Development of 1047 insertion-deletion markers for rice genetic studies and breeding

Abstract

ABSTRACT. In this study, a total of 1047 insertion-deletion (InDel) primer pairs distributed across the rice genome were developed and experimentally validated. The primer pairs were designed based on the InDel length polymorphisms between 93-11 (Oryza sativa ssp indica cv.) and Nipponbare (Oryza sativa ssp japonica cv.), aiming for utilization between indica and japonica rice, or between other inter-subspecific rice cultivars. The 1047 primer pairs were dispersed across all 12 of the rice chromosomes, with one InDel marker found every 371.3 kb on average. The InDel length of the markers varied from 3 to 39 bp: 88.2% of the markers contained 6 to 25 bp, only 6.2% of markers were ≤5 bp, and 5.6% were ≥26 bp. Six hundred and twenty-three (59.5%) of the 1047 InDel markers were shown to amplify well and were polymorphic between Taichung65 and IR8, and 476 (45.5%) markers were polymorphic between Lemont and Yangdao4, while 398 (38.0%) were polymorphic in both combinations. These results demonstrated that the polymerase chain reaction-based InDel markers developed in this study could be of immediate use for rice genetic studies and breeding programs.

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

“…The number of e-PCR validated InDel markers (>6 bp in length) in this study was 12,944, which was 11 times more than the reported 1,047 in another study (Zeng et al 2013). We further compared the 12,944 e-PCR validated markers in this study to the 986 InDels developed by Zeng et al (2013). The data we obtained from the paper of Zeng et al (2013) only contained information of primers, making it hard to obtain the exact locations of InDels and therefore prohibited us from comparing all of these InDels against our own dataset.…”

“…To confirm the efficiency of AGA-pipe, we compared the InDels/markers obtained from another two studies and our study. The number of e-PCR validated InDel markers (>6 bp in length) in this study was 12,944, which was 11 times more than the reported 1,047 in another study (Zeng et al 2013). We further compared the 12,944 e-PCR validated markers in this study to the 986 InDels developed by Zeng et al (2013).…”

“…We further compared the 12,944 e-PCR validated markers in this study to the 986 InDels developed by Zeng et al (2013). The data we obtained from the paper of Zeng et al (2013) only contained information of primers, making it hard to obtain the exact locations of InDels and therefore prohibited us from comparing all of these InDels against our own dataset. We filtered the 1,047 pairs of PCR primers developed through MFEprimer2, and after removing mismatching primers and primers whose amplification products were not on target chromosomes, only 806 InDels were accurately located Query: genome or a single DNA sequence, such as 93-11 genome sequence.…”

Mapping quantitative trait loci for sheath blight disease resistance in Yangdao 4 rice

“…Because the SSR marker polymorphisms were low between Lemont and Yangdao 4, we developed insertion-deletion (InDel) markers to augment the polymorphic markers (Zeng et al, 2013b). Using the F 2 population planted in E1, a genetic linkage map with 180 markers was constructed, including 52 SSR markers and 128 InDel markers.…”

“…org/). The forward and reverse sequences of the 128 InDel markers were previously described by Zeng et al (2013b). Based on the ShB-QTL identified in E1 and E2, the F 2 population grown in E3 was assayed using 41 markers.…”