1
|
Fang P, Arens P, Liu X, Zhang X, Lakwani D, Foucher F, Clotault J, Geike J, Kaufmann H, Debener T, Bai Y, Zhang Z, Smulders MJM. Analysis of allelic variants of RhMLO genes in rose and functional studies on susceptibility to powdery mildew related to clade V homologs. Theor Appl Genet 2021; 134:2495-2515. [PMID: 33934211 PMCID: PMC8277636 DOI: 10.1007/s00122-021-03838-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
Rose has 19 MLO genes. Of these, RhMLO1 and RhMLO2 were shown to be required for powdery mildew infection, which suggests their potential as susceptibility targets towards disease resistance. Powdery mildew, caused by Podosphaera pannosa, is one of the most serious and widespread fungal diseases for roses, especially in greenhouse-grown cut roses. It has been shown that certain MLO genes are involved in powdery mildew susceptibility and that loss of function in these genes in various crops leads to broad-spectrum, long-lasting resistance against this fungal disease. For this reason, these MLO genes are called susceptibility genes. We carried out a genome-wide identification of the MLO gene family in the Rosa chinensis genome, and screened for allelic variants among 22 accessions from seven different Rosa species using re-sequencing and transcriptome data. We identified 19 MLO genes in rose, of which four are candidate genes for functional homologs in clade V, which is the clade containing all dicot MLO susceptibility genes. We detected a total of 198 different allelic variants in the set of Rosa species and accessions, corresponding to 5-15 different alleles for each of the genes. Some diploid Rosa species shared alleles with tetraploid rose cultivars, consistent with the notion that diploid species have contributed to the formation of tetraploid roses. Among the four RhMLO genes in clade V, we demonstrated using expression study, virus-induced gene silencing as well as transient RNAi silencing that two of them, RhMLO1 and RhMLO2, are required for infection by P. pannosa and suggest their potential as susceptibility targets for powdery mildew resistance breeding in rose.
Collapse
Affiliation(s)
- Peihong Fang
- Plant Breeding, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Paul Arens
- Plant Breeding, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Xintong Liu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Xin Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | - Deepika Lakwani
- IRHS, Agrocampus-Ouest, INRAE, Université D’Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Fabrice Foucher
- IRHS, Agrocampus-Ouest, INRAE, Université D’Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Jérémy Clotault
- IRHS, Agrocampus-Ouest, INRAE, Université D’Angers, SFR 4207 QuaSaV, 49071 Beaucouzé, France
| | - Juliane Geike
- Institute of Plant Genetics, Molecular Plant Breeding Unit, Leibniz Universität Hannover, Hannover, Germany
| | - Helgard Kaufmann
- Institute of Plant Genetics, Molecular Plant Breeding Unit, Leibniz Universität Hannover, Hannover, Germany
| | - Thomas Debener
- Institute of Plant Genetics, Molecular Plant Breeding Unit, Leibniz Universität Hannover, Hannover, Germany
| | - Yuling Bai
- Plant Breeding, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
| | - Zhao Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, College of Horticulture, China Agricultural University, Beijing, 100193 China
| | | |
Collapse
|
2
|
Soufflet-Freslon V, Araou E, Jeauffre J, Thouroude T, Chastellier A, Michel G, Mikanagi Y, Kawamura K, Banfield M, Oghina-Pavie C, Clotault J, Pernet A, Foucher F. Diversity and selection of the continuous-flowering gene, RoKSN, in rose. Hortic Res 2021; 8:76. [PMID: 33790245 PMCID: PMC8012652 DOI: 10.1038/s41438-021-00512-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 01/11/2021] [Accepted: 03/01/2021] [Indexed: 05/23/2023]
Abstract
Blooming seasonality is an important trait in ornamental plants and was selected by humans. Wild roses flower only in spring whereas most cultivated modern roses can flower continuously. This trait is explained by a mutation of a floral repressor gene, RoKSN, a TFL1 homologue. In this work, we studied the origin, the diversity and the selection of the RoKSN gene. We analyzed 270 accessions, including wild and old cultivated Asian and European roses as well as modern roses. By sequencing the RoKSN gene, we proposed that the allele responsible for continuous-flowering, RoKSNcopia, originated from Chinese wild roses (Indicae section), with a recent insertion of the copia element. Old cultivated Asian roses with the RoKSNcopia allele were introduced in Europe, and the RoKSNcopia allele was progressively selected during the 19th and 20th centuries, leading to continuous-flowering modern roses. Furthermore, we detected a new allele, RoKSNA181, leading to a weak reblooming. This allele encodes a functional floral repressor and is responsible for a moderate accumulation of RoKSN transcripts. A transient selection of this RoKSNA181 allele was observed during the 19th century. Our work highlights the selection of different alleles at the RoKSN locus for recurrent blooming in rose.
