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Duraiswamy A, Sneha A. NM, Jebakani K. S, Selvaraj S, Pramitha J. L, Selvaraj R, Petchiammal K. I, Kather Sheriff S, Thinakaran J, Rathinamoorthy S, Kumar P. R. Genetic manipulation of anti-nutritional factors in major crops for a sustainable diet in future. FRONTIERS IN PLANT SCIENCE 2023; 13:1070398. [PMID: 36874916 PMCID: PMC9976781 DOI: 10.3389/fpls.2022.1070398] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 12/19/2022] [Indexed: 06/18/2023]
Abstract
The consumption of healthy food, in order to strengthen the immune system, is now a major focus of people worldwide and is essential to tackle the emerging pandemic concerns. Moreover, research in this area paves the way for diversification of human diets by incorporating underutilized crops which are highly nutritious and climate-resilient in nature. However, although the consumption of healthy foods increases nutritional uptake, the bioavailability of nutrients and their absorption from foods also play an essential role in curbing malnutrition in developing countries. This has led to a focus on anti-nutrients that interfere with the digestion and absorption of nutrients and proteins from foods. Anti-nutritional factors in crops, such as phytic acid, gossypol, goitrogens, glucosinolates, lectins, oxalic acid, saponins, raffinose, tannins, enzyme inhibitors, alkaloids, β-N-oxalyl amino alanine (BOAA), and hydrogen cyanide (HCN), are synthesized in crop metabolic pathways and are interconnected with other essential growth regulation factors. Hence, breeding with the aim of completely eliminating anti-nutrition factors tends to compromise desirable features such as yield and seed size. However, advanced techniques, such as integrated multi-omics, RNAi, gene editing, and genomics-assisted breeding, aim to breed crops in which negative traits are minimized and to provide new strategies to handle these traits in crop improvement programs. There is also a need to emphasize individual crop-based approaches in upcoming research programs to achieve smart foods with minimum constraints in future. This review focuses on progress in molecular breeding and prospects for additional approaches to improve nutrient bioavailability in major crops.
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Affiliation(s)
- Aishwarya Duraiswamy
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Nancy Mano Sneha A.
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Sherina Jebakani K.
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Sellakumar Selvaraj
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Lydia Pramitha J.
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Ramchander Selvaraj
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Indira Petchiammal K.
- Genetics and Plant Breeding, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Sharmili Kather Sheriff
- Agronomy, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Jenita Thinakaran
- Horticulture, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Samundeswari Rathinamoorthy
- Crop Physiology, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
| | - Ramesh Kumar P.
- Plant Biochemistry, School of Agricultural Sciences, Karunya Institute of Technology and Sciences, Coimbatore, India
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Sinyavina NG, Kochetov AA, Egorova KV, Kocherina NV, Chesnokov YV. Genetic-Biochemical Studies and Morphobiological Assessment of Small Radish (Raphanus sativus L.) under Artificial Light Culture Conditions. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422060102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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A Comparative Transcriptome and Metabolome Combined Analysis Reveals the Key Genes and Their Regulatory Model Responsible for Glucoraphasatin Accumulation in Radish Fleshy Taproots. Int J Mol Sci 2022; 23:ijms23062953. [PMID: 35328374 PMCID: PMC8949420 DOI: 10.3390/ijms23062953] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 02/28/2022] [Accepted: 03/07/2022] [Indexed: 02/01/2023] Open
Abstract
Radish (Raphanus sativus L.) is rich in specific glucosinolates (GSLs), which benefit human health and special flavor formation. Although the basic GSLs metabolic pathway in Brassicaceae plants is clear, the regulating mechanism for specific glucosinolates content in radish fleshy taproots is not well understood. In this study, we discovered that there was a significant difference in the GSLs profiles and the content of various GSLs components. Glucoraphasatin (GRH) is the most predominant GSL in radish taproots of different genotypes as assessed by HPLC analysis. Further, we compared the taproot transcriptomes of three radish genotypes with high and low GSLs content by employing RNA-seq. Totally, we identified forty-one differentially expressed genes related to GSLs metabolism. Among them, thirteen genes (RsBCAT4, RsIPMDH1, RsMAM1a, RsMAM1b, RsCYP79F1, RsGSTF9, RsGGP1, RsSUR1, RsUGT74C1, RsST5b, RsAPK1, RsGSL-OH, and RsMYB28) were significantly higher co-expressed in the high content genotypes than in low content genotype. Notably, correlation analysis indicated that the expression level of RsMYB28, as an R2R3 transcription factor directly regulating aliphatic glucosinolate biosynthesis, was positively correlated with the GRH content. Co-expression network showed that RsMYB28 probably positively regulated the expression of the above genes, particularly RsSUR1, and consequently the synthesis of GRH. Moreover, the molecular mechanism of the accumulation of this 4-carbon (4C) GSL in radish taproots was explored. This study provides new perspectives on the GSLs accumulation mechanism and genetic improvements in radish taproots.
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Pacifico D, Lanzanova C, Pagnotta E, Bassolino L, Mastrangelo AM, Marone D, Matteo R, Lo Scalzo R, Balconi C. Sustainable Use of Bioactive Compounds from Solanum Tuberosum and Brassicaceae Wastes and by-Products for Crop Protection-A Review. Molecules 2021; 26:2174. [PMID: 33918886 PMCID: PMC8070479 DOI: 10.3390/molecules26082174] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Revised: 03/31/2021] [Accepted: 04/01/2021] [Indexed: 12/24/2022] Open
Abstract
Defatted seed meals of oleaginous Brassicaceae, such as Eruca sativa, and potato peel are excellent plant matrices to recover potentially useful biomolecules from industrial processes in a circular strategy perspective aiming at crop protection. These biomolecules, mainly glycoalkaloids and phenols for potato and glucosinolates for Brassicaceae, have been proven to be effective against microbes, fungi, nematodes, insects, and even parasitic plants. Their role in plant protection is overviewed, together with the molecular basis of their synthesis in plant, and the description of their mechanisms of action. Possible genetic and biotechnological strategies are presented to increase their content in plants. Genetic mapping and identification of closely linked molecular markers are useful to identify the loci/genes responsible for their accumulation and transfer them to elite cultivars in breeding programs. Biotechnological approaches can be used to modify their allelic sequence and enhance the accumulation of the bioactive compounds. How the global challenges, such as reducing agri-food waste and increasing sustainability and food safety, could be addressed through bioprotector applications are discussed here.
