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Si Z, Du B, Huo J, He S, Liu Q, Zhai H. A genome-wide BAC-end sequence survey provides first insights into sweetpotato (Ipomoea batatas (L.) Lam.) genome composition. BMC Genomics 2016; 17:945. [PMID: 27871234 PMCID: PMC5117676 DOI: 10.1186/s12864-016-3302-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Accepted: 11/15/2016] [Indexed: 11/14/2022] Open
Abstract
Background Sweetpotato, Ipomoea batatas (L.) Lam., is an important food crop widely grown in the world. However, little is known about the genome of this species because it is a highly heterozygous hexaploid. Gaining a more in-depth knowledge of sweetpotato genome is therefore necessary and imperative. In this study, the first bacterial artificial chromosome (BAC) library of sweetpotato was constructed. Clones from the BAC library were end-sequenced and analyzed to provide genome-wide information about this species. Results The BAC library contained 240,384 clones with an average insert size of 101 kb and had a 7.93–10.82 × coverage of the genome, and the probability of isolating any single-copy DNA sequence from the library was more than 99%. Both ends of 8310 BAC clones randomly selected from the library were sequenced to generate 11,542 high-quality BAC-end sequences (BESs), with an accumulative length of 7,595,261 bp and an average length of 658 bp. Analysis of the BESs revealed that 12.17% of the sweetpotato genome were known repetitive DNA, including 7.37% long terminal repeat (LTR) retrotransposons, 1.15% Non-LTR retrotransposons and 1.42% Class II DNA transposons etc., 18.31% of the genome were identified as sweetpotato-unique repetitive DNA and 10.00% of the genome were predicted to be coding regions. In total, 3,846 simple sequences repeats (SSRs) were identified, with a density of one SSR per 1.93 kb, from which 288 SSRs primers were designed and tested for length polymorphism using 20 sweetpotato accessions, 173 (60.07%) of them produced polymorphic bands. Sweetpotato BESs had significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum than those of Vitis vinifera, Theobroma cacao and Arabidopsis thaliana. Conclusions The first BAC library for sweetpotato has been successfully constructed. The high quality BESs provide first insights into sweetpotato genome composition, and have significant hits to the genome sequences of I. trifida and more matches to the whole-genome sequences of Solanum lycopersicum. These resources as a robust platform will be used in high-resolution mapping, gene cloning, assembly of genome sequences, comparative genomics and evolution for sweetpotato. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3302-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zengzhi Si
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Bing Du
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Jinxi Huo
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Shaozhen He
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China
| | - Qingchang Liu
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China.
| | - Hong Zhai
- Beijing Key Laboratory of Crop Genetic Improvement/Laboratory of Crop Heterosis and Utilization, Ministry of Education, China Agricultural University, Beijing, 100193, China.
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Zhang L, Yang X, Tian L, Chen L, Yu W. Identification of peanut (Arachis hypogaea) chromosomes using a fluorescence in situ hybridization system reveals multiple hybridization events during tetraploid peanut formation. THE NEW PHYTOLOGIST 2016; 211:1424-39. [PMID: 27176118 DOI: 10.1111/nph.13999] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 03/31/2016] [Indexed: 05/17/2023]
Abstract
The cultivated peanut Arachis hypogaea (AABB) is thought to have originated from the hybridization of Arachis duranensis (AA) and Arachis ipaënsis (BB) followed by spontaneous chromosome doubling. In this study, we cloned and analyzed chromosome markers from cultivated peanut and its wild relatives. A fluorescence in situ hybridization (FISH)-based karyotyping cocktail was developed with which to study the karyotypes and chromosome evolution of peanut and its wild relatives. Karyotypes were constructed in cultivated peanut and its two putative progenitors using our FISH-based karyotyping system. Comparative karyotyping analysis revealed that chromosome organization was highly conserved in cultivated peanut and its two putative progenitors, especially in the B genome chromosomes. However, variations existed between A. duranensis and the A genome chromosomes in cultivated peanut, especially for the distribution of the interstitial telomere repeats (ITRs). A search of additional A. duranensis varieties from different geographic regions revealed both numeric and positional variations of ITRs, which were similar to the variations in tetraploid peanut varieties. The results provide evidence for the origin of cultivated peanut from the two diploid ancestors, and also suggest that multiple hybridization events of A. ipaënsis with different varieties of A. duranensis may have occurred during the origination of peanut.
