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Usovsky M, Gamage VA, Meinhardt CG, Dietz N, Triller M, Basnet P, Gillman JD, Bilyeu KD, Song Q, Dhital B, Nguyen A, Mitchum MG, Scaboo AM. Loss-of-function of an α-SNAP gene confers resistance to soybean cyst nematode. Nat Commun 2023; 14:7629. [PMID: 37993454 PMCID: PMC10665432 DOI: 10.1038/s41467-023-43295-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023] Open
Abstract
Plant-parasitic nematodes are one of the most economically impactful pests in agriculture resulting in billions of dollars in realized annual losses worldwide. Soybean cyst nematode (SCN) is the number one biotic constraint on soybean production making it a priority for the discovery, validation and functional characterization of native plant resistance genes and genetic modes of action that can be deployed to improve soybean yield across the globe. Here, we present the discovery and functional characterization of a soybean resistance gene, GmSNAP02. We use unique bi-parental populations to fine-map the precise genomic location, and a combination of whole genome resequencing and gene fragment PCR amplifications to identify and confirm causal haplotypes. Lastly, we validate our candidate gene using CRISPR-Cas9 genome editing and observe a gain of resistance in edited plants. This demonstrates that the GmSNAP02 gene confers a unique mode of resistance to SCN through loss-of-function mutations that implicate GmSNAP02 as a nematode virulence target. We highlight the immediate impact of utilizing GmSNAP02 as a genome-editing-amenable target to diversify nematode resistance in commercially available cultivars.
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Affiliation(s)
- Mariola Usovsky
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, 65211, USA
| | - Vinavi A Gamage
- Department of Plant Pathology and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA
| | - Clinton G Meinhardt
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, 65211, USA
| | - Nicholas Dietz
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, 65211, USA
| | - Marissa Triller
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, 65211, USA
| | - Pawan Basnet
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, 65211, USA
| | - Jason D Gillman
- Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, University of Missouri, Columbia, MO, 65211, USA
| | - Kristin D Bilyeu
- Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, University of Missouri, Columbia, MO, 65211, USA
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, Beltsville, MD, 20705, USA
| | - Bishnu Dhital
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, 65211, USA
| | - Alice Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, 65211, USA
| | - Melissa G Mitchum
- Department of Plant Pathology and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, 30602, USA.
| | - Andrew M Scaboo
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, 65211, USA.
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2
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Mahmood A, Bilyeu KD, Škrabišová M, Biová J, De Meyer EJ, Meinhardt CG, Usovsky M, Song Q, Lorenz AJ, Mitchum MG, Shannon G, Scaboo AM. Cataloging SCN resistance loci in North American public soybean breeding programs. FRONTIERS IN PLANT SCIENCE 2023; 14:1270546. [PMID: 38053759 PMCID: PMC10694258 DOI: 10.3389/fpls.2023.1270546] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/16/2023] [Indexed: 12/07/2023]
Abstract
Soybean cyst nematode (SCN) is a destructive pathogen of soybeans responsible for annual yield loss exceeding $1.5 billion in the United States. Here, we conducted a series of genome-wide association studies (GWASs) to understand the genetic landscape of SCN resistance in the University of Missouri soybean breeding programs (Missouri panel), as well as germplasm and cultivars within the United States Department of Agriculture (USDA) Uniform Soybean Tests-Northern Region (NUST). For the Missouri panel, we evaluated the resistance of breeding lines to SCN populations HG 2.5.7 (Race 1), HG 1.2.5.7 (Race 2), HG 0 (Race 3), HG 2.5.7 (Race 5), and HG 1.3.6.7 (Race 14) and identified seven quantitative trait nucleotides (QTNs) associated with SCN resistance on chromosomes 2, 8, 11, 14, 17, and 18. Additionally, we evaluated breeding lines in the NUST panel for resistance to SCN populations HG 2.5.7 (Race 1) and HG 0 (Race 3), and we found three SCN resistance-associated QTNs on chromosomes 7 and 18. Through these analyses, we were able to decipher the impact of seven major genetic loci, including three novel loci, on resistance to several SCN populations and identified candidate genes within each locus. Further, we identified favorable allelic combinations for resistance to individual SCN HG types and provided a list of available germplasm for integration of these unique alleles into soybean breeding programs. Overall, this study offers valuable insight into the landscape of SCN resistance loci in U.S. public soybean breeding programs and provides a framework to develop new and improved soybean cultivars with diverse plant genetic modes of SCN resistance.
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Affiliation(s)
- Anser Mahmood
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Kristin D. Bilyeu
- Plant Genetics Research Unit, United States Department of Agriculture-Agricultural Research Service, University of Missouri, Columbia, MO, United States
| | - Mária Škrabišová
- Department of Biochemistry, Faculty of Science, Palacky University Olomouc, Olomouc, Czechia
| | - Jana Biová
- Department of Biochemistry, Faculty of Science, Palacky University Olomouc, Olomouc, Czechia
| | - Elizabeth J. De Meyer
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Clinton G. Meinhardt
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Mariola Usovsky
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD, United States
| | - Aaron J. Lorenz
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - Melissa G. Mitchum
- Department of Plant Pathology and Institute of Plant Breeding, Genetics, and Genomics, University of Georgia, Athens, GA, United States
| | - Grover Shannon
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
| | - Andrew M. Scaboo
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, United States
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3
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Torabi S, Seifi S, Geddes-McAlister J, Tenuta A, Wally O, Torkamaneh D, Eskandari M. Soybean-SCN Battle: Novel Insight into Soybean's Defense Strategies against Heterodera glycines. Int J Mol Sci 2023; 24:16232. [PMID: 38003422 PMCID: PMC10671692 DOI: 10.3390/ijms242216232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/28/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
Soybean cyst nematode (SCN, Heterodera glycines, Ichinohe) poses a significant threat to global soybean production, necessitating a comprehensive understanding of soybean plants' response to SCN to ensure effective management practices. In this study, we conducted dual RNA-seq analysis on SCN-resistant Plant Introduction (PI) 437654, 548402, and 88788 as well as a susceptible line (Lee 74) under exposure to SCN HG type 1.2.5.7. We aimed to elucidate resistant mechanisms in soybean and identify SCN virulence genes contributing to resistance breakdown. Transcriptomic and pathway analyses identified the phenylpropanoid, MAPK signaling, plant hormone signal transduction, and secondary metabolite pathways as key players in resistance mechanisms. Notably, PI 437654 exhibited complete resistance and displayed distinctive gene expression related to cell wall strengthening, oxidative enzymes, ROS scavengers, and Ca2+ sensors governing salicylic acid biosynthesis. Additionally, host studies with varying immunity levels and a susceptible line shed light on SCN pathogenesis and its modulation of virulence genes to evade host immunity. These novel findings provide insights into the molecular mechanisms underlying soybean-SCN interactions and offer potential targets for nematode disease management.
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Affiliation(s)
- Sepideh Torabi
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | - Soren Seifi
- Aurora Cannabis Inc., Comox, BC V9M 4A1, Canada;
| | | | - Albert Tenuta
- Ontario Ministry of Agriculture, Food and Rural Affairs, Ridgetown, ON N0P 2C0, Canada;
| | - Owen Wally
- Harrow Research and Development Centre, Agriculture and Agri-Food Canada, London, ON N0R 1G0, Canada;
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada;
| | - Milad Eskandari
- Department of Plant Agriculture, University of Guelph, Guelph, ON N1G 2W1, Canada;
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Jiang H, Lv S, Zhou C, Qu S, Liu F, Sun H, Zhao X, Han Y. Identification of QTL, QTL-by-environment interactions, and their candidate genes for resistance HG Type 0 and HG Type 1.2.3.5.7 in soybean using 3VmrMLM. FRONTIERS IN PLANT SCIENCE 2023; 14:1177345. [PMID: 37152131 PMCID: PMC10162016 DOI: 10.3389/fpls.2023.1177345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 03/31/2023] [Indexed: 05/09/2023]
Abstract
Introduction Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is an important disease affecting soybean yield in the world. Potential SCN-related QTLs and QTL-by-environment interactions (QEIs) have been used in SCN-resistant breeding. Methods In this study, a compressed variance component mixed model, 3VmrMLM, in genome-wide association studies was used to detect QTLs and QEIs for resistance to SCN HG Type 0 and HG Type 1.2.3.5.7 in 156 different soybean cultivars materials. Results and discussion The results showed that 53 QTLs were detected in single environment analysis; 36 QTLs and 9 QEIs were detected in multi-environment analysis. Based on the statistical screening of the obtained QTLs, we obtained 10 novel QTLs and one QEI which were different from the previous studies. Based on previous studies, we identified 101 known genes around the significant/suggested QTLs and QEIs. Furthermore, used the transcriptome data of SCN-resistant (Dongnong L-10) and SCN-susceptible (Suinong 14) cultivars, 10 candidate genes related to SCN resistance were identified and verified by Quantitative real time polymerase chain reaction (qRT-PCR) analysis. Haplotype difference analysis showed that Glyma.03G005600 was associated with SCN HG Type 0 and HG Type 1.2.3.5.7 resistance and had a haplotype beneficial to multi-SCN-race resistance. These results provide a new idea for accelerating SCN disease resistance breeding.
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Affiliation(s)
- Haipeng Jiang
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Suchen Lv
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Changjun Zhou
- Daqing Branch, Heilongjiang Academy of Agricultural Science, Daqing, China
| | - Shuo Qu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Fang Liu
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Haowen Sun
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
| | - Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
- *Correspondence: Yingpeng Han, ; Xue Zhao,
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, China
- *Correspondence: Yingpeng Han, ; Xue Zhao,
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5
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Abd-Elgawad MMM. Exploiting Plant-Phytonematode Interactions to Upgrade Safe and Effective Nematode Control. LIFE (BASEL, SWITZERLAND) 2022; 12:life12111916. [PMID: 36431051 PMCID: PMC9693997 DOI: 10.3390/life12111916] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 11/19/2022]
Abstract
Plant-parasitic nematodes (PPNs) bring about substantial losses of economic crops globally. With the environmental and health issues facing the use of chemical nematicides, research efforts should focus on providing economically effective and safe control methods. The sound exploitation of plant-PPN interactions is fundamental to such efforts. Initially, proper sampling and extraction techniques should be followed to avoid misleading nematode data. Recent evolutions in plant-PPN interactions can make use of diverse non-molecular and molecular approaches to boost plant defenses. Therefore, PPN control and increasing crop yields through single, sequential, dual-purpose, and simultaneous applications of agricultural inputs, including biocontrol agents, should be seriously attempted, especially within IPM schemes. The use of biologicals would ideally be facilitated by production practices to solve related issues. The full investment of such interactions should employ new views of interdisciplinary specialties in the relevant modern disciplines to optimize the PPN management. Having an accurate grasp of the related molecular events will help in developing tools for PPN control. Nonetheless, the currently investigated molecular plant-PPN interactions favoring plant responses, e.g., resistance genes, RNA interference, marker-assisted selection, proteinase inhibitors, chemo-disruptive peptides, and plant-incorporated protectants, are key factors to expanding reliable management. They may be applied on broader scales for a substantial improvement in crop yields.
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Affiliation(s)
- Mahfouz M M Abd-Elgawad
- Plant Pathology Department, Agricultural and Biological Research Institute, National Research Centre, El-Behooth St., Dokki, Giza 12622, Egypt
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Chu S, Ma H, Li K, Li J, Liu H, Quan L, Zhu X, Chen M, Lu W, Chen X, Qu X, Xu J, Lian Y, Lu W, Xiong E, Jiao Y. Comparisons of constitutive resistances to soybean cyst nematode between PI 88788- and Peking-type sources of resistance in soybean by transcriptomic and metabolomic profilings. Front Genet 2022; 13:1055867. [PMID: 36437927 PMCID: PMC9686325 DOI: 10.3389/fgene.2022.1055867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/24/2022] [Indexed: 11/11/2022] Open
Abstract
Soybean cyst nematode (SCN) is a serious damaging disease in soybean worldwide. Peking- and PI 88788-type sources of resistance are two most important germplasm used in breeding resistant soybean cultivars against this disease. However, until now, no comparisons of constitutive resistances to soybean cyst nematode between these two types of sources had been conducted, probably due to the influences of different backgrounds. In this study, we used pooled-sample analysis strategy to minimize the influence of different backgrounds and directly compared the molecular mechanisms underlying constitutive resistance to soybean cyst nematode between these two types of sources via transcriptomic and metabolomic profilings. Six resistant soybean accessions that have identical haplotypes as Peking at Rgh1 and Rhg4 loci were pooled to represent Peking-type sources. The PI88788-type and control pools were also constructed in a same way. Through transcriptomic and metabolomics anaylses, differentially expressed genes and metabolites were identified. The molecular pathways involved in the metabolism of toxic metabolites were predicted to play important roles in conferring soybean cyst nematode resistance to soybean. Functions of two resistant candidate genes were confirmed by hairy roots transformation methods in soybean. Our studies can be helpful for soybean scientists to further learn about the molecular mechanism of resistance to soybean cyst nematode in soybean.
