Reference "Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.)"

Reference ID

7765

Title

Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.)

Source

DNA research : an international journal for rapid publication of reports on genes and genomes, 2002, vol. 9, pp. 199-207

Authors (19)

McCouch-S-R	Teytelman-L	Xu-Y	Lobos-K-B	Clare-K
Walton-M	Fu-B	Maghirang-R	Li-Z	Xing-Y
Zhang-Q	Kono-I	Yano-M	Fjellstrom-R	DeClerck-G
Schneider-D	Cartinhour-S	Ware-D	Stein-L

Abstract

A total of 2414 new di-, tri- and tetra-nucleotide non-redundant SSR primer
pairs, representing 2240 unique marker loci, have been developed and
experimentally validated for rice (Oryza sativa L.). Duplicate primer pairs are
reported for 7% (174) of the loci. The majority (92%) of primer pairs were
developed in regions flanking perfect repeats > or = 24 bp in length. Using
electronic PCR (e-PCR) to align primer pairs against 3284 publicly sequenced
rice BAC and PAC clones (representing about 83% of the total rice genome), 65%
of the SSR markers hit a BAC or PAC clone containing at least one genetically
mapped marker and could be mapped by proxy. Additional information based on
genetic mapping and "nearest marker" information provided the basis for
locating a total of 1825 (81%) of the newly designed markers along rice
chromosomes. Fifty-six SSR markers (2.8%) hit BAC clones on two or more
different chromosomes and appeared to be multiple copy. The largest proportion
of SSRs in this data set correspond to poly(GA) motifs (36%), followed by
poly(AT) (15%) and poly(CCG) (8%) motifs. AT-rich microsatellites had the
longest average repeat tracts, while GC-rich motifs were the shortest. In
combination with the pool of 500 previously mapped SSR markers, this release
makes available a total of 2740 experimentally confirmed SSR markers for rice,
or approximately one SSR every 157 kb.