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Almeida-Silva F, Prost-Boxoen L, Van de Peer Y. hybridexpress: an R/Bioconductor package for comparative transcriptomic analyses of hybrids and their progenitors. THE NEW PHYTOLOGIST 2024. [PMID: 38798271 DOI: 10.1111/nph.19862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/08/2024] [Indexed: 05/29/2024]
Abstract
Hybridization, the process of crossing individuals from diverse genetic backgrounds, plays a pivotal role in evolution, biological invasiveness, and crop breeding. At the transcriptional level, hybridization often leads to complex nonadditive effects, presenting challenges for understanding its consequences. Although standard transcriptomic analyses exist to compare hybrids to their progenitors, such analyses have not been implemented in a software package, hindering reproducibility. We introduce hybridexpress, an R/Bioconductor package designed to facilitate the analysis, visualization, and comparison of gene expression patterns in hybrid triplets (hybrids and their progenitors). hybridexpress provides users with a user-friendly and comprehensive workflow that includes all standard comparative analyses steps, including data normalization, calculation of midparent expression values, sample clustering, expression-based gene classification into categories and classes, and overrepresentation analysis for functional terms. We illustrate the utility of hybridexpress through comparative transcriptomic analyses of cotton allopolyploidization and rice root trait heterosis. hybridexpress is designed to streamline comparative transcriptomic studies of hybrid triplets, advancing our understanding of evolutionary dynamics in allopolyploids, and enhancing plant breeding strategies. hybridexpress is freely accessible from Bioconductor (https://bioconductor.org/packages/HybridExpress) and its source code is available on GitHub (https://github.com/almeidasilvaf/HybridExpress).
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Affiliation(s)
- Fabricio Almeida-Silva
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
| | - Lucas Prost-Boxoen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Department of Biology, Ghent University, 9000, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, VIB, 9052, Ghent, Belgium
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
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Kamara MM, Mansour E, Khalaf AEA, Eid MAM, Hassanin AA, Abdelghany AM, Kheir AMS, Galal AA, Behiry SI, Silvar C, El-Hendawy S. Molecular Diversity and Combining Ability in Newly Developed Maize Inbred Lines under Low-Nitrogen Conditions. Life (Basel) 2024; 14:641. [PMID: 38792661 PMCID: PMC11122723 DOI: 10.3390/life14050641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Revised: 05/14/2024] [Accepted: 05/14/2024] [Indexed: 05/26/2024] Open
Abstract
Nitrogen is an essential element for maize growth, but excessive application can lead to various environmental and ecological issues, including water pollution, air pollution, greenhouse gas emissions, and biodiversity loss. Hence, developing maize hybrids resilient to low-N conditions is vital for sustainable agriculture, particularly in nitrogen-deficient soils. Combining ability and genetic relationships among parental lines is crucial for breeding superior hybrids under diverse nitrogen levels. This study aimed to assess the genetic diversity of maize inbred lines using simple sequence repeat (SSR) markers and evaluate their combining ability to identify superior hybrids under low-N and recommended conditions. Local and exotic inbred lines were genotyped using SSR markers, revealing substantial genetic variation with high gene diversity (He = 0.60), moderate polymorphism information content (PIC = 0.54), and an average of 3.64 alleles per locus. Twenty-one F1 hybrids were generated through a diallel mating design using these diverse lines. These hybrids and a high yielding commercial check (SC-131) were field-tested under low-N and recommended N conditions. Significant variations (p < 0.01) were observed among nitrogen levels, hybrids, and their interaction for all recorded traits. Additive genetic variances predominated over non-additive genetic variances for grain yield and most traits. Inbred IL3 emerged as an effective combiner for developing early maturing genotypes with lower ear placement. Additionally, inbreds IL1, IL2, and IL3 showed promise as superior combiners for enhancing grain yield and related traits under both low-N and recommended conditions. Notably, hybrids IL1×IL4, IL2×IL5, IL2×IL6, and IL5×IL7 exhibited specific combining abilities for increasing grain yield and associated traits under low-N stress conditions. Furthermore, strong positive associations were identified between grain yield and specific traits like plant height, ear length, number of rows per ear, and number of kernels per row. Due to their straightforward measurability, these relationships underscore the potential of using these traits as proxies for indirect selection in early breeding generations, particularly under low-N stress. This research contributes to breeding nitrogen-efficient maize hybrids and advances our understanding of the genetic foundations for tolerance to nitrogen limitations.
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Affiliation(s)
- Mohamed M. Kamara
- Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt; (M.M.K.); (A.A.G.)
| | - Elsayed Mansour
- Department of Crop Science, Faculty of Agriculture, Zagazig University, Zagazig 44519, Egypt;
| | - Ahmed E. A. Khalaf
- Agronomy Department, Faculty of Agriculture, Fayoum University, Fayoum 63514, Egypt; (A.E.A.K.); (M.A.M.E.)
| | - Mohamed A. M. Eid
- Agronomy Department, Faculty of Agriculture, Fayoum University, Fayoum 63514, Egypt; (A.E.A.K.); (M.A.M.E.)
| | - Abdallah A. Hassanin
- Department of Genetics, Faculty of Agriculture, Zagazig University, Zagazig 44519, Egypt;
| | - Ahmed M. Abdelghany
- Crop Science Department, Faculty of Agriculture, Damanhour University, Damanhour 22516, Egypt;
| | - Ahmed M. S. Kheir
- Soils, Water and Environment Research Institute, Agricultural Research Center, Giza 12619, Egypt;
| | - Ahmed A. Galal
- Department of Agronomy, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh 33516, Egypt; (M.M.K.); (A.A.G.)
| | - Said I. Behiry
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria 21531, Egypt;
| | - Cristina Silvar
- Grupo de Investigación en Bioloxía Evolutiva, CICA—Centro Interdisciplinar de Química e Bioloxía, Universidade da Coruña, 15071 A Coruña, Spain;
| | - Salah El-Hendawy
- Department of Plant Production, College of Food and Agriculture Sciences, King Saud University, P.O. Box 2460, Riyadh 11451, Saudi Arabia
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Tao D, Kalendar R, Paterson AH. Editorial: Interspecific hybridization in plant biology, volume II. FRONTIERS IN PLANT SCIENCE 2024; 15:1412622. [PMID: 38736442 PMCID: PMC11088942 DOI: 10.3389/fpls.2024.1412622] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 04/22/2024] [Indexed: 05/14/2024]
Affiliation(s)
- Dayun Tao
- Yunnan Seed Laboratory/Yunnan Key Laboratory for Rice Genetic Improvement, Food Crops Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Ruslan Kalendar
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Andrew H. Paterson
- Plant Genome Mapping Laboratory, University of Georgia, Athens, GA, United States
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Peixoto MA, Leach KA, Jarquin D, Flannery P, Zystro J, Tracy WF, Bhering L, Resende MFR. Utilizing genomic prediction to boost hybrid performance in a sweet corn breeding program. FRONTIERS IN PLANT SCIENCE 2024; 15:1293307. [PMID: 38726298 PMCID: PMC11080654 DOI: 10.3389/fpls.2024.1293307] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 03/26/2024] [Indexed: 05/12/2024]
Abstract
Sweet corn breeding programs, like field corn, focus on the development of elite inbred lines to produce commercial hybrids. For this reason, genomic selection models can help the in silico prediction of hybrid crosses from the elite lines, which is hypothesized to improve the test cross scheme, leading to higher genetic gain in a breeding program. This study aimed to explore the potential of implementing genomic selection in a sweet corn breeding program through hybrid prediction in a within-site across-year and across-site framework. A total of 506 hybrids were evaluated in six environments (California, Florida, and Wisconsin, in the years 2020 and 2021). A total of 20 traits from three different groups were measured (plant-, ear-, and flavor-related traits) across the six environments. Eight statistical models were considered for prediction, as the combination of two genomic prediction models (GBLUP and RKHS) with two different kernels (additive and additive + dominance), and in a single- and multi-trait framework. Also, three different cross-validation schemes were tested (CV1, CV0, and CV00). The different models were then compared based on the correlation between the estimated breeding values/total genetic values and phenotypic measurements. Overall, heritabilities and correlations varied among the traits. The models implemented showed good accuracies for trait prediction. The GBLUP implementation outperformed RKHS in all cross-validation schemes and models. Models with additive plus dominance kernels presented a slight improvement over the models with only additive kernels for some of the models examined. In addition, models for within-site across-year and across-site performed better in the CV0 than the CV00 scheme, on average. Hence, GBLUP should be considered as a standard model for sweet corn hybrid prediction. In addition, we found that the implementation of genomic prediction in a sweet corn breeding program presented reliable results, which can improve the testcross stage by identifying the top candidates that will reach advanced field-testing stages.
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Affiliation(s)
- Marco Antônio Peixoto
- Laboratório de Biometria, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Kristen A. Leach
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | - Diego Jarquin
- Department of Agronomy, University of Florida, Gainesville, FL, United States
| | - Patrick Flannery
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Jared Zystro
- Organic Seed Alliance, Port Townsend, WA, United States
| | - William F. Tracy
- Department of Plant and Agroecosystem Sciences, University of Wisconsin-Madison, Madison, WI, United States
| | - Leonardo Bhering
- Laboratório de Biometria, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Márcio F. R. Resende
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
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Zhang D, Hu Y, Li R, Tang L, Mo L, Pan Y, Mao B, Shao Y, Zhao B, Lei D. Research on Physiological Characteristics and Differential Gene Expression of Rice Hybrids and Their Parents under Salt Stress at Seedling Stage. PLANTS (BASEL, SWITZERLAND) 2024; 13:744. [PMID: 38475590 DOI: 10.3390/plants13050744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 02/23/2024] [Accepted: 03/05/2024] [Indexed: 03/14/2024]
Abstract
Soil salinization is one of the most important abiotic stresses which can seriously affect the growth and development of rice, leading to the decrease in or even loss of a rice harvest. Increasing the rice yield of saline soil is a key issue for agricultural production. The utilization of heterosis could significantly increase crop biomass and yield, which might be an effective way to meet the demand for rice cultivation in saline soil. In this study, to elucidate the regulatory mechanisms of rice hybrids and their parents that respond to salt stress, we investigated the phenotypic characteristics, physiological and biochemical indexes, and expression level of salt-related genes at the seedling stage. In this study, two sets of materials, encapsulating the most significant differences between the rice hybrids and their parents, were screened using the salt damage index and a hybrid superiority analysis. Compared with their parents, the rice hybrids Guang-Ba-You-Hua-Zhan (BB1) and Y-Liang-You-900 (GD1) exhibited much better salt tolerance, including an increased fresh weight and higher survival rate, a better scavenging ability towards reactive oxygen species (ROS), better ionic homeostasis with lower content of Na+ in their Na+/K+ ratio, and a higher expression of salt-stress-responsive genes. These results indicated that rice hybrids developed complex regulatory mechanisms involving multiple pathways and genes to adapt to salt stress and provided a physiological basis for the utilization of heterosis for improving the yield of rice under salt stress.
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Affiliation(s)
- Dan Zhang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Yuanyi Hu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
- National Center of Technology Innovation for Salin-Alkali Tolerant Rice, Sanya 572000, China
- School of Tropical Agricultture and Forestry, Hainan University, Haikou 570228, China
| | - Ruopeng Li
- National Center of Technology Innovation for Salin-Alkali Tolerant Rice, Sanya 572000, China
- School of Tropical Agricultture and Forestry, Hainan University, Haikou 570228, China
| | - Li Tang
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
- School of Tropical Agricultture and Forestry, Hainan University, Haikou 570228, China
| | - Lin Mo
- National Center of Technology Innovation for Salin-Alkali Tolerant Rice, Sanya 572000, China
- School of Tropical Agricultture and Forestry, Hainan University, Haikou 570228, China
| | - Yinlin Pan
- National Center of Technology Innovation for Salin-Alkali Tolerant Rice, Sanya 572000, China
| | - Bigang Mao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
- School of Tropical Agricultture and Forestry, Hainan University, Haikou 570228, China
| | - Ye Shao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Bingran Zhao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha 410125, China
| | - Dongyang Lei
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
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Dickel L, Arcese P, Keller LF, Nietlisbach P, Goedert D, Jensen H, Reid JM. Multigenerational Fitness Effects of Natural Immigration Indicate Strong Heterosis and Epistatic Breakdown in a Wild Bird Population. Am Nat 2024; 203:411-431. [PMID: 38358807 DOI: 10.1086/728669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2024]
Abstract
AbstractThe fitness of immigrants and their descendants produced within recipient populations fundamentally underpins the genetic and population dynamic consequences of immigration. Immigrants can in principle induce contrasting genetic effects on fitness across generations, reflecting multifaceted additive, dominance, and epistatic effects. Yet full multigenerational and sex-specific fitness effects of regular immigration have not been quantified within naturally structured systems, precluding inference on underlying genetic architectures and population outcomes. We used four decades of song sparrow (Melospiza melodia) life history and pedigree data to quantify fitness of natural immigrants, natives, and their F1, F2, and backcross descendants and test for evidence of nonadditive genetic effects. Values of key fitness components (including adult lifetime reproductive success and zygote survival) of F1 offspring of immigrant-native matings substantially exceeded their parent mean, indicating strong heterosis. Meanwhile, F2 offspring of F1-F1 matings had notably low values, indicating surprisingly strong epistatic breakdown. Furthermore, magnitudes of effects varied among fitness components and differed between female and male descendants. These results demonstrate that strong nonadditive genetic effects on fitness can arise within weakly structured and fragmented populations experiencing frequent natural immigration. Such effects will substantially affect the net degree of effective gene flow and resulting local genetic introgression and adaptation.
