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Rêgo APB, Mora-Ocampo IY, Corrêa RX. Interactions of Different Species of Phytophthora with Cacao Induce Genetic, Biochemical, and Morphological Plant Alterations. Microorganisms 2023; 11:1172. [PMID: 37317146 DOI: 10.3390/microorganisms11051172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/22/2023] [Accepted: 04/24/2023] [Indexed: 06/16/2023] Open
Abstract
Diseases associated with Phytophthora cause considerable losses in cocoa production worldwide. Analyzing genes, proteins, and metabolites involved in Theobroma cacao's interaction with Phytophthora species is essential to explaining the molecular aspects of plant defense. Through a systematic literature review, this study aims to identify reports of genes, proteins, metabolites, morphological characteristics, and molecular and physiological processes of T. cacao involved in its interaction with species of Phytophthora. After the searches, 35 papers were selected for the data extraction stage, according to pre-established inclusion and exclusion criteria. In these studies, 657 genes and 32 metabolites, among other elements (molecules and molecular processes), were found to be involved in the interaction. The integration of this information resulted in the following conclusions: the expression patterns of pattern recognition receptors (PRRs) and a possible gene-to-gene interaction participate in cocoa resistance to Phytophthora spp.; the expression pattern of genes that encode pathogenesis-related (PRs) proteins is different between resistant and susceptible genotypes; phenolic compounds play an important role in preformed defenses; and proline accumulation may be involved in cell wall integrity. Only one proteomics study of T. cacao-Phytophthora spp. was found, and some genes proposed via QTL analysis were confirmed in transcriptomic studies.
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Affiliation(s)
- Angra Paula Bomfim Rêgo
- Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus 45662-900, Bahia, Brazil
| | - Irma Yuliana Mora-Ocampo
- Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus 45662-900, Bahia, Brazil
| | - Ronan Xavier Corrêa
- Centro de Biotecnologia e Genética (CBG), Universidade Estadual de Santa Cruz (UESC), Rodovia Jorge Amado km 16, Ilhéus 45662-900, Bahia, Brazil
- Departamento de Ciências Biológicas (DCB), Universidade Estadual de Santa Cruz, Ilhéus 45662-900, Bahia, Brazil
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Quiroz-Vera J, Morillo E, Cordoba C, Buitron J. Molecular characterization of national cocoa collection from the leading traditional growing areas in Ecuador. BIONATURA 2023. [DOI: 10.21931/rb/2023.08.01.31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
Abstract
Ecuador is the leading producer and exporter of fine cocoa, with plantations over 80 years old, preserving distinctive aroma and flavor characteristics. The research objective was to screen the genetic variability of a collection of National cocoa from Ecuador's leading traditional cocoa growing areas, denominated as Centennial National Cocoa Plants (CCNC). This germplasm collection with 243 accessions was analyzed with 20 microsatellites (SSR) markers. DNA genotyping was highly informative, generating a total of 109 SSR alleles with an average of 5.5 alleles per locus. Only 0.8% of duplicate accessions were identified. The average genetic diversity obtained was 0.447, and the polymorphic content index was 0.414, which shows a high genetic diversity. The clustering, main coordinates, and population assignment analysis revealed that the samples are classified into two subpopulations (GN and GM), differentiated by their level of heterozygosity, with a fixation index value of 0.105. The results showed that microsatellite markers and statistical tools provide useful information that favors managing and conserving genetic variability in CCNC collection.
Keywords: fine and aroma cocoa, Sabor Arriba, DNA genotyping, SSR markers
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Affiliation(s)
- James Quiroz-Vera
- Programa de Cacao. Instituto Nacional de Investigaciones Agropecuarias. Estación Experimental Litoral Sur; Yaguachi, Ecuador
| | - Eduardo Morillo
- Departamento de Biotecnología. Instituto Nacional de Investigaciones Agropecuarias.Johana Buitron
| | - Carla Cordoba
- Departamento de Biotecnología. Instituto Nacional de Investigaciones Agropecuarias.Johana Buitron
| | - Johana Buitron
- Departamento de Biotecnología. Instituto Nacional de Investigaciones Agropecuarias.Johana Buitron
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Li Y, Gu M, Liu X, Lin J, Jiang H, Song H, Xiao X, Zhou W. Sequencing and analysis of the complete mitochondrial genomes of Toona sinensis and Toona ciliata reveal evolutionary features of Toona. BMC Genomics 2023; 24:58. [PMID: 36726084 PMCID: PMC9893635 DOI: 10.1186/s12864-023-09150-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 01/24/2023] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Toona is a critical genus in the Meliaceae, and the plants of this group are an asset for both restorative and restorative purposes, the most flexible of which are Toona sinensis and Toona ciliata. To concentrate on the advancement of mitochondrial(Mt) genome variety in T.sinensis and T.ciliata, the Mt genomes of the two species were sequenced in high throughput independently, after de novo assembly and annotation to construct a Mt genome map for comparison in genome structure. Find their repetitive sequences and analyze them in comparison with the chloroplast genome, along with Maximum-likelihood(ML) phylogenetic analysis with 16 other relatives. RESULTS (1) T. sinensis and T.ciliata are both circular structures with lengths of 683482 bp and 68300 bp, respectively. They share a high degree of similarity in encoding genes and have AT preferences. All of them have the largest Phe concentration and are the most frequently used codons. (2) Both of their Mt genome are highly preserved in terms of structural and functional genes, while the main variability is reflected in the length of tRNA, the number of genes, and the value of RSCU. (3) T. siniensis and T. ciliata were detected to have 94 and 87 SSRs, respectively, of which mononucleotides accounted for the absolute proportion. Besides, the vast majority of their SSRs were found to be poly-A or poly-T. (4)10 and 11 migrating fragments were identified in the comparison with the chloroplast genome, respectively. (5) In the ML evolutionary tree, T.sinensis and T.ciliata clustered individually into a small branch with 100% support, reflecting two species of Toona are very similarly related to each other. CONCLUSIONS This research provides a basis for the exploitation of T.sinensis and T.ciliata in terms of medicinal, edible, and timber resources to avoid confusion; at the same time, it can explore the evolutionary relationship between the Toona and related species, which does not only have an important practical value, but also provides a theoretical basis for future hybrid breeding of forest trees, molecular markers, and evolutionary aspects of plants, which has great scientific significance.
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Affiliation(s)
- Youli Li
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Min Gu
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Xuanzhe Liu
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Jianna Lin
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Huier Jiang
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Huiyun Song
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
| | - Xingcui Xiao
- grid.464457.00000 0004 0445 3867Sichuan Academy of Forestry Sciences, Chengdu, 61008 Sichuan China
| | - Wei Zhou
- grid.20561.300000 0000 9546 5767College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 51000 Guangdong China
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Javaid N, Ramzan M, Khan IA, Alahmadi TA, Datta R, Fahad S, Danish S. The chloroplast genome of Farsetia hamiltonii Royle, phylogenetic analysis, and comparative study with other members of Clade C of Brassicaceae. BMC PLANT BIOLOGY 2022; 22:384. [PMID: 35918648 PMCID: PMC9344719 DOI: 10.1186/s12870-022-03750-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 07/13/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Farsetia hamiltonii Royle is a medicinally important annual plant from the Cholistan desert that belongs to the tribe Anastaticeae and clade C of the Brassicaceae family. We provide the entire chloroplast sequence of F.hamiltonii, obtained using the Illumina HiSeq2500 and paired-end sequencing. We compared F. hamiltonii to nine other clade C species, including Farsetia occidentalis, Lobularia libyca, Notoceras bicorne, Parolinia ornata, Morettia canescens, Cochlearia borzaeana, Megacarpaea polyandra, Biscutella laevigata, and Iberis amara. We conducted phylogenetic research on the 22 Brassicaceae species, which included members from 17 tribes and six clades. RESULTS The chloroplast genome sequence of F.hamiltonii of 154,802 bp sizes with 36.30% GC content and have a typical structure comprised of a Large Single Copy (LSC) of 83,906 bp, a Small Single Copy (SSC) of 17,988 bp, and two copies of Inverted Repeats (IRs) of 26,454 bp. The genomes of F. hamiltonii and F. occidentalis show shared amino acid frequencies and codon use, RNA editing sites, simple sequence repeats, and oligonucleotide repeats. The maximum likelihood tree revealed Farsetia as a monophyletic genus, closely linked to Morettia, with a bootstrap score of 100. The rate of transversion substitutions (Tv) was higher than the rate of transition substitutions (Ts), resulting in Ts/Tv less than one in all comparisons with F. hamiltonii, indicating that the species are closely related. The rate of synonymous substitutions (Ks) was greater than non-synonymous substitutions (Ka) in all comparisons with F. hamiltonii, with a Ka/Ks ratio smaller than one, indicating that genes underwent purifying selection. Low nucleotide diversity values range from 0.00085 to 0.08516, and IR regions comprise comparable genes on junctions with minimal change, supporting the conserved status of the selected chloroplast genomes of the clade C of the Brassicaceae family. We identified ten polymorphic regions, including rps8-rpl14, rps15-ycf1, ndhG-ndhI, psbK-psbI, ccsA-ndhD, rpl36-rps8, petA-psbJ, ndhF-rpl32, psaJ-rpl3, and ycf1 that might be exploited to construct genuine and inexpensive to solve taxonomic discrepancy and understand phylogenetic relationship amongst Brassicaceae species. CONCLUSION The entire chloroplast sequencing of F. hamiltonii sheds light on the divergence of genic chloroplast sequences among members of the clade C. When other Farsetia species are sequenced in the future, the full F. hamiltonii chloroplast will be used as a source for comprehensive taxonomical investigations of the genus. The comparison of F. hamiltonii and other clade C species adds new information to the phylogenetic data and evolutionary processes of the clade. The results of this study will also provide further molecular uses of clade C chloroplasts for possible plant genetic modifications and will help recognise more Brassicaceae family species.
