Abstract
Cytoplasmic male sterility (CMS) breeding systems expedite the production of hybrid seed in many crops. By taking advantage of an interaction between the nucleus and the cytoplasm that regulates the production of viable pollen, CMS eliminates the need for manual emasculation. Markers that can identify the status of cytoplasmic male sterility and nuclear restorer-of-fertility (Rf) genes are valuable for identification and development of CMS systems. In chile pepper (Capsicum annuum), reliable markers for the Rf trait have been elusive. To identify viable Rf markers for chile pepper, markers were created using identified Rf candidate genes and compared them to the most effective previously reported Rf markers. The previously reported cleaved amplified polymorphic sequence (CAPS) marker Co1Mod1-CAPS and PPR-derived CaRf648, had the highest rates of correctly predicting the Rf phenotype for an F2 segregating population. The Co1Mod1-CAPS marker detected the Rf genotype, and CaRf648 quickly and inexpensively identified Rf presence.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
The datasets generated during during the current study are available in the World Vegetable Center HARVEST repository, https://worldveg.tind.io/record/73337?ln=en.
References
Barchenger DW, Said JI, Zhang Y, Song M, Ortega FA, Ha Y, Kang BC, Bosland PW (2018) Genome-wide identification of chile pepper pentatricopeptide repeat domains provides insight into fertility restoration. J Am Soc Hort Sci 143:418–429. https://doi.org/10.21273/JASHS04522-18
Bentolila S, Alfonso AA, Hanson MR (2002) A pentatricopeptide repeat-containing gene restores fertility to cytoplasmic male-sterile plants. Proc Natl Acad Sci 99:10887–10892. https://doi.org/10.1073/pnas.102301599
Bohra A, Jha UC, Adhimoolam P, Bisht D, Singh NP (2016) Cytoplasmic male sterility (CMS) in hybrid breeding in field crops. Plant Cell Rep 35(5):967–993. https://doi.org/10.1007/s00299-016-1949-3
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. https://doi.org/10.1046/j.1365-313X.2003.01799.x
Chen L, Liu YG (2014) Male sterility and fertility restoration in crops. Annu Rev Plant Bio 65:579–606. https://doi.org/10.1146/annurev-arplant-050213-040119
Cui X, Wise RP, Schnable PS (1996) The rf2 nuclear restorer gene of male-sterile T-cytoplasm maize. Science 272:1334–1336. https://doi.org/10.1126/science.272.5266.1334
Dill CL, Wise RP, Schnable PS (1997) Rf8 and Rf* mediate unique T-urf13-transcript accumulation, revealing a conserved motif associated with RNA processing and restoration of pollen fertility in T-cytoplasm maize. Genetics 147:1367–1379
Fujii S, Yamada M, Toriyama K (2009) Cytoplasmic male sterility-related protein kinase, OsNek3, is regulated downstream of mitochondrial protein phosphatase 2C, DCW11. Plant Cell Physiol 50:828–837. https://doi.org/10.1093/pcp/pcp026
Gulyas G, Pakozdi K, Lee J-S, Hirata Y (2006) Analysis of fertility restoration by using cytoplasmic male-sterile red pepper (Capsicum annuum L.) lines. Breed Sci 56:331–334
Hu J, 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. https://doi.org/10.1105/tpc.111.093211
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 112:14984–14989. https://doi.org/10.1073/pnas.1511748112
Itabashi E, Iwata N, Fujii S, Kazama T, Toriyama K (2010) 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. https://doi.org/10.1111/j.1365-313x.2010.04427.x
Ji J-J, Huang W, Yin Y-X, Li Z, Gong Z-H (2014) Development of a SCAR marker for early identification of S-cytoplasm based on mitochondrial SRAP analysis in pepper (Capsicum annuum L.). Mol Breed 33:679–690. https://doi.org/10.1007/s11032-013-9984-z
Jo YD, Kim Y-M, Park M-N, Yoo J-H, Park M, Kim B-D, Kang B-C (2010) Development and evaluation of broadly applicable markers for Restorer-of-fertility in pepper. Mol Breed 25:187–201. https://doi.org/10.1007/s11032-009-9318-3
Jo YD, Ha Y, Lee J-H, Park M, Bergsma AC, Choi H-I, Goritsching S, Kloosterman B, van Dijk PJ, Choi D, Kang B-C (2016) 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. https://doi.org/10.1007/s00122-016-2755-6
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. https://doi.org/10.1016/S0014-5793(03)00480-0
Kazama T, Itabashi E, Fujii S, Nakamura T, Toriyama K (2016) Mitochondrial ORF79 levels determine pollen abortion in cytoplasmic male sterile rice. Plant J 85:707–716. https://doi.org/10.1111/tpj.13135
Kim DH, Kim B-D (2006) The organization of mitochondrial atp6 gene region in male fertile and CMS lines of pepper (Capsicum annuum L.). Curr Genet 49:59–67. https://doi.org/10.1007/s00294-005-0032-3
Kim DH, Kang JG, Kim B-D (2007) Isolation and characterization of the cytoplasmic male sterility-associated orf456 gene of chili pepper (Capsicum annuum L.). Plant Mol Biol 63:519–532. https://doi.org/10.1007/s11103-006-9106-y
Klein RR, Klein PE, Mullet JE, Minx P, Rooney WL, Schertz KF (2005) Fertility restorer locus Rf1of 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. https://doi.org/10.1007/s00122-005-2011-y
Komori T, Ohta S, Murai N, Takakura Y, Kuraya Y, Suzuki S, Hiel Y, Imazeki H, Nitta N (2004) Map-based cloning of a fertility restorer gene, Rf-1, in rice (Oryza sativa L.). Plant J37:315–325. https://doi.org/10.1046/j.1365-313x.2003.01961.x