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Affiliation(s)
- Daniela Pacifico
- CREA Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, 00198 Rome, Italy; (C.L.); (E.P.); (L.B.); (A.M.M.); (D.M.); (C.B.); (R.M.)
| | - Chiara Lanzanova
- CREA Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, 00198 Rome, Italy; (C.L.); (E.P.); (L.B.); (A.M.M.); (D.M.); (C.B.); (R.M.)
| | - Eleonora Pagnotta
- CREA Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, 00198 Rome, Italy; (C.L.); (E.P.); (L.B.); (A.M.M.); (D.M.); (C.B.); (R.M.)
| | - Laura Bassolino
- CREA Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, 00198 Rome, Italy; (C.L.); (E.P.); (L.B.); (A.M.M.); (D.M.); (C.B.); (R.M.)
| | - Anna Maria Mastrangelo
- CREA Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, 00198 Rome, Italy; (C.L.); (E.P.); (L.B.); (A.M.M.); (D.M.); (C.B.); (R.M.)
| | - Daniela Marone
- CREA Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, 00198 Rome, Italy; (C.L.); (E.P.); (L.B.); (A.M.M.); (D.M.); (C.B.); (R.M.)
| | - Roberto Matteo
- CREA Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, 00198 Rome, Italy; (C.L.); (E.P.); (L.B.); (A.M.M.); (D.M.); (C.B.); (R.M.)
| | - Roberto Lo Scalzo
- CREA Council for Agricultural Research and Economics—Research Centre for Engineering and Agro-Food Processing, 00198 Rome, Italy;
| | - Carlotta Balconi
- CREA Council for Agricultural Research and Economics—Research Centre for Cereal and Industrial Crops, 00198 Rome, Italy; (C.L.); (E.P.); (L.B.); (A.M.M.); (D.M.); (C.B.); (R.M.)
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Kobayashi H, Shirasawa K, Fukino N, Hirakawa H, Akanuma T, Kitashiba H. Identification of genome-wide single-nucleotide polymorphisms among geographically diverse radish accessions. DNA Res 2021; 27:5739440. [PMID: 32065621 PMCID: PMC7315352 DOI: 10.1093/dnares/dsaa001] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 02/11/2020] [Indexed: 11/24/2022] Open
Abstract
Radish (Raphanus sativus L.) is cultivated around the world as a vegetable crop and exhibits diverse morphological and physiological features. DNA polymorphisms are responsible for differences in traits among cultivars. In this study, we determined genome-wide single-nucleotide polymorphisms (SNPs) among geographically diverse radish accessions using the double-digest restriction site-associated DNA sequencing (ddRAD-Seq) method. A total of 52,559 SNPs was identified in a collection of over 500 radish accessions (cultivated and wild) from East Asia, South and Southeast Asia, and the Occident and Near East. In addition, 2,624 SNP sites without missing data (referred to as common SNP sites) were identified among 510 accessions. Genetic diversity analyses, based on the common SNP sites, divided the cultivated radish accessions into four main groups, each derived from four geographical areas (Japan, East Asia, South and Southeast Asia, and the Occident and Near East). Furthermore, we discuss the origin of cultivated radish and its migration from the West to East Asia. SNP data generated in this work will facilitate further genetic studies on the radish breeding and production of DNA markers.
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Affiliation(s)
- Hiroto Kobayashi
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 980-8572, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Nobuko Fukino
- Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu 514-2392, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, Kazusa-kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Takashi Akanuma
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 980-8572, Japan
| | - Hiroyasu Kitashiba
- Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai 980-8572, Japan
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Kim K, Kang Y, Lee SJ, Choi SH, Jeon DH, Park MY, Park S, Lim YP, Kim C. Quantitative Trait Loci (QTLs) Associated with Microspore Culture in Raphanus sativus L. (Radish). Genes (Basel) 2020; 11:genes11030337. [PMID: 32245207 PMCID: PMC7141118 DOI: 10.3390/genes11030337] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 03/19/2020] [Accepted: 03/20/2020] [Indexed: 11/25/2022] Open
Abstract
The radish is a highly self-incompatible plant, and consequently it is difficult to produce homozygous lines. Bud pollination in cross-fertilization plants should be done by opening immature pollen and attaching pollen to mature flowers. It accordingly takes a lot of time and effort to develop lines with fixed alleles. In the current study, a haploid breeding method has been applied to obtain homozygous plants in a short period of time by doubling chromosomes through the induction of a plant body in the haploid cells, in order to shorten the time to breed inbred lines. We constructed genetic maps with an F1 population derived by crossing parents that show a superior and inferior ability to regenerate microspores, respectively. Genetic maps were constructed from the maternal and parental maps, separately, using the two-way pseudo-testcross model. The phenotype of the regeneration rate was examined by microspore cultures and a quantitative trait loci (QTL) analysis was performed based on the regeneration rate. From the results of the culture of microspores in the F1 population, more than half of the group did not regenerate, and only a few showed a high regeneration rate. A total of five significant QTLs were detected in the F1 population, and five candidate genes were found based on the results. These candidate genes are divided into two classes, and appear to be related to either PRC2 subunits or auxin synthesis.
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Affiliation(s)
- Kyeongmin Kim
- Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea; (K.K.); (Y.K.); (S.-J.L.); (S.-H.C.); (D.-H.J.)
| | - Yuna Kang
- Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea; (K.K.); (Y.K.); (S.-J.L.); (S.-H.C.); (D.-H.J.)
| | - Sol-Ji Lee
- Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea; (K.K.); (Y.K.); (S.-J.L.); (S.-H.C.); (D.-H.J.)
| | - Se-Hyun Choi
- Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea; (K.K.); (Y.K.); (S.-J.L.); (S.-H.C.); (D.-H.J.)
| | - Dong-Hyun Jeon
- Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea; (K.K.); (Y.K.); (S.-J.L.); (S.-H.C.); (D.-H.J.)
| | - Min-Young Park
- National Institute of Horticultural & Herbal Science, Rural Development Administration (RDA), Wanju 55365, Korea; (M.-Y.P.); (S.P.)
| | - Suhyoung Park
- National Institute of Horticultural & Herbal Science, Rural Development Administration (RDA), Wanju 55365, Korea; (M.-Y.P.); (S.P.)
| | - Yong Pyo Lim
- Department of Horticultural Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea;
| | - Changsoo Kim
- Department of Crop Science, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea; (K.K.); (Y.K.); (S.-J.L.); (S.-H.C.); (D.-H.J.)
- Department of Smart Agriculture Systems, College of Agricultural and Life Sciences, Chungnam National University, Daejeon 34134, Korea
- Correspondence: ; Tel.: +82-42-821-5729
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Yu X, Lu L, Ma Y, Chhapekar SS, Yi SY, Lim YP, Choi SR. Fine-mapping of a major QTL (Fwr1) for fusarium wilt resistance in radish. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:329-340. [PMID: 31686113 DOI: 10.1007/s00122-019-03461-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 10/15/2019] [Indexed: 06/10/2023]
Abstract
A major radish QTL (Fwr1) for fusarium wilt resistance was fine-mapped. Sequence and expression analyses suggest that a gene encoding a serine/arginine-rich protein kinase is a candidate gene for Fwr1. Fusarium wilt resistance locus 1 (Fwr1) is a major quantitative trait locus (QTL) mediating the resistance of radish inbred line 'B2' to Fusarium oxysporum, which is responsible for fusarium wilt. We previously detected Fwr1 on radish linkage group 3 (i.e., chromosome 5). In this study, a high-resolution genetic map of the Fwr1 locus was constructed by analyzing 354 recombinant F2 plants derived from a cross between 'B2' and '835', the latter of which is susceptible to fusarium wilt. The Fwr1 QTL was fine-mapped to a 139.8-kb region between markers FM82 and FM87 in the middle part of chromosome 5. Fifteen candidate genes were predicted in this region based on a sequence comparison with the 'WK10039' radish reference genome. Additionally, we examined the time-course expression patterns of these predicted genes following an infection by the fusarium wilt pathogen. The ORF4 expression level was significantly higher in the resistant 'B2' plants than in the susceptible '835' plants. The ORF4 sequence was predicted to encode a serine/arginine-rich protein kinase and includes SNPs that result in nonsynonymous mutations, which may have important functional consequences. This study reveals a novel gene responsible for fusarium wilt resistance in radish. Further analyses of this gene may elucidate the molecular mechanisms underlying the fusarium wilt resistance of plants.