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Affiliation(s)
- Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops /College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Hui Ma
- Collaborative Innovation Center of Henan Grain Crops /College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Ke Li
- Collaborative Innovation Center of Henan Grain Crops /College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Junfeng Li
- Collaborative Innovation Center of Henan Grain Crops /College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Hongli Liu
- Collaborative Innovation Center of Henan Grain Crops /College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Leipo Quan
- Collaborative Innovation Center of Henan Grain Crops /College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuling Zhu
- Collaborative Innovation Center of Henan Grain Crops /College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Meiling Chen
- Collaborative Innovation Center of Henan Grain Crops /College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Wenyan Lu
- Collaborative Innovation Center of Henan Grain Crops /College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xiaoming Chen
- Collaborative Innovation Center of Henan Grain Crops /College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Xuelian Qu
- Collaborative Innovation Center of Henan Grain Crops /College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Jiaqi Xu
- Collaborative Innovation Center of Henan Grain Crops /College of Agronomy, Henan Agricultural University, Zhengzhou, China
| | - Yun Lian
- Zhengzhou Subcenter of National Soybean Improvement Center, Key Laboratory of Oil Crops in Huang-Huai Valleys of Ministry of Agriculture, Institute of Industrial Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Weiguo Lu
- Zhengzhou Subcenter of National Soybean Improvement Center, Key Laboratory of Oil Crops in Huang-Huai Valleys of Ministry of Agriculture, Institute of Industrial Crops, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Erhui Xiong
- Collaborative Innovation Center of Henan Grain Crops /College of Agronomy, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Yongqing Jiao, ; Erhui Xiong,
| | - Yongqing Jiao
- Collaborative Innovation Center of Henan Grain Crops /College of Agronomy, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Yongqing Jiao, ; Erhui Xiong,
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7
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Lin F, Chhapekar SS, Vieira CC, Da Silva MP, Rojas A, Lee D, Liu N, Pardo EM, Lee YC, Dong Z, Pinheiro JB, Ploper LD, Rupe J, Chen P, Wang D, Nguyen HT. Breeding for disease resistance in soybean: a global perspective. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3773-3872. [PMID: 35790543 PMCID: PMC9729162 DOI: 10.1007/s00122-022-04101-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 04/11/2022] [Indexed: 05/29/2023]
Abstract
KEY MESSAGE This review provides a comprehensive atlas of QTLs, genes, and alleles conferring resistance to 28 important diseases in all major soybean production regions in the world. Breeding disease-resistant soybean [Glycine max (L.) Merr.] varieties is a common goal for soybean breeding programs to ensure the sustainability and growth of soybean production worldwide. However, due to global climate change, soybean breeders are facing strong challenges to defeat diseases. Marker-assisted selection and genomic selection have been demonstrated to be successful methods in quickly integrating vertical resistance or horizontal resistance into improved soybean varieties, where vertical resistance refers to R genes and major effect QTLs, and horizontal resistance is a combination of major and minor effect genes or QTLs. This review summarized more than 800 resistant loci/alleles and their tightly linked markers for 28 soybean diseases worldwide, caused by nematodes, oomycetes, fungi, bacteria, and viruses. The major breakthroughs in the discovery of disease resistance gene atlas of soybean were also emphasized which include: (1) identification and characterization of vertical resistance genes reside rhg1 and Rhg4 for soybean cyst nematode, and exploration of the underlying regulation mechanisms through copy number variation and (2) map-based cloning and characterization of Rps11 conferring resistance to 80% isolates of Phytophthora sojae across the USA. In this review, we also highlight the validated QTLs in overlapping genomic regions from at least two studies and applied a consistent naming nomenclature for these QTLs. Our review provides a comprehensive summary of important resistant genes/QTLs and can be used as a toolbox for soybean improvement. Finally, the summarized genetic knowledge sheds light on future directions of accelerated soybean breeding and translational genomics studies.
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Affiliation(s)
- Feng Lin
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
| | - Sushil Satish Chhapekar
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
| | - Caio Canella Vieira
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Marcos Paulo Da Silva
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Alejandro Rojas
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Dongho Lee
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Nianxi Liu
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun,, 130033 Jilin China
| | - Esteban Mariano Pardo
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA) [Estación Experimental Agroindustrial Obispo Colombres (EEAOC) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)], Av. William Cross 3150, C.P. T4101XAC, Las Talitas, Tucumán, Argentina
| | - Yi-Chen Lee
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Zhimin Dong
- Soybean Research Institute, Jilin Academy of Agricultural Sciences, Changchun,, 130033 Jilin China
| | - Jose Baldin Pinheiro
- Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” (ESALQ/USP), PO Box 9, Piracicaba, SP 13418-900 Brazil
| | - Leonardo Daniel Ploper
- Instituto de Tecnología Agroindustrial del Noroeste Argentino (ITANOA) [Estación Experimental Agroindustrial Obispo Colombres (EEAOC) – Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)], Av. William Cross 3150, C.P. T4101XAC, Las Talitas, Tucumán, Argentina
| | - John Rupe
- Department of Entomology and Plant Pathology, University of Arkansas, Fayetteville, AR 72701 USA
| | - Pengyin Chen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
- Fisher Delta Research Center, University of Missouri, Portageville, MO 63873 USA
| | - Dechun Wang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824 USA
| | - Henry T. Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri-Columbia, Columbia, MO 65211 USA
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8
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Lu X, Torabi S, de Lima Passianotto AL, Welacky T, Eskandari M. Quantitative trait loci and gene-specific markers associated with resistance to soybean cyst nematode HG type 2.5.7. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:62. [PMID: 37313012 PMCID: PMC10248661 DOI: 10.1007/s11032-022-01330-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 09/13/2022] [Indexed: 06/15/2023]
Abstract
Soybean cyst nematode (SCN) is one of the most damaging soybean (Glycine max) pests worldwide. More than 95% of SCN-resistant commercial cultivars in North America are derived from a single source of resistance named PI 88788, and the widespread use of this source in the past three decades has led to the selection of virulent biotypes of SCN, such as HG (Heterodera glycines) type 2.5.7 that can overcome the PI 88788-type resistance. The objectives of this study were to identify quantitative trait loci (QTL) and candidate genes underlying the resistance to HG type 2.5.7 isolate and to measure the impact of the resistance factors on seed yield. To achieve the goals, a recombinant inbreed line (RIL) population was established from a cross between an SCN-susceptible high-yielding elite soybean cultivar, OAC Calypso, and the cultivar LD07-3419, resistant to SCN HG type 2.5.7. The RILs resistant to HG type 2.5.7 were identified using greenhouse bioassay tested for differentiation of resistant sources using Kompetitive Allele-Specific PCR (KASP) assay at rhg1 and Rhg4 loci and also for rhg1 copy number variation using TaqMan assay. The RILs were also genotyped using genotype-by-sequencing and three SCN-related QTL were identified on chromosomes 9, 12, and 18 using composite interval mapping. In addition, 31 genes involved in protein kinase activity were identified within QTL regions as potential causal candidate genes underlying the resistance. No significant correlation was found between seed yield and the resistance to SCN in the RIL population evaluated under non-SCN-infested environments. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01330-8.
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Affiliation(s)
- Xin Lu
- Department of Plant Agriculture, University of Guelph, Guelph, Canada
| | - Sepideh Torabi
- Department of Plant Agriculture, University of Guelph, Guelph, Canada
| | | | - Tom Welacky
- Agriculturan and Agri-Food Canada, Harrow Research Station, Essex, Canada
| | - Milad Eskandari
- Department of Plant Agriculture, University of Guelph, Guelph, Canada
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9
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Abstract
Resistance to the soybean cyst nematode (SCN) is a topic incorporating multiple mechanisms and multiple types of science. It is also a topic of substantial agricultural importance, as SCN is estimated to cause more yield damage than any other pathogen of soybean, one of the world's main food crops. Both soybean and SCN have experienced jumps in experimental tractability in the past decade, and significant advances have been made. The rhg1-b locus, deployed on millions of farm acres, has been durable and will remain important, but local SCN populations are gradually evolving to overcome rhg1-b. Multiple other SCN resistance quantitative trait loci (QTL) of proven value are now in play with soybean breeders. QTL causal gene discovery and mechanistic insights into SCN resistance are contributing to both basic and applied disciplines. Additional understanding of SCN and other cyst nematodes will also grow in importance and lead to novel disease control strategies.
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Affiliation(s)
- Andrew F Bent
- Department of Plant Pathology, University of Wisconsin-Madison, Madison, Wisconsin, USA;
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10
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Understanding Molecular Plant–Nematode Interactions to Develop Alternative Approaches for Nematode Control. PLANTS 2022; 11:plants11162141. [PMID: 36015444 PMCID: PMC9415668 DOI: 10.3390/plants11162141] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/26/2022]
Abstract
Developing control measures of plant-parasitic nematodes (PPNs) rank high as they cause big crop losses globally. The growing awareness of numerous unsafe chemical nematicides and the defects found in their alternatives are calling for rational molecular control of the nematodes. This control focuses on using genetically based plant resistance and exploiting molecular mechanisms underlying plant–nematode interactions. Rapid and significant advances in molecular techniques such as high-quality genome sequencing, interfering RNA (RNAi) and gene editing can offer a better grasp of these interactions. Efficient tools and resources emanating from such interactions are highlighted herein while issues in using them are summarized. Their revision clearly indicates the dire need to further upgrade knowledge about the mechanisms involved in host-specific susceptibility/resistance mediated by PPN effectors, resistance genes, or quantitative trait loci to boost their effective and sustainable use in economically important plant species. Therefore, it is suggested herein to employ the impacts of these techniques on a case-by-case basis. This will allow us to track and optimize PPN control according to the actual variables. It would enable us to precisely fix the factors governing the gene functions and expressions and combine them with other PPN control tactics into integrated management.
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11
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Lian Y, Koch G, Bo D, Wang J, Nguyen HT, Li C, Lu W. The Spatial Distribution and Genetic Diversity of the Soybean Cyst Nematode, Heterodera glycines, in China: It Is Time to Take Measures to Control Soybean Cyst Nematode. FRONTIERS IN PLANT SCIENCE 2022; 13:927773. [PMID: 35783986 PMCID: PMC9242501 DOI: 10.3389/fpls.2022.927773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
The continuous evolution and spread of virulent forms of the soybean cyst nematode (SCN) driven by the environment and anthropogenic intervention is a serious threat to the soybean production worldwide, including China. Especially in China, the implemented measures to control SCN are insufficient for sustainable agricultural development yet. We summarized our knowledge about the spread and spatial distribution of SCN in China and the virulence diversity in the main soybean growing areas. To reveal the genetic relatedness and diversity of SCN populations, we re-sequenced 53 SCN genomes from the Huang-Huai Valleys, one of the two main soybean growing areas in China. We identified spreading patterns linked to the local agroecosystems and topographies. Moreover, we disclosed the first evidence for the selection of complex virulence in the field even under low selection pressure in an example from North Shanxi. SCN is present in all soybean growing areas in China but SCN susceptible cultivars are still largely grown indicating that SCN-related damage and financial loss have not received the attention they deserve yet. To prevent increasing yield losses and to improve the acceptance of resistant cultivars by the growers, we emphasized that it is time to accelerate SCN resistance breeding, planting resistant cultivars to a larger extent, and to support farmers to implement a wider crop rotation for sustainable development of the soybean production in China.
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Affiliation(s)
- Yun Lian
- Henan Academy of Crops Molecular Breeding, National Centre for Plant Breeding, Zhengzhou Subcenter of National Soybean Improvement Center, Key Laboratory of Oil Crops in Huang Huaihai Plains, Ministry of Agriculture and Rural Affairs, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, China
| | - Georg Koch
- National Centre for Plant Breeding, Xinxiang, China
| | - Dexin Bo
- Hubei Key Laboratory of Agricultural Bioinformatics, Huazhong Agricultural University, Wuhan, China
| | - Jinshe Wang
- Henan Academy of Crops Molecular Breeding, National Centre for Plant Breeding, Zhengzhou Subcenter of National Soybean Improvement Center, Key Laboratory of Oil Crops in Huang Huaihai Plains, Ministry of Agriculture and Rural Affairs, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, China
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, United States
| | - Chun Li
- Henan Academy of Crops Molecular Breeding, National Centre for Plant Breeding, Zhengzhou Subcenter of National Soybean Improvement Center, Key Laboratory of Oil Crops in Huang Huaihai Plains, Ministry of Agriculture and Rural Affairs, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, China
| | - Weiguo Lu
- Henan Academy of Crops Molecular Breeding, National Centre for Plant Breeding, Zhengzhou Subcenter of National Soybean Improvement Center, Key Laboratory of Oil Crops in Huang Huaihai Plains, Ministry of Agriculture and Rural Affairs, Henan Provincial Key Laboratory for Oil Crops Improvement, Zhengzhou, China
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12
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Basnet P, Meinhardt CG, Usovsky M, Gillman JD, Joshi T, Song Q, Diers B, Mitchum MG, Scaboo AM. Epistatic interaction between Rhg1-a and Rhg2 in PI 90763 confers resistance to virulent soybean cyst nematode populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:2025-2039. [PMID: 35381870 PMCID: PMC9205835 DOI: 10.1007/s00122-022-04091-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/25/2022] [Indexed: 05/19/2023]
Abstract
KEY MESSAGE An epistatic interaction between SCN resistance loci rhg1-a and rhg2 in PI 90763 imparts resistance against virulent SCN populations which can be employed to diversify SCN resistance in soybean cultivars. With more than 95% of the $46.1B soybean market dominated by a single type of genetic resistance, breeding for soybean cyst nematode (SCN)-resistant soybean that can effectively combat the widespread increase in virulent SCN populations presents a significant challenge. Rhg genes (for Resistance to Heterodera glycines) play a key role in resistance to SCN; however, their deployment beyond the use of the rhg1-b allele has been limited. In this study, quantitative trait loci (QTL) were mapped using PI 90763 through two biparental F3:4 recombinant inbred line (RIL) populations segregating for rhg1-a and rhg1-b alleles against a SCN HG type 1.2.5.7 (Race 2) population. QTL located on chromosome 18 (rhg1-a) and chromosome 11 (rhg2) were determined to confer SCN resistance in PI 90763. The rhg2 gene was fine-mapped to a 169-Kbp region pinpointing GmSNAP11 as the strongest candidate gene. We demonstrated a unique epistatic interaction between rhg1-a and rhg2 loci that not only confers resistance to multiple virulent SCN populations. Further, we showed that pyramiding rhg2 with the conventional mode of resistance, rhg1-b, is ineffective against these virulent SCN populations. This highlights the importance of pyramiding rhg1-a and rhg2 to maximize the impact of gene pyramiding strategies toward management of SCN populations virulent on rhg1-b sources of resistance. Our results lay the foundation for the next generation of soybean resistance breeding to combat the number one pathogen of soybean.