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Affiliation(s)
- Nida Javaid
- Department of Botany, The Islamia University, Bahawalpur, Pakistan
| | - Musarrat Ramzan
- Department of Botany, The Islamia University, Bahawalpur, Pakistan
| | - Ishtiaq Ahmad Khan
- Jamil-ur-Rahman Center for Genome Research, Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences University of Karachi, Karachi, 75270 Pakistan
| | - Tahani Awad Alahmadi
- Department of Pediatrics, College of Medicine and King Khalid University Hospital, King Saud University, Medical City, PO Box-2925, Riyadh, 11461 Saudi Arabia
| | - Rahul Datta
- Department of Geology and Pedology, Faculty of Forestry and Wood Technology, Mendel University in Brno, Zemedelska1, 61300 Brno, Czech Republic
| | - Shah Fahad
- Department of Agronomy, The University of Haripur, Khyber Pakhtunkhwa, Haripur, 22620 Pakistan
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 570228 China
| | - Subhan Danish
- Hainan Key Laboratory for Sustainable Utilization of Tropical Bioresource, College of Tropical Crops, Hainan University, Haikou, 570228 China
- Department of Soil Science, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Multan, 60800 Punjab Pakistan
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Cui G, Wang C, Wei X, Wang H, Wang X, Zhu X, Li J, Yang H, Duan H. Complete chloroplast genome of Hordeum brevisubulatum: Genome organization, synonymous codon usage, phylogenetic relationships, and comparative structure analysis. PLoS One 2021; 16:e0261196. [PMID: 34898618 PMCID: PMC8668134 DOI: 10.1371/journal.pone.0261196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2021] [Accepted: 11/28/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Hordeum brevisubulatum, known as fine perennial forage, is used for soil salinity improvement in northern China. Chloroplast (cp) genome is an ideal model for assessing its genome evolution and the phylogenetic relationships. We de novo sequenced and analyzed the cp genome of H. brevisubulatum, providing a fundamental reference for further studies in genetics and molecular breeding. RESULTS The cp genome of H. brevisubulatum was 137,155 bp in length with a typical quadripartite structure. A total of 130 functional genes were annotated and the gene of accD was lost in the process of evolution. Among all the annotated genes, 16 different genes harbored introns and the genes of ycf3 and rps12 contained two introns. Parity rule 2 (PR2) plot analysis showed that majority of genes had a bias toward T over A in the coding strand in all five Hordeum species, and a slight G over C in the other four Hordeum species except for H. bogdanil. Additionally, 52 dispersed repeat sequences and 182 simple sequence repeats were identified. Moreover, some unique SSRs of each species could be used as molecular markers for further study. Compared to the other four Hordeum species, H. brevisubulatum was most closely related to H. bogdanii and its cp genome was relatively conserved. Moreover, inverted repeat regions (IRa and IRb) were less divergent than other parts and coding regions were relatively conserved compared to non-coding regions. Main divergence was presented at the SSC/IR border. CONCLUSIONS This research comprehensively describes the architecture of the H. brevisubulatum cp genome and improves our understanding of its cp biology and genetic diversity, which will facilitate biological discoveries and cp genome engineering.
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Affiliation(s)
- Guangxin Cui
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Chunmei Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Xiaoxing Wei
- Academy of Animal and Veterinary Sciences, Qinghai University, Xining, Qinghai, China
| | - Hongbo Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Laboratory of Quality & Safety Risk Assessment for Livestock Products, Ministry of Agriculture and Rural Affairs, Lanzhou, Gansu, China
| | - Xiaoli Wang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Xinqiang Zhu
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - JinHua Li
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Hongshan Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- * E-mail: (HY); (HD)
| | - Huirong Duan
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- * E-mail: (HY); (HD)
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Rono PC, Dong X, Yang JX, Mutie FM, Oulo MA, Malombe I, Kirika PM, Hu GW, Wang QF. Initial Complete Chloroplast Genomes of Alchemilla (Rosaceae): Comparative Analysis and Phylogenetic Relationships. Front Genet 2020; 11:560368. [PMID: 33362846 PMCID: PMC7756076 DOI: 10.3389/fgene.2020.560368] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Accepted: 10/15/2020] [Indexed: 11/13/2022] Open
Abstract
The genus Alchemilla L., known for its medicinal and ornamental value, is widely distributed in the Holarctic regions with a few species found in Asia and Africa. Delimitation of species within Alchemilla is difficult due to hybridization, autonomous apomixes, and polyploidy, necessitating efficient molecular-based characterization. Herein, we report the initial complete chloroplast (cp) genomes of Alchemilla. The cp genomes of two African (Afromilla) species Alchemilla pedata and Alchemilla argyrophylla were sequenced, and phylogenetic and comparative analyses were conducted in the family Rosaceae. The cp genomes mapped a typical circular quadripartite structure of lengths 152,438 and 152,427 base pairs (bp) in A. pedata and A. argyrophylla, respectively. Alchemilla cp genomes were composed of a pair of inverted repeat regions (IRa/IRb) of length 25,923 and 25,915 bp, separating the small single copy (SSC) region of 17,980 and 17,981 bp and a large single copy (LSC) region of 82,612 and 82,616 bp in A. pedata and A. argyrophylla, respectively. The cp genomes encoded 114 unique genes including 88 protein-coding genes, 37 transfer RNA (tRNA) genes, and 4 ribosomal RNA (rRNA) genes. Additionally, 88 and 95 simple sequence repeats (SSRs) and 37 and 40 tandem repeats were identified in A. pedata and A. argyrophylla, respectively. Significantly, the loss of group II intron in atpF gene in Alchemilla species was detected. Phylogenetic analysis based on 26 whole cp genome sequences and 78 protein-coding gene sequences of 27 Rosaceae species revealed a monophyletic clustering of Alchemilla nested within subfamily Rosoideae. Based on a protein-coding region, negative selective pressure (Ka/Ks < 1) was detected with an average Ka/Ks value of 0.1322 in A. argyrophylla and 0.1418 in A. pedata. The availability of complete cp genome in the genus Alchemilla will contribute to species delineation and further phylogenetic and evolutionary studies in the family Rosaceae.
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Affiliation(s)
- Peninah Cheptoo Rono
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xiang Dong
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jia-Xin Yang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Fredrick Munyao Mutie
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Millicent A Oulo
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Itambo Malombe
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Paul M Kirika
- East African Herbarium, National Museums of Kenya, Nairobi, Kenya
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
| | - Qing-Feng Wang
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China.,Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, China
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Du X, Zeng T, Feng Q, Hu L, Luo X, Weng Q, He J, Zhu B. The complete chloroplast genome sequence of yellow mustard (Sinapis alba L.) and its phylogenetic relationship to other Brassicaceae species. Gene 2020; 731:144340. [PMID: 31923575 DOI: 10.1016/j.gene.2020.144340] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 12/09/2019] [Accepted: 01/06/2020] [Indexed: 12/20/2022]
Abstract
As a member of the large Brassicaceae family, yellow mustard (Sinapis alba L.) has been used as an important gene pool for the genetic improvement of cash crops in Brassicaceae. Understanding the phylogenetic relationship between Sinapis alba (S. alba) and other Brassicaceae crops can provide guidance on the introgression of its favorable alleles into related species. The chloroplast (cp) genome is an ideal model for assessing genome evolution and the phylogenetic relationships of complex angiosperm families. Herein, we de novo assembled the complete cp genome of S. alba by integrating the PacBio and Illumina sequencing platforms. A 153,760 bp quadripartite cycle without any gap was obtained, including a pair of inverted repeats (IRa and IRb) of 26,221 bp, separated by a large single copy (LSC) region of 83,506 bp and a small single copy (SSC) region of 17,821 bp. A total of 78 protein-coding genes, 30 tRNA genes, and four rRNA genes were identified in this cp genome, as were 89 simple sequence repeat (SSR) loci of 18 types. The codon usage analysis revealed a preferential use of the Leu codon with the A/U ending. The phylogenetic analysis using 82 Brassicaceae species demonstrated that S. alba had a close relationship with important Brassica and Raphanus species; moreover, it likely originated from a separate evolutionary pathway compared with the congeneric Sinapis arvensis. The synonymous (Ks) and non-synonymous (Ks) substitution rate analysis showed that genes encoding "Subunits of cytochrome b/f complex" were under the lowest purifying selection pressure, whereas those associated with "Maturase", "Subunit of acetyl-CoA", and "Subunits of NADH-dehydrogenase" underwent relatively higher purifying selection pressures. Our results provide valuable information for fully utilizing the S. alba cp genome as a potential genetic resource for the genetic improvement of Brassica and Raphanus species.
