Identification of novel insertion–deletion markers for Dongxiang wild rice (Oryza rufipogon Griff.) using high-throughput sequencing technology

Zhang, Fantao; Zhang, Liangxing; Cui, Fenglei; Luo, Xiangdong; Zhou, Yi; Xie, Jingzhong

doi:10.1007/s12041-015-0556-3

Cited by 3 publications

(4 citation statements)

References 19 publications

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“…The most abundant chromosomes for SVs were chromosomes 1, 12, 10, and 6, with one SV per 18.24, 18.67, 18.81, and 18.99 kb, respectively (Table 1). Of these, chromosomes 1, 6, and 10 also have a high density of InDels and SNPs (Zhang et al, 2015(Zhang et al, , 2017, implying that these chromosomes had more abundant genetic variations than the other chromosomes.…”

Section: Discussionmentioning

confidence: 99%

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Application of SV markers developed from Dongxiang common wild rice in analysis of cultivated rice

Zhang

Luo

et al. 2019

Plant Genet. Resour.

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Dongxiang common wild rice (Oryza rufipogon Griff., DXWR) is an important genetic resource for the improvement of cultivated rice. For the past three decades, great achievements have been made in the field of molecular marker development. Although structural variations (SVs) had been studied between DXWR and Nipponbare (Oryza sativa L. ssp. japonica), the development and application of SV markers in DXWR has not been reported. In this study, based on the genome-wide SV loci, we developed and synthesized a total of 195 SV markers that were evenly distributed across the 12 rice chromosomes. Then, these markers were tested for their stabilities and polymorphisms. Of these 195 markers, 147 (75.4%) were successfully amplified and displayed abundant polymorphisms between DXWR and Nipponbare. Meanwhile, through the genotyping of 20 rice varieties from 13 countries and areas, we concluded that these SV markers have a wide application prospect in the analysis of cultivated rice. Therefore, these molecular markers greatly enrich the number of markers available for DXWR, which will facilitate genomic research and molecular breeding for this important and endangered germplasm resource.

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Section: Discussionmentioning

confidence: 99%

“…Whole-genome sequencing, reads filtering, and clean reads mapping to the reference genome were performed as previously (Zhang et al ., 2015). Based on the paired-end sequence method, one read should be mapped to the forward strand, and the other to the reverse strand.…”

Section: Methodsmentioning

confidence: 99%

Application of SV markers developed from Dongxiang common wild rice in analysis of cultivated rice

Zhang

Luo

et al. 2019

Plant Genet. Resour.

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“…In our previous study, whole-genome sequencing of DXWR was performed and 282,383,842 paired-end reads (90 bp per read) were obtained after filtering, and approximately 228 million reads were uniquely aligned with the reference genome of Nipponbare. An overall effective depth of 55× coverage was achieved, and the resulting consensus sequence was 357,407,193 bp, with 95.76% coverage of the Nipponbare genome (Zhang et al ., 2015).…”

Section: Discussionmentioning

confidence: 99%

“…In this study, we used data from our previous study regarding whole-genome sequencing, reads filtering, and mapping to the published rice (Nipponbare) reference genome (http://rice.plantbiology.msu.edu/) (Kawahara et al, 2013). The sequencing data of DXWR are deposited in NCBI with the accession number SRA167397 (Zhang et al, 2015). SNP loci in the consensus sequence were detected by comparing with the reference sequence and then filtered using specific requirements (quality value >20 and the result supported by at least two reads) using SoapSNP (Chagné et al, 2012).…”

Section: Methodsmentioning

confidence: 99%

Genome-wide SNPs detection by genomic comparison between Dongxiang wild rice (Oryza rufipogon) and cultivated rice Nipponbare (Oryza sativa ssp. japonica)

Zhang

Huang

Xia

et al. 2017

Plant Genet. Resour.

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Dongxiang wild rice (Oryza rufipogon, DXWR) exhibits valuable agronomic traits and represents a precious germplasm resource for rice breeding. The use of genetic markers can greatly speed up the breeding process and facilitate research on genetics and genomics. In our previous study, we identified insertion–deletion polymorphisms between DXWR and cultivated rice Nipponbare (Oryza sativa ssp. japonica), using whole-genome sequencing in DXWR. In this study, to further explore the genetic variations and enrich the available genetic markers of DXWR, we identified 1,089,478 single-nucleotide polymorphisms (SNPs) (corresponding to one SNP per 0.33 kb of the genome) by genomic comparison between DXWR and Nipponbare, using the genome sequencing data and bioinformatics approaches. Furthermore, the accuracy of the identified SNPs was also validated by polymerase chain reaction amplification and Sanger sequencing. This genome-wide SNPs identification greatly increases the number of genetic markers available for DXWR and provides new opportunities to exploit this valuable and endangered germplasm resource.

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Development of a drought stress-resistant rice restorer line through Oryza sativa–rufipogon hybridization

Luo

Lao

et al. 2019

J Genet

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Identification of novel insertion–deletion markers for Dongxiang wild rice (Oryza rufipogon Griff.) using high-throughput sequencing technology

Cited by 3 publications

References 19 publications

Application of SV markers developed from Dongxiang common wild rice in analysis of cultivated rice

Application of SV markers developed from Dongxiang common wild rice in analysis of cultivated rice

Genome-wide SNPs detection by genomic comparison between Dongxiang wild rice (Oryza rufipogon) and cultivated rice Nipponbare (Oryza sativa ssp. japonica)

Development of a drought stress-resistant rice restorer line through Oryza sativa–rufipogon hybridization

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