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Sforça DA, Vautrin S, Cardoso-Silva CB, Mancini MC, Romero-da Cruz MV, Pereira GDS, Conte M, Bellec A, Dahmer N, Fourment J, Rodde N, Van Sluys MA, Vicentini R, Garcia AAF, Forni-Martins ER, Carneiro MS, Hoffmann HP, Pinto LR, Landell MGDA, Vincentz M, Berges H, de Souza AP. Gene Duplication in the Sugarcane Genome: A Case Study of Allele Interactions and Evolutionary Patterns in Two Genic Regions. FRONTIERS IN PLANT SCIENCE 2019; 10:553. [PMID: 31134109 PMCID: PMC6514446 DOI: 10.3389/fpls.2019.00553] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 04/11/2019] [Indexed: 05/25/2023]
Abstract
Sugarcane (Saccharum spp.) is highly polyploid and aneuploid. Modern cultivars are derived from hybridization between S. officinarum and S. spontaneum. This combination results in a genome exhibiting variable ploidy among different loci, a huge genome size (~10 Gb) and a high content of repetitive regions. An approach using genomic, transcriptomic, and genetic mapping can improve our knowledge of the behavior of genetics in sugarcane. The hypothetical HP600 and Centromere Protein C (CENP-C) genes from sugarcane were used to elucidate the allelic expression and genomic and genetic behaviors of this complex polyploid. The physically linked side-by-side genes HP600 and CENP-C were found in two different homeologous chromosome groups with ploidies of eight and ten. The first region (Region01) was a Sorghum bicolor ortholog region with all haplotypes of HP600 and CENP-C expressed, but HP600 exhibited an unbalanced haplotype expression. The second region (Region02) was a scrambled sugarcane sequence formed from different noncollinear genes containing partial duplications of HP600 and CENP-C (paralogs). This duplication resulted in a non-expressed HP600 pseudogene and a recombined fusion version of CENP-C and the orthologous gene Sobic.003G299500 with at least two chimeric gene haplotypes expressed. It was also determined that it occurred before Saccharum genus formation and after the separation of sorghum and sugarcane. A linkage map was constructed using markers from nonduplicated Region01 and for the duplication (Region01 and Region02). We compare the physical and linkage maps, demonstrating the possibility of mapping markers located in duplicated regions with markers in nonduplicated region. Our results contribute directly to the improvement of linkage mapping in complex polyploids and improve the integration of physical and genetic data for sugarcane breeding programs. Thus, we describe the complexity involved in sugarcane genetics and genomics and allelic dynamics, which can be useful for understanding complex polyploid genomes.
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Affiliation(s)
| | - Sonia Vautrin
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | | | | | | | | | - Mônica Conte
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Arnaud Bellec
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | - Nair Dahmer
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Joelle Fourment
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | - Nathalie Rodde
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
| | | | | | | | | | | | - Hermann Paulo Hoffmann
- Centro de Ciências Agrárias, Universidade Federal de São Carlos (UFSCAR), Araras, Brazil
| | | | | | - Michel Vincentz
- Universidade Estadual de Campinas (UNICAMP), Campinas, Brazil
| | - Helene Berges
- Centre National de Ressources Genomiques Vegetales (CNRGV), Institut National de la Recherche Agronomique (INRA), Castanet Tolosan, France
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Zhang J, Zhang Q, Li L, Tang H, Zhang Q, Chen Y, Arrow J, Zhang X, Wang A, Miao C, Ming R. Recent polyploidization events in three Saccharum founding species. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:264-274. [PMID: 29878497 PMCID: PMC6330536 DOI: 10.1111/pbi.12962] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 05/21/2018] [Accepted: 06/04/2018] [Indexed: 05/07/2023]
Abstract
The complexity of polyploid Saccharum genomes hindered progress of genome research and crop improvement in sugarcane. To understand their genome structure, transcriptomes of 59 F1 individuals derived from S. officinarumLA Purple and S. robustum Molokai 5829 (2n = 80, x = 10 for both) were sequenced, yielding 11 157 and 8998 SNPs and 83 and 105 linkage groups, respectively. Most markers in each linkage group aligned to single sorghum chromosome. However, 71 interchromosomal rearrangements were detected between sorghum and S. officinarum or S. robustum, and 24 (33.8%) of them were shared between S. officinarum and S. robustum, indicating their occurrence before the speciation event that separated these two species. More than 2000 gene pairs from S. spontaneum, S. officinarum and S. robustum were analysed to estimate their divergence time. Saccharum officinarum and S. robustum diverged about 385 thousand years ago, and the whole-genome duplication events occurred after the speciation event because of shared interchromosomal rearrangements. The ancestor of these two species diverged from S. spontaneum about 769 thousand years ago, and the reduction in basic chromosome number from 10 to 8 in S. spontaneum occurred after the speciation event but before the two rounds of whole-genome duplication. Our results proved that S. officinarum is a legitimate species in its own right and not a selection from S. robustum during the domestication process in the past 10 000 years. Our findings rejected a long-standing hypothesis and clarified the timing of speciation and whole-genome duplication events in Saccharum.