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Affiliation(s)
- Laining Zhang
- School of Life Sciences, Institute of Plant Molecular Biology and Agricultural Biotechnology, State (China) Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Xiaoyu Yang
- School of Life Sciences, Institute of Plant Molecular Biology and Agricultural Biotechnology, State (China) Key Laboratory for Agrobiotechnology, The Chinese University of Hong Kong, Sha Tin, Hong Kong
| | - Li Tian
- Institute of Biological Chemistry, Washington State University, Pullman, WA, 99164-6340, USA
| | - Lei Chen
- Shenzhen Research Institute, the Chinese University of Hong Kong, Shenzhen, 518000, China
| | - Weichang Yu
- Shenzhen Research Institute, the Chinese University of Hong Kong, Shenzhen, 518000, China
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Chen YN, Wei WH, Ren XP, Zhao XY, Zhou XJ, Huang L, Tang XC, Jiang HF. Construction of a high-quality genomic BAC library for Chinese peanut cultivar Zhonghua 8 with high oil content. BOTANICAL STUDIES 2014; 55:8. [PMID: 28510971 PMCID: PMC5432765 DOI: 10.1186/1999-3110-55-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 07/31/2013] [Indexed: 05/30/2023]
Abstract
BACKGROUND Arachis hypogaea L. (2n = 4× = 40, AABB) is one of the most important oil and economic crop plants in the word. This species has the largest genome size of about 2,813 Mb among the oil crop species. Zhonghua 8 is a peanut cultivar planted widely in central China and has several superior traits including high oil content, high yield and disease resistance. A high-quality BAC library of Zhonghua 8 was constructed for future researches on the genomics of Chinese peanut cultivars. RESULTS A Hin d III-digested genomic BAC (bacterial artificial chromosome) library was constructed with the genomic DNA from leaves of Zhonghua 8. This BAC library consists of 160,512 clones and the average insert is estimated about 102 kb ranging from 30 to 150 kb. The library represents about 5.55× haploid genome equivalents, and provides a 99.71% probability of finding specific genes. The empty-vector rate is under 5 percent detected from 200 randomly selected clones. Probing of 384 clones with the psbA gene of barley chloroplast and the atp6 gene of rice mitochondrion indicated that the contamination with organellar DNA is insignificant. Successive subculture of three clones showed that the inserts are stable in one hundred generations. CONCLUSIONS This study presented the construction of a high-quality BAC library for the genome of Chinese cultivated peanut. Many essential experiences were summarized in the present study. This BAC library can serve as a substantial platform for development of molecular marker, isolation of genes and further genome research.
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Affiliation(s)
- Yu-Ning Chen
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Wen-Hui Wei
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Xiao-Ping Ren
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Xue-Ya Zhao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Xiao-Jing Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Li Huang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
| | - Xing-Chun Tang
- School of Life Sciences, Hubei University, Wuhan, 430062 China
| | - Hui-Fang Jiang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, 430062 China
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Ratnaparkhe MB, Lee TH, Tan X, Wang X, Li J, Kim C, Rainville LK, Lemke C, Compton RO, Robertson J, Gallo M, Bertioli DJ, Paterson AH. Comparative and evolutionary analysis of major peanut allergen gene families. Genome Biol Evol 2014; 6:2468-88. [PMID: 25193311 PMCID: PMC4202325 DOI: 10.1093/gbe/evu189] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Peanut (Arachis hypogaea L.) causes one of the most serious food allergies. Peanut seed proteins, Arah1, Arah2, and Arah3, are considered to be among the most important peanut allergens. To gain insights into genome organization and evolution of allergen-encoding genes, approximately 617 kb from the genome of cultivated peanut and 215 kb from a wild relative were sequenced including three Arah1, one Arah2, eight Arah3, and two Arah6 gene family members. To assign polarity to differences between homoeologous regions in peanut, we used as outgroups the single orthologous regions in Medicago, Lotus, common bean, chickpea, and pigeonpea, which diverged from peanut about 50 Ma and have not undergone subsequent polyploidy. These regions were also compared with orthologs in many additional dicot plant species to help clarify the timing of evolutionary events. The lack of conservation of allergenic epitopes between species, and the fact that many different proteins can be allergenic, makes the identification of allergens across species by comparative studies difficult. The peanut allergen genes are interspersed with low-copy genes and transposable elements. Phylogenetic analyses revealed lineage-specific expansion and loss of low-copy genes between species and homoeologs. Arah1 syntenic regions are conserved in soybean, pigeonpea, tomato, grape, Lotus, and Arabidopsis, whereas Arah3 syntenic regions show genome rearrangements. We infer that tandem and segmental duplications led to the establishment of the Arah3 gene family. Our analysis indicates differences in conserved motifs in allergen proteins and in the promoter regions of the allergen-encoding genes. Phylogenetic analysis and genomic organization studies provide new insights into the evolution of the major peanut allergen-encoding genes.