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Affiliation(s)
- Xiaona Yu
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
- Agronomy Department, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Lu Lu
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - Yinbo Ma
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - Sushil Satish Chhapekar
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - So Young Yi
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea
| | - Su Ryun Choi
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon, Korea.
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Luo X, Xu L, Wang Y, Dong J, Chen Y, Tang M, Fan L, Zhu Y, Liu L. An ultra-high-density genetic map provides insights into genome synteny, recombination landscape and taproot skin colour in radish (Raphanus sativus L.). PLANT BIOTECHNOLOGY JOURNAL 2020; 18:274-286. [PMID: 31218798 PMCID: PMC6920339 DOI: 10.1111/pbi.13195] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 05/30/2019] [Accepted: 06/11/2019] [Indexed: 05/19/2023]
Abstract
High-density genetic map is a valuable tool for exploring novel genomic information, quantitative trait locus (QTL) mapping and gene discovery of economically agronomic traits in plant species. However, high-resolution genetic map applied to tag QTLs associated with important traits and to investigate genomic features underlying recombination landscape in radish (Raphanus sativus) remains largely unexplored. In this study, an ultra-high-density genetic map with 378 738 SNPs covering 1306.8 cM in nine radish linkage groups (LGs) was developed by a whole-genome sequencing-based approach. A total of 18 QTLs for 11 horticulture traits were detected. The map-based cloning data indicated that the R2R3-MYB transcription factor RsMYB90 was a crucial candidate gene determining the taproot skin colour. Comparative genomics analysis among radish, Brassica rapa and B. oleracea genome revealed several genomic rearrangements existed in the radish genome. The highly uneven distribution of recombination was observed across the nine radish chromosomes. Totally, 504 recombination hot regions (RHRs) were enriched near gene promoters and terminators. The recombination rate in RHRs was positively correlated with the density of SNPs and gene, and GC content, respectively. Functional annotation indicated that genes within RHRs were mainly involved in metabolic process and binding. Three QTLs for three traits were found in the RHRs. The results provide novel insights into the radish genome evolution and recombination landscape, and facilitate the development of effective strategies for molecular breeding by targeting and dissecting important traits in radish.
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Affiliation(s)
- Xiaobo Luo
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
- Guizhou Institute of BiotechnologyGuizhou Academy of Agricultural SciencesGuiyangChina
| | | | - Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Junhui Dong
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Yinglong Chen
- The UWA Institute of Agriculture, and School of Agriculture and EnvironmentThe University of Western AustraliaPerthWAAustralia
| | - Mingjia Tang
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Lianxue Fan
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Yuelin Zhu
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Liwang Liu
- National Key Laboratory of Crop Genetics and Germplasm EnhancementKey Laboratory of Horticultural Crop Biology and Genetic Improvement (East China) of MOA, College of HorticultureNanjing Agricultural UniversityNanjingChina
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Nugroho ABD, Han N, Pervitasari AN, Kim DH, Kim J. Differential expression of major genes involved in the biosynthesis of aliphatic glucosinolates in intergeneric Baemoochae (Brassicaceae) and its parents during development. PLANT MOLECULAR BIOLOGY 2020; 102:171-184. [PMID: 31792713 DOI: 10.1007/s11103-019-00939-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/26/2019] [Indexed: 06/10/2023]
Abstract
Thus study found the temporal and spatial relationship between production of aliphatic glucosinolate compounds and the expression profile of glucosinolate-related genes during growth and development in radish, Chinese cabbage, and their intergeneric hybrid baemoochae plants. Glucosinolates (GSLs) are one of major bioactive compounds in Brassicaceae plants. GSLs play a role in defense against microbes as well as chemo-preventative activity against cancer, which draw attentions from plant scientists. We investigated the temporal relationship between production of aliphatic Glucosinolate (GSLs) compounds and the expression profile of GSL related genes during growth and development in radish, Chinese cabbage, and their intergeneric hybrid, baemoochae. Over the complete life cycle, Glucoraphasatin (GRH) and glucoraphanin (GRE) predominated in radish, whereas gluconapin (GNP), glucobrassicanapin (GBN), and glucoraphanin (GRA) abounded in Chinese cabbage. Baemoochae contained intermediate levels of all GSLs studied, indicating inheritance from both radish and Chinese cabbage. Expression patterns of BCAT4, CYP79F1, CYP83A1, UGT74B1, GRS1, FMOgs-ox1, and AOP2 genes showed a correlation to their corresponding encoded proteins in radish, Chinese cabbage, and baemoochae. Interestingly, there is a sharp change in gene expression pattern involved in side chain modification, particularly GRS1, FMOgs-ox1, and AOP2, among these plants during the vegetative and reproductive stage. For instance, the GRS1 was strongly expressed during leaf development, while both of FMOgs-ox1 and AOP2 was manifested high in floral tissues. Furthermore, expression of GRS1 gene which is responsible for GRH production was predominantly expressed in leaf tissues of radish and baemoochae, whereas it was only slightly detected in Chinese cabbage root tissue, explaining why radish has an abundance of GRH compared to other Brassica plants. Altogether, our comprehensive and comparative data proved that aliphatic GSLs biosynthesis is dynamically and precisely regulated in a tissue- and development-dependent manner in Brassicaceae family members.
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Affiliation(s)
- Adji Baskoro Dwi Nugroho
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | - Narae Han
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea
| | | | - Dong-Hwan Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea.
| | - Jongkee Kim
- Department of Plant Science and Technology, Chung-Ang University, Anseong, 17546, Republic of Korea.