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Affiliation(s)
- Jisen Zhang
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
- College of Life SciencesFujian Normal UniversityFuzhouChina
| | - Qing Zhang
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
- College of Life SciencesFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Leiting Li
- College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Haibao Tang
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Qiong Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical GardenChinese Academy of SciencesWuhanChina
| | - Yang Chen
- College of Life SciencesFujian Normal UniversityFuzhouChina
| | - Jie Arrow
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
| | - Xingtan Zhang
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Aiqin Wang
- State Key Lab for Conservation and Utilization of Subtropical Agro‐biological ResourcesGuangxi UniversityNanningChina
| | - Chenyong Miao
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
| | - Ray Ming
- FAFU and UIUC Joint Center for Genomics and BiotechnologyKey Laboratory of Sugarcane Biology and Genetic Breeding Ministry of AgricultureFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, and Key Laboratory of GeneticsBreeding and Multiple Utilization of CorpsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhouFujianChina
- Department of Plant BiologyUniversity of Illinois at Urbana‐ChampaignUrbanaILUSA
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Parida SK, Kalia S, Pandit A, Nayak P, Singh RK, Gaikwad K, Srivastava PS, Singh NK, Mohapatra T. Single nucleotide polymorphism in sugar pathway and disease resistance genes in sugarcane. PLANT CELL REPORTS 2016; 35:1629-1653. [PMID: 27289592 DOI: 10.1007/s00299-016-1978-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 03/21/2016] [Indexed: 06/06/2023]
Abstract
Single nucleotide polymorphism in sugar pathway and disease resistance genes showing genetic association with sugar content and red rot resistance would be useful in marker-assisted genetic improvement of sugarcane. Validation and genotyping of potential sequence variants in candidate genes are necessary to understand their functional significance and trait association potential. We discovered, characterized, validated and genotyped SNPs and InDels in sugar pathway and disease resistance genes of Saccharum complex and sugarcane varieties using amplicon sequencing and CAPS assays. The SNPs were abundant in the non-coding 3'UTRs than 5'UTRs and coding sequences depicting a strong bias toward C to T transition substitutions than transversions. Sequencing of cloned amplicons validated 61.6 and 45.2 % SNPs detected in silico in 21 sugar pathway and 16 disease resistance genes, respectively. Sixteen SNPs in four sugar pathway genes and 10 SNPs in nine disease resistance genes were validated through cost-effective CAPS assay. Functional and adaptive significance of SNP and protein haplotypes identified in sugar pathway and disease resistance genes was assessed by correlating their allelic variation with missense amino acid substitutions in the functional domains, alteration in protein structure models and possible modulation of catalytic enzyme activity in contrasting high and low sugar and moderately red rot resistant and highly susceptible sugarcane genotypes. A strong genetic association of five SNPs in the sugar pathway and disease resistance genes, and an InDel marker in the promoter sequence of sucrose synthase-2 gene, with sugar content and red rot resistance, was evident. The functionally relevant SNPs and InDels, detected and validated in sugar pathway and disease resistance genes, and genic CAPS markers designed, would be of immense use in marker-assisted genetic improvement of sugarcane for sugar content and disease resistance.
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Affiliation(s)
- Swarup K Parida
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sanjay Kalia
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
- Department of Biotechnology, CGO Complex, Lodhi Road, New Delhi, 110003, India
| | - Awadhesh Pandit
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
- National Centre for Biological Sciences, Bengaluru, 560065, Karnataka , India
| | - Preetam Nayak
- Utkal University, Vanivihar, Bhubaneswar, Odisha, 751004, India
| | - Ram Kushal Singh
- U.P. Council of Sugarcane Research, Shahjahanpur, Uttar Pradesh, 242001, India
| | - Kishor Gaikwad
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
| | | | - Nagendra K Singh
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India
| | - Trilochan Mohapatra
- National Research Centre on Plant Biotechnology, New Delhi, 110012, India.
