Use of Organelle Markers to Study Genetic Diversity in Soybean

Skuza, Lidia; Filip, Ewa; Szućko, Izabela

doi:10.5772/52028

Cited by 12 publications

(8 citation statements)

References 146 publications

(203 reference statements)

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“…Organelle genomes are preferentially used in DNA barcoding because they carry more information than nuclear markers, which are inherited biparentally (Skuza et al 2013). The main benefit of organelles is that there is only one allele per cell and per organism, and, consequently, no recombination between two alleles can occur (Skuza et al 2013). Moreover, organelle DNA can be retrieved more easily from low-quantity and/or degraded DNA samples than nuclear DNA, as it is present in many copies per cell.…”

Section: Introductionmentioning

confidence: 99%

“…As in seed plants, chloroplasts and mitochondria are mainly inherited uniparentally (Birky 1995). Organelle genomes are preferentially used in DNA barcoding because they carry more information than nuclear markers, which are inherited biparentally (Skuza et al 2013). The main benefit of organelles is that there is only one allele per cell and per organism, and, consequently, no recombination between two alleles can occur (Skuza et al 2013).…”

Section: Introductionmentioning

confidence: 99%

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Development of mitochondrial SNP markers in different Populus species

Kersten¹,

Voss²,

Fladung³

2014

Trees

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Key message We aim to develop, for the first time, poplar species-specific mitochondrial SNP markers which can be employed as diagnostic tool, e.g., to identify mitochondria belonging to different poplar species used in protoplast fusion experiments and for population genetics approaches. Abstract In most higher plant species, the inheritance of chloroplasts and mitochondria is maternal. In contrast to chloroplast DNA, however, the mitochondrial genome, especially for woody plants including poplar, has seldom been the object of molecular biological research. Published studies on mitochondrial DNA variation in poplar have dealt with genetic relationships using RFLP analyses for population genetic purposes, but so far not for species identification. In this study, we for the first time aim to develop poplar species-specific mitochondrial SNP markers which can be employed as a diagnostic tool, e.g., to identify mitochondria belonging to different poplar species used in protoplast fusion experiments. In total, seven mitochondrial regions were PCR amplified, sequenced and screened for SNPs differentiating clones belonging to six different poplar species from three sections. Two regions (Sc438, contig42) revealed to be monomorphic in the six Populus species. For the five other regions, SNPs could be identified that are suitable for distinguishing between Populus species, either by a SNP-related CAPS (cleaved amplified polymorphic site) marker to be employed in robust PCR-RFLPs, or simply on the basis of the sequence to be screened by PCR and subsequent Sanger sequencing. As a proof of concept, the developed mitochondrial SNP markers confirmed results obtained with chloroplast SNP markers in interspecific poplar hybrids, either with respect to the direction of the cross or the reclassification of putative pure lines as hybrid lines.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Development of mitochondrial SNP markers in different Populus species

Kersten¹,

Voss²,

Fladung³

2014

Trees

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“…We used simple sequence repeat (SSR, microsatellite) markers on the nuclear genomes to characterize the genetic diversity in Japanese aromatic rice, because among the many types of molecular marker in rice, SSRs are the most informative for distinguishing closely related rice species (Akagi et al 1997;Ni et al 2002;Jain et al 2004;Okoshi et al 2004;Garris et al 2005;Thomson et al 2007;Okoshi et al 2007;Prabakaran et al 2010). We also applied ORF100 (Kanno et al 1993;Chen et al 1993Chen et al , 1994 and 3 newly developed markers (OsC04, OsC11, and OsM04) from chloroplast and mitochondrial genomes to characterize genetic structure, as they are considered to be informative over a longer evolutionary history of crops than nuclear markers (Skuza et al 2013).…”

Section: Introductionmentioning

confidence: 99%

Genetic diversity in Japanese aromatic rice (Oryza sativa L.) as revealed by nuclear and organelle DNA markers