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Kumar R, Sharma N, Dubey AK, Sharma RM, Sethi S, Mishra GP, Mathur S, Vittal H, Shivran M, Sharma N. Fruit Quality Assessment of Novel Hybrid Pummelo × Sweet Orange and Its Molecular Characterization Using Acidity Specific Markers. Food Technol Biotechnol 2024; 62:35-45. [PMID: 38601970 PMCID: PMC11002445 DOI: 10.17113/ftb.62.01.24.8349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 01/04/2024] [Indexed: 04/12/2024] Open
Abstract
Research background There is considerable diversity in newly developed pummelo × sweet orange citrus hybrids. Most hybrids showed lower peel thickness and high juice yield but there is a lack of information on fruit quality parameters and molecular characterization. Therefore, the aim of the current study is to determine the content of antioxidants and properties of the fresh juice of 24 new pummelo × sweet orange citrus hybrids (Citrus maxima [Burm. f.] Osbeck × Citrus sinensis [L.] Osbeck) and the parental genotypes along with molecular characteristics determined using acidity specific markers. Experimental approach The correlation and estimate of inheritance of the fruit juice properties: ascorbic acid, total phenol, total flavonoid, total antioxidant, total soluble solid and sugar contents, pH, titratable acidity, along with sensory evaluation was performed. Molecular characterization of these hybrids was carried out using de novo generated acidity specific simple sequence repeat (SSR) markers. Results and conclusions The main constituents of the fruit juice of pummelo × sweet orange hybrids were observed in the range of w(ascorbic acid)=40.00-58.13 mg/100 g, total phenols expressed as gallic acid equivalents w(GAE)=40.67-107.33 mg/100 g, total antioxidants expressed as Trolox equivalents b(Trolox)=2.03-5.49 µmol/g, total flavonoids expressed as quercetin equivalents w(QE)=23.67-59.33 mg/100 g, along with other properties: total soluble solids=7.33-11.33 %, w(total sugar)=2.10-5.76 %, w(reducing sugar)=1.69-2.78 %, w(non-reducing sugar)=0.39-3.17 % and titratable acidity 1.00-2.11 %. The above parameters differed significantly in the fruit juice of the evaluated pummelo × sweet orange hybrids. Considering these parameters, the hybrids SCSH 17-9, SCSH 13-13, SCSH 11-15 and SCSH 3-15 had superior antioxidant properties in terms of these parameters. A higher heritability (≥80 %) was also observed for all juice properties. Molecular characterization of pummelo × sweet orange hybrids showed that >50 % of the hybrids were grouped with medium acidity parents. Both molecular and biochemical parameter-based clustering showed that interspecific hybrids exhibit transgressive segregation with increased antioxidants that help alleviate the health problems. Novelty and scientific contribution These newly developed pummelo × sweet orange citrus hybrids are a valuable source of high-quality antioxidants for a healthy diet. The identification of trait markers that enable selection at the seedling stage is of great benefit to citrus breeders, as the characteristic features of a mature tree are not yet visible at the juvenile stage.
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Affiliation(s)
- Raushan Kumar
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa Campus, 110012 New Delhi, Delhi, India
| | - Nimisha Sharma
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa Campus, 110012 New Delhi, Delhi, India
| | - Anil Kumar Dubey
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa Campus, 110012 New Delhi, Delhi, India
| | - Radha Mohan Sharma
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa Campus, 110012 New Delhi, Delhi, India
| | - Shruti Sethi
- Division of Food Science and Postharvest Technology, ICAR-Indian Agricultural Research Institute Pusa Campus,110012 New Delhi, Delhi, India
| | - Gyan Prakash Mishra
- Division of Seed Science and Technology, ICAR-Indian Agricultural Research Institute, Pusa Campus, 110012 New Delhi, Delhi, India
| | - Sandeep Mathur
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa Campus, 110012 New Delhi, Delhi, India
| | - Hatkari Vittal
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa Campus, 110012 New Delhi, Delhi, India
| | - Mukesh Shivran
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, Pusa Campus, 110012 New Delhi, Delhi, India
| | - Neha Sharma
- ICAR-National Institute for Plant Biotechnology, Pusa Campus, 110012 New Delhi, Delhi, India
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Liu W, He G, Deng XW. Toward understanding and utilizing crop heterosis in the age of biotechnology. iScience 2024; 27:108901. [PMID: 38533455 PMCID: PMC10964264 DOI: 10.1016/j.isci.2024.108901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/28/2024] Open
Abstract
Heterosis, a universal phenomenon in nature, mainly reflected in the superior productivity, quality, and fitness of F1 hybrids compared with their inbred parents, has been exploited in agriculture and greatly benefited human society in terms of food security. However, the flexible and efficient utilization of heterosis has remained a challenge in hybrid breeding systems because of the limitations of "three-line" and "two-line" methods. In the past two decades, rapidly developed biotechnologies have provided unprecedented conveniences for both understanding and utilizing heterosis. Notably, "third-generation" (3G) hybrid breeding technology together with high-throughput sequencing and gene editing greatly promoted the efficiency of hybrid breeding. Here, we review emerging ideas about the genetic or molecular mechanisms of heterosis and the development of 3G hybrid breeding system in the age of biotechnology. In addition, we summarized opportunities and challenges for optimal heterosis utilization in the future.
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Affiliation(s)
- Wenwen Liu
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
| | - Guangming He
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Xing Wang Deng
- School of Advanced Agricultural Sciences and School of Life Sciences, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
- National Key Laboratory of Wheat Improvement, Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Weifang, Shandong 261325, China
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Wang Y, Wang J, Sarwar R, Zhang W, Geng R, Zhu KM, Tan XL. Research progress on the physiological response and molecular mechanism of cold response in plants. FRONTIERS IN PLANT SCIENCE 2024; 15:1334913. [PMID: 38352650 PMCID: PMC10861734 DOI: 10.3389/fpls.2024.1334913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 01/10/2024] [Indexed: 02/16/2024]
Abstract
Low temperature is a critical environmental stress factor that restricts crop growth and geographical distribution, significantly impacting crop quality and yield. When plants are exposed to low temperatures, a series of changes occur in their external morphology and internal physiological and biochemical metabolism. This article comprehensively reviews the alterations and regulatory mechanisms of physiological and biochemical indices, such as membrane system stability, redox system, fatty acid content, photosynthesis, and osmoregulatory substances, in response to low-temperature stress in plants. Furthermore, we summarize recent research on signal transduction and regulatory pathways, phytohormones, epigenetic modifications, and other molecular mechanisms mediating the response to low temperatures in higher plants. In addition, we outline cultivation practices to improve plant cold resistance and highlight the cold-related genes used in molecular breeding. Last, we discuss future research directions, potential application prospects of plant cold resistance breeding, and recent significant breakthroughs in the research and application of cold resistance mechanisms.
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Affiliation(s)
| | | | | | | | | | | | - Xiao-Li Tan
- School of Life Sciences, Jiangsu University, Zhenjiang, China
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Westbrook AS, DiTommaso A. Hybridization in agricultural weeds: A review from ecological, evolutionary, and management perspectives. AMERICAN JOURNAL OF BOTANY 2023; 110:e16258. [PMID: 38031455 DOI: 10.1002/ajb2.16258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 10/22/2023] [Accepted: 10/23/2023] [Indexed: 12/01/2023]
Abstract
Agricultural weeds frequently hybridize with each other or with related crop species. Some hybrid weeds exhibit heterosis (hybrid vigor), which may be stabilized through mechanisms like genome duplication or vegetative reproduction. Even when heterosis is not stabilized, hybridization events diversify weed gene pools and often enable adaptive introgression. Consequently, hybridization may promote weed evolution and exacerbate weed-crop competition. However, hybridization does not always increase weediness. Even when viable and fertile, hybrid weeds sometimes prove unsuccessful in crop fields. This review provides an overview of weed hybridization and its management implications. We describe intrinsic and extrinsic factors that influence hybrid fitness in agroecosystems. We also survey the rapidly growing literature on crop-weed hybridization and the link between hybridization and invasiveness. These topics are increasingly relevant in this era of genetic tools for crop improvement, intensive and simplified cropping systems, and globalized trade. The review concludes with suggested research priorities, including hybridization in the context of climate change, plant-insect interactions, and redesigned weed management programs. From a weed management perspective, hybridization is one of many reasons that researchers and land managers must diversify their weed control toolkits.
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Affiliation(s)
- Anna S Westbrook
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Antonio DiTommaso
- Section of Soil and Crop Sciences, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
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Cyplik A, Piaskowska D, Czembor P, Bocianowski J. The use of weighted multiple linear regression to estimate QTL × QTL × QTL interaction effects of winter wheat (Triticum aestivum L.) doubled-haploid lines. J Appl Genet 2023; 64:679-693. [PMID: 37878169 PMCID: PMC10632291 DOI: 10.1007/s13353-023-00795-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/25/2023] [Accepted: 10/04/2023] [Indexed: 10/26/2023]
Abstract
Knowledge of the magnitude of gene effects and their interactions, their nature, and contribution to determining quantitative traits is very important in conducting an effective breeding program. In traditional breeding, information on the parameter related to additive gene effect and additive-additive interaction (epistasis) and higher-order additive interactions would be useful. Although commonly overlooked in studies, higher-order interactions have a significant impact on phenotypic traits. Failure to account for the effect of triplet interactions in quantitative genetics can significantly underestimate additive QTL effects. Understanding the genetic architecture of quantitative traits is a major challenge in the post-genomic era, especially for quantitative trait locus (QTL) effects, QTL-QTL interactions, and QTL-QTL-QTL interactions. This paper proposes using weighted multiple linear regression to estimate the effects of triple interaction (additive-additive-additive) quantitative trait loci (QTL-QTL-QTL). The material for the study consisted of 126 doubled haploid lines of winter wheat (Mandub × Begra cross). The lines were analyzed for 18 traits, including percentage of necrosis leaf area, percentage of leaf area covered by pycnidia, heading data, and height. The number of genes (the number of effective factors) was lower than the number of QTLs for nine traits, higher for four traits and equal for five traits. The number of triples for unweighted regression ranged from 0 to 9, while for weighted regression, it ranged from 0 to 13. The total aaagu effect ranged from - 14.74 to 15.61, while aaagw ranged from - 23.39 to 21.65. The number of detected threes using weighted regression was higher for two traits and lower for four traits. Forty-nine statistically significant threes of the additive-by-additive-by-additive interaction effects were observed. The QTL most frequently occurring in threes was 4407404 (9 times). The use of weighted regression improved (in absolute value) the assessment of QTL-QTL-QTL interaction effects compared to the assessment based on unweighted regression. The coefficients of determination for the weighted regression model were higher, ranging from 0.8 to 15.5%, than for the unweighted regression. Based on the results, it can be concluded that the QTL-QTL-QTL triple interaction had a significant effect on the expression of quantitative traits. The use of weighted multiple linear regression proved to be a useful statistical tool for estimating additive-additive-additive (aaa) interaction effects. The weighted regression also provided results closer to phenotypic evaluations than estimator values obtained using unweighted regression, which is closer to the true values.
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Affiliation(s)
- Adrian Cyplik
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637, Poznań, Poland
| | - Dominika Piaskowska
- Plant Breeding and Acclimatization Institute - National Research Institute, Department of Applied Biology, Radzików, 05-870, Błonie, Poland
| | - Paweł Czembor
- Plant Breeding and Acclimatization Institute - National Research Institute, Department of Applied Biology, Radzików, 05-870, Błonie, Poland
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637, Poznań, Poland.
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12
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Feng LY, Lin PF, Xu RJ, Kang HQ, Gao LZ. Comparative Genomic Analysis of Asian Cultivated Rice and Its Wild Progenitor ( Oryza rufipogon) Has Revealed Evolutionary Innovation of the Pentatricopeptide Repeat Gene Family through Gene Duplication. Int J Mol Sci 2023; 24:16313. [PMID: 38003501 PMCID: PMC10671101 DOI: 10.3390/ijms242216313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Revised: 11/10/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023] Open
Abstract
The pentatricopeptide repeat (PPR) gene family is one of the largest gene families in land plants. However, current knowledge about the evolution of the PPR gene family remains largely limited. In this study, we performed a comparative genomic analysis of the PPR gene family in O. sativa and its wild progenitor, O. rufipogon, and outlined a comprehensive landscape of gene duplications. Our findings suggest that the majority of PPR genes originated from dispersed duplications. Although segmental duplications have only expanded approximately 11.30% and 13.57% of the PPR gene families in the O. sativa and O. rufipogon genomes, we interestingly obtained evidence that segmental duplication promotes the structural diversity of PPR genes through incomplete gene duplications. In the O. sativa and O. rufipogon genomes, 10 (~33.33%) and 22 pairs of gene duplications (~45.83%) had non-PPR paralogous genes through incomplete gene duplication. Segmental duplications leading to incomplete gene duplications might result in the acquisition of domains, thus promoting functional innovation and structural diversification of PPR genes. This study offers a unique perspective on the evolution of PPR gene structures and underscores the potential role of segmental duplications in PPR gene structural diversity.
