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Kassem MA, Knizia D, Meksem K. A Summary of Two Decades of QTL and Candidate Genes That Control Seed Tocopherol Contents in Maize ( Zea mays L.). Genes (Basel) 2024; 15:472. [PMID: 38674406 PMCID: PMC11049817 DOI: 10.3390/genes15040472] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Revised: 04/04/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Tocopherols are secondary metabolites synthesized through the shikimate biosynthetic pathway in the plastids of most plants. It is well known that α-Tocopherol (vitamin E) has many health benefits for humans and animals; therefore, it is highly used in human and animal diets. Tocopherols vary considerably in most crop (and plant) species and within cultivars of the same species depending on environmental and growth conditions; tocopherol content is a polygenic, complex traits, and its inheritance is poorly understood. The objective of this review paper was to summarize all identified quantitative trait loci (QTL) that control seed tocopherols and related contents identified in maize (Zea mays) during the past two decades (2002-2022). Candidate genes identified within these QTL regions are also discussed. The QTL described here, and candidate genes identified within these genomic regions could be used in breeding programs to develop maize cultivars with high, beneficial levels of seed tocopherol contents.
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Affiliation(s)
- My Abdelmajid Kassem
- Plant Genomics and Biotechnology Laboratory, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA
| | - Dounya Knizia
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (D.K.); (K.M.)
| | - Khalid Meksem
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (D.K.); (K.M.)
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Goshika S, Meksem K, Ahmed KR, Lakhssassi N. Deep Learning Model for Classifying and Evaluating Soybean Leaf Disease Damage. Int J Mol Sci 2023; 25:106. [PMID: 38203277 PMCID: PMC10779234 DOI: 10.3390/ijms25010106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024] Open
Abstract
Soybean (Glycine max (L.) Merr.) is a major source of oil and protein for human food and animal feed; however, soybean crops face diverse factors causing damage, including pathogen infections, environmental shifts, poor fertilization, and incorrect pesticide use, leading to reduced yields. Identifying the level of leaf damage aids yield projections, pesticide, and fertilizer decisions. Deep learning models (DLMs) and neural networks mastering tasks from abundant data have been used for binary healthy/unhealthy leaf classification. However, no DLM predicts and categorizes soybean leaf damage severity (five levels) for tailored pesticide use and yield forecasts. This paper introduces a novel DLM for accurate damage prediction and classification, trained on 2930 near-field soybean leaf images. The model quantifies damage severity, distinguishing healthy/unhealthy leaves and offering a comprehensive solution. Performance metrics include accuracy, precision, recall, and F1-score. This research presents a robust DLM for soybean damage assessment, supporting informed agricultural decisions based on specific damage levels and enhancing crop management and productivity.
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Affiliation(s)
- Sandeep Goshika
- School of Computing, Southern Illinois University, Carbondale, IL 62901, USA; (S.G.); (K.R.A.)
| | - Khalid Meksem
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901, USA;
| | - Khaled R. Ahmed
- School of Computing, Southern Illinois University, Carbondale, IL 62901, USA; (S.G.); (K.R.A.)
| | - Naoufal Lakhssassi
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901, USA;
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Zhang L, Zhao J, Kong L, Huang W, Peng H, Peng D, Meksem K, Liu S. No Pairwise Interactions of GmSNAP18, GmSHMT08 and AtPR1 with Suppressed AtPR1 Expression Enhance the Susceptibility of Arabidopsis to Beet Cyst Nematode. Plants (Basel) 2023; 12:4118. [PMID: 38140445 PMCID: PMC10747334 DOI: 10.3390/plants12244118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/06/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023]
Abstract
GmSNAP18 and GmSHMT08 are two major genes conferring soybean cyst nematode (SCN) resistance in soybean. Overexpression of either of these two soybean genes would enhance the susceptibility of Arabidopsis to beet cyst nematode (BCN), while overexpression of either of their corresponding orthologs in Arabidopsis, AtSNAP2 and AtSHMT4, would suppress it. However, the mechanism by which these two pairs of orthologous genes boost or inhibit BCN susceptibility of Arabidopsis still remains elusive. In this study, Arabidopsis with simultaneously overexpressed GmSNAP18 and GmSHMT0 suppressed the growth of underground as well as above-ground parts of plants. Furthermore, Arabidopsis that simultaneously overexpressed GmSNAP18 and GmSHMT08 substantially stimulated BCN susceptibility and remarkably suppressed expression of AtPR1 in the salicylic acid signaling pathway. However, simultaneous overexpression of GmSNAP18 and GmSHMT08 did not impact the expression of AtJAR1 and AtHEL1 in the jasmonic acid and ethylene signaling pathways. GmSNAP18, GmSHMT08, and a pathogenesis-related (PR) protein, GmPR08-Bet VI, in soybean, and AtSNAP2, AtSHMT4, and AtPR1 in Arabidopsis could interact pair-wisely for mediating SCN and BCN resistance in soybean and Arabidopsis, respectively. Both AtSNAP2 and AtPR1 were localized on the plasma membrane, and AtSHMT4 was localized both on the plasma membrane and in the nucleus of cells. Nevertheless, after interactions, AtSNAP2 and AtPR1 could partially translocate into the cell nucleus. GmSNAP18 interacted with AtSHMT4, and GmSHMT4 interacted with AtSNAP2. However, neither GmSNAP18 nor GmSHMT08 interacted with AtPR1. Thus, no pairwise interactions among α-SNAPs, SHMTs, and AtPR1 occurred in Arabidopsis overexpressing either GmSNAP18 or GmSHMT08, or both of them. Transgenic Arabidopsis overexpressing either GmSNAP18 or GmSHMT08 substantially suppressed AtPR1 expression, while transgenic Arabidopsis overexpressing either AtSNAP2 or AtSHMT4 remarkably enhanced it. Taken together, no pairwise interactions of GmSNAP18, GmSHMT08, and AtPR1 with suppressed expression of AtPR1 enhanced BCN susceptibility in Arabidopsis. This study may provide a clue that nematode-resistant or -susceptible functions of plant genes likely depend on both hosts and nematode species.
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Affiliation(s)
- Liuping Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.Z.); (J.Z.); (L.K.); (W.H.); (H.P.); (D.P.)
| | - Jie Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.Z.); (J.Z.); (L.K.); (W.H.); (H.P.); (D.P.)
| | - Lingan Kong
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.Z.); (J.Z.); (L.K.); (W.H.); (H.P.); (D.P.)
| | - Wenkun Huang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.Z.); (J.Z.); (L.K.); (W.H.); (H.P.); (D.P.)
| | - Huan Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.Z.); (J.Z.); (L.K.); (W.H.); (H.P.); (D.P.)
| | - Deliang Peng
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.Z.); (J.Z.); (L.K.); (W.H.); (H.P.); (D.P.)
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA;
| | - Shiming Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (L.Z.); (J.Z.); (L.K.); (W.H.); (H.P.); (D.P.)
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Bellaloui N, Knizia D, Yuan J, Song Q, Betts F, Register T, Williams E, Lakhssassi N, Mazouz H, Nguyen HT, Meksem K, Mengistu A, Kassem MA. Genetic Mapping for QTL Associated with Seed Nickel and Molybdenum Accumulation in the Soybean 'Forrest' by 'Williams 82' RIL Population. Plants (Basel) 2023; 12:3709. [PMID: 37960065 PMCID: PMC10649706 DOI: 10.3390/plants12213709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 10/01/2023] [Accepted: 10/23/2023] [Indexed: 11/15/2023]
Abstract
Understanding the genetic basis of seed Ni and Mo is essential. Since soybean is a major crop in the world and a major source for nutrients, including Ni and Mo, the objective of the current research was to map genetic regions (quantitative trait loci, QTL) linked to Ni and Mo concentrations in soybean seed. A recombinant inbred line (RIL) population was derived from a cross between 'Forrest' and 'Williams 82' (F × W82). A total of 306 lines was used for genotyping using 5405 single nucleotides polymorphism (SNP) markers using Infinium SNP6K BeadChips. A two-year experiment was conducted and included the parents and the RIL population. One experiment was conducted in 2018 in North Carolina (NC), and the second experiment was conducted in Illinois in 2020 (IL). Logarithm of the odds (LOD) of ≥2.5 was set as a threshold to report identified QTL using the composite interval mapping (CIM) method. A wide range of Ni and Mo concentrations among RILs was observed. A total of four QTL (qNi-01, qNi-02, and qNi-03 on Chr 2, 8, and 9, respectively, in 2018, and qNi-01 on Chr 20 in 2020) was identified for seed Ni. All these QTL were significantly (LOD threshold > 2.5) associated with seed Ni, with LOD scores ranging between 2.71-3.44, and with phenotypic variance ranging from 4.48-6.97%. A total of three QTL for Mo (qMo-01, qMo-02, and qMo-03 on Chr 1, 3, 17, respectively) was identified in 2018, and four QTL (qMo-01, qMo-02, qMo-03, and qMo-04, on Chr 5, 11, 14, and 16, respectively) were identified in 2020. Some of the current QTL had high LOD and significantly contributed to the phenotypic variance for the trait. For example, in 2018, Mo QTL qMo-01 on Chr 1 had LOD of 7.8, explaining a phenotypic variance of 41.17%, and qMo-03 on Chr 17 had LOD of 5.33, with phenotypic variance explained of 41.49%. In addition, one Mo QTL (qMo-03 on Chr 14) had LOD of 9.77, explaining 51.57% of phenotypic variance related to the trait, and another Mo QTL (qMo-04 on Chr 16) had LOD of 7.62 and explained 49.95% of phenotypic variance. None of the QTL identified here were identified twice across locations/years. Based on a search of the available literature and of SoyBase, the four QTL for Ni, identified on Chr 2, 8, 9, and 20, and the five QTL associated with Mo, identified on Chr 1, 17, 11, 14, and 16, are novel and not previously reported. This research contributes new insights into the genetic mapping of Ni and Mo, and provides valuable QTL and molecular markers that can potentially assist in selecting Ni and Mo levels in soybean seeds.
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Affiliation(s)
- Nacer Bellaloui
- Crop Genetics Research Unit, USDA, Agriculture Research Service, 141 Experiment Station Road, Stoneville, MS 38776, USA
| | - Dounya Knizia
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (D.K.); (N.L.); (K.M.)
- Laboratoire de Biotechnologies & Valorisation des Bio-Ressources (BioVar), Département de Biologie, Faculté des Sciences, Université Moulay Ismail, Meknès 50000, Morocco;
| | - Jiazheng Yuan
- Plant Genomics and Biotechnology Laboratory, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (J.Y.); (F.B.); (T.R.); (E.W.); (M.A.K.)
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, USA;
| | - Frances Betts
- Plant Genomics and Biotechnology Laboratory, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (J.Y.); (F.B.); (T.R.); (E.W.); (M.A.K.)
| | - Teresa Register
- Plant Genomics and Biotechnology Laboratory, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (J.Y.); (F.B.); (T.R.); (E.W.); (M.A.K.)
| | - Earl Williams
- Plant Genomics and Biotechnology Laboratory, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (J.Y.); (F.B.); (T.R.); (E.W.); (M.A.K.)
| | - Naoufal Lakhssassi
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (D.K.); (N.L.); (K.M.)
| | - Hamid Mazouz
- Laboratoire de Biotechnologies & Valorisation des Bio-Ressources (BioVar), Département de Biologie, Faculté des Sciences, Université Moulay Ismail, Meknès 50000, Morocco;
| | - Henry T. Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA;
| | - Khalid Meksem
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (D.K.); (N.L.); (K.M.)
| | - Alemu Mengistu
- Crop Genetics Research Unit, USDA, Agricultural Research Service, Jackson, TN 38301, USA;
| | - My Abdelmajid Kassem
- Plant Genomics and Biotechnology Laboratory, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (J.Y.); (F.B.); (T.R.); (E.W.); (M.A.K.)
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Knizia D, Bellaloui N, Yuan J, Lakhssasi N, Anil E, Vuong T, Embaby M, Nguyen HT, Mengistu A, Meksem K, Kassem MA. Quantitative Trait Loci and Candidate Genes That Control Seed Sugars Contents in the Soybean 'Forrest' by 'Williams 82' Recombinant Inbred Line Population. Plants (Basel) 2023; 12:3498. [PMID: 37836238 PMCID: PMC10575016 DOI: 10.3390/plants12193498] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/03/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023]
Abstract
Soybean seed sugars are among the most abundant beneficial compounds for human and animal consumption in soybean seeds. Higher seed sugars such as sucrose are desirable as they contribute to taste and flavor in soy-based food. Therefore, the objectives of this study were to use the 'Forrest' by 'Williams 82' (F × W82) recombinant inbred line (RIL) soybean population (n = 309) to identify quantitative trait loci (QTLs) and candidate genes that control seed sugar (sucrose, stachyose, and raffinose) contents in two environments (North Carolina and Illinois) over two years (2018 and 2020). A total of 26 QTLs that control seed sugar contents were identified and mapped on 16 soybean chromosomes (chrs.). Interestingly, five QTL regions were identified in both locations, Illinois and North Carolina, in this study on chrs. 2, 5, 13, 17, and 20. Amongst 57 candidate genes identified in this study, 16 were located within 10 Megabase (MB) of the identified QTLs. Amongst them, a cluster of four genes involved in the sugars' pathway was collocated within 6 MB of two QTLs that were detected in this study on chr. 17. Further functional validation of the identified genes could be beneficial in breeding programs to produce soybean lines with high beneficial sucrose and low raffinose family oligosaccharides.
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Affiliation(s)
- Dounya Knizia
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (D.K.); (N.L.); (E.A.); (M.E.); (K.M.)
| | - Nacer Bellaloui
- USDA, Agriculture Research Service, Crop Genetics Research Unit, 141 Experiment Station Road, Stoneville, MS 38776, USA;
| | - Jiazheng Yuan
- Plant Genomics and Biotechnology Lab, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA;
| | - Naoufal Lakhssasi
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (D.K.); (N.L.); (E.A.); (M.E.); (K.M.)
| | - Erdem Anil
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (D.K.); (N.L.); (E.A.); (M.E.); (K.M.)
| | - Tri Vuong
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA; (T.V.); (H.T.N.)
| | - Mohamed Embaby
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (D.K.); (N.L.); (E.A.); (M.E.); (K.M.)
| | - Henry T. Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA; (T.V.); (H.T.N.)
| | - Alemu Mengistu
- USDA, Agriculture Research Service, Crop Genetics Research Unit, 605 Airways Blvd, Jackson, TN 38301, USA;
| | - Khalid Meksem
- School of Agricultural Sciences, Southern Illinois University, Carbondale, IL 62901, USA; (D.K.); (N.L.); (E.A.); (M.E.); (K.M.)
| | - My Abdelmajid Kassem
- Plant Genomics and Biotechnology Lab, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA;
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Piya S, Pantalone V, Zadegan SB, Shipp S, Lakhssassi N, Knizia D, Krishnan HB, Meksem K, Hewezi T. Soybean gene co-expression network analysis identifies two co-regulated gene modules associated with nodule formation and development. Mol Plant Pathol 2023; 24:628-636. [PMID: 36975024 DOI: 10.1111/mpp.13327] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 05/18/2023]
Abstract
Gene co-expression network analysis is an efficient systems biology approach for the discovery of novel gene functions and trait-associated gene modules. To identify clusters of functionally related genes involved in soybean nodule formation and development, we performed a weighted gene co-expression network analysis. Two nodule-specific modules (NSM-1 and NSM-2, containing 304 and 203 genes, respectively) were identified. The NSM-1 gene promoters were significantly enriched in cis-binding elements for ERF, MYB, and C2H2-type zinc transcription factors, whereas NSM-2 gene promoters were enriched in cis-binding elements for TCP, bZIP, and bHLH transcription factors, suggesting a role of these regulatory factors in the transcriptional activation of nodule co-expressed genes. The co-expressed gene modules included genes with potential novel roles in nodulation, including those involved in xylem development, transmembrane transport, the ethylene signalling pathway, cytoskeleton organization, cytokinesis and regulation of the cell cycle, regulation of meristem initiation and growth, transcriptional regulation, DNA methylation, and histone modifications. Functional analysis of two co-expressed genes using TILLING mutants provided novel insight into the involvement of unsaturated fatty acid biosynthesis and folate metabolism in nodule formation and development. The identified gene co-expression modules provide valuable resources for further functional genomics studies to dissect the genetic basis of nodule formation and development in soybean.
