Abstract
Key message
The Pseudo-Response Regulator 2 gene was identified in the c1 locus, representing a genetic factor regulating fruit color in pepper using GBS-based BSA-seq.
Abstract
The loci c1, c2, and y have been widely reported as genetic determinants of various ripe fruit colors in pepper. However, c1, which may impact reduced pigmentation in red, orange, and yellow fruits, is not well understood. Two cultivars showing peach or orange fruit in Capsicum chinense ‘Habanero’ were found to have c2 mutation and were hypothesized to segregate c1 locus in the F2 population. Habanero peach (HP) showed a reduced level of chlorophylls, carotenoids and total soluble solids in immature and ripe fruits. A microscopic examination of the fruit pericarps revealed smaller plastids and less stacked thylakoid grana in HP. The expression of many genes related to chlorophyll and carotenoid biosynthetic pathways were reduced in HP. To identify the genomic region of the c1 locus, bulked segregant analysis combined with genotyping-by-sequencing was employed on an F2 population derived from a cross between Habanero orange and HP. One SNP at chromosome 1 was strongly associated with the peach fruit color. Pepper Pseudo-Response Regulator 2 (PRR2) was located close to the SNP and cosegregated with the peach fruit color. A 41 bp deletion at the third exon–intron junction region of CcPRR2 in HP resulted in a premature termination codon. A nonsense mutation of CaPRR2 was found in C. annuum ‘IT158782’ which had white ripe fruit coupled with null mutations of capsanthin–capsorubin synthase (y) and phytoene synthase 1 (c2). These results will be useful for the genetic improvement in fruit color and nutritional quality in pepper.
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References
Berry HM, Rickett DV, Baxter CJ, Enfissi EMA, Fraser PD (2019) Carotenoid biosynthesis and sequestration in red chilli pepper fruit and its impact on colour intensity traits. J Exp Bot 70:2637–2650. https://doi.org/10.1093/jxb/erz086
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for illumina sequence data. Bioinformatics 30:2114–2120. https://doi.org/10.1093/bioinformatics/btu170
Borovsky Y et al (2019) The zinc-finger transcription factor CcLOL1 controls chloroplast development and immature pepper fruit color in Capsicum chinense and its function is conserved in tomato. Plant J 99:41. https://doi.org/10.1111/tpj.14305
Brand A, Borovsky Y, Meir S, Rogachev I, Aharoni A, Paran I (2012) pc8.1, a major QTL for pigment content in pepper fruit, is associated with variation in plastid compartment size. Planta 235:579–588. https://doi.org/10.1007/s00425-011-1530-9
Brand A, Borovsky Y, Hill T, Rahman KAA, Bellalou A, Van Deynze A, Paran I (2014) CaGLK2 regulates natural variation of chlorophyll content and fruit color in pepper fruit. Theor Appl Genet 127:2139–2148. https://doi.org/10.1007/s00122-014-2367-y
Britton G (1985) General carotenoid methods. Methods Enzymol 111:113–149. https://doi.org/10.1016/S0076-6879(85)11007-4
Carvalho RF et al (2011) Convergence of developmental mutants into a single tomato model system: ‘Micro-Tom’ as an effective toolkit for plant development research. Plant Methods 7:18. https://doi.org/10.1186/1746-4811-7-18
Cookson P et al (2003) Increases in cell elongation, plastid compartment size and phytoene synthase activity underlie the phenotype of the high pigment-1 mutant of tomato. Planta 217:896–903
Egea I et al (2011) Chloroplast to chromoplast transition in tomato fruit: spectral confocal microscopy analyses of carotenoids and chlorophylls in isolated plastids and time-lapse recording on intact live tissue. Ann Bot 108:291–297. https://doi.org/10.1093/aob/mcr140
Elshire RJ, Glaubitz JC, Sun Q, Poland JA, Kawamoto K, Buckler ES, Mitchell SE (2011) A robust, simple genotyping-by-sequencing (GBS) approach for high diversity species. PLoS ONE 6:e19379. https://doi.org/10.1371/journal.pone.0019379
Galpaz N, Wang Q, Menda N, Zamir D, Hirschberg J (2008) Abscisic acid deficiency in the tomato mutant high-pigment 3 leading to increased plastid number and higher fruit lycopene content. Plant J 53:717–730. https://doi.org/10.1111/j.1365-313x.2007.03362.x
Girardot C, Scholtalbers J, Sauer S, Su S-Y, Furlong EE (2016) Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers. BMC Bioinf 17:419
