title: Genome-wide characterization and linkage mapping of simple sequence repeats in mei (Prunus mume Sieb. et Zucc.).
abstract: Because of its popularity as an ornamental plant in East Asia, mei (Prunus mume Sieb. et Zucc.) has received increasing attention in genetic and genomic research with the recent shotgun sequencing of its genome. Here, we performed the genome-wide characterization of simple sequence repeats (SSRs) in the mei genome and detected a total of 188,149 SSRs occurring at a frequency of 794 SSR/Mb. Mononucleotide repeats were the most common type of SSR in genomic regions, followed by di- and tetranucleotide repeats. Most of the SSRs in coding sequences (CDS) were composed of tri- or hexanucleotide repeat motifs, but mononucleotide repeats were always the most common in intergenic regions. Genome-wide comparison of SSR patterns among the mei, strawberry (Fragaria vesca), and apple (Malus×domestica) genomes showed mei to have the highest density of SSRs, slightly higher than that of strawberry (608 SSR/Mb) and almost twice as high as that of apple (398 SSR/Mb). Mononucleotide repeats were the dominant SSR motifs in the three Rosaceae species. Using 144 SSR markers, we constructed a 670 cM-long linkage map of mei delimited into eight linkage groups (LGs), with an average marker distance of 5 cM. Seventy one scaffolds covering about 27.9% of the assembled mei genome were anchored to the genetic map, depending on which the macro-colinearity between the mei genome and Prunus T×E reference map was identified. The framework map of mei constructed provides a first step into subsequent high-resolution genetic mapping and marker-assisted selection for this ornamental species.
authors.affiliation: College of Landscape Architecture, National Engineering Research Center for Floriculture, Beijing Forestry University, Beijing, PR China.
authors.forename: Lidan
authors.initials: L
authors.lastname: Sun
authors.forename: Weiru
authors.initials: W
authors.lastname: Yang
authors.forename: Qixiang
authors.initials: Q
authors.lastname: Zhang
authors.forename: Tangren
authors.initials: T
authors.lastname: Cheng
authors.forename: Huitang
authors.initials: H
authors.lastname: Pan
authors.forename: Zongda
authors.initials: Z
authors.lastname: Xu
authors.forename: Jie
authors.initials: J
authors.lastname: Zhang
authors.forename: Chuguang
authors.initials: C
authors.lastname: Chen
mesh_terms: D018745:Genome, Plant / Q000235:genetics; D023281:Genomics; D018895:Microsatellite Repeats / Q000235:genetics*; D010802:Phylogeny; D020161:Physical Chromosome Mapping; D027861:Prunus / Q000235:genetics*; D026801:Synteny / Q000235:genetics
references.citation: BMC Genet. 2010 Jul 13;11:66
references.pmid: 20626882
references.citation: Nat Genet. 2010 Nov;42(11):1027-30
references.pmid: 20972441
references.citation: BMC Plant Biol. 2008 Jun 18;8:67
references.pmid: 18564412
references.citation: Nat Commun. 2012;3:1318
references.pmid: 23271652
references.citation: Ann Bot. 2011 Aug;108(2):321-36
references.pmid: 21788377
references.citation: Plant Physiol. 2004 Jul;135(3):1198-205
references.pmid: 15266053
references.citation: Nucleic Acids Res. 1995 Mar 25;23(6):1050-9
references.pmid: 7731793
references.citation: BMC Genomics. 2009 Aug 07;10:371
references.pmid: 19664231
references.citation: Cell. 1995 May 19;81(4):533-40
references.pmid: 7758107
references.citation: Proc Natl Acad Sci U S A. 2004 Jun 29;101(26):9891-6
references.pmid: 15159547
references.citation: Nucleic Acids Res. 1984 May 25;12(10):4127-38
references.pmid: 6328411