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Affiliation(s)
- Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Vince Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | | | - Sarah Shipp
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, 37996, USA
| | - Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, Illinois, 62901, USA
| | - Dounya Knizia
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, Illinois, 62901, USA
| | - Hari B Krishnan
- Plant Science Division, University of Missouri, Columbia, Missouri, USA
- Plant Genetics Research, USDA Agricultural Research Service, Columbia, Missouri, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, Illinois, 62901, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, 37996, USA
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Li W, Zheng X, Cheng R, Zhong C, Zhao J, Liu TH, Yi T, Zhu Z, Xu J, Meksem K, Dai L, Liu S. Soybean ZINC FINGER PROTEIN03 targets two SUPEROXIDE DISMUTASE1s and confers resistance to Phytophthora sojae. Plant Physiol 2023; 192:633-647. [PMID: 36782397 PMCID: PMC10152685 DOI: 10.1093/plphys/kiad083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 12/22/2022] [Accepted: 01/19/2023] [Indexed: 05/03/2023]
Abstract
Phytophthora sojae causes Phytophthora root and stem rot disease of soybean (Glycine max), leading to huge annual yield loss worldwide, but resistance to Phytophthora sojae (Rps) genes remains elusive. Soybean cultivar "Yudou 29" is resistant to P. sojae strain PsMC1, and this study aimed to clone, identify, and characterize the Rps gene in Yudou 29 (RpsYD29) and clarify its functional mechanism. We map-based cloned RpsYD29 (ZINC FINGER PROTEIN03, GmZFP03) using the families of a cross between Yudou 29 and a P. sojae-susceptible soybean cultivar "Jikedou 2". P. sojae resistance of GmZFP03 was functionally validated by stable soybean genetic transformation and allele-phenotype association analysis. GmZFP03 was identified as a C2H2-type zinc finger protein transcription factor, showing 4 amino acid residue polymorphisms (V79F, G122-, G123-, and D125V) and remarkably different expression patterns between resistant and susceptible soybeans. Notably boosted activity and gene expression of superoxide dismutase (SOD) in resistant-type GmZFP03-expressed transgenic soybean, substantial enhancement of P. sojae resistance of wild-type soybean by exogenous SOD treatment, and GmZFP03 binding to and activation of 2 SOD1 (Glyma.03g242900 and Glyma.19g240400) promoters demonstrated the involvement of SOD1s in GmZFP03-mediated resistance to P. sojae strain PsMC1. Thus, this study cloned the soybean P. sojae-resistant GmZFP03, the product of which specifically targets 2 SOD1 promoters. GmZFP03 can be directly used for precise P. sojae-resistance soybean breeding.
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Affiliation(s)
- Wei Li
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, P. R. China
| | - Xiang Zheng
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, P. R. China
| | - Rong Cheng
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, P. R. China
| | - Chanjuan Zhong
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, P. R. China
| | - Jie Zhao
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Tyler H Liu
- College of Letters and Science, University of Wisconsin, Madison, WI 53706, USA
| | - Tuyong Yi
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, P. R. China
| | - Zhendong Zhu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, P. R. China
| | - Jieting Xu
- Wimi Biotechnology Co., Ltd, Changzhou 213000, P. R. China
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
| | - Liangying Dai
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, P. R. China
| | - Shiming Liu
- Hunan Provincial Key Laboratory for Biology and Control of Plant Diseases and Insect Pests, College of Plant Protection, Hunan Agricultural University, Changsha 410128, P. R. China
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
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Zhou Z, Lakhssassi N, Knizia D, Cullen MA, El Baz A, Embaby MG, Liu S, Badad O, Vuong TD, AbuGhazaleh A, Nguyen HT, Meksem K. Genome-wide identification and analysis of soybean acyl-ACP thioesterase gene family reveals the role of GmFAT to improve fatty acid composition in soybean seed. Theor Appl Genet 2021; 134:3611-3623. [PMID: 34319424 DOI: 10.1007/s00122-021-03917-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/13/2021] [Indexed: 06/13/2023]
Abstract
KEY MESSAGE Soybean acyl-ACP thioesterase gene family have been characterized; GmFATA1A mutants were discovered to confer high oleic acid, while GmFATB mutants presented low palmitic and high oleic acid seed content. Soybean oil stability and quality are primarily determined by the relative proportions of saturated versus unsaturated fatty acids. Commodity soybean typically contains 11% palmitic acid, as the primary saturated fatty acids. Reducing palmitic acid content is the principal approach to minimize the levels of saturated fatty acids in soybean. Though high palmitic acid enhances oxidative stability of soybean oil, it is negatively correlated with oil and oleic acid content and can cause coronary heart diseases for humans. For plants, acyl-acyl carrier protein (ACP) thioesterases (TEs) are a group of enzymes to hydrolyze acyl group and release free fatty acid from plastid. Among them, GmFATB1A has become the main target to genetically reduce the palmitic acid content in soybean. However, the role of members in soybean acyl-ACP thioesterase gene family is largely unknown. In this study, we characterized two classes of TEs, GmFATA, and GmFATB in soybean. We also denominated two GmFATA members and discovered six additional members that belong to GmFATB gene family through phylogenetic, syntenic, and in silico analysis. Using TILLING-by-Sequencing+, we identified an allelic series of mutations in five soybean acyl-ACP thioesterase genes, including GmFATA1A, GmFATB1A, GmFATB1B, GmFATB2A, and GmFATB2B. Additionally, we discovered mutations at GmFATA1A to confer high oleic acid (up to 34.5%) content, while mutations at GmFATB presented low palmitic acid (as low as 5.6%) and high oleic acid (up to 36.5%) phenotypes. The obtained soybean mutants with altered fatty acid content can be used in soybean breeding program for improving soybean oil composition traits.
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Affiliation(s)
- Zhou Zhou
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
- Plant Science Department, McGill University, Montreal, QC, H9X 3V9, Canada
| | - Naoufal Lakhssassi
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Dounya Knizia
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Mallory A Cullen
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Abdelhalim El Baz
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Mohamed G Embaby
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Shiming Liu
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Oussama Badad
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Tri D Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Amer AbuGhazaleh
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Khalid Meksem
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA.
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9
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Knizia D, Yuan J, Bellaloui N, Vuong T, Usovsky M, Song Q, Betts F, Register T, Williams E, Lakhssassi N, Mazouz H, Nguyen HT, Meksem K, Mengistu A, Kassem MA. The Soybean High Density 'Forrest' by 'Williams 82' SNP-Based Genetic Linkage Map Identifies QTL and Candidate Genes for Seed Isoflavone Content. Plants (Basel) 2021; 10:plants10102029. [PMID: 34685837 PMCID: PMC8541105 DOI: 10.3390/plants10102029] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/13/2021] [Accepted: 09/21/2021] [Indexed: 11/26/2022]
Abstract
Isoflavones are secondary metabolites that are abundant in soybean and other legume seeds providing health and nutrition benefits for both humans and animals. The objectives of this study were to construct a single nucleotide polymorphism (SNP)-based genetic linkage map using the ‘Forrest’ by ‘Williams 82’ (F×W82) recombinant inbred line (RIL) population (n = 306); map quantitative trait loci (QTL) for seed daidzein, genistein, glycitein, and total isoflavone contents in two environments over two years (NC-2018 and IL-2020); identify candidate genes for seed isoflavone. The FXW82 SNP-based map was composed of 2075 SNPs and covered 4029.9 cM. A total of 27 QTL that control various seed isoflavone traits have been identified and mapped on chromosomes (Chrs.) 2, 4, 5, 6, 10, 12, 15, 19, and 20 in both NC-2018 (13 QTL) and IL-2020 (14 QTL). The six QTL regions on Chrs. 2, 4, 5, 12, 15, and 19 are novel regions while the other 21 QTL have been identified by other studies using different biparental mapping populations or genome-wide association studies (GWAS). A total of 130 candidate genes involved in isoflavone biosynthetic pathways have been identified on all 20 Chrs. And among them 16 have been identified and located within or close to the QTL identified in this study. Moreover, transcripts from four genes (Glyma.10G058200, Glyma.06G143000, Glyma.06G137100, and Glyma.06G137300) were highly abundant in Forrest and Williams 82 seeds. The identified QTL and four candidate genes will be useful in breeding programs to develop soybean cultivars with high beneficial isoflavone contents.
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Affiliation(s)
- Dounya Knizia
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (D.K.); (N.L.); (K.M.)
- Laboratoire de Biotechnologies & Valorisation des Bio-Ressources (BioVar), Department de Biology, Faculté des Sciences, Université Moulay Ismail, Meknès 50000, Morocco;
| | - Jiazheng Yuan
- Plant Genomics and Biotechnology Laboratory, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (J.Y.); (F.B.); (T.R.); (E.W.)
| | - Nacer Bellaloui
- Crop Genetics Research Unit, USDA, Agriculture Research Service, 141 Experiment Station Road, Stoneville, MS 38776, USA;
| | - Tri Vuong
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA; (T.V.); (M.U.); (H.T.N.)
| | - Mariola Usovsky
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA; (T.V.); (M.U.); (H.T.N.)
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, USA;
| | - Frances Betts
- Plant Genomics and Biotechnology Laboratory, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (J.Y.); (F.B.); (T.R.); (E.W.)
| | - Teresa Register
- Plant Genomics and Biotechnology Laboratory, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (J.Y.); (F.B.); (T.R.); (E.W.)
| | - Earl Williams
- Plant Genomics and Biotechnology Laboratory, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (J.Y.); (F.B.); (T.R.); (E.W.)
| | - Naoufal Lakhssassi
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (D.K.); (N.L.); (K.M.)
| | - Hamid Mazouz
- Laboratoire de Biotechnologies & Valorisation des Bio-Ressources (BioVar), Department de Biology, Faculté des Sciences, Université Moulay Ismail, Meknès 50000, Morocco;
| | - Henry T. Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA; (T.V.); (M.U.); (H.T.N.)
| | - Khalid Meksem
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (D.K.); (N.L.); (K.M.)
| | - Alemu Mengistu
- Crop Genetics Research Unit, USDA, Agricultural Research Service, Jackson, TN 38301, USA;
| | - My Abdelmajid Kassem
- Plant Genomics and Biotechnology Laboratory, Department of Biological and Forensic Sciences, Fayetteville State University, Fayetteville, NC 28301, USA; (J.Y.); (F.B.); (T.R.); (E.W.)
- Correspondence:
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10
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Badad O, Lakhssassi N, Zaid N, El Baze A, Zaid Y, Meksem J, Lightfoot DA, Tombuloglu H, Zaid EH, Unver T, Meksem K. Genome Wide MeDIP-Seq Profiling of Wild and Cultivated Olives Trees Suggests DNA Methylation Fingerprint on the Sensory Quality of Olive Oil. Plants (Basel) 2021; 10:plants10071405. [PMID: 34371608 PMCID: PMC8309279 DOI: 10.3390/plants10071405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/31/2022]
Abstract
Secondary metabolites are particularly important to humans due to their pharmaceutical properties. Moreover, secondary metabolites are key compounds in climate change adaptation in long-living trees. Recently, it has been described that the domestication of Olea subspecies had no major selection signature on coding variants and was mainly related to changes in gene expression. In addition, the phenotypic plasticity in Olea subspecies was linked to the activation of transposable elements in the genes neighboring. Here, we investigated the imprint of DNA methylation in the unassigned fraction of the phenotypic plasticity of the Olea subspecies, using methylated DNA immuno-precipitation sequencing (MeDIP-seq) for a high-resolution genome-wide DNA methylation profiling of leaves and fruits during fruit development in wild and cultivated olives from Turkey. Notably, the methylation profiling showed a differential DNA methylation in secondary metabolism responsible for the sensory quality of olive oil. Here, we highlight for the first time the imprint of DNA methylation in modulating the activity of the Linoleate 9S lipoxygenase in the biosynthesis of volatile aromatic compounds. Unprecedently, the current study reveals the methylation status of the olive genome during fruit ripening.
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Affiliation(s)
- Oussama Badad
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (O.B.); (N.L.); (A.E.B.); (D.A.L.)
- Department of Biology, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco; (N.Z.); (Y.Z.); (E.H.Z.)
| | - Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (O.B.); (N.L.); (A.E.B.); (D.A.L.)
| | - Nabil Zaid
- Department of Biology, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco; (N.Z.); (Y.Z.); (E.H.Z.)
| | - Abdelhalim El Baze
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (O.B.); (N.L.); (A.E.B.); (D.A.L.)
| | - Younes Zaid
- Department of Biology, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco; (N.Z.); (Y.Z.); (E.H.Z.)
- Research Center, Abulcasis University of Health Sciences, Rabat 10000, Morocco
| | - Jonas Meksem
- Trinity College of Arts and Sciences, Duke University, Durham, NC 27708, USA;
| | - David A Lightfoot
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (O.B.); (N.L.); (A.E.B.); (D.A.L.)
| | - Huseyin Tombuloglu
- Department of Genetics Research, Institute for Research and Medical Consultations (IRMC), Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia;
| | - El Houcine Zaid
- Department of Biology, Faculty of Sciences, Mohammed V University, Rabat 10000, Morocco; (N.Z.); (Y.Z.); (E.H.Z.)
| | - Turgay Unver
- Ficus Biotechnology, Ostim OSB Mah, 100. Yil Blv, No:55, Yenimahalle, Ankara 06000, Turkey
- Correspondence: (T.U.); (K.M.)
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (O.B.); (N.L.); (A.E.B.); (D.A.L.)
- Correspondence: (T.U.); (K.M.)