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Affiliation(s)
- Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Tuo Zeng
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China; Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qun Feng
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Lijuan Hu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Xi Luo
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Qingbei Weng
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China
| | - Jiefang He
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China.
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang 550025, China.
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Yan C, Du J, Gao L, Li Y, Hou X. The complete chloroplast genome sequence of watercress (Nasturtium officinale R. Br.): Genome organization, adaptive evolution and phylogenetic relationships in Cardamineae. Gene 2019; 699:24-36. [PMID: 30849538 DOI: 10.1016/j.gene.2019.02.075] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 02/16/2019] [Accepted: 02/18/2019] [Indexed: 12/12/2022]
Abstract
Watercress (Nasturtium officinale R. Br.), an aquatic leafy vegetable of the Brassicaceae family, is known as a nutritional powerhouse. Here, we de novo sequenced and assembled the complete chloroplast (cp) genome of watercress based on combined PacBio and Illumina data. The cp genome is 155,106 bp in length, exhibiting a typical quadripartite structure including a pair of inverted repeats (IRA and IRB) of 26,505 bp separated by a large single copy (LSC) region of 84,265 bp and a small single copy (SSC) region of 17,831 bp. The genome contained 113 unique genes, including 79 protein-coding genes, 30 tRNAs and 4 rRNAs, with 20 duplicate in the IRs. Compared with the prior cp genome of watercress deposited in GenBank, 21 single nucleotide polymorphisms (SNPs) and 27 indels were identified, mainly located in noncoding sequences. A total of 49 repeat structures and 71 simple sequence repeats (SSRs) were detected. Codon usage showed a bias for A/T-ending codons in the cp genome of watercress. Moreover, 45 RNA editing sites were predicted in 16 genes, all for C-to-U transitions. A comparative plastome study with Cardamineae species revealed a conserved gene order and high similarity of protein-coding sequences. Analysis of the Ka/Ks ratios of Cardamineae suggested positive selection exerted on the ycf2 gene in watercress, which might reflect specific adaptations of watercress to its particular living environment. Phylogenetic analyses based on complete cp genomes and common protein-coding genes from 56 species showed that the genus Nasturtium was a sister to Cardamine in the Cardamineae tribe. Our study provides valuable resources for future evolution, population genetics and molecular biology studies of watercress.
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Affiliation(s)
- Chao Yan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, Nanjing Agricultural University, Nanjing 210095, China
| | - Jianchang Du
- Provincial Key Laboratory of Agrobiology, Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Lu Gao
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Li
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, Nanjing Agricultural University, Nanjing 210095, China
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (East China), Ministry of Agriculture and Rural Affairs of the P.R. China, Nanjing Agricultural University, Nanjing 210095, China.
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9
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Wickramasuriya AM, Dunwell JM. Cacao biotechnology: current status and future prospects. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:4-17. [PMID: 28985014 PMCID: PMC5785363 DOI: 10.1111/pbi.12848] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2017] [Revised: 09/25/2017] [Accepted: 09/28/2017] [Indexed: 05/03/2023]
Abstract
Theobroma cacao-The Food of the Gods, provides the raw material for the multibillion dollar chocolate industry and is also the main source of income for about 6 million smallholders around the world. Additionally, cocoa beans have a number of other nonfood uses in the pharmaceutical and cosmetic industries. Specifically, the potential health benefits of cocoa have received increasing attention as it is rich in polyphenols, particularly flavonoids. At present, the demand for cocoa and cocoa-based products in Asia is growing particularly rapidly and chocolate manufacturers are increasing investment in this region. However, in many Asian countries, cocoa production is hampered due to many reasons including technological, political and socio-economic issues. This review provides an overview of the present status of global cocoa production and recent advances in biotechnological applications for cacao improvement, with special emphasis on genetics/genomics, in vitro embryogenesis and genetic transformation. In addition, in order to obtain an insight into the latest innovations in the commercial sector, a survey was conducted on granted patents relating to T. cacao biotechnology.
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Affiliation(s)
| | - Jim M. Dunwell
- School of Agriculture, Policy and DevelopmentUniversity of ReadingReadingUK
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10
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Livingstone D, Stack C, Mustiga GM, Rodezno DC, Suarez C, Amores F, Feltus FA, Mockaitis K, Cornejo OE, Motamayor JC. A Larger Chocolate Chip-Development of a 15K Theobroma cacao L. SNP Array to Create High-Density Linkage Maps. FRONTIERS IN PLANT SCIENCE 2017; 8:2008. [PMID: 29259608 PMCID: PMC5723429 DOI: 10.3389/fpls.2017.02008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 11/10/2017] [Indexed: 05/30/2023]
Abstract
Cacao (Theobroma cacao L.) is an important cash crop in tropical regions around the world and has a rich agronomic history in South America. As a key component in the cosmetic and confectionary industries, millions of people worldwide use products made from cacao, ranging from shampoo to chocolate. An Illumina Infinity II array was created using 13,530 SNPs identified within a small diversity panel of cacao. Of these SNPs, 12,643 derive from variation within annotated cacao genes. The genotypes of 3,072 trees were obtained, including two mapping populations from Ecuador. High-density linkage maps for these two populations were generated and compared to the cacao genome assembly. Phenotypic data from these populations were combined with the linkage maps to identify the QTLs for yield and disease resistance.
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Affiliation(s)
| | | | | | | | - Carmen Suarez
- Estación Experimental Tropical Pichilingue, National Institute of Agricultural Research, Quevedo, Ecuador
- Agricultural Faculty, Technical University of Quevedo, Quevedo, Ecuador
| | - Freddy Amores
- Estación Experimental Tropical Pichilingue, National Institute of Agricultural Research, Quevedo, Ecuador
- Universidad Técnica Estatal Quevedo (UTEQ), Quevedo, Ecuador
| | - Frank A. Feltus
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC, United States
| | - Keithanne Mockaitis
- Department of Biology and Pervasive Technology Institute, Indiana University Bloomington, Bloomington, IN, United States
| | - Omar E. Cornejo
- School of Biological Sciences, Washington State University, Pullman, WA, United States
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11
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Unver T, Wu Z, Sterck L, Turktas M, Lohaus R, Li Z, Yang M, He L, Deng T, Escalante FJ, Llorens C, Roig FJ, Parmaksiz I, Dundar E, Xie F, Zhang B, Ipek A, Uranbey S, Erayman M, Ilhan E, Badad O, Ghazal H, Lightfoot DA, Kasarla P, Colantonio V, Tombuloglu H, Hernandez P, Mete N, Cetin O, Van Montagu M, Yang H, Gao Q, Dorado G, Van de Peer Y. Genome of wild olive and the evolution of oil biosynthesis. Proc Natl Acad Sci U S A 2017; 114:E9413-E9422. [PMID: 29078332 PMCID: PMC5676908 DOI: 10.1073/pnas.1708621114] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Here we present the genome sequence and annotation of the wild olive tree (Olea europaea var. sylvestris), called oleaster, which is considered an ancestor of cultivated olive trees. More than 50,000 protein-coding genes were predicted, a majority of which could be anchored to 23 pseudochromosomes obtained through a newly constructed genetic map. The oleaster genome contains signatures of two Oleaceae lineage-specific paleopolyploidy events, dated at ∼28 and ∼59 Mya. These events contributed to the expansion and neofunctionalization of genes and gene families that play important roles in oil biosynthesis. The functional divergence of oil biosynthesis pathway genes, such as FAD2, SACPD, EAR, and ACPTE, following duplication, has been responsible for the differential accumulation of oleic and linoleic acids produced in olive compared with sesame, a closely related oil crop. Duplicated oleaster FAD2 genes are regulated by an siRNA derived from a transposable element-rich region, leading to suppressed levels of FAD2 gene expression. Additionally, neofunctionalization of members of the SACPD gene family has led to increased expression of SACPD2, 3, 5, and 7, consequently resulting in an increased desaturation of steric acid. Taken together, decreased FAD2 expression and increased SACPD expression likely explain the accumulation of exceptionally high levels of oleic acid in olive. The oleaster genome thus provides important insights into the evolution of oil biosynthesis and will be a valuable resource for oil crop genomics.