references.citation: Nat Genet. 2002 Feb;30(2):194-200
references.pmid: 11799393
references.citation: Theor Appl Genet. 1995 Jan;90(1):81-9
references.pmid: 24173787
references.citation: Genetics. 1994 Dec;138(4):1251-74
references.pmid: 7896104
references.citation: Methods Mol Biol. 2000;132:365-86
references.pmid: 10547847
references.citation: Nature. 1996 Jun 6;381(6582):483
references.pmid: 8632820
references.citation: Genome Res. 2000 Jul;10(7):967-81
references.pmid: 10899146
references.citation: Theor Appl Genet. 2002 Jan;104(1):17-29
references.pmid: 12579424
references.citation: BMC Genomics. 2006 Sep 08;7:229
references.pmid: 16961921
references.citation: PLoS One. 2012;7(7):e41213
references.pmid: 22815973
references.citation: Theor Appl Genet. 2002 Sep;105(4):622-628
references.pmid: 12582513
references.citation: FEBS Lett. 2007 May 29;581(13):2523-6
references.pmid: 17498704
references.citation: Genomics. 1990 Aug;7(4):524-30
references.pmid: 1974878
references.citation: DNA Res. 2007 Feb 28;14(1):37-45
references.pmid: 17452422
references.citation: Genome. 2000 Jun;43(3):512-20
references.pmid: 10902716
references.citation: Genome Res. 2009 Sep;19(9):1639-45
references.pmid: 19541911
references.citation: Proc Natl Acad Sci U S A. 1989 Jan;86(1):192-6
references.pmid: 2463621
references.citation: Theor Appl Genet. 1995 Jan;90(1):73-80
references.pmid: 24173786
references.citation: Anal Biochem. 1991 Jul;196(1):80-3
references.pmid: 1716076
references.citation: Genetics. 2004 Jan;166(1):419-36
references.pmid: 15020433
references.citation: Mol Biol Evol. 2001 Mar;18(3):384-92
references.pmid: 11230539
references.citation: Mol Biol Evol. 2001 Jul;18(7):1161-7
references.pmid: 11420357
references.citation: Nat Genet. 2010 Oct;42(10):833-9
references.pmid: 20802477
references.citation: PLoS One. 2011 Jan 06;6(1):e15952
references.pmid: 21253606
references.citation: BMC Genomics. 2011 Jun 10;12:304
references.pmid: 21663628
references.citation: PLoS One. 2011;6(6):e21298
references.pmid: 21713003
references.citation: Genome. 2001 Oct;44(5):783-90
references.pmid: 11681601
references.citation: Genome Res. 2000 Jan;10(1):72-80
references.pmid: 10645952
references.citation: Genome Biol Evol. 2010;2:620-35
references.pmid: 20668018
references.citation: BMC Genomics. 2009 Nov 29;10:562
references.pmid: 19943965
references.citation: Genome. 2006 Oct;49(10):1256-64
references.pmid: 17213907
references.citation: Genome Res. 2002 Apr;12(4):656-64
references.pmid: 11932250
references.citation: Nat Rev Genet. 2005 May;6(5):351-60
references.pmid: 15861207
references.citation: Theor Appl Genet. 2003 Nov;107(7):1235-42
references.pmid: 12898031
references.citation: Biochem Soc Trans. 2006 Aug;34(Pt 4):531-4
references.pmid: 16856852
references.citation: Theor Appl Genet. 2004 Apr;108(6):1120-30
references.pmid: 15067399
references.citation: PLoS One. 2012;7(1):e29453
references.pmid: 22247776
references.citation: BMC Genomics. 2011 Oct 21;12:521
references.pmid: 22014081
references.citation: BMC Genomics. 2010 Oct 15;11:569
references.pmid: 20950470
references.citation: Mol Breed. 2012 Jun;30(1):125-138
references.pmid: 22707912
references.citation: Chromosoma. 2000 Sep;109(6):365-71
references.pmid: 11072791
references.citation: Theor Appl Genet. 2002 Aug;105(2-3):182-191
references.pmid: 12582518
references.citation: Nat Genet. 2011 Feb;43(2):109-16
references.pmid: 21186353
references.citation: Science. 2008 Apr 25;320(5875):486-8
references.pmid: 18436778
references.citation: PLoS One. 2012;7(7):e40861
references.pmid: 22815847