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Affiliation(s)
- Li-Ying Feng
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China; (L.-Y.F.); (P.-F.L.)
| | - Pei-Fan Lin
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China; (L.-Y.F.); (P.-F.L.)
| | - Rong-Jing Xu
- Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou 570228, China; (R.-J.X.); (H.-Q.K.)
| | - Hai-Qi Kang
- Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou 570228, China; (R.-J.X.); (H.-Q.K.)
| | - Li-Zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou 510642, China; (L.-Y.F.); (P.-F.L.)
- Tropical Biodiversity and Genomics Research Center, Hainan University, Haikou 570228, China; (R.-J.X.); (H.-Q.K.)
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13
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Kristensen PS, Sarup P, Fé D, Orabi J, Snell P, Ripa L, Mohlfeld M, Chu TT, Herrström J, Jahoor A, Jensen J. Prediction of additive, epistatic, and dominance effects using models accounting for incomplete inbreeding in parental lines of hybrid rye and sugar beet. FRONTIERS IN PLANT SCIENCE 2023; 14:1193433. [PMID: 38162304 PMCID: PMC10756082 DOI: 10.3389/fpls.2023.1193433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 10/16/2023] [Indexed: 01/03/2024]
Abstract
Genomic models for prediction of additive and non-additive effects within and across different heterotic groups are lacking for breeding of hybrid crops. In this study, genomic prediction models accounting for incomplete inbreeding in parental lines from two different heterotic groups were developed and evaluated. The models can be used for prediction of general combining ability (GCA) of parental lines from each heterotic group as well as specific combining ability (SCA) of all realized and potential crosses. Here, GCA was estimated as the sum of additive genetic effects and within-group epistasis due to high degree of inbreeding in parental lines. SCA was estimated as the sum of across-group epistasis and dominance effects. Three models were compared. In model 1, it was assumed that each hybrid was produced from two completely inbred parental lines. Model 1 was extended to include three-way hybrids from parental lines with arbitrary levels of inbreeding: In model 2, parents of the three-way hybrids could have any levels of inbreeding, while the grandparents of the maternal parent were assumed completely inbred. In model 3, all parental components could have any levels of inbreeding. Data from commercial breeding programs for hybrid rye and sugar beet was used to evaluate the models. The traits grain yield and root yield were analyzed for rye and sugar beet, respectively. Additive genetic variances were larger than epistatic and dominance variances. The models' predictive abilities for total genetic value, for GCA of each parental line and for SCA were evaluated based on different cross-validation strategies. Predictive abilities were highest for total genetic values and lowest for SCA. Predictive abilities for SCA and for GCA of maternal lines were higher for model 2 and model 3 than for model 1. The implementation of the genomic prediction models in hybrid breeding programs can potentially lead to increased genetic gain in two different ways: I) by facilitating the selection of crossing parents with high GCA within heterotic groups and II) by prediction of SCA of all realized and potential combinations of parental lines to produce hybrids with high total genetic values.
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Affiliation(s)
| | - Pernille Sarup
- Research and Development, Nordic Seed A/S, Odder, Denmark
| | - Dario Fé
- Research Division, DLF Seeds A/S, Store Heddinge, Denmark
| | - Jihad Orabi
- Research and Development, Nordic Seed A/S, Odder, Denmark
| | - Per Snell
- Research and Development, DLF Beet Seed AB, Landskrona, Sweden
| | - Linda Ripa
- Research and Development, DLF Beet Seed AB, Landskrona, Sweden
| | | | - Thinh Tuan Chu
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | | | - Ahmed Jahoor
- Research and Development, Nordic Seed A/S, Odder, Denmark
- Breeding, Nordic Seed Germany GmbH, Nienstädt, Germany
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Just Jensen
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
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14
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Hamid R, Jacob F, Ghorbanzadeh Z, Jafari L, Alishah O. Dynamic roles of small RNAs and DNA methylation associated with heterosis in allotetraploid cotton (Gossypium hirsutum L.). BMC PLANT BIOLOGY 2023; 23:488. [PMID: 37828433 PMCID: PMC10571366 DOI: 10.1186/s12870-023-04495-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 09/28/2023] [Indexed: 10/14/2023]
Abstract
BACKGROUND Heterosis is a complex phenomenon wherein the hybrids outperform their parents. Understanding the underlying molecular mechanism by which hybridization leads to higher yields in allopolyploid cotton is critical for effective breeding programs. Here, we integrated DNA methylation, transcriptomes, and small RNA profiles to comprehend the genetic and molecular basis of heterosis in allopolyploid cotton at three developmental stages. RESULTS Transcriptome analysis revealed that numerous DEGs responsive to phytohormones (auxin and salicylic acid) were drastically altered in F1 hybrid compared to the parental lines. DEGs involved in energy metabolism and plant growth were upregulated, whereas DEGs related to basal defense were downregulated. Differences in homoeologous gene expression in F1 hybrid were greatly reduced after hybridization, suggesting that higher levels of parental expression have a vital role in heterosis. Small RNAome and methylome studies showed that the degree of DNA methylation in hybrid is higher when compared to the parents. A substantial number of allele-specific expression genes were found to be strongly regulated by CG allele-specific methylation levels. The hybrid exhibited higher 24-nt-small RNA (siRNA) expression levels than the parents. The regions in the genome with increased levels of 24-nt-siRNA were chiefly related to genes and their flanking regulatory regions, demonstrating a possible effect of these molecules on gene expression. The transposable elements correlated with siRNA clusters in the F1 hybrid had higher methylation levels but lower expression levels, which suggest that these non-additively expressed siRNA clusters, reduced the activity of transposable elements through DNA methylation in the hybrid. CONCLUSIONS These multi-omics data provide insights into how changes in epigenetic mechanisms and gene expression patterns can lead to heterosis in allopolyploid cotton. This makes heterosis a viable tool in cotton breeding.
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Affiliation(s)
- Rasmieh Hamid
- Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran.
| | - Feba Jacob
- Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, Thrissur, India
| | - Zahra Ghorbanzadeh
- Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran (ABRII), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran
| | - Leila Jafari
- Horticultural Science Department, Faculty of Agriculture and Natural Resources, University of Hormozgan, Bandar Abbas, Iran
- Research Group of Agroecology in Dryland Areas, University of Hormozgan, Bandar Abbas, Iran
| | - Omran Alishah
- Department of Plant Breeding, Cotton Research Institute of Iran (CRII), Agricultural Research, Education and Extension Organization (AREEO), Gorgan, Iran
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15
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Alseekh S, Karakas E, Zhu F, Wijesingha Ahchige M, Fernie AR. Plant biochemical genetics in the multiomics era. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:4293-4307. [PMID: 37170864 PMCID: PMC10433942 DOI: 10.1093/jxb/erad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
Our understanding of plant biology has been revolutionized by modern genetics and biochemistry. However, biochemical genetics can be traced back to the foundation of Mendelian genetics; indeed, one of Mendel's milestone discoveries of seven characteristics of pea plants later came to be ascribed to a mutation in a starch branching enzyme. Here, we review both current and historical strategies for the elucidation of plant metabolic pathways and the genes that encode their component enzymes and regulators. We use this historical review to discuss a range of classical genetic phenomena including epistasis, canalization, and heterosis as viewed through the lens of contemporary high-throughput data obtained via the array of approaches currently adopted in multiomics studies.
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Affiliation(s)
- Saleh Alseekh
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Esra Karakas
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
| | - Feng Zhu
- National R&D Center for Citrus Preservation, Key Laboratory of Horticultural Plant Biology, Ministry of Education, Huazhong Agricultural University, 430070 Wuhan, China
| | | | - Alisdair R Fernie
- Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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16
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Hudson CM, Cuenca Cambronero M, Moosmann M, Narwani A, Spaak P, Seehausen O, Matthews B. Environmentally independent selection for hybrids between divergent freshwater stickleback lineages in semi-natural ponds. J Evol Biol 2023; 36:1166-1184. [PMID: 37394735 DOI: 10.1111/jeb.14194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 05/03/2023] [Accepted: 05/31/2023] [Indexed: 07/04/2023]
Abstract
Hybridization following secondary contact of genetically divergent populations can influence the range expansion of invasive species, though specific outcomes depend on the environmental dependence of hybrid fitness. Here, using two genetically and ecologically divergent threespine stickleback lineages that differ in their history of freshwater colonization, we estimate fitness variation of parental lineages and hybrids in semi-natural freshwater ponds with contrasting histories of nutrient loading. In our experiment, we found that fish from the older freshwater lineage (Lake Geneva) and hybrids outperformed fish from the younger freshwater lineage (Lake Constance) in terms of both growth and survival, regardless of the environmental context of our ponds. Across all ponds, hybrids exhibited the highest survival. Although wild-caught adult populations differed in their functional and defence morphology, it is unclear which of these traits underlie the fitness differences observed among juveniles in our experiment. Overall, our work suggests that when hybrid fitness is insensitive to environmental conditions, as observed here, introgression may promote population expansion into unoccupied habitats and accelerate invasion success.
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Affiliation(s)
- Cameron Marshall Hudson
- Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biochemistry, Lucerne, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Zürich, Switzerland
| | - Maria Cuenca Cambronero
- Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biochemistry, Lucerne, Switzerland
- Aquatic Ecology Group, University of Vic, Central University of Catalonia, Vic, Spain
| | - Marvin Moosmann
- Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biochemistry, Lucerne, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Anita Narwani
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Zürich, Switzerland
| | - Piet Spaak
- Department of Aquatic Ecology, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Zürich, Switzerland
| | - Ole Seehausen
- Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biochemistry, Lucerne, Switzerland
- Division of Aquatic Ecology and Evolution, Institute of Ecology and Evolution, University of Bern, Bern, Switzerland
| | - Blake Matthews
- Department of Fish Ecology and Evolution, Eawag, Swiss Federal Institute of Aquatic Science and Technology, Center of Ecology, Evolution and Biochemistry, Lucerne, Switzerland
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17
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Rahimi M, AhmadiAfzadi M, Kordrostami M. Genetic diversity in Sickleweed (Falcaria vulgaris) and using stepwise regression to identify marker associated with traits. Sci Rep 2023; 13:12142. [PMID: 37495658 PMCID: PMC10372081 DOI: 10.1038/s41598-023-39419-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2023] [Accepted: 07/25/2023] [Indexed: 07/28/2023] Open
Abstract
One of the well-known medicinal plants in the Falcaria genus is Sickleweed. Falcaria species exhibit a high degree of genetic variability, posing challenges in the examination of genetic diversity due to the significant potential for hybridization and introgression among them. Utilizing morphological traits and molecular markers may prove to be a valuable approach in evaluating and harnessing germplasm, considering the current obstacles faced in breeding this medicinal herb. In 2021, fifteen Sickleweed populations were cultivated in pots under field conditions, employing a randomized complete block design with three replications. This aimed to assess genetic diversity and conduct marker-trait association analyses utilizing morpho-physiological characteristics and SSR markers. The Sickleweed populations displayed considerable genetic diversity across all traits. Through cluster analysis of traits and the utilization of the UPGMA method based on the Gower distance matrix, the population was classified into three distinct clusters. Upon examining all genotypes, 52 polymorphic bands were detected, with an average of 8.68 bands per primer. The average expected heterozygosity across all loci was 0.864, while the average PIC was 0.855. Molecular data analysis employing the Jaccard similarity index and UPGMA method revealed the division of Sickleweed populations into two major groups. Furthermore, the results of molecular variance analysis indicated that variation within the population exceeded that between populations. Thirty-two SSR fragments were found to be significantly associated with genomic regions controlling the studied traits, determined through the application of stepwise regression. Selection based on molecular markers offers a rapid method for breeding programs, with the genetic information obtained from these markers playing a crucial role. Therefore, alongside traits, selecting superior genotypes and populations of high value in breeding programs becomes feasible. The findings highlight that certain markers are linked to multiple traits, emphasizing the critical importance of this characteristic in plant breeding for the simultaneous improvement of numerous traits. The study's insights regarding markers hold potential for application in Sickleweed breeding programs.