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11
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Usovsky M, Lakhssassi N, Patil GB, Vuong TD, Piya S, Hewezi T, Robbins RT, Stupar RM, Meksem K, Nguyen HT. Dissecting nematode resistance regions in soybean revealed pleiotropic effect of soybean cyst and reniform nematode resistance genes. Plant Genome 2021; 14:e20083. [PMID: 33724721 DOI: 10.1002/tpg2.20083] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 12/04/2020] [Indexed: 06/12/2023]
Abstract
Reniform nematode (RN, Rotylenchulus reniformis Linford & Oliveira) has emerged as one of the most important plant parasitic nematodes of soybean [Glycine max (L.) Merr.]. Planting resistant varieties is the most effective strategy for nematode management. The objective of this study was to identify quantitative trait loci (QTL) for RN resistance in an exotic soybean line, PI 438489B, using two linkage maps constructed from the Universal Soybean Linkage Panel (USLP 1.0) and next-generation whole-genome resequencing (WGRS) technology. Two QTL controlling RN resistance were identified-the soybean cyst nematode (SCN, Heterodera glycines) resistance gene GmSNAP18 at the rhg1 locus and its paralog GmSNAP11. Strong association between resistant phenotype and haplotypes of the GmSNAP11 and GmSNAP18 was observed. The results indicated that GmSNAP11 possibly could have epistatic effect on GmSNAP18, or vice versa, with the presence of a significant correlation in RN resistance of rhg1-a GmSNAP18 vs. rhg1-b GmSNAP18. Most importantly, our preliminary data suggested that GmSNAP18 and GmSNAP11 proteins physically interact in planta, suggesting that they belong to the same pathway for resistance. Unlike GmSNAP18, no indication of GmSNAP11 copy number variation was found. Moreover, gene-based single nucleotide polymorphism (SNP) markers were developed for rapid detection of RN or SCN resistance at these loci. Our analysis substantiates synergic interaction between GmSNAP11 and GmSNAP18 genes and confirms their roles in RN as well as SCN resistance. These results could contribute to a better understanding of evolution and subfunctionalization of genes conferring resistance to multiple nematode species and provide a framework for further investigations.
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Affiliation(s)
- Mariola Usovsky
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Gunvant B Patil
- Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA
| | - Tri D Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Robert T Robbins
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, USA
| | - Robert M Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
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12
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Lakhssassi N, Lopes-Caitar VS, Knizia D, Cullen MA, Badad O, El Baze A, Zhou Z, Embaby MG, Meksem J, Lakhssassi A, Chen P, AbuGhazaleh A, Vuong TD, Nguyen HT, Hewezi T, Meksem K. TILLING-by-Sequencing + Reveals the Role of Novel Fatty Acid Desaturases (GmFAD2-2s) in Increasing Soybean Seed Oleic Acid Content. Cells 2021; 10:1245. [PMID: 34069320 PMCID: PMC8158723 DOI: 10.3390/cells10051245] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/15/2021] [Accepted: 05/16/2021] [Indexed: 11/17/2022] Open
Abstract
Soybean is the second largest source of oil worldwide. Developing soybean varieties with high levels of oleic acid is a primary goal of the soybean breeders and industry. Edible oils containing high level of oleic acid and low level of linoleic acid are considered with higher oxidative stability and can be used as a natural antioxidant in food stability. All developed high oleic acid soybeans carry two alleles; GmFAD2-1A and GmFAD2-1B. However, when planted in cold soil, a possible reduction in seed germination was reported when high seed oleic acid derived from GmFAD2-1 alleles were used. Besides the soybean fatty acid desaturase (GmFAD2-1) subfamily, the GmFAD2-2 subfamily is composed of five members, including GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E. Segmental duplication of GmFAD2-1A/GmFAD2-1B, GmFAD2-2A/GmFAD2-2C, GmFAD2-2A/GmFAD2-2D, and GmFAD2-2D/GmFAD2-2C have occurred about 10.65, 27.04, 100.81, and 106.55 Mya, respectively. Using TILLING-by-Sequencing+ technology, we successfully identified 12, 8, 10, 9, and 19 EMS mutants at the GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E genes, respectively. Functional analyses of newly identified mutants revealed unprecedented role of the five GmFAD2-2A, GmFAD2-2B, GmFAD2-2C, GmFAD2-2D, and GmFAD2-2E members in controlling the seed oleic acid content. Most importantly, unlike GmFAD2-1 members, subcellular localization revealed that members of the GmFAD2-2 subfamily showed a cytoplasmic localization, which may suggest the presence of an alternative fatty acid desaturase pathway in soybean for converting oleic acid content without substantially altering the traditional plastidial/ER fatty acid production.
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Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (M.A.C.); (O.B.); (A.E.B.); (Z.Z.)
| | | | - Dounya Knizia
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (M.A.C.); (O.B.); (A.E.B.); (Z.Z.)
| | - Mallory A. Cullen
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (M.A.C.); (O.B.); (A.E.B.); (Z.Z.)
| | - Oussama Badad
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (M.A.C.); (O.B.); (A.E.B.); (Z.Z.)
| | - Abdelhalim El Baze
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (M.A.C.); (O.B.); (A.E.B.); (Z.Z.)
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (M.A.C.); (O.B.); (A.E.B.); (Z.Z.)
| | - Mohamed G. Embaby
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL 62901, USA; (M.G.E.); (A.A.)
| | - Jonas Meksem
- Trinity College of Arts and Sciences, Duke University, Durham, NC 27708, USA;
| | - Aicha Lakhssassi
- Faculty of Sciences and Technologies, University of Lorraine, 54506 Nancy, France;
| | - Pengyin Chen
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (P.C.); (T.D.V.); (H.T.N.)
| | - Amer AbuGhazaleh
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL 62901, USA; (M.G.E.); (A.A.)
| | - Tri D. Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (P.C.); (T.D.V.); (H.T.N.)
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (P.C.); (T.D.V.); (H.T.N.)
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (V.S.L.-C.); (T.H.)
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (M.A.C.); (O.B.); (A.E.B.); (Z.Z.)
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13
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Lakhssassi N, Zhou Z, Cullen MA, Badad O, El Baze A, Chetto O, Embaby MG, Knizia D, Liu S, Neves LG, Meksem K. TILLING-by-Sequencing + to Decipher Oil Biosynthesis Pathway in Soybeans: A New and Effective Platform for High-Throughput Gene Functional Analysis. Int J Mol Sci 2021; 22:4219. [PMID: 33921707 PMCID: PMC8073088 DOI: 10.3390/ijms22084219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/08/2021] [Accepted: 04/13/2021] [Indexed: 12/25/2022] Open
Abstract
Reverse genetic approaches have been widely applied to study gene function in crop species; however, these techniques, including gel-based TILLING, present low efficiency to characterize genes in soybeans due to genome complexity, gene duplication, and the presence of multiple gene family members that share high homology in their DNA sequence. Chemical mutagenesis emerges as a genetically modified-free strategy to produce large-scale soybean mutants for economically important traits improvement. The current study uses an optimized high-throughput TILLING by target capture sequencing technology, or TILLING-by-Sequencing+ (TbyS+), coupled with universal bioinformatic tools to identify population-wide mutations in soybeans. Four ethyl methanesulfonate mutagenized populations (4032 mutant families) have been screened for the presence of induced mutations in targeted genes. The mutation types and effects have been characterized for a total of 138 soybean genes involved in soybean seed composition, disease resistance, and many other quality traits. To test the efficiency of TbyS+ in complex genomes, we used soybeans as a model with a focus on three desaturase gene families, GmSACPD, GmFAD2, and GmFAD3, that are involved in the soybean fatty acid biosynthesis pathway. We successfully isolated mutants from all the six gene family members. Unsurprisingly, most of the characterized mutants showed significant changes either in their stearic, oleic, or linolenic acids. By using TbyS+, we discovered novel sources of soybean oil traits, including high saturated and monosaturated fatty acids in addition to low polyunsaturated fatty acid contents. This technology provides an unprecedented platform for highly effective screening of polyploid mutant populations and functional gene analysis. The obtained soybean mutants from this study can be used in subsequent soybean breeding programs for improved oil composition traits.
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Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Zhou Zhou
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Mallory A. Cullen
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Oussama Badad
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Abdelhalim El Baze
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Oumaima Chetto
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Mohamed G. Embaby
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL 62901, USA;
| | - Dounya Knizia
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | - Shiming Liu
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
| | | | - Khalid Meksem
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (Z.Z.); (M.A.C.); (O.B.); (A.E.B.); (O.C.); (D.K.); (S.L.)
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14
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Lakhssassi N, Zhou Z, Liu S, Piya S, Cullen MA, El Baze A, Knizia D, Patil GB, Badad O, Embaby MG, Meksem J, Lakhssassi A, AbuGhazaleh A, Hewezi T, Meksem K. Soybean TILLING-by-Sequencing+ reveals the role of novel GmSACPD members in unsaturated fatty acid biosynthesis while maintaining healthy nodules. J Exp Bot 2020; 71:6969-6987. [PMID: 32898219 DOI: 10.1093/jxb/eraa402] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 08/27/2020] [Indexed: 05/07/2023]
Abstract
Developing soybean lines with high levels of stearic acid is a primary goal of the soybean industry. Most high-stearic-acid soybeans carry different GmSACPD-C mutated alleles. However, due to the dual role of GmSACPD-C in seeds and nodule development, all derived deleterious GmSACPD-C mutant alleles are of extremely poor agronomic value because of defective nodulation. The soybean stearoyl-acyl carrier protein desaturase (GmSACPD) gene family is composed of five members. Comparative genomics analysis indicated that SACPD genes were duplicated and derived from a common ancestor that is still present in chlorophytic algae. Synteny analysis showed the presence of segment duplications between GmSACPD-A/GmSACPD-B, and GmSACPD-C/GmSACPD-D. GmSACPD-E was not contained in any duplicated segment and may be the result of tandem duplication. We developed a TILLING by Target Capture Sequencing (Tilling-by-Sequencing+) technology, a versatile extension of the conventional TILLING by sequencing, and successfully identified 12, 14, and 18 ethyl methanesulfonate mutants at the GmSACPD-A, GmSACPD-B, and GmSACPD-D genes, respectively. Functional analysis of all identified mutants revealed an unprecedented role of GmSACPD-A, GmSACPD-B, and GmSACPD-D in unsaturated fatty acid biosynthesis without affecting nodule development and structure. This discovery will positively impact the development of high-stearic-acid lines to enhance soybean nutritional value without potential developmental tradeoffs.
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Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Shiming Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Mallory A Cullen
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Abdelhalim El Baze
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Dounya Knizia
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Gunvant B Patil
- Institute for Genomics of Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, USA
| | - Oussama Badad
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
| | - Mohamed G Embaby
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL, USA
| | - Jonas Meksem
- Trinity College of Arts and Sciences, Duke University, Durham, NC, USA
| | - Aicha Lakhssassi
- Faculty of Sciences and Technologies, University of Lorraine, Nancy, France
| | - Amer AbuGhazaleh
- Department of Animal Science, Food, and Nutrition, Southern Illinois University, Carbondale, IL, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, USA
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15
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Lakhssassi N, Baharlouei A, Meksem J, Hamilton-Brehm SD, Lightfoot DA, Meksem K, Liang Y. EMS-Induced Mutagenesis of Clostridium carboxidivorans for Increased Atmospheric CO 2 Reduction Efficiency and Solvent Production. Microorganisms 2020; 8:microorganisms8081239. [PMID: 32824093 PMCID: PMC7464951 DOI: 10.3390/microorganisms8081239] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/04/2020] [Accepted: 08/10/2020] [Indexed: 11/16/2022] Open
Abstract
Clostridium carboxidivorans (P7) is one of the most important solvent-producing bacteria capable of fermenting syngas (CO, CO2, and H2) to produce chemical commodities when grown as an autotroph. This study aimed to develop ethyl methanesulfonate (EMS)-induced P7 mutants that were capable of growing in the presence of CO2 as a unique source of carbon with increased solvent formation and atmospheric CO2 reduction to limit global warming. Phenotypic analysis including growth and end product characterization of the P7 wild type (WT) demonstrated that this strain grew better at 25 °C than 37 °C when CO2 served as the only source of carbon. In the current study, 55 mutagenized P7-EMS mutants were developed by using 100 mM and 120 mM EMS. Interestingly, using a forward genetic approach, three out of the 55 P7-EMS mutants showed a significant increase in ethanol, butyrate, and butanol production. The three P7-EMS mutants presented on average a 4.68-fold increase in concentrations of ethanol when compared to the P7-WT. Butyric acid production from 3 P7-EMS mutants contained an average of a 3.85 fold increase over the levels observed in the P7-WT cultures under the same conditions (CO2 only). In addition, one P7-EMS mutant presented butanol production (0.23 ± 0.02 g/L), which was absent from the P7-WT under CO2 conditions. Most of the P7-EMS mutants showed stability of the obtained end product traits after three transfers. Most importantly, the amount of reduced atmospheric CO2 increased up to 8.72 times (0.21 g/Abs) for ethanol production and up to 8.73 times higher (0.16 g/Abs) for butyrate than the levels contained in the P7-WT. Additionally, to produce butanol, the P7-EMSIII-J mutant presented 0.082 g/Abs of CO2 reduction. This study demonstrated the feasibility and effectiveness of employing EMS mutagenesis in generating solvent-producing anaerobic bacteria mutants with improved and novel product formation and increased atmospheric CO2 reduction efficiency.
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Affiliation(s)
- Naoufal Lakhssassi
- Department of Civil and Environmental Engineering, 1230 Lincoln Drive, Southern Illinois University Carbondale, Carbondale, IL 62901, USA; (N.L.); (A.B.)
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA;
| | - Azam Baharlouei
- Department of Civil and Environmental Engineering, 1230 Lincoln Drive, Southern Illinois University Carbondale, Carbondale, IL 62901, USA; (N.L.); (A.B.)
| | - Jonas Meksem
- Trinity College of Arts and Sciences, Duke University, Durham, NC 27708, USA;
| | | | - David A. Lightfoot
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA;
| | - Khalid Meksem
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA;
- Correspondence: (K.M.); (Y.L.)
| | - Yanna Liang
- Department of Civil and Environmental Engineering, 1230 Lincoln Drive, Southern Illinois University Carbondale, Carbondale, IL 62901, USA; (N.L.); (A.B.)
- Department of Environmental and Sustainable Engineering, 1400 Washington Ave, State University of New York at Albany, Albany, NY 12222, USA
- Correspondence: (K.M.); (Y.L.)
