Development of an integrated laboratory information management system for the maize mapping project

Sánchez-Villeda, Héctor; Schroeder, Steven G.; Polacco, Mary L.; McMullen, Michael D.; Havermann, Seth A.; Davis, Gregory L.; Vroh-Bi, I.; Cone, Karen C.; Sharopova, Natalya; Yim, Young Sun; Schultz, Linda; Duru, Ngozi A.; Musket, Theresa A.; Houchins, Kate; Fang, Zhiwei; Gardiner, Jack M.; Coe, E. H.

doi:10.1093/bioinformatics/btg274

Cited by 33 publications

(21 citation statements)

References 15 publications

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“…Three primer pairs, Mo17-H10.1, Mo17-H10.2, and Mo17-E22.1, were used to score a complete 94-sample IBM population (Lee et al 2002;Sanchez-Villeda et al 2003). The segregation patterns for Mo17-H10.1 and Mo17-H10.2 were identical for all 94 DNA samples, indicating that different markers from a single BAC provide consistent and reproducible data.…”

Section: T He Centromeres In Most Plants and Animalsmentioning

confidence: 99%

Precise Centromere Mapping Using a Combination of Repeat Junction Markers and Chromatin Immunoprecipitation–Polymerase Chain Reaction

et al. 2006

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Section: T He Centromeres In Most Plants and Animalsmentioning

confidence: 99%

Precise Centromere Mapping Using a Combination of Repeat Junction Markers and Chromatin Immunoprecipitation–Polymerase Chain Reaction

et al. 2006

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“…Commercial LIMS are available, but they are expensive and time-consuming to adapt to a given research lab's specificities (Weissig 2004). Some freely downloadable LIMS dedicated to mutation detection exist, such as MMP-LIMS (Sanchez-Villeda et al 2003), SNP LIMS (Barenboim et al 2003), and Genetic Susceptibility Group LIMS (Voegele et al 2007). However, these LIMS apply to very specific lab protocols or instruments that may not be common to all SNP discovery projects.…”

Section: Introductionmentioning

confidence: 99%

TreeSNPs: a laboratory information management system (LIMS) dedicated to SNP discovery in trees

Clément

Fillon

Bousquet

et al. 2010

Tree Genetics & Genomes

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TreeSNPs is a laboratory information management system with a user-friendly Web interface for the gathering and display of data generated through medium-to large-scale single nucleotide polymorphism (SNP) identification by resequencing, in the context of whole genome association, outlier detection, quantitative trait locus, and genetic mapping studies. Its multi-gene approach allows the tracking of all the steps from candidate gene classification and prioritization to SNP discovery. The system, source code, and documentation are available for download at http://treesnps-pub.arborea.ulaval.ca:3000/download. An online demo version can also be accessed from the above link.

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“…In plants, however, few extensive SNP markers have been developed and integrated into existing plant linkage maps, although a little work has been conducted in Arabidopsis, barley and maize (Cho et al 1999;Sanchez-Villeda et al 2003;Rostoks et al 2005). In soybean, a total of 280 SNPs were discovered in a 76 kb sequence among 25 diverse soybean genotypes (Zhu et al 2003) and Van et al (2004) identiWed 66 SNPs in a 33 kb sequence among nine Korean soybean genotypes.…”

Section: Introductionmentioning

confidence: 99%

SNP discovery, linkage analysis and microsynteny in tentative consensus sequences derived from roots cDNA in a supernodulating soybean mutant

et al. 2008

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A soybean transcript map with genes mainly expressed in roots of a supernodulating mutant was constructed by mapping of single nucleotide polymorphism (SNP) markers into pre-existing SSR-based map, using a recombinant inbred line (RIL) population from Pureunkong and Jinpumkong 2. For SNP discovery, primer pairs were designed from 793 tentative consensus sequences (TCs) derived from the roots of a supernodulating soybean mutant. Among 520 loci showing high-quality sequence, more than 300 SNPs were identiWed in 116 loci between the parental genotypes. Average SNP frequency between the parental genotypes was one SNP per 1,010 bp. A total of 325 markers, including 98 SNPs, 208 SSRs, 15 AFLPs and four classical markers, were used to construct a genetic linkage map with 20 linkage groups (LGs) and a total length of 2,379 cM. Ten nonsynonymous changes were detected out of these SNP markers, indicating the possible usage of these markers as functional markers. With 40 of the SNP markers, putative synteny between soybean and Medicago truncatula (Mt) was revealed by identiWcation of 19 short colinear blocks between the two genomes. This genetic map will provide the basis for the identiWcation of gene in relation to nodulation and nitrogen Wxation in partially sequenced genome like soybean by comparisons of the model genome (Mt). And, the integration of SNP markers and expression data with available genetic and phenotypic information would be helpful for clarifying function of cloned genes.

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Development of an integrated laboratory information management system for the maize mapping project

Abstract: To receive a copy of the iMap or cMap software, please fill out the form on our website. The other MMP-LIMS software is freely available at http://www.maizemap.org/bioinformatics.htm.

Cited by 33 publications

References 15 publications

Precise Centromere Mapping Using a Combination of Repeat Junction Markers and Chromatin Immunoprecipitation–Polymerase Chain Reaction

Precise Centromere Mapping Using a Combination of Repeat Junction Markers and Chromatin Immunoprecipitation–Polymerase Chain Reaction

TreeSNPs: a laboratory information management system (LIMS) dedicated to SNP discovery in trees

SNP discovery, linkage analysis and microsynteny in tentative consensus sequences derived from roots cDNA in a supernodulating soybean mutant

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