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Babu BK, Mathur RK, Anitha P, Ravichandran G, Bhagya HP. Phenomics, genomics of oil palm ( Elaeis guineensis Jacq.): way forward for making sustainable and high yielding quality oil palm. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:587-604. [PMID: 33854286 PMCID: PMC7981377 DOI: 10.1007/s12298-021-00964-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 05/17/2023]
Abstract
Oil palm (Elaeis guineensis Jacq.) is a heterogeneous, perennial crop having long breeding cycle with a genome size of 1.8 Gb. The demand for vegetable oil is steadily increasing, and expected that nearly 240-250 million tons of vegetable oil may be required by 2050. Genomics and next generation technologies plays crucial role in achieving the sustainable availability of oil palm with good yield and high quality. A successful breeding programme in oil palm depends on the availability of diverse gene pool, ex-situ conservation and their proper utilization for generating elite planting material. The major breeding methods adopted in oil palm are either modified recurrent selection or the modified reciprocal recurrent selection method. The QTLs of yield and related traits are chiefly located on chromosome 4, 10, 12 and 15 which is discussed in the current review. The probable chromosomal regions influencing the less height increment is observed to be on chromosomes 4, 10, 14 and 15. Advanced genomic approaches together with bioinformatics tools were discussed thoroughly for achieving sustainable oil palm where more efforts are needed. Major emphasis is given on oil palm crop improvement using holistic approaches of various genomic tools. Also a road map given on the milestones in the genomics and way forward for making oil palm to high yielding quality oil palm.
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Affiliation(s)
- B. Kalyana Babu
- ICAR-Indian Institute of Oil Palm Research, 534 450, Pedavegi, West Godavari (Dt), Andhra Pradesh India
| | - R. K. Mathur
- ICAR-Indian Institute of Oil Palm Research, 534 450, Pedavegi, West Godavari (Dt), Andhra Pradesh India
| | - P. Anitha
- ICAR-Indian Institute of Oil Palm Research, 534 450, Pedavegi, West Godavari (Dt), Andhra Pradesh India
| | - G. Ravichandran
- ICAR-Indian Institute of Oil Palm Research, 534 450, Pedavegi, West Godavari (Dt), Andhra Pradesh India
| | - H. P. Bhagya
- ICAR-Indian Institute of Oil Palm Research, 534 450, Pedavegi, West Godavari (Dt), Andhra Pradesh India
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Yue GH, Ye BQ, Lee M. Molecular approaches for improving oil palm for oil. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:22. [PMID: 37309424 PMCID: PMC10236033 DOI: 10.1007/s11032-021-01218-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 02/22/2021] [Indexed: 06/14/2023]
Abstract
The oil palm, originating from Africa, is the most productive oil crop species. Palm oil is an important source of edible oil. Its current global plantation area is over 23 million ha. The theoretical oil yield potential of the oil palm is 18.2 tons/ha/year. However, current average oil yield is only 3.8 tons/ha/year. In the past 100 years, conventional breeding and improvement of field management played important roles in increasing oil yield. However, conventional breeding for trait improvement was limited by its very long (10-20 years) phenotypic selection cycle, although it improved oil yield by ~10-20% per generation. Molecular breeding using novel molecular technologies will accelerate genetic improvement and may reduce the need to deforest and to use arable land for expanding oil palm plantations, which in turn makes palm oil more sustainable. Here, we comprehensively synthesize information from relevant literature of the technologies, achievements, and challenges of molecular approaches, including tissue culture, haploid breeding, mutation breeding, marker-assisted selection (MAS), genomic selection (GS), and genome editing (GE). We propose the characteristics of ideal palms and suggest a road map to breed ideal palms for sustainable palm oil.