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16
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Lakhssassi N, Piya S, Bekal S, Liu S, Zhou Z, Bergounioux C, Miao L, Meksem J, Lakhssassi A, Jones K, Kassem MA, Benhamed M, Bendahmane A, Lambert K, Boualem A, Hewezi T, Meksem K. A pathogenesis-related protein GmPR08-Bet VI promotes a molecular interaction between the GmSHMT08 and GmSNAP18 in resistance to Heterodera glycines. Plant Biotechnol J 2020; 18:1810-1829. [PMID: 31960590 PMCID: PMC7336373 DOI: 10.1111/pbi.13343] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Revised: 12/19/2019] [Accepted: 01/03/2020] [Indexed: 05/19/2023]
Abstract
Soybean cyst nematode (SCN, Heterodera glycines) is the most devastating pest affecting soybean production worldwide. SCN resistance requires both the GmSHMT08 and the GmSNAP18 in 'Peking'-type resistance. Here, we describe the molecular interaction between GmSHMT08 and GmSNAP18, which is potentiated by a pathogenesis-related protein GmPR08-Bet VI. Like GmSNAP18 and GmSHMT08, GmPR08-Bet VI expression was induced in response to SCN and its overexpression decreased SCN cysts by 65% in infected transgenic soybean roots. Overexpression of GmPR08-Bet VI did not have an effect on SCN resistance when the two cytokinin-binding sites in GmPR08-Bet VI were mutated, indicating a new role of GmPR08-Bet VI in SCN resistance. GmPR08-Bet VI was mapped to a QTL for resistance to SCN using different mapping populations. GmSHMT08, GmSNAP18 and GmPR08-Bet VI localize to the cytosol and plasma membrane. GmSNAP18 expression and localization hyper-accumulated at the plasma membrane and was specific to the root cells surrounding the nematode in SCN-resistant soybeans. Genes encoding key components of the salicylic acid signalling pathway were induced under SCN infection. GmSNAP18 and GmPR08-Bet VI were also induced under salicylic acid and cytokinin exogenous treatments, while GmSHMT08 was induced only when the resistant GmSNAP18 was present, pointing to the presence of a molecular crosstalk between SCN-resistant genes and defence genes. Expression analysis of GmSHMT08 and GmSNAP18 identified the need of a minimum expression requirement to trigger the SCN resistance reaction. These results provide insight into a new response mechanism towards plant nematode resistance involving haplotype compatibility, gene dosage and hormone signalling.
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Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Sarbottam Piya
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Sadia Bekal
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Shiming Liu
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Catherine Bergounioux
- INRAInstitute of Plant Sciences Paris‐Saclay (IPS2)CNRSUniversité Paris‐SudOrsayFrance
| | - Long Miao
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | | | - Aicha Lakhssassi
- Faculty of Sciences and TechnologiesUniversity of LorraineNancyFrance
| | - Karen Jones
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | | | - Moussa Benhamed
- INRAInstitute of Plant Sciences Paris‐Saclay (IPS2)CNRSUniversité Paris‐SudOrsayFrance
| | - Abdelhafid Bendahmane
- INRAInstitute of Plant Sciences Paris‐Saclay (IPS2)CNRSUniversité Paris‐SudOrsayFrance
| | - Kris Lambert
- Department of Crop SciencesUniversity of IllinoisUrbanaILUSA
| | - Adnane Boualem
- INRAInstitute of Plant Sciences Paris‐Saclay (IPS2)CNRSUniversité Paris‐SudOrsayFrance
| | - Tarek Hewezi
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
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Rambani A, Pantalone V, Yang S, Rice JH, Song Q, Mazarei M, Arelli PR, Meksem K, Stewart CN, Hewezi T. Identification of introduced and stably inherited DNA methylation variants in soybean associated with soybean cyst nematode parasitism. New Phytol 2020; 227:168-184. [PMID: 32112408 DOI: 10.1111/nph.16511] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 02/18/2020] [Indexed: 06/10/2023]
Abstract
DNA methylation is a widespread epigenetic mark that contributes to transcriptome reprogramming during plant-pathogen interactions. However, the distinct role of DNA methylation in establishing resistant and susceptible responses remains largely unexplored. Here, we developed and used a pair of near-isogenic lines (NILs) to characterize DNA methylome landscapes of soybean roots during the susceptible and resistant interactions with soybean cyst nematode (SCN; Heterodera glycines). We also compared the methylomes of the NILs and their parents to identify introduced and stably inherited methylation variants. The genomes of the NILs were substantially differentially methylated under uninfected conditions. This difference was associated with differential gene expression that may prime the NIL responses to SCN infection. In response to SCN infection, the susceptible line exhibited reduced global methylation levels in both protein-coding genes and transposable elements, whereas the resistant line showed the opposite response, increased global methylation levels. Heritable and novel nonparental differentially methylated regions overlapping with genes associated with soybean response to SCN infection were identified and validated using transgenic hairy root system. Our analyses indicate that DNA methylation patterns associated with the susceptible and resistant interactions are highly specific and that novel and stably inherited methylation variants are of biological significance.
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Affiliation(s)
- Aditi Rambani
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Vince Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Songnan Yang
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - J Hollis Rice
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville Agricultural Research Center, Beltsville, MD, 20705, USA
| | - Mitra Mazarei
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | | | - Khalid Meksem
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - C Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
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18
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Lakhssassi N, Piya S, Knizia D, El Baze A, Cullen MA, Meksem J, Lakhssassi A, Hewezi T, Meksem K. Mutations at the Serine Hydroxymethyltransferase Impact its Interaction with a Soluble NSF Attachment Protein and a Pathogenesis-Related Protein in Soybean. Vaccines (Basel) 2020; 8:vaccines8030349. [PMID: 32629961 PMCID: PMC7563484 DOI: 10.3390/vaccines8030349] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 06/24/2020] [Accepted: 06/25/2020] [Indexed: 01/01/2023] Open
Abstract
Resistance to soybean cyst nematodes (SCN) in “Peking-type” resistance is bigenic, requiring Rhg4-a and rhg1-a. Rhg4-a encodes a serine hydroxymethyltransferase (GmSHMT08) and rhg1-a encodes a soluble NSF attachment protein (GmSNAP18). Recently, it has been shown that a pathogenesis-related protein, GmPR08-Bet VI, potentiates the interaction between GmSHMT08 and GmSNAP18. Mutational analysis using spontaneously occurring and ethyl methanesulfonate (EMS)-induced mutations was carried out to increase our knowledge of the interacting GmSHMT08/GmSNAP18/GmPR08-Bet VI multi-protein complex. Mutations affecting the GmSHMT08 protein structure (dimerization and tetramerization) and interaction sites with GmSNAP18 and GmPR08-Bet VI proteins were found to impact the multi-protein complex. Interestingly, mutations affecting the PLP/THF substrate binding and catalysis did not affect the multi-protein complex, although they resulted in increased susceptibility to SCN. Most importantly, GmSHMT08 and GmSNAP18 from PI88788 were shown to interact within the cell, being potentiated in the presence of GmPR08-Bet VI. In addition, we have shown the presence of incompatibility between the GmSNAP18 (rhg1-b) of PI88788 and GmSHMT08 (Rhg4-a) from Peking. Components of the reactive oxygen species (ROS) pathway were shown to be induced in the SCN incompatible reaction and were mapped to QTLs for resistance to SCN using different mapping populations.
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Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (A.E.B.); (M.A.C.)
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (S.P.); (T.H.)
| | - Dounya Knizia
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (A.E.B.); (M.A.C.)
| | - Abdelhalim El Baze
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (A.E.B.); (M.A.C.)
| | - Mallory A. Cullen
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (A.E.B.); (M.A.C.)
| | - Jonas Meksem
- Trinity College of Arts and Sciences, Duke University, Durham, NC 27708, USA;
| | - Aicha Lakhssassi
- Faculty of Sciences and Technologies, University of Lorraine, 54000 Nancy, France;
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA; (S.P.); (T.H.)
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (N.L.); (D.K.); (A.E.B.); (M.A.C.)
- Correspondence: ; Tel.: +1-618-453-3103
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19
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Zhou Z, Lakhssassi N, Cullen MA, El Baz A, Vuong TD, Nguyen HT, Meksem K. Assessment of Phenotypic Variations and Correlation among Seed Composition Traits in Mutagenized Soybean Populations. Genes (Basel) 2019; 10:E975. [PMID: 31783508 PMCID: PMC6947669 DOI: 10.3390/genes10120975] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 11/22/2019] [Accepted: 11/22/2019] [Indexed: 01/31/2023] Open
Abstract
Soybean [Glycine max (L.) Merr.] seed is a valuable source of protein and oil worldwide. Traditionally, the natural variations were heavily used in conventional soybean breeding programs to select desired traits. However, traditional plant breeding is encumbered with low frequencies of spontaneous mutations. In mutation breeding, genetic variations from induced mutations provide abundant sources of alterations in important soybean traits; this facilitated the development of soybean germplasm with modified seed composition traits to meet the different needs of end users. In this study, a total of 2366 'Forrest'-derived M2 families were developed for both forward and reverse genetic studies. A subset of 881 M3 families was forward genetically screened to measure the contents of protein, oil, carbohydrates, and fatty acids. A total of 14 mutants were identified to have stable seed composition phenotypes observed in both M3 and M4 generations. Correlation analyses have been conducted among ten seed composition traits and compared to a collection of 103 soybean germplasms. Mainly, ethyl methanesulfonate (EMS) mutagenesis had a strong impact on the seed-composition correlation that was observed among the 103 soybean germplasms, which offers multiple benefits for the soybean farmers and industry to breed for desired multiple seed phenotypes.
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Affiliation(s)
- Zhou Zhou
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (Z.Z.); (N.L.); (M.A.C.); (A.E.B.)
| | - Naoufal Lakhssassi
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (Z.Z.); (N.L.); (M.A.C.); (A.E.B.)
| | - Mallory A. Cullen
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (Z.Z.); (N.L.); (M.A.C.); (A.E.B.)
| | - Abdelhalim El Baz
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (Z.Z.); (N.L.); (M.A.C.); (A.E.B.)
| | - Tri D. Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (T.D.V.); (H.T.N.)
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA; (T.D.V.); (H.T.N.)
| | - Khalid Meksem
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA; (Z.Z.); (N.L.); (M.A.C.); (A.E.B.)
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20
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Patil GB, Lakhssassi N, Wan J, Song L, Zhou Z, Klepadlo M, Vuong TD, Stec AO, Kahil SS, Colantonio V, Valliyodan B, Rice JH, Piya S, Hewezi T, Stupar RM, Meksem K, Nguyen HT. Whole-genome re-sequencing reveals the impact of the interaction of copy number variants of the rhg1 and Rhg4 genes on broad-based resistance to soybean cyst nematode. Plant Biotechnol J 2019; 17:1595-1611. [PMID: 30688400 PMCID: PMC6662113 DOI: 10.1111/pbi.13086] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 05/19/2023]
Abstract
Soybean cyst nematode (SCN) is the most devastating plant-parasitic nematode. Most commercial soybean varieties with SCN resistance are derived from PI88788. Resistance derived from PI88788 is breaking down due to narrow genetic background and SCN population shift. PI88788 requires mainly the rhg1-b locus, while 'Peking' requires rhg1-a and Rhg4 for SCN resistance. In the present study, whole genome re-sequencing of 106 soybean lines was used to define the Rhg haplotypes and investigate their responses to the SCN HG-Types. The analysis showed a comprehensive profile of SNPs and copy number variations (CNV) at these loci. CNV of rhg1 (GmSNAP18) only contributed towards resistance in lines derived from PI88788 and 'Cloud'. At least 5.6 copies of the PI88788-type rhg1 were required to confer SCN resistance, regardless of the Rhg4 (GmSHMT08) haplotype. However, when the GmSNAP18 copies dropped below 5.6, a 'Peking'-type GmSHMT08 haplotype was required to ensure SCN resistance. This points to a novel mechanism of epistasis between GmSNAP18 and GmSHMT08 involving minimum requirements for copy number. The presence of more Rhg4 copies confers resistance to multiple SCN races. Moreover, transcript abundance of the GmSHMT08 in root tissue correlates with more copies of the Rhg4 locus, reinforcing SCN resistance. Finally, haplotype analysis of the GmSHMT08 and GmSNAP18 promoters inferred additional levels of the resistance mechanism. This is the first report revealing the genetic basis of broad-based resistance to SCN and providing new insight into epistasis, haplotype-compatibility, CNV, promoter variation and its impact on broad-based disease resistance in plants.
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Affiliation(s)
- Gunvant B. Patil
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
- Department Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Jinrong Wan
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - Li Song
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | | | - Tri D. Vuong
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - Adrian O. Stec
- Department Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Sondus S. Kahil
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Vincent Colantonio
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Babu Valliyodan
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
| | - J. Hollis Rice
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Sarbottam Piya
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Tarek Hewezi
- Department of Plant SciencesUniversity of TennesseeKnoxvilleTNUSA
| | - Robert M. Stupar
- Department Agronomy and Plant GeneticsUniversity of MinnesotaSt. PaulMNUSA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural SystemsSouthern Illinois UniversityCarbondaleILUSA
| | - Henry T. Nguyen
- Division of Plant SciencesUniversity of MissouriColumbiaMOUSA
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21
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Lakhssassi N, Patil G, Piya S, Zhou Z, Baharlouei A, Kassem MA, Lightfoot DA, Hewezi T, Barakat A, Nguyen HT, Meksem K. Genome reorganization of the GmSHMT gene family in soybean showed a lack of functional redundancy in resistance to soybean cyst nematode. Sci Rep 2019; 9:1506. [PMID: 30728404 PMCID: PMC6365578 DOI: 10.1038/s41598-018-37815-w] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 12/13/2018] [Indexed: 12/21/2022] Open
Abstract
In soybeans, eighteen members constitute the serine hydroxymethyltransferase (GmSHMT) gene family, of which the cytosolic-targeted GmSHMT08c member has been reported to mediate resistance to soybean cyst nematode (SCN). This work presents a comprehensive study of the SHMT gene family members, including synteny, phylogeny, subcellular localizations, haplotypes, protein homology modeling, mutational, and expression analyses. Phylogenetic analysis showed that SHMT genes are divided into four classes reflecting their subcellular distribution (cytosol, nucleus, mitochondrion, and chloroplast). Subcellular localization of selected GmSHMT members supports their in-silico predictions and phylogenetic distribution. Expression and functional analyses showed that GmSHMT genes display many overlapping, but some divergent responses during SCN infection. Furthermore, mutational analysis reveals that all isolated EMS mutants that lose their resistance to SCN carry missense and nonsense mutations at the GmSHMT08c, but none of the Gmshmt08c mutants carried mutations in the other GmSHMT genes. Haplotype clustering analysis using the whole genome resequencing data from a collection of 106 diverse soybean germplams (15X) was performed to identify allelic variants and haplotypes within the GmSHMT gene family. Interestingly, only the cytosolic-localized GmSHMT08c presented SNP clusters that were associated with SCN resistance, supporting our mutational analysis. Although eight GmSHMT members respond to the nematode infestation, functional and mutational analysis has shown the absence of functional redundancy in resistance to SCN. Structural analysis and protein homology modeling showed the presence of spontaneous mutations at important residues within the GmSHMT proteins, suggesting the presence of altered enzyme activities based on substrate affinities. Due to the accumulation of mutations during the evolution of the soybean genome, the other GmSHMT members have undergone neofunctionalization and subfunctionalization events.
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Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Gunvant Patil
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65201, USA
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Sarbottam Piya
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Azam Baharlouei
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - My Abdelmajid Kassem
- Department of Biological Sciences, Fayetteville State University, Fayetteville, NC, 28301, USA
| | - David A Lightfoot
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Tarek Hewezi
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996, USA
| | - Abdelali Barakat
- Department of Biology, University of South Dakota, Vermillion, SD, 57069, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65201, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA.