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Affiliation(s)
- Pawan Basnet
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, 65211, USA
| | - Clinton G Meinhardt
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, 65211, USA
| | - Mariola Usovsky
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, 65211, USA
| | | | - Trupti Joshi
- Department of Health Management and Informatics, MUIDSI, and Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, 65211, USA
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, Beltsville Agricultural Research Center, USDA-ARS, Beltsville, MD, USA
| | - Brian Diers
- Department of Crop Sciences, University of Illinois, Urbana-Champaign, IL, USA
| | - Melissa G Mitchum
- Department of Plant Pathology and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, USA
| | - Andrew M Scaboo
- Division of Plant Science and Technology, University of Missouri, Columbia, MO, 65211, USA.
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13
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Wei H, Lian Y, Li J, Li H, Song Q, Wu Y, Lei C, Wang S, Zhang H, Wang J, Lu W. Identification of Candidate Genes Controlling Soybean Cyst Nematode Resistance in "Handou 10" Based on Genome and Transcriptome Analyzes. FRONTIERS IN PLANT SCIENCE 2022; 13:860034. [PMID: 35371127 PMCID: PMC8965568 DOI: 10.3389/fpls.2022.860034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/21/2022] [Indexed: 06/14/2023]
Abstract
Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) is a highly destructive pathogen for soybean production worldwide. The use of resistant varieties is the most effective way of preventing yield loss. Handou 10 is a commercial soybean variety with desirable agronomic traits and SCN resistance, however genes underlying the SCN resistance in the variety are unknown. An F2:8 recombinant inbred line (RIL) population derived from a cross between Zheng 9525 (susceptible) and Handou 10 was developed and its resistance to SCN HG type 2.5.7 (race 1) and 1.2.5.7 (race 2) was identified. We identified seven quantitative trait loci (QTLs) with additive effects. Among these, three QTLs on Chromosomes 7, 8, and 18 were resistant to both races. These QTLs could explain 1.91-7.73% of the phenotypic variation of SCN's female index. The QTLs on chromosomes 8 and 18 have already been reported and were most likely overlapped with rhg1 and Rhg4 loci, respectively. However, the QTL on chromosome 7 was novel. Candidate genes for the three QTLs were predicted through genes functional analysis and transcriptome analysis of infected roots of Handou 10 vs. Zheng 9525. Transcriptome analysis performed also indicated that the plant-pathogen interaction played an important role in the SCN resistance for Handou 10. The information will facilitate SCN-resistant gene cloning, and the novel resistant gene will be a source for improving soybeans' resistance to SCN.
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Affiliation(s)
- He Wei
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Yun Lian
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Jinying Li
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Haichao Li
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Qijian Song
- Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD, United States
| | - Yongkang Wu
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Chenfang Lei
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Shiwei Wang
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Hui Zhang
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Jinshe Wang
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
| | - Weiguo Lu
- Henan Academy of Crops Molecular Breeding, Henan Academy of Agricultural Sciences/National Centre for Plant Breeding/Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of Ministry of Agriculture, Zhengzhou, China
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14
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Usovsky M, Robbins RT, Fultz Wilkes J, Crippen D, Shankar V, Vuong TD, Agudelo P, Nguyen HT. Classification Methods and Identification of Reniform Nematode Resistance in Known Soybean Cyst Nematode-Resistant Soybean Genotypes. PLANT DISEASE 2022; 106:382-389. [PMID: 34494868 DOI: 10.1094/pdis-01-21-0051-re] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Plant parasitic nematodes are a major yield-limiting factor of soybean in the United States and Canada. It has been indicated that soybean cyst nematode (SCN; Heterodera glycines Ichinohe) and reniform nematode (RN; Rotylenchulus reniformis Linford and Oliveira) resistance could be genetically related. For many years, fragmentary data have shown this relationship. This report evaluates RN reproduction on 418 plant introductions (PIs) selected from the U.S. Department of Agriculture Soybean Germplasm Collection with reported SCN resistance. The germplasm was divided into two tests of 214 PIs reported as resistant and 204 PIs reported as moderately resistant to SCN. The defining and reporting of RN resistance changed several times in the last 30 years, causing inconsistencies in RN resistance classification among multiple experiments. Comparison of four RN resistance classification methods was performed: (i) ≤10% as compared with the susceptible check, (ii) using normalized reproduction index (RI) values, and using (iii) transformed data log10(x), and (iv) transformed data log10(x + 1) in an optimal univariate k-means clustering analysis. The method of transformed data log10(x) was selected as the most accurate for classification of RN resistance. Among 418 PIs with reported SCN resistance, the log10(x) method grouped 59 PIs (15%) as resistant and 130 PIs (31%) as moderately resistant to RN. Genotyping of a subset of the most resistant PIs to both nematode species revealed their strong correlation with rhg1-a allele. This research identified genotypes with resistance to two nematode species and potential new sources of RN resistance that could be valuable to breeders in developing resistant cultivars.
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Affiliation(s)
- Mariola Usovsky
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211
| | - Robert T Robbins
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701
| | - Juliet Fultz Wilkes
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
| | - Devany Crippen
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR 72701
| | - Vijay Shankar
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634
| | - Tri D Vuong
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211
| | - Paula Agudelo
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634
| | - Henry T Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211
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15
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Salgotra RK, Thompson M, Chauhan BS. Unravelling the genetic potential of untapped crop wild genetic resources for crop improvement. CONSERV GENET RESOUR 2021. [DOI: 10.1007/s12686-021-01242-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Razzaq A, Wani SH, Saleem F, Yu M, Zhou M, Shabala S. Rewilding crops for climate resilience: economic analysis and de novo domestication strategies. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6123-6139. [PMID: 34114599 DOI: 10.1093/jxb/erab276] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/09/2021] [Indexed: 05/08/2023]
Abstract
To match predicted population growth, annual food production should be doubled by 2050. This is not achievable by current agronomical and breeding practices, due to the impact of climate changes and associated abiotic stresses on agricultural production systems. Here, we analyze the impact of global climate trends on crop productivity and show that the overall loss in crop production from climate-driven abiotic stresses may exceed US$170 billion year-1 and represents a major threat to global food security. We also show that abiotic stress tolerance had been present in wild progenitors of modern crops but was lost during their domestication. We argue for a major shift in our paradigm of crop breeding, focusing on climate resilience, and call for a broader use of wild relatives as a major tool in this process. We argue that, while molecular tools are currently in place to harness the potential of climate-resilient genes present in wild relatives, the complex polygenic nature of tolerance traits remains a major bottleneck in this process. Future research efforts should be focused not only on finding appropriate wild relatives but also on development of efficient cell-based high-throughput phenotyping platforms allowing assessment of the in planta operation of key genes.
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Affiliation(s)
- Ali Razzaq
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisald 38040,Pakistan
| | - Shabir Hussain Wani
- Mountain Research Center for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, J&K,India
| | - Fozia Saleem
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisald 38040,Pakistan
| | - Min Yu
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000,China
| | - Meixue Zhou
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tas 7001,Australia
| | - Sergey Shabala
- International Research Centre for Environmental Membrane Biology, Foshan University, Foshan 528000,China
- Tasmanian Institute of Agriculture, University of Tasmania, Hobart, Tas 7001,Australia
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17
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Ali S, Tyagi A, Bae H. Ionomic Approaches for Discovery of Novel Stress-Resilient Genes in Plants. Int J Mol Sci 2021; 22:7182. [PMID: 34281232 PMCID: PMC8267685 DOI: 10.3390/ijms22137182] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 01/03/2023] Open
Abstract
Plants, being sessile, face an array of biotic and abiotic stresses in their lifespan that endanger their survival. Hence, optimized uptake of mineral nutrients creates potential new routes for enhancing plant health and stress resilience. Recently, minerals (both essential and non-essential) have been identified as key players in plant stress biology, owing to their multifaceted functions. However, a realistic understanding of the relationship between different ions and stresses is lacking. In this context, ionomics will provide new platforms for not only understanding the function of the plant ionome during stresses but also identifying the genes and regulatory pathways related to mineral accumulation, transportation, and involvement in different molecular mechanisms under normal or stress conditions. This article provides a general overview of ionomics and the integration of high-throughput ionomic approaches with other "omics" tools. Integrated omics analysis is highly suitable for identification of the genes for various traits that confer biotic and abiotic stress tolerance. Moreover, ionomics advances being used to identify loci using qualitative trait loci and genome-wide association analysis of element uptake and transport within plant tissues, as well as genetic variation within species, are discussed. Furthermore, recent developments in ionomics for the discovery of stress-tolerant genes in plants have also been addressed; these can be used to produce more robust crops with a high nutritional value for sustainable agriculture.
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Affiliation(s)
- Sajad Ali
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea;
| | - Anshika Tyagi
- National Institute for Plant Biotechnology, New Delhi 110012, India;
| | - Hanhong Bae
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Korea;
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18
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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. THE 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] [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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Huang M, Qin R, Li C, Liu C, Jiang Y, Yu J, Chang D, Roberts PA, Chen Q, Wang C. Transgressive resistance to Heterodera glycines in chromosome segment substitution lines derived from susceptible soybean parents. THE PLANT GENOME 2021; 14:e20091. [PMID: 33817979 DOI: 10.1002/tpg2.20091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Accepted: 01/31/2021] [Indexed: 06/12/2023]
Abstract
Chromosome segment substitution lines (CSSLs) are valuable genetic resources for quantitative trait loci (QTL) mapping of complex agronomic traits especially suitable for minor effect QTL. Here, 162 BC3 F7 -BC7 F3 CSSLs derived from crossing two susceptible parent lines, soybean [Glycine max (L.) Merr.] 'Suinong14' (recurrent parent) × wild soybean (G. soja Siebold & Zucc.) ZYD00006, were used for QTL mapping of soybean cyst nematode (SCN, Heterodera glycine Ichinohe) resistance based on female index (FI) and cysts per gram root (CGR) through phenotypic screening and whole-genome resequencing of CSSLs. Phenotypic results displayed a wide range of distribution and transgressive lines in both HG Type 2.5.7 FI and CGR and demonstrated a higher correlation between CGR and root weight (R2 = .5424) compared with than between FI and CGR (R2 = .0018). Using the single-marker analysis nonparametric mapping test, 33 significant QTL were detected on 18 chromosomes contributing resistance to FI and CGR. Fourteen QTL contributing 5.6-15.5% phenotypic variance (PVE) to FI were revealed on 11 chromosomes, and 16 QTL accounting for 6.1-36.2% PVE in CGR were detected on 14 chromosomes with strong additive effect by multiple-QTL model (MQM) mapping. Twenty-five and 13 out of all 38 QTL identified for FI and CGR on 20 chromosomes were from ZYD00006 and Suinong14, respectively. The CSSLs with the combination of positive alleles for FI, CGR, and root weight exhibited low nematode reproduction. For the first time, QTL associated with CGR have been detected, and both FI and CGR should be considered for breeding purposes in the absence of strong resistance genes such as rhg1 and Rhg4.
