Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice

<p>Abstract</p> <p>Background</p> <p>We report the development of a microarray platform for rapid and cost-effective genetic mapping, and its evaluation using rice as a model. In contrast to methods employing whole-genome tiling microarrays for genotyping, our method is based on low-cost spotted microarray production, focusing only on known polymorphic features.</p> <p>Results</p> <p>We have produced a genotyping microarray for rice, comprising 880 single feature polymorphism (SFP) elements derived from insertions/deletions identified by aligning genomic sequences of the <it>japonica </it>cultivar Nipponbare and the <it>indica </it>cultivar 93-11. The SFPs were experimentally verified by hybridization with labeled genomic DNA prepared from the two cultivars. Using the genotyping microarrays, we found high levels of polymorphism across diverse rice accessions, and were able to classify all five subpopulations of rice with high bootstrap support. The microarrays were used for mapping of a gene conferring resistance to <it>Magnaporthe grisea</it>, the causative organism of rice blast disease, by quantitative genotyping of samples from a recombinant inbred line population pooled by phenotype.</p> <p>Conclusion</p> <p>We anticipate this microarray-based genotyping platform, based on its low cost-per-sample, to be particularly useful in applications requiring whole-genome molecular marker coverage across large numbers of individuals.</p

Molecular and morphometric analyses reveal discrete grouping of pomegranate (Punica granatum) genebank accessions away from cultivars

Management of germplasm in the field genebanks is greatly assisted by genetic analysis. Estimation of genetic diversity and assessment of genetic relationships among 45 accessions of pomegranate (Punica granatum L.) that included cultivars and germplasm collections were carried out using nine morphometric, 241 ISSR and six SSR markers. The average genetic distance values based on ANOVA sum of squares (Ward) were 3.94 and 5.10 for morphometric and DNA markers respectively. Hierarchical clustering based on genetic distances grouped the accessions into at least three distinct clusters; the two-way clustering showing the contribution of individual markers in genetic grouping. Discrete grouping of field genebank accessions (with IC numbers) away from cultivars was evident based both on quantitative traits data as well as DNA marker data. The findings suggested the possibility of broadening genetic base of cultivated varieties by augmenting the breeding programmes in India with diverse as well as trait- specific pomegranate germplasm

Mapping and QTL Analysis of Gynoecy and Earliness in Bitter Gourd (Momordica charantia L.) Using Genotyping-by-Sequencing (GBS) Technology

A high-density, high-resolution genetic map was constructed for bitter gourd (Momordica charantia L.). A total of 2013 high quality SNP markers binned to 20 linkage groups (LG) spanning a cumulative distance of 2329.2 cM were developed. Each LG ranging from 185.2 cM (LG-12) to 46.2 cM (LG-17) and average LG span of 116.46 cM. The number of SNP markers mapped in each LG varied from 23 markers in LG-20 to 146 markers in LG-1 with an average of 100.65 SNPs per LG. The average distance between markers was 1.16 cM across 20 LGs and average distance between the markers ranged from 0.70 (LG-4) to 2.92 (LG-20). A total of 22 QTLs for four traits (gynoecy, sex ratio, node and days at first female flower appearance) were identified and mapped on 20 LGs. The gynoecious (gy-1) locus is flanked by markers TP_54865 and TP_54890 on LG 12 at a distance of 3.04 cM to TP_54890 and the major QTLs identified for the earliness traits will be extremely useful in marker development and MAS for rapid development of various gynoecious lines with different genetic background of best combiner for development of early and high yielding hybrids in bitter gourd

Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice-1

Wn as grey.<p><b>Copyright information:</b></p><p>Taken from "Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice"</p><p>http://www.plantmethods.com/content/4/1/13</p><p>Plant Methods 2008;4():13-13.</p><p>Published online 29 May 2008</p><p>PMCID:PMC2435114.</p><p></p

Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice-2

<p><b>Copyright information:</b></p><p>Taken from "Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice"</p><p>http://www.plantmethods.com/content/4/1/13</p><p>Plant Methods 2008;4():13-13.</p><p>Published online 29 May 2008</p><p>PMCID:PMC2435114.</p><p></p

Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice-5

Wn in grey. SFPs confirmed by PCR are shown in blue (Nipponbare) and red (93-11). The positions of the centromeres are indicated with an "X".<p><b>Copyright information:</b></p><p>Taken from "Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice"</p><p>http://www.plantmethods.com/content/4/1/13</p><p>Plant Methods 2008;4():13-13.</p><p>Published online 29 May 2008</p><p>PMCID:PMC2435114.</p><p></p

Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice-0

Wn in grey. SFPs confirmed by PCR are shown in blue (Nipponbare) and red (93-11). The positions of the centromeres are indicated with an "X".<p><b>Copyright information:</b></p><p>Taken from "Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice"</p><p>http://www.plantmethods.com/content/4/1/13</p><p>Plant Methods 2008;4():13-13.</p><p>Published online 29 May 2008</p><p>PMCID:PMC2435114.</p><p></p

Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice-3

linkage model of STRUCTURE.<p><b>Copyright information:</b></p><p>Taken from "Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice"</p><p>http://www.plantmethods.com/content/4/1/13</p><p>Plant Methods 2008;4():13-13.</p><p>Published online 29 May 2008</p><p>PMCID:PMC2435114.</p><p></p

Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice-4

Nd association with the susceptible parent allele (LTH) with the resistant pool are assigned negative values. The line is drawn using loess smoothing.<p><b>Copyright information:</b></p><p>Taken from "Development and evaluation of a high-throughput, low-cost genotyping platform based on oligonucleotide microarrays in rice"</p><p>http://www.plantmethods.com/content/4/1/13</p><p>Plant Methods 2008;4():13-13.</p><p>Published online 29 May 2008</p><p>PMCID:PMC2435114.</p><p></p