Collapse
Affiliation(s)
- Vanessa Soufflet-Freslon
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000 Angers, France, 49071, Beaucouzé, France.
| | - Emilie Araou
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000 Angers, France, 49071, Beaucouzé, France
| | - Julien Jeauffre
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000 Angers, France, 49071, Beaucouzé, France
| | - Tatiana Thouroude
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000 Angers, France, 49071, Beaucouzé, France
| | - Annie Chastellier
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000 Angers, France, 49071, Beaucouzé, France
| | - Gilles Michel
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000 Angers, France, 49071, Beaucouzé, France
| | | | | | - Mark Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich Research Park, Norwich, UK
| | | | - Jérémy Clotault
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000 Angers, France, 49071, Beaucouzé, France
| | - Alix Pernet
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000 Angers, France, 49071, Beaucouzé, France
| | - Fabrice Foucher
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAV, F-49000 Angers, France, 49071, Beaucouzé, France.
| |
Collapse
|
3
|
Menz I, Lakhwani D, Clotault J, Linde M, Foucher F, Debener T. Analysis of the Rdr1 gene family in different Rosaceae genomes reveals an origin of an R-gene cluster after the split of Rubeae within the Rosoideae subfamily. PLoS One 2020; 15:e0227428. [PMID: 31971947 PMCID: PMC6977733 DOI: 10.1371/journal.pone.0227428] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 12/18/2019] [Indexed: 11/20/2022] Open
Abstract
The Rdr1 gene confers resistance to black spot in roses and belongs to a large TNL gene family, which is organized in two major clusters at the distal end of chromosome 1. We used the recently available chromosome scale assemblies for the R. chinensis 'Old Blush' genome, re-sequencing data for nine rose species and genome data for Fragaria, Rubus, Malus and Prunus to identify Rdr1 homologs from different taxa within Rosaceae. Members of the Rdr1 gene family are organized into two major clusters in R. chinensis and at a syntenic location in the Fragaria genome. Phylogenetic analysis indicates that the two clusters existed prior to the split of Rosa and Fragaria and that one cluster has a more recent origin than the other. Genes belonging to cluster 2, such as the functional Rdr1 gene muRdr1A, were subject to a faster evolution than genes from cluster 1. As no Rdr1 homologs were found in syntenic positions for Prunus persica, Malus x domestica and Rubus occidentalis, a translocation of the Rdr1 clusters to the current positions probably happened after the Rubeae split from other groups within the Rosoideae approximately 70-80 million years ago during the Cretaceous period.
Collapse
Affiliation(s)
- Ina Menz
- Institute for Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Deepika Lakhwani
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, Beaucouzé, France
| | - Jérémy Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, Beaucouzé, France
| | - Marcus Linde
- Institute for Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Fabrice Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d’Angers, Beaucouzé, France
| | - Thomas Debener
- Institute for Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| |
Collapse
|
4
|
Debray K, Marie-Magdelaine J, Ruttink T, Clotault J, Foucher F, Malécot V. Identification and assessment of variable single-copy orthologous (SCO) nuclear loci for low-level phylogenomics: a case study in the genus Rosa (Rosaceae). BMC Evol Biol 2019; 19:152. [PMID: 31340752 PMCID: PMC6657147 DOI: 10.1186/s12862-019-1479-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 07/16/2019] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND With an ever-growing number of published genomes, many low levels of the Tree of Life now contain several species with enough molecular data to perform shallow-scale phylogenomic studies. Moving away from using just a few universal phylogenetic markers, we can now target thousands of other loci to decipher taxa relationships. Making the best possible selection of informative sequences regarding the taxa studied has emerged as a new issue. Here, we developed a general procedure to mine genomic data, looking for orthologous single-copy loci capable of deciphering phylogenetic relationships below the generic rank. To develop our strategy, we chose the genus Rosa, a rapid-evolving lineage of the Rosaceae family in which several species genomes have recently been sequenced. We also compared our loci to conventional plastid markers, commonly used for phylogenetic inference in this genus. RESULTS We generated 1856 sequence tags in putative single-copy orthologous nuclear loci. Associated in silico primer pairs can potentially amplify fragments able to resolve a wide range of speciation events within the genus Rosa. Analysis of parsimony-informative site content showed the value of non-coding genomic regions to obtain variable sequences despite the fact that they may be more difficult to target in less related species. Dozens of nuclear loci outperform the conventional plastid phylogenetic markers in terms of phylogenetic informativeness, for both recent and ancient evolutionary divergences. However, conflicting phylogenetic signals were found between nuclear gene tree topologies and the species-tree topology, shedding light on the many patterns of hybridization and/or incomplete lineage sorting that occur in the genus Rosa. CONCLUSIONS With recently published genome sequence data, we developed a set of single-copy orthologous nuclear loci to resolve species-level phylogenomics in the genus Rosa. This genome-wide scale dataset contains hundreds of highly variable loci which phylogenetic interest was assessed in terms of phylogenetic informativeness and topological conflict. Our target identification procedure can easily be reproduced to identify new highly informative loci for other taxonomic groups and ranks.