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Affiliation(s)
- Turgay Unver
- İzmir International Biomedicine and Genome Institute, Dokuz Eylül University, 35340 İzmir, Turkey;
| | | | - Lieven Sterck
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Mine Turktas
- Department of Biology, Faculty of Science, Cankiri Karatekin University, 18100 Cankiri, Turkey
| | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Ming Yang
- BGI Shenzhen, 518038 Shenzhen, China
| | - Lijuan He
- BGI Shenzhen, 518038 Shenzhen, China
| | | | | | | | | | - Iskender Parmaksiz
- Department of Molecular Biology and Genetics, Faculty of Science, Gaziosmanpasa University, 60250 Tokat, Turkey
| | - Ekrem Dundar
- Department of Molecular Biology and Genetics, Faculty of Science, Balikesir University, 10145 Balikesir, Turkey
| | - Fuliang Xie
- Department of Biology, East Carolina University, Greenville, NC 27858
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858
| | - Arif Ipek
- Department of Biology, Faculty of Science, Cankiri Karatekin University, 18100 Cankiri, Turkey
| | - Serkan Uranbey
- Department of Field Crops, Faculty of Agriculture, Ankara University, 06120 Ankara, Turkey
| | - Mustafa Erayman
- Department of Biology, Faculty of Arts and Science, Mustafa Kemal University, 31060 Hatay, Turkey
| | - Emre Ilhan
- Department of Biology, Faculty of Arts and Science, Mustafa Kemal University, 31060 Hatay, Turkey
| | - Oussama Badad
- Laboratory of Plant Physiology, University Mohamed V, 10102 Rabat, Morocco
| | - Hassan Ghazal
- Polydisciplinary Faculty of Nador, University Mohamed Premier, 62700 Nador, Morocco
| | - David A Lightfoot
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901
| | - Pavan Kasarla
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901
| | - Vincent Colantonio
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901
| | - Huseyin Tombuloglu
- Institute for Research and Medical Consultation, University of Dammam, 34212 Dammam, Saudi Arabia
| | - Pilar Hernandez
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas, 14004 Córdoba, Spain
| | - Nurengin Mete
- Olive Research Institute of Bornova, 35100 Izmir, Turkey
| | - Oznur Cetin
- Olive Research Institute of Bornova, 35100 Izmir, Turkey
| | - Marc Van Montagu
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | | | - Qiang Gao
- BGI Shenzhen, 518038 Shenzhen, China
| | - Gabriel Dorado
- Departamento Bioquímica y Biología Molecular, Campus de Excelencia Internacional Agroalimentario, Universidad de Córdoba, 14071 Córdoba, Spain
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium;
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
- Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria 0028, South Africa
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12
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da Costa ZP, Munhoz CDF, Vieira MLC. Report on the development of putative functional SSR and SNP markers in passion fruits. BMC Res Notes 2017; 10:445. [PMID: 28874179 PMCID: PMC5585897 DOI: 10.1186/s13104-017-2771-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 08/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Passionflowers Passiflora edulis and Passiflora alata are diploid, outcrossing and understudied fruit bearing species. In Brazil, passion fruit cultivation began relatively recently and has earned the country an outstanding position as the world's top producer of passion fruit. The fruit's main economic value lies in the production of juice, an essential exotic ingredient in juice blends. Currently, crop improvement strategies, including those for underexploited tropical species, tend to incorporate molecular genetic approaches. In this study, we examined a set of P. edulis transcripts expressed in response to infection by Xanthomonas axonopodis, (the passion fruit's main bacterial pathogen that attacks the vines), aiming at the development of putative functional markers, i.e. SSRs (simple sequence repeats) and SNPs (single nucleotide polymorphisms). RESULTS A total of 210 microsatellites were found in 998 sequences, and trinucleotide repeats were found to be the most frequent (31.4%). Of the sequences selected for designing primers, 80.9% could be used to develop SSR markers, and 60.6% SNP markers for P. alata. SNPs were all biallelic and found within 15 gene fragments of P. alata. Overall, gene fragments generated 10,003 bp. SNP frequency was estimated as one SNP every 294 bp. Polymorphism rates revealed by SSR and SNP loci were 29.4 and 53.6%, respectively. CONCLUSIONS Passiflora edulis transcripts were useful for the development of putative functional markers for P. alata, suggesting a certain level of sequence conservation between these cultivated species. The markers developed herein could be used for genetic mapping purposes and also in diversity studies.
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Affiliation(s)
- Zirlane Portugal da Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Carla de Freitas Munhoz
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil.
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Liu LX, Li R, Worth JRP, Li X, Li P, Cameron KM, Fu CX. The Complete Chloroplast Genome of Chinese Bayberry ( Morella rubra, Myricaceae): Implications for Understanding the Evolution of Fagales. FRONTIERS IN PLANT SCIENCE 2017; 8:968. [PMID: 28713393 PMCID: PMC5492642 DOI: 10.3389/fpls.2017.00968] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 05/23/2017] [Indexed: 05/18/2023]
Abstract
Morella rubra (Myricaceae), also known as Chinese bayberry, is an economically important, subtropical, evergreen fruit tree. The phylogenetic placement of Myricaceae within Fagales and the origin of Chinese bayberry's domestication are still unresolved. In this study, we report the chloroplast (cp) genome of M. rubra and take advantage of several previously reported chloroplast genomes from related taxa to examine patterns of evolution in Fagales. The cp genomes of three M. rubra individuals were 159,478, 159,568, and 159.586 bp in length, respectively, comprising a pair of inverted repeat (IR) regions (26,014-26,069 bp) separated by a large single-copy (LSC) region (88,683-88,809 bp) and a small single-copy (SSC) region (18,676-18,767 bp). Each cp genome encodes the same 111 unique genes, consisting of 77 different protein-coding genes, 30 transfer RNA genes and four ribosomal RNA genes, with 18 duplicated in the IRs. Comparative analysis of chloroplast genomes from four representative Fagales families revealed the loss of infA and the pseudogenization of ycf15 in all analyzed species, and rpl22 has been pseudogenized in M. rubra and Castanea mollissima, but not in Juglans regia or Ostrya rehderiana. The genome size variations are detected mainly due to the length of intergenic spacers rather than gene loss, gene pseudogenization, IR expansion or contraction. The phylogenetic relationships yielded by the complete genome sequences strongly support the placement of Myricaceae as sister to Juglandaceae. Furthermore, seven cpDNA markers (trnH-psbA, psbA-trnK, rps2-rpoC2, ycf4-cemA, petD-rpoA, ndhE-ndhG, and ndhA intron) with relatively high levels of variation and variable cpSSR loci were identified within M. rubra, which will be useful in future research characterizing the population genetics of M. rubra and investigating the origin of domesticated Chinese bayberry.
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Affiliation(s)
- Lu-Xian Liu
- Laboratory of Plant Germplasm and Genetic Engineering, College of Life Sciences, Henan UniversityKaifeng, China
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang UniversityHangzhou, China
| | - Rui Li
- Food Inspection and Testing Institute of Henan ProvinceZhengzhou, China
| | - James R. P. Worth
- Department of Forest Molecular Genetics and Biotechnology, Forestry and Forest Products Research InstituteIbaraki, Japan
| | - Xian Li
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang UniversityHangzhou, China
| | - Pan Li
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang UniversityHangzhou, China
- *Correspondence: Pan Li,
| | | | - Cheng-Xin Fu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education, College of Life Sciences, Zhejiang UniversityHangzhou, China
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14
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Wei S, Wang X, Bi C, Xu Y, Wu D, Ye N. Assembly and analysis of the complete Salix purpurea L. (Salicaceae) mitochondrial genome sequence. SPRINGERPLUS 2016; 5:1894. [PMID: 27843751 PMCID: PMC5084139 DOI: 10.1186/s40064-016-3521-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2016] [Accepted: 10/11/2016] [Indexed: 11/10/2022]
Abstract
Plant mitochondrial (mt) genomes possess several complex features, including a variable size, a dynamic genome structure, and complicated patterns of gene loss and gain throughout evolutionary history. Studies of plant mt genomes can, therefore, provide unique insights into organelle evolution. We assembled the complete Salix purpurea L. mt genome by screening genomic sequence reads generated by a Roche-454 pyrosequencing platform. The pseudo-molecule obtained has a typical circular structure 598,970 bp long, with an overall GC content of 55.06%. The S. purpurea mt genome contains 52 genes: 31 protein-coding, 18 tRNAs, and three rRNAs. Eighteen tandem repeats and 404 microsatellites are distributed unevenly throughout the S. purpurea mt genome. A phylogenetic tree of 23 representative terrestrial plants strongly supports S. purpurea inclusion in the Malpighiales clade. Our analysis contributes toward understanding the organization and evolution of organelle genomes in Salicaceae species.
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Affiliation(s)
- Suyun Wei
- College of Forestry, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Xuelin Wang
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Changwei Bi
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Yiqing Xu
- College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; School of Computer Science and Engineering, Southeast University, Nanjing, 211189 Jiangsu China
| | - Dongyang Wu
- College of Forestry, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
| | - Ning Ye
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037 Jiangsu China ; College of Information Science and Technology, Nanjing Forestry University, Nanjing, 210037 Jiangsu China
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15
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The Whole Genome Assembly and Comparative Genomic Research of Thellungiella parvula (Extremophile Crucifer) Mitochondrion. Int J Genomics 2016; 2016:5283628. [PMID: 27148547 PMCID: PMC4842374 DOI: 10.1155/2016/5283628] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/03/2016] [Accepted: 03/10/2016] [Indexed: 11/17/2022] Open
Abstract
The complete nucleotide sequences of the mitochondrial (mt) genome of an extremophile species Thellungiella parvula (T. parvula) have been determined with the lengths of 255,773 bp. T. parvula mt genome is a circular sequence and contains 32 protein-coding genes, 19 tRNA genes, and three ribosomal RNA genes with a 11.5% coding sequence. The base composition of 27.5% A, 27.5% T, 22.7% C, and 22.3% G in descending order shows a slight bias of 55% AT. Fifty-three repeats were identified in the mitochondrial genome of T. parvula, including 24 direct repeats, 28 tandem repeats (TRs), and one palindromic repeat. Furthermore, a total of 199 perfect microsatellites have been mined with a high A/T content (83.1%) through simple sequence repeat (SSR) analysis and they were distributed unevenly within this mitochondrial genome. We also analyzed other plant mitochondrial genomes' evolution in general, providing clues for the understanding of the evolution of organelles genomes in plants. Comparing with other Brassicaceae species, T. parvula is related to Arabidopsis thaliana whose characters of low temperature resistance have been well documented. This study will provide important genetic tools for other Brassicaceae species research and improve yields of economically important plants.