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Affiliation(s)
- Mehdi Rahimi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran.
| | - Masoud AhmadiAfzadi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Mojtaba Kordrostami
- Nuclear Science and Technology Research Institute (NSTRI), Nuclear Agriculture Research School, Karaj, Iran
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18
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Adams J, de Vries M, van Eeuwijk F. Efficient Genomic Prediction of Yield and Dry Matter in Hybrid Potato. PLANTS (BASEL, SWITZERLAND) 2023; 12:2617. [PMID: 37514232 PMCID: PMC10385487 DOI: 10.3390/plants12142617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/27/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023]
Abstract
There is an ongoing endeavor within the potato breeding sector to rapidly adapt potato from a clonal polyploid crop to a diploid hybrid potato crop. While hybrid breeding allows for the efficient generation and selection of parental lines, it also increases breeding program complexity and results in longer breeding cycles. Over the past two decades, genomic prediction has revolutionized hybrid crop breeding through shorter breeding cycles, lower phenotyping costs, and better population improvement, resulting in increased genetic gains for genetically complex traits. In order to accelerate the genetic gains in hybrid potato, the proper implementation of genomic prediction is a crucial milestone in the rapid improvement of this crop. The authors of this paper set out to test genomic prediction in hybrid potato using current genotyped material with two alternative models: one model that predicts the general combining ability effects (GCA) and another which predicts both the general and specific combining ability effects (GCA+SCA). Using a training set comprising 769 hybrids and 456 genotyped parental lines, we found that reasonable a prediction accuracy could be achieved for most phenotypes with both zero common parents (ρ=0.36-0.61) and one (ρ=0.50-0.68) common parent between the training and test sets. There was no benefit with the inclusion of non-additive genetic effects in the GCA+SCA model despite SCA variance contributing between 9% and 19% of the total genetic variance. Genotype-by-environment interactions, while present, did not appear to affect the prediction accuracy, though prediction errors did vary across the trial's targets. These results suggest that genomically estimated breeding values on parental lines are sufficient for hybrid yield prediction.
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Affiliation(s)
- James Adams
- Biometris, Mathematical and Statistical Methods, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
- Solynta, Dreijenlaan 2, 6703 HA Wageningen, The Netherlands
| | | | - Fred van Eeuwijk
- Biometris, Mathematical and Statistical Methods, Wageningen University and Research, 6708 PB Wageningen, The Netherlands
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19
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Guo Y, Zhao G, Gao X, Zhang L, Zhang Y, Cai X, Yuan X, Guo X. CRISPR/Cas9 gene editing technology: a precise and efficient tool for crop quality improvement. PLANTA 2023; 258:36. [PMID: 37395789 DOI: 10.1007/s00425-023-04187-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 06/18/2023] [Indexed: 07/04/2023]
Abstract
MAIN CONCLUSION This review provides a direction for crop quality improvement and ideas for further research on the application of CRISPR/Cas9 gene editing technology for crop improvement. Various important crops, such as wheat, rice, soybean and tomato, are among the main sources of food and energy for humans. Breeders have long attempted to improve crop yield and quality through traditional breeding methods such as crossbreeding. However, crop breeding progress has been slow due to the limitations of traditional breeding methods. In recent years, clustered regularly spaced short palindromic repeat (CRISPR)/Cas9 gene editing technology has been continuously developed. And with the refinement of crop genome data, CRISPR/Cas9 technology has enabled significant breakthroughs in editing specific genes of crops due to its accuracy and efficiency. Precise editing of certain key genes in crops by means of CRISPR/Cas9 technology has improved crop quality and yield and has become a popular strategy for many breeders to focus on and adopt. In this paper, the present status and achievements of CRISPR/Cas9 gene technology as applied to the improvement of quality in several crops are reviewed. In addition, the shortcomings, challenges and development prospects of CRISPR/Cas9 gene editing technology are discussed.
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Affiliation(s)
- Yingxin Guo
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Guangdong Zhao
- College of Life Sciences, Linyi University, Linyi, 276000, Shandong, People's Republic of China
| | - Xing Gao
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Lin Zhang
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Yanan Zhang
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Xiaoming Cai
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China
| | - Xuejiao Yuan
- College of Biological and Chemical Engineering, Qilu Institute of Technology, Jinan, 250200, Shandong, People's Republic of China.
| | - Xingqi Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, 271018, Shandong, People's Republic of China.
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20
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Zhang Z, Wang L. A simulation framework for reciprocal recurrent selection-based hybrid breeding under transparent and opaque simulators. FRONTIERS IN PLANT SCIENCE 2023; 14:1174168. [PMID: 37441181 PMCID: PMC10333587 DOI: 10.3389/fpls.2023.1174168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 06/02/2023] [Indexed: 07/15/2023]
Abstract
Hybrid breeding is an established and effective process to improve offspring performance, while it is resource-intensive and time-consuming for the recurrent process in reality. To enable breeders and researchers to evaluate the effectiveness of competing decision-making strategies, we present a modular simulation framework for reciprocal recurrent selection-based hybrid breeding. Consisting of multiple modules such as heterotic separation, genomic prediction, and genomic selection, this simulation framework allows breeders to efficiently simulate the hybrid breeding process with multiple options of simulators and decision-making strategies. We also integrate the recently proposed concepts of transparent and opaque simulators into the framework in order to reflect the breeding process more realistically. Simulation results show the performance comparison among different breeding strategies under the two simulators.
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Affiliation(s)
- Zerui Zhang
- Program of Bioinformatics and Computational Biology, Iowa State University, Ames, IA, United States
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, IA, United States
- Department of Statistics, Iowa State University, Ames, IA, United States
| | - Lizhi Wang
- Program of Bioinformatics and Computational Biology, Iowa State University, Ames, IA, United States
- Department of Industrial and Manufacturing Systems Engineering, Iowa State University, Ames, IA, United States
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21
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Cyplik A, Bocianowski J. A Comparison of Methods to Estimate Additive-by-Additive-by-Additive of QTL×QTL×QTL Interaction Effects by Monte Carlo Simulation Studies. Int J Mol Sci 2023; 24:10043. [PMID: 37373191 DOI: 10.3390/ijms241210043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/05/2023] [Accepted: 06/11/2023] [Indexed: 06/29/2023] Open
Abstract
The goal of the breeding process is to obtain new genotypes with traits improved over the parental forms. Parameters related to the additive effect of genes as well as their interactions (such as epistasis of gene-by-gene interaction effect and additive-by-additive-by-additive of gene-by-gene-by-gene interaction effect) can influence decisions on the suitability of breeding material for this purpose. Understanding the genetic architecture of complex traits is a major challenge in the post-genomic era, especially for quantitative trait locus (QTL) effects, QTL-by-QTL interactions and QTL-by-QTL-by-QTL interactions. With regards to the comparing methods for estimating additive-by-additive-by-additive of QTL×QTL×QTL interaction effects by Monte Carlo simulation studies, there are no publications in the open literature. The parameter combinations assumed in the presented simulation studies represented 84 different experimental situations. The use of weighted regression may be the preferred method for estimating additive-by-additive-by-additive of QTL-QTL-QTL triples interaction effects, as it provides results closer to the true values of total additive-by-additive-by-additive interaction effects than using unweighted regression. This is also indicated by the obtained values of the determination coefficients of the proposed models.
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Affiliation(s)
- Adrian Cyplik
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland
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Labroo MR, Endelman JB, Gemenet DC, Werner CR, Gaynor RC, Covarrubias-Pazaran GE. Clonal diploid and autopolyploid breeding strategies to harness heterosis: insights from stochastic simulation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:147. [PMID: 37291402 DOI: 10.1007/s00122-023-04377-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 05/05/2023] [Indexed: 06/10/2023]
Abstract
KEY MESSAGE Reciprocal recurrent selection sometimes increases genetic gain per unit cost in clonal diploids with heterosis due to dominance, but it typically does not benefit autopolyploids. Breeding can change the dominance as well as additive genetic value of populations, thus utilizing heterosis. A common hybrid breeding strategy is reciprocal recurrent selection (RRS), in which parents of hybrids are typically recycled within pools based on general combining ability. However, the relative performances of RRS and other breeding strategies have not been thoroughly compared. RRS can have relatively increased costs and longer cycle lengths, but these are sometimes outweighed by its ability to harness heterosis due to dominance. Here, we used stochastic simulation to compare genetic gain per unit cost of RRS, terminal crossing, recurrent selection on breeding value, and recurrent selection on cross performance considering different amounts of population heterosis due to dominance, relative cycle lengths, time horizons, estimation methods, selection intensities, and ploidy levels. In diploids with phenotypic selection at high intensity, whether RRS was the optimal breeding strategy depended on the initial population heterosis. However, in diploids with rapid-cycling genomic selection at high intensity, RRS was the optimal breeding strategy after 50 years over almost all amounts of initial population heterosis under the study assumptions. Diploid RRS required more population heterosis to outperform other strategies as its relative cycle length increased and as selection intensity and time horizon decreased. The optimal strategy depended on selection intensity, a proxy for inbreeding rate. Use of diploid fully inbred parents vs. outbred parents with RRS typically did not affect genetic gain. In autopolyploids, RRS typically did not outperform one-pool strategies regardless of the initial population heterosis.
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Affiliation(s)
- Marlee R Labroo
- Excellence in Breeding Platform, Consultative Group of International Agricultural Research, Texcoco, Mexico
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Jeffrey B Endelman
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Dorcus C Gemenet
- Excellence in Breeding Platform, Consultative Group of International Agricultural Research, Texcoco, Mexico
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | - Christian R Werner
- Excellence in Breeding Platform, Consultative Group of International Agricultural Research, Texcoco, Mexico
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico
| | | | - Giovanny E Covarrubias-Pazaran
- Excellence in Breeding Platform, Consultative Group of International Agricultural Research, Texcoco, Mexico.
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, Mexico.
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23
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Dwivedi SL, Heslop-Harrison P, Spillane C, McKeown PC, Edwards D, Goldman I, Ortiz R. Evolutionary dynamics and adaptive benefits of deleterious mutations in crop gene pools. TRENDS IN PLANT SCIENCE 2023; 28:685-697. [PMID: 36764870 DOI: 10.1016/j.tplants.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 12/03/2022] [Accepted: 01/18/2023] [Indexed: 05/13/2023]
Abstract
Mutations with deleterious consequences in nature may be conditionally deleterious in crop plants. That is, while some genetic variants may reduce fitness under wild conditions and be subject to purifying selection, they can be under positive selection in domesticates. Such deleterious alleles can be plant breeding targets, particularly for complex traits. The difficulty of distinguishing favorable from unfavorable variants reduces the power of selection, while favorable trait variation and heterosis may be attributable to deleterious alleles. Here, we review the roles of deleterious mutations in crop breeding and discuss how they can be used as a new avenue for crop improvement with emerging genomic tools, including HapMaps and pangenome analysis, aiding the identification, removal, or exploitation of deleterious mutations.
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Affiliation(s)
| | - Pat Heslop-Harrison
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China; Department of Genetics and Genome Biology, University of Leicester, Leicester, LE1 7RH, UK
| | - Charles Spillane
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - Peter C McKeown
- Agriculture and Bioeconomy Research Centre, Ryan Institute, University of Galway, University Road, Galway, H91 REW4, Ireland
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA 6009, Australia
| | - Irwin Goldman
- Department of Horticulture, College of Agricultural and Life Sciences, University of Wisconsin Madison, WI 53706, USA
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, SE 23053, Sweden.
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24
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Sorsa Z, Mohammed W, Wegary D, Tarkegne A. Performances of three-way cross hybrids over their respective single crosses and related heterosis of maize ( Zea mays L.) hybrids evaluated in Ethiopia. Heliyon 2023; 9:e15513. [PMID: 37144203 PMCID: PMC10151324 DOI: 10.1016/j.heliyon.2023.e15513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/17/2023] [Accepted: 04/12/2023] [Indexed: 05/06/2023] Open
Abstract
Less attention had been given to the performances of three-way crosses and its comparative advantages of these hybrids over single crosses. This study was carried out to evaluate the performances of three-way crosses in comparison to single crosses for yield and related agronomic traits and to estimate the magnitude of heterosis. The trial was laid out in a simple alpha lattice design of 10 × 6 for lines, 6 × 5 for single crosses (SC), and 9 × 5 for three way-crosses and planted in adjacent plots in the 2019 cropping season in three locations namely Ambo, Abala-Farcha and Melkassa. Single cross hybrids showed a highly significant (P<1%) variation for grain yield, plant height, ear height, and ear length at three locations. These single cross hybrids had showed also a highly significant genotype by environment interaction (P < 1%) for grain yield, plant height, ear height and kernel per ear. Regarding three-way crosses, there was a significant variation (P<5%) on grain yield in Ambo and Melkassa but on ear height and rows per ear in Abala-Faracho. The genotype × environment interaction was significantly varied for grain yield, ear height and ear length. In the comparison, 80% crosses in Ambo, 73% in Abala-Faracho and 67% in Melkassa showed that three-way crosses were better in their performance than that of their respective single crosses. On the other hand, the single crosses that out-performed their respective three-way crosses were higher in Melkassa than Abala-Faracho and the least were reported from Ambo. Similarly, the maximum better and mid-parent heterosis was from single cross 1(769%) in Ambo and single cross 7 (104%) in Melkassa whereas TWC 14 (52%) and TWC 24 (78%) were the highest better and mid-parent heterosis, respectively in Ambo, TWC1 (56%), and TWC30 (25%) were the highest BPH, and MPH, respectively in Melkassa.