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22
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Anderson J, Lakhssassi N, Kantartzi SK, Meksem K. Nonhypothesis Analysis of a Mutagenic Soybean ( Glycine max[L.]) Population for Protein and Fatty-Acid Composition. J AM OIL CHEM SOC 2018. [DOI: 10.1002/aocs.12063] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- James Anderson
- Department of Plant Soil and Agricultural Systems; Southern Illinois University, 1205 Lincoln Drive, Mail Code 4415; Carbondale IL 62901 USA
| | - Naoufal Lakhssassi
- Department of Plant Soil and Agricultural Systems; Southern Illinois University, 1205 Lincoln Drive, Mail Code 4415; Carbondale IL 62901 USA
| | - Stella K. Kantartzi
- Department of Plant Soil and Agricultural Systems; Southern Illinois University, 1205 Lincoln Drive, Mail Code 4415; Carbondale IL 62901 USA
| | - Khalid Meksem
- Department of Plant Soil and Agricultural Systems; Southern Illinois University, 1205 Lincoln Drive, Mail Code 4415; Carbondale IL 62901 USA
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23
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Kandoth PK, Liu S, Prenger E, Ludwig A, Lakhssassi N, Heinz R, Zhou Z, Howland A, Gunther J, Eidson S, Dhroso A, LaFayette P, Tucker D, Johnson S, Anderson J, Alaswad A, Cianzio SR, Parrott WA, Korkin D, Meksem K, Mitchum MG. Systematic Mutagenesis of Serine Hydroxymethyltransferase Reveals an Essential Role in Nematode Resistance. Plant Physiol 2017; 175:1370-1380. [PMID: 28912378 PMCID: PMC5664460 DOI: 10.1104/pp.17.00553] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 09/11/2017] [Indexed: 05/27/2023]
Abstract
Rhg4 is a major genetic locus that contributes to soybean cyst nematode (SCN) resistance in the Peking-type resistance of soybean (Glycine max), which also requires the rhg1 gene. By map-based cloning and functional genomic approaches, we previously showed that the Rhg4 gene encodes a predicted cytosolic serine hydroxymethyltransferase (GmSHMT08); however, the novel gain of function of GmSHMT08 in SCN resistance remains to be characterized. Using a forward genetic screen, we identified an allelic series of GmSHMT08 mutants that shed new light on the mechanistic aspects of GmSHMT08-mediated resistance. The new mutants provide compelling genetic evidence that Peking-type rhg1 resistance in cv Forrest is fully dependent on the GmSHMT08 gene and demonstrates that this resistance is mechanistically different from the PI 88788-type of resistance that only requires rhg1 We also demonstrated that rhg1-a from cv Forrest, although required, does not exert selection pressure on the nematode to shift from HG type 7, which further validates the bigenic nature of this resistance. Mapping of the identified mutations onto the SHMT structural model uncovered key residues for structural stability, ligand binding, enzyme activity, and protein interactions, suggesting that GmSHMT08 has additional functions aside from its main enzymatic role in SCN resistance. Lastly, we demonstrate the functionality of the GmSHMT08 SCN resistance gene in a transgenic soybean plant.
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Affiliation(s)
- Pramod K Kandoth
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Shiming Liu
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Elizabeth Prenger
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Andrew Ludwig
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Naoufal Lakhssassi
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Robert Heinz
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Zhou Zhou
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Amanda Howland
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
| | - Joshua Gunther
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Samantha Eidson
- Mathematics and Computer Science Department, Fontbonne University, St. Louis, Missouri 63105
| | - Andi Dhroso
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Peter LaFayette
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Donna Tucker
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Sarah Johnson
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - James Anderson
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Alaa Alaswad
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | | | - Wayne A Parrott
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia 30602
| | - Dmitry Korkin
- Department of Computer Science and Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, Massachusetts 01609
| | - Khalid Meksem
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211
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24
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Mirzaei S, Batley J, El-Mellouki T, Liu S, Meksem K, Ferguson BJ, Gresshoff PM. Neodiversification of homeologous CLAVATA1-like receptor kinase genes in soybean leads to distinct developmental outcomes. Sci Rep 2017; 7:8878. [PMID: 28827708 PMCID: PMC5566472 DOI: 10.1038/s41598-017-08252-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 06/29/2017] [Indexed: 11/09/2022] Open
Abstract
The CLAVATA pathway that regulates stem cell numbers of the shoot apical meristem has exclusively been studied in Arabidopsis; as such insight into other species is warranted. In this study, a GmCLV1A mutant (F-S562L) with altered lateral organ development, and two mutants of GmNARK, isolated from a Forrest M2 population (EMS-mutated soybean) were studied. GmCLV1A and GmNARK encode for LRR receptor kinases, and share 92% of protein sequence. While GmNARK is critical for systemic regulation of nodulation (new organ made on the root through symbiosis), we show that GmCLV1A functions locally and has no apparent function in nodulation or root development. However, a recessive, loss-of-function mutation (S562L) in a putative S-glycosylation site of GmCLV1A causes stem nodal identity alterations as well as flower and pod abnormalities (deformed flower and pod). The mutant also exhibits a homeotic phenotype, displaying abnormal leaf development/number, vein-derived leaf emergence, and a thick, faciated stem. The mutant phenotype is also temperature-sensitive. Interestingly, a novel truncated version of GmCLV1A was identified upstream of GmCLV1A that is absent from GmNARK, but is present upstream of the GmNARK orthologues, MtSUNN and PvNARK. Taken together, our findings indicate that GmCLV1A acts on shoot architecture, whereas GmNARK, functions in controlling nodule numbers.
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Affiliation(s)
- Saeid Mirzaei
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
- Department of Biotechnology, Institute of Science, High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Jacqueline Batley
- School of Biological Sciences, University of Western Australia, Crawley, WA, 6009, Australia
| | - Tarik El-Mellouki
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Shiming Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901, USA
| | - Brett J Ferguson
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia
| | - Peter M Gresshoff
- Centre for Integrative Legume Research, School of Agriculture and Food Sciences, The University of Queensland, St Lucia, Brisbane, QLD, 4072, Australia.
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25
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Lakhssassi N, Colantonio V, Flowers ND, Zhou Z, Henry J, Liu S, Meksem K. Stearoyl-Acyl Carrier Protein Desaturase Mutations Uncover an Impact of Stearic Acid in Leaf and Nodule Structure. Plant Physiol 2017; 174:1531-1543. [PMID: 28461402 PMCID: PMC5490888 DOI: 10.1104/pp.16.01929] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 04/26/2017] [Indexed: 05/20/2023]
Abstract
Stearoyl-acyl carrier protein desaturase (SACPD-C) has been reported to control the accumulation of seed stearic acid; however, no study has previously reported its involvement in leaf stearic acid content and impact on leaf structure and morphology. A subset of an ethyl methanesulfonate mutagenized population of soybean (Glycine max) 'Forrest' was screened to identify mutants within the GmSACPD-C gene. Using a forward genetics approach, one nonsense and four missense Gmsacpd-c mutants were identified to have high levels of seed, nodule, and leaf stearic acid content. Homology modeling and in silico analysis of the GmSACPD-C enzyme revealed that most of these mutations were localized near or at conserved residues essential for diiron ion coordination. Soybeans carrying Gmsacpd-c mutations at conserved residues showed the highest stearic acid content, and these mutations were found to have deleterious effects on nodule development and function. Interestingly, mutations at nonconserved residues show an increase in stearic acid content yet retain healthy nodules. Thus, random mutagenesis and mutational analysis allows for the achievement of high seed stearic acid content with no associated negative agronomic characteristics. Additionally, expression analysis demonstrates that nodule leghemoglobin transcripts were significantly more abundant in soybeans with deleterious mutations at conserved residues of GmSACPD-C. Finally, we report that Gmsacpd-c mutations cause an increase in leaf stearic acid content and an alteration of leaf structure and morphology in addition to differences in nitrogen-fixing nodule structure.
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Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Vincent Colantonio
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
- Department of Microbiology, Southern Illinois University, Carbondale, Illinois 62901
| | - Nicholas D Flowers
- Department of Plant Biology, Southern Illinois University, Carbondale, Illinois 62901
| | - Zhou Zhou
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Jason Henry
- Department of Plant Biology, Southern Illinois University, Carbondale, Illinois 62901
| | - Shiming Liu
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
| | - Khalid Meksem
- Department of Plant, Soil, and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901
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26
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Brensha W, Kantartzi SK, Meksem K, Grier IV RL, Barakat A, Lightfoot DA, Kassem MA. Genetic Analysis of Root and Shoot Traits in the ‘Essex’ By ‘Forrest’ Recombinant Inbred Line (RIL) Population of Soybean [Glycine max (L.) Merr.]. ACTA ACUST UNITED AC 2017. [DOI: 10.5147/pggb.v1i1.146] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Crop productivity is severely reduced by water deficit and drought in many plant species including soybean. Improved root and shoot traits can contribute to drought tolerance ability of the plant. This research was conducted to identify QTL that underlie several root and shoot traits in the ‘Essex’ by ‘Forrest’ (ExF RILs, n=94) recombinant inbred line (RIL) soybean population. Field collected samples were used for gathering phenotypic data of basal root thickness (BRT), lateral root number (LRN), maximum root length (MRL), root fresh weight (RFW), root dry weight (RDW), shoot fresh weight (SFW), shoot dry weight (SDW), and calculating RFW/SFW, and RDW/SDW ratios. All traits and ratios were compared against DNA markers using the composite interval mapping (CIM). A total of 12 QTL: 3 for MRL, 1 QTL for LRN, 1 QTL for BRT, 2 QTL for RFW, 2 QTL for RDW, 4 QTL for SFW, 3 QTL for SDW, and 3 QTL for SFW/SDW were identified and mapped on different linkage groups (LGs) A2, B2, C2, D1a, F, G, and N. The LOD scores of these QTL ranged from 2.5 to 6.0. No QTL were associated with RFW/RDW. The root and shoot trait QTL of this study may benefit breeding programs for producing cultivars tolerant to water deficit and high yield. Preliminary analyses of genes the QTL regions using GO annotation gave insight into genes that may underlie some of these QTLs.
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27
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Liu S, Kandoth PK, Lakhssassi N, Kang J, Colantonio V, Heinz R, Yeckel G, Zhou Z, Bekal S, Dapprich J, Rotter B, Cianzio S, Mitchum MG, Meksem K. The soybean GmSNAP18 gene underlies two types of resistance to soybean cyst nematode. Nat Commun 2017; 8:14822. [PMID: 28345654 PMCID: PMC5378975 DOI: 10.1038/ncomms14822] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 02/06/2017] [Indexed: 12/24/2022] Open
Abstract
Two types of resistant soybean (Glycine max (L.) Merr.) sources are widely used against soybean cyst nematode (SCN, Heterodera glycines Ichinohe). These include Peking-type soybean, whose resistance requires both the rhg1-a and Rhg4 alleles, and PI 88788-type soybean, whose resistance requires only the rhg1-b allele. Multiple copy number of PI 88788-type GmSNAP18, GmAAT, and GmWI12 in one genomic segment simultaneously contribute to rhg1-b resistance. Using an integrated set of genetic and genomic approaches, we demonstrate that the rhg1-a Peking-type GmSNAP18 is sufficient for resistance to SCN in combination with Rhg4. The two SNAPs (soluble NSF attachment proteins) differ by only five amino acids. Our findings suggest that Peking-type GmSNAP18 is performing a different role in SCN resistance than PI 88788-type GmSNAP18. As such, this is an example of a pathogen resistance gene that has evolved to underlie two types of resistance, yet ensure the same function within a single plant species.
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Affiliation(s)
- Shiming Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, 1205 Lincoln Drive RM176, Carbondale, Illinois 62901, USA
| | - Pramod K. Kandoth
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, 1205 Lincoln Drive RM176, Carbondale, Illinois 62901, USA
| | - Jingwen Kang
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Vincent Colantonio
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, 1205 Lincoln Drive RM176, Carbondale, Illinois 62901, USA
| | - Robert Heinz
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Greg Yeckel
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, 1205 Lincoln Drive RM176, Carbondale, Illinois 62901, USA
| | - Sadia Bekal
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, 1205 Lincoln Drive RM176, Carbondale, Illinois 62901, USA
| | | | - Bjorn Rotter
- GenXPro-GmbH, Altenhöferallee 3, 60438 Frankfurt am Main, Germany
| | - Silvia Cianzio
- Department of Agronomy, Iowa State University, Ames, Iowa 50011, USA
| | - Melissa G. Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, Missouri 65211, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, 1205 Lincoln Drive RM176, Carbondale, Illinois 62901, USA
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28
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Lakhssassi N, Liu S, Bekal S, Zhou Z, Colantonio V, Lambert K, Barakat A, Meksem K. Characterization of the Soluble NSF Attachment Protein gene family identifies two members involved in additive resistance to a plant pathogen. Sci Rep 2017; 7:45226. [PMID: 28338077 PMCID: PMC5364553 DOI: 10.1038/srep45226] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 02/21/2017] [Indexed: 11/15/2022] Open
Abstract
Proteins with Tetratricopeptide-repeat (TPR) domains are encoded by large gene families and distributed in all plant lineages. In this study, the Soluble NSF-Attachment Protein (SNAP) subfamily of TPR containing proteins is characterized. In soybean, five members constitute the SNAP gene family: GmSNAP18, GmSNAP11, GmSNAP14, GmSNAP02, and GmSNAP09. Recently, GmSNAP18 has been reported to mediate resistance to soybean cyst nematode (SCN). Using a population of recombinant inbred lines from resistant and susceptible parents, the divergence of the SNAP gene family is analysed over time. Phylogenetic analysis of SNAP genes from 22 diverse plant species showed that SNAPs were distributed in six monophyletic clades corresponding to the major plant lineages. Conservation of the four TPR motifs in all species, including ancestral lineages, supports the hypothesis that SNAPs were duplicated and derived from a common ancestor and unique gene still present in chlorophytic algae. Syntenic analysis of regions harbouring GmSNAP genes in soybean reveals that this family expanded from segmental and tandem duplications following a tetraploidization event. qRT-PCR analysis of GmSNAPs indicates a co-regulation following SCN infection. Finally, genetic analysis demonstrates that GmSNAP11 contributes to an additive resistance to SCN. Thus, GmSNAP11 is identified as a novel minor gene conferring resistance to SCN.