Collapse
Affiliation(s)
- Kevin Debray
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France.
| | | | - Tom Ruttink
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - Jérémy Clotault
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Fabrice Foucher
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - Valéry Malécot
- IRHS, Agrocampus-Ouest, INRA, UNIV Angers, SFR 4207 QuaSaV, Beaucouzé, France.
| |
Collapse
|
5
|
Proïa F, Panloup F, Trabelsi C, Clotault J. Probabilistic reconstruction of genealogies for polyploid plant species. J Theor Biol 2019; 462:537-551. [PMID: 30500601 DOI: 10.1016/j.jtbi.2018.11.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 11/20/2018] [Accepted: 11/27/2018] [Indexed: 10/27/2022]
Abstract
A probabilistic reconstruction of genealogies in a polyploid population (from 2x to 4x) is investigated, by considering genetic data analyzed as the probability of allele presence in a given genotype. Based on the likelihood of all possible crossbreeding patterns, our model enables us to infer and to quantify the whole potential genealogies in the population. We explain in particular how to deal with the uncertain allelic multiplicity that may occur with polyploids. Then we build an ad hoc penalized likelihood to compare genealogies and to decide whether a particular individual brings sufficient information to be included in the taken genealogy. This decision criterion enables us in a next part to suggest a greedy algorithm in order to explore missing links and to rebuild some connections in the genealogies, retrospectively. As a by-product, we also give a way to infer the individuals that may have been favored by breeders over the years. In the last part we highlight the results given by our model and our algorithm, firstly on a simulated population and then on a real population of rose bushes. Most of the methodology relies on the maximum likelihood principle and on graph theory.
Collapse
Affiliation(s)
- Frédéric Proïa
- LAREMA, Faculté des Sciences, 2 Boulevard Lavoisier, 49045 Angers, France.
| | - Fabien Panloup
- LAREMA, Faculté des Sciences, 2 Boulevard Lavoisier, 49045 Angers, France.
| | - Chiraz Trabelsi
- LAREMA, Faculté des Sciences, 2 Boulevard Lavoisier, 49045 Angers, France.
| | - Jérémy Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, 49071, France.
| |
Collapse
|
6
|
Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Arens P, Voorrips RE, Maliepaard C, Neu E, Linde M, Le Paslier MC, Bérard A, Bounon R, Clotault J, Choisne N, Quesneville H, Kawamura K, Aubourg S, Sakr S, Smulders MJM, Schijlen E, Bucher E, Debener T, De Riek J, Foucher F. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. Nat Plants 2018; 4:473-484. [PMID: 29892093 DOI: 10.1101/254102] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/01/2018] [Indexed: 05/27/2023]
Abstract
Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.
Collapse
Affiliation(s)
- L Hibrand Saint-Oyant
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Ruttink
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - L Hamama
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - I Kirov
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
- Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - D Lakhwani
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N N Zhou
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - P M Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - N Daccord
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Leus
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - D Schulz
- Leibniz Universität, Hannover, Germany
| | - H Van de Geest
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - T Hesselink
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - K Van Laere
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - K Debray
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Balzergue
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Thouroude
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - A Chastellier
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - J Jeauffre
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Voisine
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Gaillard
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T J A Borm
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - P Arens
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - R E Voorrips
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - C Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Neu
- Leibniz Universität, Hannover, Germany
| | - M Linde
- Leibniz Universität, Hannover, Germany
| | - M C Le Paslier
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - A Bérard
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - R Bounon
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - J Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N Choisne
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - H Quesneville
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - K Kawamura
- Osaka Institute of Technology, Osaka, Japan
| | - S Aubourg
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Sakr
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - M J M Smulders
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Schijlen
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - E Bucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Debener
- Leibniz Universität, Hannover, Germany
| | - J De Riek
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - F Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France.
| |
Collapse
|
7
|
Hibrand Saint-Oyant L, Ruttink T, Hamama L, Kirov I, Lakhwani D, Zhou NN, Bourke PM, Daccord N, Leus L, Schulz D, Van de Geest H, Hesselink T, Van Laere K, Debray K, Balzergue S, Thouroude T, Chastellier A, Jeauffre J, Voisine L, Gaillard S, Borm TJA, Arens P, Voorrips RE, Maliepaard C, Neu E, Linde M, Le Paslier MC, Bérard A, Bounon R, Clotault J, Choisne N, Quesneville H, Kawamura K, Aubourg S, Sakr S, Smulders MJM, Schijlen E, Bucher E, Debener T, De Riek J, Foucher F. A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits. Nat Plants 2018; 4:473-484. [PMID: 29892093 PMCID: PMC6786968 DOI: 10.1038/s41477-018-0166-1] [Citation(s) in RCA: 141] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 05/01/2018] [Indexed: 05/18/2023]
Abstract
Rose is the world's most important ornamental plant, with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.