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Affiliation(s)
- Milind B Ratnaparkhe
- Plant Genome Mapping Laboratory, University of Georgia Directorate of Soybean Research, Indian Council of Agriculture Research (ICAR), Indore, (M.P.), India
| | - Tae-Ho Lee
- Plant Genome Mapping Laboratory, University of Georgia
| | - Xu Tan
- Plant Genome Mapping Laboratory, University of Georgia
| | - Xiyin Wang
- Plant Genome Mapping Laboratory, University of Georgia Center for Genomics and Computational Biology, School of Life Sciences, School of Sciences, Hebei United University, Tangshan, Hebei, China
| | - Jingping Li
- Plant Genome Mapping Laboratory, University of Georgia
| | - Changsoo Kim
- Plant Genome Mapping Laboratory, University of Georgia
| | | | | | | | - Jon Robertson
- Plant Genome Mapping Laboratory, University of Georgia
| | - Maria Gallo
- Department of Molecular Biosciences and Bioengineering, University of Hawaii at Mānoa
| | - David J Bertioli
- University of Brasília, Campus Universitário Darcy Ribeiro, DF, Brazil
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Bertioli DJ, Vidigal B, Nielen S, Ratnaparkhe MB, Lee TH, Leal-Bertioli SCM, Kim C, Guimarães PM, Seijo G, Schwarzacher T, Paterson AH, Heslop-Harrison P, Araujo ACG. The repetitive component of the A genome of peanut (Arachis hypogaea) and its role in remodelling intergenic sequence space since its evolutionary divergence from the B genome. ANNALS OF BOTANY 2013; 112:545-59. [PMID: 23828319 PMCID: PMC3718217 DOI: 10.1093/aob/mct128] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
BACKGROUND AND AIMS Peanut (Arachis hypogaea) is an allotetraploid (AABB-type genome) of recent origin, with a genome of about 2·8 Gb and a high repetitive content. This study reports an analysis of the repetitive component of the peanut A genome using bacterial artificial chromosome (BAC) clones from A. duranensis, the most probable A genome donor, and the probable consequences of the activity of these elements since the divergence of the peanut A and B genomes. METHODS The repetitive content of the A genome was analysed by using A. duranensis BAC clones as probes for fluorescence in situ hybridization (BAC-FISH), and by sequencing and characterization of 12 genomic regions. For the analysis of the evolutionary dynamics, two A genome regions are compared with their B genome homeologues. KEY RESULTS BAC-FISH using 27 A. duranensis BAC clones as probes gave dispersed and repetitive DNA characteristic signals, predominantly in interstitial regions of the peanut A chromosomes. The sequences of 14 BAC clones showed complete and truncated copies of ten abundant long terminal repeat (LTR) retrotransposons, characterized here. Almost all dateable transposition events occurred <3·5 million years ago, the estimated date of the divergence of A and B genomes. The most abundant retrotransposon is Feral, apparently parasitic on the retrotransposon FIDEL, followed by Pipa, also non-autonomous and probably parasitic on a retrotransposon we named Pipoka. The comparison of the A and B genome homeologous regions showed conserved segments of high sequence identity, punctuated by predominantly indel regions without significant similarity. CONCLUSIONS A substantial proportion of the highly repetitive component of the peanut A genome appears to be accounted for by relatively few LTR retrotransposons and their truncated copies or solo LTRs. The most abundant of the retrotransposons are non-autonomous. The activity of these retrotransposons has been a very significant driver of genome evolution since the evolutionary divergence of the A and B genomes.
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Affiliation(s)
- David J. Bertioli
- University of Brasilia, Department of Genetics, Campus Universitário, Brasília DF, Brazil
| | - Bruna Vidigal
- University of Brasilia, Department of Genetics, Campus Universitário, Brasília DF, Brazil
- Embrapa Genetic Resources and Biotechnology, Brasilia, DF, Brazil
| | - Stephan Nielen
- Embrapa Genetic Resources and Biotechnology, Brasilia, DF, Brazil
| | | | - Tae-Ho Lee
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA 30605, USA
| | | | - Changsoo Kim
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA 30605, USA
| | | | - Guillermo Seijo
- Plant Cytogenetic and Evolution Laboratory, Instituto de Botánica del Nordeste and Faculty of Exact and Natural Sciences, National University of the Northeast, Corrientes, Argentina
| | | | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, The University of Georgia, Athens, GA 30605, USA
| | | | - Ana C. G. Araujo
- Embrapa Genetic Resources and Biotechnology, Brasilia, DF, Brazil
- For correspondence. E-mail
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Guo B, Pandey MK, He G, Zhang X, Liao B, Culbreath A, Varshney RK, Nwosu V, Wilson RF, Stalker HT. Recent Advances in Molecular Genetic Linkage Maps of Cultivated Peanut. ACTA ACUST UNITED AC 2013. [DOI: 10.3146/ps13-03.1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
ABSTRACT
The competitiveness of peanuts in domestic and global markets has been threatened by losses in productivity and quality that are attributed to diseases, pests, environmental stresses and allergy or food safety issues. Narrow genetic diversity and a deficiency of polymorphic DNA markers severely hindered construction of dense genetic maps and quantitative trait loci (QTL) mapping in order to deploy linked markers in marker-assisted peanut improvement. The U.S. Peanut Genome Initiative (PGI) was launched in 2004, and expanded to a global effort in 2006 to address these issues through coordination of international efforts in genome research beginning with molecular marker development and improvement of map resolution and coverage. Ultimately, a peanut genome sequencing project was launched in 2012 by the Peanut Genome Consortium (PGC). We reviewed the progress for accelerated development of peanut genomic resources in peanut, such as generation of expressed sequenced tags (ESTs) (252,832 ESTs as December 2012 in the public NCBI EST database), development of molecular markers (over 15,518 SSRs), and construction of peanut genetic linkage maps, in particular for cultivated peanut. Several consensus genetic maps have been constructed, and there are examples of recent international efforts to develop high density maps. An international reference consensus genetic map was developed recently with 897 marker loci based on 11 published mapping populations. Furthermore, a high-density integrated consensus map of cultivated peanut and wild diploid relatives also has been developed, which was enriched further with 3693 marker loci on a single map by adding information from five new genetic mapping populations to the published reference consensus map.