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Affiliation(s)
- Gen Hua Yue
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604 Singapore
- School of Biological Sciences, Nanyang Technological University, 6 Nanyang Drive, Singapore, 637551 Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, 117543 Singapore
| | - Bao Qing Ye
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604 Singapore
| | - May Lee
- Molecular Population Genetics and Breeding Group, Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore, 117604 Singapore
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Senthilvel S, Ghosh A, Shaik M, Shaw RK, Bagali PG. Development and validation of an SNP genotyping array and construction of a high-density linkage map in castor. Sci Rep 2019; 9:3003. [PMID: 30816245 PMCID: PMC6395776 DOI: 10.1038/s41598-019-39967-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/06/2019] [Indexed: 02/01/2023] Open
Abstract
Castor is a commercially important oilseed crop that provides raw materials for several industries. Currently, the availability of genomic resources for castor is very limited. In this study, genome-wide SNPs were discovered in castor via whole-genome sequencing of 14 diverse lines to an average of 34X coverage. A total of 2,179,759 putative SNPs were detected, and a genotyping array was designed with 6,000 high-quality SNPs representing 2,492 scaffolds of the draft castor genome (87.5% genome coverage). The array was validated by genotyping a panel of 314 inbred castor lines, which resulted in 5,025 scorable SNPs with a high call rate (98%) and reproducibility (100%). Using this array, a consensus linkage map consisting of 1,978 SNP loci was constructed with an average inter-marker distance of 0.55 cM. The genome-wide SNP data, the genotyping array and the dense linkage map are valuable genomic tools for promoting high-throughput genomic research and molecular breeding in castor.
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Affiliation(s)
- S Senthilvel
- ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad, 500030, India.
| | - Arpita Ghosh
- Xcelris Labs Ltd., Xcellon building, Navrangpura, Ahmedabad, 380009, India
| | - Mobeen Shaik
- ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad, 500030, India
| | - Ranjan K Shaw
- ICAR-Indian Institute of Oilseeds Research, Rajendranagar, Hyderabad, 500030, India
| | - Prashanth G Bagali
- Xcelris Labs Ltd., Xcellon building, Navrangpura, Ahmedabad, 380009, India
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Ramakrishna G, Kaur P, Nigam D, Chaduvula PK, Yadav S, Talukdar A, Singh NK, Gaikwad K. Genome-wide identification and characterization of InDels and SNPs in Glycine max and Glycine soja for contrasting seed permeability traits. BMC PLANT BIOLOGY 2018; 18:141. [PMID: 29986650 PMCID: PMC6038289 DOI: 10.1186/s12870-018-1341-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2017] [Accepted: 06/05/2018] [Indexed: 05/03/2023]
Abstract
BACKGROUND Water permeability governed by seed coat is a major facet of seed crops, especially soybean, whose seeds lack physiological dormancy and experience rapid deterioration in seed viability under prolonged storage. Moreover, the physiological and chemical characteristics of soybean seeds are known to vary with seed coat color. Thus, to underpin the genes controlling water permeability in soybean seeds, we carried out an in-depth characterization of the associated genomic variation. RESULTS In the present study, we have analyzed genomic variation between cultivated soybean and its wild progenitor with implications on seed permeability, a trait related to seed storability. Whole genome resequencing of G.max and G. soja, identified SNPs and InDels which were further characterized on the basis of their genomic location and impact on gene expression. Chromosomal density distribution of the variation was assessed across the genome and genes carrying SNPs and InDels were characterized into different metabolic pathways. Seed hardiness is a complex trait that is affected by the allelic constitution of a genetic locus as well as by a tricky web of plant hormone interactions. Seven genes that hold a probable role in the determination of seed permeability were selected and their expression differences at different stages of water imbibition were analyzed. Variant interaction network derived 205 downstream interacting partners of 7 genes confirmed their role in seed related traits. Interestingly, genes encoding for Type I- Inositol polyphosphate 5 phosphatase1 and E3 Ubiquitin ligase could differentiate parental genotypes, revealed protein conformational deformations and were found to segregate among RILs in coherence with their permeability scores. The 2 identified genes, thus showed a preliminary association with the desirable permeability characteristics. CONCLUSION In the light of above outcomes, 2 genes were identified that revealed preliminary, but a relevant association with soybean seed permeability trait and hence could serve as a primary material for understanding the molecular pathways controlling seed permeability traits in soybean.