Okoshi

Matsuno

Okuno

et al. 2015

Genet Resour Crop Evol

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Aromatic rice (Oryza sativa L.) cultivated in Japan is regionally differentiated by geographical distribution and characteristics. We aimed to characterize the lineage of Japanese aromatic rice using DNA markers. Based on analyses with nuclear SSR markers, we found that Japanese aromatic rice cultivars belong, with one exception, to japonica but showed some differences from authentic japonica and were divided into two clades that were distributed in western and eastern Japan, respectively. Further analyses with organelle markers showed that most of the cultivars in eastern Japan had cytoplasm characterized by tropical japonica, whereas most of those in western Japan had cytoplasm characterized by temperate japonica. We postulate that the ancestor of the cultivars in eastern Japan differs from those of the cultivars in western Japan, and that the two groups may have been separately introduced from Taiwan into Japan. The cytoplasm of aromatic rice cultivars in western Japan may have originated from tropical japonica and been substituted into the cytoplasm of temperate japonica through hybridization between tropical japonica as a male parent and temperate japonica as a female parent.

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“…Chloroplasts and mitochondria are mainly inherited uniparentally in seeded plants [ 64 ]. The chloroplast genome is usually maternally inherited in most angiosperm species, including cruciferous crops, such as cabbage, broccoli, and cauliflower [ 47 , 65 ], although it can also be paternally [ 66 – 67 ] or biparentally inherited [ 68 – 69 ]. Mitochondrial DNA is maternally inherited or passed via paternal transmission [ 67 ].…”

Section: Discussionmentioning

confidence: 99%

“…The main advantage of organelle genomes is that no recombination can occur between two alleles, because there is only one allele per cell and per organism [ 69 ]. Furthermore, organelle DNA can be easily obtained because it exists in many copies in each cell.…”

Section: Discussionmentioning

confidence: 99%

Organelle Simple Sequence Repeat Markers Help to Distinguish Carpelloid Stamen and Normal Cytoplasmic Male Sterile Sources in Broccoli

Shu

Liu

et al. 2015

PLoS ONE

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We previously discovered carpelloid stamens when breeding cytoplasmic male sterile lines in broccoli (Brassica oleracea var. italica). In this study, hybrids and multiple backcrosses were produced from different cytoplasmic male sterile carpelloid stamen sources and maintainer lines. Carpelloid stamens caused dysplasia of the flower structure and led to hooked or coiled siliques with poor seed setting, which were inherited in a maternal fashion. Using four distinct carpelloid stamens and twelve distinct normal stamens from cytoplasmic male sterile sources and one maintainer, we used 21 mitochondrial simple sequence repeat (mtSSR) primers and 32 chloroplast SSR primers to identify a mitochondrial marker, mtSSR2, that can differentiate between the cytoplasm of carpelloid and normal stamens. Thereafter, mtSSR2 was used to identify another 34 broccoli accessions, with an accuracy rate of 100%. Analysis of the polymorphic sequences revealed that the mtSSR2 open reading frame of carpelloid stamen sterile sources had a deletion of 51 bases (encoding 18 amino acids) compared with normal stamen materials. The open reading frame is located in the coding region of orf125 and orf108 of the mitochondrial genomes in Brassica crops and had the highest similarity with Raphanus sativus and Brassica carinata. The current study has not only identified a useful molecular marker to detect the cytoplasm of carpelloid stamens during broccoli breeding, but it also provides evidence that the mitochondrial genome is maternally inherited and provides a basis for studying the effect of the cytoplasm on flower organ development in plants.

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Use of Organelle Markers to Study Genetic Diversity in Soybean

Cited by 12 publications

References 146 publications

Development of mitochondrial SNP markers in different Populus species

Development of mitochondrial SNP markers in different Populus species

Genetic diversity in Japanese aromatic rice (Oryza sativa L.) as revealed by nuclear and organelle DNA markers

Organelle Simple Sequence Repeat Markers Help to Distinguish Carpelloid Stamen and Normal Cytoplasmic Male Sterile Sources in Broccoli

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