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Lipps S, Lipka AE, Mideros S, Jamann T. Inhibition of ethylene involved in resistance to E. turcicum in an exotic-derived double haploid maize population. FRONTIERS IN PLANT SCIENCE 2023; 14:1272951. [PMID: 37868313 PMCID: PMC10587583 DOI: 10.3389/fpls.2023.1272951] [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: 08/04/2023] [Accepted: 09/19/2023] [Indexed: 10/24/2023]
Abstract
Northern corn leaf blight (NCLB) is an economically important disease of maize. While the genetic architecture of NCLB has been well characterized, the pathogen is known to overcome currently deployed resistance genes, and the role of hormones in resistance to NCLB is an area of active research. The objectives of the study were (i) to identify significant markers associated with resistance to NCLB, (ii) to identify metabolic pathways associated with NCLB resistance, and (iii) to examine role of ethylene in resistance to NCLB. We screened 252 lines from the exotic-derived double haploid BGEM maize population for resistance to NCLB in both field and greenhouse environments. We used a genome wide association study (GWAS) and stepwise regression to identify four markers associated with resistance, followed by a pathway association study tool (PAST) to identify important metabolic pathways associated with disease severity and incubation period. The ethylene synthesis pathway was significant for disease severity and incubation period. We conducted a greenhouse assay in which we inhibited ethylene to examine the role of ethylene in resistance to NCLB. We observed a significant increase in incubation period and a significant decrease in disease severity between plants treated with the ethylene inhibitor and mock-treated plants. Our study confirms the potential of the BGEM population as a source of novel alleles for resistance. We also confirm the role of ethylene in resistance to NCLB and contribute to the growing body of literature on ethylene and disease resistance in monocots.
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Affiliation(s)
| | | | | | - Tiffany Jamann
- Department of Crop Sciences, University of Illinois, Urbana, IL, United States
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2
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Jin M, Liu H, Liu X, Guo T, Guo J, Yin Y, Ji Y, Li Z, Zhang J, Wang X, Qiao F, Xiao Y, Zan Y, Yan J. Complex genetic architecture underlying the plasticity of maize agronomic traits. PLANT COMMUNICATIONS 2023; 4:100473. [PMID: 36642074 DOI: 10.1016/j.xplc.2022.100473] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/21/2022] [Accepted: 11/07/2022] [Indexed: 05/11/2023]
Abstract
Phenotypic plasticity is the ability of a given genotype to produce multiple phenotypes in response to changing environmental conditions. Understanding the genetic basis of phenotypic plasticity and establishing a predictive model is highly relevant to future agriculture under a changing climate. Here we report findings on the genetic basis of phenotypic plasticity for 23 complex traits using a diverse maize population planted at five sites with distinct environmental conditions. We found that latitude-related environmental factors were the main drivers of across-site variation in flowering time traits but not in plant architecture or yield traits. For the 23 traits, we detected 109 quantitative trait loci (QTLs), 29 for mean values, 66 for plasticity, and 14 for both parameters, and 80% of the QTLs interacted with latitude. The effects of several QTLs changed in magnitude or sign, driving variation in phenotypic plasticity. We experimentally validated one plastic gene, ZmTPS14.1, whose effect was likely mediated by the compensation effect of ZmSPL6 from a downstream pathway. By integrating genetic diversity, environmental variation, and their interaction into a joint model, we could provide site-specific predictions with increased accuracy by as much as 9.9%, 2.2%, and 2.6% for days to tassel, plant height, and ear weight, respectively. This study revealed a complex genetic architecture involving multiple alleles, pleiotropy, and genotype-by-environment interaction that underlies variation in the mean and plasticity of maize complex traits. It provides novel insights into the dynamic genetic architecture of agronomic traits in response to changing environments, paving a practical way toward precision agriculture.