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Affiliation(s)
- Zemach Sorsa
- Department of Plant Science, Wolaita Sodo University, Wolaita Sodo, Ethiopia
- Corresponding author.
| | - Wassu Mohammed
- School of Plant Sciences, Haramaya University, Dire Dawa, Ethiopia
| | - Dagne Wegary
- International Maize and Wheat Improvement Centre (CIMMYT), Harare, Zimbabwe
| | - Amsal Tarkegne
- Zambia Seed Company Limited, Ingwezi 11066A, Roma, Lusaka, Zambia
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25
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Lanctot A. A lotus by any other color: Gene regulation divergence in lotus petal development. PLANT PHYSIOLOGY 2023; 191:1470-1472. [PMID: 36567508 PMCID: PMC10022601 DOI: 10.1093/plphys/kiac596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 12/06/2022] [Indexed: 06/17/2023]
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26
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Cortés AJ, Barnaby JY. Editorial: Harnessing genebanks: High-throughput phenotyping and genotyping of crop wild relatives and landraces. FRONTIERS IN PLANT SCIENCE 2023; 14:1149469. [PMID: 36968416 PMCID: PMC10036837 DOI: 10.3389/fpls.2023.1149469] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/22/2023] [Accepted: 01/26/2023] [Indexed: 06/18/2023]
Affiliation(s)
- Andrés J. Cortés
- Corporación Colombiana de Investigación Agropecuaria – AGROSAVIA, C.I. La Selva, Rionegro, Colombia
| | - Jinyoung Y. Barnaby
- U.S. Department of Agriculture, U.S. National Arboretum, Floral and Nursery Plants Research Unit, Beltsville, MD, United States
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Castro-Urrea FA, Urricariet MP, Stefanova KT, Li L, Moss WM, Guzzomi AL, Sass O, Siddique KHM, Cowling WA. Accuracy of Selection in Early Generations of Field Pea Breeding Increases by Exploiting the Information Contained in Correlated Traits. PLANTS (BASEL, SWITZERLAND) 2023; 12:1141. [PMID: 36903999 PMCID: PMC10005560 DOI: 10.3390/plants12051141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Accuracy of predicted breeding values (PBV) for low heritability traits may be increased in early generations by exploiting the information available in correlated traits. We compared the accuracy of PBV for 10 correlated traits with low to medium narrow-sense heritability (h2) in a genetically diverse field pea (Pisum sativum L.) population after univariate or multivariate linear mixed model (MLMM) analysis with pedigree information. In the contra-season, we crossed and selfed S1 parent plants, and in the main season we evaluated spaced plants of S0 cross progeny and S2+ (S2 or higher) self progeny of parent plants for the 10 traits. Stem strength traits included stem buckling (SB) (h2 = 0.05), compressed stem thickness (CST) (h2 = 0.12), internode length (IL) (h2 = 0.61) and angle of the main stem above horizontal at first flower (EAngle) (h2 = 0.46). Significant genetic correlations of the additive effects occurred between SB and CST (0.61), IL and EAngle (-0.90) and IL and CST (-0.36). The average accuracy of PBVs in S0 progeny increased from 0.799 to 0.841 and in S2+ progeny increased from 0.835 to 0.875 in univariate vs MLMM, respectively. An optimized mating design was constructed with optimal contribution selection based on an index of PBV for the 10 traits, and predicted genetic gain in the next cycle ranged from 1.4% (SB), 5.0% (CST), 10.5% (EAngle) and -10.5% (IL), with low achieved parental coancestry of 0.12. MLMM improved the potential genetic gain in annual cycles of early generation selection in field pea by increasing the accuracy of PBV.
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Affiliation(s)
- Felipe A. Castro-Urrea
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Maria P. Urricariet
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
- General Genetics Unit, Pontificia Universidad Católica Argentina, Buenos Aires C1107AAZ, Argentina
| | - Katia T. Stefanova
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- SAGI West, School of Molecular and Life Sciences, Curtin University, Perth, WA 6845, Australia
| | - Li Li
- Animal Genetics and Breeding Unit, University of New England, Armidale, NSW 2351, Australia
| | - Wesley M. Moss
- Centre for Engineering Innovation: Agriculture & Ecological Restoration, The University of Western Australia, Shenton Park, WA 6008, Australia
- School of Engineering, The University of Western Australia, Perth, WA 6009, Australia
| | - Andrew L. Guzzomi
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- Centre for Engineering Innovation: Agriculture & Ecological Restoration, The University of Western Australia, Shenton Park, WA 6008, Australia
- School of Engineering, The University of Western Australia, Perth, WA 6009, Australia
| | - Olaf Sass
- Norddeutsche Pflanzenzucht Hans-Georg Lembke KG, Hohenlieth-Hof 1, 24363 Holtsee, Germany
| | - Kadambot H. M. Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
| | - Wallace A. Cowling
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia
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28
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Jiménez NP, Feldmann MJ, Famula RA, Pincot DDA, Bjornson M, Cole GS, Knapp SJ. Harnessing underutilized gene bank diversity and genomic prediction of cross usefulness to enhance resistance to Phytophthora cactorum in strawberry. THE PLANT GENOME 2023; 16:e20275. [PMID: 36480594 DOI: 10.1002/tpg2.20275] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/19/2022] [Indexed: 05/10/2023]
Abstract
The development of strawberry (Fragaria × ananassa Duchesne ex Rozier) cultivars resistant to Phytophthora crown rot (PhCR), a devastating disease caused by the soil-borne pathogen Phytophthora cactorum (Lebert & Cohn) J. Schröt., has been challenging partly because the resistance phenotypes are quantitative and only moderately heritable. To develop deeper insights into the genetics of resistance and build the foundation for applying genomic selection, a genetically diverse training population was screened for resistance to California isolates of the pathogen. Here we show that genetic gains in breeding for resistance to PhCR have been negligible (3% of the cultivars tested were highly resistant and none surpassed early 20th century cultivars). Narrow-sense genomic heritability for PhCR resistance ranged from 0.41 to 0.75 among training population individuals. Using multivariate genome-wide association studies (GWAS), we identified a large-effect locus (predicted to be RPc2) that explained 43.6-51.6% of the genetic variance, was necessary but not sufficient for resistance, and was associated with calcium channel and other candidate genes with known plant defense functions. The addition of underutilized gene bank resources to our training population doubled additive genetic variance, increased the accuracy of genomic selection, and enabled the discovery of individuals carrying favorable alleles that are either rare or not present in modern cultivars. The incorporation of an RPc2-associated single-nucleotide polymorphism (SNP) as a fixed effect increased genomic prediction accuracy from 0.40 to 0.55. Finally, we show that parent selection using genomic-estimated breeding values, genetic variances, and cross usefulness holds promise for enhancing resistance to PhCR in strawberry.
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Affiliation(s)
- Nicolás P Jiménez
- Dep. of Plant Sciences, Univ. of California, One Shields Ave, Davis, CA, 95616, USA
| | - Mitchell J Feldmann
- Dep. of Plant Sciences, Univ. of California, One Shields Ave, Davis, CA, 95616, USA
| | - Randi A Famula
- Dep. of Plant Sciences, Univ. of California, One Shields Ave, Davis, CA, 95616, USA
| | - Dominique D A Pincot
- Dep. of Plant Sciences, Univ. of California, One Shields Ave, Davis, CA, 95616, USA
| | - Marta Bjornson
- Dep. of Plant Sciences, Univ. of California, One Shields Ave, Davis, CA, 95616, USA
| | - Glenn S Cole
- Dep. of Plant Sciences, Univ. of California, One Shields Ave, Davis, CA, 95616, USA
| | - Steven J Knapp
- Dep. of Plant Sciences, Univ. of California, One Shields Ave, Davis, CA, 95616, USA
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29
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Rahimi M, Ranjbaran E. Investigating the geographical, phenotypic and genetic diversity of Sickleweed populations by bioclimatic parameters, morphological traits and SCoT molecular markers. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:421-433. [PMID: 37033768 PMCID: PMC10073401 DOI: 10.1007/s12298-023-01296-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/20/2023] [Accepted: 03/11/2023] [Indexed: 06/19/2023]
Abstract
Sickleweed (Falcaria vulgaris) is important due to its nutritional value and medicinal effects on the human body. The 15 different Sickleweed populations were collected based on an unbalanced nest design with 10 replications and nine morphological traits were measured on them. The diversity was investigated with 15 primers of SCoT marker. The genetic diversity was investigated by ANOVA, cluster analysis and Bayesian statistical model based on morphological traits, bioclimatic and SCoT. Grouping the study areas based on bioclimatic parameters by UPGMA method showed that these areas were divided into two groups and were similar in terms of climatic similarities and bioclimatic information. The results of analysis of variance showed that there was a significant difference between populations at the level of one percent for the studied traits. The cluster analysis based traits by the UPGMA method divided these populations into two groups. The phenotypic diversity of these populations was largely consistent with the geographical diversity. The primers used for SCoT marker produced 137 polymorphic bands on the populations, The UPGMA cluster analysis with molecular data placed the studied populations into three groups and four subgroups. Grouping based on the Bayesian method placed the populations into nine groups, although the populations were not differentiated and were a mixture of all nine groups. High genetic diversity for the studied Sickleweed populations have showed valuable insights into the evolution of this plant and provides basic data for designing appropriate management practices for breeding Sickleweed populations.
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Affiliation(s)
- Mehdi Rahimi
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
| | - Elaheh Ranjbaran
- Department of Biotechnology, Institute of Science and High Technology and Environmental Sciences, Graduate University of Advanced Technology, Kerman, Iran
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30
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dos Santos Junior DR, do Amaral Junior AT, de Lima VJ, Leite JT, Bispo RB, Azeredo VC, de Almeida Filho JE, Kamphorst SH, Viana FN, Ribeiro RM, Viana AP, Gravina GDA. Recurrent Interpopulation Selection in Popcorn: From Heterosis to Genetic Gains. PLANTS (BASEL, SWITZERLAND) 2023; 12:1056. [PMID: 36903916 PMCID: PMC10005362 DOI: 10.3390/plants12051056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/09/2023] [Accepted: 02/15/2023] [Indexed: 06/18/2023]
Abstract
In view of the need to develop new popcorn cultivars and considering the uncertainties in choosing the most appropriate breeding methods to ensure consistent genetic progress, simultaneously for both popping expansion and grain yield, this study addressed the efficiency of interpopulation recurrent selection regarding genetic gains, the study of the response in genetic parameters as well as heterotic effects on the control of the main agronomic traits of popcorn. Two populations were established, Pop1 and Pop2. A total of 324 treatments were evaluated, which consisted of 200 half-sib families (100 from Pop1 and 100 from Pop2), 100 full-sib families from the two populations and 24 controls. The field experiment was arranged in a lattice design with three replications in two environments, in the north and northwest regions of the State of Rio de Janeiro, Brazil. The genotype × environment interaction was partitioned and the genetic parameters, heterosis and predicted gains were estimated by the Mulamba and Mock index, based on selection results in both environments. The genetic parameters detected variability that can be explored in successive interpopulation recurrent selection cycles. Exploring heterosis for GY, PE and yield components is a promising option to increase grain yield and quality. The Mulamba and Mock index was efficient in predicting the genetic gains in GY and PE. Interpopulation recurrent selection proved effective to provide genetic gains for traits with predominantly additive and dominance inheritance.
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Huo X, Wang J, Zhang L. Combined QTL mapping on bi-parental immortalized heterozygous populations to detect the genetic architecture on heterosis. FRONTIERS IN PLANT SCIENCE 2023; 14:1157778. [PMID: 37082336 PMCID: PMC10112513 DOI: 10.3389/fpls.2023.1157778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/20/2023] [Indexed: 05/03/2023]
Abstract
From bi-parental pure-inbred lines (PIL), immortalized backcross (i.e., IB1 and IB2, representing the two directions of backcrossing) and F2 (i.e., IF2) populations can be developed. These populations are suitable for genetic studies on heterosis, due to the present of both homozygous and heterozygous genotypes, and in the meantime allow repeated phenotyping trials across multiple locations and years. In this study, we developed a combined approach of quantitative trait locus (QTL) mapping, when some or all of the four immortalized populations (i.e., PIL, IB1, IB2, and IF2) are available. To estimate the additive and dominant effects simultaneously and accurately, suitable transformations are made on phenotypic values from different populations. When IB1 and IB2 are present, summation and subtraction are used. When IF2 and PIL are available, mid-parental values and mid-parental heterosis are used. One-dimensional genomic scanning is performed to detect the additive and dominant QTLs, based on the algorithm of inclusive composite interval mapping (ICIM). The proposed approach was applied to one IF2 population together with PIL in maize, and identified ten QTLs on ear length, showing varied degrees of dominance. Simulation studies indicated the proposed approach is similar to or better than individual population mapping by QTL detection power, false discovery rate (FDR), and estimated QTL position and effects.