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Affiliation(s)
- G. Ramakrishna
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Parampreet Kaur
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Deepti Nigam
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Pavan K. Chaduvula
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Sangita Yadav
- ICAR- IARI, Division of Seed Science and Technology, Pusa Campus, New Delhi, 110012 India
| | - Akshay Talukdar
- ICAR- IARI, Division of Genetics, Pusa Campus, New Delhi, India
| | - Nagendra Kumar Singh
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
| | - Kishor Gaikwad
- ICAR- National Research Centre on Plant Biotechnology, Pusa Campus, New Delhi, 110012 India
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Bhardwaj A, Dhar YV, Asif MH, Bag SK. In Silico identification of SNP diversity in cultivated and wild tomato species: insight from molecular simulations. Sci Rep 2016; 6:38715. [PMID: 27929054 PMCID: PMC5144076 DOI: 10.1038/srep38715] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Accepted: 11/15/2016] [Indexed: 12/12/2022] Open
Abstract
Single Nucleotide Polymorphisms (SNPs), an important source of genetic variations, are often used in crop improvement programme. The present study represented comprehensive In silico analysis of nucleotide polymorphisms in wild (Solanum habrochaites) and cultivated (Solanum lycopersicum) species of tomato to explore the consequence of substitutions both at sequence and structure level. A total of 8978 SNPs having Ts/Tv (Transition/Transversion) ratio 1.75 were identified from the Expressed Sequence Tag (EST) and Next Generation Sequence (NGS) data of both the species available in public databases. Out of these, 1838 SNPs were non-synonymous and distributed in 988 protein coding genes. Among these, 23 genes containing 96 SNPs were involved in traits markedly different between the two species. Furthermore, there were 28 deleterious SNPs distributed in 27 genes and a few of these genes were involved in plant pathogen interaction and plant hormone pathways. Molecular docking and simulations of several selected proteins showed the effect of SNPs in terms of compactness, conformation and interaction ability. Observed SNPs exhibited various types of motif binding effects due to nucleotide changes. SNPs that provide the evidence of differential motif binding and interaction behaviour could be effectively used for the crop improvement program.
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Affiliation(s)
- Archana Bhardwaj
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Yogeshwar Vikram Dhar
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Mehar Hasan Asif
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
| | - Sumit K Bag
- Academy of Scientific and Innovative Research (AcSIR), CSIR-NBRI Campus, Lucknow, India
- Council of Scientific and Industrial Research - National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India
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Pootakham W, Jomchai N, Ruang-Areerate P, Shearman JR, Sonthirod C, Sangsrakru D, Tragoonrung S, Tangphatsornruang S. Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS). Genomics 2015; 105:288-95. [PMID: 25702931 DOI: 10.1016/j.ygeno.2015.02.002] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 02/03/2015] [Accepted: 02/12/2015] [Indexed: 11/24/2022]
Abstract
Oil palm has become one of the most important oil crops in the world. Marker-assisted selections have played a pivotal role in oil palm breeding programs. Here, we report the use of genotyping-by-sequencing (GBS) approach for a large-scale SNP discovery and genotyping of a mapping population. Reduced representation libraries of 108 F2 progeny were sequenced and a total of 524 million reads were obtained. We detected 21,471 single nucleotide substitutions, most of which (62.6%) represented transition events. Of 3417 fully informative SNP markers, we were able to place 1085 on a linkage map, which spanned 1429.6 cM and had an average of one marker every 1.26 cM. Three QTL affecting trunk height were detected on LG 10, 14 and 15, whereas a single QTL associated with fruit bunch weight was identified on LG 3. The use of GBS approach proved to be rapid, cost-effective and highly reproducible in this species.
