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Wirojsirasak W, Songsri P, Jongrungklang N, Tangphatsornruang S, Klomsa-ard P, Ukoskit K. A Large-Scale Candidate-Gene Association Mapping for Drought Tolerance and Agronomic Traits in Sugarcane. Int J Mol Sci 2023; 24:12801. [PMID: 37628982 PMCID: PMC10454574 DOI: 10.3390/ijms241612801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 08/09/2023] [Accepted: 08/12/2023] [Indexed: 08/27/2023] Open
Abstract
Dissection of the genetic loci controlling drought tolerance traits with a complex genetic inheritance is important for drought-tolerant sugarcane improvement. In this study, we conducted a large-scale candidate gene association study of 649 candidate genes in a sugarcane diversity panel to identify genetic variants underlying agronomic traits and drought tolerance indices evaluated in plant cane and ratoon cane under water-stressed (WS) and non-stressed (NS) environments. We identified 197 significant marker-trait associations (MTAs) in 141 candidate genes associated with 18 evaluated traits with the Bonferroni correction threshold (α = 0.05). Out of the total, 95 MTAs in 78 candidate genes and 62 MTAs in 58 candidate genes were detected under NS and WS conditions, respectively. Most MTAs were found only in specific water regimes and crop seasons. These MTAs explained 7.93-30.52% of phenotypic variation. Association mapping results revealed that 34, 59, and 104 MTAs involved physiological and molecular adaptation, phytohormone metabolism, and drought-inducible genes. They identified 19 pleiotropic genes associated with more than one trait and many genes related to drought tolerance indices. The genetic and genomic resources identified in this study will enable the combining of yield-related traits and sugar-related traits with agronomic value to optimize the yield of sugarcane cultivars grown under drought-stressed and non-stressed environments.
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Affiliation(s)
- Warodom Wirojsirasak
- Department of Biotechnology, Faculty of Science and Technology, Rangsit Campus, Thammasat University, Pathum Thani 12120, Thailand;
- Mitr Phol Innovation and Research Center, Chaiyaphum 36110, Thailand;
| | - Patcharin Songsri
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (P.S.); (N.J.)
- Northeast Thailand Cane and Sugar Research Center, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Nakorn Jongrungklang
- Department of Agronomy, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (P.S.); (N.J.)
- Northeast Thailand Cane and Sugar Research Center, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Pathum Thani 12120, Thailand;
| | | | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Rangsit Campus, Thammasat University, Pathum Thani 12120, Thailand;
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Lee C, Cheon KS, Shin Y, Oh H, Jeong YM, Jang H, Park YC, Kim KY, Cho HC, Won YJ, Baek J, Cha YS, Kim SL, Kim KH, Ji H. Development and Application of a Target Capture Sequencing SNP-Genotyping Platform in Rice. Genes (Basel) 2022; 13:genes13050794. [PMID: 35627177 PMCID: PMC9141132 DOI: 10.3390/genes13050794] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 12/25/2022] Open
Abstract
The development of efficient, robust, and high-throughput SNP genotyping platforms is pivotal for crop genetics and breeding. Recently, SNP genotyping platforms based on target capture sequencing, which is very flexible in terms of the number of SNP markers, have been developed for maize, cassava, and fava bean. We aimed to develop a target capture sequencing SNP genotyping platform for rice. A target capture sequencing panel containing 2565 SNPs, including 1225 SNPs informative for japonica and 1339 SNPs informative for indica, was developed. This platform was used in diversity analysis of 50 rice varieties. Of the 2565 SNP markers, 2341 (91.3%) produced useful polymorphic genotype data, enabling the production of a phylogenetic tree of the 50 varieties. The mean number of markers polymorphic between any two varieties was 854. The platform was used for QTL mapping of preharvest sprouting (PHS) resistance in an F8 recombinant inbred line population derived from the cross Odae × Joun. A genetic map comprising 475 markers was constructed, and two QTLs for PHS resistance were identified on chromosomes 4 and 11. This system is a powerful tool for rice genetics and breeding and will facilitate QTL studies and gene mapping, germplasm diversity analysis, and marker-assisted selection.
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Affiliation(s)
- Chaewon Lee
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
- Department of Crop Science and Biotechnology, Chonbuk National University, Jeonju 54896, Korea
| | - Kyeong-Seong Cheon
- Division of Forest Tree Improvement and Biotechnology, Department of Forest Bioresources, National Institute of Forest Science, Suwon 16631, Korea;
| | - Yunji Shin
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
- Genecell Biotech Inc., Wanju, 55322, Korea
| | - Hyoja Oh
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Young-Min Jeong
- Seed Industry Promotion Center, Korea Agriculture Technology Promotion Agency (KOAT), Gimje 54324, Korea;
| | - Hoon Jang
- CELEMICS, Seoul 08506, Korea; (H.J.); (Y.-C.P.)
| | | | - Kyung-Yun Kim
- INSILICOGEN, Yongin 16954, Korea; (K.-Y.K.); (H.-C.C.)
| | - Hang-Chul Cho
- INSILICOGEN, Yongin 16954, Korea; (K.-Y.K.); (H.-C.C.)
| | - Yong-Jae Won
- Cheorwon Branch, National Institute of Crop Science, Rural Development Administration (RDA), Cheorwon 24010, Korea;
| | - Jeongho Baek
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Young-Soon Cha
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Song-Lim Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Kyung-Hwan Kim
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
| | - Hyeonso Ji
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration (RDA), Jeonju 54874, Korea; (C.L.); (Y.S.); (H.O.); (J.B.); (Y.-S.C.); (S.-L.K.); (K.-H.K.)
- Correspondence: ; Tel.: +82-63-238-4657
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Saxesena RR, Mishra VK, Chand R, Kumar U, Chowdhury AK, Bhati J, Budhlakoti N, Joshi AK. SNP Discovery Using BSR-Seq Approach for Spot Blotch Resistance in Wheat ( Triticum aestivum L.), an Essential Crop for Food Security. Front Genet 2022; 13:859676. [PMID: 35450212 PMCID: PMC9016274 DOI: 10.3389/fgene.2022.859676] [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: 01/21/2022] [Accepted: 02/17/2022] [Indexed: 11/13/2022] Open
Abstract
The pathogenic fungus, Bipolaris sorokiniana, that causes spot blotch (SB) disease of wheat, is a major production constraint in the Eastern Gangetic Plains of South Asia and other warm, humid regions of the world. A recombinant inbred line population was developed and phenotyped at three SB-prone locations in India. The single nucleotide polymorphism (SNP) for SB resistance was identified using a bulked segregant RNA-Seq-based approach, referred to as “BSR-Seq.” Transcriptome sequencing of the resistant parent (YS#24), the susceptible parent (YS#58), and their resistant and susceptible bulks yielded a total of 429.67 million raw reads. The bulk frequency ratio (BFR) of SNPs between the resistant and susceptible bulks was estimated, and selection of SNPs linked to resistance was done using sixfold enrichments in the corresponding bulks (BFR >6). With additional filtering criteria, the number of transcripts was further reduced to 506 with 1055 putative polymorphic SNPs distributed on 21 chromosomes of wheat. Based on SNP enrichment on chromosomal loci, five transcripts were found to be associated with SB resistance. Among the five SB resistance-associated transcripts, four were distributed on the 5B chromosome with putative 52 SNPs, whereas one transcript with eight SNPs was present on chromosome 3B. The SNPs linked to the trait were exposed to a tetra-primer ARMS-PCR assay, and an SNP-based allele-specific marker was identified for SB resistance. The in silico study of these five transcripts showed homology with pathogenesis-related genes; the metabolic pathway also exhibits similar results, suggesting their role in the plant defense mechanism.
