Development of genome‐wide insertion/deletion markers in rice based on graphic pipeline platform

Abstract

DNA markers play important roles in plant breeding and genetics. The Insertion/Deletion (InDel) marker is one kind of co-dominant DNA markers widely used due to its low cost and high precision. However, the canonical way of searching for InDel markers is time-consuming and laborintensive. We developed an end-to-end computational solution (InDel Markers Development Platform, IMDP) to identify genome-wide InDel markers under a graphic pipeline environment. IMDP constitutes assembled genome sequences alignment pipeline (AGA-pipe) and next-generation resequencing data mapping pipeline (NGS-pipe). With AGA-pipe we are able to identify 12,944 markers between the genome of rice cultivars Nipponbare and 93-11. Using NGS-pipe, we reported 34,794 InDels from re-sequencing data of rice cultivars Wu-Yun-Geng7 and Guang-Lu-Ai4. Combining AGApipe and NGS-pipe, we developed 205,659 InDels in eight japonica and nine indica cultivars and 2,681 InDels showed a subgroup-specific pattern. Polymerase chain reaction (PCR) analysis of subgroup-specific markers indicated that the precision reached 90% (86 of 95). Finally, to make them available to the public, we have integrated the InDels/markers information into a website (Rice InDel Marker Database, RIMD, http://202.120.45.71/). The application of IMDP in rice will facilitate efficiency for development of genome-wide InDel markers, in addition it can be used in other species with reference genome sequences and NGS data.

A Rice Glutamyl-tRNA Synthetase Modulates Early Anther Cell Division and Patterning

“…The OsERS1 gene was initially located to 546 chromosome 10 between two InDel molecular markers, 10tys14 and 10tys2, 547 and finer mapping narrowed down the gene to the region between RM25267 548 and 10tys28. Mapping combined with genome sequencing was performed 549 using the previously published method (Abe et al, 2012;Lü et al, 2015). 550…”

Analysis of ‘Fuji’ apple somatic variants from next-generation sequencing

“…The application of NGS (next-generation sequencing) technologies has led to the effective discovery of numerous genome-wide DNA polymorphisms, such as single nucleotide polymorphisms (SNPs), and insertions or deletions (InDels) (Varshney et al, 2009), which reduce the cost of marker development (Gao et al, 2012;Lü et al, 2015). SNPs are the most abundant type of DNA sequence polymorphism (Lijavetzky et al, 2007).…”

Indel Group in Genomes (IGG) Molecular Genetic Markers

“…Testing pairs of known unique primers for amplicon size differences is done within other indel marker programs (Liu et al, 2015;Lü et al, 2015;Zhou et al, 2015), but it is normally limited to very short distances and single indel spans. The actual limits on amplicon sizes and size differences are parameters specified when IGGPIPE is run to generate the markers, providing user flexibility while also allowing length limits like those of traditional indel markers to be obtained when desired.…”

“…We compared the features and performance of IGGPIPE with two other marker creation tools, IMDP (Lü et al, 2015) and PolyMarker (Ramirez-Gonzalez et al, 2015), that also process whole-genome data in silico (Table X). Markers are discovered by IGGPIPE and IMDP, whereas PolyMarker requires SNPs as input and generates primers.…”

“…Available tools include the Indel Markers Development Platform (IMDP) for indel markers (Lü et al, 2015), PolyMarker to generate SNP-specific primers around known SNPs (Ramirez-Gonzalez et al, 2015b), the EST SSR Marker Pipeline to find short sequence repeats for Reference to the article defining the marker technique and in some cases to the article first using the marker acronym. The marker acronym may have originated later than the invention of the marker technique, and the identification of the polymorphism upon which the marker is based may have occurred earlier than the invention of the technique.…”