An annotated genetic map of loblolly pine based on microsatellite and cDNA markers.
BACKGROUND
Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety of sources and published cDNA markers into a composite P. taeda genetic map constructed from two reference mapping pedigrees. A dense genetic map that incorporates SSR loci will benefit complete pine genome sequencing, pine population genetics studies, and pine breeding programs. Careful marker annotation using a variety of references further enhances the utility of the integrated SSR map.


RESULTS
The updated P. taeda genetic map, with an estimated genome coverage of 1,515 cM(Kosambi) across 12 linkage groups, incorporated 170 new SSR markers and 290 previously reported SSR, RFLP, and ESTP markers. The average marker interval was 3.1 cM. Of 233 mapped SSR loci, 84 were from cDNA-derived sequences (EST-SSRs) and 149 were from non-transcribed genomic sequences (genomic-SSRs). Of all 311 mapped cDNA-derived markers, 77% were associated with NCBI Pta UniGene clusters, 67% with RefSeq proteins, and 62% with functional Gene Ontology (GO) terms. Duplicate (i.e., redundant accessory) and paralogous markers were tentatively identified by evaluating marker sequences by their UniGene cluster IDs, clone IDs, and relative map positions. The average gene diversity, He, among polymorphic SSR loci, including those that were not mapped, was 0.43 for 94 EST-SSRs and 0.72 for 83 genomic-SSRs. The genetic map can be viewed and queried at http://www.conifergdb.org/pinemap.


CONCLUSIONS
Many polymorphic and genetically mapped SSR markers are now available for use in P. taeda population genetics, studies of adaptive traits, and various germplasm management applications. Annotating mapped genes with UniGene clusters and GO terms allowed assessment of redundant and paralogous EST markers and further improved the quality and utility of the genetic map for P. taeda.
Southern Institute of Forest Genetics, Southern Research Station, USDA Forest Service, Saucier, MS 39574, USA. cecht@fs.fed.us
Craig S
CS
Echt
Surya
S
Saha
Konstantin V
KV
Krutovsky
Kokulapalan
K
Wimalanathan
John E
JE
Erpelding
Chun
C
Liang
C Dana
CD
Nelson
D002874:Chromosome Mapping; D018076:DNA, Complementary; D008040:Genetic Linkage; D005819:Genetic Markers; D005838:Genotype; D018598:Minisatellite Repeats; D041603:Pinus taeda / Q000235:genetics*; D011110:Polymorphism, Genetic
D018076:DNA, Complementary; D005819:Genetic Markers
Genetics. 1999 Jan;151(1):321-30
9872970
BMC Bioinformatics. 2008 May 29;9:253
18510760
Bioinformatics. 2009 Jan 15;25(2):288-9
19033274
Nat Rev Genet. 2007 Sep;8(9):699-710
17703239
Bioinformatics. 2009 Nov 15;25(22):3040-2
19648141
Nat Genet. 2000 May;25(1):25-9
10802651
Genome. 1997 Feb;40(1):9-17
9061909
Nucleic Acids Res. 2006 Jan 1;34(Database issue):D173-80
16381840
Plant J. 2007 Jun;50(6):1063-78
17488239
Genome. 2003 Oct;46(5):809-16
14608397
Theor Appl Genet. 1994 Jun;88(3-4):273-8
24186005
Theor Appl Genet. 1999 Jun;98(8):1279-92
12238515
Theor Appl Genet. 2003 Aug;107(4):667-78
12827250
Nature. 2005 Aug 11;436(7052):793-800
16100779
Bioinformatics. 2012 Oct 1;28(19):2537-9
22820204
Genome Res. 2001 May;11(5):904-18
11337484
Nat Biotechnol. 2000 Feb;18(2):233-4
10657137
Genetics. 1991 May;128(1):175-82
2060775
Am J Hum Genet. 1982 Nov;34(6):842-5
6960692
Plant Cell. 2008 Nov;20(11):2931-45
19017747
Genome. 2000 Jun;43(3):550-5
10902720
Bioresour Technol. 2008 Jul;99(11):5051-7
18206369
Genetics. 2001 Oct;159(2):799-809
11606554
Genetics. 1994 Dec;138(4):1293-300
7896107
Theor Appl Genet. 2004 Jul;109(2):361-9
15045175
Am J Hum Genet. 1994 Sep;55(3):582-3
8079998
Heredity (Edinb). 2003 Jan;90(1):33-8
12522423
Nucleic Acids Res. 2005 Jan 1;33(Database issue):D501-4
15608248
Theor Appl Genet. 2004 Oct;109(6):1204-14
15448894
J Hered. 2001 Jul-Aug;92(4):327-32
11535645
Genetics. 2004 Sep;168(1):447-61
15454556
Genome. 1996 Dec;39(6):1102-8
8983182
Int J Plant Genomics. 2008;2008:412875
18725987
Theor Appl Genet. 1999 Aug;99(3-4):656-62
22665202
Proc Natl Acad Sci U S A. 1992 Apr 15;89(8):3419-23
1314388
Genetics. 2008 May;179(1):83-93
18493042
Genome. 2007 Feb;50(2):241-51
17546089
Theor Appl Genet. 2005 Nov;111(8):1466-88
16215729
Biotechniques. 1996 Jun;20(6):1004-6, 1008-10
8780871
Genetics. 2003 Aug;164(4):1537-46
12930758
J Hered. 2002 Jan-Feb;93(1):77-8
12011185
Theor Appl Genet. 2006 Nov;113(8):1371-93
17061103