- Indian Council of Agricultural Research, Krishi Bhavan, New Delhi, 110001, India.
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Genetic analysis of diversity within a Chinese local sugarcane germplasm based on start codon targeted polymorphism. BIOMED RESEARCH INTERNATIONAL 2014; 2014:468375. [PMID: 24779012 PMCID: PMC3980922 DOI: 10.1155/2014/468375] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 12/14/2013] [Accepted: 01/03/2014] [Indexed: 11/17/2022]
Abstract
In-depth information on sugarcane germplasm is the basis for its conservation and utilization. Data on sugarcane molecular markers are limited for the Chinese sugarcane germplasm collections. In the present study, 20 start codon targeted (SCoT) marker primers were designed to assess the genetic diversity among 107 sugarcane accessions within a local sugarcane germplasm collection. These primers amplified 176 DNA fragments, of which 163 were polymorphic (92.85%). Polymorphic information content (PIC) values ranged from 0.783 to 0.907 with a mean of 0.861. Unweighted pair group method of arithmetic averages (UPGMA) cluster analysis of the SCoT marker data divided the 107 sugarcane accessions into six clusters at 0.674 genetic similarity coefficient level. Relatively abundant genetic diversity was observed among ROC22, ROC16, and ROC10, which occupied about 80% of the total sugarcane acreage in China, indicating their potential breeding value on Mainland China. Principal component analysis (PCA) partitioned the 107 sugarcane accessions into two major groups, the Domestic Group and the Foreign Introduction Group. Each group was further divided based on institutions, where the sugarcane accessions were originally developed. The knowledge of genetic diversity among the local sugarcane germplasm provided foundation data for managing sugarcane germplasm, including construction of a core collection and regional variety distribution and subrogation.
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Garvin MR, Saitoh K, Gharrett AJ. Application of single nucleotide polymorphisms to non-model species: a technical review. Mol Ecol Resour 2013; 10:915-34. [PMID: 21565101 DOI: 10.1111/j.1755-0998.2010.02891.x] [Citation(s) in RCA: 159] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Single nucleotide polymorphisms (SNPs) have gained wide use in humans and model species and are becoming the marker of choice for applications in other species. Technology that was developed for work in model species may provide useful tools for SNP discovery and genotyping in non-model organisms. However, SNP discovery can be expensive, labour intensive, and introduce ascertainment bias. In addition, the most efficient approaches to SNP discovery will depend on the research questions that the markers are to resolve as well as the focal species. We discuss advantages and disadvantages of several past and recent technologies for SNP discovery and genotyping and summarize a variety of SNP discovery and genotyping studies in ecology and evolution.
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Affiliation(s)
- M R Garvin
- Fisheries Division, School of Fisheries and Ocean Sciences, University of Alaska Fairbanks, 17101 Point Lena Loop Road, Juneau, AK 99801, USA National Research Institute of Fisheries Science, Fukuura, Kanazawa, Yokohama 236-8648 Japan
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Zhang J, Arro J, Chen Y, Ming R. Haplotype analysis of sucrose synthase gene family in three Saccharum species. BMC Genomics 2013; 14:314. [PMID: 23663250 PMCID: PMC3668173 DOI: 10.1186/1471-2164-14-314] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Accepted: 04/29/2013] [Indexed: 11/10/2022] Open
Abstract
Background Sugarcane is an economically important crop contributing about 80% and 40% to the world sugar and ethanol production, respectively. The complicated genetics consequential to its complex polyploid genome, however, have impeded efforts to improve sugar yield and related important agronomic traits. Modern sugarcane cultivars are complex hybrids derived mainly from crosses among its progenitor species, S. officinarum and S. spontanuem, and to a lesser degree, S. robustom. Atypical of higher plants, sugarcane stores its photoassimilates as sucrose rather than as starch in its parenchymous stalk cells. In the sugar biosynthesis pathway, sucrose synthase (SuSy, UDP-glucose: D-fructose 2-a-D-glucosyltransferase, EC 2.4.1.13) is a key enzyme in the regulation of sucrose accumulation and partitioning by catalyzing the reversible conversion of