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Affiliation(s)
- Baozhu Guo
- USDA- Agricultural Research Service, Crop Protection and Management Research Unit, Tifton, GA 31793
| | - Manish K. Pandey
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Guohao He
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL 36088
| | - Xinyou Zhang
- Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Boshou Liao
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Albert Culbreath
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | - Victor Nwosu
- Plant Science Program, Global Chocolate Science & Technology, Mars Chocolate North America, Hackettstown, NJ 07840
| | - Richard F. Wilson
- Oilseeds & Bioscience Consulting, 5517 Hickory Leaf Drive, Raleigh, NC 27606
| | - H. Thomas Stalker
- Department of Crop Science, North Carolina State University, Raleigh, NC 27695
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Varshney RK, Mohan SM, Gaur PM, Gangarao NVPR, Pandey MK, Bohra A, Sawargaonkar SL, Chitikineni A, Kimurto PK, Janila P, Saxena KB, Fikre A, Sharma M, Rathore A, Pratap A, Tripathi S, Datta S, Chaturvedi SK, Mallikarjuna N, Anuradha G, Babbar A, Choudhary AK, Mhase MB, Bharadwaj C, Mannur DM, Harer PN, Guo B, Liang X, Nadarajan N, Gowda CLL. Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics. Biotechnol Adv 2013; 31:1120-34. [PMID: 23313999 DOI: 10.1016/j.biotechadv.2013.01.001] [Citation(s) in RCA: 157] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 12/16/2012] [Accepted: 01/03/2013] [Indexed: 10/27/2022]
Abstract
Advances in next-generation sequencing and genotyping technologies have enabled generation of large-scale genomic resources such as molecular markers, transcript reads and BAC-end sequences (BESs) in chickpea, pigeonpea and groundnut, three major legume crops of the semi-arid tropics. Comprehensive transcriptome assemblies and genome sequences have either been developed or underway in these crops. Based on these resources, dense genetic maps, QTL maps as well as physical maps for these legume species have also been developed. As a result, these crops have graduated from 'orphan' or 'less-studied' crops to 'genomic resources rich' crops. This article summarizes the above-mentioned advances in genomics and genomics-assisted breeding applications in the form of marker-assisted selection (MAS) for hybrid purity assessment in pigeonpea; marker-assisted backcrossing (MABC) for introgressing QTL region for drought-tolerance related traits, Fusarium wilt (FW) resistance and Ascochyta blight (AB) resistance in chickpea; late leaf spot (LLS), leaf rust and nematode resistance in groundnut. We critically present the case of use of other modern breeding approaches like marker-assisted recurrent selection (MARS) and genomic selection (GS) to utilize the full potential of genomics-assisted breeding for developing superior cultivars with enhanced tolerance to various environmental stresses. In addition, this article recommends the use of advanced-backcross (AB-backcross) breeding and development of specialized populations such as multi-parents advanced generation intercross (MAGIC) for creating new variations that will help in developing superior lines with broadened genetic base. In summary, we propose the use of integrated genomics and breeding approach in these legume crops to enhance crop productivity in marginal environments ensuring food security in developing countries.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India; CGIAR Generation Challenge Programme (GCP), c/o CIMMYT, DF 06600, Mexico; The University of Western Australia, Crawley 6009, Australia; Crops Research Institute, Guangdong Academy of Agricultural Sciences (GAAS), Guangzhou 510640, China.
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Zhao Y, Prakash CS, He G. Characterization and compilation of polymorphic simple sequence repeat (SSR) markers of peanut from public database. BMC Res Notes 2012; 5:362. [PMID: 22818284 PMCID: PMC3500262 DOI: 10.1186/1756-0500-5-362] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Accepted: 06/25/2012] [Indexed: 12/22/2022] Open
Abstract
Background There are several reports describing thousands of SSR markers in the peanut (Arachis hypogaea L.) genome. There is a need to integrate various research reports of peanut DNA polymorphism into a single platform. Further, because of lack of uniformity in the labeling of these markers across the publications, there is some confusion on the identities of many markers. We describe below an effort to develop a central comprehensive database of polymorphic SSR markers in peanut. Findings We compiled 1,343 SSR markers as detecting polymorphism (14.5%) within a total of 9,274 markers. Amongst all polymorphic SSRs examined, we found that AG motif (36.5%) was the most abundant followed by AAG (12.1%), AAT (10.9%), and AT (10.3%).The mean length of SSR repeats in dinucleotide SSRs was significantly longer than that in trinucleotide SSRs. Dinucleotide SSRs showed higher polymorphism frequency for genomic SSRs when compared to trinucleotide SSRs, while for EST-SSRs, the frequency of polymorphic SSRs was higher in trinucleotide SSRs than in dinucleotide SSRs. The correlation of the length of SSR and the frequency of polymorphism revealed that the frequency of polymorphism was decreased as motif repeat number increased. Conclusions The assembled polymorphic SSRs would enhance the density of the existing genetic maps of peanut, which could also be a useful source of DNA markers suitable for high-throughput QTL mapping and marker-assisted selection in peanut improvement and thus would be of value to breeders.
