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High-resolution genetic mapping and physical map construction for the fertility restorer Rfm1 locus in barley

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High-resolution genetic linkage mapping and BAC physical mapping narrowed the fertility restorer locus Rfm1 in barley to a sub-centimorgan genetic interval and a 208-kb physical interval.

Abstract

Rfm1 restores the fertility of msm1 and msm2 male-sterile cytoplasms in barley. The fertility restoration gene is located on the short arm of chromosome 6H (6HS), and we pursued a positional cloning of this gene. Starting from a previous result that has delimited Rfm1 within a 10.8 cM region on 6HS, we developed novel CAPS and SSR markers tightly linked to the gene in barley using the sequence information from the syntenic region of rice and barley genome assemblies. Next, we performed fine mapping of the Rfm1 locus. To isolate recombinants, we surveyed 3,638 F2 plants derived from a cross between the CMS strain and the Rf strain with adjacent markers (NAS2090 and NAS1080). This analysis identified 175 recombinant plants from the F2 population to build a high-resolution map with nine markers tightly linked to the Rfm1 locus. Rfm1 was located within the 0.14 cM region delimited by two markers (NAS9113 and NAS9200). Using these flanking markers as well as marker cosegregating with Rfm1 (NAS9133), we screened the BAC libraries of the cultivar Morex, an rfm1 carrier. We isolated 11 BAC clones and constructed a BAC physical map using their fingerprints. Finally, we delimited the Rfm1 locus encompassing the rfm1 allele on a 208-kb contig composed of three minimally overlapping BAC clones. This precise localization of the Rfm1 locus in the barley genome is expected to greatly accelerate the future map-based cloning of the Rfm1 gene by sequence analysis and its genetic transformation for the complementation of cytoplasmic male-sterile plants.

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References

  • Ahokas H (1979) Cytoplasmic male sterility in barley. Acta Agric Scand 29:219–224

    Article  Google Scholar 

  • Ahokas H (1982) Cytoplasmic male sterility in barley. Xi. The msm2 cytoplasm. Genetics 102:285–295

    CAS  PubMed Central  PubMed  Google Scholar 

  • Akagi H, Nakamura A, Yokozeki-Misono Y, Inagaki A, Takahashi H, Mori K, Fujimura T (2004) Positional cloning of the rice Rf-1 gene, a restorer of BT-type cytoplasmic male sterility that encodes a mitochondria-targeting PPR protein. Theor Appl Genet 108:1449–1457

    Article  CAS  PubMed  Google Scholar 

  • Ariyadasa R, Mascher M, Nussbaumer T, Schulte D, Frenkel Z, Poursarebani N, Zhou R, Steuernagel B, Gundlach H, Taudien S, Felder M, Platzer M, Himmelbach A, Schmutzer T, Hedley PE, Muehlbauer GJ, Scholz U, Korol A, Mayer KFX, Waugh R, Langridge P, Graner A, Stein N (2014) A sequence-ready physical map of barley anchored genetically by two million SNPs. Plant Physiol 164:412–423

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Bentolila S, Alfonso AA, Hanson MR (2002) A pentatricopeptide repeat-containing gene restores fertility to cytoplasmic male-sterile plants. Proc Natl Acad Sci USA 99:10887–10892

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Brown G, Formanová N, Jin H, Wargachuk R, Dendy C, Patil P, Laforest M, Zhang J, Cheung WY, Landry BS (2003) The radish Rfo restorer gene of Ogura cytoplasmic male sterility encodes a protein with multiple pentatricopeptide repeats. Plant J 35:262–272

    Article  CAS  PubMed  Google Scholar 

  • Desloire S, Gherbi H, Laloui W, Marhadour S, Clouet V, Cattolico L, Falentin C, Giancola S, Renard M, Budar F, Small I, Caboche M, Delourme R, Bendahmane A (2003) Identification of the fertility restoration locus, Rfo, in radish, as a member of the pentatricopeptide-repeat protein family. EMBO Rep 4:588–594

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Fujii S, Toriyama K (2009) Suppressed expression of retrograde-regulated male sterility restores pollen fertility in cytoplasmic male sterile rice plants. Proc Natl Acad Sci USA 106:9513–9518