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Affiliation(s)
- Ravi Ranjan Saxesena
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Vinod Kumar Mishra
- Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Ramesh Chand
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, India
| | - Uttam Kumar
- Borlaug Institute for South Asia (BISA), Ludhiana, India
| | | | - Jyotika Bhati
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Neeraj Budhlakoti
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Arun Kumar Joshi
- Borlaug Institute for South Asia (BISA), Ludhiana, India.,International Maize and Wheat Improvement Center (CIMMYT) and Borlaug Institute for South Asia (BISA), DPS Marg, New Delhi, India
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Luo S, Ma Q, Zhong Y, Jing J, Wei Z, Zhou W, Lu X, Tian Y, Zhang P. Editing of the starch branching enzyme gene SBE2 generates high-amylose storage roots in cassava. PLANT MOLECULAR BIOLOGY 2022; 108:429-442. [PMID: 34792751 DOI: 10.1007/s11103-021-01215-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
The production of high-amylose cassava through CRISPR/Cas9-mediated mutagenesis of the starch branching enzyme gene SBE2 was firstly achieved. High-amylose cassava (Manihot esculenta Crantz) is desirable for starch industrial applications and production of healthier processed food for human consumption. In this study, we report the production of high-amylose cassava through CRISPR/Cas9-mediated mutagenesis of the starch branching enzyme 2 (SBE2). Mutations in two targeted exons of SBE2 were identified in all regenerated plants; these mutations, which included nucleotide insertions, and short or long deletions in the SBE2 gene, were classified into eight mutant lines. Three mutants, M6, M7 and M8, with long fragment deletions in the second exon of SBE2 showed no accumulation of SBE2 protein. After harvest from the field, significantly higher amylose (up to 56% in apparent amylose content) and resistant starch (up to 35%) was observed in these mutants compared with the wild type, leading to darker blue coloration of starch granules after quick iodine staining and altered starch viscosity with a higher pasting temperature and peak time. Further 1H-NMR analysis revealed a significant reduction in the degree of starch branching, together with fewer short chains (degree of polymerization [DP] 15-25) and more long chains (DP>25 and especially DP>40) of amylopectin, which indicates that cassava SBE2 catalyzes short chain formation during amylopectin biosynthesis. Transition from A- to B-type crystallinity was also detected in the starches. Our study showed that CRISPR/Cas9-mediated mutagenesis of starch biosynthetic genes in cassava is an effective approach for generating novel varieties with valuable starch properties for food and industrial applications.
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Affiliation(s)
- Shu Luo
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Qiuxiang Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Yingying Zhong
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Shanghai Sanshu Biotechnology Co., LTD, Shanghai, 201210, China
| | - Jianling Jing
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zusheng Wei
- Guangxi Subtropical Crops Research Institute, Nanning, 530001, China
| | - Wenzhi Zhou
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- Shanghai Sanshu Biotechnology Co., LTD, Shanghai, 201210, China
| | - Xinlu Lu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yinong Tian
- Guangxi Subtropical Crops Research Institute, Nanning, 530001, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China.
- University of Chinese Academy of Sciences, Beijing, China.
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Shaibu AS, Ibrahim H, Miko ZL, Mohammed IB, Mohammed SG, Yusuf HL, Kamara AY, Omoigui LO, Karikari B. Assessment of the Genetic Structure and Diversity of Soybean ( Glycine max L.) Germplasm Using Diversity Array Technology and Single Nucleotide Polymorphism Markers. PLANTS (BASEL, SWITZERLAND) 2021; 11:68. [PMID: 35009071 PMCID: PMC8747349 DOI: 10.3390/plants11010068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/11/2021] [Accepted: 12/14/2021] [Indexed: 11/20/2022]
Abstract
Knowledge of the genetic structure and diversity of germplasm collections is crucial for sustainable genetic improvement through hybridization programs and rapid adaptation to changing breeding objectives. The objective of this study was to determine the genetic diversity and population structure of 281 International Institute of Tropical Agriculture (IITA) soybean accessions using diversity array technology (DArT) and single nucleotide polymorphism (SNP) markers for the efficient utilization of these accessions. From the results, the SNP and DArT markers were well distributed across the 20 soybean chromosomes. The cluster and principal component analyses revealed the genetic diversity among the 281 accessions by grouping them into two stratifications, a grouping that was also evident from the population structure analysis, which divided the 281 accessions into two distinct groups. The analysis of molecular variance revealed that 97% and 98% of the genetic variances using SNP and DArT markers, respectively, were within the population. Genetic diversity indices such as Shannon's diversity index, diversity and unbiased diversity revealed the diversity among the different populations of the soybean accessions. The SNP and DArT markers used provided similar information on the structure, diversity and polymorphism of the accessions, which indicates the applicability of the DArT marker in genetic diversity studies. Our study provides information about the genetic structure and diversity of the IITA soybean accessions that will allow for the efficient utilization of these accessions in soybean improvement programs, especially in Africa.
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Affiliation(s)
- Abdulwahab S. Shaibu
- Department of Agronomy, Bayero University Kano, Kano 700001, Nigeria; (H.I.); (Z.L.M.); (I.B.M.)
| | - Hassan Ibrahim
- Department of Agronomy, Bayero University Kano, Kano 700001, Nigeria; (H.I.); (Z.L.M.); (I.B.M.)
| | - Zainab L. Miko
- Department of Agronomy, Bayero University Kano, Kano 700001, Nigeria; (H.I.); (Z.L.M.); (I.B.M.)
| | - Ibrahim B. Mohammed
- Department of Agronomy, Bayero University Kano, Kano 700001, Nigeria; (H.I.); (Z.L.M.); (I.B.M.)
| | - Sanusi G. Mohammed
- Centre for Dryland Agriculture, Bayero University Kano, Kano 700001, Nigeria;
| | - Hauwa L. Yusuf
- Department of Food Science and Technology, Bayero University Kano, Kano 700001, Nigeria;
| | - Alpha Y. Kamara
- International Institute of Tropical Agriculture, Ibadan 200211, Nigeria; (A.Y.K.); (L.O.O.)
| | - Lucky O. Omoigui
- International Institute of Tropical Agriculture, Ibadan 200211, Nigeria; (A.Y.K.); (L.O.O.)
| | - Benjamin Karikari
- Department of Crop Science, Faculty of Agriculture, Food and Consumer Sciences, University for Development Studies, P.O. Box TL 1882, Tamale 00233, Ghana;
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Mbanjo EGN, Rabbi IY, Ferguson ME, Kayondo SI, Eng NH, Tripathi L, Kulakow P, Egesi C. Technological Innovations for Improving Cassava Production in Sub-Saharan Africa. Front Genet 2021; 11:623736. [PMID: 33552138 PMCID: PMC7859516 DOI: 10.3389/fgene.2020.623736] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/23/2020] [Indexed: 11/17/2022] Open
Abstract
Cassava is crucial for food security of millions of people in sub-Saharan Africa. The crop has great potential to contribute to African development and is increasing its income-earning potential for small-scale farmers and related value chains on the continent. Therefore, it is critical to increase cassava production, as well as its quality attributes. Technological innovations offer great potential to drive this envisioned change. This paper highlights genomic tools and resources available in cassava. The paper also provides a glimpse of how these resources have been used to screen and understand the pattern of cassava genetic diversity on the continent. Here, we reviewed the approaches currently used for phenotyping cassava traits, highlighting the methodologies used to link genotypic and phenotypic information, dissect the genetics architecture of key cassava traits, and identify quantitative trait loci/markers significantly associated with those traits. Additionally, we examined how knowledge acquired is utilized to contribute to crop improvement. We explored major approaches applied in the field of molecular breeding for cassava, their promises, and limitations. We also examined the role of national agricultural research systems as key partners for sustainable cassava production.
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Affiliation(s)
| | | | | | | | - Ng Hwa Eng
- CGIAR Excellence in Breeding Platform, El Batan, Mexico
| | - Leena Tripathi
- International Institute of Tropical Agriculture, Nairobi, Kenya
| | - Peter Kulakow
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Chiedozie Egesi
- International Institute of Tropical Agriculture, Ibadan, Nigeria
- National Root Crops Research Institute, Umudike, Nigeria
- Department of Global Development, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, United States
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Suksamran R, Saithong T, Thammarongtham C, Kalapanulak S. Genomic and Transcriptomic Analysis Identified Novel Putative Cassava lncRNAs Involved in Cold and Drought Stress. Genes (Basel) 2020; 11:E366. [PMID: 32231066 PMCID: PMC7230406 DOI: 10.3390/genes11040366] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 01/09/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play important roles in the regulation of complex cellular processes, including transcriptional and post-transcriptional regulation of gene expression relevant for development and stress response, among others. Compared to other important crops, there is limited knowledge of cassava lncRNAs and their roles in abiotic stress adaptation. In this study, we performed a genome-wide study of ncRNAs in cassava, integrating genomics- and transcriptomics-based approaches. In total, 56,840 putative ncRNAs were identified, and approximately half the number were verified using expression data or previously known ncRNAs. Among these were 2229 potential novel lncRNA transcripts with unmatched sequences, 250 of which were differentially expressed in cold or drought conditions, relative to controls. We showed that lncRNAs might be involved in post-transcriptional regulation of stress-induced transcription factors (TFs) such as zinc-finger, WRKY, and nuclear factor Y gene families. These findings deepened our knowledge of cassava lncRNAs and shed light on their stress-responsive roles.