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16
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Royaert S, Jansen J, da Silva DV, de Jesus Branco SM, Livingstone DS, Mustiga G, Marelli JP, Araújo IS, Corrêa RX, Motamayor JC. Identification of candidate genes involved in Witches' broom disease resistance in a segregating mapping population of Theobroma cacao L. in Brazil. BMC Genomics 2016; 17:107. [PMID: 26865216 PMCID: PMC4750280 DOI: 10.1186/s12864-016-2415-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 01/26/2016] [Indexed: 01/17/2023] Open
Abstract
Background Witches’ broom disease (WBD) caused by the fungus Moniliophthora perniciosa is responsible for considerable economic losses for cacao producers. One of the ways to combat WBD is to plant resistant cultivars. Resistance may be governed by a few genetic factors, mainly found in wild germplasm. Results We developed a dense genetic linkage map with a length of 852.8 cM that contains 3,526 SNPs and is based on the MP01 mapping population, which counts 459 trees from a cross between the resistant ‘TSH 1188’ and the tolerant ‘CCN 51’ at the Mars Center for Cocoa Science in Barro Preto, Bahia, Brazil. Seven quantitative trait loci (QTL) that are associated with WBD were identified on five different chromosomes using a multi-trait QTL analysis for outbreeders. Phasing of the haplotypes at the major QTL region on chromosome IX on a diversity panel of genotypes clearly indicates that the major resistance locus comes from a well-known source of WBD resistance, the clone ‘SCAVINA 6’. Various potential candidate genes identified within all QTL may be involved in different steps leading to disease resistance. Preliminary expression data indicate that at least three of these candidate genes may play a role during the first 12 h after infection, with clear differences between ‘CCN 51’ and ‘TSH 1188’. Conclusions We combined the information from a large mapping population with very distinct parents that segregate for WBD, a dense set of mapped markers, rigorous phenotyping capabilities and the availability of a sequenced genome to identify several genomic regions that are involved in WBD resistance. We also identified a novel source of resistance that most likely comes from the ‘CCN 51’ parent. Thanks to the large population size of the MP01 population, we were able to pick up QTL and markers with relatively small effects that can contribute to the creation and selection of more tolerant/resistant plant material. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2415-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stefan Royaert
- Mars Center for Cocoa Science, CP 55, Itajuípe, BA, CEP 45.630-000, Brazil.
| | - Johannes Jansen
- Biometris, Wageningen University and Research Centre, P.O. Box 100, 6700 AC, Wageningen, The Netherlands.
| | - Daniela Viana da Silva
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, Km 16, Bairro Salobrinho, Ilhéus, BA, CEP 45.662-900, Brazil.
| | - Samuel Martins de Jesus Branco
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, Km 16, Bairro Salobrinho, Ilhéus, BA, CEP 45.662-900, Brazil.
| | | | - Guiliana Mustiga
- Mars, Incorporated, 13601 Old Cutler Road, Miami, FL, 33158, USA.
| | | | - Ioná Santos Araújo
- Departamento de Ciências Vegetais, Universidade Federal Rural do Semi-Arido, BR 110 - Km 47, Bairro Pres. Costa e Silva, Mossoró, RN, CEP 59.625-900, Brazil.
| | - Ronan Xavier Corrêa
- Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Ilhéus-Itabuna, Km 16, Bairro Salobrinho, Ilhéus, BA, CEP 45.662-900, Brazil.
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17
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Chen J, Hao Z, Xu H, Yang L, Liu G, Sheng Y, Zheng C, Zheng W, Cheng T, Shi J. The complete chloroplast genome sequence of the relict woody plant Metasequoia glyptostroboides Hu et Cheng. FRONTIERS IN PLANT SCIENCE 2015; 6:447. [PMID: 26136762 PMCID: PMC4468836 DOI: 10.3389/fpls.2015.00447] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Accepted: 05/31/2015] [Indexed: 05/03/2023]
Abstract
Metasequoia glyptostroboides Hu et Cheng is the only species in the genus Metasequoia Miki ex Hu et Cheng, which belongs to the Cupressaceae family. There were around 10 species in the Metasequoia genus, which were widely spread across the Northern Hemisphere during the Cretaceous of the Mesozoic and in the Cenozoic. M. glyptostroboides is the only remaining representative of this genus. Here, we report the complete chloroplast (cp) genome sequence and the cp genomic features of M. glyptostroboides. The M. glyptostroboides cp genome is 131,887 bp in length, with a total of 117 genes comprised of 82 protein-coding genes, 31 tRNA genes and four rRNA genes. In this genome, 11 forward repeats, nine palindromic repeats, and 15 tandem repeats were detected. A total of 188 perfect microsatellites were detected through simple sequence repeat (SSR) analysis and these were distributed unevenly within the cp genome. Comparison of the cp genome structure and gene order to those of several other land plants indicated that a copy of the inverted repeat (IR) region, which was found to be IR region A (IRA), was lost in the M. glyptostroboides cp genome. The five most divergent and five most conserved genes were determined and further phylogenetic analysis was performed among plant species, especially for related species in conifers. Finally, phylogenetic analysis demonstrated that M. glyptostroboides is a sister species to Cryptomeria japonica (L. F.) D. Don and to Taiwania cryptomerioides Hayata. The complete cp genome sequence information of M. glyptostroboides will be great helpful for further investigations of this endemic relict woody plant and for in-depth understanding of the evolutionary history of the coniferous cp genomes, especially for the position of M. glyptostroboides in plant systematics and evolution.
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Affiliation(s)
- Jinhui Chen
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry UniversityNanjing, China
| | - Zhaodong Hao
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry UniversityNanjing, China
| | - Haibin Xu
- College of Biology and the Environment, Nanjing Forestry UniversityNanjing, China
| | - Liming Yang
- School of Life Sciences, Huaiyin Normal UniversityHuaian, China
| | - Guangxin Liu
- College of Biology and the Environment, Nanjing Forestry UniversityNanjing, China
| | - Yu Sheng
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry UniversityNanjing, China
| | - Chen Zheng
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry UniversityNanjing, China
| | - Weiwei Zheng
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry UniversityNanjing, China
| | - Tielong Cheng
- College of Biology and the Environment, Nanjing Forestry UniversityNanjing, China
| | - Jisen Shi
- Key Laboratory of Forest Genetics and Biotechnology, Ministry of Education, Nanjing Forestry UniversityNanjing, China
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18
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Herrmann L, Felbinger C, Haase I, Rudolph B, Biermann B, Fischer M. Food Fingerprinting: Characterization of the Ecuadorean Type CCN-51 of Theobroma cacao L. Using Microsatellite Markers. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:4539-4544. [PMID: 25892108 DOI: 10.1021/acs.jafc.5b01462] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The cocoa type "Colección Castro Naranjal 51" (CCN-51) is known for its resistance to specific climate conditions and its high yield, but it shows a weaker flavor profile and therefore is marketed as bulk cocoa. In a previous study, the two cocoa types Arriba and CCN-51 could easily be distinguished, but differences among the CCN-51 samples were observed. This was unexpected, as CCN-51 is reported to be a clone. To confirm whether CCN-51 is a pure clone, 10 simple sequence repeats (SSR) located on the nuclear genome were used to analyze various CCN-51 samples in comparison to the cocoa varieties Arriba and Criollo. As expected, there are differences in the SSR pattern among CCN-51, Arriba, and Criollo, but a variability within the CCN-51 sample set was detected as well. The previously described sequence variation in the chloroplast genome was confirmed by a variability in the microsatellite loci of the nuclear genome for a comprehensive cultivar collection of CCN-51 of both bean and leaf samples. In summary, beneath somaclonal variation, misidentification of plant collections and also sexual reproduction of CCN-51 can be suggested.
