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Fine mapping of Restorer-of-fertility in pepper (Capsicum annuum L.) identified a candidate gene encoding a pentatricopeptide repeat (PPR)-containing protein

Abstract

Key message

Using fine mapping techniques, the genomic region co-segregating with Restorer - of - fertility ( Rf ) in pepper was delimited to a region of 821 kb in length. A PPR gene in this region, CaPPR6 , was identified as a strong candidate for Rf based on expression pattern and characteristics of encoding sequence.

Abstract

Cytoplasmic-genic male sterility (CGMS) has been used for the efficient production of hybrid seeds in peppers (Capsicum annuum L.). Although the mitochondrial candidate genes that might be responsible for cytoplasmic male sterility (CMS) have been identified, the nuclear Restorer-of-fertility (Rf) gene has not been isolated. To identify the genomic region co-segregating with Rf in pepper, we performed fine mapping using an Rf-segregating population consisting of 1068 F2 individuals, based on BSA-AFLP and a comparative mapping approach. Through six cycles of chromosome walking, the co-segregating region harboring the Rf locus was delimited to be within 821 kb of sequence. Prediction of expressed genes in this region based on transcription analysis revealed four candidate genes. Among these, CaPPR6 encodes a pentatricopeptide repeat (PPR) protein with PPR motifs that are repeated 14 times. Characterization of the CaPPR6 protein sequence, based on alignment with other homologs, showed that CaPPR6 is a typical Rf-like (RFL) gene reported to have undergone diversifying selection during evolution. A marker developed from a sequence near CaPPR6 showed a higher prediction rate of the Rf phenotype than those of previously developed markers when applied to a panel of breeding lines of diverse origin. These results suggest that CaPPR6 is a strong candidate for the Rf gene in pepper.

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References

  1. Barkan A, Small I (2014) Pentatricopeptide repeat proteins in plants. Annu Rev Plant Biol 65:415–442

  2. Barkan A, Rojas M, Fujii S, Yap A, Chong YS, Bond CS, Small I (2012) A combinatorial amino acid code for RNA recognition by pentatricopeptide repeat proteins. PLoS Genet 8:e1002910

  3. Barr CM, Fishman L (2010) Cytoplasmic male sterility in Mimulus hybrids has pleiotropic effects on corolla and pistil traits. Heredity (Edinb) 106:886–893

  4. 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

  5. Brown GG, Formanova 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

  6. Chen L, Liu YG (2014) Male sterility and fertility restoration in crops. Annu Rev Plant Biol 65:579–606

  7. Cui X, Wise RP, Schnable PS (1996) The rf2 nuclear restorer gene of male-sterile T-cytoplasm maize. Science 272:1334–1336

  8. Dahan J, Mireau H (2013) The Rf and Rf-like PPR in higher plants, a fast-evolving subclass of PPR genes. RNA Biol 10:1469–1476

  9. 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

  10. 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

  11. 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

  12. Geddy R, Brown GG (2007) Genes encoding pentatricopeptide repeat (PPR) proteins are not conserved in location in plant genomes and may be subject to diversifying selection. BMC Genom 8:130

  13. Gulyas G, Pakozdi K, Lee JS, Hirata Y (2006) Analysis of fertility restoration by using cytoplasmic male-sterile red pepper (Capsicum annuum L.) lines. Breed Sci 56:331–334

  14. Hanson MR, Bentolila S (2004) Interactions of mitochondrial and nuclear genes that affect male gametophyte development. Plant Cell 16(Suppl):S154–169

  15. Holzle A, Jonietz C, Torjek O, Altmann T, Binder S, Forner J (2011) A RESTORER OF FERTILITY-like PPR gene is required for 5′-end processing of the nad4 mRNA in mitochondria of Arabidopsis thaliana. Plant J 65:737–744

  16. Hu J, Wang K, Huang W, Liu G, Gao Y, Wang J, Huang Q, Ji Y, Qin X, Wan L, Zhu R, Li S, Yang D, Zhu Y (2012) The rice pentatricopeptide repeat protein RF5 restores fertility in Hong-Lian cytoplasmic male-sterile lines via a complex with the glycine-rich protein GRP162. Plant Cell 24:109–122

  17. Huang W, Yu C, Hu J, Wang L, Dan Z, Zhou W, He C, Zeng Y, Yao G, Qi J, Zhang Z, Zhu R, Chen X, Zhu Y (2015) Pentatricopeptide-repeat family protein RF6 functions with hexokinase 6 to rescue rice cytoplasmic male sterility. Proc Natl Acad Sci USA 112:14984–14989

  18. 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

  19. Jeong HJ, Jo YD, Kang BC (2010) Identification of Capsicum species using SNP markers based on high resolution melting analysis. Genome 53:1029–1040

  20. Jo YD, Kim YM, Park MN, Yoo JH, Park M, Kim BD, Kang BC (2010) Development and evaluation of broadly applicable markers for Restorer-of-fertility in pepper. Mol Breed 25:187–201