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Affiliation(s)
- Rungaroon Suksamran
- Biotechnology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang KhunThian), Bangkok 10150, Thailand
| | - Treenut Saithong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang KhunThian), Bangkok 10150, Thailand
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (Bang KhunThian), Bangkok 10150, Thailand
| | - Chinae Thammarongtham
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology at King Mongkut's University of Technology Thonburi (Bang KhunThian), Bangkok 10150, Thailand
| | - Saowalak Kalapanulak
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang KhunThian), Bangkok 10150, Thailand
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (Bang KhunThian), Bangkok 10150, Thailand
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Alves‐Pereira A, Clement CR, Picanço‐Rodrigues D, Veasey EA, Dequigiovanni G, Ramos SLF, Pinheiro JB, de Souza AP, Zucchi MI. A population genomics appraisal suggests independent dispersals for bitter and sweet manioc in Brazilian Amazonia. Evol Appl 2020; 13:342-361. [PMID: 31993081 PMCID: PMC6976959 DOI: 10.1111/eva.12873] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2019] [Accepted: 09/14/2019] [Indexed: 12/19/2022] Open
Abstract
Amazonia is a major world centre of plant domestication, but the genetics of domestication remains unclear for most Amazonian crops. Manioc (Manihot esculenta) is the most important staple food crop that originated in this region. Although manioc is relatively well-studied, little is known about the diversification of bitter and sweet landraces and how they were dispersed across Amazonia. We evaluated single nucleotide polymorphisms (SNPs) in wild and cultivated manioc to identify outlier SNPs putatively under selection and to assess the neutral genetic structure of landraces to make inferences about the evolution of the crop in Amazonia. Some outlier SNPs were in putative manioc genes possibly related to plant architecture, transcriptional regulation and responses to stress. The neutral SNPs revealed contrasting genetic structuring for bitter and sweet landraces. The outlier SNPs may be signatures of the genomic changes resulting from domestication, while the neutral genetic structure suggests independent dispersals for sweet and bitter manioc, possibly related to the earlier domestication and diversification of the former. Our results highlight the role of ancient peoples and current smallholders in the management and conservation of manioc genetic diversity, including putative genes and specific genetic resources with adaptive potential in the context of climate change.
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Affiliation(s)
- Alessandro Alves‐Pereira
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
- Departamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de Campinas (UNICAMP)CampinasBrazil
| | | | | | - Elizabeth Ann Veasey
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - Gabriel Dequigiovanni
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - Santiago Linorio Ferreyra Ramos
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - José Baldin Pinheiro
- Departamento de GenéticaEscola Superior de Agricultura “Luiz de Queiróz”Universidade de São Paulo (ESALQ‐USP)PiracicabaBrazil
| | - Anete Pereira de Souza
- Departamento de Biologia VegetalInstituto de BiologiaUniversidade Estadual de Campinas (UNICAMP)CampinasBrazil
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Bragina MK, Afonnikov DA, Salina EA. Progress in plant genome sequencing: research directions. Vavilovskii Zhurnal Genet Selektsii 2019. [DOI: 10.18699/vj19.459] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Since the first plant genome of Arabidopsis thaliana has been sequenced and published, genome sequencing technologies have undergone significant changes. New algorithms, sequencing technologies and bioinformatic approaches were adopted to obtain genome, transcriptome and exome sequences for model and crop species, which have permitted deep inferences into plant biology. As a result of an improved genome assembly and analysis methods, genome sequencing costs plummeted and the number of high-quality plant genome sequences is constantly growing. Consequently, more than 300 plant genome sequences have been published over the past twenty years. Although many of the published genomes are considered incomplete, they proved to be a valuable tool for identifying genes involved in the formation of economically valuable plant traits, for marker-assisted and genomic selection and for comparative analysis of plant genomes in order to determine the basic patterns of origin of various plant species. Since a high coverage and resolution of a genome sequence is not enough to detect all changes in complex samples, targeted sequencing, which consists in the isolation and sequencing of a specific region of the genome, has begun to develop. Targeted sequencing has a higher detection power (the ability to identify new differences/variants) and resolution (up to one basis). In addition, exome sequencing (the method of sequencing only protein-coding genes regions) is actively developed, which allows for the sequencing of non-expressed alleles and genes that cannot be found with RNA-seq. In this review, an analysis of sequencing technologies development and the construction of “reference” genomes of plants is performed. A comparison of the methods of targeted sequencing based on the use of the reference DNA sequence is accomplished.
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Affiliation(s)
| | - D. A. Afonnikov
- Institute of Cytology and Genetics, SB RAS; Novosibirsk State University
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Tappiban P, Smith DR, Triwitayakorn K, Bao J. Recent understanding of starch biosynthesis in cassava for quality improvement: A review. Trends Food Sci Technol 2019. [DOI: 10.1016/j.tifs.2018.11.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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11
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OLIVEIRA PAULOHENRIQUEGDE, BARBOSA ANACLAUDIAO, DINIZ RAFAELP, OLIVEIRA EDERJDE, FERREIRA CLAUDIAF. Molecular marker assisted selection for increasing inbreeding in S1 populations of cassava. AN ACAD BRAS CIENC 2018; 90:3853-3869. [PMID: 30427393 DOI: 10.1590/0001-3765201820180278] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 07/02/2018] [Indexed: 01/15/2023] Open
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12
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Giles JAD, Oliosi G, Rodrigues WP, Braun H, Ribeiro-Barros AI, Partelli FL. Agronomic performance and genetic divergence between genotypes of Manihot esculenta. AN ACAD BRAS CIENC 2018; 90:3639-3648. [PMID: 30184017 DOI: 10.1590/0001-3765201820180099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 05/21/2018] [Indexed: 11/21/2022] Open
Abstract
The morphoagronomic characterization of 12 genotypes of M. esculenta was performed during the 2013/2014 and 2014/2015 crop years. The 12 genotypes were planted in a randomized block design, with four replicates per genotype. Number of tuberous roots per plant, weight of tuberous roots, root yield, total plant weight, harvest index, plant height, height of first branch, number of shoots, stem diameter, number of buds, leaf dry weight and petiole length were evaluated. Genotypes "Camuquem" and "Goiás" were the most productive, and "Amarela" and "Gema de Ovo" were the most divergent. Seventy percent of genetic diversity was due to petiole length (22.86%), root yield (19.20%), weight of tuberous roots (14.89%) and number of buds (13.72%). Overall, the present results indicate a broad genetic basis for the evaluated genotypes, so that such genetic variation benefits the plant breeding for future scenarios Further studies of the evaluated genotypes should be performed under environmental limitations, using biochemical and molecular tools to identify markers for genetic improvement.
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Affiliation(s)
- João Antonio D Giles
- Departmento de Ciências Agrárias e Biológicas, Centro Universitário Norte do Espírito Santo, Universidade Federal do Espírito Santo/UFES, Rod. BR 101, Km 60, Litorâneo, 29932-540 São Mateus, ES, Brazil
| | - Gleison Oliosi
- Departmento de Ciências Agrárias e Biológicas, Centro Universitário Norte do Espírito Santo, Universidade Federal do Espírito Santo/UFES, Rod. BR 101, Km 60, Litorâneo, 29932-540 São Mateus, ES, Brazil
| | - Weverton P Rodrigues
- Centro de Ciências e Tecnologias Agropecuárias, Universidade Estadual Norte Fluminense-Darcy Ribeiro, Av. Alberto Lamego, 2000, 28013-602 Campos dos Goytacazes, RJ, Brazil
| | - Heder Braun
- Departamento de Fitotecnia e Fitossanidade, Universidade Estadual do Maranhão, Cidade Universitária Paulo VI, Caixa Postal 09, 65055-098 São Luíz, MA, Brazil
| | - Ana I Ribeiro-Barros
- Grupo Interações Planta-Ambiente & Biodiversidade/PlantStress&Biodiversity, Centro de Investigação em Agronomia, Alimentos, Ambiente e Paisagem/LEAF, Departamento de Recursos Naturais, Ambiente e Território/DRAT, Instituto Superior de Agronomia/ISA, Universidade de Lisboa/ULisboa, Qta. Marquês, Av. República, 2784-505 Oeiras, Portugal.,GeoBioTec, Fac. Ciências Tecnologia/FCT, Universidade Nova de Lisboa/UNL, 2829-516 Caparica, Portugal
| | - Fábio L Partelli
- Departmento de Ciências Agrárias e Biológicas, Centro Universitário Norte do Espírito Santo, Universidade Federal do Espírito Santo/UFES, Rod. BR 101, Km 60, Litorâneo, 29932-540 São Mateus, ES, Brazil
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13
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Yoodee S, Kobayashi Y, Songnuan W, Boonchird C, Thitamadee S, Kobayashi I, Narangajavana J. Phytohormone priming elevates the accumulation of defense-related gene transcripts and enhances bacterial blight disease resistance in cassava. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 122:65-77. [PMID: 29190504 DOI: 10.1016/j.plaphy.2017.11.016] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 11/25/2017] [Accepted: 11/25/2017] [Indexed: 05/26/2023]
Abstract
Cassava bacterial blight (CBB) disease caused by Xanthomonas axonopodis pv. manihotis (Xam) is a severe disease in cassava worldwide. In addition to causing significant cassava yield loss, CBB disease has not been extensively studied, especially in terms of CBB resistance genes. The present research demonstrated the molecular mechanisms underlining the defense response during Xam infection in two cassava cultivars exhibiting different degrees of disease resistance, Huay Bong60 (HB60) and Hanatee (HN). Based on gene expression analysis, ten of twelve putative defense-related genes including, leucine-rich repeat receptor-like kinases (LRR-RLKs), resistance (R), WRKY and pathogenesis-related (PR) genes, were differentially expressed between these two cassava cultivars during Xam infection. The up-regulation of defense-related genes observed in HB60 may be the mechanism required for the reduction of disease severity in the resistant cultivar. Interestingly, priming with salicylic acid (SA) or methyl jasmonate (MeJA) for 24 h before Xam inoculation could enhance the defense response in both cassava cultivars. The disease severity was decreased 10% in the resistant cultivar (HB60) and was remarkably reduced 21% in the susceptible cultivar (HN) by SA/MeJA priming. Priming with Xam inoculation modulated cassava4.1_013417, cassava4.1_030866 and cassava4.1_020555 (highest similarity to MeWRKY59, MePR1 and AtPDF2.2, respectively) expression and led to enhanced resistance of the susceptible cultivar in the second infection. The putative cis-regulatory elements were predicted in an upstream region of these three defense-related genes. The different gene expression levels in these genes between the two cultivars were due to the differences in cis-regulatory elements in their promoter regions. Taken together, our study strongly suggested that the induction of defense-related genes correlated with defense resistance against Xam infection, and exogenous application of SA or MeJA could elevate the defense response in both cultivars of cassava. This finding should pave the way for management to reduce yield loss from disease and genetic improvement in cassava.