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Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
| | - Shiming Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
| | - Sadia Bekal
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
| | - Vincent Colantonio
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
| | - Kris Lambert
- Department of Crop Sciences, University of Illinois, Urbana, IL 61801, USA
| | - Abdelali Barakat
- Department of Biology, University of South Dakota, Vermillion, SD 57069, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
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29
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Lakhssassi N, Zhou Z, Liu S, Colantonio V, AbuGhazaleh A, Meksem K. Characterization of the FAD2 Gene Family in Soybean Reveals the Limitations of Gel-Based TILLING in Genes with High Copy Number. Front Plant Sci 2017; 8:324. [PMID: 28348573 PMCID: PMC5346563 DOI: 10.3389/fpls.2017.00324] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 02/23/2017] [Indexed: 05/21/2023]
Abstract
Soybean seed oil typically contains 18-20% oleic acid. Increasing the content of oleic acid is beneficial for health and biodiesel production. Mutations in FAD2-1 genes have been reported to increase seed oleic acid content. A subset of 1,037 mutant families from a mutagenized soybean cultivar (cv.) Forrest population was screened using reverse genetics (TILLING) to identify mutations within FAD2 genes. Although no fad2 mutants were identified using gel-based TILLING, four fad2-1A and one fad2-1B mutants were identified to have high seed oleic acid content using forward genetic screening and subsequent target sequencing. TILLING has been successfully used as a non-transgenic reverse genetic approach to identify mutations in genes controlling important agronomic traits. However, this technique presents limitations in traits such as oil composition due to gene copy number and similarities within the soybean genome. In soybean, FAD2 are present as two copies, FAD2-1 and FAD2-2. Two FAD2-1 members: FAD2-1A and FAD2-1B; and three FAD2-2 members: FAD2-2A, FAD2-2B, and FAD2-2C have been reported. Syntenic, phylogenetic, and in silico analysis revealed two additional members constituting the FAD2 gene family: GmFAD2-2D and GmFAD2-2E, located on chromosomes 09 and 15, respectively. They are presumed to have diverged from other FAD2-2 members localized on chromosomes 19 (GmFAD2-2A and GmFAD2-2B) and 03 (GmFAD2-2C). This work discusses alternative solutions to the limitations of gel-based TILLING in functional genomics due to high copy number and multiple paralogs of the FAD2 gene family in soybean.
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Affiliation(s)
- Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois UniversityCarbondale, IL, USA
| | - Zhou Zhou
- Department of Plant, Soil and Agricultural Systems, Southern Illinois UniversityCarbondale, IL, USA
| | - Shiming Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois UniversityCarbondale, IL, USA
| | - Vincent Colantonio
- Department of Plant, Soil and Agricultural Systems, Southern Illinois UniversityCarbondale, IL, USA
| | - Amer AbuGhazaleh
- Department of Animal Science, Food and Nutrition, Southern Illinois UniversityCarbondale, IL, USA
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois UniversityCarbondale, IL, USA
- *Correspondence: Khalid Meksem
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30
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Gan X, Hay A, Kwantes M, Haberer G, Hallab A, Ioio RD, Hofhuis H, Pieper B, Cartolano M, Neumann U, Nikolov LA, Song B, Hajheidari M, Briskine R, Kougioumoutzi E, Vlad D, Broholm S, Hein J, Meksem K, Lightfoot D, Shimizu KK, Shimizu-Inatsugi R, Imprialou M, Kudrna D, Wing R, Sato S, Huijser P, Filatov D, X Mayer KF, Mott R, Tsiantis M. Erratum: The Cardamine hirsuta genome offers insight into the evolution of morphological diversity. Nat Plants 2016; 2:16189. [PMID: 27819656 PMCID: PMC9119268 DOI: 10.1038/nplants.2016.189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
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31
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Gan X, Hay A, Kwantes M, Haberer G, Hallab A, Ioio RD, Hofhuis H, Pieper B, Cartolano M, Neumann U, Nikolov LA, Song B, Hajheidari M, Briskine R, Kougioumoutzi E, Vlad D, Broholm S, Hein J, Meksem K, Lightfoot D, Shimizu KK, Shimizu-Inatsugi R, Imprialou M, Kudrna D, Wing R, Sato S, Huijser P, Filatov D, Mayer KFX, Mott R, Tsiantis M. The Cardamine hirsuta genome offers insight into the evolution of morphological diversity. Nat Plants 2016; 2:16167. [PMID: 27797353 PMCID: PMC8826541 DOI: 10.1038/nplants.2016.167] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 09/30/2016] [Indexed: 05/18/2023]
Abstract
Finding causal relationships between genotypic and phenotypic variation is a key focus of evolutionary biology, human genetics and plant breeding. To identify genome-wide patterns underlying trait diversity, we assembled a high-quality reference genome of Cardamine hirsuta, a close relative of the model plant Arabidopsis thaliana. We combined comparative genome and transcriptome analyses with the experimental tools available in C. hirsuta to investigate gene function and phenotypic diversification. Our findings highlight the prevalent role of transcription factors and tandem gene duplications in morphological evolution. We identified a specific role for the transcriptional regulators PLETHORA5/7 in shaping leaf diversity and link tandem gene duplication with differential gene expression in the explosive seed pod of C. hirsuta. Our work highlights the value of comparative approaches in genetically tractable species to understand the genetic basis for evolutionary change.
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Affiliation(s)
- Xiangchao Gan
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Angela Hay
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Michiel Kwantes
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Georg Haberer
- Plant Genome and Systems Biology, Helmholtz Zentrum Munich, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Asis Hallab
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Raffaele Dello Ioio
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
- Present Address: †Present address: Department of Biology and Biotechnology, Università La Sapienza, P.le Aldo Moro, 5, 00185 Rome, Italy (R.D.I.). The Global Food Security, BBSRC, Polaris House, North Star Avenue, Swindon SN2 1UH, UK (E.K.). Institute of Biotechnology, Viikinkaari 1, 00014 University of Helsinki, Finland (S.B.),
| | - Hugo Hofhuis
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Bjorn Pieper
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Maria Cartolano
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Ulla Neumann
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Lachezar A. Nikolov
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Baoxing Song
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Mohsen Hajheidari
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Roman Briskine
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Evangelia Kougioumoutzi
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford UK
- Present Address: †Present address: Department of Biology and Biotechnology, Università La Sapienza, P.le Aldo Moro, 5, 00185 Rome, Italy (R.D.I.). The Global Food Security, BBSRC, Polaris House, North Star Avenue, Swindon SN2 1UH, UK (E.K.). Institute of Biotechnology, Viikinkaari 1, 00014 University of Helsinki, Finland (S.B.),
| | - Daniela Vlad
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford UK
| | - Suvi Broholm
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford UK
- Present Address: †Present address: Department of Biology and Biotechnology, Università La Sapienza, P.le Aldo Moro, 5, 00185 Rome, Italy (R.D.I.). The Global Food Security, BBSRC, Polaris House, North Star Avenue, Swindon SN2 1UH, UK (E.K.). Institute of Biotechnology, Viikinkaari 1, 00014 University of Helsinki, Finland (S.B.),
| | - Jotun Hein
- Department of Statistics, University of Oxford, 1 South Parks Road, OX1 3TG Oxford UK
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, 62901 Illinois USA
| | - David Lightfoot
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, 62901 Illinois USA
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Rie Shimizu-Inatsugi
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Martha Imprialou
- Department of Statistics, University of Oxford, 1 South Parks Road, OX1 3TG Oxford UK
| | - David Kudrna
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, 85721 Arizona USA
| | - Rod Wing
- Arizona Genomics Institute, School of Plant Sciences and BIO5 Institute for Collaborative Research, University of Arizona, 1657 East Helen Street, Tucson, 85721 Arizona USA
| | - Shusei Sato
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford UK
| | - Peter Huijser
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | - Dmitry Filatov
- Department of Plant Sciences, University of Oxford, South Parks Road, OX1 3RB Oxford UK
| | - Klaus F. X. Mayer
- Plant Genome and Systems Biology, Helmholtz Zentrum Munich, Ingolstädter Landstrasse 1, 85764 Neuherberg, Germany
| | - Richard Mott
- UCL Genetics Institute, University College London, Gower Street, WC1E 6BT London UK
| | - Miltos Tsiantis
- Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
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Nordine A, Udupa SM, Iraqi D, Meksem K, Hmamouchi M, ElMeskaoui A. Correlation between the Chemical and Genetic Relationships amongThymus saturejoidesGenotypes Cultured underin vitroandin vivoEnvironments. Chem Biodivers 2016; 13:387-94. [DOI: 10.1002/cbdv.201500102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2015] [Accepted: 09/04/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Aicha Nordine
- Phytobiotechnology Unit; National Agency of Medicinal and Aromatic Plants; PB 159 Taounate Morocco
- University of Sidi Mohamed Ben Abdellah; Imouzzer Road PB 2626, 30000 Fez Morocco
| | - Sripada M. Udupa
- ICARDA-INRA Cooperative Research Project; International Center for Agricultural Research in the Dry Areas (ICARDA); PB 6299 Rabat Morocco
| | - Driss Iraqi
- Biotechnology Research Unit; National Institute of Agronomic Research; PB 415 Rabat Morocco
| | - Khalid Meksem
- Department of Plant, Soil & General Agriculture; Southern Illinois University; Carbondale IL 62901-6899 USA
| | - Mohamed Hmamouchi
- Faculty of Medicine and Pharmacy; Mohamed V University; Mohamed Belarbi El Alaoui ST PB 6203, Rabat Morocco
| | - Abdelmalek ElMeskaoui
- Phytobiotechnology Unit; National Agency of Medicinal and Aromatic Plants; PB 159 Taounate Morocco
- University of Sidi Mohamed Ben Abdellah; Imouzzer Road PB 2626, 30000 Fez Morocco
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Zenis A, Kantartzi S, Meksem K, Kassem MA. Influence of Drought Stress on Several Root Traits and their Correlation with Seed Protein and Oil Contents in Soybean. ACTA ACUST UNITED AC 2016. [DOI: 10.5147/ajb.v0i0.37] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Bekal S, Domier LL, Gonfa B, Lakhssassi N, Meksem K, Lambert KN. A SNARE-Like Protein and Biotin Are Implicated in Soybean Cyst Nematode Virulence. PLoS One 2015; 10:e0145601. [PMID: 26714307 PMCID: PMC4699853 DOI: 10.1371/journal.pone.0145601] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 12/07/2015] [Indexed: 11/24/2022] Open
Abstract
Phytoparasitic nematodes that are able to infect and reproduce on plants that are considered resistant are referred to as virulent. The mechanism(s) that virulent nematodes employ to evade or suppress host plant defenses are not well understood. Here we report the use of a genetic strategy (allelic imbalance analysis) to associate single nucleotide polymorphisms (SNPs) with nematode virulence genes in Heterodera glycines, the soybean cyst nematode (SCN). To accomplish this analysis, a custom SCN SNP array was developed and used to genotype SCN F3-derived populations grown on resistant and susceptible soybean plants. Three SNPs reproducibly showed allele imbalances between nematodes grown on resistant and susceptible plants. Two candidate SCN virulence genes that were tightly linked to the SNPs were identified. One SCN gene encoded biotin synthase (HgBioB), and the other encoded a bacterial-like protein containing a putative SNARE domain (HgSLP-1). The two genes mapped to two different linkage groups. HgBioB contained sequence polymorphisms between avirulent and virulent nematodes. However, the gene encoding HgSLP-1 had reduced copy number in virulent nematode populations and appears to produce multiple forms of the protein via intron retention and alternative splicing. We show that HgSLP-1 is an esophageal-gland protein that is secreted by the nematode during plant parasitism. Furthermore, in bacterial co-expression experiments, HgSLP-1 co-purified with the SCN resistance protein Rhg1 α-SNAP, suggesting that these two proteins physically interact. Collectively our data suggest that multiple SCN genes are involved in SCN virulence, and that HgSLP-1 may function as an avirulence protein and when absent it helps SCN evade host defenses.
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Affiliation(s)
- Sadia Bekal
- Department of Plant, Soil and Agricultural Systems, 1205 Lincoln Dr. Southern Illinois University, Carbondale, IL, 62901, United States of America
| | - Leslie L. Domier
- Department of Crop Sciences, University of Illinois, 1102 South Goodwin Ave. Urbana, IL, 61801, United States of America
| | - Biruk Gonfa
- Department of Crop Sciences, University of Illinois, 1102 South Goodwin Ave. Urbana, IL, 61801, United States of America
| | - Naoufal Lakhssassi
- Department of Plant, Soil and Agricultural Systems, 1205 Lincoln Dr. Southern Illinois University, Carbondale, IL, 62901, United States of America
| | - Khalid Meksem
- Department of Plant, Soil and Agricultural Systems, 1205 Lincoln Dr. Southern Illinois University, Carbondale, IL, 62901, United States of America
| | - Kris N. Lambert
- Department of Crop Sciences, University of Illinois, 1102 South Goodwin Ave. Urbana, IL, 61801, United States of America
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Shi Z, Liu S, Noe J, Arelli P, Meksem K, Li Z. SNP identification and marker assay development for high-throughput selection of soybean cyst nematode resistance. BMC Genomics 2015; 16:314. [PMID: 25903750 PMCID: PMC4407462 DOI: 10.1186/s12864-015-1531-3] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2014] [Accepted: 04/13/2015] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Soybean cyst nematode (SCN) is the most economically devastating pathogen of soybean. Two resistance loci, Rhg1 and Rhg4 primarily contribute resistance to SCN race 3 in soybean. Peking and PI 88788 are the two major sources of SCN resistance with Peking requiring both Rhg1 and Rhg4 alleles and PI 88788 only the Rhg1 allele. Although simple sequence repeat (SSR) markers have been reported for both loci, they are linked markers and limited to be applied in breeding programs due to accuracy, throughput and cost of detection methods. The objectives of this study were to develop robust functional marker assays for high-throughput selection of SCN resistance and to differentiate the sources of resistance. RESULTS Based on the genomic DNA sequences of 27 soybean lines with known SCN phenotypes, we have developed Kompetitive Allele Specific PCR (KASP) assays for two Single nucleotide polymorphisms (SNPs) from Glyma08g11490 for the selection of the Rhg4 resistance allele. Moreover, the genomic DNA of Glyma18g02590 at the Rhg1 locus from 11 soybean lines and cDNA of Forrest, Essex, Williams 82 and PI 88788 were fully sequenced. Pairwise sequence alignment revealed seven SNPs/insertion/deletions (InDels), five in the 6th exon and two in the last exon. Using the same 27 soybean lines, we identified one SNP that can be used to select the Rhg1 resistance allele and another SNP that can be employed to differentiate Peking and PI 88788-type resistance. These SNP markers have been validated and a strong correlation was observed between the SNP genotypes and reactions to SCN race 3 using a panel of 153 soybean lines, as well as a bi-parental population, F5-derived recombinant inbred lines (RILs) from G00-3213xLG04-6000. CONCLUSIONS Three functional SNP markers (two for Rhg1 locus and one for Rhg4 locus) were identified that could provide genotype information for the selection of SCN resistance and differentiate Peking from PI 88788 source for most germplasm lines. The robust KASP SNP marker assays were developed. In most contexts, use of one or two of these markers is sufficient for high-throughput marker-assisted selection of plants that will exhibit SCN resistance.
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Affiliation(s)
- Zi Shi
- Center for Applied Genetic Technologies & Dep. of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
| | - Shiming Liu
- Department of Plant, Soil and Agriculture Systems, Southern Illinois University, Carbondale, IL, 62901, USA.
| | - James Noe
- Department of Plant Pathology, University of Georgia, Athens, GA, 30602, USA.
| | | | - Khalid Meksem
- Department of Plant, Soil and Agriculture Systems, Southern Illinois University, Carbondale, IL, 62901, USA.
| | - Zenglu Li
- Center for Applied Genetic Technologies & Dep. of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA.