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Affiliation(s)
- Yongli Zhao
- Department of Agricultural and Environmental Sciences, Tuskegee University, Tuskegee, AL 36088, USA
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Shirasawa K, Hirakawa H, Tabata S, Hasegawa M, Kiyoshima H, Suzuki S, Sasamoto S, Watanabe A, Fujishiro T, Isobe S. Characterization of active miniature inverted-repeat transposable elements in the peanut genome. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:1429-38. [PMID: 22294450 PMCID: PMC3336055 DOI: 10.1007/s00122-012-1798-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2011] [Accepted: 01/05/2012] [Indexed: 05/19/2023]
Abstract
Miniature inverted-repeat transposable elements (MITEs), some of which are known as active nonautonomous DNA transposons, are found in the genomes of plants and animals. In peanut (Arachis hypogaea), Ah-MITE1 has been identified in a gene for fatty-acid desaturase, and possessed excision activity. However, the AhMITE1 distribution and frequency of excision have not been determined for the peanut genome. In order to characterize AhMITE1s, their genomic diversity and transposition ability was investigated. Southern blot analysis indicated high AhMITE1 copy number in the genomes of A. hypogaea, A. magna and A. monticola, but not in A. duranensis. A total of 504 AhMITE1s were identified from the MITE-enriched genomic libraries of A. hypogaea. The representative AhMITE1s exhibited a mean length of 205.5 bp and a GC content of 30.1%, with AT-rich, 9 bp target site duplications and 25 bp terminal inverted repeats. PCR analyses were performed using primer pairs designed against both flanking sequences of each AhMITE1. These analyses detected polymorphisms at 169 out of 411 insertional loci in the four peanut lines. In subsequent analyses of 60 gamma-irradiated mutant lines, four Ah-MITE1 excisions showed footprint mutations at the 109 loci tested. This study characterizes AhMITE1s in peanut and discusses their use as DNA markers and mutagens for the genetics, genomics and breeding of peanut and its relatives.
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Affiliation(s)
- Kenta Shirasawa
- Department of Plant Genome Research, Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan.
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Advances in BAC-based physical mapping and map integration strategies in plants. J Biomed Biotechnol 2012; 2012:184854. [PMID: 22500080 PMCID: PMC3303678 DOI: 10.1155/2012/184854] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2011] [Revised: 10/26/2011] [Accepted: 11/11/2011] [Indexed: 12/29/2022] Open
Abstract
In the advent of next-generation sequencing (NGS) platforms, map-based sequencing strategy has been recently suppressed being too expensive and laborious. The detailed studies on NGS drafts alone indicated these assemblies remain far from gold standard reference quality, especially when applied on complex genomes. In this context the conventional BAC-based physical mapping has been identified as an important intermediate layer in current hybrid sequencing strategy. BAC-based physical map construction and its integration with high-density genetic maps have benefited from NGS and high-throughput array platforms. This paper addresses the current advancements of BAC-based physical mapping and high-throughput map integration strategies to obtain densely anchored well-ordered physical maps. The resulted maps are of immediate utility while providing a template to harness the maximum benefits of the current NGS platforms.
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Matita, a new retroelement from peanut: characterization and evolutionary context in the light of the Arachis A-B genome divergence. Mol Genet Genomics 2011; 287:21-38. [PMID: 22120641 DOI: 10.1007/s00438-011-0656-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2011] [Accepted: 10/20/2011] [Indexed: 12/16/2022]
Abstract
Cultivated peanut is an allotetraploid with an AB-genome. In order to learn more of the genomic structure of peanut, we characterized and studied the evolution of a retrotransposon originally isolated from a resistance gene analog (RGA)-containing bacterial artificial chromosome (BAC) clone. It is a moderate copy number Ty1-copia retrotransposon from the Bianca lineage and we named it Matita. Fluorescent in situ hybridization (FISH) experiments showed that Matita is mainly located on the distal regions of chromosome arms and is of approximately equal frequency on both A- and B-chromosomes. Its chromosome-specific hybridization pattern facilitates the identification of individual chromosomes, a useful cytogenetic tool considering that chromosomes in peanut are mostly metacentric and of similar size. Phylogenetic analysis of Matita elements, molecular dating of transposition events, and an estimation of the evolutionary divergence of the most probable A- and B-donor species suggest that Matita underwent its last major burst of transposition activity at around the same time of the A- and B-genome divergence about 3.5 million years ago. By probing BAC libraries with overgos probes for Matita, resistance gene analogues, and single- or low-copy genes, it was demonstrated that Matita is not randomly distributed in the genome but exhibits a significant tendency of being more abundant near resistance gene homologues than near single-copy genes. The described work is a further step towards broadening the knowledge on genomic and chromosomal structure of peanut and on its evolution.
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Pandey MK, Monyo E, Ozias-Akins P, Liang X, Guimarães P, Nigam SN, Upadhyaya HD, Janila P, Zhang X, Guo B, Cook DR, Bertioli DJ, Michelmore R, Varshney RK. Advances in Arachis genomics for peanut improvement. Biotechnol Adv 2011; 30:639-51. [PMID: 22094114 DOI: 10.1016/j.biotechadv.2011.11.001] [Citation(s) in RCA: 191] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2011] [Revised: 10/24/2011] [Accepted: 11/01/2011] [Indexed: 01/01/2023]
Abstract
Peanut genomics is very challenging due to its inherent problem of genetic architecture. Blockage of gene flow from diploid wild relatives to the tetraploid; cultivated peanut, recent polyploidization combined with self pollination, and the narrow genetic base of the primary genepool have resulted in low genetic diversity that has remained a major bottleneck for genetic improvement of peanut. Harnessing the rich source of wild relatives has been negligible due to differences in ploidy level as well as genetic drag and undesirable alleles for low yield. Lack of appropriate genomic resources has severely hampered molecular breeding activities, and this crop remains among the less-studied crops. The last five years, however, have witnessed accelerated development of genomic resources such as development of molecular markers, genetic and physical maps, generation of expressed sequenced tags (ESTs), development of mutant resources, and functional genomics platforms that facilitate the identification of QTLs and discovery of genes associated with tolerance/resistance to abiotic and biotic stresses and agronomic traits. Molecular breeding has been initiated for several traits for development of superior genotypes. The genome or at least gene space sequence is expected to be available in near future and this will further accelerate use of biotechnological approaches for peanut improvement.