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Affiliation(s)
- Minliang Jin
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Haijun Liu
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna BioCenter, 1030 Vienna, Austria
| | - Xiangguo Liu
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Tingting Guo
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jia Guo
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Yuejia Yin
- Institute of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Yan Ji
- Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266000, China
| | - Zhenxian Li
- Institute of Agricultural Sciences of Xishuangbanna Prefecture of Yunnan Province, Jinghong 666100, China
| | - Jinhong Zhang
- Institute of Agricultural Sciences of Xishuangbanna Prefecture of Yunnan Province, Jinghong 666100, China
| | - Xiaqing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Feng Qiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
| | - Yingjie Xiao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yanjun Zan
- Umeå Plant Science Center, Department of Forestry Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90736 Umeå, Sweden; Key Laboratory of Tobacco Improvement and Biotechnology, Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266000, China.
| | - Jianbing Yan
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China; Hubei Hongshan Laboratory, Wuhan 430070, China.
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3
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Tan B, Ingvarsson PK. Integrating genome-wide association mapping of additive and dominance genetic effects to improve genomic prediction accuracy in Eucalyptus. THE PLANT GENOME 2022; 15:e20208. [PMID: 35441826 DOI: 10.1002/tpg2.20208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Genome-wide association studies (GWAS) is a powerful and widely used approach to decipher the genetic control of complex traits. Still, a significant challenge for dissecting quantitative traits in forest trees is statistical power. This study uses a population consisting of 1,123 samples derived from two successive generations of crosses between Eucalyptus grandis (W. Hill) and E. urophylla (S.T. Blake). All samples have been phenotyped for growth and wood property traits and genotyped using the EuChip60K chip, yielding 37,832 informative single nucleotide polymorphisms (SNPs). We use multi-locus GWAS models to assess additive and dominance effects to identify markers associated with growth and wood property traits in the eucalypt hybrids. Additive and dominance association models identified 78 and 82 significant SNPs across all traits, respectively, which captured between 39 and 86% of the genomic-based heritability. We also used SNPs identified from the GWAS and SNPs using less stringent significance thresholds to evaluate predictive abilities in a genomic selection framework. Genomic selection models based on the top 1% SNPs captured a substantially greater proportion of the genetic variance of traits compared with when we used all SNPs for model training. The prediction ability of estimated breeding values improved significantly for all traits when using either the top 1% SNPs or SNPs identified using a relaxed p value threshold (p < 10-3 ). This study also highlights the added value of incorporating dominance effects for identifying genomic regions controlling growth traits in trees. Moreover, integrating GWAS results into genomic selection method provides enhanced power relative to discrete associations for identifying genomic variation potentially valuable for forest tree breeding.
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Affiliation(s)
- Biyue Tan
- Umeå Plant Science Centre, Dep. of Ecology and Environmental Science, Umeå Univ., Umeå, SE-90187, Sweden
- Stora Enso AB, Nacka, SE-131 04, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Dep. of Plant Biology, Uppsala BioCenter, Swedish Univ. of Agricultural Sciences, Uppsala, SE-750 07, Sweden
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Khan SU, Khan MU, Kalsoom F, Khan MI, Gao S, Unar A, Zubair M, Bilal M. Mechanisms of gene regulation by histone degradation in adaptation of yeast: an overview of recent advances. Arch Microbiol 2022; 204:287. [PMID: 35482104 DOI: 10.1007/s00203-022-02897-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/12/2022] [Accepted: 04/04/2022] [Indexed: 02/07/2023]
Abstract
Histones are important component of eukaryotic cells chromatin and consist of arginine and lysine residues. Histones play an important role in the protection of DNA. Their contents significantly affect high-level chromatin structure formation, gene expression, DNA replication, and other important life activities. Protein degradation is an important regulatory mechanism of histone content. Recent studies have revealed that modification of amino acid sequence is directly related to histone breakdown. In addition, histone degradation is closely related to covalent modifications, such as ubiquitination and acetylation, which are considered to be driving factors in gene regulation. Gene regulation is an important mechanism in adaptation to the environment and survival of species. With the introduction of highly efficient technology, various mutations in histones have been identified in yeast. In the field of epigenetics and the transmission of chromatin states, two widely used model organisms are the budding yeast Saccharomyces cerevisiae and Schizosaccharomyces pombe. Higher eukaryotes can use their silent loci to maintain their epigenetic states and providing the base to investigate mechanisms underlying development. Therfore, both species have contributed a plethora of information on these mechanisms in both yeast and higher eukaryotes. This study focuses on the role of histone modifications in controlling telomeric silencing in Saccharomyces cerevisiae and centromeric silencing in S. pombe as examples of genetic loci that demonstrate epigenetic inheritance. In view of recent advances, this review focuses on the post-translational modification of histone amino acid residues and reviews the relationship between histone degradation and amino acid residue modification.
