Abstract
The Capsicum genus comprises approximately thirty species with different ploidy and chromosome base number for which the understanding of the phylogenetic relationships has been a target of many researches since forty years. The earliest morphological, biochemical, and molecular studies allowed to identify three main groups (Annuum, Baccatum, and Pubescens) enclosing the most widely used species in terms of consumption and breeding. The advent of molecular markers gave new insight into the taxonomy of the genus better clarifying previous classifications. In addition, the progress made in the field of biology and the release of whole genome sequences have accelerated comparative mapping between pepper and the major solanaceous species such as tomato, potato, and eggplant. This chapter is a review of modern approaches that contributed to study the phylogenentic relationships and evolution of Capsicum species. Main comparative studies in pepperĀ using genetic and genomic approaches are also discussed.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Barboza GE, Bianchetti LDB (2005) Three new species of Capsicum (Solanaceae) and a key to the wild species from Brazil. Syst Bot 30:863ā871
Ben-Chaim A, Brodsky Y, Falise M, Mazourek M et al (2006) QTL analysis for capsaicinoid content in Capsicum. Theor Appl Genet 113:1481ā1490
Caranta C, Thabuis A, Palloix A (1999) Development of a CAPS marker for the Pvr4 locus: a tool for pyramiding potyvirus resistance genes in pepper. Genome 42:1111ā1116
Carrizo GC, Barfuss HJ, Sehr EM, Barboza GE, Samuel R, Moscone EA, Ehrendorfer F (2016) Phylogenetic relationships, diversification and expansion of chili peppers (Capsicum, Solanaceae). Ann Bot 118:35ā51
Di Dato F, Parisi M, Cardi T, Tripodi P (2015) Genetic diversity and assessment of markers linked to resistance and pungency genes in Capsicum germplasm. Euphytica 1:103ā119
Djian-Caporalino C, Pijarowski L, Fazari A, Samson M, Gaveau L, OāByrne C, Lefebvre V, Caranta C, Palloix A, Abad P (2001) High-resolution genetic mapping of the pepper (Capsicum annuum L.) resistance loci Me3 and Me4 conferring heat-stable resistance to root-knot nematodes (Meloidogyne spp.). Theor Appl Genet 103(4):592ā600
Gonzalez-PĆ©rez S, GarceĆ©s-Claver A, Mallor C, SĆ enz de Miera LE, Fayos O, Pomar F, Merino F, Silvar C (2014) New insights into Capsicum spp. relatedness and the diversification process of Capsicum annuum in Spain. PLoS One 9(12):116276
Hill T, Ashrafi H, Chin-Wo SR, Stoffel K, Truco MJ, Kozik A, Michelmore R, Van Deynze A (2015) Ultra-high density, transcript-based genetic maps of pepper define recombination in the genome and synteny among related species. Genes Genomes Genet 5(11):2341ā2355
Hunziker AT (2001) Genera Solanacearum: the genera of Solanaceae illustrated, arranged according to a new system. Gantner Verlag, Ruggell, Liechtenstein
Ibiza VP, Blanca J, Canizares J, Nuez F (2012) Taxonomy and genetic diversity of domesticated Capsicum species in the Andean region. Genet Resour Crop Evol 59:1077ā1088
Ince AG, Karaca M, Onus AN (2010) Genetic relationships within and between Capsicum species. Biochem Genet 48:83ā95
Jarret RL (2008) DNA barcoding in a crop genebank: the Capsicum annuum species complex. Opin Biol J 1:35ā42
Jeong HJ, Jo YD, Park SW, Kang BC (2010) Identification of Capsicum species using SNP markers based on high resolution melting analysis. Genome 53:1029ā1040
Kim S, Park M, Yeom SI, Kim YM, Lee JM, Lee HA et al (2014) Genome sequence of the hot pepper provides insights into the evolution of pungency in Capsicum species. Nat Genet 46:270ā278
Kim S, Park J, Yeom SI, Kim YM, Seo E, Kim KT et al (2017) New reference genome sequences of hot pepper reveal the massive evolution of plant disease-resistance genes by retroduplication. Genome Biol 18:210
Lanteri S, Pickersgill B (1993) Chromosomal structural-changes in Capsicum annuum L. and C. chinense Jacq. Euphytica 67:155ā160
Lee HY, Ro NY, Jeong HJ, Kwon JK, Jo J, Ha Y, Jung A, Han JW, Venkatesh J, Kang BC (2016) Genetic diversity and population structure analysis to construct a core collection from a large Capsicum germplasm. BMC Genet 17:142
Lefebvre V, Palloix A, Caranta C, Pochard E (1995) Construction of an intra-specific integrated linkage map of pepper using molecular markers and double dhaploid progenies. Genome 38:112ā121