Collapse
Affiliation(s)
- L Hibrand Saint-Oyant
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Ruttink
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - L Hamama
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - I Kirov
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
- Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia
| | - D Lakhwani
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N N Zhou
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - P M Bourke
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - N Daccord
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Leus
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - D Schulz
- Leibniz Universität, Hannover, Germany
| | - H Van de Geest
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - T Hesselink
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - K Van Laere
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - K Debray
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Balzergue
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Thouroude
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - A Chastellier
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - J Jeauffre
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - L Voisine
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Gaillard
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T J A Borm
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - P Arens
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - R E Voorrips
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - C Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Neu
- Leibniz Universität, Hannover, Germany
| | - M Linde
- Leibniz Universität, Hannover, Germany
| | - M C Le Paslier
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - A Bérard
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - R Bounon
- INRA, US 1279 EPGV, Université Paris-Saclay, Evry, France
| | - J Clotault
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - N Choisne
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - H Quesneville
- URGI, INRA, Université Paris-Saclay, Versailles, France
| | - K Kawamura
- Osaka Institute of Technology, Osaka, Japan
| | - S Aubourg
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - S Sakr
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - M J M Smulders
- Plant Breeding, Wageningen University & Research, Wageningen, The Netherlands
| | - E Schijlen
- Wageningen University & Research, Business Unit Bioscience, Wageningen, The Netherlands
| | - E Bucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France
| | - T Debener
- Leibniz Universität, Hannover, Germany
| | - J De Riek
- ILVO, Flanders Research Institute for Agriculture, Fisheries and Food, Plant Sciences Unit, Melle, Belgium
| | - F Foucher
- IRHS, Agrocampus-Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, Beaucouzé, France.
| |
Collapse
|
8
|
Varshney RK, Shi C, Thudi M, Mariac C, Wallace J, Qi P, Zhang H, Zhao Y, Wang X, Rathore A, Srivastava RK, Chitikineni A, Fan G, Bajaj P, Punnuri S, Gupta SK, Wang H, Jiang Y, Couderc M, Katta MAVSK, Paudel DR, Mungra KD, Chen W, Harris-Shultz KR, Garg V, Desai N, Doddamani D, Kane NA, Conner JA, Ghatak A, Chaturvedi P, Subramaniam S, Yadav OP, Berthouly-Salazar C, Hamidou F, Wang J, Liang X, Clotault J, Upadhyaya HD, Cubry P, Rhoné B, Gueye MC, Sunkar R, Dupuy C, Sparvoli F, Cheng S, Mahala RS, Singh B, Yadav RS, Lyons E, Datta SK, Hash CT, Devos KM, Buckler E, Bennetzen JL, Paterson AH, Ozias-Akins P, Grando S, Wang J, Mohapatra T, Weckwerth W, Reif JC, Liu X, Vigouroux Y, Xu X. Pearl millet genome sequence provides a resource to improve agronomic traits in arid environments. Nat Biotechnol 2017; 35:969-976. [PMID: 28922347 PMCID: PMC6871012 DOI: 10.1038/nbt.3943] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 07/17/2017] [Indexed: 01/21/2023]
Abstract
Draft genome, 994 re-sequenced lines and GWAS for yield-traits provide a resource of genetics and genomics tools for pearl millet researchers and breeders. Pearl millet [Cenchrus americanus (L.) Morrone] is a staple food for more than 90 million farmers in arid and semi-arid regions of sub-Saharan Africa, India and South Asia. We report the ∼1.79 Gb draft whole genome sequence of reference genotype Tift 23D2B1-P1-P5, which contains an estimated 38,579 genes. We highlight the substantial enrichment for wax biosynthesis genes, which may contribute to heat and drought tolerance in this crop. We resequenced and analyzed 994 pearl millet lines, enabling insights into population structure, genetic diversity and domestication. We use these resequencing data to establish marker trait associations for genomic selection, to define heterotic pools, and to predict hybrid performance. We believe that these resources should empower researchers and breeders to improve this important staple crop.