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Anderson J, Akond M, Kassem MA, Meksem K, Kantartzi SK. Quantitative trait loci underlying resistance to sudden death syndrome (SDS) in MD96-5722 by 'Spencer' recombinant inbred line population of soybean. 3 Biotech 2015; 5:203-210. [PMID: 28324582 PMCID: PMC4362743 DOI: 10.1007/s13205-014-0211-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2014] [Accepted: 03/21/2014] [Indexed: 11/06/2022] Open
Abstract
The best way to protect yield loss of soybean [Glycine max (L.) Merr.] due to sudden death syndrome (SDS), caused by Fusarium virguliforme (Aoki, O'Donnel, Homma & Lattanzi), is the development and use of resistant lines. Mapping quantitative trait loci (QTL) linked to SDS help developing resistant soybean germplasm through molecular marker-assisted selection strategy. QTL for SDS presented herein are from a high-density SNP-based genetic linkage map of MD 96-5722 (a.k.a 'Monocacy') by 'Spencer' recombinant inbred line using SoySNP6K Illumina Infinium BeadChip genotyping array. Ninety-four F5:7 lines were evaluated for 2 years (2010 and 2011) at two locations (Carbondale and Valmeyer) in southern Illinois, USA to identify QTL controlling SDS resistance using disease index (DX). Composite interval mapping identified 19 SDS controlling QTL which were mapped on 11 separate linkage group (LG) or chromosomes (Chr) out of 20 LG or Chr of soybean genome. Many of these significant QTL identified in one environment/year were confirmed in another year or environment, which suggests a common genetic effects and modes of the pathogen. These new QTL are useful sources for SDS resistance studies in soybean breeding, complementing previously reported loci.
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Affiliation(s)
- J Anderson
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901-4415, USA
| | - M Akond
- Plant Genomics and Biotechnology Lab, Department of Biological Sciences, Fayetteville State University, Fayetteville, NC, 28301-4298, USA
| | - M A Kassem
- Plant Genomics and Biotechnology Lab, Department of Biological Sciences, Fayetteville State University, Fayetteville, NC, 28301-4298, USA
| | - K Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901-4415, USA
| | - S K Kantartzi
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL, 62901-4415, USA.
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Akond M, Liu S, Kantartzi SK, Meksem K, Bellaloui N, Lightfoot DA, Yuan J, Wang D, Kassem MA. Quantitative trait loci for seed isoflavone contents in 'MD96-5722' by 'Spencer' recombinant inbred lines of soybean. J Agric Food Chem 2014; 62:1464-1468. [PMID: 24499298 DOI: 10.4236/fns.2015.611100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Isoflavones from soybeans [ Glycine max (L.) Merr.] have a significant impact on human health to reduce the risk of several major diseases. Breeding soybean for high isoflavone content in the seed is possible through marker-assisted selection (MAS) which can be based on quantitative trait loci (QTL). The objective of this study was to identify QTL controlling isoflavone content in a set of 'MD96-5722' by 'Spencer' recombinant inbred line (RIL) populations of soybean. Wide variations were found for seed concentrations of daidzein, glycitein, genistein, and total isoflavones among the RIL populations. Three QTL were identified on three different linkage groups (LG) represented by three different chromosomes (Chr). One QTL that controlled daidzein content was identified on LG A1 (Chr 5), and two QTL that underlay glycitein content were identified on LG K (Chr 9) and LG B2 (Chr 14). Identified QTL could be functional in developing soybean with preferable isoflavone concentrations in the seeds through MAS.
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Affiliation(s)
- Masum Akond
- Plant Genomics and Biotechnology Laboratory, Department of Biological Sciences, Fayetteville State University , Fayetteville, North Carolina 28301-4298, United States
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Akond M, Liu S, Kantartzi SK, Meksem K, Bellaloui N, Lightfoot DA, Yuan J, Wang D, Kassem MA. Quantitative trait loci for seed isoflavone contents in 'MD96-5722' by 'Spencer' recombinant inbred lines of soybean. J Agric Food Chem 2014; 62:1464-8. [PMID: 24499298 DOI: 10.1021/jf4040173] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Isoflavones from soybeans [ Glycine max (L.) Merr.] have a significant impact on human health to reduce the risk of several major diseases. Breeding soybean for high isoflavone content in the seed is possible through marker-assisted selection (MAS) which can be based on quantitative trait loci (QTL). The objective of this study was to identify QTL controlling isoflavone content in a set of 'MD96-5722' by 'Spencer' recombinant inbred line (RIL) populations of soybean. Wide variations were found for seed concentrations of daidzein, glycitein, genistein, and total isoflavones among the RIL populations. Three QTL were identified on three different linkage groups (LG) represented by three different chromosomes (Chr). One QTL that controlled daidzein content was identified on LG A1 (Chr 5), and two QTL that underlay glycitein content were identified on LG K (Chr 9) and LG B2 (Chr 14). Identified QTL could be functional in developing soybean with preferable isoflavone concentrations in the seeds through MAS.
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Affiliation(s)
- Masum Akond
- Plant Genomics and Biotechnology Laboratory, Department of Biological Sciences, Fayetteville State University , Fayetteville, North Carolina 28301-4298, United States
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Ragin B, Akond M, Kantartzi S, Meksem K, Herrera H, Akbay C, Lightfoot DA, Kassem MA. Effect of Row Spacing on Seed Isoflavone Contents in Soybean [Glycine max (L.) Merr.]. ACTA ACUST UNITED AC 2014. [DOI: 10.4236/ajps.2014.526418] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Njiti VN, Meksem K, Yuan J, Lightfoot DA, Banz WJ, Winters TA. DNA markers associated with Loci underlying seed phytoestrogen content in soybeans. J Med Food 2013; 2:185-7. [PMID: 19281376 DOI: 10.1089/jmf.1999.2.185] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- V N Njiti
- Department of Plant, Soil, and General Agriculture, Southern Illinois University, Carbondale, IL, USA
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Liu S, Kandoth PK, Warren SD, Yeckel G, Heinz R, Alden J, Yang C, Jamai A, El-Mellouki T, Juvale PS, Hill J, Baum TJ, Cianzio S, Whitham SA, Korkin D, Mitchum MG, Meksem K. A soybean cyst nematode resistance gene points to a new mechanism of plant resistance to pathogens. Nature 2012; 492:256-60. [PMID: 23235880 DOI: 10.1038/nature11651] [Citation(s) in RCA: 225] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2012] [Accepted: 09/27/2012] [Indexed: 12/26/2022]
Abstract
Soybean (Glycine max (L.) Merr.) is an important crop that provides a sustainable source of protein and oil worldwide. Soybean cyst nematode (Heterodera glycines Ichinohe) is a microscopic roundworm that feeds on the roots of soybean and is a major constraint to soybean production. This nematode causes more than US$1 billion in yield losses annually in the United States alone, making it the most economically important pathogen on soybean. Although planting of resistant cultivars forms the core management strategy for this pathogen, nothing is known about the nature of resistance. Moreover, the increase in virulent populations of this parasite on most known resistance sources necessitates the development of novel approaches for control. Here we report the map-based cloning of a gene at the Rhg4 (for resistance to Heterodera glycines 4) locus, a major quantitative trait locus contributing to resistance to this pathogen. Mutation analysis, gene silencing and transgenic complementation confirm that the gene confers resistance. The gene encodes a serine hydroxymethyltransferase, an enzyme that is ubiquitous in nature and structurally conserved across kingdoms. The enzyme is responsible for interconversion of serine and glycine and is essential for cellular one-carbon metabolism. Alleles of Rhg4 conferring resistance or susceptibility differ by two genetic polymorphisms that alter a key regulatory property of the enzyme. Our discovery reveals an unprecedented plant resistance mechanism against a pathogen. The mechanistic knowledge of the resistance gene can be readily exploited to improve nematode resistance of soybean, an increasingly important global crop.
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Affiliation(s)
- Shiming Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University, Carbondale, Illinois 62901, USA
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Liu X, Liu S, Jamai A, Bendahmane A, Lightfoot DA, Mitchum MG, Meksem K. Soybean cyst nematode resistance in soybean is independent of the Rhg4 locus LRR-RLK gene. Funct Integr Genomics 2011; 11:539-49. [PMID: 21541782 DOI: 10.1007/s10142-011-0225-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Revised: 04/04/2011] [Accepted: 04/05/2011] [Indexed: 01/08/2023]
Abstract
To test the function of candidate genes in soybean for resistance to the soybean cyst nematode (SCN), a large collection of EMS-mutants from the SCN-resistant soybean cultivar "Forrest" was developed for Targeting Induced Local Lesions IN Genomes (TILLING). Additionally, due to the complexity of the soybean genome, an integrated set of genomic and genetic analysis tools was employed to complement the TILLING approach. The efficiency of this integrated set of tools was tested using a candidate soybean gene for resistance to SCN, encoding a leucine-rich repeat receptor-like kinase (LRR-RLK) that was identified by map-based cloning at the Rhg4 locus. The Rhg4 locus is one of the major quantitative trait loci controlling soybean resistance against SCN race 3 (HG type 0) in cv. Forrest, but the gene(s) sequence for resistance remains to be determined. Using TILLING, a Forrest mutant containing a nonsense mutation in the LRR domain of the candidate resistance protein was identified and confirmed; however, the SCN-resistant phenotype of the mutant was not altered. Haplotyping and EcoTILLING of recombinant inbred lines along with complementation analysis corroborated the TILLING result and ruled out the possibility of functional redundancy by a second copy of the LRR-RLK gene identified in the soybean genome. This study validates the use of TILLING, in combination with an integrated set of genomic tools, as an efficient means of testing candidate genes for SCN resistance in soybean.
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Affiliation(s)
- Xiaohong Liu
- Division of Plant Sciences and Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
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Chang YL, Chuang HW, Meksem K, Wu FC, Chang CY, Zhang M, Zhang HB. Characterization of a plant-transformation-ready large-insert BIBAC library of Arabidopsis and bombardment transformation of a large-insert BIBAC of the library into tobacco. Genome 2011; 54:437-47. [PMID: 21585277 DOI: 10.1139/g11-011] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Plant-transformation-ready, large-insert binary bacterial artificial chromosome (BIBAC) libraries are of significance for functional and network analysis of large genomic regions, gene clusters, large-spanning genes, and complex loci in the post-genome era. Here, we report the characterization of a plant-transformation-ready BIBAC library of the sequenced Arabidopsis genome for which such a library is not available to the public, the transformation of a large-insert BIBAC of the library into tobacco by biolistic bombardment, and the expression analysis of its containing genes in transgenic plants. The BIBAC library was constructed from nuclear DNA partially digested with BamHI in the BIBAC vector pCLD04541. It contains 6144 clones and has a mean insert size of 108 kb, representing 5.2× equivalents of the Arabidopsis genome or a probability of greater than 99% of obtaining at least one positive clone from the library using a single-copy sequence as a probe. The transformation of the large-insert BIBAC and analyses of the transgenic plants showed that not only did transgenic plants have intact BIBAC DNA, but also could the BIBAC be transmitted stably into progenies and its containing genes be expressed actively. These results suggest that the large-insert BIBAC library, combined with the biolistic bombardment transformation method, could provide a useful tool for large-scale functional analysis of the Arabidopsis genome sequence and applications in plant-molecular breeding.
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Affiliation(s)
- Yueh-Long Chang
- Institute of Agricultural Biotechnology, National Chiayi University, Chiayi 600, Taiwan.
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Ruben E, Jamai A, Afzal J, Njiti VN, Triwitayakorn K, Iqbal MJ, Yaegashi S, Bashir R, Kazi S, Arelli P, Town CD, Ishihara H, Meksem K, Lightfoot DA. Erratum to: Genomic analysis of the rhg1 locus: candidate genes that underlie soybean resistance to the cyst nematode. Mol Genet Genomics 2011. [DOI: 10.1007/s00438-011-0606-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Iqbal MJ, Ahsan R, Afzal AJ, Jamai A, Meksem K, El-Shemy HA, Lightfoot DA. Multigeneic QTL: the laccase encoded within the soybean Rfs2/rhg1 locus inferred to underlie part of the dual resistance to cyst nematode and sudden death syndrome. Curr Issues Mol Biol 2009; 11 Suppl 1:i11-19. [PMID: 19193960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2008] [Revised: 10/05/2008] [Accepted: 10/12/2008] [Indexed: 05/27/2023] Open
Abstract
Multigeneic QTL present significant problems to analysis. Resistance to soybean (Glycine max (L) Merr.) sudden death syndrome (SDS) caused by Fusarium virguliforme was partly underlain by QRfs2 that was clustered with, or pleiotropic to, the multigeneic rhg1 locus providing resistance to soybean cyst nematode (SCN; Heterodera glycines). A group of five genes were found between the two markers that delimited the Rfs2/rhg1 locus. One of the five genes was predicted to encode an unusual diphenol oxidase (laccase; EC 1.10.3.2). The aim of this study was to characterize this member of the soybean laccase gene-family and explore its involvement in SDS resistance. A genomic clone and a full length cDNA was isolated from resistant cultivar 'Forrest' that were different among susceptible cultivars 'Asgrow 3244' and 'Williams 82' at four residues R/H168, I/M271, R/H330, E/K470. Additional differences were found in six of the seven introns and the promoter region. Transcript abundance (TA) among genotypes that varied for resistance to SDS or SCN did not differ significantly. Therefore the protein activity was inferred to underlie resistance. Protein expressed in yeast pYES2/NTB had weak enzyme activity with common substrates but good activity with root phenolics. The Forrest isoform may underlie both QRfs2 and rhg1.
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Affiliation(s)
- M J Iqbal
- Institute for Sustainable and Renewable Resources (ISRR), Institute for Advanced Learning and Research (IALR), Danville, VA 24540, USA
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Tomita R, Murai J, Miura Y, Ishihara H, Liu S, Kubotera Y, Honda A, Hatta R, Kuroda T, Hamada H, Sakamoto M, Munemura I, Nunomura O, Ishikawa K, Genda Y, Kawasaki S, Suzuki K, Meksem K, Kobayashi K. Fine mapping and DNA fiber FISH analysis locates the tobamovirus resistance gene L3 of Capsicum chinense in a 400-kb region of R-like genes cluster embedded in highly repetitive sequences. Theor Appl Genet 2008; 117:1107-1118. [PMID: 18663424 PMCID: PMC2755798 DOI: 10.1007/s00122-008-0848-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2008] [Accepted: 07/11/2008] [Indexed: 05/26/2023]
Abstract
The tobamovirus resistance gene L(3) of Capsicum chinense was mapped using an intra-specific F2 population (2,016 individuals) of Capsicum annuum cultivars, into one of which had been introduced the C. chinense L(3) gene, and an inter-specific F2 population (3,391 individuals) between C. chinense and Capsicum frutescence. Analysis of a BAC library with an AFLP marker closely linked to L(3)-resistance revealed the presence of homologs of the tomato disease resistance gene I2. Partial or full-length coding sequences were cloned by degenerate PCR from 35 different pepper I2 homologs and 17 genetic markers were generated in the inter-specific combination. The L(3) gene was mapped between I2 homolog marker IH1-04 and BAC-end marker 189D23M, and located within a region encompassing two different BAC contigs consisting of four and one clones, respectively. DNA fiber FISH analysis revealed that these two contigs are separated from each other by about 30 kb. DNA fiber FISH results and Southern blotting of the BAC clones suggested that the L(3) locus-containing region is rich in highly repetitive sequences. Southern blot analysis indicated that the two BAC contigs contain more than ten copies of the I2 homologs. In contrast to the inter-specific F2 population, no recombinant progeny were identified to have a crossover point within two BAC contigs consisting of seven and two clones in the intra-specific F2 population. Moreover, distribution of the crossover points differed between the two populations, suggesting linkage disequilibrium in the region containing the L locus.