Lefebvre V, Pflieger S, Thabuis A, Caranta C, Blattes A, Chauvet JC, DaubĆØze AM, Palloix A (2002) Towards the saturation of the pepper linkage map by alignment of three intraspecific maps including known-function genes. Genome 45:839ā854
McLeod MJ, Guttman SI, Eshbaugh WH (1982) Early evolution of chili peppers (Capsicum). Econ Bot 36:361ā368
Minamiyama Y, Tsuro M, Hirai M (2006) An SSR-based linkage map of Capsicum annuum. Mol Breed 18:157ā169
Moscone EA, Baranyi M, Ebert I, Greilhuber J, Ehrendorfer F, Hunziker AT (2003) Analysis of nuclear DNA content in Capsicum (Solanaceae) by flow cytometry and Feulgen densitometry. Ann Bot 92:21ā29
Moury B, Pflieger S, Blattes A, Lefebvre V, Palloix A (2000) A CAPS marker to assist selection of Tomato spotted wilt virus (TSWV) resistance in pepper. Genome 43:137ā142
Nicolai M, Cantet M, Lefebvre V, Sage-Palloix AM, Palloix A (2013) Genotyping a large collection of pepper (Capsicum spp.) with SSR loci brings new evidence for the wild origin of cultivated C. annuum and the structuring of genetic diversity by human selection of cultivar types. Genet Resour Crop Evol 60:2375ā2390
Paran I, Van der Voort JR, Lefebvre V, Jahn M et al (2004) An integrated genetic linkage map of pepper (Capsicum spp.). Mol Breed 13:251ā261
Park Y-K, Park K-C, Park C-H, Kim N-S (2000) Chromosomal localization and sequence variation of 5Sr RNA gene in five Capsicum species. Mol Cells 10:18ā24
Pickersgill B (1971) Relationships between weedy and cultivated forms in some species of chili peppers (genus Capsicum). Evolution 25:683ā691
Pickersgill B (1988) The genus Capsicum: a multidisciplinary approach to the taxonomy of cultivated and wild plants. Biol Zentrabl 107:381ā389
Pochard E (1970) Description of trisomic individuals of Capsicum annuum L. obtained in progeny of a haploid plant. Ann Amel Plantes 20:233ā256
Qin C, Yu C, Shen Y, Fang X, Chen L, Min J et al (2014) Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci USA 111:5135ā5140
Rinaldi R, Van Deynze A, Portis E, Rotino GL, Toppino L, Hill T, Ashrafi H, Barchi L, Lanteri S (2016) New insights on eggplant/tomato/pepper synteny and identification of eggplant and pepper orthologous QTL. Front Plant Sci 7:1031
Tanksley SD, Bernatzky R, Lapitan NL, Prince JP (1988) Conservation of gene repertoire but not gene order in pepper and tomato. Proc Natl Acad Sci USA 85:6419ā6423
Thabuis A, Palloix A, Servin B, DaubĆØze AM, Signoret P, Hospital F, Lefebvre V (2004) Marker-assisted introgression of 4 Phytophthora capsici resistance QTL alleles into a bell pepper line: validation of additive and epistatic effects. Mol Breed 14:9ā20
Thorup T, Tanyolac B, Livingstone K, Popovsky S, Paran I, Jahn M (2000) Candidate gene analysis of organ pigmentation loci in the Solanaceae. Proc Natl Acad Sci USA 97:11192ā11197
Walsh BM, Hoot SB (2001) Phylogenetic relationships of Capsicum (Solanaceae) using DNA sequences from two non-coding regions: the chloroplast atpB-rbcL spacer region and nuclear waxy introns. Int J Plant Sci 162:1409ā1418
Wu FN, Tanksley SD (2010) Chromosomal evolution in the plant family Solanaceae. BMC Genom 11:182
Wu FN, Mueller LA, Crouzillat D, Petiard V, Tanksley SD (2006) Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics 174:1407ā1420
Wu FN, Eannetta NT, Xu YM, Durrett R, Mazourek M, Jahn M, Tanksley S (2009) A high density COSII map of the pepper genome provides a detailed picture of synteny with tomato and new insights into recent chromosome evolution in the genus. Theor Appl Genet 118:1279ā1293
Yoon JB, Park HG (2005) Trispecies bridge crosses, (Capsicum annuum Ć C. chinense) Ć C. baccatum, as an alternative for introgression of anthracnose resistance from C. baccatum into C. annuum. J Kor Soc Hort Sci 46:5ā9
Zygier S, Ben Chaim A, Efrati A, Kaluzky G et al (2005) QTL mapping for fruit size and shape in chromosomes 2 and 4 in pepper and a comparison of the pepper QTL map with that of tomato. Theor Appl Genet 111:437ā445
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
Ā© 2019 Springer Nature Switzerland AG
About this chapter
Cite this chapter
Tripodi, P. (2019). Revisiting Origin, Evolution, and Phylogenetics of Capsicums in the Genomics Era. In: Ramchiary, N., Kole, C. (eds) The Capsicum Genome. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-319-97217-6_12
Download citation
DOI: https://doi.org/10.1007/978-3-319-97217-6_12
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-319-97216-9
Online ISBN: 978-3-319-97217-6
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)