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Fujii S, Bond CS, Small ID (2011) Selection patterns on restorer-like genes reveal a conflict between nuclear and mitochondrial genomes throughout angiosperm evolution. Proc Natl Acad Sci USA 108:1723–1728

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Hanson M, Bentolila S (2004) Interactions of mitochondrial and nuclear genes that affect male gametophyte development. Plant Cell 16:S154–S169

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436:793–800

    Article  Google Scholar 

  • Itabashi E, Iwata N, Fujii S, Kazama T, Toriyama K (2011) The fertility restorer gene, Rf2, for lead rice-type cytoplasmic male sterility of rice encodes a mitochondrial glycine-rich protein. Plant J 65:359–367

    Article  CAS  PubMed  Google Scholar 

  • Iwata H, Ninomiya S (2006) AntMap: constructing genetic linkage maps using an ant colony optimization algorithm. Breed Sci 56:371–377

    Article  Google Scholar 

  • Kazama T, Toriyama K (2003) A pentatricopeptide repeat-containing gene that promotes the processing of aberrant atp6 RNA of cytoplasmic male-sterile rice. FEBS Lett 544:99–102

    Article  CAS  PubMed  Google Scholar 

  • Koizuka N, Imai R, Fujimoto H, Hayakawa T, Kimura Y, Kohno-Murase J, Sakai T, Kawasaki S, Imamura J (2003) Genetic characterization of a pentatricopeptide repeat protein gene, orf687, that restores fertility in the cytoplasmic male-sterile Kosena radish. Plant J 34:407–415

    Article  CAS  PubMed  Google Scholar 

  • Komatsuda T, Pourkheirandish M, He C, Azhaguvel P, Kanamori H, Perovic D, Stein N, Graner A, Wicker T, Tagiri A, Lundqvist U, Fujimura T, Matsuoka M, Matsumoto T, Yano M (2007) Six-rowed barley originated from a mutation in a homeodomain-leucine zipper I-class homeobox gene. Proc Natl Acad Sci USA 104:1424–1429

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Komori T, Ohta S, Murai N, Takakura Y, Kuraya Y, Suzuki S, Hiei Y, Imaseki H, Nitta N (2004) Map-based cloning of a fertility restorer gene, Rf-1, in rice (Oryza sativa L.). Plant J 37:315–325

    Article  CAS  PubMed  Google Scholar 

  • Konieczny A, Ausubel FM (1993) A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 4:403–410

    Article  CAS  PubMed  Google Scholar 

  • Kosambi DD (1943) The estimation of map distances from recombination values. Ann Eugen 12:172–175

    Article  Google Scholar 

  • Künzel G, Korzun L, Meister A (2000) Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints. Genetics 154:397–412

    PubMed Central  PubMed  Google Scholar 

  • Lurin C, Andrés C, Aubourg S, Bellaoui M, Bitton F, Bruyère C, Caboche M, Debast C, Gualberto J, Hoffmann B, Lecharny A, Le Ret M, Martin-Magniette M-L, Mireau H, Peeters N, Renou J-P, Szurek B, Taconnat L, Small I (2004) Genome-wide analysis of Arabidopsis pentatricopeptide repeat proteins reveals their essential role in organelle biogenesis. Plant Cell 16:2089–2103

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Matsuhira H, Kagami H, Kurata M, Kitazaki K, Matsunaga M, Hamaguchi Y, Hagihara E, Ueda M, Harada M, Muramatsu A, Yui-Kurino R, Taguchi K, Tamagake H, Mikami T, Kubo T (2012) Unusual and typical features of a novel restorer-of-fertility gene of sugar beet (Beta vulgaris L.). Genetics 192:1347–1358

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Matsui K, Mano Y, Taketa S, Kawada N, Komatsuda T (2001) Molecular mapping of a fertility restoration locus (Rfm1) for cytoplasmic male sterility in barley (Hordeum vulgare L.). Theor Appl Genet 102:477–482

    Article  CAS  Google Scholar 

  • Mayer K, Martis M, Hedley P, imková H, Liu H, Morris JA, Steuernagel B, Taudien S, Roessner S, Gundlach H, Kubaláková M, Suchánková P, Murat F, Felder M, Nussbaumer T, Graner A, Salse J, Endo T, Sakai H, Tanaka T, Itoh T, Sato K, Platzer M, Matsumoto T, Scholz U, Dolezel J, Waugh R, Stein N (2011) Unlocking the barley genome by chromosomal and comparative genomics. Plant Cell 23:1249–1263