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Affiliation(s)
- Minghui Huang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ruifeng Qin
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chunjie Li
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
| | - Chunyan Liu
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Ye Jiang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinyao Yu
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
| | - Doudou Chang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Philip A Roberts
- Department of Nematology, University of California, Riverside, CA, 92521, USA
| | - Qingshan Chen
- College of Agronomy, Northeast Agricultural University, Harbin, Heilongjiang, 150030, China
| | - Congli Wang
- Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, Heilongjiang, 150081, China
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20
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Rosso ML, Shang C, Song Q, Escamilla D, Gillenwater J, Zhang B. Development of Breeder-Friendly KASP Markers for Low Concentration of Kunitz Trypsin Inhibitor in Soybean Seeds. Int J Mol Sci 2021; 22:2675. [PMID: 33800919 PMCID: PMC7961957 DOI: 10.3390/ijms22052675] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2020] [Revised: 02/18/2021] [Accepted: 03/03/2021] [Indexed: 11/18/2022] Open
Abstract
Trypsin inhibitors (TI), a common anti-nutritional factor in soybean, prevent animals' protein digestibility reducing animal growth performance. No commercial soybean cultivars with low or null concentration of TI are available. The availability of a high throughput genotyping assay will be beneficial to incorporate the low TI trait into elite breeding lines. The aim of this study is to develop and validate a breeder friendly Kompetitive Allele Specific PCR (KASP) assay linked to low Kunitz trypsin inhibitor (KTI) in soybean seeds. A total of 200 F3:5 lines derived from PI 547656 (low KTI) X Glenn (normal KTI) were genotyped using the BARCSoySNP6K_v2 Beadchip. F3:4 and F3:5 lines were grown in Blacksburg and Orange, Virginia in three years, respectively, and were measured for KTI content using a quantitative HPLC method. We identified three SNP markers tightly linked to the major QTL associated to low KTI in the mapping population. Based on these SNPs, we developed and validated the KASP assays in a set of 93 diverse germplasm accessions. The marker Gm08_44814503 has 86% selection efficiency for the accessions with low KTI and could be used in marker assisted breeding to facilitate the incorporation of low KTI content in soybean seeds.
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Affiliation(s)
- M. Luciana Rosso
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (M.L.R.); (C.S.)
| | - Chao Shang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (M.L.R.); (C.S.)
| | - Qijian Song
- Beltsville Agricultural Research Center, Soybean Genomics and Improvement Laboratory, USDA-ARS, Beltsville, MD 20705, USA;
| | - Diana Escamilla
- Department of Agronomy, Purdue University, West Lafayette, IN 47907, USA;
| | - Jay Gillenwater
- Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695, USA;
| | - Bo Zhang
- School of Plant and Environmental Sciences, Virginia Tech, Blacksburg, VA 24061, USA; (M.L.R.); (C.S.)
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Zhou L, Song L, Lian Y, Ye H, Usovsky M, Wan J, Vuong TD, Nguyen HT. Genetic characterization of qSCN10 from an exotic soybean accession PI 567516C reveals a novel source conferring broad-spectrum resistance to soybean cyst nematode. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:859-874. [PMID: 33394061 DOI: 10.1007/s00122-020-03736-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
KEY MESSAGE The qSCN10 locus with broad-spectrum SCN resistance was fine-mapped to a 379-kb region on chromosome 10 in soybean accession PI 567516C. Candidate genes and potential application benefits of this locus were discussed. Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most devastating pests of soybean, causing significant yield losses worldwide every year. Genetic resistance has been the major strategy to control this pest. However, the overuse of the same genetic resistance derived primarily from PI 88788 has led to the genetic shifts in nematode populations and resulted in the reduced effectiveness in soybean resistance to SCN. Therefore, novel genetic resistance resources, especially those with broad-spectrum resistance, are needed to develop new resistant cultivars to cope with the genetic shifts in nematode populations. In this study, a quantitative trait locus (QTL) qSCN10 previously identified from a soybean landrace PI 567516C was confirmed to confer resistance to multiple SCN HG Types. This QTL was further fine-mapped to a 379-kb region. There are 51 genes in this region. Four of them are defense-related and were regulated by SCN infection, suggesting their potential role in mediating resistance to SCN. The phylogenetic and haplotype analyses of qSCN10 as well as other information indicate that this locus is different from other reported resistance QTL or genes. There was no yield drag or other unfavorable traits associated with this QTL when near-isogenic lines with and without qSCN10 were tested in a SCN-free field. Therefore, our study not only provides further insight into the genetic basis of soybean resistance to SCN, but also identifies a novel genetic resistance resource for breeding soybean for durable, broad-spectrum resistance to this pest.
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Affiliation(s)
- Lijuan Zhou
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Li Song
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Yangzhou University, Yangzhou, 225009, China
| | - Yun Lian
- Institute of Industrial Crops, Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Heng Ye
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Mariola Usovsky
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jinrong Wan
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Tri D Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
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22
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Usovsky M, Ye H, Vuong TD, Patil GB, Wan J, Zhou L, Nguyen HT. Fine-mapping and characterization of qSCN18, a novel QTL controlling soybean cyst nematode resistance in PI 567516C. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:621-631. [PMID: 33185711 DOI: 10.1007/s00122-020-03718-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Accepted: 10/27/2020] [Indexed: 06/11/2023]
Abstract
KEY MESSAGE The qSCN18 QTL from PI 56756C was confirmed and fine-mapped to improve soybean resistance to the SCN population HG Type 2.5.7 using near-isogenic lines carrying recombination crossovers within the QTL region. The QTL underlying resistance was fine-mapped to a 166-Kbp region on chromosome 18, and the candidate genes were selected based on genomic analyses. Soybean cyst nematode (SCN, Heterodera glycines, Ichinohe) is the most devastating pathogen of soybean. Understanding the genetic basis of SCN resistance is crucial for managing this parasite in the field. Two major loci, rhg1 and Rhg4, were previously characterized as valuable resources for SCN resistance. However, their continuous use has caused shifts in the virulence of SCN populations, which can overcome the resistance conferred by these two major loci. Reduced effectiveness became a major concern in the soybean industry due to continuous use of rhg1 for decades. Thus, it is imperative to identify sources of SCN resistance for durable SCN management. A novel QTL qSCN18 was identified in PI567516C. To fine-map qSCN18 and identify resistance genes, a large backcross population was developed. Nineteen near-isogenic lines (NILs) carrying recombination crossovers within the QTL region were identified. The first phase of fine-mapping narrowed the QTL region to 549-Kbp, whereas the second phase confined the region to 166-Kbp containing 23 genes. Two flanking markers, MK-1 and MK-6, were developed and validated to detect the presence of the qSCN18 resistance allele. Haplotype analysis clustered the fine-mapped qSCN18 region from PI 567516C with the cqSCN-007 locus previously mapped in the wild soybean accession PI 468916. The NILs were developed to further characterize the causal gene(s) harbored in this QTL. This study also confirmed the previously identified qSCN18. The results will facilitate marker-assisted selection (MAS) introducing the qSCN18 locus from PI 567516C into high-yielding soybean cultivars with durable resistance to SCN.
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Affiliation(s)
- Mariola Usovsky
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Heng Ye
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Tri D Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Gunvant B Patil
- Institute for Genomics of Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, Lubbock, TX, 79415, USA
| | - Jinrong Wan
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Lijuan Zhou
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, USA.
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23
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Whiting RM, Torabi S, Lukens L, Eskandari M. Genomic regions associated with important seed quality traits in food-grade soybeans. BMC PLANT BIOLOGY 2020; 20:485. [PMID: 33096978 PMCID: PMC7583236 DOI: 10.1186/s12870-020-02681-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 09/30/2020] [Indexed: 05/26/2023]
Abstract
BACKGROUND The production of soy-based food products requires specific physical and chemical characteristics of the soybean seed. Identification of quantitative trait loci (QTL) associated with value-added traits, such as seed weight, seed protein and sucrose concentration, could accelerate the development of competitive high-protein soybean cultivars for the food-grade market through marker-assisted selection (MAS). The objectives of this study were to identify and validate QTL associated with these value-added traits in two high-protein recombinant inbred line (RIL) populations. RESULTS The RIL populations were derived from the high-protein cultivar 'AC X790P' (49% protein, dry weight basis), and two high-yielding commercial cultivars, 'S18-R6' (41% protein) and 'S23-T5' (42% protein). Fourteen large-effect QTL (R2 > 10%) were identified associated with seed protein concentration. Of these QTL, seven QTL were detected in both populations, and eight of them were co-localized with QTL associated with either seed sucrose concentration or seed weight. None of the protein-related QTL was found to be associated with seed yield in either population. Sixteen candidate genes with putative roles in protein metabolism were identified within seven of these protein-related regions: qPro_Gm02-3, qPro_Gm04-4, qPro_Gm06-1, qPro_Gm06-3, qPro_Gm06-6, qPro_Gm13-4 and qPro-Gm15-3. CONCLUSION The use of RIL populations derived from high-protein parents created an opportunity to identify four novel QTL that may have been masked by large-effect QTL segregating in populations developed from diverse parental cultivars. In total, we have identified nine protein QTL that were detected either in both populations in the current study or reported in other studies. These QTL may be useful in the curated selection of new soybean cultivars for optimized soy-based food products.
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Affiliation(s)
- Rachel M Whiting
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Sepideh Torabi
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Lewis Lukens
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Milad Eskandari
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada.
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24
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Lian Y, Wei H, Wang J, Lei C, Li H, Li J, Wu Y, Wang S, Zhang H, Wang T, Du P, Guo J, Lu W. Chromosome-level reference genome of X12, a highly virulent race of the soybean cyst nematode Heterodera glycines. Mol Ecol Resour 2019; 19:1637-1646. [PMID: 31339217 PMCID: PMC6899682 DOI: 10.1111/1755-0998.13068] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2019] [Revised: 07/09/2019] [Accepted: 07/15/2019] [Indexed: 12/22/2022]
Abstract
Soybean cyst nematode (SCN, Heterodera glycines) is a major pest of soybean that is spreading across major soybean production regions worldwide. Increased SCN virulence has recently been observed in both the United States and China. However, no study has reported a genome assembly for H. glycines at the chromosome scale. Herein, the first chromosome-level reference genome of X12, an unusual SCN race with high infection ability, is presented. Using whole-genome shotgun (WGS) sequencing, Pacific Biosciences (PacBio) sequencing, Illumina paired-end sequencing, 10X Genomics linked reads and high-throughput chromatin conformation capture (Hi-C) genome scaffolding techniques, a 141.01-megabase (Mb) assembled genome was obtained with scaffold and contig N50 sizes of 16.27 Mb and 330.54 kilobases (kb), respectively. The assembly showed high integrity and quality, with over 90% of Illumina reads mapped to the genome. The assembly quality was evaluated using Core Eukaryotic Genes Mapping Approach and Benchmarking Universal Single-Copy Orthologs. A total of 11,882 genes were predicted using de novo, homolog and RNAseq data generated from eggs, second-stage juveniles (J2), third-stage juveniles (J3) and fourth-stage juveniles (J4) of X12, and 79.0% of homologous sequences were annotated in the genome. These high-quality X12 genome data will provide valuable resources for research in a broad range of areas, including fundamental nematode biology, SCN-plant interactions and co-evolution, and also contribute to the development of technology for overall SCN management.
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Affiliation(s)
- Yun Lian
- Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of the Ministry of Agriculture/Institute of Industrial CropsHenan Academy of Agricultural SciencesZhengzhouChina
| | - He Wei
- Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of the Ministry of Agriculture/Institute of Industrial CropsHenan Academy of Agricultural SciencesZhengzhouChina
| | - Jinshe Wang
- Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of the Ministry of Agriculture/Institute of Industrial CropsHenan Academy of Agricultural SciencesZhengzhouChina
| | - Chenfang Lei
- Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of the Ministry of Agriculture/Institute of Industrial CropsHenan Academy of Agricultural SciencesZhengzhouChina
| | - Haichao Li
- Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of the Ministry of Agriculture/Institute of Industrial CropsHenan Academy of Agricultural SciencesZhengzhouChina
| | - Jinying Li
- Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of the Ministry of Agriculture/Institute of Industrial CropsHenan Academy of Agricultural SciencesZhengzhouChina
| | - Yongkang Wu
- Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of the Ministry of Agriculture/Institute of Industrial CropsHenan Academy of Agricultural SciencesZhengzhouChina
| | - Shufeng Wang
- Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of the Ministry of Agriculture/Institute of Industrial CropsHenan Academy of Agricultural SciencesZhengzhouChina
| | - Hui Zhang
- Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of the Ministry of Agriculture/Institute of Industrial CropsHenan Academy of Agricultural SciencesZhengzhouChina
| | - Tingfeng Wang
- Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of the Ministry of Agriculture/Institute of Industrial CropsHenan Academy of Agricultural SciencesZhengzhouChina
| | - Pei Du
- Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of the Ministry of Agriculture/Institute of Industrial CropsHenan Academy of Agricultural SciencesZhengzhouChina
| | - Jianqiu Guo
- Luoyang Academy of Agriculture and Forestry SciencesLuoyangChina
| | - Weiguo Lu
- Zhengzhou Subcenter of National Soybean Improvement Center/Key Laboratory of Oil Crops in Huanghuaihai Plains of the Ministry of Agriculture/Institute of Industrial CropsHenan Academy of Agricultural SciencesZhengzhouChina
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25
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Tian Y, Liu B, Shi X, Reif JC, Guan R, Li YH, Qiu LJ. Deep genotyping of the gene GmSNAP facilitates pyramiding resistance to cyst nematode in soybean. ACTA ACUST UNITED AC 2019. [DOI: 10.1016/j.cj.2019.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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26
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Neupane S, Purintun JM, Mathew FM, Varenhorst AJ, Nepal MP. Molecular Basis of Soybean Resistance to Soybean Aphids and Soybean Cyst Nematodes. PLANTS 2019; 8:plants8100374. [PMID: 31561499 PMCID: PMC6843664 DOI: 10.3390/plants8100374] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/05/2019] [Accepted: 09/17/2019] [Indexed: 01/25/2023]
Abstract
Soybean aphid (SBA; Aphis glycines Matsumura) and soybean cyst nematode (SCN; Heterodera glycines Ichninohe) are major pests of the soybean (Glycine max [L.] Merr.). Substantial progress has been made in identifying the genetic basis of limiting these pests in both model and non-model plant systems. Classical linkage mapping and genome-wide association studies (GWAS) have identified major and minor quantitative trait loci (QTLs) in soybean. Studies on interactions of SBA and SCN effectors with host proteins have identified molecular cues in various signaling pathways, including those involved in plant disease resistance and phytohormone regulations. In this paper, we review the molecular basis of soybean resistance to SBA and SCN, and we provide a synthesis of recent studies of soybean QTLs/genes that could mitigate the effects of virulent SBA and SCN populations. We also review relevant studies of aphid–nematode interactions, particularly in the soybean–SBA–SCN system.