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Affiliation(s)
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Nukoon Jomchai
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Panthita Ruang-Areerate
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Jeremy R Shearman
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
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High density SNP and SSR-based genetic maps of two independent oil palm hybrids. BMC Genomics 2014; 15:309. [PMID: 24767304 PMCID: PMC4234488 DOI: 10.1186/1471-2164-15-309] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2013] [Accepted: 03/25/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Oil palm is an important perennial oil crop with an extremely long selection cycle of 10 to 12 years. As such, any tool that speeds up its genetic improvement process, such as marker-assisted breeding is invaluable. Previously, genetic linkage maps based on AFLP, RFLP and SSR markers were developed and QTLs for fatty acid composition and yield components identified. High density genetic maps of crosses of different genetic backgrounds are indispensable tools for investigating oil palm genetics. They are also useful for comparative mapping analyses to identify markers closely linked to traits of interest. RESULTS A 4.5 K customized oil palm SNP array was developed using the Illumina Infinium platform. The SNPs and 252 SSRs were genotyped on two mapping populations, an intraspecific cross with 87 palms and an interspecific cross with 108 palms. Parental maps with 16 linkage groups (LGs), were constructed for the three fruit forms of E. guineensis (dura, pisifera and tenera). Map resolution was further increased by integrating the dura and pisifera maps into an intraspecific integrated map with 1,331 markers spanning 1,867 cM. We also report the first map of a Colombian E. oleifera, comprising 10 LGs with 65 markers spanning 471 cM. Although not very dense due to the high level of homozygosity in E. oleifera, the LGs were successfully integrated with the LGs of the tenera map. Direct comparison between the parental maps identified 603 transferable markers polymorphic in at least two of the parents. Further analysis revealed a high degree of marker transferability covering 1,075 cM, between the intra- and interspecific integrated maps. The interspecific cross displayed higher segregation distortion than the intraspecific cross. However, inclusion of distorted markers in the genetic maps did not disrupt the marker order and no map expansion was observed. CONCLUSIONS The high density SNP and SSR-based genetic maps reported in this paper have greatly improved marker density and genome coverage in comparison with the first reference map based on AFLP and SSR markers. Therefore, it is foreseen that they will be more useful for fine mapping of QTLs and whole genome association mapping studies in oil palm.
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Low ETL, Rosli R, Jayanthi N, Mohd-Amin AH, Azizi N, Chan KL, Maqbool NJ, Maclean P, Brauning R, McCulloch A, Moraga R, Ong-Abdullah M, Singh R. Analyses of hypomethylated oil palm gene space. PLoS One 2014; 9:e86728. [PMID: 24497974 PMCID: PMC3907425 DOI: 10.1371/journal.pone.0086728] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2013] [Accepted: 12/15/2013] [Indexed: 12/21/2022] Open
Abstract
Demand for palm oil has been increasing by an average of ∼8% the past decade and currently accounts for about 59% of the world's vegetable oil market. This drives the need to increase palm oil production. Nevertheless, due to the increasing need for sustainable production, it is imperative to increase productivity rather than the area cultivated. Studies on the oil palm genome are essential to help identify genes or markers that are associated with important processes or traits, such as flowering, yield and disease resistance. To achieve this, 294,115 and 150,744 sequences from the hypomethylated or gene-rich regions of Elaeis guineensis and E. oleifera genome were sequenced and assembled into contigs. An additional 16,427 shot-gun sequences and 176 bacterial artificial chromosomes (BAC) were also generated to check the quality of libraries constructed. Comparison of these sequences revealed that although the methylation-filtered libraries were sequenced at low coverage, they still tagged at least 66% of the RefSeq supported genes in the BAC and had a filtration power of at least 2.0. A total 33,752 microsatellites and 40,820 high-quality single nucleotide polymorphism (SNP) markers were identified. These represent the most comprehensive collection of microsatellites and SNPs to date and would be an important resource for genetic mapping and association studies. The gene models predicted from the assembled contigs were mined for genes of interest, and 242, 65 and 14 oil palm transcription factors, resistance genes and miRNAs were identified respectively. Examples of the transcriptional factors tagged include those associated with floral development and tissue culture, such as homeodomain proteins, MADS, Squamosa and Apetala2. The E. guineensis and E. oleifera hypomethylated sequences provide an important resource to understand the molecular mechanisms associated with important agronomic traits in oil palm.
