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

By Susan McCouch, Leonid Teytelman, Yunbi Xu, K. B. Lobos, K. Clare, M. Walton, B. Fu, R. Maghirang, Zhikang Li, Yongzhong Xing and 9 more. DNA Research, 2002

1,575 citations recorded by the source corpus.

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.

Subfields: Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/162ba96cfff6aff24bb4a5ca1e747fe6ede51a8a

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Citations in the corpus

A QTL Cluster for Plant Architecture and Its Ecological Significance in Asian Wild Rice (2007, methodology): “The map covered most of the whole genome of rice, based on the reported map (McCouch et al. 2002).”
Development of DNA Markers Suitable for Marker Assisted Selection of Three Pi Genes Conferring Resistance to Multiple Pyricularia grisea Pathotypes (2004, methodology): “Ifby the presence or absence of several resistance gene factors found at this chromosomal location. one wants to detect recombination around a resistance gene, markers flanking a Pi locus can be tested, suchAlthough not directly presented in this research, vari- ability within pathogen races for agg”
Molecular Marker based Genetic Diversity Analysis in Rice (Oryza sativa L.) using RAPD and SSR markers (2003, methodology): “Like the RAPD markers, SSR markers were also employed in rice because of their polyallelic nature and greater allelic diversity over RFLPs ( McCouch et al., 1997 ).”
Mapping of a Major Resistance Gene to the Brown Planthopper in the Rice Cultivar Rathu Heenati (2005, methodology): “The original sources and motifs for all the SSR markers used in this study could be found in the gramene database (http://www.gramene. org/) and the report of McCouch et al. (2002) (http://www. dna_res.kazusa.or.jp/9/6/05/spl_table1/table1.pdf).”
Quantitative trait loci controlling rice seed germination under salt stress (2011, methodology): “The SSR markers were used as described by Temnykh et al. (2000), McCouch et al. (2002) and the Gramene Database (http://www.gramene.org/).”
Advances in Drought Resistance of Rice (2009, background): “The rice genetic map is well covered by microsatellite markers (McCouch et al., 2003), and rice researchers worldwide have developed diverse mapping populations and related databases (Ware et al., 2002).”
Highly variable SSR markers suitable for rice genotyping using agarose gels (2009, methodology): “The SSR markers have been used widely for rice germplasm evaluation, interpreting population structure and genetic dissection of quantitative trait loci (QTL) for important agronomic traits (Akkaya et al. 1992 ;Y ang et al.1994; McCouch et al. 1997, 2002; Cho et al. 2000).”
Molecular diversity and genome-wide linkage disequilibrium patterns in a worldwide collection of Oryza sativa and its wild relatives (2008, methodology): “For LD between two multi-allelic loci, D was applied in Oryza (Thomson et al. 2007), Triticum (Maccaferri et al. 2005) and Zea mays L. ( Maurer et al. 2006; Stich et al. 2005).”
QTLs mapping of physiological traits related to salt tolerance in young rice seedlings (2009, methodology): “The position of most SSR markers on chromosomes was identical with the previous reports (Chen et al. 1997, Temnykh et al. 2000, McCouch et al. 2002) but its order was not identical.”
Molecular fingerprinting of hybrids and assessment of genetic purity of hybrid seeds in rice using microsatellite markers (2004, background): “Availability of more than 2740 mapped microsatellite markers with an average density of one STMS for every 157 kb (<1 cM) of the rice genome (Cho et al., 2000; McCouch et al., 2002; Temnykh et al., 2000) has greatly improved their utility.”
Development of Chromosome Segment Substitution Lines Derived from Backcross between indica Donor Rice Cultivar ‘Nona Bokra’ and japonica Recipient Cultivar ‘Koshihikari’ (2007, methodology): “The SSR markers, developed by McCouch et al. (2002), are denoted by “RM” followed by a four-digit-number.”
Development of rice introgression lines with brown planthopper resistance and KDML105 grain quality characteristics through marker-assisted selection (2009, methodology): “Based on the high-resolution rice linkage map with SSR markers (McCouch et al., 2002), about 120 SSR primer sets were selected and tested on the parental cultivars RH and KD.”