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Transcriptome analysis for identifying possible gene regulations during maize root emergence and formation at the initial growth stage. Genes Genomics 2018; 40:755-766. [PMID: 29934814 DOI: 10.1007/s13258-018-0687-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 03/15/2018] [Indexed: 10/17/2022]
Abstract
The root plays an important role during plant development and growth, i.e., the plant body maintenance, nutrient storage, absorption of water, oxygen and nutrient from the soil, and storage of water and carbohydrates, etc. The objective of this study was attempted to determine root-specific genes at the initial developmental stages of maize by using network-based transcriptome analysis. The raw data obtained using RNA-seq were filtered for quality control of the reads with the FASTQC tool, and the filtered reads were pre-proceed using the TRIMMOMATIC tool. The enriched BINs of the DEGs were detected using PageMan analysis with the ORA_FISHER statistical test, and genes were assigned to metabolic pathways by using the MapMan tool, which was also used for detecting transcription factors (TFs). For reconstruction of the co-expression network, we used the algorithm for the reconstruction of accurate cellular networks (ARACNE) in the R package, and then the reconstructed co-expression network was visualized using the Cytoscape tool. RNA-seq. was performed using maize shoots and roots at different developmental stages of root emergence (6-10 days after planting, VE) and 1 week after plant emergence (V2). A total of 1286 differentially expressed genes (DEGs) were detected in both tissues. Many DEGs involved in metabolic pathways exhibited altered mRNA levels between VE and V2. In addition, we observed gene expression changes for 113 transcription factors and found five enriched cis-regulatory elements in the 1-kb upstream regions of both DEGs. The network-based transcriptome analysis showed two modules as co-expressed gene clusters differentially expressed between the shoots and roots during plant development. The DEGs of one module exhibited gene expressional coherence in the maize root tips, suggesting that their functional relationships are associated with the initial developmental stage of the maize root. Finally, we confirmed reliable mRNA levels of the hub genes in the potential sub-network related to initial root development at the different developmental stages of VE, V2, and 2 weeks after plant emergence.
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Kumar S, Knox RE, Singh AK, DePauw RM, Campbell HL, Isidro-Sanchez J, Clarke FR, Pozniak CJ, N’Daye A, Meyer B, Sharpe A, Ruan Y, Cuthbert RD, Somers D, Fedak G. High-density genetic mapping of a major QTL for resistance to multiple races of loose smut in a tetraploid wheat cross. PLoS One 2018; 13:e0192261. [PMID: 29485999 PMCID: PMC5828438 DOI: 10.1371/journal.pone.0192261] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Accepted: 01/19/2018] [Indexed: 11/28/2022] Open
Abstract
Loose smut, caused by Ustilago tritici (Pers.) Rostr., is a systemic disease of tetraploid durum wheat (Triticum turgidum L.). Loose smut can be economically controlled by growing resistant varieties, making it important to find and deploy new sources of resistance. Blackbird, a variety of T. turgidum L. subsp. carthlicum (Nevski) A. Love & D. Love, carries a high level of resistance to loose smut. Blackbird was crossed with the loose smut susceptible durum cultivar Strongfield to produce a doubled haploid (DH) mapping population. The parents and progenies were inoculated with U. tritici races T26, T32 and T33 individually and as a mixture at Swift Current, Canada in 2011 and 2012 and loose smut incidence (LSI) was assessed. Genotyping of the DH population and parents using an Infinium iSelect 90K single nucleotide polymorphism (SNP) array identified 12,952 polymorphic SNPs. The SNPs and 426 SSRs (previously genotyped in the same population) were mapped to 16 linkage groups spanning 3008.4 cM at an average inter-marker space of 0.2 cM in a high-density genetic map. Composite interval mapping analysis revealed three significant quantitative trait loci (QTL) for loose smut resistance on chromosomes 3A, 6B and 7A. The loose smut resistance QTL on 6B (QUt.spa-6B.2) and 7A (QUt.spa-7A.2) were derived from Blackbird. Strongfield contributed the minor QTL on 3A (QUt.spa-3A.2). The resistance on 6B was a stable major QTL effective against all individual races and the mixture of the three races; it explained up to 74% of the phenotypic variation. This study is the first attempt in durum wheat to identify and map loose smut resistance QTL using a high-density genetic map. The QTL QUt.spa-6B.2 would be an effective source for breeding resistance to multiple races of the loose smut pathogen because it provides near-complete broad resistance to the predominant virulence on the Canadian prairies.
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Affiliation(s)
- Sachin Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut, Uttar Pradesh, India
- * E-mail: (RK); (SK)
| | - Ron E. Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
- * E-mail: (RK); (SK)
| | - Asheesh K. Singh
- 1501 Agronomy Hall, Iowa State University, Ames, Iowa, United States of America
| | - Ron M. DePauw
- Advancing Wheat Technology, Swift Current, Saskatchewan, Canada
| | - Heather L. Campbell
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - Julio Isidro-Sanchez
- School of Agriculture and Food Science, University College Dublin, Belfield, Dublin, Ireland
| | - Fran R. Clarke
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - Curtis J. Pozniak
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Amidou N’Daye
- Department of Plant Sciences and Crop Development Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Brad Meyer
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - Andrew Sharpe
- Global Institute of Food Security, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - Richard D. Cuthbert
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, Saskatchewan, Canada
| | - Daryl Somers
- Vineland Research and Innovation Centre, Vineland Station, Ontario, Canada
| | - George Fedak
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, Ontario, Canada
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13
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Kakizaki T, Kitashiba H, Zou Z, Li F, Fukino N, Ohara T, Nishio T, Ishida M. A 2-Oxoglutarate-Dependent Dioxygenase Mediates the Biosynthesis of Glucoraphasatin in Radish. PLANT PHYSIOLOGY 2017; 173:1583-1593. [PMID: 28100450 PMCID: PMC5338677 DOI: 10.1104/pp.16.01814] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 01/16/2017] [Indexed: 05/22/2023]
Abstract
Glucosinolates (GSLs) are secondary metabolites whose degradation products confer intrinsic flavors and aromas to Brassicaceae vegetables. Several structures of GSLs are known in the Brassicaceae, and the biosynthetic pathway and regulatory networks have been elucidated in Arabidopsis (Arabidopsis thaliana). GSLs are precursors of chemical defense substances against herbivorous pests. Specific GSLs can act as feeding blockers or stimulants, depending on the pest species. Natural selection has led to diversity in the GSL composition even within individual species. However, in radish (Raphanus sativus), glucoraphasatin (4-methylthio-3-butenyl glucosinolate) accounts for more than 90% of the total GSLs, and little compositional variation is observed. Because glucoraphasatin is not contained in other members of the Brassicaceae, like Arabidopsis and cabbage (Brassica oleracea), the biosynthetic pathways for glucoraphasatin remain unclear. In this report, we identified and characterized a gene encoding GLUCORAPHASATIN SYNTHASE 1 (GRS1) by genetic mapping using a mutant that genetically lacks glucoraphasatin. Transgenic Arabidopsis, which overexpressed GRS1 cDNA, accumulated glucoraphasatin in the leaves. GRS1 encodes a 2-oxoglutarate-dependent dioxygenase, and it is abundantly expressed in the leaf. To further investigate the biosynthesis and transportation of GSLs in radish, we grafted a grs1 plant onto a wild-type plant. The grafting experiment revealed a leaf-to-root long-distance glucoraphasatin transport system in radish and showed that the composition of GSLs differed among the organs. Based on these observations, we propose a characteristic biosynthesis pathway for glucoraphasatin in radish. Our results should be useful in metabolite engineering for breeding of high-value vegetables.
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Affiliation(s)
- Tomohiro Kakizaki
- Division of Vegetable Breeding, Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu, Mie 514-2392, Japan (T.K., N.F., T.O., M.I.);
- and Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845, Japan (H.K., Z.Z., F.L., T.N.)
| | - Hiroyasu Kitashiba
- Division of Vegetable Breeding, Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu, Mie 514-2392, Japan (T.K., N.F., T.O., M.I.)