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Affiliation(s)
- R. Tomita
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
| | - J. Murai
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
- Research Institute, Osaka Medical Center for Cancer and Cardiovascular Diseases, Osaka, Osaka 537-8511 Japan
| | - Y. Miura
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
- Nippon Flour Mills Co., Ltd, Central Laboratory, Atsugi, Kanagawa 243-0041 Japan
| | - H. Ishihara
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University at Carbondale, Carbondale, IL 62901-4415 USA
- Max Planck Institute for Molecular Plant Physiology, Am Muehlenberg 1, 14476 Potsdam, Germany
| | - S. Liu
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University at Carbondale, Carbondale, IL 62901-4415 USA
| | - Y. Kubotera
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
| | - A. Honda
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
| | - R. Hatta
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
| | - T. Kuroda
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
- Crop Center, Niigata Agricultural Research Institute, Nagaoka, Niigata 940-0826 Japan
| | - H. Hamada
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
- National Agricultural Research Center, Tsukuba, Ibaraki 305-8666 Japan
| | - M. Sakamoto
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
| | - I. Munemura
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
| | - O. Nunomura
- Japan Horticultural Production and Research Institute, Matsudo, Chiba 270-2221 Japan
| | - K. Ishikawa
- Japan Horticultural Production and Research Institute, Matsudo, Chiba 270-2221 Japan
| | - Y. Genda
- Japan Horticultural Production and Research Institute, Matsudo, Chiba 270-2221 Japan
| | - S. Kawasaki
- National Institute of Agrobiological Resources, Tsukuba, Ibaraki 305-8602 Japan
| | - K. Suzuki
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
- School of Environmental Science, University of Shiga Prefecture, Hikone, Shiga 522-8533 Japan
| | - K. Meksem
- Department of Plant, Soil and Agricultural Systems, Southern Illinois University at Carbondale, Carbondale, IL 62901-4415 USA
| | - K. Kobayashi
- Iwate Biotechnology Research Center, 22-174-4 Narita, Kitakami, Iwate 024-0003 Japan
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Yuan J, Zhu M, Lightfoot DA, Iqbal MJ, Yang JY, Meksem K. In silico comparison of transcript abundances during Arabidopsis thaliana and Glycine max resistance to Fusarium virguliforme. BMC Genomics 2008; 9 Suppl 2:S6. [PMID: 18831797 PMCID: PMC2559896 DOI: 10.1186/1471-2164-9-s2-s6] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Sudden death syndrome (SDS) of soybean (Glycine max L. Merr.) is an economically important disease, caused by the semi-biotrophic fungus Fusarium solani f. sp. glycines, recently renamed Fusarium virguliforme (Fv). Due to the complexity and length of the soybean-Fusarium interaction, the molecular mechanisms underlying plant resistance and susceptibility to the pathogen are not fully understood. F. virguliforme has a very wide host range for the ability to cause root rot and a very narrow host range for the ability to cause a leaf scorch. Arabidopsis thaliana is a host for many types of phytopathogens including bacteria, fungi, viruses and nematodes. Deciphering the variations among transcript abundances (TAs) of functional orthologous genes of soybean and A. thaliana involved in the interaction will provide insights into plant resistance to F. viguliforme. RESULTS In this study, we reported the analyses of microarrays measuring TA in whole plants after A. thaliana cv 'Columbia' was challenged with fungal pathogen F. virguliforme. Infection caused significant variations in TAs. The total number of increased transcripts was nearly four times more than that of decreased transcripts in abundance. A putative resistance pathway involved in responding to the pathogen infection in A. thaliana was identified and compared to that reported in soybean. CONCLUSION Microarray experiments allow the interrogation of tens of thousands of transcripts simultaneously and thus, the identification of plant pathways is likely to be involved in plant resistance to Fusarial pathogens. Dissection of the set functional orthologous genes between soybean and A. thaliana enabled a broad view of the functional relationships and molecular interactions among plant genes involved in F. virguliforme resistance.
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Affiliation(s)
- Jiazheng Yuan
- Department of Plant, Soil Sciences and Agriculture System, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
- Department of Plant Biology, Southern Illinois University at Carbondale, IL 62901, USA
| | - Mengxia Zhu
- Department of Computer Science, Southern Illinois University at Carbondale, IL 62901, USA
| | - David A Lightfoot
- Department of Plant, Soil Sciences and Agriculture System, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
- Department of Plant Biology, Southern Illinois University at Carbondale, IL 62901, USA
| | - M Javed Iqbal
- Department of Plant, Soil Sciences and Agriculture System, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
| | - Jack Y Yang
- Harvard Medical School, Harvard University, Cambridge, MA 02140, USA
| | - Khalid Meksem
- Department of Plant, Soil Sciences and Agriculture System, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
- Plants and Microbes Genomics and Genetics lab, Department of Plant, Soil Sciences, and Agriculture System, Southern Illinois University at Carbondale, Carbondale, IL 62901, USA
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48
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Cooper JL, Till BJ, Laport RG, Darlow MC, Kleffner JM, Jamai A, El-Mellouki T, Liu S, Ritchie R, Nielsen N, Bilyeu KD, Meksem K, Comai L, Henikoff S. TILLING to detect induced mutations in soybean. BMC Plant Biol 2008; 8:9. [PMID: 18218134 PMCID: PMC2266751 DOI: 10.1186/1471-2229-8-9] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2007] [Accepted: 01/24/2008] [Indexed: 05/18/2023]
Abstract
BACKGROUND Soybean (Glycine max L. Merr.) is an important nitrogen-fixing crop that provides much of the world's protein and oil. However, the available tools for investigation of soybean gene function are limited. Nevertheless, chemical mutagenesis can be applied to soybean followed by screening for mutations in a target of interest using a strategy known as Targeting Induced Local Lesions IN Genomes (TILLING). We have applied TILLING to four mutagenized soybean populations, three of which were treated with ethyl methanesulfonate (EMS) and one with N-nitroso-N-methylurea (NMU). RESULTS We screened seven targets in each population and discovered a total of 116 induced mutations. The NMU-treated population and one EMS mutagenized population had similar mutation density (approximately 1/140 kb), while another EMS population had a mutation density of approximately 1/250 kb. The remaining population had a mutation density of approximately 1/550 kb. Because of soybean's polyploid history, PCR amplification of multiple targets could impede mutation discovery. Indeed, one set of primers tested in this study amplified more than a single target and produced low quality data. To address this problem, we removed an extraneous target by pretreating genomic DNA with a restriction enzyme. Digestion of the template eliminated amplification of the extraneous target and allowed the identification of four additional mutant alleles compared to untreated template. CONCLUSION The development of four independent populations with considerable mutation density, together with an additional method for screening closely related targets, indicates that soybean is a suitable organism for high-throughput mutation discovery even with its extensively duplicated genome.
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Affiliation(s)
| | - Bradley J Till
- Fred Hutchinson Cancer Research Center, Seattle, WA 98107, USA
- Department of Biology, University of Washington, Box 355325, Seattle, WA 98195, USA
| | - Robert G Laport
- Fred Hutchinson Cancer Research Center, Seattle, WA 98107, USA
| | | | - Justin M Kleffner
- National Center for Soybean Biotechnology, Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Aziz Jamai
- Department of Plant Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
| | - Tarik El-Mellouki
- Department of Plant Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
| | - Shiming Liu
- Department of Plant Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
| | - Rae Ritchie
- USDA-ARS Crop Production and Pest Control Research Unit, Purdue University, West Lafayette, IN 47907, USA
| | - Niels Nielsen
- USDA-ARS Crop Production and Pest Control Research Unit, Purdue University, West Lafayette, IN 47907, USA
| | | | - Khalid Meksem
- Department of Plant Soil and Agricultural Systems, Southern Illinois University, Carbondale, IL 62901, USA
| | - Luca Comai
- Department of Biology, University of Washington, Box 355325, Seattle, WA 98195, USA
- Current address: Department of Plant Biology and Genome Center, UC Davis, Davis, CA 95616, USA
| | - Steven Henikoff
- Fred Hutchinson Cancer Research Center, Seattle, WA 98107, USA
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49
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Coyne CJ, McClendon MT, Walling JG, Timmerman-Vaughan GM, Murray S, Meksem K, Lightfoot DA, Shultz JL, Keller KE, Martin RR, Inglis DA, Rajesh PN, McPhee KE, Weeden NF, Grusak MA, Li CM, Storlie EW. Construction and characterization of two bacterial artificial chromosome libraries of pea (Pisum sativum L.) for the isolation of economically important genes. Genome 2007; 50:871-5. [PMID: 17893728 DOI: 10.1139/g07-063] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Pea (Pisum sativum L.) has a genome of about 4 Gb that appears to share conserved synteny with model legumes having genomes of 0.2-0.4 Gb despite extensive intergenic expansion. Pea plant inventory (PI) accession 269818 has been used to introgress genetic diversity into the cultivated germplasm pool. The aim here was to develop pea bacterial artificial chromosome (BAC) libraries that would enable the isolation of genes involved in plant disease resistance or control of economically important traits. The BAC libraries encompassed about 3.2 haploid genome equivalents consisting of partially HindIII-digested DNA fragments with a mean size of 105 kb that were inserted in 1 of 2 vectors. The low-copy oriT-based T-DNA vector (pCLD04541) library contained 55 680 clones. The single-copy oriS-based vector (pIndigoBAC-5) library contained 65 280 clones. Colony hybridization of a universal chloroplast probe indicated that about 1% of clones in the libraries were of chloroplast origin. The presence of about 0.1% empty vectors was inferred by white/blue colony plate counts. The usefulness of the libraries was tested by 2 replicated methods. First, high-density filters were probed with low copy number sequences. Second, BAC plate-pool DNA was used successfully to PCR amplify 7 of 9 published pea resistance gene analogs (RGAs) and several other low copy number pea sequences. Individual BAC clones encoding specific sequences were identified. Therefore, the HindIII BAC libraries of pea, based on germplasm accession PI 269818, will be useful for the isolation of genes underlying disease resistance and other economically important traits.
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Affiliation(s)
- C J Coyne
- USDA-ARS Plant Germplasm Introduction and Testing Unit, Washington State University, Pullman, WA 99164-6402, USA.
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50
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Ballvora A, Jöcker A, Viehöver P, Ishihara H, Paal J, Meksem K, Bruggmann R, Schoof H, Weisshaar B, Gebhardt C. Comparative sequence analysis of Solanum and Arabidopsis in a hot spot for pathogen resistance on potato chromosome V reveals a patchwork of conserved and rapidly evolving genome segments. BMC Genomics 2007; 8:112. [PMID: 17474978 PMCID: PMC3225836 DOI: 10.1186/1471-2164-8-112] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2006] [Accepted: 05/02/2007] [Indexed: 11/10/2022] Open
Abstract
Background Quantitative phenotypic variation of agronomic characters in crop plants is controlled by environmental and genetic factors (quantitative trait loci = QTL). To understand the molecular basis of such QTL, the identification of the underlying genes is of primary interest and DNA sequence analysis of the genomic regions harboring QTL is a prerequisite for that. QTL mapping in potato (Solanum tuberosum) has identified a region on chromosome V tagged by DNA markers GP21 and GP179, which contains a number of important QTL, among others QTL for resistance to late blight caused by the oomycete Phytophthora infestans and to root cyst nematodes. Results To obtain genomic sequence for the targeted region on chromosome V, two local BAC (bacterial artificial chromosome) contigs were constructed and sequenced, which corresponded to parts of the homologous chromosomes of the diploid, heterozygous genotype P6/210. Two contiguous sequences of 417,445 and 202,781 base pairs were assembled and annotated. Gene-by-gene co-linearity was disrupted by non-allelic insertions of retrotransposon elements, stretches of diverged intergenic sequences, differences in gene content and gene order. The latter was caused by inversion of a 70 kbp genomic fragment. These features were also found in comparison to orthologous sequence contigs from three homeologous chromosomes of Solanum demissum, a wild tuber bearing species. Functional annotation of the sequence identified 48 putative open reading frames (ORF) in one contig and 22 in the other, with an average of one ORF every 9 kbp. Ten ORFs were classified as resistance-gene-like, 11 as F-box-containing genes, 13 as transposable elements and three as transcription factors. Comparing potato to Arabidopsis thaliana annotated proteins revealed five micro-syntenic blocks of three to seven ORFs with A. thaliana chromosomes 1, 3 and 5. Conclusion Comparative sequence analysis revealed highly conserved collinear regions that flank regions showing high variability and tandem duplicated genes. Sequence annotation revealed that the majority of the ORFs were members of multiple gene families. Comparing potato to Arabidopsis thaliana annotated proteins suggested fragmented structural conservation between these distantly related plant species.
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Affiliation(s)
- Agim Ballvora
- Max-Planck Institut für Züchtungsforschung, Carl von Linné Weg 10, 50829 Köln, Germany
| | - Anika Jöcker
- Max-Planck Institut für Züchtungsforschung, Carl von Linné Weg 10, 50829 Köln, Germany
| | - Prisca Viehöver
- Max-Planck Institut für Züchtungsforschung, Carl von Linné Weg 10, 50829 Köln, Germany
- Institut für Genomforschung, Universität Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Hirofumi Ishihara
- Institut für Genomforschung, Universität Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
- Southern Illinois University at Carbondale, Dept. of Plant, Soil and General Agriculture, Carbondale, IL62901-4415, USA
| | - Jürgen Paal
- Max-Planck Institut für Züchtungsforschung, Carl von Linné Weg 10, 50829 Köln, Germany
| | - Khalid Meksem
- Southern Illinois University at Carbondale, Dept. of Plant, Soil and General Agriculture, Carbondale, IL62901-4415, USA
| | - Rémy Bruggmann
- GSF Forschungszentrum für Umwelt und Gesundheit, Institut für Bioinformatik, Ingolstädter Landstr. 1, 85764 Neuherberg, Germany
| | - Heiko Schoof
- Max-Planck Institut für Züchtungsforschung, Carl von Linné Weg 10, 50829 Köln, Germany
| | - Bernd Weisshaar
- Max-Planck Institut für Züchtungsforschung, Carl von Linné Weg 10, 50829 Köln, Germany
- Institut für Genomforschung, Universität Bielefeld, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Christiane Gebhardt
- Max-Planck Institut für Züchtungsforschung, Carl von Linné Weg 10, 50829 Köln, Germany
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