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Moore G, Devos KM, Wang Z, Gale MD (1995) Cereal genome evolution. Grasses, line up and form a circle. Curr Biol 5:737–739

    Article  CAS  PubMed  Google Scholar 

  • Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Neff MM, Neff JD, Chory J, Pepper AE (1998) dCAPS, a simple technique for the genetic analysis of single nucleotide polymorphisms: experimental applications in Arabidopsis thaliana genetics. Plant J 14:387–392

    Article  CAS  PubMed  Google Scholar 

  • O’Toole N, Hattori M, Andres C, Iida K, Lurin C, Schmitz-Linneweber C, Sugita M, Small I (2008) On the expansion of the pentatricopeptide repeat gene family in plants. Mol Biol Evol 25:1120–1128

    Article  PubMed  Google Scholar 

  • Ramage RT (1983) Heterosis and hybrid seed production in barley. In: Frankel R (ed) Heterosis: reappraisal of theory and practice. Series: monographs on theoretical and applied genetics vol 6. Springer, Berlin, pp 71–93

    Google Scholar 

  • Schulte D, Ariyadasa R, Shi B, Fleury D, Saski C, Atkins M, de Jong P, Wu CC, Graner A, Langridge P, Stein N (2011) BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.). BMC Genom 12:247

    Article  CAS  Google Scholar 

  • The International Barley Genome Sequencing Consortium (2012) A physical, genetic and functional sequence assembly of the barley genome. Nature 491:711–716

    Google Scholar 

  • Touzet P, Budar F (2004) Unveiling the molecular arms race between two conflicting genomes in cytoplasmic male sterility? Trends Plant Sci 9:568–570

    Article  CAS  PubMed  Google Scholar 

  • Yu Y, Tomkins JP, Waugh R, Frisch DA, Kudrna D, Kleinhofs A, Brueggeman RS, Muehlbauer GJ, Wise RP, Wing RA (2000) A bacterial artificial chromosome library for barley (Hordeum vulgare L.) and the identification of clones containing putative resistance genes. Theor Appl Genet 101:1093–1099

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported in part by a grant from the Ministry of Agriculture, Forestry, and Fisheries of Japan (Genomics-based Technology for Agricultural Improvement, TRS-1002).

Conflict of interest

The authors have declared no conflict of interest.

Author information

Author notes

  1. Mohammad Sameri

    Present address: Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences, Box 7080, 750 07, Uppsala, Sweden

  2. Mohammad Pourkheirandish

    Present address: Wheat and Barley Research Division, National Institute of Crop Sciences, 2-1-18, Kan-non-dai, Tsukuba, 305-8518, Japan

Authors and Affiliations

  1. Plant Genome Research Unit, National Institute of Agrobiological Sciences, 2-1-2, Kan-non-dai, Tsukuba, 305-8602, Japan

    Hajime Ui, Mohammad Sameri, Mohammad Pourkheirandish, Takao Komatsuda & Hirokazu Handa

  2. Department of Biological Science and Technology, Tokyo University of Science, 6-3-1, Niijuku, Katsushika, Tokyo, 125-8585, Japan

    Hajime Ui & Hiroaki Shimada

  3. Department of Agronomy, National Taiwan University, No.1, Sec.4, Roosevelt Road, Taipei 106, Taiwan

    Men-Chi Chang

  4. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland (OT Gatersleben), 06466, Germany

    Nils Stein

  5. Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1, Ten-noh-dai, Tsukuba, 305-8572, Japan

    Hirokazu Handa

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  1. Hajime Ui
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Correspondence to Hirokazu Handa.

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Communicated by Peter Langridge.

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Ui, H., Sameri, M., Pourkheirandish, M. et al. High-resolution genetic mapping and physical map construction for the fertility restorer Rfm1 locus in barley. Theor Appl Genet 128, 283–290 (2015). https://doi.org/10.1007/s00122-014-2428-2

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  • DOI: https://doi.org/10.1007/s00122-014-2428-2

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