- and Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845, Japan (H.K., Z.Z., F.L., T.N.)
| | - Zhongwei Zou
- Division of Vegetable Breeding, Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu, Mie 514-2392, Japan (T.K., N.F., T.O., M.I.)
- and Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845, Japan (H.K., Z.Z., F.L., T.N.)
| | - Feng Li
- Division of Vegetable Breeding, Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu, Mie 514-2392, Japan (T.K., N.F., T.O., M.I.)
- and Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845, Japan (H.K., Z.Z., F.L., T.N.)
| | - Nobuko Fukino
- Division of Vegetable Breeding, Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu, Mie 514-2392, Japan (T.K., N.F., T.O., M.I.)
- and Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845, Japan (H.K., Z.Z., F.L., T.N.)
| | - Takayoshi Ohara
- Division of Vegetable Breeding, Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu, Mie 514-2392, Japan (T.K., N.F., T.O., M.I.)
- and Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845, Japan (H.K., Z.Z., F.L., T.N.)
| | - Takeshi Nishio
- Division of Vegetable Breeding, Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu, Mie 514-2392, Japan (T.K., N.F., T.O., M.I.)
- and Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845, Japan (H.K., Z.Z., F.L., T.N.)
| | - Masahiko Ishida
- Division of Vegetable Breeding, Institute of Vegetable and Floriculture Science, NARO, Ano, Tsu, Mie 514-2392, Japan (T.K., N.F., T.O., M.I.)
- and Graduate School of Agricultural Science, Tohoku University, Aoba-ku, Sendai, Miyagi 980-0845, Japan (H.K., Z.Z., F.L., T.N.)
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14
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Identification of a nuclear-recessive gene locus for male sterility on A2 chromosome using the Brassica 60 K SNP array in non-heading Chinese cabbage. Genes Genomics 2016. [DOI: 10.1007/s13258-016-0459-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Recent Perspective of Next Generation Sequencing: Applications in Molecular Plant Biology and Crop Improvement. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s40011-016-0770-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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16
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Sharma S, Shrivastava N. Renaissance in phytomedicines: promising implications of NGS technologies. PLANTA 2016; 244:19-38. [PMID: 27002972 DOI: 10.1007/s00425-016-2492-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 02/19/2016] [Indexed: 06/05/2023]
Abstract
Medicinal plant research is growing significantly in faith to discover new and more biologically compatible phytomedicines. Deposition of huge genome/trancriptome sequence data assisted by NGS technologies has revealed the new possibilities for producing upgraded bioactive molecules in medicinal plants. Growing interest of investors and consumers in the herbal drugs raises the need for extensive research to open the facts and details of every inch of life canvas of medicinal plants to produce improved quality of phytomedicines. As in agriculture crops, knowledge emergence from medicinal plant's genome/transcriptome, can be used to assure their amended quality and these improved varieties are then transported to the fields for cultivation. Genome studies generate huge sequence data which can be exploited further for obtaining information regarding genes/gene clusters involved in biosynthesis as well as regulation. This can be achieved rapidly at a very large scale with NGS platforms. Identification of new RNA molecules has become possible, which can lead to the discovery of novel compounds. Sequence information can be combined with advanced phytochemical and bioinformatics tools to discover functional herbal drugs. Qualitative and quantitative analysis of small RNA species put a light on the regulatory aspect of biosynthetic pathways for phytomedicines. Inter or intra genomic as well as transcriptomic interactive processes for biosynthetic pathways can be elucidated in depth. Quality management of herbal material will also become rapid and high throughput. Enrichment of sequence information will be used to engineer the plants to get more efficient phytopharmaceuticals. The present review comprises of role of NGS technologies to boost genomic studies of pharmaceutically important plants and further, applications of sequence information aiming to produce enriched phytomedicines. Emerging knowledge from the medicinal plants genome/transcriptome can give birth to deep understanding of the processes responsible for biosynthesis of medicinally important compounds.
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Affiliation(s)
- Sonal Sharma
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India
- Nirma University, Ahmedabad, Gujarat, India
| | - Neeta Shrivastava
- B.V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Sarkhej - Gandhinagar Highway, Ahmedabad, Gujarat, India.
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17
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Seo MS, Jin M, Chun JH, Kim SJ, Park BS, Shon SH, Kim JS. Functional analysis of three BrMYB28 transcription factors controlling the biosynthesis of glucosinolates in Brassica rapa. PLANT MOLECULAR BIOLOGY 2016; 90:503-16. [PMID: 26820138 PMCID: PMC4766241 DOI: 10.1007/s11103-016-0437-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 01/09/2016] [Indexed: 05/09/2023]
Abstract
Glucosinolates (GSLs) are secondary metabolites that have anticarcinogenic activity and play defense roles in plants of the Brassicaceae family. MYB28 is known as a transcription factor that regulates aliphatic GSL biosynthesis in Arabidopsis thaliana. Brassicaceae plants have three orthologous copies of AtMYB28 derived from recent genome triplication. These BrMYB28 genes have a high level of sequence homology, with 81-87% similarities in the coding DNA sequence compared to Arabidopsis. Overexpression of three paralogous BrMYB28 genes in transgenic Chinese cabbage increased the total GSL content in all T1 generation plants and in two inbred lines of homozygous T2 plants. The highest total GSL contents were detected in homozygous T2 lines overexpressing BrMYB28.1, which showed an approximate fivefold increase compared to that of nontransgenic plants. The homozygous T2 lines with overexpressed BrMYB28.1 also showed an increased content of aliphatic, indolic, and aromatic GSLs compared to that of nontransgenic plants. Furthermore, all of the three BrMYB28 genes were identified as negative regulators of BrAOP2 and positive regulators of BrGSL-OH in the homozygous T2 lines. These data indicate the regulatory mechanism of GSL biosynthesis in B. rapa is unlike that in A. thaliana. Our results will provide useful information for elucidating the regulatory mechanism of GSL biosynthesis in polyploid plants.
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Affiliation(s)
- Mi-Suk Seo
- Genomics Division, Department of Agricultural Bio-resources, National Academy of Agricultural Science, Rural Development Administration (RDA), Wansan-gu, Jeonju, Korea.
| | - Mina Jin
- Genomics Division, Department of Agricultural Bio-resources, National Academy of Agricultural Science, Rural Development Administration (RDA), Wansan-gu, Jeonju, Korea.
| | - Jin-Hyuk Chun
- Department of Biological Environment and Chemistry, College of Agriculture and Life Science, Chungnam National University, Yuseong-gu, Daejeon, Korea.
| | - Sun-Ju Kim
- Department of Biological Environment and Chemistry, College of Agriculture and Life Science, Chungnam National University, Yuseong-gu, Daejeon, Korea.
| | - Beom-Seok Park
- Genomics Division, Department of Agricultural Bio-resources, National Academy of Agricultural Science, Rural Development Administration (RDA), Wansan-gu, Jeonju, Korea.
| | - Seong-Han Shon
- Genomics Division, Department of Agricultural Bio-resources, National Academy of Agricultural Science, Rural Development Administration (RDA), Wansan-gu, Jeonju, Korea.
| | - Jung Sun Kim
- Genomics Division, Department of Agricultural Bio-resources, National Academy of Agricultural Science, Rural Development Administration (RDA), Wansan-gu, Jeonju, Korea.