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Affiliation(s)
- Manish K Pandey
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, India
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Schulte D, Ariyadasa R, Shi B, Fleury D, Saski C, Atkins M, deJong P, Wu CC, Graner A, Langridge P, Stein N. BAC library resources for map-based cloning and physical map construction in barley (Hordeum vulgare L.). BMC Genomics 2011; 12:247. [PMID: 21595870 PMCID: PMC3224359 DOI: 10.1186/1471-2164-12-247] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2011] [Accepted: 05/19/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although second generation sequencing (2GS) technologies allow re-sequencing of previously gold-standard-sequenced genomes, whole genome shotgun sequencing and de novo assembly of large and complex eukaryotic genomes is still difficult. Availability of a genome-wide physical map is therefore still a prerequisite for whole genome sequencing for genomes like barley. To start such an endeavor, large insert genomic libraries, i.e. Bacterial Artificial Chromosome (BAC) libraries, which are unbiased and representing deep haploid genome coverage, need to be ready in place. RESULT Five new BAC libraries were constructed for barley (Hordeum vulgare L.) cultivar Morex. These libraries were constructed in different cloning sites (HindIII, EcoRI, MboI and BstXI) of the respective vectors. In order to enhance unbiased genome representation and to minimize the number of gaps between BAC contigs, which are often due to uneven distribution of restriction sites, a mechanically sheared library was also generated. The new BAC libraries were fully characterized in depth by scrutinizing the major quality parameters such as average insert size, degree of contamination (plate wide, neighboring, and chloroplast), empty wells and off-scale clones (clones with <30 or >250 fragments). Additionally a set of gene-based probes were hybridized to high density BAC filters and showed that genome coverage of each library is between 2.4 and 6.6 X. CONCLUSION BAC libraries representing >20 haploid genomes are available as a new resource to the barley research community. Systematic utilization of these libraries in high-throughput BAC fingerprinting should allow developing a genome-wide physical map for the barley genome, which will be instrumental for map-based gene isolation and genome sequencing.
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Affiliation(s)
- Daniela Schulte
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
- KWS SAAT AG, Grimsehlstr. 31, 37555 Einbeck, Germany
| | - Ruvini Ariyadasa
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
| | - Bujun Shi
- Australian Centre of Plant Functional Genomics, University of Adelaide, PMB 1 Glen Osmond SA 5064, Australia
| | - Delphine Fleury
- Australian Centre of Plant Functional Genomics, University of Adelaide, PMB 1 Glen Osmond SA 5064, Australia
| | - Chris Saski
- Clemson University Genomics Institute (CUGI), 51 New Cherry St. BRC 310, Clemson, SC 29634, USA
| | - Michael Atkins
- Clemson University Genomics Institute (CUGI), 51 New Cherry St. BRC 310, Clemson, SC 29634, USA
| | - Pieter deJong
- BACPAC Resources, Children's Hospital Oakland, 747 52nd St. Oakland, CA 94609, USA
| | - Cheng-Cang Wu
- Lucigen Corporation, 2120 West Greenview Dr., Middleton, WI 53562, USA
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
| | - Peter Langridge
- Australian Centre of Plant Functional Genomics, University of Adelaide, PMB 1 Glen Osmond SA 5064, Australia
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466 Gatersleben, Germany
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Lin J, Kudrna D, Wing RA. Construction, characterization, and preliminary BAC-end sequence analysis of a bacterial artificial chromosome library of the tea plant (Camellia sinensis). J Biomed Biotechnol 2010; 2011:476723. [PMID: 21234344 PMCID: PMC3017946 DOI: 10.1155/2011/476723] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 10/28/2010] [Indexed: 12/17/2022] Open
Abstract
We describe the construction and characterization of a publicly available BAC library for the tea plant, Camellia sinensis. Using modified methods, the library was constructed with the aim of developing public molecular resources to advance tea plant genomics research. The library consists of a total of 401,280 clones with an average insert size of 135 kb, providing an approximate coverage of 13.5 haploid genome equivalents. No empty vector clones were observed in a random sampling of 576 BAC clones. Further analysis of 182 BAC-end sequences from randomly selected clones revealed a GC content of 40.35% and low chloroplast and mitochondrial contamination. Repetitive sequence analyses indicated that LTR retrotransposons were the most predominant sequence class (86.93%-87.24%), followed by DNA retrotransposons (11.16%-11.69%). Additionally, we found 25 simple sequence repeats (SSRs) that could potentially be used as genetic markers.
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Affiliation(s)
- Jinke Lin
- School of Plant Sciences, Arizona Genomics Institute, The University of Arizona, Tucson AZ 85721, USA
- Department of Tea Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Dave Kudrna
- School of Plant Sciences, Arizona Genomics Institute, The University of Arizona, Tucson AZ 85721, USA
| | - Rod A. Wing
- School of Plant Sciences, Arizona Genomics Institute, The University of Arizona, Tucson AZ 85721, USA
- BIO5 Institute, University of Arizona, Tucson AZ 85721, USA
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Varshney RK, Glaszmann JC, Leung H, Ribaut JM. More genomic resources for less-studied crops. Trends Biotechnol 2010; 28:452-60. [PMID: 20692061 DOI: 10.1016/j.tibtech.2010.06.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 06/23/2010] [Accepted: 06/27/2010] [Indexed: 01/14/2023]
Abstract
Many of the crop species considered to be minor on a global scale, yet are important locally for food security in the developing world, have remained less-studied crops. Recent years have witnessed the development of large-scale genomic and genetic resources, including simple sequence repeat, single nucleotide polymorphism and diversity array technology markers, expressed sequence tags or transcript reads, bacterial artificial chromosome libraries, genetic and physical maps, and genetic stocks with rich genetic diversity, such as core reference sets and introgression lines in these crops. These resources have the potential to accelerate gene discovery and initiate molecular breeding in these crops, thereby enhancing crop productivity to ensure food security in developing countries.