sucrose and UDP into UDP-glucose and fructose. However, little is known about the sugarcane SuSy gene family members and hence no definitive studies have been reported regarding allelic diversity of SuSy gene families in Saccharum species. Results We identified and characterized a total of five sucrose synthase genes in the three sugarcane progenitor species through gene annotation and PCR haplotype analysis by analyzing 70 to 119 PCR fragments amplified from intron-containing target regions. We detected all but one (i.e. ScSuSy5) of ScSuSy transcripts in five tissue types of three Saccharum species. The average SNP frequency was one SNP per 108 bp, 81 bp, and 72 bp in S. officinarum, S. robustom, and S. spontanuem respectively. The average shared SNP is 15 between S. officinarum and S. robustom, 7 between S. officinarum and S. spontanuem , and 11 between S. robustom and S. spontanuem. We identified 27, 35, and 32 haplotypes from the five ScSuSy genes in S. officinarum, S. robustom, and S. spontanuem respectively. Also, 12, 11, and 9 protein sequences were translated from the haplotypes in S. officinarum, S. robustom, S. spontanuem, respectively. Phylogenetic analysis showed three separate clusters composed of SbSuSy1 and SbSuSy2, SbSuSy3 and SbSuSy5, and SbSuSy4. Conclusions The five members of the SuSy gene family evolved before the divergence of the genera in the tribe Andropogoneae at least 12 MYA. Each ScSuSy gene showed at least one non-synonymous substitution in SNP haplotypes. The SNP frequency is the lowest in S. officinarum, intermediate in S. robustum, and the highest in S. spontaneum, which may reflect the timing of the two rounds of whole genome duplication in these octoploids. The higher rate of shared SNP frequency between S. officinarum and S. robustum than between S. officinarum and in S. spontaneum confirmed that the speciation event separating S. officinarum and S. robustum occurred after their common ancestor diverged from S. spontaneum. The SNP and haplotype frequencies in three Saccharum species provide fundamental information for designing strategies to sequence these autopolyploid genomes.
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Affiliation(s)
- Jisen Zhang
- College of Life Sciences, Fujian Normal University, Fuzhou 350108, China
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Allen AM, Barker GLA, Wilkinson P, Burridge A, Winfield M, Coghill J, Uauy C, Griffiths S, Jack P, Berry S, Werner P, Melichar JPE, McDougall J, Gwilliam R, Robinson P, Edwards KJ. Discovery and development of exome-based, co-dominant single nucleotide polymorphism markers in hexaploid wheat (Triticum aestivum L.). PLANT BIOTECHNOLOGY JOURNAL 2013; 11:279-95. [PMID: 23279710 DOI: 10.1111/pbi.12009] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2012] [Revised: 08/06/2012] [Accepted: 08/10/2012] [Indexed: 05/19/2023]
Abstract
Globally, wheat is the most widely grown crop and one of the three most important crops for human and livestock feed. However, the complex nature of the wheat genome has, until recently, resulted in a lack of single nucleotide polymorphism (SNP)-based molecular markers of practical use to wheat breeders. Recently, large numbers of SNP-based wheat markers have been made available via the use of next-generation sequencing combined with a variety of genotyping platforms. However, many of these markers and platforms have difficulty distinguishing between heterozygote and homozygote individuals and are therefore of limited use to wheat breeders carrying out commercial-scale breeding programmes. To identify exome-based co-dominant SNP-based assays, which are capable of distinguishing between heterozygotes and homozygotes, we have used targeted re-sequencing of the wheat exome to generate large amounts of genomic sequences from eight varieties. Using a bioinformatics approach, these sequences have been used to identify 95 266 putative single nucleotide polymorphisms, of which 10 251 were classified as being putatively co-dominant. Validation of a subset of these putative co-dominant markers confirmed that 96% were true polymorphisms and 65% were co-dominant SNP assays. The new co-dominant markers described here are capable of genotypic classification of a segregating locus in polyploid wheat and can be used on a variety of genotyping platforms; as such, they represent a powerful tool for wheat breeders. These markers and related information have been made publically available on an interactive web-based database to facilitate their use on genotyping programmes worldwide.