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18
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Recent advances in molecular marker techniques: Insight into QTL mapping, GWAS and genomic selection in plants. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s12892-015-0037-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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19
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Zhang W, Kwon ST, Chen F, Kliebenstein DJ. Isolate Dependency of Brassica rapa Resistance QTLs to Botrytis cinerea. FRONTIERS IN PLANT SCIENCE 2016; 7:161. [PMID: 26925079 PMCID: PMC4756292 DOI: 10.3389/fpls.2016.00161] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 01/30/2016] [Indexed: 05/04/2023]
Abstract
Generalist necrotrophic pathogens including Botrytis cinerea cause significant yield and financial losses on Brassica crops. However, there is little knowledge about the mechanisms underlying the complex interactions encoded by both host and pathogen genomes in this interaction. This potentially includes multiple layers of plant defense and pathogen virulence mechanisms that could complicate in breeding broad spectrum resistance within Brassica species. Glucosinolates (GSLs) are a diverse group of defense metabolites that play a key role in interaction between Brassica and biotic attackers. In this study, we utilized a collection of diverse B. cinerea isolates to investigate resistance within the Brassica rapa R500 × IMB211 recombinant inbred line population. We tested variation on lesion development and glucosinolate accumulation in parental lines and all population lines. We then mapped quantitative trait loci (QTL) for both resistances to B. cinerea and defense metabolites in this population. Phenotypic analysis and QTL mapping demonstrate that the genetic basis of resistance to B. cinerea in B. rapa is isolate specific and polygenic with transgressive segregation that both parents contribute resistance alleles. QTLs controlling defensive GSLs are highly dependent on pathogen infection. An overlap of two QTLs identified between resistance to B. cinerea and defense metabolites also showed isolate specific effects. This work suggests that directly searching for resistance loci may not be the best approach at improving resistance in B. rapa to necrotrophic pathogen.
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Affiliation(s)
- Wei Zhang
- Department of Plant Sciences, University of California, Davis, DavisCA, USA
- National and Local Joint Engineering Laboratory for Energy Plant Bio-oil Production and Application, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan UniversityChengdu, China
| | - Soon-Tae Kwon
- Department of Plant Sciences, University of California, Davis, DavisCA, USA
- Department of Horticulture and Breeding, Andong National UniversityAndong, South Korea
| | - Fang Chen
- National and Local Joint Engineering Laboratory for Energy Plant Bio-oil Production and Application, Key Laboratory of Bio-resource and Eco-environment, Ministry of Education, College of Life Sciences, Sichuan UniversityChengdu, China
| | - Daniel J. Kliebenstein
- Department of Plant Sciences, University of California, Davis, DavisCA, USA
- DynaMo Center of Excellence, University of CopenhagenCopenhagen, Denmark
- *Correspondence: Daniel J. Kliebenstein,
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20
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Yu X, Choi SR, Dhandapani V, Rameneni JJ, Li X, Pang W, Lee JY, Lim YP. Quantitative Trait Loci for Morphological Traits and their Association with Functional Genes in Raphanus sativus. FRONTIERS IN PLANT SCIENCE 2016; 7:255. [PMID: 26973691 PMCID: PMC4777717 DOI: 10.3389/fpls.2016.00255] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 02/15/2016] [Indexed: 05/04/2023]
Abstract
Identification of quantitative trait loci (QTLs) governing morphologically important traits enables to comprehend their potential genetic mechanisms in the genetic breeding program. In this study, we used 210 F2 populations derived from a cross between two radish inbred lines (Raphanus sativus) "835" and "B2," including 258 SSR markers were used to detect QTLs for 11 morphological traits that related to whole plant, leaf, and root yield in 3 years of replicated field test. Total 55 QTLs were detected which were distributed on each linkage group of the Raphanus genome. Individual QTLs accounted for 2.69-12.6 of the LOD value, and 0.82-16.25% of phenotypic variation. Several genomic regions have multiple traits that clustered together, suggested the existence of pleiotropy linkage. Synteny analysis of the QTL regions with A. thaliana genome selected orthologous genes in radish. InDels and SNPs in the parental lines were detected in those regions by Illumina genome sequence. Five identified candidate gene-based markers were validated by co-mapping with underlying QTLs affecting different traits. Semi-quantitative reverse transcriptase PCR analysis showed the different expression levels of these five genes in parental lines. In addition, comparative QTL analysis with B. rapa revealed six common QTL regions and four key major evolutionarily conserved crucifer blocks (J, U, R, and W) harboring QTL for morphological traits. The QTL positions identified in this study will provide a valuable resource for identifying more functional genes when whole radish genome sequence is released. Candidate genes identified in this study that co-localized in QTL regions are expected to facilitate in radish breeding programs.
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Affiliation(s)
- Xiaona Yu
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National UniversityDaejeon, South Korea
| | - Su Ryun Choi
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National UniversityDaejeon, South Korea
| | - Vignesh Dhandapani
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National UniversityDaejeon, South Korea
| | - Jana Jeevan Rameneni
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National UniversityDaejeon, South Korea
| | - Xiaonan Li
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National UniversityDaejeon, South Korea
| | - Wenxing Pang
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National UniversityDaejeon, South Korea
| | - Ji-Young Lee
- School of Biological Sciences, College of Natural Science, Seoul National UniversitySeoul, South Korea
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National UniversityDaejeon, South Korea
- *Correspondence: Yong Pyo Lim
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21
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Ishida M, Kakizaki T, Morimitsu Y, Ohara T, Hatakeyama K, Yoshiaki H, Kohori J, Nishio T. Novel glucosinolate composition lacking 4-methylthio-3-butenyl glucosinolate in Japanese white radish (Raphanus sativus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2037-2046. [PMID: 26152572 DOI: 10.1007/s00122-015-2564-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2015] [Accepted: 06/13/2015] [Indexed: 06/04/2023]
Abstract
Genetic analysis and gene mapping of the 4-methylthio-3-butenyl glucosinolate-less trait of white radish were performed and a white radish cultivar with new glucosinolate composition was developed. A spontaneous mutant having significantly low 4-methylthio-3-butenyl glucosinolate (4MTB-GSL) content was identified from a landrace of Japanese white radish (Raphanus sativus L.) through intensive evaluation of glucosinolate profiles of 632 lines including genetic resources and commercial cultivars using high-performance liquid chromatography (HPLC) analysis. A line lacking 4MTB-GSL was developed using the selected mutant as a gene source. Genetic analyses of F1, F2, and BC1F1 populations of this line suggested that the 4MTB-GSL-less trait is controlled by a single recessive allele. Using SNP and SCAR markers, 96 F2 plants were genotyped, and a linkage map having nine linkage groups with a total map distance of 808.3 cM was constructed. A gene responsible for the 4MTB-GSL-less trait was mapped between CL1753 and CL5895 at the end of linkage group 1. The genetic distance between these markers was 4.2 cM. By selfing and selection of plants lacking 4MTB-GSL, a new cultivar, 'Daikon parental line No. 5', was successfully developed. This cultivar was characterized by glucoerucin, which accounted for more than 90% of the total glucosinolates (GSLs). The total GSL content in roots was ca. 12 μmol/g DW, significantly lower than those in common white radish cultivars. Significance of this line in radish breeding is discussed.