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Affiliation(s)
- Rajeev K Varshney
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru 502324, A.P., India.
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Stalker HT, Weissinger AK, Milla-Lewis S, Holbrook CC. Genomics: An Evolving Science in Peanut. ACTA ACUST UNITED AC 2009. [DOI: 10.3146/at07-006.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Abstract
Genomic spcience offers new research tools to explore the function of genes and their effects on plants and animals. Arachis hypogaea is a polyploid species of relatively recent origin and molecular analyses with technologies available in the 1980s and 1990s resulted in little progress in the cultivated species because of apparent lack of molecular variation. Large numbers of polymorphisms existing in wild Arachis species led to evolutionary and gene introgression studies. High throughput genomic sequencing technologies have greatly expanded the possibilities for investigating gene function, but techniques are sufficiently expensive that most federal funding has been directed toward model species and ‘major’ crops. Peanut has lagged behind many other crops, but the number of researchers working on the species in the U.S. and internationally has greatly increased during recent years. In an effort to bring researchers who work with a number of legume crops together to discuss common goals, a national strategic planning workshop was held in 2001 which led to the U.S. Legume Crops Genomics Initiative. A second workshop was held in 2004 to develop a plan with specific objectives for cross-legume genomics research and to outline milestones for accomplishments. Specifically for peanut, a genomics strategic planning workshop was organized at Atlanta in 2004 by the American Peanut Council. A broad view of genomic science was adopted and goals were set by participants to include (a) improving the utility of genetic tools for peanut genomics research, (b) improving the efficacy of technology for gene manipulation in genomics, (c) developing a framework for assembling the peanut genetic blueprint, (d) improving knowledge of gene identification and regulation, and (e) providing bioinformatic management of peanut biological information. Teams of researchers, including molecular biologists, plant breeders, pathologists, and many other disciplines need to be developed to fully utilize the potential of genomics for peanut improvement.
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Jang CS, Kamps TL, Tang H, Bowers JE, Lemke C, Paterson AH. Evolutionary fate of rhizome-specific genes in a non-rhizomatous Sorghum genotype. Heredity (Edinb) 2008; 102:266-73. [PMID: 19002204 DOI: 10.1038/hdy.2008.119] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
What is the fate of organ-specific genes after the organ is lost? For Sorghum propinquum and Sorghum halepense genes that were previously shown to have rhizome-enriched expression, we have conducted comparative analysis of both coding regions and regulatory sequences in Sorghum bicolor (non-rhizomatousness) and S. propinquum (rhizomatousness). Most genes with rhizome-enriched expression appear to have similar numbers of paralogous copies in both genotypes, with only three of 24 genes studied showing significant differences in copy numbers. We detected no greater propensity for mutation in S. bicolor than in S. propinquum of genes with rhizome-enriched expression in the latter. Several cis-acting regulatory elements, particularly an Myb-binding core (AACGG) that is involved in the regulation of the mitotic cyclin, were more abundant in promoters of S. propinquum than in non-rhizomatous S. bicolor or Oryza sativa (rice). We suggest that many genes with rhizome-enriched expression in S. propinquum may serve multiple functions, with partial loss of some of these functions in S. bicolor but ongoing purifying selection acting to preserve the remaining functions. Expressed genes in polyploid S. halepense rhizomes appeared to be more frequently derived from the S. propinquum than the S. bicolor progenitor, but there was some evidence of formation of novel alleles and 'recruitment' of S. bicolor genes to rhizome-enriched expression in S. halepense, suggesting that polyploidy may have offered new evolutionary potential to S. halepense.
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Affiliation(s)
- C S Jang
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA 30602, USA
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A BAC library of Beta vulgaris L. for the targeted isolation of centromeric DNA and molecular cytogenetics of Beta species. Genetica 2008; 135:157-67. [DOI: 10.1007/s10709-008-9265-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2007] [Accepted: 03/18/2008] [Indexed: 10/22/2022]
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Guimarães PM, Garsmeur O, Proite K, Leal-Bertioli SCM, Seijo G, Chaine C, Bertioli DJ, D'Hont A. BAC libraries construction from the ancestral diploid genomes of the allotetraploid cultivated peanut. BMC PLANT BIOLOGY 2008; 8:14. [PMID: 18230166 PMCID: PMC2254395 DOI: 10.1186/1471-2229-8-14] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2007] [Accepted: 01/29/2008] [Indexed: 05/19/2023]
Abstract
BACKGROUND Cultivated peanut, Arachis hypogaea is an allotetraploid of recent origin, with an AABB genome. In common with many other polyploids, it seems that a severe genetic bottle-neck was imposed at the species origin, via hybridisation of two wild species and spontaneous chromosome duplication. Therefore, the study of the genome of peanut is hampered both by the crop's low genetic diversity and its polyploidy. In contrast to cultivated peanut, most wild Arachis species are diploid with high genetic diversity. The study of diploid Arachis genomes is therefore attractive, both to simplify the construction of genetic and physical maps, and for the isolation and characterization of wild alleles. The most probable wild ancestors of cultivated peanut are A. duranensis and A. ipaënsis with genome types AA and BB respectively. RESULTS We constructed and characterized two large-insert libraries in Bacterial Artificial Chromosome (BAC) vector, one for each of the diploid ancestral species. The libraries (AA and BB) are respectively c. 7.4 and c. 5.3 genome equivalents with low organelle contamination and average insert sizes of 110 and 100 kb. Both libraries were used for the isolation of clones containing genetically mapped legume anchor markers (single copy genes), and resistance gene analogues. CONCLUSION These diploid BAC libraries are important tools for the isolation of wild alleles conferring resistances to biotic stresses, comparisons of orthologous regions of the AA and BB genomes with each other and with other legume species, and will facilitate the construction of a physical map.