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Affiliation(s)
- Sunisa Yoodee
- Department of Biotechnology, Faculty of Science, Mahidol University, Phayathai, Bangkok, Thailand
| | - Yohko Kobayashi
- Center for Molecular Biology and Genetics, Graduate School of Regional Innovation Studies, Mie University, Japan
| | - Wisuwat Songnuan
- Department of Plant Science, Faculty of Science, Mahidol University, Phayathai, Bangkok, Thailand
| | - Chuenchit Boonchird
- Department of Biotechnology, Faculty of Science, Mahidol University, Phayathai, Bangkok, Thailand
| | - Siripong Thitamadee
- Department of Biotechnology, Faculty of Science, Mahidol University, Phayathai, Bangkok, Thailand
| | - Issei Kobayashi
- Center for Molecular Biology and Genetics, Graduate School of Regional Innovation Studies, Mie University, Japan
| | - Jarunya Narangajavana
- Department of Biotechnology, Faculty of Science, Mahidol University, Phayathai, Bangkok, Thailand; Center of Excellence on Agricultural Biotechnology: (AG-BIO/PERDO-CHE), Bangkok, Thailand.
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14
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Zhang S, Chen X, Lu C, Ye J, Zou M, Lu K, Feng S, Pei J, Liu C, Zhou X, Ma P, Li Z, Liu C, Liao Q, Xia Z, Wang W. Genome-Wide Association Studies of 11 Agronomic Traits in Cassava ( Manihot esculenta Crantz). FRONTIERS IN PLANT SCIENCE 2018; 9:503. [PMID: 29725343 PMCID: PMC5917017 DOI: 10.3389/fpls.2018.00503] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/03/2018] [Indexed: 05/21/2023]
Abstract
Cassava (Manihot esculenta Crantz) is a major tuberous crop produced worldwide. In this study, we sequenced 158 diverse cassava varieties and identified 349,827 single-nucleotide polymorphisms (SNPs) and indels. In each chromosome, the number of SNPs and the physical length of the respective chromosome were in agreement. Population structure analysis indicated that this panel can be divided into three subgroups. Genetic diversity analysis indicated that the average nucleotide diversity of the panel was 1.21 × 10-4 for all sampled landraces. This average nucleotide diversity was 1.97 × 10-4, 1.01 × 10-4, and 1.89 × 10-4 for subgroups 1, 2, and 3, respectively. Genome-wide linkage disequilibrium (LD) analysis demonstrated that the average LD was about ∼8 kb. We evaluated 158 cassava varieties under 11 different environments. Finally, we identified 36 loci that were related to 11 agronomic traits by genome-wide association analyses. Four loci were associated with two traits, and 62 candidate genes were identified in the peak SNP sites. We found that 40 of these genes showed different expression profiles in different tissues. Of the candidate genes related to storage roots, Manes.13G023300, Manes.16G000800, Manes.02G154700, Manes.02G192500, and Manes.09G099100 had higher expression levels in storage roots than in leaf and stem; on the other hand, of the candidate genes related to leaves, Manes.05G164500, Manes.05G164600, Manes.04G057300, Manes.01G202000, and Manes.03G186500 had higher expression levels in leaves than in storage roots and stem. This study provides basis for research on genetics and the genetic improvement of cassava.
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Affiliation(s)
- Shengkui Zhang
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xin Chen
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Cheng Lu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jianqiu Ye
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences, Danzhou, China
| | - Meiling Zou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Kundian Lu
- Wuming Agricultural Technology Extension Center, Nanning, China
| | - Subin Feng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Jinli Pei
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Chen Liu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Xincheng Zhou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Ping’an Ma
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
| | - Zhaogui Li
- Wuming Agricultural Technology Extension Center, Nanning, China
| | - Cuijuan Liu
- Hepu Institute of Agricultural Science, Beihai, China
| | - Qi Liao
- Hepu Institute of Agricultural Science, Beihai, China
| | - Zhiqiang Xia
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- *Correspondence: Zhiqiang Xia, Wenquan Wang,
| | - Wenquan Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- *Correspondence: Zhiqiang Xia, Wenquan Wang,
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15
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da Costa ZP, Munhoz CDF, Vieira MLC. Report on the development of putative functional SSR and SNP markers in passion fruits. BMC Res Notes 2017; 10:445. [PMID: 28874179 PMCID: PMC5585897 DOI: 10.1186/s13104-017-2771-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 08/31/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Passionflowers Passiflora edulis and Passiflora alata are diploid, outcrossing and understudied fruit bearing species. In Brazil, passion fruit cultivation began relatively recently and has earned the country an outstanding position as the world's top producer of passion fruit. The fruit's main economic value lies in the production of juice, an essential exotic ingredient in juice blends. Currently, crop improvement strategies, including those for underexploited tropical species, tend to incorporate molecular genetic approaches. In this study, we examined a set of P. edulis transcripts expressed in response to infection by Xanthomonas axonopodis, (the passion fruit's main bacterial pathogen that attacks the vines), aiming at the development of putative functional markers, i.e. SSRs (simple sequence repeats) and SNPs (single nucleotide polymorphisms). RESULTS A total of 210 microsatellites were found in 998 sequences, and trinucleotide repeats were found to be the most frequent (31.4%). Of the sequences selected for designing primers, 80.9% could be used to develop SSR markers, and 60.6% SNP markers for P. alata. SNPs were all biallelic and found within 15 gene fragments of P. alata. Overall, gene fragments generated 10,003 bp. SNP frequency was estimated as one SNP every 294 bp. Polymorphism rates revealed by SSR and SNP loci were 29.4 and 53.6%, respectively. CONCLUSIONS Passiflora edulis transcripts were useful for the development of putative functional markers for P. alata, suggesting a certain level of sequence conservation between these cultivated species. The markers developed herein could be used for genetic mapping purposes and also in diversity studies.
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Affiliation(s)
- Zirlane Portugal da Costa
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Carla de Freitas Munhoz
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil
| | - Maria Lucia Carneiro Vieira
- Departamento de Genética, Escola Superior de Agricultura "Luiz de Queiroz", Universidade de São Paulo, 13418-900, Piracicaba, Brazil.
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16
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Chanroj V, Rattanawong R, Phumichai T, Tangphatsornruang S, Ukoskit K. Genome-wide association mapping of latex yield and girth in Amazonian accessions of Hevea brasiliensis grown in a suboptimal climate zone. Genomics 2017; 109:475-484. [PMID: 28751185 DOI: 10.1016/j.ygeno.2017.07.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 07/07/2017] [Accepted: 07/21/2017] [Indexed: 12/29/2022]
Abstract
Latex yield and growth are the key complex traits in commercial rubber production. The present study is the first to report genome-wide association mapping of latex yield and girth, for 170 Amazonian accessions grown in a suboptimal area characterized by limited rainfall and a lengthy dry season. Targeted sequence enrichment to capture gene transcripts generated 14,155 high quality filtered single nucleotide polymorphisms (SNPs) of which 94.3% resided in coding regions. The rapid decay of linkage disequilibrium over physical and genetic distance found in the accessions was comparable to those previously reported for several outcrossing species. A mixed linear model detected three significant SNPs in three candidate genes involved in plant adaptation to drought stress, individually explaining 12.7-15.7% of the phenotypic variance. The SNPs identified in the study will help to extend understanding, and to support genetic improvement of rubber trees grown in drought-affected regions.