Collapse
Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana State, India
| | | | - Mahendar Thudi
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana State, India
| | - Cedric Mariac
- Institut de recherche pour le développement (IRD), Montpellier, France
| | | | - Peng Qi
- University of Georgia, Athens, Georgia, USA
| | | | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Xiyin Wang
- University of Georgia, Athens, Georgia, USA
| | - Abhishek Rathore
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana State, India
| | - Rakesh K Srivastava
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana State, India
| | - Annapurna Chitikineni
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana State, India
| | | | - Prasad Bajaj
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana State, India
| | | | - S K Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana State, India
| | - Hao Wang
- Cornell University, Ithaca, New York, USA
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Marie Couderc
- Institut de recherche pour le développement (IRD), Montpellier, France
| | - Mohan A V S K Katta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana State, India
| | - Dev R Paudel
- University of Florida, Gainesville, Florida, USA
| | - K D Mungra
- Junagadh Agricultural University, Jamnagar, Gujarat, India
| | | | - Karen R Harris-Shultz
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Tifton, Georgia, USA
| | - Vanika Garg
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana State, India
| | - Neetin Desai
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Amity University, Mumbai, Maharashtra, India
| | - Dadakhalandar Doddamani
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana State, India
| | - Ndjido Ardo Kane
- Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
| | | | - Arindam Ghatak
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,School of Bioinformatics and Biotechnology, D.Y. Patil University, Mumbai, Maharashtra, India
| | - Palak Chaturvedi
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Sabarinath Subramaniam
- University of Arizona, Tucson, Arizona, USA.,Phoenix Bioinformatics, Redwood City, California, USA
| | - Om Parkash Yadav
- Indian Council of Agricultural Research (ICAR)-Central Arid Zone Research Institute (CAZRI), Jodhpur, Rajasthan, India
| | - Cécile Berthouly-Salazar
- Institut de recherche pour le développement (IRD), Montpellier, France.,Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux, Centre de Recherche de Bel Air, Dakar, Senegal
| | - Falalou Hamidou
- ICRISAT Sahelian Center, Niamey, Niger.,Faculty of Sciences and Techniques, University Abdou Moumouni, Niamey, Niger
| | | | | | - Jérémy Clotault
- Institut de recherche pour le développement (IRD), Montpellier, France.,University of Montpellier, Montpellier, France
| | - Hari D Upadhyaya
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana State, India
| | - Philippe Cubry
- Institut de recherche pour le développement (IRD), Montpellier, France
| | - Bénédicte Rhoné
- Institut de recherche pour le développement (IRD), Montpellier, France.,Laboratoire de biométrie et Biologie Evolutive, Université Lyon 1, Villeurbanne, France
| | - Mame Codou Gueye
- Institut Sénégalais de Recherches Agricoles (ISRA), Dakar, Senegal
| | | | | | - Francesca Sparvoli
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biologia e Biotecnologia Agraria, Milan, Italy
| | | | - R S Mahala
- Pioneer Hi-Bred Private Limited, Hyderabad, Telangana State, India
| | - Bharat Singh
- Fort Valley State University, Fort Valley, Georgia, USA
| | - Rattan S Yadav
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth University, Ceredigion, UK
| | - Eric Lyons
- University of Arizona, Tucson, Arizona, USA
| | | | | | | | - Edward Buckler
- Cornell University, Ithaca, New York, USA.,USDA-ARS, Ithaca, New York, USA
| | | | | | | | - Stefania Grando
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, Telangana State, India
| | | | | | - Wolfram Weckwerth
- Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.,Vienna Metabolomics Center (VIME), University of Vienna, Vienna, Austria
| | - Jochen C Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Xin Liu
- BGI-Shenzhen, Shenzhen, China.,BGI-Qingdao, Qingdao, China
| | - Yves Vigouroux
- Institut de recherche pour le développement (IRD), Montpellier, France.,University of Montpellier, Montpellier, France
| | - Xun Xu
- BGI-Shenzhen, Shenzhen, China.,BGI-Qingdao, Qingdao, China.,China National GeneBank (CNGB), Shenzen, China
| |
Collapse
|
9
|
Liorzou M, Pernet A, Li S, Chastellier A, Thouroude T, Michel G, Malécot V, Gaillard S, Briée C, Foucher F, Oghina-Pavie C, Clotault J, Grapin A. Nineteenth century French rose (Rosa sp.) germplasm shows a shift over time from a European to an Asian genetic background. J Exp Bot 2016; 67:4711-25. [PMID: 27406785 PMCID: PMC4973750 DOI: 10.1093/jxb/erw269] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Hybridization with introduced genetic resources is commonly practiced in ornamental plant breeding to introgress desired traits. The 19th century was a golden age for rose breeding in France. The objective here was to study the evolution of rose genetic diversity over this period, which included the introduction of Asian genotypes into Europe. A large sample of 1228 garden roses encompassing the conserved diversity cultivated during the 18th and 19th centuries was genotyped with 32 microsatellite primer pairs. Its genetic diversity and structure were clarified. Wide diversity structured in 16 genetic groups was observed. Genetic differentiation was detected between ancient European and Asian accessions, and a temporal shift from a European to an Asian genetic background was observed in cultivated European hybrids during the 19th century. Frequent crosses with Asian roses throughout the 19th century and/or selection for Asiatic traits may have induced this shift. In addition, the consistency of the results with respect to a horticultural classification is discussed. Some horticultural groups, defined according to phenotype and/or knowledge of their pedigree, seem to be genetically more consistent than others, highlighting the difficulty of classifying cultivated plants. Therefore, the horticultural classification is probably more appropriate for commercial purposes rather than genetic relatedness, especially to define preservation and breeding strategies.