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Affiliation(s)
- Xuexue Huo
- National Key Facility for Crop Gene Resources and Genetic Improvement, and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Jiankang Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences (CAAS), Sanya, Hainan, China
- *Correspondence: Jiankang Wang, ; Luyan Zhang,
| | - Luyan Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, and Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
- *Correspondence: Jiankang Wang, ; Luyan Zhang,
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Ge D, Wen Z, Feijó A, Lissovsky A, Zhang W, Cheng J, Yan C, She H, Zhang D, Cheng Y, Lu L, Wu X, Mu D, Zhang Y, Xia L, Qu Y, Vogler AP, Yang Q. Genomic Consequences of and Demographic Response to Pervasive Hybridization Over Time in Climate-Sensitive Pikas. Mol Biol Evol 2022; 40:6958644. [PMID: 36562771 PMCID: PMC9847633 DOI: 10.1093/molbev/msac274] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 11/13/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022] Open
Abstract
Rare and geographically restricted species may be vulnerable to genetic effects from inbreeding depression in small populations or from genetic swamping through hybridization with common species, but a third possibility is that selective gene flow can restore fitness (genetic rescue). Climate-sensitive pikas (Ochotona spp.) of the Qinghai-Tibetan Plateau (QHTP) and its vicinity have been reduced to residual populations through the movement of climatic zones during the Pleistocene and recent anthropogenic disturbance, whereas the plateau pika (O. curzoniae) remains common. Population-level whole-genome sequencing (n = 142) of six closely related species in the subgenus Ochotona revealed several phases of ancient introgression, lineage replacement, and bidirectional introgression. The strength of gene flow was the greatest from the dominant O. curzoniae to ecologically distinct species in areas peripheral to the QHTP. Genetic analyses were consistent with environmental reconstructions of past population movements. Recurrent periods of introgression throughout the Pleistocene revealed an increase in genetic variation at first but subsequent loss of genetic variation in later phases. Enhanced dispersion of introgressed genomic regions apparently contributed to demographic recovery in three peripheral species that underwent range shifts following climate oscillations on the QHTP, although it failed to drive recovery of northeastern O. dauurica and geographically isolated O. sikimaria. Our findings highlight differences in timescale and environmental background to determine the consequence of hybridization and the unique role of the QHTP in conserving key evolutionary processes of sky island species.
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Affiliation(s)
| | | | | | | | | | - Jilong Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Chaochao Yan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, China
| | - Huishang She
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Dezhi Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Yalin Cheng
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Liang Lu
- State Key Laboratory for Infectious Diseases Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China
| | - Xinlai Wu
- The Key Laboratory of Zoological Systematics and Application, School of Life Science, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Danping Mu
- Xinjiang Key Laboratory of Biological Resources and Genetic Engineering, College of Life Science and Technology, Xinjiang University, Urumqi, 830046, China
| | - Yubo Zhang
- State Key Laboratory for Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences at College of Life Sciences, Peking University, Beijing, 100871, China
| | - Lin Xia
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
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Adigoun RFR, Houdegbe AC, Fassinou Hotegni NV, Segnon AC, N'Danikou S, Adjé CAO, Adadja RPM, Achigan-Dako EG. Enabling effective maize seed system in low-income countries of West Africa: Insights from Benin. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.1045629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
IntroductionAccess to high-quality seeds remains a key constraint to the intensification of crop production in low-income countries. In this study, we analyzed maize seed production and distribution systems in Benin to identify leverage points for effective seed systems, a prerequisite for improving maize production.MethodsSemi-structured interviews were conducted with 81 seed producers selected in seven municipalities across the three phytogeographical zones of Benin. Key informant interviews were also conducted with ten public and private stakeholders involved in maize seed systems in Benin.Results and discussionFindings showed that the legal and institutional frameworks governing seed systems in Benin were recently reinforced with a national seed policy, the creation and operationalization of the National Committee of Plant Seeds and the existence of regulations and rules on the production, quality control, certification, trade, and packaging of seeds. In addition, enabling conditions to facilitate the involvement of the private sector have been greatly improved with the revision of modalities for obtaining approval for the production and distribution of seeds in Benin. While the seed sector is improving and both public and private stakeholders are involved in maize seed production and distribution, synergies among stakeholders need to be strengthened. Strengthening business and marketing skills of seed producers through training and promoting the comparative advantages of improved seeds in increasing yield and production among maize farmers could be a promising avenue. Connecting seed producers with maize farmers' organizations coupled with ICT-based agro-advisories could boost the development of the maize seed sector, and ultimately the maize value chain.
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Orantes-Bonilla M, Makhoul M, Lee H, Chawla HS, Vollrath P, Langstroff A, Sedlazeck FJ, Zou J, Snowdon RJ. Frequent spontaneous structural rearrangements promote rapid genome diversification in a Brassica napus F1 generation. FRONTIERS IN PLANT SCIENCE 2022; 13:1057953. [PMID: 36466276 PMCID: PMC9716091 DOI: 10.3389/fpls.2022.1057953] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 10/31/2022] [Indexed: 05/26/2023]
Abstract
In a cross between two homozygous Brassica napus plants of synthetic and natural origin, we demonstrate that novel structural genome variants from the synthetic parent cause immediate genome diversification among F1 offspring. Long read sequencing in twelve F1 sister plants revealed five large-scale structural rearrangements where both parents carried different homozygous alleles but the heterozygous F1 genomes were not identical heterozygotes as expected. Such spontaneous rearrangements were part of homoeologous exchanges or segmental deletions and were identified in different, individual F1 plants. The variants caused deletions, gene copy-number variations, diverging methylation patterns and other structural changes in large numbers of genes and may have been causal for unexpected phenotypic variation between individual F1 sister plants, for example strong divergence of plant height and leaf area. This example supports the hypothesis that spontaneous de novo structural rearrangements after de novo polyploidization can rapidly overcome intense allopolyploidization bottlenecks to re-expand crops genetic diversity for ecogeographical expansion and human selection. The findings imply that natural genome restructuring in allopolyploid plants from interspecific hybridization, a common approach in plant breeding, can have a considerably more drastic impact on genetic diversity in agricultural ecosystems than extremely precise, biotechnological genome modifications.
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Affiliation(s)
- Mauricio Orantes-Bonilla
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Manar Makhoul
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - HueyTyng Lee
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Harmeet Singh Chawla
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Paul Vollrath
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Anna Langstroff
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Fritz J. Sedlazeck
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, United States
| | - Jun Zou
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science & Technology, Huazhong Agricultural University, Wuhan, China
| | - Rod J. Snowdon
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
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Vinci G, Marques I, Rodrigues AP, Martins S, Leitão AE, Semedo MC, Silva MJ, Lidon FC, DaMatta FM, Ribeiro-Barros AI, Ramalho JC. Protective Responses at the Biochemical and Molecular Level Differ between a Coffea arabica L. Hybrid and Its Parental Genotypes to Supra-Optimal Temperatures and Elevated Air [CO 2]. PLANTS (BASEL, SWITZERLAND) 2022; 11:2702. [PMID: 36297726 PMCID: PMC9610391 DOI: 10.3390/plants11202702] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/06/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
Climate changes with global warming associated with rising atmospheric [CO2] can strongly impact crop performance, including coffee, which is one of the most world's traded agricultural commodities. Therefore, it is of utmost importance to understand the mechanisms of heat tolerance and the potential role of elevated air CO2 (eCO2) in the coffee plant response, particularly regarding the antioxidant and other protective mechanisms, which are crucial for coffee plant acclimation. For that, plants of Coffea arabica cv. Geisha 3, cv. Marsellesa and their hybrid (Geisha 3 × Marsellesa) were grown for 2 years at 25/20 °C (day/night), under 400 (ambient CO2, aCO2) or 700 µL (elevated CO2, eCO2) CO2 L-1, and then gradually submitted to a temperature increase up to 42/30 °C, followed by recovery periods of 4 (Rec4) and 14 days (Rec14). Heat (37/28 °C and/or 42/30 °C) was the major driver of the response of the studied protective molecules and associated genes in all genotypes. That was the case for carotenoids (mostly neoxanthin and lutein), but the maximal (α + β) carotenes pool was found at 37/28 °C only in Marsellesa. All genes (except VDE) encoding for antioxidative enzymes (catalase, CAT; superoxide dismutases, CuSODs; ascorbate peroxidases, APX) or other protective proteins (HSP70, ELIP, Chape20, Chape60) were strongly up-regulated at 37/28 °C, and, especially, at 42/30 °C, in all genotypes, but with maximal transcription in Hybrid plants. Accordingly, heat greatly stimulated the activity of APX and CAT (all genotypes) and glutathione reductase (Geisha3, Hybrid) but not of SOD. Notably, CAT activity increased even at 42/30 °C, concomitantly with a strongly declined APX activity. Therefore, increased thermotolerance might arise through the reinforcement of some ROS-scavenging enzymes and other protective molecules (HSP70, ELIP, Chape20, Chape60). Plants showed low responsiveness to single eCO2 under unstressed conditions, while heat promoted changes in aCO2 plants. Only eCO2 Marsellesa plants showed greater contents of lutein, the pool of the xanthophyll cycle components (V + A + Z), and β-carotene, compared to aCO2 plants at 42/30 °C. This, together with a lower CAT activity, suggests a lower presence of H2O2, likely also associated with the higher photochemical use of energy under eCO2. An incomplete heat stress recovery seemed evident, especially in aCO2 plants, as judged by the maintenance of the greater expression of all genes in all genotypes and increased levels of zeaxanthin (Marsellesa and Hybrid) relative to their initial controls. Altogether, heat was the main response driver of the addressed protective molecules and genes, whereas eCO2 usually attenuated the heat response and promoted a better recovery. Hybrid plants showed stronger gene expression responses, especially at the highest temperature, when compared to their parental genotypes, but altogether, Marsellesa showed a greater acclimation potential. The reinforcement of antioxidative and other protective molecules are, therefore, useful biomarkers to be included in breeding and selection programs to obtain coffee genotypes to thrive under global warming conditions, thus contributing to improved crop sustainability.
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Affiliation(s)
- Gabriella Vinci
- Department of Biological, Geological and Environmental Sciences (BiGeA), Alma Mater Studiorum, The University of Bologna, Via Irnerio 42, 40126 Bologna, Italy
- Plant Stress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Oeiras, 2784-505 Lisboa, Portugal
- Plant Stress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Isabel Marques
- Plant Stress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Oeiras, 2784-505 Lisboa, Portugal
- Plant Stress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Ana P. Rodrigues
- Plant Stress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Oeiras, 2784-505 Lisboa, Portugal
- Plant Stress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Tapada da Ajuda, 1349-017 Lisboa, Portugal
| | - Sónia Martins
- Departamento de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516 Caparica, Portugal
| | - António E. Leitão
- Plant Stress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Oeiras, 2784-505 Lisboa, Portugal
- Plant Stress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Tapada da Ajuda, 1349-017 Lisboa, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516 Caparica, Portugal
| | - Magda C. Semedo
- Departamento de Engenharia Química, Instituto Superior de Engenharia de Lisboa, Instituto Politécnico de Lisboa, R. Conselheiro Emídio Navarro 1, 1959-007 Lisboa, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516 Caparica, Portugal
| | - Maria J. Silva
- Plant Stress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Oeiras, 2784-505 Lisboa, Portugal
- Plant Stress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Tapada da Ajuda, 1349-017 Lisboa, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516 Caparica, Portugal
| | - Fernando C. Lidon
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516 Caparica, Portugal
| | - Fábio M. DaMatta
- Departamento de Biologia Vegetal, Universidade Federal Viçosa (UFV), Viçosa 36570-900, MG, Brazil
| | - Ana I. Ribeiro-Barros
- Plant Stress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Oeiras, 2784-505 Lisboa, Portugal
- Plant Stress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Tapada da Ajuda, 1349-017 Lisboa, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516 Caparica, Portugal
| | - José C. Ramalho
- Plant Stress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Oeiras, 2784-505 Lisboa, Portugal
- Plant Stress & Biodiversity Lab, Centro de Estudos Florestais (CEF), Instituto Superior Agronomia (ISA), Universidade de Lisboa (ULisboa), Quinta do Marquês, Av. República, Tapada da Ajuda, 1349-017 Lisboa, Portugal
- Unidade de Geobiociências, Geoengenharias e Geotecnologias (GeoBioTec), Faculdade de Ciências e Tecnologia (FCT), Universidade NOVA de Lisboa (UNL), Monte de Caparica, 2829-516 Caparica, Portugal
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Xiao R, Yuan Y, Xia H, Ge Q, Chen L, Zhu F, Xu J, Wang X, Fan Y, Wang Q, Yang Y, Chen K. Comparative transcriptome and proteome reveal synergistic functions of differentially expressed genes and proteins implicated in an over-dominant silkworm heterosis of increased silk yield. INSECT MOLECULAR BIOLOGY 2022; 31:551-567. [PMID: 35445454 DOI: 10.1111/imb.12779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 03/09/2022] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
We previously observed an over-dominant silkworm heterosis of increased yield in a cross of Bombyx mori nuclear polyhydrosis virus-resistant strain NB with a susceptible strain 306. In the present study, we found that heterosis also exists in crosses of NB with other susceptible strains, indicating it is a more general phenomenon. We performed comparative transcriptome and proteome and identified 1624 differentially expressed genes (DEGs) and 298 differentially expressed proteins (DEPs) in silk glands between parents and F1 hybrids, of which 24 DEGs/DEPs showed consistent expression at mRNA and protein levels revealed by Venn joint analysis. Their expressions are completely non-additive, mainly transgressive and under low-parent, suggesting recombination of parental genomes may be the major genetic mechanism for the heterosis. GO and KEGG analyses revealed that they may function in generally similar but distinctive aspects of metabolisms and processes with signal transduction and translation being most affected. Notably, they may not only up-regulate biosynthesis and transport of silk proteins but also down-regulate other unrelated processes, synergistically and globally remodelling the silk gland to increase yield and cause the heterosis. Our findings contribute insights into the understanding of silkworm heterosis and silk gland development and provide targets for transgenic manipulation to further increase the silk yield.