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Affiliation(s)
- Masahiko Ishida
- NARO Institute of Vegetable and Tea Science, Tsukuba Vegetable Research Station, 3-1-1 Kannondai, Tsukuba, 305-8666, Japan
| | - Tomohiro Kakizaki
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Yasujiro Morimitsu
- The Department of Food and Nutritional Sciences, The Graduate School of Humanities and Sciences, Ochanomizu University, 2-1-1 Otsuka, Bunkyo-ku, Tokyo, 112-8610, Japan
| | - Takayoshi Ohara
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Katsunori Hatakeyama
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Hitoshi Yoshiaki
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Junna Kohori
- NARO Institute of Vegetable and Tea Science, 360 Kusawa, Ano, Tsu, Mie, 514-2392, Japan
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori Amamiya-machi, Aoba-ku, Sendai, Miyagi, 981-8555, Japan.
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22
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Mitsui Y, Shimomura M, Komatsu K, Namiki N, Shibata-Hatta M, Imai M, Katayose Y, Mukai Y, Kanamori H, Kurita K, Kagami T, Wakatsuki A, Ohyanagi H, Ikawa H, Minaka N, Nakagawa K, Shiwa Y, Sasaki T. The radish genome and comprehensive gene expression profile of tuberous root formation and development. Sci Rep 2015; 5:10835. [PMID: 26056784 PMCID: PMC4650646 DOI: 10.1038/srep10835] [Citation(s) in RCA: 103] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2015] [Accepted: 04/08/2015] [Indexed: 12/23/2022] Open
Abstract
Understanding the processes that regulate plant sink formation and development at the molecular level will contribute to the areas of crop breeding, food production and plant evolutionary studies. We report the annotation and analysis of the draft genome sequence of the radish Raphanus sativus var. hortensis (long and thick root radish) and transcriptome analysis during root development. Based on the hybrid assembly approach of next-generation sequencing, a total of 383 Mb (N50 scaffold: 138.17 kb) of sequences of the radish genome was constructed containing 54,357 genes. Syntenic and phylogenetic analyses indicated that divergence between Raphanus and Brassica coincide with the time of whole genome triplication (WGT), suggesting that WGT triggered diversification of Brassiceae crop plants. Further transcriptome analysis showed that the gene functions and pathways related to carbohydrate metabolism were prominently activated in thickening roots, particularly in cell proliferating tissues. Notably, the expression levels of sucrose synthase 1 (SUS1) were correlated with root thickening rates. We also identified the genes involved in pungency synthesis and their transcription factors.
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Affiliation(s)
- Yuki Mitsui
- Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Michihiko Shimomura
- Mitsubishi Space Software Co., Ltd., 1-6-1, Takezono, Tsukuba, Ibaraki 305-0032, Japan
| | - Kenji Komatsu
- Junior College of Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Nobukazu Namiki
- Mitsubishi Space Software Co., Ltd., 1-6-1, Takezono, Tsukuba, Ibaraki 305-0032, Japan
| | - Mari Shibata-Hatta
- Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Misaki Imai
- Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yuichi Katayose
- National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Yoshiyuki Mukai
- National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Hiroyuki Kanamori
- National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Kanako Kurita
- National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki, 305-8634, Japan
| | - Tsutomu Kagami
- Sakata Seed Corporation, 2-7-1, Nakamachidai, Tuzuki-ku, Yokohama, 224-0041, Japan
| | - Akihito Wakatsuki
- Sakata Seed Corporation, 2-7-1, Nakamachidai, Tuzuki-ku, Yokohama, 224-0041, Japan
| | - Hajime Ohyanagi
- Mitsubishi Space Software Co., Ltd., 1-6-1, Takezono, Tsukuba, Ibaraki 305-0032, Japan
| | - Hiroshi Ikawa
- Mitsubishi Space Software Co., Ltd., 1-6-1, Takezono, Tsukuba, Ibaraki 305-0032, Japan
| | - Nobuhiro Minaka
- 1] Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan [2] National Institute for Agro-Environmental Science, 3-1-3, Tukuba, 305-8604, Japan
| | - Kunihiro Nakagawa
- Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Yu Shiwa
- Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan
| | - Takuji Sasaki
- 1] Tokyo University of Agriculture, 1-1-1, Sakuragaoka, Setagaya-ku, Tokyo 156-8502, Japan [2] National Institute of Agrobiological Sciences, 1-2, Owashi, Tsukuba, Ibaraki, 305-8634, Japan
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Kitashiba H, Li F, Hirakawa H, Kawanabe T, Zou Z, Hasegawa Y, Tonosaki K, Shirasawa S, Fukushima A, Yokoi S, Takahata Y, Kakizaki T, Ishida M, Okamoto S, Sakamoto K, Shirasawa K, Tabata S, Nishio T. Draft sequences of the radish (Raphanus sativus L.) genome. DNA Res 2014; 21:481-90. [PMID: 24848699 PMCID: PMC4195494 DOI: 10.1093/dnares/dsu014] [Citation(s) in RCA: 136] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Radish (Raphanus sativus L., n = 9) is one of the major vegetables in Asia. Since the genomes of Brassica and related species including radish underwent genome rearrangement, it is quite difficult to perform functional analysis based on the reported genomic sequence of Brassica rapa. Therefore, we performed genome sequencing of radish. Short reads of genomic sequences of 191.1 Gb were obtained by next-generation sequencing (NGS) for a radish inbred line, and 76,592 scaffolds of ≥300 bp were constructed along with the bacterial artificial chromosome-end sequences. Finally, the whole draft genomic sequence of 402 Mb spanning 75.9% of the estimated genomic size and containing 61,572 predicted genes was obtained. Subsequently, 221 single nucleotide polymorphism markers and 768 PCR-RFLP markers were used together with the 746 markers produced in our previous study for the construction of a linkage map. The map was combined further with another radish linkage map constructed mainly with expressed sequence tag-simple sequence repeat markers into a high-density integrated map of 1,166 cM with 2,553 DNA markers. A total of 1,345 scaffolds were assigned to the linkage map, spanning 116.0 Mb. Bulked PCR products amplified by 2,880 primer pairs were sequenced by NGS, and SNPs in eight inbred lines were identified.