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Affiliation(s)
- Patricia M Guimarães
- Biotechnology Unit, Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
| | - Olivier Garsmeur
- Centre de Coopération International en Recherche Agronomique pour le Developpement (CIRAD), Montpellier, France
| | - Karina Proite
- Biotechnology Unit, Embrapa Genetic Resources and Biotechnology, Brasília, DF, Brazil
- Cell Biology Department, IB-University of Brasília (UnB), Brasília, DF, Brazil
| | | | - Guilhermo Seijo
- Plant Cytogenetics and Evolution Laboratory, Instituto de Botánica del Nordeste, Corrientes, Argentina
| | - Christian Chaine
- Centre de Coopération International en Recherche Agronomique pour le Developpement (CIRAD), Montpellier, France
| | - David J Bertioli
- Biotechnology and Genomic Sciences Department, Campus II Catholic University of Brasília, Brasília, DF, Brazil
| | - Angelique D'Hont
- Centre de Coopération International en Recherche Agronomique pour le Developpement (CIRAD), Montpellier, France
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Wang XF, Ma J, Wang WS, Zheng YM, Zhang GY, Liu CJ, Ma ZY. Construction and characterization of the first bacterial artificial chromosome library for the cotton species Gossypium barbadense L. Genome 2006; 49:1393-8. [PMID: 17426754 DOI: 10.1139/g06-113] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
As the second most widely cultivated cotton, Gossypium barbadense is well known for its superior fiber properties and its high levels of resistance to Fusarium and Verticillium wilts. To enhance our ability to exploit these properties in breeding programs, we constructed the first bacterial artificial chromosome (BAC) library for this species. The library contains 167 424 clones (49 920 BamHI and 117 504 HindIII clones), with an estimated average insert size of 130 kb. About 94.0% of the clones had inserts over 100 kb, and the empty clones accounted for less than 4.0%. Contamination of the library with chloroplast clones was very low (0.2%). Screening the library with locus-specific probes showed that BAC clones represent 6.5-fold genome equivalents. This high-quality library provides an additional asset with which to exploit genetic variation for cotton improvement.
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Affiliation(s)
- X F Wang
- Key Laboratory of Crop Germplasm Resources of Hebei Province, Agricultural University of Hebei, Baoding 071001, China
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Feng J, Vick BA, Lee MK, Zhang HB, Jan CC. Construction of BAC and BIBAC libraries from sunflower and identification of linkage group-specific clones by overgo hybridization. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 113:23-32. [PMID: 16612648 DOI: 10.1007/s00122-006-0265-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2005] [Accepted: 03/09/2006] [Indexed: 05/04/2023]
Abstract
Complementary BAC and BIBAC libraries were constructed from nuclear DNA of sunflower cultivar HA 89. The BAC library, constructed with BamHI in the pECBAC1 vector, contains 107,136 clones and has an average insert size of 140 kb. The BIBAC library was constructed with HindIII in the plant-transformation-competent binary vector pCLD04541 and contains 84,864 clones, with an average insert size of 137 kb. The two libraries combined contain 192,000 clones and are equivalent to approximately 8.9 haploid genomes of sunflower (3,000 Mb/1C), and provide a greater than 99% probability of obtaining a clone of interest. The frequencies of BAC and BIBAC clones carrying chloroplast or mitochondrial DNA sequences were estimated to be 2.35 and 0.04%, respectively, and insert-empty clones were less than 0.5%. To facilitate chromosome engineering and anchor the sunflower genetic map to its chromosomes, one to three single- or low-copy RFLP markers from each linkage group of sunflower were used to design pairs of overlapping oligonucleotides (overgos). Thirty-six overgos were designed and pooled as probes to screen a subset (5.1x) of the BAC and BIBAC libraries. Of the 36 overgos, 33 (92%) gave at least one positive clone and 3 (8%) failed to hit any clone. As a result, 195 BAC and BIBAC clones representing 19 linkage groups were identified, including 76 BAC clones and 119 BIBAC clones, further verifying the genome coverage and utility of the libraries. These BAC and BIBAC libraries and linkage group-specific clones provide resources essential for comprehensive research of the sunflower genome.
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Affiliation(s)
- Jiuhuan Feng
- Department of Plant Sciences, North Dakota State University, Fargo, ND 58105, USA
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