Nonrandom distribution and frequencies of genomic and EST-derived microsatellite markers in rice, wheat, and barley.
BACKGROUND
Earlier comparative maps between the genomes of rice (Oryza sativa L.), barley (Hordeum vulgare L.) and wheat (Triticum aestivum L.) were linkage maps based on cDNA-RFLP markers. The low number of polymorphic RFLP markers has limited the development of dense genetic maps in wheat and the number of available anchor points in comparative maps. Higher density comparative maps using PCR-based anchor markers are necessary to better estimate the conservation of colinearity among cereal genomes. The purposes of this study were to characterize the proportion of transcribed DNA sequences containing simple sequence repeats (SSR or microsatellites) by length and motif for wheat, barley and rice and to determine in-silico rice genome locations for primer sets developed for wheat and barley Expressed Sequence Tags.


RESULTS
The proportions of SSR types (di-, tri-, tetra-, and penta-nucleotide repeats) and motifs varied with the length of the SSRs within and among the three species, with trinucleotide SSRs being the most frequent. Distributions of genomic microsatellites (gSSRs), EST-derived microsatellites (EST-SSRs), and transcribed regions in the contiguous sequence of rice chromosome 1 were highly correlated. More than 13,000 primer pairs were developed for use by the cereal research community as potential markers in wheat, barley and rice.


CONCLUSIONS
Trinucleotide SSRs were the most common type in each of the species; however, the relative proportions of SSR types and motifs differed among rice, wheat, and barley. Genomic microsatellites were found to be primarily located in gene-rich regions of the rice genome. Microsatellite markers derived from the use of non-redundant EST-SSRs are an economic and efficient alternative to RFLP for comparative mapping in cereals.
La Rota
Mauricio
M
Department of Plant Breeding and Genetics, 240 Emerson Hall, Cornell University, Ithaca, NY 14853, USA. cml22@cornell.edu
Kantety
Ramesh V
RV
Yu
Ju-Kyung
JK
Sorrells
Mark E
ME
D020816:Amino Acid Motifs; D002874:Chromosome Mapping; D032461:Chromosomes, Plant; D017931:DNA Primers / Q000737:chemistry; D020224:Expressed Sequence Tags; D017343:Genes, Plant; D008040:Genetic Linkage; D005819:Genetic Markers; D018745:Genome, Plant; D001467:Hordeum / Q000235:genetics*; D018895:Microsatellite Repeats; D008957:Models, Genetic; D015233:Models, Statistical; D009711:Nucleotides / Q000235:genetics; D012275:Oryza / Q000235:genetics*; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic; D012150:Polymorphism, Restriction Fragment Length; D012044:Regression Analysis; D014158:Transcription, Genetic; D014908:Triticum / Q000235:genetics*
D017931:DNA Primers; D005819:Genetic Markers; D009711:Nucleotides
Genome. 2000 Aug;43(4):689-97
10984182
Plant Mol Biol. 2002 Mar-Apr;48(5-6):501-10
11999831
Cell Mol Biol Lett. 2002;7(2A):537-46
12378259
J Comput Biol. 2000 Feb-Apr;7(1-2):203-14
10890397
Theor Appl Genet. 2002 Nov;105(6-7):898-905
12582915
Nucleic Acids Res. 2003 Jan 1;31(1):23-7
12519940
Genome Res. 2001 Aug;11(8):1441-52
11483586
Mol Genet Genomics. 2003 Dec;270(4):315-23
14508680
Theor Appl Genet. 2004 Aug;109(4):783-91
15205737
Mol Genet Genomics. 2004 Jul;271(6):742-51
15197579
Am J Hum Genet. 2002 Oct;71(4):923-32
12232854
Plant Mol Biol. 1997 Sep;35(1-2):3-15
9291955
Proc Natl Acad Sci U S A. 1998 Mar 3;95(5):1971-4
9482816
Mol Genet Genomics. 2004 Oct;272(3):308-27
15368122
Anim Genet. 2002 Oct;33(5):372-6
12354146
Nature. 2002 Nov 21;420(6913):312-6
12447438
Theor Appl Genet. 2004 Feb;108(3):414-22
13679975
Genome Res. 2003 Aug;13(8):1818-27
12902377
Funct Integr Genomics. 2004 Mar;4(1):34-46
14740255
Theor Appl Genet. 2002 Jan;104(1):61-6
12579429
Mol Genet Genomics. 2001 Nov;266(3):471-80
11713677
Methods Mol Biol. 2000;132:365-86
10547847
Plant Sci. 2001 May;160(6):1115-1123
11337068
Mol Genet Genomics. 2002 Nov;268(3):331-43
12436255
Plant Mol Biol. 1998 Oct;38(3):407-15
9747848
Nat Genet. 2002 Feb;30(2):194-200
11799393
Nucleic Acids Res. 2001 Jan 1;29(1):159-64
11125077
Mol Genet Metab. 2001 Sep-Oct;74(1-2):281-91
11592825
Hum Mol Genet. 2000 Apr 12;9(6):909-16
10767314
Nucleic Acids Res. 2003 Jan 1;31(1):183-6
12519977
Theor Appl Genet. 2003 Feb;106(3):411-22
12589540
Mol Gen Genet. 1993 Dec;241(5-6):483-90
7903411
Theor Appl Genet. 2002 Feb;104(2-3):399-407
12582712