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Affiliation(s)
- Luise Herrmann
- †Hamburg School of Food Science; Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Christine Felbinger
- †Hamburg School of Food Science; Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Ilka Haase
- †Hamburg School of Food Science; Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Barbara Rudolph
- ‡Biozentrum Klein Flottbek, University of Hamburg, Ohnhorststr. 18, 22609 Hamburg, Germany
| | - Bernhard Biermann
- †Hamburg School of Food Science; Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
| | - Markus Fischer
- †Hamburg School of Food Science; Institute of Food Chemistry, University of Hamburg, Grindelallee 117, 20146 Hamburg, Germany
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19
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Herrmann L, Haase I, Blauhut M, Barz N, Fischer M. DNA-based differentiation of the Ecuadorian cocoa types CCN-51 and Arriba based on sequence differences in the chloroplast genome. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2014; 62:12118-12127. [PMID: 25404556 DOI: 10.1021/jf504258w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Two cocoa types, Arriba and CCN-51, are being cultivated in Ecuador. With regard to the unique aroma, Arriba is considered a fine cocoa type, while CCN-51 is a bulk cocoa because of its weaker aroma. Because it is being assumed that Arriba is mixed with CCN-51, there is an interest in the analytical differentiation of the two types. Two methods to identify CCN-51 adulterations in Arriba cocoa were developed on the basis of differences in the chloroplast DNA. On the one hand, a different repeat of the sequence TAAAG in the inverted repeat region results in a different length of amplicons for the two cocoa types, which can be detected by agarose gel electrophoresis, capillary gel electrophoresis, and denaturing high-performance liquid chromatography. On the other hand, single nucleotide polymorphisms (SNPs) between the CCN-51 and Arriba sequences represent restriction sites, which can be used for restriction fragment length polymorphism analysis. A semi-quantitative analysis based on these SNPs is feasible. A method for an exact quantitation based on these results is not realizable. These sequence variations were confirmed for a comprehensive cultivar collection of Arriba and CCN-51, for both bean and leaf samples.
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Affiliation(s)
- Luise Herrmann
- Hamburg School of Food Science, Institut für Lebensmittelchemie, Universität Hamburg , Grindelallee 117, 20146 Hamburg, Germany
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Mejía LC, Herre EA, Sparks JP, Winter K, García MN, Van Bael SA, Stitt J, Shi Z, Zhang Y, Guiltinan MJ, Maximova SN. Pervasive effects of a dominant foliar endophytic fungus on host genetic and phenotypic expression in a tropical tree. Front Microbiol 2014; 5:479. [PMID: 25309519 PMCID: PMC4162356 DOI: 10.3389/fmicb.2014.00479] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 08/25/2014] [Indexed: 12/05/2022] Open
Abstract
It is increasingly recognized that macro-organisms (corals, insects, plants, vertebrates) consist of both host tissues and multiple microbial symbionts that play essential roles in their host's ecological and evolutionary success. Consequently, identifying benefits and costs of symbioses, as well as mechanisms underlying them are research priorities. All plants surveyed under natural conditions harbor foliar endophytic fungi (FEF) in their leaf tissues, often at high densities. Despite producing no visible effects on their hosts, experiments have nonetheless shown that FEF reduce pathogen and herbivore damage. Here, combining results from three genomic, and two physiological experiments, we demonstrate pervasive genetic and phenotypic effects of the apparently asymptomatic endophytes on their hosts. Specifically, inoculation of endophyte-free (E−) Theobroma cacao leaves with Colletotrichum tropicale (E+), the dominant FEF species in healthy T. cacao, induces consistent changes in the expression of hundreds of host genes, including many with known defensive functions. Further, E+ plants exhibited increased lignin and cellulose content, reduced maximum rates of photosynthesis (Amax), and enrichment of nitrogen-15 and carbon-13 isotopes. These phenotypic changes observed in E+ plants correspond to changes in expression of specific functional genes in related pathways. Moreover, a cacao gene (Tc00g04254) highly up-regulated by C. tropicale also confers resistance to pathogen damage in the absence of endophytes or their products in host tissues. Thus, the benefits of increased pathogen resistance in E+ plants are derived in part from up-regulation of intrinsic host defense responses, and appear to be offset by potential costs including reduced photosynthesis, altered host nitrogen metabolism, and endophyte heterotrophy of host tissues. Similar effects are likely in most plant-endophyte interactions, and should be recognized in the design and interpretation of genetic and phenotypic studies of plants.
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Affiliation(s)
- Luis C Mejía
- Smithsonian Tropical Research Institute Unit 9100, USA ; Department of Plant Science and The Huck Institutes of the Life Sciences, The Pennsylvania State University University Park, PA, USA
| | | | - Jed P Sparks
- Department of Ecology and Evolution, Cornell University Ithaca, NY, USA
| | - Klaus Winter
- Smithsonian Tropical Research Institute Unit 9100, USA
| | | | - Sunshine A Van Bael
- Smithsonian Tropical Research Institute Unit 9100, USA ; Department of Ecology and Evolutionary Biology, Tulane University New Orleans, LA, USA
| | - Joseph Stitt
- Social, Life and Engineering Sciences Imaging Center, Materials Research Institute University Park, PA, USA
| | - Zi Shi
- Department of Plant Science and The Huck Institutes of the Life Sciences, The Pennsylvania State University University Park, PA, USA
| | - Yufan Zhang
- Department of Plant Science and The Huck Institutes of the Life Sciences, The Pennsylvania State University University Park, PA, USA
| | - Mark J Guiltinan
- Department of Plant Science and The Huck Institutes of the Life Sciences, The Pennsylvania State University University Park, PA, USA
| | - Siela N Maximova
- Department of Plant Science and The Huck Institutes of the Life Sciences, The Pennsylvania State University University Park, PA, USA
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Abstract
In accordance with pseudo-testcross strategy, the first genetic linkage map of Eucommia ulmoides Oliv. was constructed by an F1 population of 122 plants using amplified fragment length polymorphism (AFLP) markers. A total of 22 AFLP primer combinations generated 363 polymorphic markers. We selected 289 markers segregating as 1:1 and used them for constructing the parent-specific linkage maps. Among the candidate markers, 127 markers were placed on the maternal map LF and 108 markers on the paternal map Q1. The maternal map LF spanned 1116.1 cM in 14 linkage groups with a mean map distance of 8.78 cM; the paternal map Q1 spanned 929.6 cM in 12 linkage groups with an average spacing of 8.61 cM. The estimated coverage of the genome through two methods was 78.5 and 73.9% for LF, and 76.8 and 71.2% for Q1, respectively. This map is the first linkage map of E. ulmoides and provides a basis for mapping quantitative-trait loci and breeding applications.
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Affiliation(s)
- Dawei Wang
- College of Forestry, Northwest A and F University, Yangling, Shaanxi 712100, People's Republic of China.
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22
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Allegre M, Argout X, Boccara M, Fouet O, Roguet Y, Bérard A, Thévenin JM, Chauveau A, Rivallan R, Clement D, Courtois B, Gramacho K, Boland-Augé A, Tahi M, Umaharan P, Brunel D, Lanaud C. Discovery and mapping of a new expressed sequence tag-single nucleotide polymorphism and simple sequence repeat panel for large-scale genetic studies and breeding of Theobroma cacao L. DNA Res 2011; 19:23-35. [PMID: 22210604 PMCID: PMC3276266 DOI: 10.1093/dnares/dsr039] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Theobroma cacao is an economically important tree of several tropical countries. Its genetic improvement is essential to provide protection against major diseases and improve chocolate quality. We discovered and mapped new expressed sequence tag-single nucleotide polymorphism (EST-SNP) and simple sequence repeat (SSR) markers and constructed a high-density genetic map. By screening 149 650 ESTs, 5246 SNPs were detected in silico, of which 1536 corresponded to genes with a putative function, while 851 had a clear polymorphic pattern across a collection of genetic resources. In addition, 409 new SSR markers were detected on the Criollo genome. Lastly, 681 new EST-SNPs and 163 new SSRs were added to the pre-existing 418 co-dominant markers to construct a large consensus genetic map. This high-density map and the set of new genetic markers identified in this study are a milestone in cocoa genomics and for marker-assisted breeding. The data are available at http://tropgenedb.cirad.fr.
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Affiliation(s)
- Mathilde Allegre
- CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France
| | - Xavier Argout
- CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France
- To whom correspondence should be addressed. Fax. +33 4-67-61-56-05.