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Affiliation(s)
- Vipavee Chanroj
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand
| | - Ratchanee Rattanawong
- Nong Khai Rubber Research Center, Rubber Research Institute of Thailand, Rattanawapi District, Nong Khai, 43120, Thailand
| | | | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, 113 Phaholyothin Rd., Klong 1, Klong Luang, Pathumthani 12120, Thailand
| | - Kittipat Ukoskit
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Rangsit Campus, Klong Luang, Pathumtani 12121, Thailand.
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17
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Bechoff A, Tomlins K, Fliedel G, Becerra Lopez-Lavalle LA, Westby A, Hershey C, Dufour D. Cassava traits and end-user preference: Relating traits to consumer liking, sensory perception, and genetics. Crit Rev Food Sci Nutr 2017; 58:547-567. [PMID: 27494196 DOI: 10.1080/10408398.2016.1202888] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Breeding efforts have focused on improving agronomic traits of the cassava plant however little research has been done to enhance the crop palatability. This review investigates the links between cassava traits and end-user preference in relation with sensory characteristics. The main trait is starch and its composition related to the textural properties of the food. Pectin degradation during cooking resulted in increased mealiness. Nutritional components such as carotenoids made the cassava yellow but also altered sweetness and softness; however, yellow cassava was more appreciated by consumers than traditional (white) varieties. Components formed during processing such as organic acids gave fermented cassava products an acidic taste that was appreciated but the fermented smell was not always liked. Anti-nutritional compounds such as cyanogenic glucosides were mostly related to bitter taste. Post-harvest Physiological Deterioration (PPD) affected the overall sensory characteristics and acceptability. Genes responsible for some of these traits were also investigated. Diversity in cassava food products can provide a challenge to identifying acceptance criteria. Socio-economic factors such as gender may also be critical. This review leads to questions in relation to the adaptation of cassava breeding to meet consumer needs and preference in order to maximize income, health and food security.
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Affiliation(s)
- Aurélie Bechoff
- a Natural Resources Institute (NRI), University of Greenwich , Central Avenue, Chatham Maritime, Kent , United Kingdom
| | - Keith Tomlins
- a Natural Resources Institute (NRI), University of Greenwich , Central Avenue, Chatham Maritime, Kent , United Kingdom
| | - Geneviève Fliedel
- b UMR Qualisud, Centre International de Recherche Agronomique pour le Développement (CIRAD) , Breton Montpellier , France
| | | | - Andrew Westby
- a Natural Resources Institute (NRI), University of Greenwich , Central Avenue, Chatham Maritime, Kent , United Kingdom
| | - Clair Hershey
- b UMR Qualisud, Centre International de Recherche Agronomique pour le Développement (CIRAD) , Breton Montpellier , France
| | - Dominique Dufour
- b UMR Qualisud, Centre International de Recherche Agronomique pour le Développement (CIRAD) , Breton Montpellier , France.,c International Center for Tropical Agriculture (CIAT), Recta Cali-Palmira , Cali , Colombia
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18
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Peng Z, Fan W, Wang L, Paudel D, Leventini D, Tillman BL, Wang J. Target enrichment sequencing in cultivated peanut (Arachis hypogaea L.) using probes designed from transcript sequences. Mol Genet Genomics 2017; 292:955-965. [PMID: 28492983 DOI: 10.1007/s00438-017-1327-z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Accepted: 05/07/2017] [Indexed: 11/29/2022]
Abstract
Enabled by the next generation sequencing, target enrichment sequencing (TES) is a powerful method to enrich genomic regions of interest and to identify sequence variations. The objective of this study was to explore the feasibility of probe design from transcript sequences for TES application in calling sequence variants in peanut, an important allotetraploid crop with a large genome size. In this study, we applied an in-solution hybridization method to enrich DNA sequences of seven peanut genotypes. Our results showed that it is feasible to apply TES with probes designed from transcript sequences in polyploid peanut. Using a set of 31,123 probes, a total of 5131 and 7521 genes were targeted in peanut A and B genomes, respectively. For each genotype used in this study, the probe target capture regions were efficiently covered with high depth. The average on-target rate of sequencing reads was 42.47%, with a significant amount of off-target reads coming from genomic regions homologous to target regions. In this study, when given predefined genomic regions of interest and the same amount of sequencing data, TES provided the highest coverage of target regions when compared to whole genome sequencing, RNA sequencing, and genotyping by sequencing. Single nucleotide polymorphism (SNP) calling and subsequent validation revealed a high validation rate (85.71%) of homozygous SNPs, providing valuable markers for peanut genotyping. This study demonstrated the success of applying TES for SNP identification in peanut, which shall provide valuable suggestions for TES application in other non-model species without a genome reference available.
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Affiliation(s)
- Ze Peng
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Wen Fan
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Liping Wang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Dev Paudel
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Dante Leventini
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Barry L Tillman
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA
| | - Jianping Wang
- Agronomy Department, University of Florida, Gainesville, FL, 32610, USA.
- Genetics Institute, Plant Molecular and Cellular Biology Program, University of Florida, Gainesville, FL, 32610, USA.
- Center for Genomics and Biotechnology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China.
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19
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Ruggieri V, Anzar I, Paytuvi A, Calafiore R, Cigliano RA, Sanseverino W, Barone A. Exploiting the great potential of Sequence Capture data by a new tool, SUPER-CAP. DNA Res 2017; 24:81-91. [PMID: 28011720 PMCID: PMC5381350 DOI: 10.1093/dnares/dsw050] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 10/26/2016] [Indexed: 01/08/2023] Open
Abstract
The recent development of Sequence Capture methodology represents a powerful strategy for enhancing data generation to assess genetic variation of targeted genomic regions. Here, we present SUPER-CAP, a bioinformatics web tool aimed at handling Sequence Capture data, fine calculating the allele frequency of variations and building genotype-specific sequence of captured genes. The dataset used to develop this in silico strategy consists of 378 loci and related regulative regions in a collection of 44 tomato landraces. About 14,000 high-quality variants were identified. The high depth (>40×) of coverage and adopting the correct filtering criteria allowed identification of about 4,000 rare variants and 10 genes with a different copy number variation. We also show that the tool is capable to reconstruct genotype-specific sequences for each genotype by using the detected variants. This allows evaluating the combined effect of multiple variants in the same protein. The architecture and functionality of SUPER-CAP makes the software appropriate for a broad set of analyses including SNP discovery and mining. Its functionality, together with the capability to process large data sets and efficient detection of sequence variation, makes SUPER-CAP a valuable bioinformatics tool for genomics and breeding purposes.
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Affiliation(s)
- Valentino Ruggieri
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici (NA), Italy.,Sequentia Biotech SL, Calle Compte d'Urgell, 240, 08035 Barcelona, Spain
| | - Irantzu Anzar
- Sequentia Biotech SL, Calle Compte d'Urgell, 240, 08035 Barcelona, Spain
| | - Andreu Paytuvi
- Sequentia Biotech SL, Calle Compte d'Urgell, 240, 08035 Barcelona, Spain
| | - Roberta Calafiore
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici (NA), Italy
| | | | - Walter Sanseverino
- Sequentia Biotech SL, Calle Compte d'Urgell, 240, 08035 Barcelona, Spain
| | - Amalia Barone
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055 Portici (NA), Italy
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20
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Wang B, Guo X, Zhao P, Ruan M, Yu X, Zou L, Yang Y, Li X, Deng D, Xiao J, Xiao Y, Hu C, Wang X, Wang X, Wang W, Peng M. Molecular diversity analysis, drought related marker-traits association mapping and discovery of excellent alleles for 100-day old plants by EST-SSRs in cassava germplasms (Manihot esculenta Cranz). PLoS One 2017; 12:e0177456. [PMID: 28493955 PMCID: PMC5426748 DOI: 10.1371/journal.pone.0177456] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Accepted: 04/27/2017] [Indexed: 11/19/2022] Open
Abstract
Cassava is the third largest food crop of the world and has strong ability of drought tolerance. In order to evaluate the molecular diversity and to discover novel alleles for drought tolerance in cassava germplasms, we examined a total of 107 abiotic stress related expressed sequence tags-simple sequence repeat (EST-SSR) markers in 134 cassava genotypes coming from planting regions worldwide and performed drought related marker-traits association mapping. As results, we successfully amplified 98 of 107 markers in 97 polymorphic loci and 279 alleles, with 2.87 alleles per locus, gene diversity of 0.48 and polymorphic information content (PIC) of 0.41 on average. The genetic coefficient between every two lines was 0.37 on average, ranging from 0.21 to 0.82. According to our population structure analysis, these samples could be divided into three sub-populations showing obvious gene flow between them. We also performed water stress experiments using 100-day old cassava plants in two years and calculated the drought tolerance coefficients (DTCs) and used them as phenotypes for marker-trait association mapping. We found that 53 markers were significantly associated with these drought-related traits, with a contribution rate for trait variation of 8.60% on average, ranging between 2.66 and 28.09%. Twenty-four of these 53 associated genes showed differential transcription or protein levels which were confirmed by qRT-PCR under drought stress when compared to the control conditions in cassava. Twelve of twenty-four genes were the same differential expression patterns in omics data and results of qRT-PCR. Out of 33 marker-traits combinations on 24 loci, 34 were positive and 53 negative alleles according to their phenotypic effects and we also obtained the typical materials which carried these elite alleles. We also found 23 positive average allele effects while 10 loci were negative according to their allele effects (AAEs). Our results on molecular diversity, locus association and differential expression under drought can prove beneficial to select excellent materials through marker assisted selection and for functional genes research in the future.