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Affiliation(s)
- Eng-Ti L. Low
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Rozana Rosli
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Nagappan Jayanthi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Ab Halim Mohd-Amin
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Norazah Azizi
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Kuang-Lim Chan
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | | | - Paul Maclean
- AgResearch Ruakura Research Centre, Hamilton, New Zealand
| | - Rudi Brauning
- AgResearch Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Alan McCulloch
- AgResearch Invermay Agricultural Centre, Mosgiel, New Zealand
| | - Roger Moraga
- AgResearch Grasslands Research Centre, Palmerston North, New Zealand
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
| | - Rajinder Singh
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board, Kajang, Selangor, Malaysia
- * E-mail:
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Garcia-Lor A, Curk F, Snoussi-Trifa H, Morillon R, Ancillo G, Luro F, Navarro L, Ollitrault P. A nuclear phylogenetic analysis: SNPs, indels and SSRs deliver new insights into the relationships in the 'true citrus fruit trees' group (Citrinae, Rutaceae) and the origin of cultivated species. ANNALS OF BOTANY 2013; 111:1-19. [PMID: 23104641 PMCID: PMC3523644 DOI: 10.1093/aob/mcs227] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Accepted: 09/12/2012] [Indexed: 05/20/2023]
Abstract
BACKGROUND AND AIMS Despite differences in morphology, the genera representing 'true citrus fruit trees' are sexually compatible, and their phylogenetic relationships remain unclear. Most of the important commercial 'species' of Citrus are believed to be of interspecific origin. By studying polymorphisms of 27 nuclear genes, the average molecular differentiation between species was estimated and some phylogenetic relationships between 'true citrus fruit trees' were clarified. METHODS Sanger sequencing of PCR-amplified fragments from 18 genes involved in metabolite biosynthesis pathways and nine putative genes for salt tolerance was performed for 45 genotypes of Citrus and relatives of Citrus to mine single nucleotide polymorphisms (SNPs) and indel polymorphisms. Fifty nuclear simple sequence repeats (SSRs) were also analysed. KEY RESULTS A total of 16 238 kb of DNA was sequenced for each genotype, and 1097 single nucleotide polymorphisms (SNPs) and 50 indels were identified. These polymorphisms were more valuable than SSRs for inter-taxon differentiation. Nuclear phylogenetic analysis revealed that Citrus reticulata and Fortunella form a cluster that is differentiated from the clade that includes three other basic taxa of cultivated citrus (C. maxima, C. medica and C. micrantha). These results confirm the taxonomic subdivision between the subgenera Metacitrus and Archicitrus. A few genes displayed positive selection patterns within or between species, but most of them displayed neutral patterns. The phylogenetic inheritance patterns of the analysed genes were inferred for commercial Citrus spp. CONCLUSIONS Numerous molecular polymorphisms (SNPs and indels), which are potentially useful for the analysis of interspecific genetic structures, have been identified. The nuclear phylogenetic network for Citrus and its sexually compatible relatives was consistent with the geographical origins of these genera. The positive selection observed for a few genes will help further works to analyse the molecular basis of the variability of the associated traits. This study presents new insights into the origin of C. sinensis.
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Affiliation(s)
- Andres Garcia-Lor
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain
| | - Franck Curk
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain
- INRA, UR1103 Génétique et Ecophysiologie de la Qualité des Agrumes, F-20230 San Giuliano, France
| | - Hager Snoussi-Trifa
- Horticultural Laboratory, Tunisian National Agronomic Research Institute (INRAT), Rue Hedi Karray, 2049 Ariana, Tunisia
| | - Raphael Morillon
- UMR AGAP, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), TA A-108/02, 34398 Montpellier, Cedex 5, France
| | - Gema Ancillo
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain
| | - François Luro
- INRA, UR1103 Génétique et Ecophysiologie de la Qualité des Agrumes, F-20230 San Giuliano, France
| | - Luis Navarro
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain
- For correspondence. E-mail or
| | - Patrick Ollitrault
- Centro de Protección Vegetal y Biotecnología, Instituto Valenciano de Investigaciones Agrarias (IVIA), 46113 Moncada (Valencia), Spain
- UMR AGAP, Centre de coopération Internationale en Recherche Agronomique pour le Développement (CIRAD), TA A-108/02, 34398 Montpellier, Cedex 5, France
- For correspondence. E-mail or
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Computational identification and analysis of single-nucleotide polymorphisms and insertions/deletions in expressed sequence tag data of Eucalyptus. J Genet 2011. [DOI: 10.1007/s12041-011-0052-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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