| | - Michel Boccara
- CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France
- University of the West Indies, Cocoa Research Unit (CRU), St Augustine, Trinidad and Tobago
| | - Olivier Fouet
- CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France
| | - Yolande Roguet
- CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France
| | - Aurélie Bérard
- INRA, UR 1279 Etude du Polymorphisme des Génomes Végétaux, CEA Institut de Génomique, Centre National de Génotypage, 2, rue Gaston Crémieux, CP5724, 91057 Evry, France
| | - Jean Marc Thévenin
- CIRAD, Biological Systems Department, UPR Bioagresseurs, 97387 Kourou Cedex, French Guiana
| | - Aurélie Chauveau
- INRA, UR 1279 Etude du Polymorphisme des Génomes Végétaux, CEA Institut de Génomique, Centre National de Génotypage, 2, rue Gaston Crémieux, CP5724, 91057 Evry, France
| | - Ronan Rivallan
- CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France
| | - Didier Clement
- CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France
- Comissão Executiva de Planejamento da Lavoura Cacaueira (CEPLAC), Km 22 Rod. Ilheus Itabuna, Cx. postal 07, Itabuna 45600-00, Bahia, Brazil
| | | | - Karina Gramacho
- Comissão Executiva de Planejamento da Lavoura Cacaueira (CEPLAC), Km 22 Rod. Ilheus Itabuna, Cx. postal 07, Itabuna 45600-00, Bahia, Brazil
| | - Anne Boland-Augé
- INRA, UR 1279 Etude du Polymorphisme des Génomes Végétaux, CEA Institut de Génomique, Centre National de Génotypage, 2, rue Gaston Crémieux, CP5724, 91057 Evry, France
| | - Mathias Tahi
- Centre National de la Recherche Agronomique (CNRA), B.P. 808, Divo, Côte d'Ivoire
| | - Pathmanathan Umaharan
- University of the West Indies, Cocoa Research Unit (CRU), St Augustine, Trinidad and Tobago
| | - Dominique Brunel
- INRA, UR 1279 Etude du Polymorphisme des Génomes Végétaux, CEA Institut de Génomique, Centre National de Génotypage, 2, rue Gaston Crémieux, CP5724, 91057 Evry, France
| | - Claire Lanaud
- CIRAD, UMR 1334 AGAP, TA 108/03-34398, Montpellier Cedex 5, France
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Abstract
We sequenced and assembled the draft genome of Theobroma cacao, an economically important tropical-fruit tree crop that is the source of chocolate. This assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of these genes anchored on the 10 T. cacao chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example, flavonoid-related genes. It also provides a major source of candidate genes for T. cacao improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten T. cacao chromosomes were shaped from an ancestor through eleven chromosome fusions.
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Zhan A, Hu J, Hu X, Hui M, Wang M, Peng W, Huang X, Wang S, Lu W, Sun C, Bao Z. Construction of microsatellite-based linkage maps and identification of size-related quantitative trait loci for Zhikong scallop (Chlamys farreri). Anim Genet 2009; 40:821-31. [PMID: 19515089 DOI: 10.1111/j.1365-2052.2009.01920.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A Zhan
- Key Laboratory of Marine Genetics and Gene Resource Exploitation (Ocean University of China), Ministry of Education, Qingdao 266003, China.
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25
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Mining of expressed sequence tag libraries of cacao for microsatellite markers using five computational tools. J Genet 2009; 88:217-25. [PMID: 19700860 DOI: 10.1007/s12041-009-0030-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Expressed sequence tags (ESTs) provide researchers with a quick and inexpensive route for discovering new genes, data on gene expression and regulation, and also provide genic markers that help in constructing genome maps. Cacao is an important perennial crop of humid tropics. Cacao EST sequences, as available in the public domain, were downloaded and made into contigs. Microsatellites were located in these ESTs and contigs using five softwares (MISA, TRA, TROLL, SSRIT and SSR primer). MISA gave maximum coverage of SSRs in cacao ESTs and contigs, although TRA was able to detect higher order (5-mer) repeats. The frequency of SSRs was one per 26.9 kb in the known set of ESTs. One-third of the repeats in EST-contigs were found to be trimeric. A few rare repeats like 21-mer repeat were also located. A/T repeats were most abundant among the mononucleotide repeats and the AG/GA/TC/CT type was the most frequent among dimerics. Flanking primers were designed using Primer3 program and verified experimentally for PCR amplification. The results of the study are made available freely online database (http://riju.byethost31.com/cocoa/). Seven primer pairs amplified genomic DNA isolated from leaves were used to screen a representative set of 12 accessions of cacao.
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26
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Kuhn DN, Motamayor JC, Meerow AW, Borrone JW, Schnell RJ. SSCP markers provide a useful alternative to microsatellites in genotyping and estimating genetic diversity in populations and germplasm collections of plant specialty crops. Electrophoresis 2008; 29:4096-108. [PMID: 18958880 DOI: 10.1002/elps.200700937] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
For well-studied plant species with whole genome sequence or extensive EST data, SNP markers are the logical choice for both genotyping and whole genome association studies. However, SNP markers may not address the needs of researchers working on specialty crops with limited available genomic information. Microsatellite markers have been frequently employed due to their robustness, but marker development can be difficult and may result in few polymorphic markers. SSCP markers, such as microsatellites, are PCR-based and scored by electrophoretic mobility but, because they are based on SNPs rather than length differences, occur more frequently and are easier to develop than microsatellites. We have examined how well correlated the estimation of genetic diversity and genetic distance are in a population or germplasm collection when measured by 13 highly polymorphic microsatellite markers or 20 SSCP markers. We observed a significant correlation in pairwise genetic distances of 82 individuals in an international cacao germplasm collection (Mantel test Rxy=0.59, p<0.0001 for 10 000 permutations). Both sets of markers could distinguish each individual in the population. These data provide strong support for the use of SSCP markers in the genotyping of plant species where development of microsatellites would be difficult or expensive.
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Affiliation(s)
- David N Kuhn
- USDA-ARS Subtropical Horticultural Research Station, Miami, FL, USA.
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27
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Motamayor JC, Lachenaud P, da Silva E Mota JW, Loor R, Kuhn DN, Brown JS, Schnell RJ. Geographic and genetic population differentiation of the Amazonian chocolate tree (Theobroma cacao L). PLoS One 2008; 3:e3311. [PMID: 18827930 PMCID: PMC2551746 DOI: 10.1371/journal.pone.0003311] [Citation(s) in RCA: 155] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2008] [Accepted: 08/29/2008] [Indexed: 11/19/2022] Open
Abstract
Numerous collecting expeditions of Theobroma cacao L. germplasm have been undertaken in Latin-America. However, most of this germplasm has not contributed to cacao improvement because its relationship to cultivated selections was poorly understood. Germplasm labeling errors have impeded breeding and confounded the interpretation of diversity analyses. To improve the understanding of the origin, classification, and population differentiation within the species, 1241 accessions covering a large geographic sampling were genotyped with 106 microsatellite markers. After discarding mislabeled samples, 10 genetic clusters, as opposed to the two genetic groups traditionally recognized within T. cacao, were found by applying Bayesian statistics. This leads us to propose a new classification of the cacao germplasm that will enhance its management. The results also provide new insights into the diversification of Amazon species in general, with the pattern of differentiation of the populations studied supporting the palaeoarches hypothesis of species diversification. The origin of the traditional cacao cultivars is also enlightened in this study.
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Affiliation(s)
- Juan C Motamayor
- National Germplasm Repository, US Department of Agriculture, Agricultural Research Service, Subtropical Horticulture Research Station, Miami, Florida, USA.
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28
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Schnell RJ, Kuhn DN, Brown JS, Olano CT, Phillips-Mora W, Amores FM, Motamayor JC. Development of a marker assisted selection program for cacao. PHYTOPATHOLOGY 2007; 97:1664-9. [PMID: 18943731 DOI: 10.1094/phyto-97-12-1664] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
ABSTRACT Production of cacao in tropical America has been severely affected by fungal pathogens causing diseases known as witches' broom (WB, caused by Moniliophthora perniciosa), frosty pod (FP, caused by M. roreri) and black pod (BP, caused by Phytophthora spp.). BP is pan-tropical and causes losses in all producing areas. WB is found in South America and parts of the Caribbean, while FP is found in Central America and parts of South America. Together, these diseases were responsible for over 700 million US dollars in losses in 2001 (4). Commercial cacao production in West Africa and South Asia are not yet affected by WB and FP, but cacao grown in these regions is susceptible to both. With the goal of providing new disease resistant cultivars the USDA-ARS and Mars, Inc. have developed a marker assisted selection (MAS) program. Quantitative trait loci have been identified for resistance to WB, FP, and BP. The potential usefulness of these markers in identifying resistant individuals has been confirmed in an experimental F(1) family in Ecuador.
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29
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Gesteira AS, Micheli F, Carels N, Da Silva AC, Gramacho KP, Schuster I, Macêdo JN, Pereira GAG, Cascardo JCM. Comparative analysis of expressed genes from cacao meristems infected by Moniliophthora perniciosa. ANNALS OF BOTANY 2007; 100:129-40. [PMID: 17557832 PMCID: PMC2735303 DOI: 10.1093/aob/mcm092] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS Witches' broom disease is caused by the hemibiotrophic basidiomycete Moniliophthora perniciosa, and is one of the most important diseases of cacao in the western hemisphere. Because very little is known about the global process of such disease development, expressed sequence tags (ESTs) were used to identify genes expressed during the Theobroma cacao-Moniliophthora perniciosa interaction. METHODS Two cDNA libraries corresponding to the resistant (RT) and susceptible (SP) cacao-M. perniciosa interactions were constructed from total RNA, using the DB SMART Creator cDNA library kit (Clontech). Clones were randomly selected, sequenced from the 5' end and analysed using bioinformatics tools including in silico analysis of the differential gene expression. KEY RESULTS A total of 6884 ESTs were generated from the RT and SP cDNA libraries. These ESTs were composed of 2585 singlets and 341 contigs for a total of 2926 non-redundant sequences. The redundancy of the libraries was low and their specificity high when compared with the few other cacao libraries already published. Sequence analysis allowed the assignment of a putative functional category for 54 % of sequences, whereas approx. 22 % of sequences corresponded to unknown function and approx. 24 % of sequences did not show any significant similarity with other proteins present in the database. Despite the similar overall distribution of the sequences in functional categories between the two libraries, qualitative differences were observed. Genes involved during the defence response to pathogen infection or in programmed cell death were identified, such as pathogenesis related-proteins, trypsin inhibitor or oxalate oxidase, and some of them showed an in silico differential expression between the resistant and the susceptible interactions. CONCLUSIONS As far as is known this is the first EST resource from the cacao-M. perniciosa interaction and it is believed that it will provide a significant contribution to the understanding of the molecular mechanisms of the resistance and susceptibility of cacao to M. perniciosa, to develop strategies to control witches' broom, and as a source of polymorphism for molecular marker development and marker-assisted selection.