Kumar R, Kumar S, Dwivedi N, Kumar S, Rai A, Singh M, Yadav DS, Rai M (2009) Validation of SCAR markers, diversity analysis of male sterile (S-) cytoplasms and isolation of an alloplasmic S-cytoplasm in Capsicum. Sci Hortic 120:167–172. https://doi.org/10.1016/j.scienta.2008.10.012
Lee J, Yoon JB, Park HG (2008) A CAPS marker associated with the partial restoration of cytoplasmic male sterility in chili pepper (Capsicum annuum L.). Mol Breed 21:95–104. https://doi.org/10.1007/s11032-007-9111-0
Liu Z, Liu P, Long F, Hong D, He Q, Yang G (2012) Fine mapping and candidate gene analysis of the nuclear restorer gene Rfp for pol CMS in rapeseed (Brassica napus L.). Theor Appl Genet 125:773–779. https://doi.org/10.1007/s00122-012-1870-2
Lin S-W, Shieh H-C, Wang Y-W, Tan C-W, Schafleitner R, Yang W-J, Kumar S (2015) Restorer breeding in sweet pepper: introgressing Rf allele from hot pepper through marker-assisted backcrossing. Sci Hortic 197:170–175. https://doi.org/10.1016/j.scienta.2015.09.036
Liu Z, Yang Z, Wang X, Li K, An H, Liu J, Yang G, Fu T, Yi B, Hong D (2016) A mitochondria-targeted PPR protein restores pol cytoplasmic male sterility by reducing orf224 transcript levels in oilseed rape. Mol Plant 9:1082–1084. https://doi.org/10.1016/j.molp.2016.04.004
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 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. https://doi.org/10.1105/tpc.104.022236
Meyer J, Pei D, Wise RP (2011) Rf8-mediated T-urf13 transcript accumulation coincides with a pentatricopeptide repeat cluster on maize chromosome 2L. Plant Genome J 4:283. https://doi.org/10.3835/plantgenome2011.05.0017
Min W-K, Kim S, Sung S-K, Kim B-D, 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. https://doi.org/10.1007/s00122-009-1134-y
Novak F (1971) Cytoplasmic male sterility in sweet pepper (Capsicum annuum L.). II. Tapetal development in male sterile anthers. Z Pflanzenzucht 65:221–232
Ortega FA, Hayano-Kanashiro AC, Bosland PW (2019) An improved extraction that increases DNA yield in chile pepper (Capsicum sp.). J Adv Plant Sci 2:106
Peterson PA (1958) Cytoplasmically inherited male sterility in capsicum. Am Nat 92:111–119. https://doi.org/10.1086/282017
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, González-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-Hernández S, Leyva-González 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 111(14):5135–5140. https://doi.org/10.1073/pnas.1400975111
R Core Team (2017) R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. https://www.R-project.org/. Accessed 10 Jan 2020
Rubinson EH, Eichman BF (2012) Nucleic acid recognition by tandem helical repeats. Curr Opin Struc Biol 22:101–109. https://doi.org/10.1016/j.sbi.2011.11.005
Shifriss C (1997) Male sterility in pepper (Capsicum annuum L.). Euphytica 93:83–88. https://doi.org/10.1023/A:1002947907046
Small ID, Peeters N (2000) The PPR motif—a TPR-related motif prevalent in plant organellar proteins. Trends Biochem Sci 25:45–47. https://doi.org/10.1016/s0968-0004(99)01520-0
Tuteja R, Saxena RK, Davila J, Shah T, Chen W, Xiao Y-L, Fan G, Saxena KB, Alverson AJ, Spillane C, Town C, Varshney RK (2013) Cytoplasmic male sterility-associated chimeric open reading frames identified by mitochondrial genome sequencing of four cajanus genotypes. DNA Res 20:485–495. https://doi.org/10.1093/dnares/dst025
Wang LH, Zhang BX, Lefebvre V, Huang SW, Daubeze AM, Palloix A (2004) QTL analysis of fertility restoration in cytoplasmic male sterile pepper. Theor Appl Genet 109:1058–1063. https://doi.org/10.1007/s00122-004-1715-8
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 Y-G (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. https://doi.org/10.1105/tpc.105.038240
Yeh T, Lin S, Shieh H, Teoh Y, Kumar S (2016) Markers for cytoplasmic male sterility (CMS) traits in chili peppers (Capsicum annuum L.). I: multiplex PCR and validation. SABRAO J Breed Genet 48:465–473
Zhang B, Huang S, Yang G, Guo J (2000) Two RAPD markers linked to a major fertility restorer gene in pepper. Euphytica 113:155–161. https://doi.org/10.1023/A:1003945723196
Acknowledgements
Funding for this research was provided by the long-term strategic donors to the World Vegetable Center, Republic of China (Taiwan); UK aid from the UK government; U.S. Agency for International Development (USAID); Australian Centre for International Agricultural Research (ACIAR), Germany, Thailand, Philippines, Korea, and Japan.
Author information
Authors and Affiliations
Contributions
FAO, DWB, and PWB conceptualized and designed the research, FAO and BW conducted the experiments. FAO wrote the paper and all authors have read, edited, and approved of the final manuscript.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that they have no conflicts of interest.
Human and animal rights
This research did not involve experiments with human or animal participants.
Additional information
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
Rights and permissions
About this article
Cite this article
Ortega, F.A., Barchenger, D.W., Wei, B. et al. Development of a genotype-specific molecular marker associated with restoration-of-fertility (Rf) in chile pepper (Capsicum annuum). Euphytica 216, 43 (2020). https://doi.org/10.1007/s10681-020-2579-y
Received:
Accepted:
Published:
DOI: https://doi.org/10.1007/s10681-020-2579-y