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Affiliation(s)
- Rui Xiao
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yi Yuan
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Hengchuan Xia
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Qi Ge
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Liang Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Feifei Zhu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Jia Xu
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Xueqi Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yixuan Fan
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Qiang Wang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Yanhua Yang
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, Zhenjiang, Jiangsu, China
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Lye Z, Choi JY, Purugganan MD. Deleterious mutations and the rare allele burden on rice gene expression. Mol Biol Evol 2022; 39:6693943. [PMID: 36073358 PMCID: PMC9512150 DOI: 10.1093/molbev/msac193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Deleterious genetic variation is maintained in populations at low frequencies. Under a model of stabilizing selection, rare (and presumably deleterious) genetic variants are associated with increase or decrease in gene expression from some intermediate optimum. We investigate this phenomenon in a population of largely Oryza sativa ssp. indica rice landraces under normal unstressed wet and stressful drought field conditions. We include single nucleotide polymorphisms, insertion/deletion mutations, and structural variants in our analysis and find a stronger association between rare variants and gene expression outliers under the stress condition. We also show an association of the strength of this rare variant effect with linkage, gene expression levels, network connectivity, local recombination rate, and fitness consequence scores, consistent with the stabilizing selection model of gene expression.
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Affiliation(s)
- Zoe Lye
- Center for Genomics and Systems Biology, New York University, New York, NY 10003
| | - Jae Young Choi
- Center for Genomics and Systems Biology, New York University, New York, NY 10003
| | - Michael D Purugganan
- Center for Genomics and Systems Biology, New York University, New York, NY 10003.,Center for Genomics and Systems Biology, New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
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Heterosis for capsacinoids accumulation in chili pepper hybrids is dependent on parent-of-origin effect. Sci Rep 2022; 12:14450. [PMID: 36002476 PMCID: PMC9402712 DOI: 10.1038/s41598-022-18711-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 08/18/2022] [Indexed: 11/09/2022] Open
Abstract
Heterosis for agronomic traits is a widespread phenomenon that underpins hybrid crop breeding. However, heterosis at the level of cellular metabolites has not yet been fully explored. Some metabolites are highly sought after, like capsaicinoids found in peppers of the Capsicum genus, which confer the characteristic pungent ('hot') flavour of the fruits. We analysed the metabolic profile of the fruit placenta and pericarp of inter- and intra-specific hybrids of two species of Capsicum peppers, C. chinense (cv. Habanero and cv. Biquinho) and C. annuum var. annuum (cv. Jalapeño and cv. Cascadura Ikeda) in complete diallel crosses with reciprocals. The parents and hybrids were grown in a glasshouse and the profile of primary metabolites (sugars, amino acids and organic acids) and capsaicinoids was generated via gas chromatography-time of flight-mass spectrometry (GC-TOF-MS) and ultra-performance liquid chromatography coupled to a mass spectrometer (UPLC-MS), respectively. We found considerable heterotic effects specifically for capsaicinoids accumulation in the fruit placenta of the hybrids, including those derived from non-pungent parents. Furthermore, a large fraction of fruit primary metabolism was influenced by the specific cross combination, with marked parent-of-origin effects, i.e. whether a specific genotype was used as the pistillate or pollen parent. The differences in metabolite levels between the hybrids and their parents provide a snapshot of heterosis for primary and secondary metabolites and may contribute to explain the manifestation of whole-plant heterotic phenotypes.
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Nerkar G, Devarumath S, Purankar M, Kumar A, Valarmathi R, Devarumath R, Appunu C. Advances in Crop Breeding Through Precision Genome Editing. Front Genet 2022; 13:880195. [PMID: 35910205 PMCID: PMC9329802 DOI: 10.3389/fgene.2022.880195] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 05/02/2022] [Indexed: 11/13/2022] Open
Abstract
The global climate change and unfavourable abiotic and biotic factors are limiting agricultural productivity and therefore intensifying the challenges for crop scientists to meet the rising demand for global food supply. The introduction of applied genetics to agriculture through plant breeding facilitated the development of hybrid varieties with improved crop productivity. However, the development of new varieties with the existing gene pools poses a challenge for crop breeders. Genetic engineering holds the potential to broaden genetic diversity by the introduction of new genes into crops. But the random insertion of foreign DNA into the plant's nuclear genome often leads to transgene silencing. Recent advances in the field of plant breeding include the development of a new breeding technique called genome editing. Genome editing technologies have emerged as powerful tools to precisely modify the crop genomes at specific sites in the genome, which has been the longstanding goal of plant breeders. The precise modification of the target genome, the absence of foreign DNA in the genome-edited plants, and the faster and cheaper method of genome modification are the remarkable features of the genome-editing technology that have resulted in its widespread application in crop breeding in less than a decade. This review focuses on the advances in crop breeding through precision genome editing. This review includes: an overview of the different breeding approaches for crop improvement; genome editing tools and their mechanism of action and application of the most widely used genome editing technology, CRISPR/Cas9, for crop improvement especially for agronomic traits such as disease resistance, abiotic stress tolerance, herbicide tolerance, yield and quality improvement, reduction of anti-nutrients, and improved shelf life; and an update on the regulatory approval of the genome-edited crops. This review also throws a light on development of high-yielding climate-resilient crops through precision genome editing.
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Affiliation(s)
- Gauri Nerkar
- Molecular Biology and Genetic Engineering Laboratory, Vasantdada Sugar Institute, Pune, India
| | - Suman Devarumath
- Vidya Pratishthan's College of Agricultural Biotechnology, Baramati, India
| | - Madhavi Purankar
- Molecular Biology and Genetic Engineering Laboratory, Vasantdada Sugar Institute, Pune, India
| | - Atul Kumar
- Molecular Biology and Genetic Engineering Laboratory, Vasantdada Sugar Institute, Pune, India
| | - R Valarmathi
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
| | - Rachayya Devarumath
- Molecular Biology and Genetic Engineering Laboratory, Vasantdada Sugar Institute, Pune, India
| | - C Appunu
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
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Ter Steeg EMS, Struik PC, Visser RGF, Lindhout P. Crucial factors for the feasibility of commercial hybrid breeding in food crops. NATURE PLANTS 2022; 8:463-473. [PMID: 35513713 DOI: 10.1038/s41477-022-01142-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 03/22/2022] [Indexed: 05/26/2023]
Abstract
There is an ongoing societal debate about plant breeding systems and their impact on stakeholders in food systems. Hybrid breeding and hybrid seed have become controversial topics as they are believed to mostly serve high-tech agricultural systems. This article focuses on the perspective of commercial plant breeders when developing new cultivars of food crops. Arguably, hybrid breeding is the most effective breeding system for genetic improvement of crops, enhancing yields, improving product quality and increasing resistance against (a)biotic stresses. Nonetheless, hybrid breeding is not commercially applied in all crops. We analyse how biological and economic factors determine whether a commercial plant breeder opts for the hybrid system or not. We show that the commercial feasibility of hybrid breeding depends on the crop and business case. In conclusion, the commercial application of hybrid breeding in crops seems to be hampered mostly by high costs of seed production. Case studies regarding the hybrid transitions in maize, wheat and potato are included to illustrate these findings.
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Affiliation(s)
- Emily M S Ter Steeg
- Development Economics, Wageningen University & Research, Wageningen, the Netherlands.
| | - Paul C Struik
- Centre for Crop Systems Analysis, Wageningen University & Research, Wageningen, the Netherlands
| | - Richard G F Visser
- Plant Breeding, Wageningen University & Research, Wageningen, the Netherlands
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Genetic variability, combining ability and molecular diversity-based parental line selection for heterosis breeding in field corn (Zea mays L.). Mol Biol Rep 2022; 49:4517-4524. [PMID: 35474052 PMCID: PMC9262758 DOI: 10.1007/s11033-022-07295-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 02/23/2022] [Indexed: 11/04/2022]
Abstract
Background The demand of maize crop is increasing day by day, hence to reduce the production and demand gap, there is a need to extract the high yielding parental lines to improve per se yield of the hybrids, which could help to enhance the productivity in maize crops. Methods and results The present investigation was carried out to select the best medium maturing inbred lines, among a set of 118 inbred lines. Based on the Duncan multiple range test, out of 118 lines, 16 inbred lines were selected on the basis of its high yield per se and flowering time. The molecular diversity was carried out using SSR markers linked to heterotic QTL and up on diversity analysis it classified selected genotypes in to three distinct groups. Among the selected inbred lines, a wider genetic variability and molecular diversity were observed. A total of 39 test crosses were generated after classifying 16 inbred lines in to three testers and thirteen lines (based on per se grain yield and molecular diversity) and crossing them in line × tester manner. Conclusion Combining ability analysis of these parental lines showed that female parents, PML 109, PML 110, PML 111, PML 114 and PML 116 showed additive effect for KRN and grain yield, whereas male parents, PML 46, and PML 93 showed epistatic effect for KRN and PML 102 showed epistatic effect for grain yield. The generated information in the present investigation may be exploited for heterosis breeding in filed corn. Key messages To tackle the balanced dietary requirement of Indian population; we focused to enhance the productivity of maize hybrids using genetically broad based, elite, diverse inbred lines. Combination of selection criterion, not only augment the productivity but also improves the quality of hybrid/s. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-022-07295-3.
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Adams JR, de Vries ME, Zheng C, van Eeuwijk FA. Little heterosis found in diploid hybrid potato: The genetic underpinnings of a new hybrid crop. G3 (BETHESDA, MD.) 2022; 12:6572814. [PMID: 35460241 PMCID: PMC9157145 DOI: 10.1093/g3journal/jkac076] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 03/27/2022] [Indexed: 11/17/2022]
Abstract
Hybrid potato breeding has become a novel alternative to conventional potato breeding allowing breeders to overcome intractable barriers (e.g. tetrasomic inheritance, masked deleterious alleles, obligate clonal propagation) with the benefit of seed-based propagule, flexible population design, and the potential of hybrid vigor. Until now, however, no formal inquiry has adequately examined the relevant genetic components for complex traits in hybrid potato populations. In this present study, we use a 2-step multivariate modeling approach to estimate the variance components to assess the magnitude of the general and specific combining abilities in diploid hybrid potato. Specific combining ability effects were identified for all yield components studied here warranting evidence of nonadditive genetic effects in hybrid potato yield. However, the estimated general combining ability effects were on average 2 times larger than their respective specific combining ability quantile across all yield phenotypes. Tuber number general combining abilities and specific combining abilities were found to be highly correlated with total yield's genetic components. Tuber volume was shown to have the largest proportion of additive and nonadditive genetic variation suggesting under-selection of this phenotype in this population. The prominence of additive effects found for all traits presents evidence that the mid-parent value alone is useful for hybrid potato evaluation. Heterotic vigor stands to be useful in bolstering simpler traits but this will be dependent on target phenotypes and market requirements. This study represents the first diallel analysis of its kind in diploid potato using material derived from a commercial hybrid breeding program.
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Affiliation(s)
- James R Adams
- Biometris, Mathematical and Statistical Methods, Wageningen University and Research, 6700 HB Wageningen, The Netherlands,Solynta, 6703 HA Wageningen, The Netherlands,Corresponding author: Biometris, Mathematical and Statistical Methods, Wageningen University and Research, 6700 HB Wageningen, The Netherlands.
| | | | - Chaozhi Zheng
- Biometris, Mathematical and Statistical Methods, Wageningen University and Research, 6700 HB Wageningen, The Netherlands
| | - Fred A van Eeuwijk
- Biometris, Mathematical and Statistical Methods, Wageningen University and Research, 6700 HB Wageningen, The Netherlands
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Cheng A, Mohd Hanafiah N, Harikrishna JA, Eem LP, Baisakh N, Mispan MS. A Reappraisal of Polyploidy Events in Grasses (Poaceae) in a Rapidly Changing World. BIOLOGY 2022; 11:biology11050636. [PMID: 35625365 PMCID: PMC9138248 DOI: 10.3390/biology11050636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 11/16/2022]
Abstract
Around 80% of megaflora species became extinct at the Cretaceous–Paleogene (K–Pg) boundary. Subsequent polyploidy events drove the survival of thousands of plant species and played a significant historical role in the development of the most successful modern cereal crops. However, current and rapid global temperature change poses an urgent threat to food crops worldwide, including the world’s big three cereals: rice, wheat, and maize, which are members of the grass family, Poaceae. Some minor cereals from the same family (such as teff) have grown in popularity in recent years, but there are important knowledge gaps regarding the similarities and differences between major and minor crops, including how polyploidy affects their biological processes under natural and (a)biotic stress conditions and thus the potential to harness polyploidization attributes for improving crop climate resilience. This review focuses on the impact of polyploidy events on the Poaceae family, which includes the world’s most important food sources, and discusses the past, present, and future of polyploidy research for major and minor crops. The increasing accessibility to genomes of grasses and their wild progenitors together with new tools and interdisciplinary research on polyploidy can support crop improvement for global food security in the face of climate change.