Gupta P, Sreelakshmi Y, Sharma R (2015) A rapid and sensitive method for determination of carotenoids in plant tissues by high performance liquid chromatography. Plant Methods 11:5. https://doi.org/10.1186/s13007-015-0051-0
Ha SH, Kim JB, Park JS, Lee SW, Cho KJ (2007) A comparison of the carotenoid accumulation in Capsicum varieties that show different ripening colours: deletion of the capsanthin–capsorubin synthase gene is not a prerequisite for the formation of a yellow pepper. J Exp Bot 58:3135–3144. https://doi.org/10.1093/jxb/erm132
He J, Zhao X, Laroche A, Lu ZX, Liu H, Li Z (2014) Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding. Front Plant Sci 5:484. https://doi.org/10.3389/fpls.2014.00484
Huh JH, Kang BC, Nahm SH, Kim S, Ha KS, Lee MH, Kim BD (2001) A candidate gene approach identified phytoene synthase as the locus for mature fruit color in red pepper (Capsicum spp.). Theor Appl Genet 102:524–530. https://doi.org/10.1007/s001220051677
Hurtado-Hernandez H, Smith PG (1985) Inheritance of mature fruit color in Capsicum annuum L. J Hered 76:211–213
Jeong HB et al (2019) Single-molecule real-time sequencing reveals diverse allelic variations in carotenoid biosynthetic genes in pepper (Capsicum spp.). Plant Biotechnol J 17:1081–1093. https://doi.org/10.1111/pbi.13039
Kim OR, Cho MC, Kim BD, Huh JH (2010) A splicing mutation in the gene encoding phytoene synthase causes orange coloration in Habanero pepper fruits. Mol Cells 30:569–574. https://doi.org/10.1007/s10059-010-0154-4
Kim S et al (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 46:270–278. https://doi.org/10.1038/ng.2877
Kim JE, Yoo HJ, Kang BC, Lee JM (2017a) A new nonsense mutation in capsanthin/capsorubin synthase controlling orange pepper. Horticul Sci Technol 35:599–607
Kim S et al (2017b) New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. Genome Biol 18:210. https://doi.org/10.1186/s13059-017-1341-9
Knaus BJ, Grünwald NJ (2017) vcfr: a package to manipulate and visualize variant call format data in R molecular. Ecol Resour 17:44–53
Kolotilin I et al (2007) Transcriptional profiling of high pigment-2dg tomato mutant links early fruit plastid biogenesis with its overproduction of phytonutrients. Plant Physiol 145:389–401. https://doi.org/10.1104/pp.107.102962
Lang Y-Q, Yanagawa S, Sasanuma T, Sasakuma T (2004) Orange fruit color in Capsicum due to deletion of capsanthin–capsorubin synthesis gene. Breed Sci 54:33–39
Lefebvre V, Kuntz M, Camara B, Palloix A (1998) The capsanthin–capsorubin synthase gene: a candidate gene for the y locus controlling the red fruit colour in pepper. Plant Mol Biol 36:785–789
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760. https://doi.org/10.1093/bioinformatics/btp324
Liu Y et al (2004) Manipulation of light signal transduction as a means of modifying fruit nutritional quality in tomato. Proc Natl Acad Sci USA 101:9897–9902. https://doi.org/10.1073/pnas.0400935101
Liu L, Shao Z, Zhang M, Wang Q (2015) Regulation of carotenoid metabolism in tomato. Mol Plant 8:28–39. https://doi.org/10.1016/j.molp.2014.11.006
Liu H et al (2016) Map-based cloning, identification and characterization of the w gene controlling white immature fruit color in cucumber (Cucumis sativus L.). Theor Appl Genet 129:1247–1256. https://doi.org/10.1007/s00122-016-2700-8
Lopez-Juez E, Pyke KA (2005) Plastids unleashed: their development and their integration in plant development. Int J Dev Biol 49:557–577. https://doi.org/10.1387/ijdb.051997el
McKenna A et al (2010) The genome analysis toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20:1297–1303. https://doi.org/10.1101/gr.107524.110
Meng L et al (2018) BEL1-LIKE HOMEODOMAIN 11 regulates chloroplast development and chlorophyll synthesis in tomato fruit. Plant J 94:1126–1140. https://doi.org/10.1111/tpj.13924
Michelmore RW, Paran I, Kesseli R (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci 88:9828–9832
Mizuno T (2005) Two-component phosphorelay signal transduction systems in plants: from hormone responses to circadian rhythms. Biosci Biotechnol Biochem 69:2263–2276. https://doi.org/10.1271/bbb.69.2263
Mustilli AC, Fenzi F, Ciliento R, Alfano F, Bowler C (1999) Phenotype of the tomato high pigment-2 mutant is caused by a mutation in the tomato homolog of DEETIOLATED1. Plant Cell 11:145–157. https://doi.org/10.1105/tpc.11.2.145