Collapse
Affiliation(s)
- Mathilde Liorzou
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Alix Pernet
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Shubin Li
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France Flower Research Institute, Yunnan Academy of Agricultural Sciences, Kunming 650205, China
| | - Annie Chastellier
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Tatiana Thouroude
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Gilles Michel
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Valéry Malécot
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Sylvain Gaillard
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Céline Briée
- Université d'Angers, UMR CNRS 6258 CERHIO, Centre de recherches historiques de l'Ouest, 5 bis Bd Lavoisier 49045 Angers, France
| | - Fabrice Foucher
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Cristiana Oghina-Pavie
- Université d'Angers, UMR CNRS 6258 CERHIO, Centre de recherches historiques de l'Ouest, 5 bis Bd Lavoisier 49045 Angers, France
| | - Jérémy Clotault
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Agnès Grapin
- IRHS, Agrocampus Ouest, INRA, Université d'Angers, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| |
Collapse
|
10
|
Saïdou AA, Clotault J, Couderc M, Mariac C, Devos KM, Thuillet AC, Amoukou IA, Vigouroux Y. Association mapping, patterns of linkage disequilibrium and selection in the vicinity of the PHYTOCHROME C gene in pearl millet. Theor Appl Genet 2014; 127:19-32. [PMID: 24114050 DOI: 10.1007/s00122-013-2197-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Accepted: 09/13/2013] [Indexed: 05/09/2023]
Abstract
Linkage analysis confirmed the association in the region of PHYC in pearl millet. The comparison of genes found in this region suggests that PHYC is the best candidate. Major efforts are currently underway to dissect the phenotype-genotype relationship in plants and animals using existing populations. This method exploits historical recombinations accumulated in these populations. However, linkage disequilibrium sometimes extends over a relatively long distance, particularly in genomic regions containing polymorphisms that have been targets for selection. In this case, many genes in the region could be statistically associated with the trait shaped by the selected polymorphism. Statistical analyses could help in identifying the best candidate genes into such a region where an association is found. In a previous study, we proposed that a fragment of the PHYTOCHROME C gene (PHYC) is associated with flowering time and morphological variations in pearl millet. In the present study, we first performed linkage analyses using three pearl millet F2 families to confirm the presence of a QTL in the vicinity of PHYC. We then analyzed a wider genomic region of ~100 kb around PHYC to pinpoint the gene that best explains the association with the trait in this region. A panel of 90 pearl millet inbred lines was used to assess the association. We used a Markov chain Monte Carlo approach to compare 75 markers distributed along this 100-kb region. We found the best candidate markers on the PHYC gene. Signatures of selection in this region were assessed in an independent data set and pointed to the same gene. These results foster confidence in the likely role of PHYC in phenotypic variation and encourage the development of functional studies.
Collapse
Affiliation(s)
- Abdoul-Aziz Saïdou
- Institut de Recherche pour le Développement, UMR DIADE, 911 avenue Agropolis, BP 64501, 34394, Montpellier, France
| | | | | | | | | | | | | | | |
Collapse
|
11
|
Soufflet-Freslon V, Jourdan M, Clotault J, Huet S, Briard M, Peltier D, Geoffriau E. Functional gene polymorphism to reveal species history: the case of the CRTISO gene in cultivated carrots. PLoS One 2013; 8:e70801. [PMID: 23940644 PMCID: PMC3733727 DOI: 10.1371/journal.pone.0070801] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Accepted: 06/24/2013] [Indexed: 01/01/2023] Open
Abstract
Background Carrot is a vegetable cultivated worldwide for the consumption of its root. Historical data indicate that root colour has been differentially selected over time and according to geographical areas. Root pigmentation depends on the relative proportion of different carotenoids for the white, yellow, orange and red types but only internally for the purple one. The genetic control for root carotenoid content might be partially associated with carotenoid biosynthetic genes. Carotenoid isomerase (CRTISO) has emerged as a regulatory step in the carotenoid biosynthesis pathway and could be a good candidate to show how a metabolic pathway gene reflects a species genetic history. Methodology/Principal Findings In this study, the nucleotide polymorphism and the linkage disequilibrium among the complete CRTISO sequence, and the deviation from neutral expectation were analysed by considering population subdivision revealed with 17 microsatellite markers. A sample of 39 accessions, which represented different geographical origins and root colours, was used. Cultivated carrot was divided into two genetic groups: one from Middle East and Asia (Eastern group), and another one mainly from Europe (Western group). The Western and Eastern genetic groups were suggested to be differentially affected by selection: a signature of balancing selection was detected within the first group whereas the second one showed no selection. A focus on orange-rooted carrots revealed that cultivars cultivated in Asia were mainly assigned to the Western group but showed CRTISO haplotypes common to Eastern carrots. Conclusion The carotenoid pathway CRTISO gene data proved to be complementary to neutral markers in order to bring critical insight in the cultivated carrot history. We confirmed the occurrence of two migration events since domestication. Our results showed a European background in material from Japan and Central Asia. While confirming the introduction of European carrots in Japanese resources, the history of Central Asia material remains unclear.