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Affiliation(s)
- Acga Cheng
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (N.M.H.); (J.A.H.)
| | - Noraikim Mohd Hanafiah
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (N.M.H.); (J.A.H.)
| | - Jennifer Ann Harikrishna
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (N.M.H.); (J.A.H.)
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Lim Phaik Eem
- Institute of Ocean and Earth Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia;
| | - Niranjan Baisakh
- School of Plant, Environmental, and Soil Science, Louisiana State University Agricultural Center, Baton Rouge, LA 70803, USA
- Correspondence: (N.B.); (M.S.M.)
| | - Muhamad Shakirin Mispan
- Faculty of Science, Institute of Biological Sciences, Universiti Malaya, Kuala Lumpur 50603, Malaysia; (A.C.); (N.M.H.); (J.A.H.)
- Centre for Research in Biotechnology for Agriculture (CEBAR), Universiti Malaya, Kuala Lumpur 50603, Malaysia
- Correspondence: (N.B.); (M.S.M.)
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Castillo-Bravo R, Fort A, Cashell R, Brychkova G, McKeown PC, Spillane C. Parent-of-Origin Effects on Seed Size Modify Heterosis Responses in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:835219. [PMID: 35330872 PMCID: PMC8940307 DOI: 10.3389/fpls.2022.835219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 01/19/2022] [Indexed: 05/05/2023]
Abstract
Parent-of-origin effects arise when a phenotype depends on whether it is inherited maternally or paternally. Parent-of-origin effects can exert a strong influence on F1 seed size in flowering plants, an important agronomic and life-history trait that can contribute to biomass heterosis. Here we investigate the natural variation in the relative contributions of the maternal and paternal genomes to F1 seed size across 71 reciprocal pairs of F1 hybrid diploids and the parental effect on F1 seed size heterosis. We demonstrate that the paternally derived genome influences F1 seed size more significantly than previously appreciated. We further demonstrate (by disruption of parental genome dosage balance in F1 triploid seeds) that hybridity acts as an enhancer of genome dosage effects on F1 seed size, beyond that observed from hybridity or genome dosage effects on their own. Our findings indicate that interactions between genetic hybridity and parental genome dosage can enhance heterosis effects in plants, opening new avenues for boosting heterosis breeding in crop plants.
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Singh M, Avtar R, Kumar N, Punia R, Pal A, Lakra N, Kumari N, Kumar D, Naruka A, Bishnoi M, Khedwal RS, Choudhary RR, Singh A, Meena RK, Dhillon A, Singh VK. Genetic Analysis for Resistance to Sclerotinia Stem Rot, Yield and Its Component Traits in Indian Mustard [ Brassica juncea (L.) Czern & Coss.]. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11050671. [PMID: 35270141 PMCID: PMC8912491 DOI: 10.3390/plants11050671] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 02/17/2022] [Accepted: 02/23/2022] [Indexed: 06/12/2023]
Abstract
Understanding the mode of gene action that controls seed yield and Sclerotinia stem rot resistance in Indian mustard is critical for boosting yield potential. In a line × tester mating design, ten susceptible lines and four resistant testers were used to conduct genetic analysis. The significance of general combining ability (GCA) and specific combining ability (SCA) variances revealed that both additive and non-additive gene actions were involved in the inheritance of Sclerotinia stem rot resistance and yield attributing traits. In addition to 1000-seed weight and number of primary and secondary branches/plant, the genotypes RH 1569 (line) and DRMR 2035 (tester) appeared to be the strongest general combiners for Sclerotinia stem rot resistance. RH 1657 × EC 597317 was the only cross among several that demonstrated a significant desired SCA value for Sclerotinia rot resistance. Regarding SCA effects for yield and component traits, the cross RH 1658 × EC 597328 performed best, with a non-significant but acceptable negative SCA effect for resistance. DRMR 2035, RH 1222-28, RH 1569, RH 1599-41, RH 1657, RH 1658, and EC 597328 are promising genotypes to use as parents in future heterosis breeding and for obtaining populations with high yield potential and greater resistance to Sclerotinia stem rot disease in Indian mustard, based on GCA effects of parents, per se performance, and SCA effects of hybrids. Days to 50% flowering, number of primary branches/plant, main shoot length, and 1000-seed weight all had a high genotypic coefficient of variability (GCV), broad-sense heritability (h2bs), and genetic advance as percent of the mean (GAM) values, as well as significant and desirable correlations and direct effects on seed yield. As a result, these traits have been recognized as the most critical selection criterion for Indian mustard breeding programs.
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Affiliation(s)
- Manjeet Singh
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Ram Avtar
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Neeraj Kumar
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Rakesh Punia
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Ajay Pal
- Department of Biochemistry, CCS Haryana Agricultural University, Hisar 125004, India;
| | - Nita Lakra
- Department of Molecular Biology, Biotechnology and Bioinformatics, CCS Haryana Agricultural University, Hisar 125004, India;
| | - Nisha Kumari
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Dalip Kumar
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Anu Naruka
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Mahavir Bishnoi
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Rajbir Singh Khedwal
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Raju Ram Choudhary
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Anoop Singh
- Department of Botany, Maharshi Dayanand University, Rohtak 124001, India;
| | - Ravindra Kumar Meena
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Ankit Dhillon
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
| | - Vivek K. Singh
- Department of Genetics and Plant Breeding, CCS Haryana Agricultural University, Hisar 125004, India; (R.A.); (N.K.); (R.P.); (N.K.); (D.K.); (A.N.); (M.B.); (R.S.K.); (R.R.C.); (R.K.M.); (A.D.)
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Effect of Chitosan-Poly(Acrylic Acid) Complexes and Two Nutrient Solutions on the Growth and Yield of Two Habanero Pepper Cultivars. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8030201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Chitosan (CS) is a natural polymer used in agriculture as a biostimulant that has been evaluated in different plant models. In this study, we evaluated the effect of the foliar application of chitosan–poly(acrylic acid) complexes (CS–PAA) and two nutrient solutions (A and B) on the parameters of growth and yield of two habanero pepper cultivars (Chichen Itza and Jaguar) in a greenhouse. Over the course of the experiment, eight foliar applications were carried out at 15-day intervals. Our results showed that foliar applications of CS–PAA complexes have a biostimulant effect on the habanero pepper crop by increasing the total dry biomass of the plant and the number of fruits of the two cultivars. Regarding nutrient solutions, the nutrient solution A increased the yield of the Chichen Itza cultivar; this effect was because it had a better balance of potassium and calcium compared to the nutrient solution B. These results provide advances on the use of CS–PAA complexes as a biostimulant and the management of nutrient solutions in the crop of habanero peppers.
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Roth M, Beugnot A, Mary-Huard T, Moreau L, Charcosset A, Fiévet JB. Improving genomic predictions with inbreeding and nonadditive effects in two admixed maize hybrid populations in single and multienvironment contexts. Genetics 2022; 220:6527635. [PMID: 35150258 PMCID: PMC8982028 DOI: 10.1093/genetics/iyac018] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 01/28/2022] [Indexed: 11/12/2022] Open
Abstract
Genetic admixture, resulting from the recombination between structural groups, is frequently encountered in breeding populations. In hybrid breeding, crossing admixed lines can generate substantial nonadditive genetic variance and contrasted levels of inbreeding which can impact trait variation. This study aimed at testing recent methodological developments for the modeling of inbreeding and nonadditive effects in order to increase prediction accuracy in admixed populations. Using two maize (Zea mays L.) populations of hybrids admixed between dent and flint heterotic groups, we compared a suite of five genomic prediction models incorporating (or not) parameters accounting for inbreeding and nonadditive effects with the natural and orthogonal interaction approach in single and multienvironment contexts. In both populations, variance decompositions showed the strong impact of inbreeding on plant yield, height, and flowering time which was supported by the superiority of prediction models incorporating this effect (+0.038 in predictive ability for mean yield). In most cases dominance variance was reduced when inbreeding was accounted for. The model including additivity, dominance, epistasis, and inbreeding effects appeared to be the most robust for prediction across traits and populations (+0.054 in predictive ability for mean yield). In a multienvironment context, we found that the inclusion of nonadditive and inbreeding effects was advantageous when predicting hybrids not yet observed in any environment. Overall, comparing variance decompositions was helpful to guide model selection for genomic prediction. Finally, we recommend the use of models including inbreeding and nonadditive parameters following the natural and orthogonal interaction approach to increase prediction accuracy in admixed populations.
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Affiliation(s)
- Morgane Roth
- Plant Breeding Research Division, Agroscope, Wädenswil, 8820 Zurich, Switzerland,Corresponding author: INRAE GAFL, 67 Allée des Chênes 84140 Montfavet, France.
| | - Aurélien Beugnot
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, UMR GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Tristan Mary-Huard
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, UMR GQE-Le Moulon, 91190 Gif-sur-Yvette, France,Université Paris-Saclay, INRAE, AgroParisTech, UMR MIA-Paris Paris, 75005 Paris, France
| | - Laurence Moreau
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, UMR GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Alain Charcosset
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, UMR GQE-Le Moulon, 91190 Gif-sur-Yvette, France
| | - Julie B Fiévet
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, UMR GQE-Le Moulon, 91190 Gif-sur-Yvette, France
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Carlsen FM, Johansen IE, Yang Z, Liu Y, Westberg IN, Kieu NP, Jørgensen B, Lenman M, Andreasson E, Nielsen KL, Blennow A, Petersen BL. Strategies for Efficient Gene Editing in Protoplasts of Solanum tuberosum Theme: Determining gRNA Efficiency Design by Utilizing Protoplast (Research). Front Genome Ed 2022; 3:795644. [PMID: 35128523 PMCID: PMC8811252 DOI: 10.3389/fgeed.2021.795644] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 11/24/2021] [Indexed: 11/13/2022] Open
Abstract
Potato, Solanum tuberosum is a highly diverse tetraploid crop. Elite cultivars are extremely heterozygous with a high prevalence of small length polymorphisms (indels) and single nucleotide polymorphisms (SNPs) within and between cultivars, which must be considered in CRISPR/Cas gene editing strategies and designs to obtain successful gene editing. In the present study, in-depth sequencing of the gene encoding glucan water dikinase (GWD) 1 and the downy mildew resistant 6 (DMR6-1) genes in the potato cultivars Saturna and Wotan, respectively, revealed both indels and a 1.3–2.8 higher SNP prevalence when compared to the heterozygous diploid RH genome sequence as expected for a tetraploid compared to a diploid. This complicates guide RNA (gRNA) and diagnostic PCR designs. At the same time, high editing efficiencies at the cell pool (protoplast) level are pivotal for achieving full allelic knock-out in tetraploids. Furthermore, high editing efficiencies reduce the downstream cumbersome and delicate ex-plant regeneration. Here, CRISPR/Cas ribonucleoprotein particles (RNPs) were delivered transiently to protoplasts by polyethylene glycol (PEG) mediated transformation. For each of GWD1 and the DMR6-1, 6–10 gRNAs were designed to target regions comprising the 5′ and the 3′ end of the two genes. Similar to other studies including several organisms, editing efficiency of the individual RNPs varied significantly, and some generated specific indel patterns. RNP’s targeting the 5′ end of GWD1 yielded significantly higher editing efficiency as compared to targeting the 3′ end. For DMR6-1, such an effect was not seen. Simultaneously targeting each of the two target regions with two RNPs (multiplexing) yielded a clear positive synergistic effect on the total editing when targeting the 3′ end of the GWD1 gene only. Multiplexing of the two genes, residing on different chromosomes, yielded no or a slightly negative effect on editing from the single or combined gRNA/RNPs. These initial findings may instigate much larger studies needed for facilitating and optimizing precision breeding in plants.
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Affiliation(s)
- Frida Meijer Carlsen
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Ida Elisabeth Johansen
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
- Kartoffel Mel Centralen Amba, Brande, Denmark
| | - Zhang Yang
- Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ying Liu
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Ida Nøhr Westberg
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Nam Phuong Kieu
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Bodil Jørgensen
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Marit Lenman
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Erik Andreasson
- Department of Plant Protection Biology, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Andreas Blennow
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
| | - Bent Larsen Petersen
- Department of Plant and Environmental Sciences, Faculty of Science, The University of Copenhagen, Copenhagen, Denmark
- *Correspondence: Bent Larsen Petersen,
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