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Affiliation(s)
- Surendra Neupane
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Jordan M Purintun
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
| | - Febina M Mathew
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA.
| | - Adam J Varenhorst
- Department of Agronomy, Horticulture and Plant Science, South Dakota State University, Brookings, SD 57007, USA.
| | - Madhav P Nepal
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD 57007, USA.
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Bayless AM, Zapotocny RW, Han S, Grunwald DJ, Amundson KK, Bent AF. The rhg1-a ( Rhg1 low-copy) nematode resistance source harbors a copia-family retrotransposon within the Rhg1-encoded α-SNAP gene. PLANT DIRECT 2019; 3:e00164. [PMID: 31468029 PMCID: PMC6712407 DOI: 10.1002/pld3.164] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/13/2019] [Accepted: 08/02/2019] [Indexed: 05/14/2023]
Abstract
Soybean growers widely use the Resistance to Heterodera glycines 1 (Rhg1) locus to reduce yield losses caused by soybean cyst nematode (SCN). Rhg1 is a tandemly repeated four gene block. Two classes of SCN resistance-conferring Rhg1 haplotypes are recognized: rhg1-a ("Peking-type," low-copy number, three or fewer Rhg1 repeats) and rhg1-b ("PI 88788-type," high-copy number, four or more Rhg1 repeats). The rhg1-a and rhg1-b haplotypes encode α-SNAP (alpha-Soluble NSF Attachment Protein) variants α-SNAP Rhg1 LC and α-SNAP Rhg1 HC, respectively, with differing atypical C-terminal domains, that contribute to SCN resistance. Here we report that rhg1-a soybean accessions harbor a copia retrotransposon within their Rhg1 Glyma.18G022500 (α-SNAP-encoding) gene. We termed this retrotransposon "RAC," for Rhg1 alpha-SNAP copia. Soybean carries multiple RAC-like retrotransposon sequences. The Rhg1 RAC insertion is in the Glyma.18G022500 genes of all true rhg1-a haplotypes we tested and was not detected in any examined rhg1-b or Rhg1WT (single-copy) soybeans. RAC is an intact element residing within intron 1, anti-sense to the rhg1-a α-SNAP open reading frame. RAC has intrinsic promoter activities, but overt impacts of RAC on transgenic α-SNAP Rhg1 LC mRNA and protein abundance were not detected. From the native rhg1-a RAC+ genomic context, elevated α-SNAP Rhg1 LC protein abundance was observed in syncytium cells, as was previously observed for α-SNAP Rhg1 HC (whose rhg1-b does not carry RAC). Using a SoySNP50K SNP corresponding with RAC presence, just ~42% of USDA accessions bearing previously identified rhg1-a SoySNP50K SNP signatures harbor the RAC insertion. Subsequent analysis of several of these putative rhg1-a accessions lacking RAC revealed that none encoded α-SNAPRhg1LC, and thus, they are not rhg1-a. rhg1-a haplotypes are of rising interest, with Rhg4, for combating SCN populations that exhibit increased virulence against the widely used rhg1-b resistance. The present study reveals another unexpected structural feature of many Rhg1 loci, and a selectable feature that is predictive of rhg1-a haplotypes.
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Affiliation(s)
- Adam M. Bayless
- Department of Plant PathologyUniversity of Wisconsin – MadisonMadisonWIUSA
| | - Ryan W. Zapotocny
- Department of Plant PathologyUniversity of Wisconsin – MadisonMadisonWIUSA
| | - Shaojie Han
- Department of Plant PathologyUniversity of Wisconsin – MadisonMadisonWIUSA
| | | | - Kaela K. Amundson
- Department of Plant PathologyUniversity of Wisconsin – MadisonMadisonWIUSA
| | - Andrew F. Bent
- Department of Plant PathologyUniversity of Wisconsin – MadisonMadisonWIUSA
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28
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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 BIOTECHNOLOGY JOURNAL 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] [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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29
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Tran DT, Steketee CJ, Boehm JD, Noe J, Li Z. Genome-Wide Association Analysis Pinpoints Additional Major Genomic Regions Conferring Resistance to Soybean Cyst Nematode ( Heterodera glycines Ichinohe). FRONTIERS IN PLANT SCIENCE 2019; 10:401. [PMID: 31031779 PMCID: PMC6470319 DOI: 10.3389/fpls.2019.00401] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Accepted: 03/18/2019] [Indexed: 05/31/2023]
Abstract
Soybean cyst nematode (Heterodera glycines Ichinohe) (SCN) is the most destructive pest affecting soybeans [Glycine max (L.) Merr.] in the U.S. To date, only two major SCN resistance alleles, rhg1 and Rhg4, identified in PI 88788 (rhg1) and Peking (rhg1/Rhg4), residing on chromosomes (Chr) 18 and 8, respectively, have been widely used to develop SCN resistant cultivars in the U.S. Thus, some SCN populations have evolved to overcome the PI 88788 and Peking derived resistance, making it a priority for breeders to identify new alleles and sources of SCN resistance. Toward that end, 461 soybean accessions from various origins were screened using a greenhouse SCN bioassay and genotyped with Illumina SoySNP50K iSelect BeadChips and three KASP SNP markers developed at the Rhg1 and Rhg4 loci to perform a genome-wide association study (GWAS) and a haplotype analysis at the Rhg1 and Rhg4 loci. In total, 35,820 SNPs were used for GWAS, which identified 12 SNPs at four genomic regions on Chrs 7, 8, 10, and 18 that were significantly associated with SCN resistance (P < 0.001). Of those, three SNPs were located at Rhg1 and Rhg4, and 24 predicted genes were found near the significant SNPs on Chrs 7 and 10. KASP SNP genotyping results of the 462 accessions at the Rhg1 and Rhg4 loci identified 30 that carried PI 88788-type resistance, 50 that carried Peking-type resistance, and 58 that carried neither the Peking-type nor the PI 88788-type resistance alleles, indicating they may possess novel SCN resistance alleles. By using two subsets of SNPs near the Rhg1 and Rhg4 loci obtained from SoySNP iSelect BeadChips, a haplotype analysis of 461 accessions grouped those 58 accessions differently from the accessions carrying Peking or PI 88788 derived resistance, thereby validating the genotyping results at Rhg1 and Rhg4. The significant SNPs, candidate genes, and newly characterized SCN resistant accessions will be beneficial for the development of DNA markers to be used for marker-assisted breeding and developing soybean cultivars carrying novel sources of SCN resistance.
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Affiliation(s)
- Dung T. Tran
- Institute of Plant Breeding, Genetics and Genomics and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Clinton J. Steketee
- Institute of Plant Breeding, Genetics and Genomics and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Jeffrey D. Boehm
- Institute of Plant Breeding, Genetics and Genomics and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - James Noe
- Department of Plant Pathology, University of Georgia, Athens, GA, United States
| | - Zenglu Li
- Institute of Plant Breeding, Genetics and Genomics and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
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Arsenault-Labrecque G, Sonah H, Lebreton A, Labbé C, Marchand G, Xue A, Belzile F, Knaus BJ, Grünwald NJ, Bélanger RR. Stable predictive markers for Phytophthora sojae avirulence genes that impair infection of soybean uncovered by whole genome sequencing of 31 isolates. BMC Biol 2018; 16:80. [PMID: 30049268 PMCID: PMC6060493 DOI: 10.1186/s12915-018-0549-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 07/19/2018] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The interaction between oomycete plant pathogen Phytophthora sojae and soybean is characterized by the presence of avirulence (Avr) genes in P. sojae, which encode for effectors that trigger immune responses and resistance in soybean via corresponding resistance genes (Rps). A recent survey highlighted a rapid diversification of P. sojae Avr genes in soybean fields and the need to deploy new Rps genes. However, the full genetic diversity of P. sojae isolates remains complex and dynamic and is mostly characterized on the basis of phenotypic associations with differential soybean lines. RESULTS We sequenced the genomes of 31 isolates of P. sojae, representing a large spectrum of the pathotypes found in soybean fields, and compared all the genetic variations associated with seven Avr genes (1a, 1b, 1c, 1d, 1k, 3a, 6) and how the derived haplotypes matched reported phenotypes in 217 interactions. We discovered new variants, copy number variations and some discrepancies with the virulence of previously described isolates with Avr genes, notably with Avr1b and Avr1c. In addition, genomic signatures revealed 11.5% potentially erroneous phenotypes. When these interactions were re-phenotyped, and the Avr genes re-sequenced over time and analyzed for expression, our results showed that genomic signatures alone accurately predicted 99.5% of the interactions. CONCLUSIONS This comprehensive genomic analysis of seven Avr genes of P. sojae in a population of 31 isolates highlights that genomic signatures can be used as accurate predictors of phenotypes for compatibility with Rps genes in soybean. Our findings also show that spontaneous mutations, often speculated as a source of aberrant phenotypes, did not occur within the confines of our experiments and further suggest that epigenesis or gene silencing do not account alone for previous discordance between genotypes and phenotypes. Furthermore, on the basis of newly identified virulence patterns within Avr1c, our results offer an explanation why Rps1c has failed more rapidly in the field than the reported information on virulence pathotypes.
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Affiliation(s)
| | - Humira Sonah
- Département de Phytologie, Université Laval, Québec, QC Canada
| | | | - Caroline Labbé
- Département de Phytologie, Université Laval, Québec, QC Canada
| | | | - Allen Xue
- Agriculture and Agri-Food Canada, Ontario, ON Canada
| | | | - Brian J. Knaus
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR USA
| | - Niklaus J. Grünwald
- Horticultural Crops Research Laboratory, USDA Agricultural Research Service, Corvallis, OR USA
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31
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Swaminathan S, Abeysekara NS, Knight JM, Liu M, Dong J, Hudson ME, Bhattacharyya MK, Cianzio SR. Mapping of new quantitative trait loci for sudden death syndrome and soybean cyst nematode resistance in two soybean populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1047-1062. [PMID: 29582113 DOI: 10.1007/s00122-018-3057-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2017] [Accepted: 01/12/2018] [Indexed: 05/07/2023]
Abstract
KEY MESSAGE Novel QTL conferring resistance to both the SDS and SCN was detected in two RIL populations. Dual resistant RILs could be used in breeding programs for developing resistant soybean cultivars. Soybean cultivars, susceptible to the fungus Fusarium virguliforme, which causes sudden death syndrome (SDS), and to the soybean cyst nematode (SCN) (Heterodera glycines), suffer yield losses valued over a billion dollars annually. Both pathogens may occur in the same production fields. Planting of cultivars genetically resistant to both pathogens is considered one of the most effective means to control the two pathogens. The objective of the study was to map quantitative trait loci (QTL) underlying SDS and SCN resistances. Two recombinant inbred line (RIL) populations were developed by crossing 'A95-684043', a high-yielding maturity group (MG) II line resistant to SCN, with 'LS94-3207' and 'LS98-0582' of MG IV, resistant to both F. virguliforme and SCN. Two hundred F7 derived recombinant inbred lines from each population AX19286 (A95-684043 × LS94-3207) and AX19287 (A95-684043 × LS98-0582) were screened for resistance to each pathogen under greenhouse conditions. Five hundred and eighty and 371 SNP markers were used for mapping resistance QTL in each population. In AX19286, one novel SCN resistance QTL was mapped to chromosome 8. In AX19287, one novel SDS resistance QTL was mapped to chromosome 17 and one novel SCN resistance QTL was mapped to chromosome 11. Previously identified additional SDS and SCN resistance QTL were also detected in the study. Lines possessing superior resistance to both pathogens were also identified and could be used as germplasm sources for breeding SDS- and SCN-resistant soybean cultivars.
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Affiliation(s)
| | - Nilwala S Abeysekara
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011, USA
- Department of Plant Pathology and Microbiology, University of California, Riverside, CA, 92507, USA
| | - Joshua M Knight
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
| | - Min Liu
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA
- Department of Agronomy, Shenyang Agricultural University, 120 Dongling Ave, Shenyang, 110866, Liaoning, China
| | - Jia Dong
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Matthew E Hudson
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | | | - Silvia R Cianzio
- Department of Agronomy, Iowa State University, Ames, IA, 50011, USA.