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Affiliation(s)
- Hiroyasu Kitashiba
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Feng Li
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Hideki Hirakawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Takahiro Kawanabe
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Zhongwei Zou
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Yoichi Hasegawa
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Kaoru Tonosaki
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Sachiko Shirasawa
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Aki Fukushima
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
| | - Shuji Yokoi
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Yoshihito Takahata
- Faculty of Agriculture, Iwate University, 3-18-8 Ueda, Morioka, Iwate 020-8550, Japan
| | - Tomohiro Kakizaki
- National Institute of Vegetable and Tea Science, 360, Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Masahiko Ishida
- National Institute of Vegetable and Tea Science, 360, Kusawa, Ano, Tsu, Mie 514-2392, Japan
| | - Shunsuke Okamoto
- Plant Breeding Experimental Station, Takii Seed Co. Ltd, Kohsei, Kohka-gun, Shiga 520-20, Japan
| | - Koji Sakamoto
- Plant Breeding Experimental Station, Takii Seed Co. Ltd, Kohsei, Kohka-gun, Shiga 520-20, Japan
| | - Kenta Shirasawa
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Satoshi Tabata
- Kazusa DNA Research Institute, 2-6-7 Kazusa-Kamatari, Kisarazu, Chiba 292-0818, Japan
| | - Takeshi Nishio
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
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24
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Ishida M, Hara M, Fukino N, Kakizaki T, Morimitsu Y. Glucosinolate metabolism, functionality and breeding for the improvement of Brassicaceae vegetables. BREEDING SCIENCE 2014; 64:48-59. [PMID: 24987290 PMCID: PMC4031110 DOI: 10.1270/jsbbs.64.48] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 02/24/2014] [Indexed: 05/18/2023]
Abstract
Unique secondary metabolites, glucosinolates (S-glucopyranosyl thiohydroximates), are naturally occurring S-linked glucosides found mainly in Brassicaceae plants. They are enzymatically hydrolyzed to produce sulfate ions, D-glucose, and characteristic degradation products such as isothiocyanates. The functions of glucosinolates in the plants remain unclear, but isothiocyanates possessing a pungent or irritating taste and odor might be associated with plant defense from microbes. Isothiocyanates have been studied extensively in experimental in vitro and in vivo carcinogenesis models for their cancer chemopreventive properties. The beneficial isothiocyanates, glucosinolates that are functional for supporting human health, have received attention from many scientists studying plant breeding, plant physiology, plant genetics, and food functionality. This review presents a summary of recent topics related with glucosinolates in the Brassica family, along with a summary of the chemicals, metabolism, and genes of glucosinolates in Brassicaceae. The bioavailabilities of isothiocyanates from certain functional glucosinolates and the importance of breeding will be described with emphasis on glucosinolates.
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Affiliation(s)
- Masahiko Ishida
- NARO Institute of Vegetable and Tea Science, Tsukuba Vegetable Research Station,
3-1-1 Kannondai, Tsukuba, Ibaraki 305-8666,
Japan
- Corresponding author (e-mail: )
| | - Masakazu Hara
- Research Institute of Green Science and Technology, Shizuoka University,
836 Ohya, Shizuoka 422-8529,
Japan
| | - Nobuko Fukino
- NARO Institute of Vegetable and Tea Science,
360 Kusawa, Ano, Tsu, Mie 514-2392,
Japan
| | - Tomohiro Kakizaki
- NARO Institute of Vegetable and Tea Science,
360 Kusawa, Ano, Tsu, Mie 514-2392,
Japan
| | - Yasujiro Morimitsu
- The Department of Food and Nutritional Sciences, The Graduate School of Humanities and Sciences, Ochanomizu University,
2-1-1 Otsuka, Bunkyo, Tokyo 112-8610,
Japan
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25
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Sharma A, Li X, Lim YP. Comparative genomics of Brassicaceae crops. BREEDING SCIENCE 2014; 64:3-13. [PMID: 24987286 PMCID: PMC4031108 DOI: 10.1270/jsbbs.64.3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/06/2013] [Accepted: 02/16/2014] [Indexed: 06/03/2023]
Abstract
The family Brassicaceae is one of the major groups of the plant kingdom and comprises diverse species of great economic, agronomic and scientific importance, including the model plant Arabidopsis. The sequencing of the Arabidopsis genome has revolutionized our knowledge in the field of plant biology and provides a foundation in genomics and comparative biology. Genomic resources have been utilized in Brassica for diversity analyses, construction of genetic maps and identification of agronomic traits. In Brassicaceae, comparative sequence analysis across the species has been utilized to understand genome structure, evolution and the detection of conserved genomic segments. In this review, we focus on the progress made in genetic resource development, genome sequencing and comparative mapping in Brassica and related species. The utilization of genomic resources and next-generation sequencing approaches in improvement of Brassica crops is also discussed.
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Affiliation(s)
- Ashutosh Sharma
- Graduate School of Agricultural Science, Tohoku University,
Aoba, Sendai, Miyagi 981-8555,
Japan
- Present address: Institute of Molecular, Cell, and Systems Biology, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
| | - Xiaonan Li
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University,
Daejeon 305-764,
Republic of Korea
| | - Yong Pyo Lim
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University,
Daejeon 305-764,
Republic of Korea
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26
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Wang Y, Pan Y, Liu Z, Zhu X, Zhai L, Xu L, Yu R, Gong Y, Liu L. De novo transcriptome sequencing of radish (Raphanus sativus L.) and analysis of major genes involved in glucosinolate metabolism. BMC Genomics 2013; 14:836. [PMID: 24279309 PMCID: PMC4046679 DOI: 10.1186/1471-2164-14-836] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 11/14/2013] [Indexed: 12/20/2022] Open
Abstract
Background Radish (Raphanus sativus L.), is an important root vegetable crop worldwide. Glucosinolates in the fleshy taproot significantly affect the flavor and nutritional quality of radish. However, little is known about the molecular mechanisms underlying glucosinolate metabolism in radish taproots. The limited availability of radish genomic information has greatly hindered functional genomic analysis and molecular breeding in radish. Results In this study, a high-throughput, large-scale RNA sequencing technology was employed to characterize the de novo transcriptome of radish roots at different stages of development. Approximately 66.11 million paired-end reads representing 73,084 unigenes with a N50 length of 1,095 bp, and a total length of 55.73 Mb were obtained. Comparison with the publicly available protein database indicates that a total of 67,305 (about 92.09% of the assembled unigenes) unigenes exhibit similarity (e –value ≤ 1.0e-5) to known proteins. The functional annotation and classification including Gene Ontology (GO), Clusters of Orthologous Group (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed that the main activated genes in radish taproots are predominately involved in basic physiological and metabolic processes, biosynthesis of secondary metabolite pathways, signal transduction mechanisms and other cellular components and molecular function related terms. The majority of the genes encoding enzymes involved in glucosinolate (GS) metabolism and regulation pathways were identified in the unigene dataset by targeted searches of their annotations. A number of candidate radish genes in the glucosinolate metabolism related pathways were also discovered, from which, eight genes were validated by T-A cloning and sequencing while four were validated by quantitative RT-PCR expression profiling. Conclusions The ensuing transcriptome dataset provides a comprehensive sequence resource for molecular genetics research in radish. It will serve as an important public information platform to further understanding of the molecular mechanisms involved in biosynthesis and metabolism of the related nutritional and flavor components during taproot formation in radish. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-14-836) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yan Wang
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Horticulture, Nanjing Agricultural University, Nanjing 210095, P,R, China.
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