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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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Singh RK, Singh RB, Singh SP, Sharma ML. Genes tagging and molecular diversity of red rot susceptible/tolerant sugarcane hybrids using c-DNA and unigene derived markers. World J Microbiol Biotechnol 2011; 28:1669-79. [DOI: 10.1007/s11274-011-0974-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 12/02/2011] [Indexed: 10/14/2022]
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Engineering Advantages, Challenges and Status of Sugarcane and other Sugar-Based Biomass Resources. ACTA ACUST UNITED AC 2010. [DOI: 10.1007/978-3-642-13440-1_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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12
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Westermeier P, Wenzel G, Mohler V. Development and evaluation of single-nucleotide polymorphism markers in allotetraploid rapeseed (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:1301-11. [PMID: 19756476 DOI: 10.1007/s00122-009-1135-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 08/12/2009] [Indexed: 05/08/2023]
Abstract
Single-nucleotide polymorphisms (SNPs) and insertion-deletions (INDELs) are currently the important classes of genetic markers for major crop species. In this study, methods for developing SNP markers in rapeseed (Brassica napus L.) and their in silico mapping and use for genotyping are demonstrated. For the development of SNP and INDEL markers, 181 fragments from 121 different gene sequences spanning 86 kb were examined. A combination of different selection methods (genome-specific amplification, hetero-duplex analysis and sequence analysis) allowed the detection of 18 singular fragments that showed a total of 87 SNPs and 6 INDELs between 6 different rapeseed varieties. The average frequency of sequence polymorphism was estimated to be one SNP every 247 bp and one INDEL every 3,583 bp. Most SNPs and INDELs were found in non-coding regions. Polymorphism information content values for SNP markers ranged between 0.02 and 0.50 in a set of 86 varieties. Using comparative genetics data for B. napus and Arabidopsis thaliana, an allocation of SNP markers to linkage groups in rapeseed was achieved: a unique location was determined for seven gene sequences; two and three possible locations were found for six and four sequences, respectively. The results demonstrate the usefulness of existing genomic resources for SNP discovery in rapeseed.
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Affiliation(s)
- Peter Westermeier
- Plant Breeding, Department of Plant Sciences, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Am Hochanger 4, 85350 Freising, Germany.
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Bundock PC, Eliott FG, Ablett G, Benson AD, Casu RE, Aitken KS, Henry RJ. Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. PLANT BIOTECHNOLOGY JOURNAL 2009; 7:347-54. [PMID: 19386042 DOI: 10.1111/j.1467-7652.2009.00401.x] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Discovering single nucleotide polymorphisms (SNPs) in specific genes in a heterozygous polyploid plant species, such as sugarcane, is challenging because of the presence of a large number of homologues. To discover SNPs for mapping genes of interest, 454 sequencing of 307 polymerase chain reaction (PCR) amplicons (> 59 kb of sequence) was undertaken. One region of a four-gasket sequencing run, on a 454 Genome Sequencer FLX, was used for pooled PCR products amplified from each parent of a quantitative trait locus (QTL) mapping population (IJ76-514 x Q165). The sequencing yielded 96,755 (IJ76-514) and 86,241 (Q165) sequences with perfect matches to a PCR primer used in amplification, with an average sequence depth of approximately 300 and an average read length of 220 bases. Further analysis was carried out on amplicons whose sequences clustered into a single contig using an identity of 80% with the program cap3. In the more polymorphic sugarcane parent (Q165), 94% of amplicons (227/242) had evidence of a reliable SNP--an average of one every 35 bases. Significantly fewer SNPs were found in the pure Saccharum officinarum parent--with one SNP every 58 bases and SNPs in 86% (213/247) of amplicons. Using automatic SNP detection, 1632 SNPs were detected in Q165 sequences and 1013 in IJ76-514. From 225 candidate SNP sites tested, 209 (93%) were validated as polymorphic using the Sequenom MassARRAY system. Amplicon re-sequencing using the 454 system enables cost-effective SNP discovery that can be targeted to genes of interest and is able to perform in the highly challenging area of polyploid genomes.
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Affiliation(s)
- Peter C Bundock
- Co-operative Research Centre for Sugar Industry Innovation through Biotechnology, Southern Cross University, Lismore, NSW 2480, Australia.