Nadakuduti SS, Holdsworth WL, Klein CL, Barry CS (2014) KNOX genes influence a gradient of fruit chloroplast development through regulation of GOLDEN2-LIKE expression in tomato. Plant J 78:1022–1033. https://doi.org/10.1111/tpj.12529
Nguyen CV, Vrebalov JT, Gapper NE, Zheng Y, Zhong S, Fei Z, Giovannoni JJ (2014) Tomato GOLDEN2-LIKE transcription factors reveal molecular gradients that function during fruit development and ripening. Plant Cell 26:585–601
Nisar N, Li L, Lu S, Khin NC, Pogson BJ (2015) Carotenoid metabolism in plants. Mol Plant 8:68–82. https://doi.org/10.1016/j.molp.2014.12.007
Oren E et al (2019) The multi-allelic APRR2 gene is associated with fruit pigment accumulation in melon and watermelon. J Exp Bot 70:3781. https://doi.org/10.1093/jxb/erz182
Pan Y et al (2013) Network inference analysis identifies an APRR2-like gene linked to pigment accumulation in tomato and pepper fruits. Plant Physiol 161:1476–1485
Perochon A, Dieterle S, Pouzet C, Aldon D, Galaud JP, Ranty B (2010) Interaction of a plant pseudo-response regulator with a calmodulin-like protein. Biochem Biophys Res Commun 398:747–751. https://doi.org/10.1016/j.bbrc.2010.07.016
Popovsky S, Paran I (2000) Molecular genetics of the y locus in pepper: its relation to capsanthin–capsorubin synthase and to fruit color. Theor Appl Genet 101:86–89
Powell AL et al (2012) Uniform ripening encodes a Golden 2-like transcription factor regulating tomato fruit chloroplast development. Science 336:1711–1715. https://doi.org/10.1126/science.1222218
Qin C et al (2014) Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci USA 111:5135–5140. https://doi.org/10.1073/pnas.1400975111
Rodriguez-Concepcion M et al (2018) A global perspective on carotenoids: metabolism, biotechnology, and benefits for nutrition and health. Prog Lipid Res 70:62–93. https://doi.org/10.1016/j.plipres.2018.04.004
Sun T, Yuan H, Cao H, Yazdani M, Tadmor Y, Li L (2018) Carotenoid metabolism in plants: the role of plastids. Mol Plant 11:58–74. https://doi.org/10.1016/j.molp.2017.09.010
Takagi H et al (2013) QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations. Plant J 74:174–183. https://doi.org/10.1111/tpj.12105
Tang HY et al (2018) Fine mapping and candidate gene prediction for white immature fruit skin in cucumber (Cucumis sativus L.). Int J Mol Sci. https://doi.org/10.3390/ijms19051493
Team RC (2013) R: A language and environment for statistical computing. R foundation for statistical computing, Vienna. http://www.R-project.org/
Thorup TA, Tanyolac B, Livingstone KD, Popovsky S, Paran I, Jahn M (2000) Candidate gene analysis of organ pigmentation loci in the Solanaceae. Proc Natl Acad Sci USA 97:11192–11197. https://doi.org/10.1073/pnas.97.21.11192
Truong HT et al (2012) Sequence-based genotyping for marker discovery and co-dominant scoring in germplasm and populations. PLoS ONE 7:e37565. https://doi.org/10.1371/journal.pone.0037565
Vranova E, Coman D, Gruissem W (2012) Structure and dynamics of the isoprenoid pathway network. Mol Plant 5:318–333. https://doi.org/10.1093/mp/sss015
Yoo HJ et al (2017) Inferring the genetic determinants of fruit colors in tomato by carotenoid profiling. Molecules 22:764. https://doi.org/10.3390/molecules22050764
Acknowledgements
We thank Prof. Doil Choi (Seoul National University) for sharing the C. chinense genome data and Prof. Byoung-Cheorl Kang (Seoul National University) for helping preparation of GBS library. This work was supported by the National Research Foundation of Korea (2018R1A2B6002620), Republic of Korea.
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JML conceived and designed the experiments: SBL, JEK and GML performed the experiments; HTK conducted GBS and BSA-seq analysis; BSK provided plant materials; JML, HTK, and JEK wrote the first draft of the manuscript, and all co-authors contributed and approved the final draft of the manuscript.
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Communicated by Sanwen Huang.
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Lee, S.B., Kim, J.E., Kim, H.T. et al. Genetic mapping of the c1 locus by GBS-based BSA-seq revealed Pseudo-Response Regulator 2 as a candidate gene controlling pepper fruit color. Theor Appl Genet 133, 1897–1910 (2020). https://doi.org/10.1007/s00122-020-03565-5
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DOI: https://doi.org/10.1007/s00122-020-03565-5