Collapse
Affiliation(s)
- Vanessa Soufflet-Freslon
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Beaucouzé, France
| | - Matthieu Jourdan
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Beaucouzé, France
| | - Jérémy Clotault
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Beaucouzé, France
| | - Sébastien Huet
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Beaucouzé, France
| | - Mathilde Briard
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Beaucouzé, France
| | - Didier Peltier
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Beaucouzé, France
| | - Emmanuel Geoffriau
- Agrocampus Ouest, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Angers, France
- Université d’Angers, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Angers, France
- INRA, UMR1345 Institut de Recherche en Horticulture et Semences, SFR4207 QUASAV, Beaucouzé, France
- * E-mail:
| |
Collapse
|
12
|
Clotault J, Peltier D, Soufflet-Freslon V, Briard M, Geoffriau E. Differential selection on carotenoid biosynthesis genes as a function of gene position in the metabolic pathway: a study on the carrot and dicots. PLoS One 2012; 7:e38724. [PMID: 22737218 PMCID: PMC3377682 DOI: 10.1371/journal.pone.0038724] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2011] [Accepted: 05/14/2012] [Indexed: 11/19/2022] Open
Abstract
Background Selection of genes involved in metabolic pathways could target them differently depending on the position of genes in the pathway and on their role in controlling metabolic fluxes. This hypothesis was tested in the carotenoid biosynthesis pathway using population genetics and phylogenetics. Methodology/Principal Findings Evolutionary rates of seven genes distributed along the carotenoid biosynthesis pathway, IPI, PDS, CRTISO, LCYB, LCYE, CHXE and ZEP, were compared in seven dicot taxa. A survey of deviations from neutrality expectations at these genes was also undertaken in cultivated carrot (Daucus carota subsp. sativus), a species that has been intensely bred for carotenoid pattern diversification in its root during its cultivation history. Parts of sequences of these genes were obtained from 46 individuals representing a wide diversity of cultivated carrots. Downstream genes exhibited higher deviations from neutral expectations than upstream genes. Comparisons of synonymous and nonsynonymous substitution rates between genes among dicots revealed greater constraints on upstream genes than on downstream genes. An excess of intermediate frequency polymorphisms, high nucleotide diversity and/or high differentiation of CRTISO, LCYB1 and LCYE in cultivated carrot suggest that balancing selection may have targeted genes acting centrally in the pathway. Conclusions/Significance Our results are consistent with relaxed constraints on downstream genes and selection targeting the central enzymes of the carotenoid biosynthesis pathway during carrot breeding history.
Collapse
Affiliation(s)
- Jérémy Clotault
- UMR1345 Institut de Recherche en Horticulture et Semences, Université d'Angers, PRES L'UNAM, Angers, France.
| | | | | | | | | |
Collapse
|
13
|
Clotault J, Thuillet AC, Buiron M, De Mita S, Couderc M, Haussmann BIG, Mariac C, Vigouroux Y. Evolutionary history of pearl millet (Pennisetum glaucum [L.] R. Br.) and selection on flowering genes since its domestication. Mol Biol Evol 2011; 29:1199-212. [PMID: 22114357 DOI: 10.1093/molbev/msr287] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The plant domestication process is associated with considerable modifications of plant phenotype. The identification of the genetic basis of this adaptation is of great interest for evolutionary biology. One of the methods used to identify such genes is the detection of signatures of selection. However, domestication is generally associated with major demographic effects. It is therefore crucial to disentangle the effects of demography and selection on diversity. In this study, we investigated selection in a flowering time pathway during domestication of pearl millet. We first used a random set of 20 genes to model pearl millet domestication using approximate Bayesian computation. This analysis showed that a model with exponential growth and wild-cultivated gene flow was well supported by our data set. Under this model, the domestication date of pearl millet is estimated at around 4,800 years ago. We assessed selection in 15 pearl millet DNA sequences homologous to flowering time genes and showed that these genes underwent selection more frequently than expected. We highlighted significant signatures of selection in six pearl millet flowering time genes associated with domestication or improvement of pearl millet. Moreover, higher deviations from neutrality were found for circadian clock-associated genes. Our study provides new insights into the domestication process of pearl millet and shows that a category of genes of the flowering pathway were preferentially selected during pearl millet domestication.