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Ganal MW, Altmann T, Röder MS. SNP identification in crop plants. CURRENT OPINION IN PLANT BIOLOGY 2009; 12:211-7. [PMID: 19186095 DOI: 10.1016/j.pbi.2008.12.009] [Citation(s) in RCA: 148] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2008] [Revised: 12/18/2008] [Accepted: 12/20/2008] [Indexed: 05/18/2023]
Abstract
In many plants, single nucleotide polymorphism (SNP) markers are increasingly becoming the marker system of choice. However, for many crop plants there are surprisingly low numbers of validated SNP markers available although they are needed in large numbers for studies regarding genetic variation, linkage mapping, population structure analysis, association genetics, map-based gene isolation, and plant breeding. This review summarizes the current status of SNP marker development technologies for major crop plants. It will also provide an outlook into the future regarding possible SNP identification approaches in crop plants on the basis of current development in model systems such as Arabidopsis which will become available with the full sequencing of more plant genomes, genome resequencing, and in conjunction with the next-generation sequencing technologies.
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Affiliation(s)
- Martin W Ganal
- TraitGenetics GmbH, Am Schwabeplan 1b, D-06466 Gatersleben, Germany.
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Fusari CM, Lia VV, Hopp HE, Heinz RA, Paniego NB. Identification of single nucleotide polymorphisms and analysis of linkage disequilibrium in sunflower elite inbred lines using the candidate gene approach. BMC PLANT BIOLOGY 2008; 8:7. [PMID: 18215288 PMCID: PMC2266750 DOI: 10.1186/1471-2229-8-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 01/23/2008] [Indexed: 05/04/2023]
Abstract
BACKGROUND Association analysis is a powerful tool to identify gene loci that may contribute to phenotypic variation. This includes the estimation of nucleotide diversity, the assessment of linkage disequilibrium structure (LD) and the evaluation of selection processes. Trait mapping by allele association requires a high-density map, which could be obtained by the addition of Single Nucleotide Polymorphisms (SNPs) and short insertion and/or deletions (indels) to SSR and AFLP genetic maps. Nucleotide diversity analysis of randomly selected candidate regions is a promising approach for the success of association analysis and fine mapping in the sunflower genome. Moreover, knowledge of the distance over which LD persists, in agronomically meaningful sunflower accessions, is important to establish the density of markers and the experimental design for association analysis. RESULTS A set of 28 candidate genes related to biotic and abiotic stresses were studied in 19 sunflower inbred lines. A total of 14,348 bp of sequence alignment was analyzed per individual. In average, 1 SNP was found per 69 nucleotides and 38 indels were identified in the complete data set. The mean nucleotide polymorphism was moderate (theta = 0.0056), as expected for inbred materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 +/- 1.88). Model-based population structure analysis allowed detection of admixed individuals within the set of accessions examined. Two putative gene pools were identified (G1 and G2), with a large proportion of the inbred lines being assigned to one of them (G1). Consistent with the absence of population sub-structuring, LD for G1 decayed more rapidly (r2 = 0.48 at 643 bp; trend line, pooled data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance). CONCLUSION Knowledge about the patterns of diversity and the genetic relationships between breeding materials could be an invaluable aid in crop improvement strategies. The relatively high frequency of SNPs within the elite inbred lines studied here, along with the predicted extent of LD over distances of 100 kbp (r2 approximately 0.1) suggest that high resolution association mapping in sunflower could be achieved with marker densities lower than those usually reported in the literature.
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Affiliation(s)
- Corina M Fusari
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
| | - Verónica V Lia
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - H Esteban Hopp
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ruth A Heinz
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Norma B Paniego
- Instituto Nacional de Tecnología Agropecuaria (INTA), Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina
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Fusari CM, Lia VV, Hopp HE, Heinz RA, Paniego NB. Identification of single nucleotide polymorphisms and analysis of linkage disequilibrium in sunflower elite inbred lines using the candidate gene approach. BMC PLANT BIOLOGY 2008; 8:7. [PMID: 18215288 DOI: 10.1186/147-2229.8-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 10/22/2007] [Accepted: 01/23/2008] [Indexed: 05/20/2023]
Abstract