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Affiliation(s)
- Bin Wang
- College of plant science & technology, Huazhong Agricultrural University, Wuhan, Hubei, PR China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xin Guo
- College of plant science & technology, Huazhong Agricultrural University, Wuhan, Hubei, PR China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Pingjuan Zhao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Mengbin Ruan
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xiaoling Yu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Liangping Zou
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Yiling Yang
- College of plant science & technology, Huazhong Agricultrural University, Wuhan, Hubei, PR China
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xiao Li
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Deli Deng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Jixiang Xiao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Yiwei Xiao
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Chunji Hu
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xue Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Xiaolin Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Wenquan Wang
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
| | - Ming Peng
- Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, PR China
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Ministry of Agriculture, Haikou, PR China
- * E-mail:
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Fudge J, Mangel N, Gruissem W, Vanderschuren H, Fitzpatrick TB. Rationalising vitamin B6 biofortification in crop plants. Curr Opin Biotechnol 2017; 44:130-137. [DOI: 10.1016/j.copbio.2016.12.004] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/17/2016] [Accepted: 12/19/2016] [Indexed: 12/31/2022]
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In Silico identification and annotation of non-coding RNAs by RNA-seq and De Novo assembly of the transcriptome of Tomato Fruits. PLoS One 2017; 12:e0171504. [PMID: 28187155 PMCID: PMC5302821 DOI: 10.1371/journal.pone.0171504] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 01/21/2017] [Indexed: 12/12/2022] Open
Abstract
The complexity of the tomato (Solanum lycopersicum) transcriptome has not yet been fully elucidated. To gain insights into the diversity and features of coding and non-coding RNA molecules of tomato fruits, we generated strand-specific libraries from berries of two tomato cultivars grown in two open-field conditions with different soil type. Following high-throughput Illumina RNA-sequencing (RNA-seq), more than 90% of the reads (over one billion, derived from twelve dataset) were aligned to the tomato reference genome. We report a comprehensive analysis of the transcriptome, improved with 39,095 transcripts, which reveals previously unannotated novel transcripts, natural antisense transcripts, long non-coding RNAs and alternative splicing variants. In addition, we investigated the sequence variants between the cultivars under investigation to highlight their genetic difference. Our strand-specific analysis allowed us to expand the current tomato transcriptome annotation and it is the first to reveal the complexity of the poly-adenylated RNA world in tomato. Moreover, our work demonstrates the usefulness of strand specific RNA-seq approach for the transcriptome-based genome annotation and provides a resource valuable for further functional studies.
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Lim SL, D'Agui HM, Enright NJ, He T. Characterization of Leaf Transcriptome in Banksia hookeriana. GENOMICS PROTEOMICS & BIOINFORMATICS 2017; 15:49-56. [PMID: 28161492 PMCID: PMC5339403 DOI: 10.1016/j.gpb.2016.11.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Revised: 11/06/2016] [Accepted: 11/24/2016] [Indexed: 12/23/2022]
Abstract
Banksia is a significant element in vegetation of southwestern Australia, a biodiversity hotspot with global significance. In particular, Banksia hookeriana represents a species with significant economic and ecological importance in the region. For better conservation and management, we reported an overview of transcriptome of B. hookeriana using RNA-seq and de novo assembly. We have generated a total of 202.7 million reads (18.91 billion of nucleotides) from four leaf samples in four plants of B. hookeriana, and assembled 59,063 unigenes (average size = 1098 bp) through de novotranscriptome assembly. Among them, 39,686 unigenes were annotated against the Swiss-Prot, Clusters of Orthologous Groups (COG), and NCBI non-redundant (NR) protein databases. We showed that there was approximately one single nucleotide polymorphism (SNP) per 5.6–7.1 kb in the transcriptome, and the ratio of transitional to transversional polymorphisms was approximately 1.82. We compared unigenes of B. hookeriana to those of Arabidopsis thaliana and Nelumbo nucifera through sequence homology, Gene Ontology (GO) annotation, and KEGG pathway analyses. The comparative analysis revealed that unigenes of B. hookeriana were closely related to those of N. nucifera. B. hookeriana, N. nucifera, and A. thaliana shared similar GO annotations but different distributions in KEGG pathways, indicating that B. hookeriana has adapted to dry-Mediterranean type shrublands via regulating expression of specific genes. In total 1927 potential simple sequence repeat (SSR) markers were discovered, which could be used in the genotype and genetic diversity studies of the Banksia genus. Our results provide valuable sequence resource for further study in Banksia.
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Affiliation(s)
- Sim Lin Lim
- Department of Environment and Agriculture, Curtin University, Perth, WA 6845, Australia
| | - Haylee M D'Agui
- Department of Environment and Agriculture, Curtin University, Perth, WA 6845, Australia
| | - Neal J Enright
- School of Veterinary and Life Sciences, Murdoch University, Perth, WA 6150, Australia
| | - Tianhua He
- Department of Environment and Agriculture, Curtin University, Perth, WA 6845, Australia.
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Duitama J, Kafuri L, Tello D, Leiva AM, Hofinger B, Datta S, Lentini Z, Aranzales E, Till B, Ceballos H. Deep Assessment of Genomic Diversity in Cassava for Herbicide Tolerance and Starch Biosynthesis. Comput Struct Biotechnol J 2017; 15:185-194. [PMID: 28179981 PMCID: PMC5295625 DOI: 10.1016/j.csbj.2017.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 12/26/2016] [Accepted: 01/10/2017] [Indexed: 12/16/2022] Open
Abstract
Cassava is one of the most important food security crops in tropical countries, and a competitive resource for the starch, food, feed and ethanol industries. However, genomics research in this crop is much less developed compared to other economically important crops such as rice or maize. The International Center for Tropical Agriculture (CIAT) maintains the largest cassava germplasm collection in the world. Unfortunately, the genetic potential of this diversity for breeding programs remains underexploited due to the difficulties in phenotypic screening and lack of deep genomic information about the different accessions. A chromosome-level assembly of the cassava reference genome was released this year and only a handful of studies have been made, mainly to find quantitative trait loci (QTL) on breeding populations with limited variability. This work presents the results of pooled targeted resequencing of more than 1500 cassava accessions from the CIAT germplasm collection to obtain a dataset of more than 2000 variants within genes related to starch functional properties and herbicide tolerance. Results of twelve bioinformatic pipelines for variant detection in pooled samples were compared to ensure the quality of the variant calling process. Predictions of functional impact were performed using two separate methods to prioritize interesting variation for genotyping and cultivar selection. Targeted resequencing, either by pooled samples or by similar approaches such as Ecotilling or capture, emerges as a cost effective alternative to whole genome sequencing to identify interesting alleles of genes related to relevant traits within large germplasm collections.
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Affiliation(s)
- Jorge Duitama
- Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Systems and Computing Engineering Department, Universidad de los Andes, Bogotá, Colombia
| | - Lina Kafuri
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Seibersdorf, Austria
- Department of Biological Sciences, School of Natural Sciences, Universidad Icesi, Cali, Colombia
| | - Daniel Tello
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Seibersdorf, Austria
- Department of Biological Sciences, School of Natural Sciences, Universidad Icesi, Cali, Colombia
| | - Ana María Leiva
- Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Bernhard Hofinger
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Seibersdorf, Austria
| | - Sneha Datta
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Seibersdorf, Austria
| | - Zaida Lentini
- Department of Biological Sciences, School of Natural Sciences, Universidad Icesi, Cali, Colombia
| | - Ericson Aranzales
- Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Bradley Till
- Plant Breeding and Genetics Laboratory, Joint FAO/IAEA Division, International Atomic Energy Agency, Seibersdorf, Austria
| | - Hernán Ceballos
- Agrobiodiversity Research Area, International Center for Tropical Agriculture (CIAT), Cali, Colombia
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Kaur P, Gaikwad K. From Genomes to GENE-omes: Exome Sequencing Concept and Applications in Crop Improvement. FRONTIERS IN PLANT SCIENCE 2017; 8:2164. [PMID: 29312405 PMCID: PMC5742236 DOI: 10.3389/fpls.2017.02164] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 12/08/2017] [Indexed: 05/13/2023]
Abstract
Exome sequencing represents targeted capture and sequencing of 1-2% of 'high-value genomic regions' (subset of the genome) which are enriched for functional variants and harbors low level of repetitive regions. We discuss here an overview of exome sequencing, ways to approach plant exomes, and advantages and applicability of this powerful approach in deciphering functional regions of genomes. Though initially this approach was developed as an alternative to whole genome sequencing (WGS), but the multitude of benefits conferred by sequence capture via hybridization approaches created a niche for itself to solve many of biological riddles, particularly for resolving phylogenetic distances. The technique has also proved to be successful in understanding the basis of natural and induced molecular variation, marker development and developing genomic resources for complex, wild and non-model species, which are still intractable for WGS efforts. Thus, with profound applications of this powerful sequencing strategy, near future is expected to witness a collective expansion of both techniques, i.e., sequence capture via hybridization for evolutionary and ecological research and WGS approaches for its universal accessibility.