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Santos RB, Pires AS, Abranches R. Addition of a histone deacetylase inhibitor increases recombinant protein expression in Medicago truncatula cell cultures. Sci Rep 2017; 7:16756. [PMID: 29196720 PMCID: PMC5711867 DOI: 10.1038/s41598-017-17006-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 11/20/2017] [Indexed: 01/02/2023] Open
Abstract
Plant cell cultures are an attractive platform for the production of recombinant proteins. A major drawback, hindering the establishment of plant cell suspensions as an industrial platform, is the low product yield obtained thus far. Histone acetylation is associated with increased transcription levels, therefore it is expected that the use of histone deacetylase inhibitors would result in an increase in mRNA and protein levels. Here, this hypothesis was tested by adding a histone deacetylase inhibitor, suberanilohydroxamic acid (SAHA), to a cell line of the model legume Medicago truncatula expressing a recombinant human protein. Histone deacetylase inhibition by SAHA and histone acetylation levels were studied, and the effect of SAHA on gene expression and recombinant protein levels was assessed by digital PCR. SAHA addition effectively inhibited histone deacetylase activity resulting in increased histone acetylation. Higher levels of transgene expression and accumulation of the associated protein were observed. This is the first report describing histone deacetylase inhibitors as inducers of recombinant protein expression in plant cell suspensions as well as the use of digital PCR in these biological systems. This study paves the way for employing epigenetic strategies to improve the final yields of recombinant proteins produced by plant cell cultures.
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Affiliation(s)
- Rita B Santos
- Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Av República, 2780-157, Oeiras, Portugal
| | - Ana Sofia Pires
- Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Av República, 2780-157, Oeiras, Portugal
| | - Rita Abranches
- Plant Cell Biology Laboratory, Instituto de Tecnologia Química e Biológica António Xavier (ITQB NOVA), Av República, 2780-157, Oeiras, Portugal.
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Ohtsu M, Sato Y, Kurihara D, Suzaki T, Kawaguchi M, Maruyama D, Higashiyama T. Spatiotemporal deep imaging of syncytium induced by the soybean cyst nematode Heterodera glycines. PROTOPLASMA 2017; 254:2107-2115. [PMID: 28343256 DOI: 10.1007/s00709-017-1105-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 03/13/2017] [Indexed: 05/17/2023]
Abstract
Parasite infections cause dramatic anatomical and ultrastructural changes in host plants. Cyst nematodes are parasites that invade host roots and induce a specific feeding structure called a syncytium. A syncytium is a large multinucleate cell formed by cell wall dissolution-mediated cell fusion. The soybean cyst nematode (SCN), Heterodera glycines, is a major soybean pathogen. To investigate SCN infection and the syncytium structure, we established an in planta deep imaging system using a clearing solution ClearSee and two-photon excitation microscopy (2PEM). Using this system, we found that several cells were incorporated into the syncytium; the nuclei increased in size and the cell wall openings began to be visible at 2 days after inoculation (DAI). Moreover, at 14 DAI, in the syncytium developed in the cortex, there were thickened concave cell wall pillars that resembled "Parthenon pillars." In contrast, there were many thick board-like cell walls and rarely Parthenon pillars in the syncytium developed in the stele. We revealed that the syncytia were classified into two types based on the pattern of the cell wall structures, which appeared to be determined by the position of the syncytium inside roots. Our results provide new insights into the developmental process of syncytium induced by cyst nematode and a better understanding of the three-dimensional structure of the syncytium in host roots.
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Affiliation(s)
- Mina Ohtsu
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.
| | - Yoshikatsu Sato
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
| | - Daisuke Kurihara
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
- JST ERATO Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
| | - Takuya Suzaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai, Tsukuba, Ibaraki, 305-8577, Japan
| | - Masayoshi Kawaguchi
- Division of Symbiotic Systems, National Institute for Basic Biology (NIBB), Okazaki, Aichi, 444-8585, Japan
| | - Daisuke Maruyama
- Kihara Institute for Biological Research, Yokohama City University, 641-12 Maioka-cho, Totsuka-ku, Yokohama, Kanagawa, 244-0813, Japan
| | - Tetsuya Higashiyama
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
- Institute of Transformative Bio-Molecules (ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8601, Japan
- JST ERATO Higashiyama Live-Holonics Project, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
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Patil G, Mian R, Vuong T, Pantalone V, Song Q, Chen P, Shannon GJ, Carter TC, Nguyen HT. Molecular mapping and genomics of soybean seed protein: a review and perspective for the future. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:1975-1991. [PMID: 28801731 PMCID: PMC5606949 DOI: 10.1007/s00122-017-2955-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/26/2017] [Indexed: 05/16/2023]
Abstract
KEY MESSAGE Genetic improvement of soybean protein meal is a complex process because of negative correlation with oil, yield, and temperature. This review describes the progress in mapping and genomics, identifies knowledge gaps, and highlights the need of integrated approaches. Meal protein derived from soybean [Glycine max (L) Merr.] seed is the primary source of protein in poultry and livestock feed. Protein is a key factor that determines the nutritional and economical value of soybean. Genetic improvement of soybean seed protein content is highly desirable, and major quantitative trait loci (QTL) for soybean protein have been detected and repeatedly mapped on chromosomes (Chr.) 20 (LG-I), and 15 (LG-E). However, practical breeding progress is challenging because of seed protein content's negative genetic correlation with seed yield, other seed components such as oil and sucrose, and interaction with environmental effects such as temperature during seed development. In this review, we discuss rate-limiting factors related to soybean protein content and nutritional quality, and potential control factors regulating seed storage protein. In addition, we describe advances in next-generation sequencing technologies for precise detection of natural variants and their integration with conventional and high-throughput genotyping technologies. A syntenic analysis of QTL on Chr. 15 and 20 was performed. Finally, we discuss comprehensive approaches for integrating protein and amino acid QTL, genome-wide association studies, whole-genome resequencing, and transcriptome data to accelerate identification of genomic hot spots for allele introgression and soybean meal protein improvement.
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Affiliation(s)
- Gunvant Patil
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Rouf Mian
- Soybean and Nitrogen Fixation Unit, USDA-ARS, Raleigh, NC, 27607, USA.
| | - Tri Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Vince Pantalone
- Department of Plant Sciences, University of Tennessee, Knoxville, TN, 37996-4561, USA
| | - Qijian Song
- Agricultural Research Service, Department of Agriculture United States, Beltsville, MD, 20705, USA
| | - Pengyin Chen
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Grover J Shannon
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Tommy C Carter
- Soybean and Nitrogen Fixation Unit, USDA-ARS, Raleigh, NC, 27607, USA
| | - Henry T Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO, 65211, USA.
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Nguyen THN, Schulz D, Winkelmann T, Debener T. Genetic dissection of adventitious shoot regeneration in roses by employing genome-wide association studies. PLANT CELL REPORTS 2017. [PMID: 28647832 DOI: 10.1007/s00299-017-2170-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We analysed the capacity to regenerate adventitious shoots in 96 rose genotypes and found 88 SNP markers associated with QTLs, some of which are derived from candidate genes for shoot regeneration. In an association panel of 96 rose genotypes previously analysed for petal colour, we conducted a genome-wide association study on the capacity of leaf petioles for direct shoot regeneration. Shoot regeneration rate and shoot ratio (number of shoots/total number of explants) were used as phenotypic descriptors for regeneration capacity. Two independent experiments were carried out with six replicates of ten explants each. We found significant variation between the genotypes ranging from 0.88 to 88.33% for the regeneration rate and from 0.008 to 1.2 for the shoot ratio, which exceeded the rates reported so far. Furthermore, we found 88 SNP markers associated with either the shoot regeneration rate or the shoot ratio. In this association analysis, we found 12 SNP markers from ESTs (expressed sequence tags) matching known candidate genes that are involved in shoot morphogenesis. The best markers explained more than 51% of the variance in the shoot regeneration rate and more than 0.65 of the variance in the shoot regeneration ratio between the homozygote marker classes. The genes underlying some of the best markers such as a GT-transcription factor or an LRR receptor-like protein kinase are novel candidate genes putatively involved in the observed phenotypic differences. The associated markers were mapped to the closely related genome of Fragaria vesca and revealed many distinct clusters, which also comprised the known candidate genes that functioned in the organogenesis of plant shoots. However, the validation of candidate genes and their functional relationship to shoot regeneration require further analysis in independent rose populations and functional analyses.
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Affiliation(s)
- Thi Hong Nhung Nguyen
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
- Institute of Agricultural Genetics, Hanoi, Vietnam
| | - Dietmar Schulz
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany
| | - Traud Winkelmann
- Institute of Horticultural Production Systems, Woody Plant and Propagation Physiology, Leibniz Universität Hannover, Hannover, Germany
| | - Thomas Debener
- Institute of Plant Genetics, Leibniz Universität Hannover, Hannover, Germany.
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Zhao X, Teng W, Li Y, Liu D, Cao G, Li D, Qiu L, Zheng H, Han Y, Li W. Loci and candidate genes conferring resistance to soybean cyst nematode HG type 2.5.7. BMC Genomics 2017; 18:462. [PMID: 28615053 PMCID: PMC5471737 DOI: 10.1186/s12864-017-3843-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 06/05/2017] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Soybean (Glycine max L. Merr.) cyst nematode (SCN, Heterodera glycines I,) is a major pest of soybean worldwide. The most effective strategy to control this pest involves the use of resistant cultivars. The aim of the present study was to investigate the genome-wide genetic architecture of resistance to SCN HG Type 2.5.7 (race 1) in landrace and elite cultivated soybeans. RESULTS A total of 200 diverse soybean accessions were screened for resistance to SCN HG Type 2.5.7 and genotyped through sequencing using the Specific Locus Amplified Fragment Sequencing (SLAF-seq) approach with a 6.14-fold average sequencing depth. A total of 33,194 SNPs were identified with minor allele frequencies (MAF) over 4%, covering 97% of all the genotypes. Genome-wide association mapping (GWAS) revealed thirteen SNPs associated with resistance to SCN HG Type 2.5.7. These SNPs were distributed on five chromosomes (Chr), including Chr7, 8, 14, 15 and 18. Four SNPs were novel resistance loci and nine SNPs were located near known QTL. A total of 30 genes were identified as candidate genes underlying SCN resistance. CONCLUSIONS A total of sixteen novel soybean accessions were identified with significant resistance to HG Type 2.5.7. The beneficial alleles and candidate genes identified by GWAS might be valuable for improving marker-assisted breeding efficiency and exploring the molecular mechanisms underlying SCN resistance.
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Affiliation(s)
- Xue Zhao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
| | - Weili Teng
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
| | - Yinghui Li
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Dongyuan Liu
- Bioinformatics Division, Biomarker Technologies Corporation, Beijing, 101300 China
| | - Guanglu Cao
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
| | - Dongmei Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
| | - Lijuan Qiu
- Institute of Crop Science, National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Hongkun Zheng
- Bioinformatics Division, Biomarker Technologies Corporation, Beijing, 101300 China
| | - Yingpeng Han
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
| | - Wenbin Li
- Key Laboratory of Soybean Biology in Chinese Ministry of Education (Key Laboratory of Soybean Biology and Breeding/Genetics of Chinese Agriculture Ministry), Northeast Agricultural University, Harbin, 150030 China
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Kadam S, Abril A, Dhanapal AP, Koester RP, Vermerris W, Jose S, Fritschi FB. Characterization and Regulation of Aquaporin Genes of Sorghum [ Sorghum bicolor (L.) Moench] in Response to Waterlogging Stress. FRONTIERS IN PLANT SCIENCE 2017; 8:862. [PMID: 28611797 PMCID: PMC5447673 DOI: 10.3389/fpls.2017.00862] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 05/09/2017] [Indexed: 05/25/2023]
Abstract
Waterlogging is a significant environmental constraint to crop production, and a better understanding of plant responses is critical for the improvement of crop tolerance to waterlogged soils. Aquaporins (AQPs) are a class of channel-forming proteins that play an important role in water transport in plants. This study aimed to examine the regulation of AQP genes under waterlogging stress and to characterize the genetic variability of AQP genes in sorghum (Sorghum bicolor). Transcriptional profiling of AQP genes in response to waterlogging stress in nodal root tips and nodal root basal regions of two tolerant and two sensitive sorghum genotypes at 18 and 96 h after waterlogging stress imposition revealed significant gene-specific pattern with regard to genotype, root tissue sample, and time point. For some tissue sample and time point combinations, PIP2-6, PIP2-7, TIP2-2, TIP4-4, and TIP5-1 expression was differentially regulated in tolerant compared to sensitive genotypes. The differential response of these AQP genes suggests that they may play a tissue specific role in mitigating waterlogging stress. Genetic analysis of sorghum revealed that AQP genes were clustered into the same four subfamilies as in maize (Zea mays) and rice (Oryza sativa) and that residues determining the AQP channel specificity were largely conserved across species. Single nucleotide polymorphism (SNP) data from 50 sorghum accessions were used to build an AQP gene-based phylogeny of the haplotypes. Phylogenetic analysis based on single nucleotide polymorphisms of sorghum AQP genes placed the tolerant and sensitive genotypes used for the expression study in distinct groups. Expression analyses suggested that selected AQPs may play a pivotal role in sorghum tolerance to water logging stress. Further experimentation is needed to verify their role and to leverage phylogenetic analyses and AQP expression data to improve waterlogging tolerance in sorghum.
