia revealed by randomly amplified polymorphic DNA markers. J Am Soc Hortic Sci. 2002;127(2):262–70.
CAS
Google Scholar
Jiang S, Zong Y, Yue X, Postman J, Teng Y, Cai D. Prediction of retrotransposons and assessment of genetic variability based on developed retrotransposon-based insertion polymorphism (RBIP) markers in Pyrus L. Mol Genet Genomics. 2015;290(1):225–37.
Article
CAS
Google Scholar
Kimura T, Shi YZ, Shoda M, Kotobuki K, Matsuta N, Hayashi T, Ban Y, Yamamoto T. Identification of Asian pear varieties by SSR analysis. Breed Sci. 2002;52(2):115–21.
Article
CAS
Google Scholar
Bao L, Chen K, Zhang D, Li X, Teng Y. An assessment of genetic variability and relationships within Asian pears based on AFLP (amplified fragment length polymorphism) markers. Sci Hortic. 2008;116(4):374–80.
Article
CAS
Google Scholar
Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable JC, Schnable PS, Lyons E, Lu J. ALLMAPS: robust scaffold ordering based on multiple maps. Genome Biol. 2015;16:3.
Article
CAS
Google Scholar
Pop M, Kosack DS, Salzberg SL. Hierarchical scaffolding with Bambus. Genome Res. 2004;14(1):149–59.
Article
CAS
Google Scholar
Rahman AYA, Usharraj AO, Misra BB, Thottathil GP, Jayasekaran K, Feng Y, Hou S, Ong SY, Ng FL, Lee LS. Draft genome sequence of the rubber tree Hevea brasiliensis. BMC Genomics. 2013;14(1):75.
Article
Google Scholar
Pootakham W, Ruang-Areerate P, Jomchai N, Sonthirod C, Sangsrakru D, Yoocha T, Theerawattanasuk K, Nirapathpongporn K, Romruensukharom P, Tragoonrung S. Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS). Front Plant Sci. 2015;6:367.
Article
Google Scholar
Westbrook JW, Chhatre VE, Wu LS, Chamala S, Neves LG, Munoz P, Martinez-Garcia PJ, Neale DB, Kirst M, Mockaitis KA. Consensus genetic map for Pinus taeda and Pinus elliottii and extent of linkage disequilibrium in two genotype-phenotype discovery populations of Pinus taeda. G3 (Bethesda, Md). 2015;5(8):1685–94.
Article
Google Scholar
Montanari S, Brewer L, Lamberts R, Velasco R, Malnoy M, Perchepied L, Guerif P, Durel CE, Bus VG, Gardiner SE. Genome mapping of postzygotic hybrid necrosis in an interspecific pear population. Hortic Res. 2016;3:15064.
Article
Google Scholar
Doyle JJ. A rapid DNA isolation procedure for small quantities of fresh leaf tissue. Phytochem Bull. 1987;19:11–5.
Google Scholar
Poland JA, Brown PJ, Sorrells ME, Jannink JL. Development of high-density genetic maps for barley and wheat using a novel two-enzyme genotyping-by-sequencing approach. PLoS One. 2012;7(2):e32253.
Article
CAS
Google Scholar
Li H, Durbin R. Fast and accurate short read alignment with burrows-wheeler transform. Bioinformatics. 2009;25(14):1754–60.
Article
CAS
Google Scholar
McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M. The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res. 2010;20(9):1297–303.
Article
CAS
Google Scholar
Wang K, Li M, Hakonarson HANNOVAR. Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38(16):e164.
Article
Google Scholar
Wu R, Ma CX, Painter I, Zeng ZB. Simultaneous maximum likelihood estimation of linkage and linkage phases in outcrossing species. Theor Popul Biol. 2002;61(3):349–63.
Article
Google Scholar
Van Ooijen JW. Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species. Genet Res. 2011;93(5):343–9.
Article
CAS
Google Scholar
Takagi H, Abe A, Yoshida K, Kosugi S, Natsume S, Mitsuoka C, Uemura A, Utsushi H, Tamiru M, Takuno S. QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J. 2013;74(1):174–83.
Article
CAS
Google Scholar