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Onda Y, Mochida K. Exploring Genetic Diversity in Plants Using High-Throughput Sequencing Techniques. Curr Genomics 2016; 17:358-67. [PMID: 27499684 PMCID: PMC4955029 DOI: 10.2174/1389202917666160331202742] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 07/19/2015] [Accepted: 07/21/2015] [Indexed: 12/31/2022] Open
Abstract
Food security has emerged as an urgent concern because of the rising world population. To meet the food demands of the near future, it is required to improve the productivity of various crops, not just of staple food crops. The genetic diversity among plant populations in a given species allows the plants to adapt to various environmental conditions. Such diversity could therefore yield valuable traits that could overcome the food-security challenges. To explore genetic diversity comprehensively and to rapidly identify useful genes and/or allele, advanced high-throughput sequencing techniques, also called next-generation sequencing (NGS) technologies, have been developed. These provide practical solutions to the challenges in crop genomics. Here, we review various sources of genetic diversity in plants, newly developed genetic diversity-mining tools synergized with NGS techniques, and related genetic approaches such as quantitative trait locus analysis and genome-wide association study.
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Affiliation(s)
- Yoshihiko Onda
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa,Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa,Japan
| | - Keiichi Mochida
- Cellulose Production Research Team, Biomass Engineering Research Division, RIKEN Center for Sustainable Resource Science, Kanagawa,Japan
- Kihara Institute for Biological Research, Yokohama City University, Kanagawa,Japan
- Gene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Kanagawa,Japan
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Gasc C, Peyretaillade E, Peyret P. Sequence capture by hybridization to explore modern and ancient genomic diversity in model and nonmodel organisms. Nucleic Acids Res 2016; 44:4504-18. [PMID: 27105841 PMCID: PMC4889952 DOI: 10.1093/nar/gkw309] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 04/07/2016] [Accepted: 04/12/2016] [Indexed: 12/25/2022] Open
Abstract
The recent expansion of next-generation sequencing has significantly improved biological research. Nevertheless, deep exploration of genomes or metagenomic samples remains difficult because of the sequencing depth and the associated costs required. Therefore, different partitioning strategies have been developed to sequence informative subsets of studied genomes. Among these strategies, hybridization capture has proven to be an innovative and efficient tool for targeting and enriching specific biomarkers in complex DNA mixtures. It has been successfully applied in numerous areas of biology, such as exome resequencing for the identification of mutations underlying Mendelian or complex diseases and cancers, and its usefulness has been demonstrated in the agronomic field through the linking of genetic variants to agricultural phenotypic traits of interest. Moreover, hybridization capture has provided access to underexplored, but relevant fractions of genomes through its ability to enrich defined targets and their flanking regions. Finally, on the basis of restricted genomic information, this method has also allowed the expansion of knowledge of nonreference species and ancient genomes and provided a better understanding of metagenomic samples. In this review, we present the major advances and discoveries permitted by hybridization capture and highlight the potency of this approach in all areas of biology.
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Affiliation(s)
- Cyrielle Gasc
- EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, 63001, France
| | | | - Pierre Peyret
- EA 4678 CIDAM, Université d'Auvergne, Clermont-Ferrand, 63001, France
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Castro JC, Maddox JD, Cobos M, Requena D, Zimic M, Bombarely A, Imán SA, Cerdeira LA, Medina AE. De novo assembly and functional annotation of Myrciaria dubia fruit transcriptome reveals multiple metabolic pathways for L-ascorbic acid biosynthesis. BMC Genomics 2015; 16:997. [PMID: 26602763 PMCID: PMC4658800 DOI: 10.1186/s12864-015-2225-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 11/17/2015] [Indexed: 01/13/2023] Open
Abstract
Background Myrciaria dubia is an Amazonian fruit shrub that produces numerous bioactive phytochemicals, but is best known by its high L-ascorbic acid (AsA) content in fruits. Pronounced variation in AsA content has been observed both within and among individuals, but the genetic factors responsible for this variation are largely unknown. The goals of this research, therefore, were to assemble, characterize, and annotate the fruit transcriptome of M. dubia in order to reconstruct metabolic pathways and determine if multiple pathways contribute to AsA biosynthesis. Results In total 24,551,882 high-quality sequence reads were de novo assembled into 70,048 unigenes (mean length = 1150 bp, N50 = 1775 bp). Assembled sequences were annotated using BLASTX against public databases such as TAIR, GR-protein, FB, MGI, RGD, ZFIN, SGN, WB, TIGR_CMR, and JCVI-CMR with 75.2 % of unigenes having annotations. Of the three core GO annotation categories, biological processes comprised 53.6 % of the total assigned annotations, whereas cellular components and molecular functions comprised 23.3 and 23.1 %, respectively. Based on the KEGG pathway assignment of the functionally annotated transcripts, five metabolic pathways for AsA biosynthesis were identified: animal-like pathway, myo-inositol pathway, L-gulose pathway, D-mannose/L-galactose pathway, and uronic acid pathway. All transcripts coding enzymes involved in the ascorbate-glutathione cycle were also identified. Finally, we used the assembly to identified 6314 genic microsatellites and 23,481 high quality SNPs. Conclusions This study describes the first next-generation sequencing effort and transcriptome annotation of a non-model Amazonian plant that is relevant for AsA production and other bioactive phytochemicals. Genes encoding key enzymes were successfully identified and metabolic pathways involved in biosynthesis of AsA, anthocyanins, and other metabolic pathways have been reconstructed. The identification of these genes and pathways is in agreement with the empirically observed capability of M. dubia to synthesize and accumulate AsA and other important molecules, and adds to our current knowledge of the molecular biology and biochemistry of their production in plants. By providing insights into the mechanisms underpinning these metabolic processes, these results can be used to direct efforts to genetically manipulate this organism in order to enhance the production of these bioactive phytochemicals. The accumulation of AsA precursor and discovery of genes associated with their biosynthesis and metabolism in M. dubia is intriguing and worthy of further investigation. The sequences and pathways produced here present the genetic framework required for further studies. Quantitative transcriptomics in concert with studies of the genome, proteome, and metabolome under conditions that stimulate production and accumulation of AsA and their precursors are needed to provide a more comprehensive view of how these pathways for AsA metabolism are regulated and linked in this species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2225-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Juan C Castro
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú. .,Círculo de Investigación en Plantas con Efecto en Salud (FONDECYT N° 010-2014), Lima, Perú.
| | - J Dylan Maddox
- Pritzker Laboratory for Molecular Systematics and Evolution, The Field Museum of Natural History, Chicago, IL, USA.
| | - Marianela Cobos
- Laboratorio de Biotecnología y Bioenergética, Universidad Científica del Perú (UCP), Av. Abelardo Quiñones km 2.5, San Juan Bautista, Iquitos, Perú.
| | - David Requena
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo (LID), Facultad de Ciencias, Universidad Peruana Cayetano Heredia (UPCH), Av. Honorio Delgado 430, San Martín de Porres, Lima, Perú. .,FARVET S.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta, Ica, Perú.
| | - Mirko Zimic
- Laboratorio de Bioinformática y Biología Molecular, Laboratorios de Investigación y Desarrollo (LID), Facultad de Ciencias, Universidad Peruana Cayetano Heredia (UPCH), Av. Honorio Delgado 430, San Martín de Porres, Lima, Perú. .,FARVET S.A.C. Carretera Panamericana Sur N° 766 Km 198.5, Chincha Alta, Ica, Perú.
| | | | - Sixto A Imán
- Área de Conservación de Recursos Fitogenéticos, Instituto Nacional de Innovación Agraria (INIA), Calle San Roque 209, Iquitos, Perú.
| | - Luis A Cerdeira
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú.
| | - Andersson E Medina
- Unidad Especializada de Biotecnología, Centro de Investigaciones de Recursos Naturales de la Amazonía (CIRNA), Universidad Nacional de la Amazonía Peruana (UNAP), Pasaje Los Paujiles S/N, San Juan Bautista, Iquitos, Perú.