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Affiliation(s)
- Suhas Kadam
- Division of Plant Sciences, University of Missouri, ColumbiaMO, United States
| | - Alejandra Abril
- Graduate Program in Plant Molecular and Cellular Biology, University of Florida, GainesvilleFL, United States
| | - Arun P. Dhanapal
- Division of Plant Sciences, University of Missouri, ColumbiaMO, United States
| | - Robert P. Koester
- Division of Plant Sciences, University of Missouri, ColumbiaMO, United States
| | - Wilfred Vermerris
- Department of Microbiology and Cell Science – Institute of Food and Agricultural Sciences, University of Florida, GainesvilleFL, United States
- University of Florida Genetics Institute, University of Florida, GainesvilleFL, United States
| | - Shibu Jose
- The Center for Agroforestry, University of Missouri, ColumbiaMO, United States
| | - Felix B. Fritschi
- Division of Plant Sciences, University of Missouri, ColumbiaMO, United States
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Cheng P, Gedling CR, Patil G, Vuong TD, Shannon JG, Dorrance AE, Nguyen HT. Genetic mapping and haplotype analysis of a locus for quantitative resistance to Fusarium graminearum in soybean accession PI 567516C. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:999-1010. [PMID: 28275816 DOI: 10.1007/s00122-017-2866-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 01/24/2017] [Indexed: 05/16/2023]
Abstract
KEY MESSAGE A major novel quantitative disease resistance locus, qRfg_Gm06, for Fusarium graminearum was genetically mapped to chromosome 6. Genomic-assisted haplotype analysis within this region identified three putative candidate genes. Fusarium graminearum causes seed, root rot, and seedling damping-off in soybean which contributes to reduced stands and yield. A cultivar Magellan and PI 567516C were identified with low and high levels of partial resistance to F. graminearum, respectively. Quantitative disease resistance loci (QDRL) were mapped with 241 F7:8 recombinant inbred lines (RILs) derived from a cross of Magellan × PI 567516C. Phenotypic evaluation for resistance to F. graminearum used the rolled towel assay in a randomized incomplete block design. The genetic map was constructed from 927 polymorphic single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers. One major QDRL qRfg_Gm06 was detected and mapped to chromosome 6 with a LOD score of 20.3 explaining 40.2% of the total phenotypic variation. This QDRL was mapped to a ~400 kb genomic region of the Williams 82 reference genome. Genome mining of this region identified 14 putative candidate disease resistance genes. Haplotype analysis of this locus using whole genome re-sequencing (WGRS) of 106 diverse soybean lines narrowed the list to three genes. A SNP genotyping Kompetitive allele-specific PCR (KASP) assay was designed for one of the genes and was validated in a subset of the RILs and all 106 diverse lines.
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Affiliation(s)
- Peng Cheng
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - Cassidy R Gedling
- Department of Plant Pathology, The Ohio State University, 1680 Madison Avenue, Wooster, OH, 44691, USA
| | - Gunvant Patil
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - Tri D Vuong
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - J Grover Shannon
- Division of Plant Sciences, University of Missouri-Fisher Delta Research Center, Portageville, MO, 63873, USA
| | - Anne E Dorrance
- Department of Plant Pathology, The Ohio State University, 1680 Madison Avenue, Wooster, OH, 44691, USA.
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
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Santos C, Duarte S, Tedesco S, Fevereiro P, Costa RL. Expression Profiling of Castanea Genes during Resistant and Susceptible Interactions with the Oomycete Pathogen Phytophthora cinnamomi Reveal Possible Mechanisms of Immunity. FRONTIERS IN PLANT SCIENCE 2017; 8:515. [PMID: 28443110 PMCID: PMC5387079 DOI: 10.3389/fpls.2017.00515] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Accepted: 03/23/2017] [Indexed: 05/28/2023]
Abstract
The most dangerous pathogen affecting the production of chestnuts is Phytophthora cinnamomi a hemibiotrophic that causes root rot, also known as ink disease. Little information has been acquired in chestnut on the molecular defense strategies against this pathogen. The expression of eight candidate genes potentially involved in the defense to P. cinnamomi was quantified by digital PCR in Castanea genotypes showing different susceptibility to the pathogen. Seven of the eight candidate genes displayed differentially expressed levels depending on genotype and time-point after inoculation. Cast_Gnk2-like revealed to be the most expressed gene across all experiments and the one that best discriminates between susceptible and resistant genotypes. Our data suggest that the pre-formed defenses are crucial for the resistance of C. crenata to P. cinnamomi. A lower and delayed expression of the eight studied genes was found in the susceptible Castanea sativa, which may be related with the establishment and spread of the disease in this species. A working model integrating the obtained results is presented.
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Affiliation(s)
- Carmen Santos
- Molecular Biology Lab, Instituto Nacional de Investigação Agrária e Veterinária, I.P.Oeiras, Portugal
- Plant Cell Biotechnology Lab, Instituto de Tecnologia Química e Biológica António Xavier (Green-it Unit), Universidade Nova de LisboaOeiras, Portugal
| | - Sofia Duarte
- Molecular Biology Lab, Instituto Nacional de Investigação Agrária e Veterinária, I.P.Oeiras, Portugal
| | - Sara Tedesco
- Molecular Biology Lab, Instituto Nacional de Investigação Agrária e Veterinária, I.P.Oeiras, Portugal
| | - Pedro Fevereiro
- Plant Cell Biotechnology Lab, Instituto de Tecnologia Química e Biológica António Xavier (Green-it Unit), Universidade Nova de LisboaOeiras, Portugal
- Departamento Biologia Vegetal, Faculdade de Ciências da Universidade de LisboaCampo Grande, Portugal
| | - Rita L. Costa
- Molecular Biology Lab, Instituto Nacional de Investigação Agrária e Veterinária, I.P.Oeiras, Portugal
- Centro de Estudos Florestais, Instituto Superior de Agronomia, Universidade de Lisboa - Tapada da AjudaLisboa, Portugal
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LIAN YUN, GUO JIANQIU, LI HAICHAO, WU YONGKANG, WEI HE, WANG JINSHE, LI JINYING, LU WEIGUO. A New Race (X12) of Soybean Cyst Nematode in China. J Nematol 2017. [DOI: 10.21307/jofnem-2017-079] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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Patil G, Chaudhary J, Vuong TD, Jenkins B, Qiu D, Kadam S, Shannon GJ, Nguyen HT. Development of SNP Genotyping Assays for Seed Composition Traits in Soybean. INTERNATIONAL JOURNAL OF PLANT GENOMICS 2017; 2017:6572969. [PMID: 28630621 PMCID: PMC5463095 DOI: 10.1155/2017/6572969] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2016] [Revised: 03/20/2017] [Accepted: 03/30/2017] [Indexed: 05/20/2023]
Abstract
Seed composition is one of the most important determinants of the economic values in soybean. The quality and quantity of different seed components, such as oil, protein, and carbohydrates, are crucial ingredients in food, feed, and numerous industrial products. Soybean researchers have successfully developed and utilized a diverse set of molecular markers for seed trait improvement in soybean breeding programs. It is imperative to design and develop molecular assays that are accurate, robust, high-throughput, cost-effective, and available on a common genotyping platform. In the present study, we developed and validated KASP (Kompetitive allele-specific polymerase chain reaction) genotyping assays based on previously known functional mutant alleles for the seed composition traits, including fatty acids, oligosaccharides, trypsin inhibitor, and lipoxygenase. These assays were validated on mutant sources as well as mapping populations and precisely distinguish the homozygotes and heterozygotes of the mutant genes. With the obvious advantages, newly developed KASP assays in this study can substitute the genotyping assays that were previously developed for marker-assisted selection (MAS). The functional gene-based assay resource developed using common genotyping platform will be helpful to accelerate efforts to improve soybean seed composition traits.
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Affiliation(s)
- Gunvant Patil
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
- Department of Agronomy and Genetics, University of Minnesota, St. Paul, MN 55108, USA
| | - Juhi Chaudhary
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Tri D. Vuong
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Brian Jenkins
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Dan Qiu
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Suhas Kadam
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Grover J. Shannon
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
| | - Henry T. Nguyen
- Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA
- *Henry T. Nguyen:
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Zhang H, Mittal N, Leamy LJ, Barazani O, Song B. Back into the wild-Apply untapped genetic diversity of wild relatives for crop improvement. Evol Appl 2017; 10:5-24. [PMID: 28035232 PMCID: PMC5192947 DOI: 10.1111/eva.12434] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 09/07/2016] [Indexed: 12/18/2022] Open
Abstract
Deleterious effects of climate change and human activities, as well as diverse environmental stresses, present critical challenges to food production and the maintenance of natural diversity. These challenges may be met by the development of novel crop varieties with increased biotic or abiotic resistance that enables them to thrive in marginal lands. However, considering the diverse interactions between crops and environmental factors, it is surprising that evolutionary principles have been underexploited in addressing these food and environmental challenges. Compared with domesticated cultivars, crop wild relatives (CWRs) have been challenged in natural environments for thousands of years and maintain a much higher level of genetic diversity. In this review, we highlight the significance of CWRs for crop improvement by providing examples of CWRs that have been used to increase biotic and abiotic stress resistance/tolerance and overall yield in various crop species. We also discuss the surge of advanced biotechnologies, such as next-generation sequencing technologies and omics, with particular emphasis on how they have facilitated gene discovery in CWRs. We end the review by discussing the available resources and conservation of CWRs, including the urgent need for CWR prioritization and collection to ensure continuous crop improvement for food sustainability.
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Affiliation(s)
- Hengyou Zhang
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Neha Mittal
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Larry J. Leamy
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
| | - Oz Barazani
- The Institute for Plant SciencesIsrael Plant Gene BankAgricultural Research OrganizationBet DaganIsrael
| | - Bao‐Hua Song
- Department of Biological SciencesUniversity of North Carolina at CharlotteCharlotteNCUSA
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Kumawat G, Gupta S, Ratnaparkhe MB, Maranna S, Satpute GK. QTLomics in Soybean: A Way Forward for Translational Genomics and Breeding. FRONTIERS IN PLANT SCIENCE 2016; 7:1852. [PMID: 28066449 PMCID: PMC5174554 DOI: 10.3389/fpls.2016.01852] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/23/2016] [Indexed: 05/19/2023]
Abstract
Food legumes play an important role in attaining both food and nutritional security along with sustainable agricultural production for the well-being of humans globally. The various traits of economic importance in legume crops are complex and quantitative in nature, which are governed by quantitative trait loci (QTLs). Mapping of quantitative traits is a tedious and costly process, however, a large number of QTLs has been mapped in soybean for various traits albeit their utilization in breeding programmes is poorly reported. For their effective use in breeding programme it is imperative to narrow down the confidence interval of QTLs, to identify the underlying genes, and most importantly allelic characterization of these genes for identifying superior variants. In the field of functional genomics, especially in the identification and characterization of gene responsible for quantitative traits, soybean is far ahead from other legume crops. The availability of genic information about quantitative traits is more significant because it is easy and effective to identify homologs than identifying shared syntenic regions in other crop species. In soybean, genes underlying QTLs have been identified and functionally characterized for phosphorous efficiency, flowering and maturity, pod dehiscence, hard-seededness, α-Tocopherol content, soybean cyst nematode, sudden death syndrome, and salt tolerance. Candidate genes have also been identified for many other quantitative traits for which functional validation is required. Using the sequence information of identified genes from soybean, comparative genomic analysis of homologs in other legume crops could discover novel structural variants and useful alleles for functional marker development. The functional markers may be very useful for molecular breeding in soybean and harnessing benefit of translational research from soybean to other leguminous crops. Thus, soybean crop can act as a model crop for translational genomics and breeding of quantitative traits in legume crops. In this review, we summarize current status of identification and characterization of genes underlying QTLs for various quantitative traits in soybean and their significance in translational genomics and breeding of other legume crops.