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Affiliation(s)
| | - Fabienne Micheli
- DCB/UESC, Laboratório de Genômica e Expressão Gênica, Ilhéus, Bahia, Brasil
- CIRAD-CP, UMR PIA, Montpellier, France
- For correspondence. E-mail
| | | | - Aline C. Da Silva
- DCB/UESC, Laboratório de Genômica e Expressão Gênica, Ilhéus, Bahia, Brasil
| | | | | | - Joci N. Macêdo
- DCB/UESC, Laboratório de Genômica e Expressão Gênica, Ilhéus, Bahia, Brasil
| | - Gonçalo A. G. Pereira
- Universidade Estadual de Campinas, Instituto de Biologia, Departamento de Genética e Evolução-UNICAMP, Campinas, São Paulo, Brasil
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30
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Marcano M, Pugh T, Cros E, Morales S, Portillo Páez EA, Courtois B, Glaszmann JC, Engels JMM, Phillips W, Astorga C, Risterucci AM, Fouet O, González V, Rosenberg K, Vallat I, Dagert M, Lanaud C. Adding value to cocoa (Theobroma cacao L.) germplasm information with domestication history and admixture mapping. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 114:877-84. [PMID: 17252253 DOI: 10.1007/s00122-006-0486-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2006] [Accepted: 12/16/2006] [Indexed: 05/13/2023]
Abstract
A sound understanding of crop history can provide the basis for deriving novel genetic information through admixture mapping. We confirmed this, by using characterization data from an international collection of cocoa, collected 25 years ago, and from a contemporary plantation. We focus on the trees derived from three centuries of admixture between Meso-American Criollo and South American Forastero genomes. In both cacao sets of individuals, linkage disequilibrium extended over long genetic distances along chromosome regions, as expected in populations derived from recent admixture. Based on loose genome scans, genomic regions involved in useful traits were identified. Fifteen genomic regions involved in seed and fruit weight variation were highlighted. They correspond to ten previously identified QTLs and five novel ones. Admixture mapping can help to add value to genetic resources and thus, help to encourage investment in their conservation.
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Affiliation(s)
- Maria Marcano
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, (CIRAD) TA 40/03, 34398, Montpellier Cedex 5, France.
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ALVES RAFAELM, SEBBENN ALEXANDREM, ARTERO ANGELAS, FIGUEIRA ANTONIO. Microsatellite loci transferability from Theobroma cacao to Theobroma grandiflorum. ACTA ACUST UNITED AC 2006. [DOI: 10.1111/j.1471-8286.2006.01496.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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32
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Loridon K, McPhee K, Morin J, Dubreuil P, Pilet-Nayel ML, Aubert G, Rameau C, Baranger A, Coyne C, Lejeune-Hènaut I, Burstin J. Microsatellite marker polymorphism and mapping in pea (Pisum sativum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2005; 111:1022-31. [PMID: 16133320 DOI: 10.1007/s00122-005-0014-3] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2005] [Accepted: 06/09/2005] [Indexed: 05/03/2023]
Abstract
This paper aims at providing reliable and cost effective genotyping conditions, level of polymorphism in a range of genotypes and map position of newly developed microsatellite markers in order to promote broad application of these markers as a common set for genetic studies in pea. Optimal PCR conditions were determined for 340 microsatellite markers based on amplification in eight genotypes. Levels of polymorphism were determined for 309 of these markers. Compared to data obtained for other species, levels of polymorphism detected in a panel of eight genotypes were high with a mean number of 3.8 alleles per polymorphic locus and an average PIC value of 0.62, indicating that pea represents a rather polymorphic autogamous species. One of our main objectives was to locate a maximum number of microsatellite markers on the pea genetic map. Data obtained from three different crosses were used to build a composite genetic map of 1,430 cM (Haldane) comprising 239 microsatellite markers. These include 216 anonymous SSRs developed from enriched genomic libraries and 13 SSRs located in genes. The markers are quite evenly distributed throughout the seven linkage groups of the map, with 85% of intervals between the adjacent SSR markers being smaller than 10 cM. There was a good conservation of marker order and linkage group assignment across the three populations. In conclusion, we hope this report will promote wide application of these markers and will allow information obtained by different laboratories worldwide in diverse fields of pea genetics, such as QTL mapping studies and genetic resource surveys, to be easily aligned.
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Affiliation(s)
- K Loridon
- INRA URLEG, Domaine d'Epoisses, 21110 Bretenières, France
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Cryer NC, Butler DR, Wilkinson MJ. High throughput, high resolution selection of polymorphic microsatellite loci for multiplex analysis. PLANT METHODS 2005; 1:3. [PMID: 16270924 PMCID: PMC1277016 DOI: 10.1186/1746-4811-1-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Accepted: 08/18/2005] [Indexed: 05/05/2023]
Abstract
BACKGROUND Large-scale genetic profiling, mapping and genetic association studies require access to a series of well-characterised and polymorphic microsatellite markers with distinct and broad allele ranges. Selection of complementary microsatellite markers with non-overlapping allele ranges has historically proved to be a bottleneck in the development of multiplex microsatellite assays. The characterisation process for each microsatellite locus can be laborious and costly given the need for numerous, locus-specific fluorescent primers. RESULTS Here, we describe a simple and inexpensive approach to select useful microsatellite markers. The system is based on the pooling of multiple unlabelled PCR amplicons and their subsequent ligation into a standard cloning vector. A second round of amplification utilising generic labelled primers targeting the vector and unlabelled locus-specific primers targeting the microsatellite flanking region yield allelic profiles that are representative of all individuals contained within the pool. Suitability of various DNA pool sizes was then tested for this purpose. DNA template pools containing between 8 and 96 individuals were assessed for the determination of allele ranges of individual microsatellite markers across a broad population. This helped resolve the balance between using pools that are large enough to allow the detection of many alleles against the risk of including too many individuals in a pool such that rare alleles are over-diluted and so do not appear in the pooled microsatellite profile. Pools of DNA from 12 individuals allowed the reliable detection of all alleles present in the pool. CONCLUSION The use of generic vector-specific fluorescent primers and unlabelled locus-specific primers provides a high resolution, rapid and inexpensive approach for the selection of highly polymorphic microsatellite loci that possess non-overlapping allele ranges for use in large-scale multiplex assays.
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Affiliation(s)
- Nicholas C Cryer
- School of Biological Sciences, University of Reading, Reading, Berkshire, RG6 6AS, UK
| | - David R Butler
- Cocoa Research Unit, The University of West Indies, St. Augustine, Trinidad and Tobago
| | - Mike J Wilkinson
- School of Biological Sciences, University of Reading, Reading, Berkshire, RG6 6AS, UK
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Clément D, Lanaud C, Sabau X, Fouet O, Le Cunff L, Ruiz E, Risterucci AM, Glaszmann JC, Piffanelli P. Creation of BAC genomic resources for cocoa ( Theobroma cacao L.) for physical mapping of RGA containing BAC clones. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2004; 108:1627-1634. [PMID: 15235775 DOI: 10.1007/s00122-004-1593-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2003] [Accepted: 01/05/2004] [Indexed: 05/24/2023]
Abstract
We have constructed and validated the first cocoa ( Theobroma cacao L.) BAC library, with the aim of developing molecular resources to study the structure and evolution of the genome of this perennial crop. This library contains 36,864 clones with an average insert size of 120 kb, representing approximately ten haploid genome equivalents. It was constructed from the genotype Scavina-6 (Sca-6), a Forastero clone highly resistant to cocoa pathogens and a parent of existing mapping populations. Validation of the BAC library was carried out with a set of 13 genetically-anchored single copy and one duplicated markers. An average of nine BAC clones per probe was identified, giving an initial experimental estimation of the genome coverage represented in the library. Screening of the library with a set of resistance gene analogues (RGAs), previously mapped in cocoa and co-localizing with QTL for resistance to Phytophthora traits, confirmed at the physical level the tight clustering of RGAs in the cocoa genome and provided the first insights into the relationships between genetic and physical distances in the cocoa genome. This library represents an available BAC resource for structural genomic studies or map-based cloning of genes corresponding to important QTLs for agronomic traits such as resistance genes to major cocoa pathogens like Phytophthora spp ( palmivora and megakarya), Crinipellis perniciosa and Moniliophthora roreri.
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Affiliation(s)
- D Clément
- TA 43/02, Centre de coopération internationale en recherche pour le développement (CIRAD), Avenue d'Agropolis, 34398 Montpellier, Cedex 5, France.
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