PIP: a database of potential intron polymorphism markers

Yang, Long; Jin, Gulei; Zhao, Xiaojing; Zheng, Yan; Xu, Zhigao; Wu, Weiren

doi:10.1093/bioinformatics/btm296

Cited by 93 publications

(69 citation statements)

References 12 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…The capability of the ITP markers to amplify intronic regions pointed to its efficiency in primer template alignment which could be attributed to accuracy and reliability of the program. This result further indicates that intron positions are highly conserved in plants and therefore using model plants to predict intron positions in nonmodel plants is feasible (Yang et al 2007).…”

Section: Discussionmentioning

confidence: 83%

“…Moreover, the ITP markers were also found to be highly suitable for cross-transferability studies and thus useful for identification of genetic determinants of a trait even in less-studied taxa (Choi et al 2004;Wang et al 2005). With the development of web-based programs like PIP (Yang et al 2007) and GeMProspector (Fredslund et al 2006), the designing of ITPs accelerated more rapidly even in orphan crops. Similarly in this study of chickpea, a high success rate of validation of ITP markers was observed (151/220; 68.6%) which was comparable with an earlier study in chickpea which reported 71.9% .…”

Section: Discussionmentioning

confidence: 99%

“…For the development of ITPs in this study, the online program 'PIP' (Yang et al 2007) was utilized. The program designed a total of 220 intron-flanking exon-exon based chickpea primers that were predicted to amplify approx.…”

Section: Development Of Est-derived Itp and Estp Markersmentioning

confidence: 99%

“…For designing the ITP primers, the Potential Intron Polymorphism (PIP) program (Yang et al 2007) was used. The program predicts the intron-exon junctions in the query species by comparing the query sequences (in this case, chickpea EST sequences) against the Arabidopsis thaliana genomic sequences and then designs intron-flanking exon-exon based primers in the query EST sequences.…”

Section: Intron Targeted Polymorphismmentioning

confidence: 99%

See 3 more Smart Citations

EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea

et al. 2012

View full text Add to dashboard Cite

Well-saturated linkage maps especially those based on expressed sequence tag (EST)-derived genic molecular markers (GMMs) are a pre-requisite for molecular breeding. This is especially true in important legumes such as chickpea where few simple sequence repeats (SSR) and even fewer GMM-based maps have been developed. Therefore, in this study, 2,496 ESTs were generated from chickpea seeds and utilized for the development of 487 novel EST-derived functional markers which included 125 EST-SSRs, 151 intron targeted primers (ITPs), 109 expressed sequence tag polymorphisms (ESTPs), and 102 single nucleotide polymorphisms (SNPs). Whereas ESTSSRs, ITPs, and ESTPs were developed by in silico analysis of the developed EST sequences, SNPs were identified by allele resequencing and their genotyping was performedusing the Illumina GoldenGate Assay. Parental polymorphism was analyzed between C. arietinum ICC4958 and C. reticulatum PI489777, parents of the reference chickpea mapping population, using a total of 872 markers: 487 new gene-based markers developed in this study along with 385 previously published markers, of which 318 (36.5%) were found to be polymorphic and were used for genotyping. The genotypic data were integrated with the previously published data of 108 markers and an advanced linkage map was generated that contained 406 loci distributed on eight linkage groups that spanned 1,497.7 cM. The average marker density was 3.68 cM and the average number of markers per LG was 50.8. Among the mapped markers, 303 new genomic locations were defined that included 177 gene-based and 126 gSSRs (genomic SSRs) thereby producing the most advanced gene-rich map of chickpea solely based on co-dominant markers.

show abstract

Section: Discussionmentioning

confidence: 83%

Section: Discussionmentioning

confidence: 99%

Section: Development Of Est-derived Itp and Estp Markersmentioning

confidence: 99%

Section: Intron Targeted Polymorphismmentioning

confidence: 99%

See 2 more Smart Citations

EST-derived genic molecular markers: development and utilization for generating an advanced transcript map of chickpea

et al. 2012

View full text Add to dashboard Cite

show abstract

“…Availability of whole-genome (Wang et al 2005 ) and soybean (Shu et al 2010 ). A database of potential intron polymorphism (PIP) in plants was developed by Yang et al ( 2007 ). At present, this database has a total of 57,658 PIP markers for 59 plant species that can be readily used by the researchers.…”

Section: Development Of Intron Polymorphism Markersmentioning

confidence: 99%