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Affiliation(s)
- Safir Ullah Khan
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Munir Ullah Khan
- MOE Key Laboratory of Macromolecular Synthesis and Functionalization, Department of Polymer Science and Engineering, Zhejiang University, Hangzhou, 310027, People's Republic of China
| | - Fadia Kalsoom
- Department of Microbiology, Ajou University School of Medicine, Suwon, 16499, Republic of Korea
| | - Muhammad Imran Khan
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China.
- Hefei National Laboratory for Physical Sciences at Microscale and the Center for Biomedical Engineering, University of Science and Technology of China, Hefei, 230027, People's Republic of China.
- Department of Pathology, District headquarters hospital, Jhang, 35200, Punjab Province, Islamic Republic of Pakistan.
| | - Shuang Gao
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Ahsanullah Unar
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Muhammad Zubair
- School of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230027, People's Republic of China
- The First Affiliated Hospital of USTC, Hefei National Laboratory for Physical Sciences at Microscale, School of Basic Medical Sciences, University of Science and Technology of China, Hefei, 230027, People's Republic of China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian, 223003, People's Republic of China.
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5
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Zhao H, Savin KW, Li Y, Breen EJ, Maharjan P, Tibbits JF, Kant S, Hayden MJ, Daetwyler HD. Genome-wide association studies dissect the G × E interaction for agronomic traits in a worldwide collection of safflowers ( Carthamus tinctorius L.). MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2022; 42:24. [PMID: 37309464 PMCID: PMC10248593 DOI: 10.1007/s11032-022-01295-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Genome-wide association studies were conducted using a globally diverse safflower (Carthamus tinctorius L.) Genebank collection for grain yield (YP), days to flowering (DF), plant height (PH), 500 seed weight (SW), seed oil content (OL), and crude protein content (PR) in four environments (sites) that differed in water availability. Phenotypic variation was observed for all traits. YP exhibited low overall genetic correlations (rGoverall) across sites, while SW and OL had high rGoverall and high pairwise genetic correlations (rGij) across all pairwise sites. In total, 92 marker-trait associations (MTAs) were identified using three methods, single locus genome-wide association studies (GWAS) using a mixed linear model (MLM), the Bayesian multi-locus method (BayesR), and meta-GWAS. MTAs with large effects across all sites were detected for OL, SW, and PR, and MTAs specific for the different water stress sites were identified for all traits. Five MTAs were associated with multiple traits; 4 of 5 MTAs were variously associated with the three traits of SW, OL, and PR. This study provided insights into the phenotypic variability and genetic architecture of important safflower agronomic traits under different environments. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-022-01295-8.
