Construction of a high-resolution linkage map of Rfd1, a restorer-of-fertility locus for cytoplasmic male sterility conferred by DCGMS cytoplasm in radish (Raphanus sativus L.) using synteny between radish and Arabidopsis genomes

Cho, Youngcho; Lee, Young-Pyo; Park, Beom-Seok; Han, Tae-Ho; Kim, Sunggil

doi:10.1007/s00122-012-1846-2

Cited by 15 publications

(5 citation statements)

References 60 publications

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“…We constructed a linkage map with a total of 1384 markers ( Supplementary Table S16 ) including 630 markers from the Kazusa DNA laboratory 75 , 746 markers from Tohoku University 25 and 8 markers from Chonnam National University 76 . If the assigned linkage number and direction differed from the Kazusa and Tohoku linkage maps, we used the Kazusa linkage map information, which was published previously 75 .…”

Section: Methodsmentioning

confidence: 99%

The radish genome and comprehensive gene expression profile of tuberous root formation and development

Mitsui

Shimomura

Kono

et al. 2015

Sci Rep

168

146

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Understanding the processes that regulate plant sink formation and development at the molecular level will contribute to the areas of crop breeding, food production and plant evolutionary studies. We report the annotation and analysis of the draft genome sequence of the radish Raphanus sativus var. hortensis (long and thick root radish) and transcriptome analysis during root development. Based on the hybrid assembly approach of next-generation sequencing, a total of 383 Mb (N50 scaffold: 138.17 kb) of sequences of the radish genome was constructed containing 54,357 genes. Syntenic and phylogenetic analyses indicated that divergence between Raphanus and Brassica coincide with the time of whole genome triplication (WGT), suggesting that WGT triggered diversification of Brassiceae crop plants. Further transcriptome analysis showed that the gene functions and pathways related to carbohydrate metabolism were prominently activated in thickening roots, particularly in cell proliferating tissues. Notably, the expression levels of sucrose synthase 1 (SUS1) were correlated with root thickening rates. We also identified the genes involved in pungency synthesis and their transcription factors.

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Section: Methodsmentioning

confidence: 99%

The radish genome and comprehensive gene expression profile of tuberous root formation and development

Mitsui

Shimomura

Kono

et al. 2015

Sci Rep

168

146

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“…In many cases, synteny between the genomes of crop and model species has been used to identify orthologous genes and putative exon-intron boundaries. For example, a high-resolution linkage map of radish was constructed using the synteny between radish and Arabidopsis (Cho et al, 2012). In the case of onion, rice is the most closely related model species, but the syntenic relationship between the two genomes was reported to be very low (Martin et al, 2005;Jakše et al, 2006).…”

Section: Discussionmentioning

confidence: 99%

Application of the Molecular Marker in Linkage Disequilibrium with Ms, a Restorer-of-fertility Locus, for Improvement of Onion Breeding Efficiency

Kim

Kim²

2015

HST

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To analyze the linkage relationships among molecular markers recently reported to be linked to onion (Allium cepa L.) Ms, a restorer-of-fertility locus, in onion (Allium cepa L.), three single nucleotide polymorphism markers were converted into cleaved amplified polymorphic sequence (CAPS) markers based on onion transcriptome sequences and the rice genome database. Analysis of the recombinants selected from 4,273 segregating plants using CAPS and other linked markers demonstrated the jnurf13 and jnurf610 markers to perfectly co-segregate with the Ms locus. In contrast to jnurf13, the jnurf610 marker was not in perfect linkage disequilibrium with the Ms locus in diverse breeding lines. Thus, the jnurf13 marker and the marker for identification of cytoplasm types were utilized to enhance the efficiency of onion breeding through four applications. First, 89 maintainer lines containing the normal cytoplasm and homozygous recessive Ms genotypes were successfully identified from 100 breeding lines. Second, these two molecular markers were used to analyze the main sources of male-fertile contaminants frequently found in the male-sterile parental lines during F1 hybrid seed production. The majority of the contaminants contained heterozygous Ms genotypes, indicating that pollen grains harboring the dominant Ms genotype may have been introduced during propagation of the maintainer lines. Therefore, the genetic purity of the two maintainer lines was analyzed in the third application, and the results showed that both maintainer lines contained 13-21% off-types. Finally, the two markers were used to increase the seed yield potentials of two open-pollinated varieties containing sterile cytoplasms by removing the plants harboring homozygous recessive and heterozygous Ms genotypes.

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“…However, such instability was not reported in two previous articles (Lee et al 2008, Wang et al 2020. To better understand fertility restoration, cloning of the Rf genes is needed, and the DNA markers developed by Cho et al (2012) would be useful for such a purpose.…”

Section: Rf Genes For Orf463mentioning

confidence: 97%

Appearance of male sterile and black radishes in the progeny of cross between <i>Raphanus raphanistrum</i> and <i>Raphanus sativus</i>

et al. 2020

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In addition to Ogura cytoplasmic male sterility (CMS), which is used extensively for F 1 hybrid seed production in Brassicaceae crops, two other CMS systems, NWB CMS and DCGMS, have also been identified. The causal gene for the latter two CMS systems has been identified as a novel chimeric gene, orf463 . We previously reported that orf463 is specific to black radish cultivars and that it is present in line ‘RS-5’ of Raphanus raphanistrum ; however, the orf463 sequence in ‘RS-5’ differed from that of black radish cultivars. Though, R. raphanistrum with an orf463 sequence identical to that found in black radish cultivars was recently identified. We therefore sought to determine whether the orf463 gene in line ‘RS-5’ induces CMS in radishes. We crossed ‘RS-5’ as a female parent with a cultivated radish, ‘Uchiki-Gensuke’, as a male parent, and examined the gross plant morphology and pollen fertility of the resulting progeny. The F 2 population contained both male sterile plants and plants with black roots. The findings showed that R. raphanistrum contains two types of orf463 genes that induce CMS, and that the origin of black radishes could be attributed to R. raphanistrum having orf463 gene.

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Construction of a high-resolution linkage map of Rfd1, a restorer-of-fertility locus for cytoplasmic male sterility conferred by DCGMS cytoplasm in radish (Raphanus sativus L.) using synteny between radish and Arabidopsis genomes

Cited by 15 publications

References 60 publications

The radish genome and comprehensive gene expression profile of tuberous root formation and development

The radish genome and comprehensive gene expression profile of tuberous root formation and development

Application of the Molecular Marker in Linkage Disequilibrium with Ms, a Restorer-of-fertility Locus, for Improvement of Onion Breeding Efficiency

Appearance of male sterile and black radishes in the progeny of cross between <i>Raphanus raphanistrum</i> and <i>Raphanus sativus</i>

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