Collapse
Affiliation(s)
- Jérémy Clotault
- Institut de Recherche pour le Développement, Unité Mixte de Recherche Diversité Adaptation et Développement des Plantes, Montpellier, France
| | | | | | | | | | | | | | | |
Collapse
|
14
|
Clotault J, Geoffriau E, Lionneton E, Briard M, Peltier D. Carotenoid biosynthesis genes provide evidence of geographical subdivision and extensive linkage disequilibrium in the carrot. Theor Appl Genet 2010; 121:659-72. [PMID: 20411232 DOI: 10.1007/s00122-010-1338-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2009] [Accepted: 04/03/2010] [Indexed: 05/15/2023]
Abstract
According to the history of the cultivated carrot, root colour can be considered as a structural factor of carrot germplasm. Therefore, molecular variations of carotenoid biosynthesis genes, these being involved in colour traits, represent a good putative source of polymorphism related to diversity structure. Seven candidate genes involved in the carotenoid biosynthesis pathway have been analysed from a sample of 48 individual plants, each one from a different cultivar of carrot (Daucus carota L. ssp. sativus). The cultivars were chosen to represent a large diversity and a wide range of root colour. A high single nucleotide polymorphism (SNP) frequency of 1 SNP per 22 bp (mean pi (sil) = 0.020) was found on average within these genes. The analysis of genetic structure from carotenoid biosynthesis gene sequences and 17 putatively neutral microsatellites showed moderate genetic differentiation between cultivars originating from the West and the East (F (ST) = 0.072), this being consistent with breeding history, but not previously evidenced by molecular tools. Surprisingly, carotenoid biosynthesis genes did not exhibit decay of LD (mean r (2) = 0.635) within the 700-1,000 bp analysed, even though a fast decay level of LD is expected in outcrossing species. The high level of intralocus LD found for carotenoid biosynthesis genes implies that candidate-gene association mapping for carrot root colour should be useful to validate gene function, but may be unable to identify precisely the causative variations involved in trait determinism. Finally this study affords the first molecular evidence of a genetic structure in cultivated carrot germplasm related to phylogeography.
Collapse
Affiliation(s)
- Jérémy Clotault
- Agrocampus Ouest, INHP, IFR 149 Quasav, UMR 1259 GenHort, 2 Rue Le Nôtre, 49045, Angers, France
| | | | | | | | | |
Collapse
|
15
|
Clotault J, Peltier D, Berruyer R, Thomas M, Briard M, Geoffriau E. Expression of carotenoid biosynthesis genes during carrot root development. J Exp Bot 2008; 59:3563-73. [PMID: 18757491 DOI: 10.1093/jxb/ern210] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Carotenogenesis has been extensively studied in fruits and flower petals. Transcriptional regulation is thought to be the major factor in carotenoid accumulation in these organs. However, little is known about regulation in root organs. The root carotenoid content of carrot germplasm varies widely. The present study was conducted to investigate transcriptional regulation of carotenoid biosynthesis genes in relation to carotenoid accumulation during early carrot root development and up to 3 months after sowing. HPLC carotenoid content analysis and quantitative RT-PCR were compared to quantify the expression of eight genes encoding carotenoid biosynthesis enzymes during the development of white, yellow, orange, and red carrot roots. The genes chosen encode phytoene synthase (PSY1 and PSY2), phytoene desaturase (PDS), zeta-carotene desaturase (ZDS1 and ZDS2), lycopene epsilon-cyclase (LCYE), lycopene beta-cyclase (LCYB1), and zeaxanthin epoxidase (ZEP). All eight genes were expressed in the white cultivar even though it did not contain carotenoids. By contrast with fruit maturation, the expression of carotenogenic genes began during the early stages of development and then progressively increased for most of these genes during root development as the total carotenoid level increased in coloured carrots. The high expression of genes encoding LCYE and ZDS noted in yellow and red cultivars, respectively, might be consistent with the accumulation of lutein and lycopene, respectively. The results showed that the accumulation of total carotenoids during development and the accumulation of major carotenoids in the red and yellow cultivars might partially be explained by the transcriptional level of genes directing the carotenoid biosynthesis pathway.
Collapse
Affiliation(s)
- Jérémy Clotault
- Institut National d'Horticulture, IFR 149 Quasav, UMR 1259 GenHort, F-49045 Angers, France
| | | | | | | | | | | |
Collapse
|