BACKGROUND Association analysis is a powerful tool to identify gene loci that may contribute to phenotypic variation. This includes the estimation of nucleotide diversity, the assessment of linkage disequilibrium structure (LD) and the evaluation of selection processes. Trait mapping by allele association requires a high-density map, which could be obtained by the addition of Single Nucleotide Polymorphisms (SNPs) and short insertion and/or deletions (indels) to SSR and AFLP genetic maps. Nucleotide diversity analysis of randomly selected candidate regions is a promising approach for the success of association analysis and fine mapping in the sunflower genome. Moreover, knowledge of the distance over which LD persists, in agronomically meaningful sunflower accessions, is important to establish the density of markers and the experimental design for association analysis. RESULTS A set of 28 candidate genes related to biotic and abiotic stresses were studied in 19 sunflower inbred lines. A total of 14,348 bp of sequence alignment was analyzed per individual. In average, 1 SNP was found per 69 nucleotides and 38 indels were identified in the complete data set. The mean nucleotide polymorphism was moderate (theta = 0.0056), as expected for inbred materials. The number of haplotypes per region ranged from 1 to 9 (mean = 3.54 +/- 1.88). Model-based population structure analysis allowed detection of admixed individuals within the set of accessions examined. Two putative gene pools were identified (G1 and G2), with a large proportion of the inbred lines being assigned to one of them (G1). Consistent with the absence of population sub-structuring, LD for G1 decayed more rapidly (r2 = 0.48 at 643 bp; trend line, pooled data) than the LD trend line for the entire set of 19 individuals (r2 = 0.64 for the same distance). CONCLUSION Knowledge about the patterns of diversity and the genetic relationships between breeding materials could be an invaluable aid in crop improvement strategies. The relatively high frequency of SNPs within the elite inbred lines studied here, along with the predicted extent of LD over distances of 100 kbp (r2 approximately 0.1) suggest that high resolution association mapping in sunflower could be achieved with marker densities lower than those usually reported in the literature.
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Affiliation(s)
- Corina M Fusari
- Instituto Nacional de Tecnología Agropecuaria, Instituto de Biotecnología (CNIA), CC 25, Castelar (B1712WAA), Buenos Aires, Argentina.
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Pavy N, Pelgas B, Beauseigle S, Blais S, Gagnon F, Gosselin I, Lamothe M, Isabel N, Bousquet J. Enhancing genetic mapping of complex genomes through the design of highly-multiplexed SNP arrays: application to the large and unsequenced genomes of white spruce and black spruce. BMC Genomics 2008; 9:21. [PMID: 18205909 PMCID: PMC2246113 DOI: 10.1186/1471-2164-9-21] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2007] [Accepted: 01/18/2008] [Indexed: 11/24/2022] Open
Abstract
Background To explore the potential value of high-throughput genotyping assays in the analysis of large and complex genomes, we designed two highly multiplexed Illumina bead arrays using the GoldenGate SNP assay for gene mapping in white spruce (Picea glauca [Moench] Voss) and black spruce (Picea mariana [Mill.] B.S.P.). Results Each array included 768 SNPs, identified by resequencing genomic DNA from parents of each mapping population. For white spruce and black spruce, respectively, 69.2% and 77.1% of genotyped SNPs had valid GoldenGate assay scores and segregated in the mapping populations. For each of these successful SNPs, on average, valid genotyping scores were obtained for over 99% of progeny. SNP data were integrated to pre-existing ALFP, ESTP, and SSR markers to construct two individual linkage maps and a composite map for white spruce and black spruce genomes. The white spruce composite map contained 821 markers including 348 gene loci. Also, 835 markers including 328 gene loci were positioned on the black spruce composite map. In total, 215 anchor markers (mostly gene markers) were shared between the two species. Considering lineage divergence at least 10 Myr ago between the two spruces, interspecific comparison of homoeologous linkage groups revealed remarkable synteny and marker colinearity. Conclusion The design of customized highly multiplexed Illumina SNP arrays appears as an efficient procedure to enhance the mapping of expressed genes and make linkage maps more informative and powerful in such species with poorly known genomes. This genotyping approach will open new avenues for co-localizing candidate genes and QTLs, partial genome sequencing, and comparative mapping across conifers.
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Affiliation(s)
- Nathalie Pavy
- Arborea and Canada Research Chair in Forest and Environmental Genomics, Centre d'Etude de la Forêt, Pavillon Charles-Eugène-Marchand, Université Laval, Québec, Québec G1V 0A6, Canada.