  21. Jonietz C, Forner J, Hildebrandt T, Binder S (2011) RNA PROCESSING FACTOR3 is crucial for the accumulation of mature ccmC transcripts in mitochondria of Arabidopsis accession Columbia. Plant Physiol 157:1430–1439

  22. 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

  23. Kim DS (2005) Development of RAPD and AFLP markers linked to fertility restorer (Rf) gene in chili pepper (Capsicum annuum L.). Thesis, Seoul National University

  24. Kim DH, Kim BD (2006) The organization of mitochondrial atp6 gene region in male fertile and CMS lines of pepper (Capsicum annuum L.). Curr Genet 49:59–67

  25. Kim DS, Kim DH, Yoo JH, Kim BD (2006) Cleaved amplified polymorphic sequence and amplified fragment length polymorphism markers linked to the fertility restorer gene in chili pepper (Capsicum annuum L.). Mol Cells 21:135–140

  26. Kim DH, Kang JG, Kim BD (2007) Isolation and characterization of the cytoplasmic male sterility-associated orf456 gene of chili pepper (Capsicum annuum L.). Plant Mol Biol 63:519–532

  27. Kim HJ, Baek KH, Lee SW, Kim J, Lee BW, Cho HS, Kim WT, Choi D, Hur CG (2008) Pepper EST database: comprehensive in silico tool for analyzing the chili pepper (Capsicum annuum) transcriptome. BMC Plant Biol 8:101

  28. Kim YM, Jo YD, Kwon JK, Kim IT, Kang BC (2013) Characterization and inheritance of a novel thermo-sensitive restoration of cytoplasmic male sterility in Capsicum annuum. Sci Hortic 164:512–520

  29. Kim S, Park M, Yeom SI, Kim YM, Lee JM, Lee HA, Seo E, Choi J, Cheong K, Kim KT, Jung K, Lee GW, Oh SK, Bae C, Kim SB, Lee HY, Kim SY, Kim MS, Kang BC, Jo YD, Yang HB, Jeong HJ, Kang WH, Kwon JK, Shin C, Lim JY, Park JH, Huh JH, Kim JS, Kim BD, Cohen O, Paran I, Suh MC, Lee SB, Kim YK, Shin Y, Noh SJ, Park J, Seo YS, Kwon SY, Kim HA, Park JM, Kim HJ, Choi SB, Bosland PW, Reeves G, Jo SH, Lee BW, Cho HT, Choi HS, Lee MS, Yu Y, Do Choi Y, Park BS, van Deynze A, Ashrafi H, Hill T, Kim WT, Pai HS, Ahn HK, Yeam I, Giovannoni JJ, Rose JK, Sorensen I, Lee SJ, Kim RW, Choi IY, Choi BS, Lim JS, Lee YH, Choi D (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 46:270–278

  30. Klein RR, Klein PE, Mullet JE, Minx P, Rooney WL, Schertz KF (2005) Fertility restorer locus Rf1 [corrected] of sorghum (Sorghum bicolor L.) encodes a pentatricopeptide repeat protein not present in the colinear region of rice chromosome 12. Theor Appl Genet 111:994–1012

  31. 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

  32. 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

  33. Kubo T, Kitazaki K, Matsunaga M, Kagami H, Mikami T (2011) Male sterility-inducing mitochondrial genomes: how do they differ? Crit Rev Plant Sci 30:378–400

  34. Lee J, Yoon JB, Park HG (2008a) A CAPS marker associated with the partial restoration of cytoplasmic male sterility in chili pepper (Capsicum annuum L.). Mol Breed 21:95–104

  35. Lee J, Yoon JB, Park HG (2008b) Linkage analysis between the partial restoration (pr) and the restorer-of-fertility (Rf) loci in pepper cytoplasmic male sterility. Theor Appl Genet 117:383–389

  36. Li J, Pandeya D, Jo YD, Liu WY, Kang BC (2013) Reduced activity of ATP synthase in mitochondria causes cytoplasmic male sterility in chili pepper. Planta 237:1097–1109

  37. Liu C, Ma N, Wang PY, Fu N, Shen HL (2013) Transcriptome sequencing and de novo analysis of a cytoplasmic male sterile line and its near-isogenic restorer line in chili pepper (Capsicum annuum L.). PLoS ONE 8:e65209

  38. Luo D, Xu H, Liu Z, Guo J, Li H, Chen L, Fang C, Zhang Q, Bai M, Yao N, Wu H, Wu H, Ji C, Zheng H, Chen Y, Ye S, Li X, Zhao X, Li R, Liu YG (2013) A detrimental mitochondrial-nuclear interaction causes cytoplasmic male sterility in rice. Nat Genet 45:573–577

  39. Lurin C, Andres C, Aubourg S, Bellaoui M, Bitton F, Bruyere C, Caboche M, Debast C, Gualberto J, Hoffmann B, Lecharny A, Le Ret M, Martin-Magniette ML, Mireau H, Peeters N, Renou JP, 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

  40. 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

  41. Min WK, Lim H, Lee YP, Sung SK, Kim BD, Kim S (2008) Identification of a third haplotype of the sequence linked to the Restorer-of-fertility (Rf) gene and its implications for male-sterility phenotypes in peppers (Capsicum annuum L.). Mol Cells 25:20–29