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Curci PL, De Paola D, Sonnante G. Development of chloroplast genomic resources for Cynara. Mol Ecol Resour 2015; 16:562-73. [PMID: 26354522 DOI: 10.1111/1755-0998.12457] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 07/31/2015] [Accepted: 08/14/2015] [Indexed: 12/17/2022]
Abstract
In this study, new chloroplast (cp) resources were developed for the genus Cynara, using whole cp genomes from 20 genotypes, by means of high-throughput sequencing technologies. Our target species included seven globe artichokes, two cultivated cardoons, eight wild artichokes, and three other wild Cynara species (C. baetica, C. cornigera and C. syriaca). One complete cp genome was isolated using short reads from a whole-genome sequencing project, while the others were obtained by means of long-range PCR, for which primer pairs are provided here. A de novo assembly strategy combined with a reference-based assembly allowed us to reconstruct each cp genome. Comparative analyses among the newly sequenced genotypes and two additional Cynara cp genomes ('Brindisino' artichoke and C. humilis) retrieved from public databases revealed 126 parsimony informative characters and 258 singletons in Cynara, for a total of 384 variable characters. Thirty-nine SSR loci and 34 other INDEL events were detected. After data analysis, 37 primer pairs for SSR amplification were designed, and these molecular markers were subsequently validated in our Cynara genotypes. Phylogenetic analysis based on all cp variable characters provided the best resolution when compared to what was observed using only parsimony informative characters, or only short 'variable' cp regions. The evaluation of the molecular resources obtained from this study led us to support the 'super-barcode' theory and consider the total cp sequence of Cynara as a reliable and valuable molecular marker for exploring species diversity and examining variation below the species level.
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Affiliation(s)
- Pasquale L Curci
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola, 165/A, 70126, Bari, Italy
| | - Domenico De Paola
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola, 165/A, 70126, Bari, Italy
| | - Gabriella Sonnante
- Institute of Biosciences and Bioresources, National Research Council, Via Amendola, 165/A, 70126, Bari, Italy
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Shearman JR, Sangsrakru D, Jomchai N, Ruang-areerate P, Sonthirod C, Naktang C, Theerawattanasuk K, Tragoonrung S, Tangphatsornruang S. SNP identification from RNA sequencing and linkage map construction of rubber tree for anchoring the draft genome. PLoS One 2015; 10:e0121961. [PMID: 25831195 PMCID: PMC4382108 DOI: 10.1371/journal.pone.0121961] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Accepted: 02/07/2015] [Indexed: 12/21/2022] Open
Abstract
Hevea brasiliensis, or rubber tree, is an important crop species that accounts for the majority of natural latex production. The rubber tree nuclear genome consists of 18 chromosomes and is roughly 2.15 Gb. The current rubber tree reference genome assembly consists of 1,150,326 scaffolds ranging from 200 to 531,465 bp and totalling 1.1 Gb. Only 143 scaffolds, totalling 7.6 Mb, have been placed into linkage groups. We have performed RNA-seq on 6 varieties of rubber tree to identify SNPs and InDels and used this information to perform target sequence enrichment and high throughput sequencing to genotype a set of SNPs in 149 rubber tree offspring from a cross between RRIM 600 and RRII 105 rubber tree varieties. We used this information to generate a linkage map allowing for the anchoring of 24,424 contigs from 3,009 scaffolds, totalling 115 Mb or 10.4% of the published sequence, into 18 linkage groups. Each linkage group contains between 319 and 1367 SNPs, or 60 to 194 non-redundant marker positions, and ranges from 156 to 336 cM in length. This linkage map includes 20,143 of the 69,300 predicted genes from rubber tree and will be useful for mapping studies and improving the reference genome assembly.
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Affiliation(s)
- Jeremy R. Shearman
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand
| | - Nukoon Jomchai
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand
| | - Panthita Ruang-areerate
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand
| | - Chaiwat Naktang
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand
| | - Kanikar Theerawattanasuk
- Rubber Research Institute of Thailand (RRIT), Department of Agriculture, Ministry of Agriculture and Cooperatives, 50 Phaholyothin Road, Chatuchack, Bangkok, 10900, Thailand
| | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Paholyothin Road, Khlong Nueng, Khlong Luang, Pathumthani, 12120, Thailand
- * E-mail:
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Pootakham W, Jomchai N, Ruang-Areerate P, Shearman JR, Sonthirod C, Sangsrakru D, Tragoonrung S, Tangphatsornruang S. Genome-wide SNP discovery and identification of QTL associated with agronomic traits in oil palm using genotyping-by-sequencing (GBS). Genomics 2015; 105:288-95. [PMID: 25702931 DOI: 10.1016/j.ygeno.2015.02.002] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 02/03/2015] [Accepted: 02/12/2015] [Indexed: 11/24/2022]
Abstract
Oil palm has become one of the most important oil crops in the world. Marker-assisted selections have played a pivotal role in oil palm breeding programs. Here, we report the use of genotyping-by-sequencing (GBS) approach for a large-scale SNP discovery and genotyping of a mapping population. Reduced representation libraries of 108 F2 progeny were sequenced and a total of 524 million reads were obtained. We detected 21,471 single nucleotide substitutions, most of which (62.6%) represented transition events. Of 3417 fully informative SNP markers, we were able to place 1085 on a linkage map, which spanned 1429.6 cM and had an average of one marker every 1.26 cM. Three QTL affecting trunk height were detected on LG 10, 14 and 15, whereas a single QTL associated with fruit bunch weight was identified on LG 3. The use of GBS approach proved to be rapid, cost-effective and highly reproducible in this species.
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Affiliation(s)
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Nukoon Jomchai
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Panthita Ruang-Areerate
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Jeremy R Shearman
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology, 113 Thailand Science Park, Pathum Thani 12120, Thailand.
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Pootakham W, Ruang-Areerate P, Jomchai N, Sonthirod C, Sangsrakru D, Yoocha T, Theerawattanasuk K, Nirapathpongporn K, Romruensukharom P, Tragoonrung S, Tangphatsornruang S. Construction of a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis) using genotyping-by-sequencing (GBS). FRONTIERS IN PLANT SCIENCE 2015; 6:367. [PMID: 26074933 PMCID: PMC4444744 DOI: 10.3389/fpls.2015.00367] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2015] [Accepted: 05/09/2015] [Indexed: 05/18/2023]
Abstract
Construction of linkage maps is crucial for genetic studies and marker-assisted breeding programs. Recent advances in next generation sequencing technologies allow for the generation of high-density linkage maps, especially in non-model species lacking extensive genomic resources. Here, we constructed a high-density integrated genetic linkage map of rubber tree (Hevea brasiliensis), the sole commercial producer of high-quality natural rubber. We applied a genotyping-by-sequencing (GBS) technique to simultaneously discover and genotype single nucleotide polymorphism (SNP) markers in two rubber tree populations. A total of 21,353 single nucleotide substitutions were identified, 55% of which represented transition events. GBS-based genetic maps of populations P and C comprised 1704 and 1719 markers and encompassed 2041 cM and 1874 cM, respectively. The average marker densities of these two maps were one SNP in 1.23-1.25 cM. A total of 1114 shared SNP markers were used to merge the two component maps. An integrated linkage map consisted of 2321 markers and spanned the cumulative length of 2052 cM. The composite map showed a substantial improvement in marker density, with one SNP marker in every 0.89 cM. To our knowledge, this is the most saturated genetic map in rubber tree to date. This integrated map allowed us to anchor 28,965 contigs, covering 135 Mb or 12% of the published rubber tree genome. We demonstrated that GBS is a robust and cost-effective approach for generating a common set of genome-wide SNP data suitable for constructing integrated linkage maps from multiple populations in a highly heterozygous agricultural species.
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Affiliation(s)
- Wirulda Pootakham
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Panthita Ruang-Areerate
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Nukoon Jomchai
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Chutima Sonthirod
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Duangjai Sangsrakru
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Thippawan Yoocha
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Kanikar Theerawattanasuk
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Kanlaya Nirapathpongporn
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Phayao Romruensukharom
- Department of Agriculture, Rubber Research Institute of Thailand, Ministry of Agriculture and CooperativesBangkok, Thailand
| | - Somvong Tragoonrung
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
| | - Sithichoke Tangphatsornruang
- National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development AgencyPathum Thani, Thailand
- *Correspondence: Sithichoke Tangphatsornruang, National Center for Genetic Engineering and Biotechnology (BIOTEC), 113 Thailand Science Park, Phahonyothin Rd., Khlong Nueng, Khlong Luang, Pathum Thani 12120, Thailand
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