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Menossi M, Silva-Filho MC, Vincentz M, Van-Sluys MA, Souza GM. Sugarcane functional genomics: gene discovery for agronomic trait development. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2008; 2008:458732. [PMID: 18273390 PMCID: PMC2216073 DOI: 10.1155/2008/458732] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2007] [Accepted: 11/21/2007] [Indexed: 05/04/2023]
Abstract
Sugarcane is a highly productive crop used for centuries as the main source of sugar and recently to produce ethanol, a renewable bio-fuel energy source. There is increased interest in this crop due to the impending need to decrease fossil fuel usage. Sugarcane has a highly polyploid genome. Expressed sequence tag (EST) sequencing has significantly contributed to gene discovery and expression studies used to associate function with sugarcane genes. A significant amount of data exists on regulatory events controlling responses to herbivory, drought, and phosphate deficiency, which cause important constraints on yield and on endophytic bacteria, which are highly beneficial. The means to reduce drought, phosphate deficiency, and herbivory by the sugarcane borer have a negative impact on the environment. Improved tolerance for these constraints is being sought. Sugarcane's ability to accumulate sucrose up to 16% of its culm dry weight is a challenge for genetic manipulation. Genome-based technology such as cDNA microarray data indicates genes associated with sugar content that may be used to develop new varieties improved for sucrose content or for traits that restrict the expansion of the cultivated land. The genes can also be used as molecular markers of agronomic traits in traditional breeding programs.
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Affiliation(s)
- M. Menossi
- Departmento de Genetica e Evolução IB-Unicamp, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas,
C.P. 6010, CEP 13083-970 Campinas, SP, Brazil
| | - M. C. Silva-Filho
- Departamento de Genética,
Escola Superior de Agricultura Luiz de Queiroz,
Universidade de São Paulo,
Av. Pádua Dias, 11, C.P. 83, 13400-970 Piracicaba, SP, Brazil
| | - M. Vincentz
- Departmento de Genetica e Evolução IB-Unicamp, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas,
C.P. 6010, CEP 13083-970 Campinas, SP, Brazil
| | - M.-A. Van-Sluys
- Departamento de Botânica, Instituto de Biociências,
Universidade de São Paulo,
Rua do Matão 277, 05508-090 São Paulo, SP, Brazil
| | - G. M. Souza
- Departamento de Bioquímica,
Instituto de Química,
Universidade de São Paulo,
Av. Prof. Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil
- *G. M. Souza:
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Jones ES, Sullivan H, Bhattramakki D, Smith JSC. A comparison of simple sequence repeat and single nucleotide polymorphism marker technologies for the genotypic analysis of maize (Zea mays L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2007; 115:361-71. [PMID: 17639299 DOI: 10.1007/s00122-007-0570-9] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Accepted: 04/25/2007] [Indexed: 05/16/2023]
Abstract
We report on the comparative utilities of simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers for characterizing maize germplasm in terms of their informativeness, levels of missing data, repeatability and the ability to detect expected alleles in hybrids and DNA pools. Two different SNP chemistries were compared; single-base extension detected by Sequenom MassARRAY, and invasive cleavage detected by Invader chemistry with PCR. A total of 58 maize inbreds and four hybrids were genotyped with 80 SSR markers, 69 Invader SNP markers and 118 MassARRAY SNP markers, with 64 SNP loci being common to the two SNP marker chemistries. Average expected heterozygosity values were 0.62 for SSRs, 0.43 for SNPs (pre-selected for their high level of polymorphism) and 0.63 for the underlying sequence haplotypes. All individual SNP markers within the same set of sequences had an average expected heterozygosity value of 0.26. SNP marker data had more than a fourfold lower level of missing data (2.1-3.1%) compared with SSRs (13.8%). Data repeatability was higher for SNPs (98.1% for MassARRAY SNPs and 99.3% for Invader) than for SSRs (91.7%). Parental alleles were observed in hybrid genotypes in 97.0% of the cases for MassARRAY SNPs, 95.5% for Invader SNPs and 81.9% for SSRs. In pooled samples with mixtures of alleles, SSRs, MassARRAY SNPs and Invader SNPs were equally capable of detecting alleles at mid to high frequencies. However, at low frequencies, alleles were least likely to be detected using Invader SNP markers, and this technology had the highest level of missing data. Collectively, these results showed that SNP technologies can provide increased marker data quality and quantity compared with SSRs. The relative loss in polymorphism compared with SSRs can be compensated by increasing SNP numbers and by using SNP haplotypes. Determining the most appropriate SNP chemistry will be dependent upon matching the technical features of the method within the context of application, particularly in consideration of whether genotypic samples will be pooled or assayed individually.
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Affiliation(s)
- E S Jones
- Pioneer Hi-Bred International Inc. (DuPont Agriculture and Nutrition), 7300 NW 62nd Avenue, Johnston, IA 51031-1004, USA.
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