  42. Min WK, Kim S, Sung SK, Kim BD, Lee S (2009) Allelic discrimination of the Restorer-of-fertility gene and its inheritance in peppers (Capsicum annuum L.). Theor Appl Genet 119:1289–1299

  43. Ohgami T, UchiyamaD Ue S, Yui-Kurino R, Yoshida Y, Kamei Y, Kuroda Y, Taguchi K, Kubo T (2016) Identification of molecular variants of the nonrestoring restorer-of-fertility 1 allele in sugar beet (Beta vulgaris L.). Theor Appl Genet 129:675–688

  44. Peterson PA (1958) Cytoplasmically inherited male sterility in Capsicum. Am Nat 92:111–119

  45. Qin C, Yu C, Shen Y, Fang X, Chen L, Min J, Cheng J, Zhao S, Xu M, Luo Y, Yang Y, Wu Z, Mao L, Wu H, Ling-Hu C, Zhou H, Lin H, Gonzalez-Morales S, Trejo-Saavedra DL, Tian H, Tang X, Zhao M, Huang Z, Zhou A, Yao X, Cui J, Li W, Chen Z, Feng Y, Niu Y, Bi S, Yang X, Li W, Cai H, Luo X, Montes-Hernandez S, Leyva-Gonzalez MA, Xiong Z, He X, Bai L, Tan S, Tang X, Liu D, Liu J, Zhang S, Chen M, Zhang L, Zhang L, Zhang Y, Liao W, Zhang Y, Wang M, Lv X, Wen B, Liu H, Luan H, Zhang Y, Yang S, Wang X, Xu J, Li X, Li S, Wang J, Palloix A, Bosland PW, Li Y, Krogh A, Rivera-Bustamante RF, Herrera-Estrella L, Yin Y, Yu J, Hu K, Zhang Z (2014) Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci USA 111:5135–5140

  46. Shifriss C (1997) Male sterility in pepper (Capsicum annuum L.). Euphytica 93:83–88

  47. Small ID, Peeters N (2000) The PPR motif—a TPR-related motif prevalent in plant organellar proteins. Trends Biochem Sci 25:46–47

  48. Tomato Genome C (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641

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

  50. Vos P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M et al (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414

  51. Wang Z, Zou Y, Li X, Zhang Q, Chen L, Wu H, Su D, Chen Y, Guo J, Luo D, Long Y, Zhong Y, Liu YG (2006) Cytoplasmic male sterility of rice with boro II cytoplasm is caused by a cytotoxic peptide and is restored by two related PPR motif genes via distinct modes of mRNA silencing. Plant Cell 18:676–687

  52. Xu XB, Liu ZX, Zhang DF, Liu Y, Song WB, Li JS, Dai JR (2009) Isolation and analysis of rice Rf1-orthologus PPR genes co-segregating with Rf3 in maize. Plant Mol Biol Rep 27:511–517

  53. Yoo EY, Kim S, Kim YH, Lee CJ, Kim BD (2003) Construction of a deep coverage BAC library from Capsicum annuum, ‘CM334’. Theor Appl Genet 107:540–543

  54. Zhang BX, Huang SW, Yang GM, Guo JZ (2000) Two RAPD markers linked to a major fertility restorer gene in pepper. Euphytica 113:155–161

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Acknowledgments

This research was supported by the Golden Seed Project (213002-04-3-CG900), the Ministry of Agriculture, Food and Rural Affairs (MAFRA), the Ministry of Oceans and Fisheries (MOF), the Rural Development Administration (RDA), and the Korea Forest Service (KFS), Republic of Korea, and a grant (710001-07) from the Vegetable Breeding Research Center through the Agriculture, Food and Rural Affairs Research Center Support Program, Ministry of Agriculture, Food and Rural Affairs.

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Correspondence to Byoung-Cheorl Kang.

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Conflict of interest

This research was supported by the Golden Seed Project (213002-04-3-CG900), the Ministry of Agriculture, Food and Rural Affairs (MAFRA), the Ministry of Oceans and Fisheries (MOF), the Rural Development Administration (RDA), and the Korea Forest Service (KFS), Republic of Korea, and a grant (710001-07) from the Vegetable Breeding Research Center through the Agriculture, Food and Rural Affairs Research Center Support Program, Ministry of Agriculture, Food and Rural Affairs.

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Communicated by M. J. Havey.

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Jo, Y.D., Ha, Y., Lee, J. et al. Fine mapping of Restorer-of-fertility in pepper (Capsicum annuum L.) identified a candidate gene encoding a pentatricopeptide repeat (PPR)-containing protein. Theor Appl Genet 129, 2003–2017 (2016). https://doi.org/10.1007/s00122-016-2755-6

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Keywords

  • Amplify Fragment Length Polymorphism
  • Bacterial Artificial Chromosome
  • Cytoplasmic Male Sterility
  • Bacterial Artificial Chromosome Clone
  • Amplify Fragment Length Polymorphism Marker