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Affiliation(s)
- Giriraj Kumawat
- Crop Improvement Section, ICAR—Indian Institute of Soybean ResearchIndore, India
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Kim KS, Vuong TD, Qiu D, Robbins RT, Grover Shannon J, Li Z, Nguyen HT. Advancements in breeding, genetics, and genomics for resistance to three nematode species in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:2295-2311. [PMID: 27796432 DOI: 10.1007/s00122-016-2816-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2016] [Accepted: 10/18/2016] [Indexed: 05/24/2023]
Abstract
KEY MESSAGE Integration of genetic analysis, molecular biology, and genomic approaches drastically enhanced our understanding of genetic control of nematode resistance and provided effective breeding strategies in soybeans. Three nematode species, including soybean cyst (SCN, Heterodera glycine), root-knot (RKN, Meloidogyne incognita), and reniform (RN, Rotylenchulus reniformis), are the most destructive pests and have spread to soybean growing areas worldwide. Host plant resistance has played an important role in their control. This review focuses on genetic, genomic studies, and breeding efforts over the past two decades to identify and improve host resistance to these three nematode species. Advancements in genetics, genomics, and bioinformatics have improved our understanding of the molecular and genetic mechanisms of nematode resistance and enabled researchers to generate large-scale genomic resources and marker-trait associations. Whole-genome resequencing, genotyping-by-sequencing, genome-wide association studies, and haplotype analyses have been employed to map and dissect genomic locations for nematode resistance. Recently, two major SCN-resistant loci, Rhg1 and Rhg4, were cloned and other novel resistance quantitative trait loci (QTL) have been discovered. Based on these discoveries, gene-specific DNA markers have been developed for both Rhg1 and Rhg4 loci, which were useful for marker-assisted selection. With RKN resistance QTL being mapped, candidate genes responsible for RKN resistance were identified, leading to the development of functional single nucleotide polymorphism markers. So far, three resistances QTL have been genetically mapped for RN resistance. With nematode species overcoming the host plant resistance, continuous efforts in the identification and deployment of new resistance genes are required to support the development of soybean cultivars with multiple and durable resistance to these pests.
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Affiliation(s)
- Ki-Seung Kim
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
- KSK's Current Address: LG Chem-FarmHannong, Ltd., Daejeon, 34115, Korea.
| | - Tri D Vuong
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - Dan Qiu
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA
| | - Robert T Robbins
- Department of Plant Pathology, University of Arkansas, Fayetteville, AR, 72701, USA
| | - J Grover Shannon
- Division of Plant Sciences, University of Missouri-Fisher Delta Research Center, Portageville, MO, 63873, USA
| | - Zenglu Li
- Center for Applied Genetic Technologies and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, 30602, USA
| | - Henry T Nguyen
- Division of Plant Sciences and National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, 65211, USA.
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Mitchum MG. Soybean Resistance to the Soybean Cyst Nematode Heterodera glycines: An Update. PHYTOPATHOLOGY 2016; 106:1444-1450. [PMID: 27392178 DOI: 10.1094/phyto-06-16-0227-rvw] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The soybean cyst nematode (SCN), Heterodera glycines, remains a serious threat to soybean production throughout the world. A lack of genetic diversity in resistant soybean cultivars has led to a widespread shift toward virulence in SCN populations, leaving farmers with few proven options other than nonhost rotation to manage this nematode. Recent advances in our understanding of the genes controlling resistance to the nematode have led to improved molecular markers, which are, in turn, increasing the efficiency and precision of the breeding pipeline. A better understanding of the molecular and biochemical basis of SCN resistance and nematode virulence will provide information useful for the development of a long-term strategic plan for diversification and the deployment of cultivars that protect current sources of natural resistance while identifying new targets for engineering novel resistance.
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Affiliation(s)
- Melissa G Mitchum
- Division of Plant Sciences and Bond Life Sciences Center, Columbia, MO 65211
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Lee TG, Diers BW, Hudson ME. An efficient method for measuring copy number variation applied to improvement of nematode resistance in soybean. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:143-153. [PMID: 27310152 DOI: 10.1111/tpj.13240] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2016] [Revised: 06/09/2016] [Accepted: 06/13/2016] [Indexed: 05/22/2023]
Abstract
Copy number variation (CNV) is implicated in important traits in multiple crop plants, but can be challenging to genotype using conventional methods. The Rhg1 locus of soybean, which confers resistance to soybean cyst nematode (SCN), is a CNV of multiple 31.2-kb genomic units each containing four genes. Reliable, high-throughput methods to quantify Rhg1 and other CNVs for selective breeding were developed. The CNV genotyping assay described here uses a homeologous gene copy within the paleopolyploid soybean genome to provide the internal control for a single-tube TaqMan copy number assay. Using this assay, CNV in breeding populations can be tracked with high precision. We also show that extensive CNV exists within Fayette, a released, inbred SCN-resistant soybean cultivar with a high copy number at Rhg1 derived from a single donor parent. Copy number at Rhg1 is therefore unstable within a released variety over a relatively small number of generations. Using this assay to select for individuals with altered copy number, plants were obtained with both increased copy number and increased SCN resistance relative to control plants. Thus, CNV genotyping technologies can be used as a new type of marker-assisted selection to select for desirable traits in breeding populations, and to control for undesirable variation within cultivars.
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Affiliation(s)
- Tong Geon Lee
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Brian W Diers
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Matthew E Hudson
- Department of Crop Sciences, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA.
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Zhang H, Li C, Davis EL, Wang J, Griffin JD, Kofsky J, Song BH. Genome-Wide Association Study of Resistance to Soybean Cyst Nematode (Heterodera glycines) HG Type 2.5.7 in Wild Soybean (Glycine soja). FRONTIERS IN PLANT SCIENCE 2016; 7:1214. [PMID: 27582748 PMCID: PMC4987380 DOI: 10.3389/fpls.2016.01214] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/02/2016] [Indexed: 05/07/2023]
Abstract
Soybean cyst nematode (SCN) is the most destructive soybean pest worldwide. Host plant resistance is the most environmentally friendly and cost-effective way of mitigating SCN damage to soybeans. However, overuse of the resistant soybean [Glycine max (L.) Merr.] cultivars from limited genetic resources has resulted in SCN race shifts in many soybean-growing areas. Thus, exploration of novel sources of SCN resistance and dissection of the genetic basis are urgently needed. In this study, we screened 235 wild soybean (Glycine soja Sieb. & Zucc.) accessions to identify genotypes resistant to SCN HG Type 2.5.7 (race 5), a less investigated type but is prevalent in the southeastern US. We also dissected the genetic basis of SCN resistance using a genome-wide association study with SNPs genotyped by SoySNP50k iSelect BeadChip. In total, 43 resistant accessions (female index < 30) were identified, with 10 SNPs being significantly associated with SCN HG 2.5.7 resistance in this wild species. Furthermore, four significant SNPs were localized to linked regions of the known quantitative trait locus (QTL) rhg1 on chromosome 18. The other four SNPs on chromosome 18 and two SNPs on chromosome 19 are novel. Genes encoding disease resistance-related proteins with a leucine-rich region, a mitogen-activated protein kinase (MAPK) on chromosome 18, and a MYB transcription factor on chromosome 19 were identified as promising candidate genes. The identified SNPs and candidate genes will benefit future marker-assisted breeding and dissection of the molecular mechanisms underlying the soybean-SCN interaction.
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Affiliation(s)
- Hengyou Zhang
- Bao-Hua Song Lab, Department of Biological Sciences, University of North Carolina at CharlotteCharlotte, NC, USA
| | - Chunying Li
- Eric Davis Lab, Department of Plant Pathology, North Carolina State UniversityRaleigh, NC, USA
| | - Eric L. Davis
- Eric Davis Lab, Department of Plant Pathology, North Carolina State UniversityRaleigh, NC, USA
| | - Jinshe Wang
- Institute of Industrial Crops, Henan Academy of Agricultural Sciences, National Subcenter for Soybean Improvement/Key Laboratory of Oil CropsZhengzhou, China
| | | | - Janice Kofsky
- Bao-Hua Song Lab, Department of Biological Sciences, University of North Carolina at CharlotteCharlotte, NC, USA
| | - Bao-Hua Song
- Bao-Hua Song Lab, Department of Biological Sciences, University of North Carolina at CharlotteCharlotte, NC, USA
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Song J, Liu Z, Hong H, Ma Y, Tian L, Li X, Li YH, Guan R, Guo Y, Qiu LJ. Identification and Validation of Loci Governing Seed Coat Color by Combining Association Mapping and Bulk Segregation Analysis in Soybean. PLoS One 2016; 11:e0159064. [PMID: 27404272 PMCID: PMC4942065 DOI: 10.1371/journal.pone.0159064] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 06/27/2016] [Indexed: 02/05/2023] Open
Abstract
Soybean seed coat exists in a range of colors from yellow, green, brown, black, to bicolor. Classical genetic analysis suggested that soybean seed color was a moderately complex trait controlled by multi-loci. However, only a couple of loci could be detected using a single biparental segregating population. In this study, a combination of association mapping and bulk segregation analysis was employed to identify genes/loci governing this trait in soybean. A total of 14 loci, including nine novel and five previously reported ones, were identified using 176,065 coding SNPs selected from entire SNP dataset among 56 soybean accessions. Four of these loci were confirmed and further mapped using a biparental population developed from the cross between ZP95-5383 (yellow seed color) and NY279 (brown seed color), in which different seed coat colors were further dissected into simple trait pairs (green/yellow, green/black, green/brown, yellow/black, yellow/brown, and black/brown) by continuously developing residual heterozygous lines. By genotyping entire F2 population using flanking markers located in fine-mapping regions, the genetic basis of seed coat color was fully dissected and these four loci could explain all variations of seed colors in this population. These findings will be useful for map-based cloning of genes as well as marker-assisted breeding in soybean. This work also provides an alternative strategy for systematically isolating genes controlling relative complex trait by association analysis followed by biparental mapping.
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Affiliation(s)
- Jian Song
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Zhangxiong Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Huilong Hong
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Yansong Ma
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Long Tian
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Xinxiu Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Ying-Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Rongxia Guan
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Yong Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI) and MOA Key Lab of Soybean Biology (Beijing), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, P. R. China
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Sonah H, Deshmukh RK, Bélanger RR. Computational Prediction of Effector Proteins in Fungi: Opportunities and Challenges. FRONTIERS IN PLANT SCIENCE 2016; 7:126. [PMID: 26904083 PMCID: PMC4751359 DOI: 10.3389/fpls.2016.00126] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2015] [Accepted: 01/23/2016] [Indexed: 05/20/2023]
Abstract
Effector proteins are mostly secretory proteins that stimulate plant infection by manipulating the host response. Identifying fungal effector proteins and understanding their function is of great importance in efforts to curb losses to plant diseases. Recent advances in high-throughput sequencing technologies have facilitated the availability of several fungal genomes and 1000s of transcriptomes. As a result, the growing amount of genomic information has provided great opportunities to identify putative effector proteins in different fungal species. There is little consensus over the annotation and functionality of effector proteins, and mostly small secretory proteins are considered as effector proteins, a concept that tends to overestimate the number of proteins involved in a plant-pathogen interaction. With the characterization of Avr genes, criteria for computational prediction of effector proteins are becoming more efficient. There are 100s of tools available for the identification of conserved motifs, signature sequences and structural features in the proteins. Many pipelines and online servers, which combine several tools, are made available to perform genome-wide identification of effector proteins. In this review, available tools and pipelines, their strength and limitations for effective identification of fungal effector proteins are discussed. We also present an exhaustive list of classically secreted proteins along with their key conserved motifs found in 12 common plant pathogens (11 fungi and one oomycete) through an analytical pipeline.
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Affiliation(s)
| | | | - Richard R. Bélanger
- Département de Phytologie, Faculté des Sciences de l’Agriculture et de l’Alimentation, Centre de Recherche en Horticulture, Université Laval, QuébecQC, Canada
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Welling MT, Shapter T, Rose TJ, Liu L, Stanger R, King GJ. A Belated Green Revolution for Cannabis: Virtual Genetic Resources to Fast-Track Cultivar Development. FRONTIERS IN PLANT SCIENCE 2016; 7:1113. [PMID: 27524992 PMCID: PMC4965456 DOI: 10.3389/fpls.2016.01113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 07/13/2016] [Indexed: 05/18/2023]
Abstract
Cannabis is a predominantly diecious phenotypically diverse domesticated genus with few if any extant natural populations. International narcotics conventions and associated legislation have constrained the establishment, characterization, and use of Cannabis genetic resource collections. This has resulted in the underutilization of genepool variability in cultivar development and has limited the inclusion of secondary genepools associated with genetic improvement strategies of the Green Revolution. The structured screening of ex situ germplasm and the exploitation of locally-adapted intraspecific traits is expected to facilitate the genetic improvement of Cannabis. However, limited attempts have been made to establish the full extent of genetic resources available for pre-breeding. We present a thorough critical review of Cannabis ex situ genetic resources, and discuss recommendations for conservation, pre-breeding characterization, and genetic analysis that will underpin future cultivar development. We consider East Asian germplasm to be a priority for conservation based on the prolonged historical cultivation of Cannabis in this region over a range of latitudes, along with the apparent high levels of genetic diversity and relatively low representation in published genetic resource collections. Seed cryopreservation could improve conservation by reducing hybridization and genetic drift that may occur during Cannabis germplasm regeneration. Given the unique legal status of Cannabis, we propose the establishment of a global virtual core collection based on the collation of consistent and comprehensive provenance meta-data and the adoption of high-throughput DNA sequencing technologies. This would enable representative core collections to be used for systematic phenotyping, and so underpin breeding strategies for the genetic improvement of Cannabis.
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Affiliation(s)
- Matthew T. Welling
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Tim Shapter
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
- Ecofibre Industries Operations Pty LtdMaleny, QLD, Australia
| | - Terry J. Rose
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Lei Liu
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Rhia Stanger
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
| | - Graham J. King
- Southern Cross Plant Science, Southern Cross UniversityLismore, NSW, Australia
- *Correspondence: Graham J. King
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