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Affiliation(s)
- Huanhuan Zhao
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083 Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
| | - Keith W. Savin
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
| | - Yongjun Li
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
| | - Edmond J. Breen
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
| | - Pankaj Maharjan
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC 3400 Australia
| | - Josquin F. Tibbits
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
| | - Surya Kant
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083 Australia
- Agriculture Victoria, Grains Innovation Park, Horsham, VIC 3400 Australia
| | - Matthew J. Hayden
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083 Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
| | - Hans D. Daetwyler
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083 Australia
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC 3083 Australia
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6
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Volk GM, Byrne PF, Coyne CJ, Flint-Garcia S, Reeves PA, Richards C. Integrating Genomic and Phenomic Approaches to Support Plant Genetic Resources Conservation and Use. PLANTS (BASEL, SWITZERLAND) 2021; 10:2260. [PMID: 34834625 PMCID: PMC8619436 DOI: 10.3390/plants10112260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 10/20/2021] [Accepted: 10/20/2021] [Indexed: 05/17/2023]
Abstract
Plant genebanks provide genetic resources for breeding and research programs worldwide. These programs benefit from having access to high-quality, standardized phenotypic and genotypic data. Technological advances have made it possible to collect phenomic and genomic data for genebank collections, which, with the appropriate analytical tools, can directly inform breeding programs. We discuss the importance of considering genebank accession homogeneity and heterogeneity in data collection and documentation. Citing specific examples, we describe how well-documented genomic and phenomic data have met or could meet the needs of plant genetic resource managers and users. We explore future opportunities that may emerge from improved documentation and data integration among plant genetic resource information systems.
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Affiliation(s)
- Gayle M. Volk
- United States Department of Agriculture, Agricultural Research Service, National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, USA; (P.A.R.); (C.R.)
| | - Patrick F. Byrne
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA;
| | - Clarice J. Coyne
- United States Department of Agriculture, Agricultural Research Service, Western Regional Plant Introduction Station, Pullman, WA 99164, USA;
| | - Sherry Flint-Garcia
- Plant Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service, Columbia, MO 65211, USA;
| | - Patrick A. Reeves
- United States Department of Agriculture, Agricultural Research Service, National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, USA; (P.A.R.); (C.R.)
| | - Chris Richards
- United States Department of Agriculture, Agricultural Research Service, National Laboratory for Genetic Resources Preservation, Fort Collins, CO 80521, USA; (P.A.R.); (C.R.)
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7
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Lopez MA, Freitas Moreira F, Rainey KM. Genetic Relationships Among Physiological Processes, Phenology, and Grain Yield Offer an Insight Into the Development of New Cultivars in Soybean ( Glycine max L. Merr). FRONTIERS IN PLANT SCIENCE 2021; 12:651241. [PMID: 33903802 PMCID: PMC8064921 DOI: 10.3389/fpls.2021.651241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 02/25/2021] [Indexed: 06/12/2023]
Abstract
Soybean grain yield has steadily increased during the last century because of enhanced cultivars and better agronomic practices. Increases in the total biomass, shorter cultivars, late maturity, and extended seed-filling period are frequently reported as main contributors for better soybean performance. However, there are still processes associated with crop physiology to be improved. From the theoretical standpoint, yield is the product of efficiency of light interception (Ei), radiation use efficiency (RUE), and harvest index (HI). The relative contribution of these three parameters on the final grain yield (GY), their interrelation with other phenological-physiological traits, and their environmental stability have not been well established for soybean. In this study, we determined the additive-genetic relationship among 14 physiological and phenological traits including photosynthesis (A) and intrinsic water use efficiency (iWUE) in a panel of 383 soybean recombinant inbred lines (RILs) through direct (path analyses) and indirect learning methods [least absolute shrinkage and selection operator (LASSO) algorithm]. We evaluated the stability of Ei, RUE, and HI through the slope from the Finley and Wilkinson joint regression and the genetic correlation between traits evaluated in different environments. Results indicate that both supervised and unsupervised methods effectively establish the main relationships underlying changes in Ei, RUE, HI, and GY. Variations in the average growth rate of canopy coverage for the first 40 days after planting (AGR40) explain most of the changes in Ei. RUE is primarily influenced by phenological traits of reproductive length (RL) and seed-filling (SFL) as well as iWUE, light extinction coefficient (K), and A. HI showed a strong relationship with A, AGR40, SFL, and RL. According to the path analysis, an increase in one standard unit of HI promotes changes in 0.5 standard units of GY, while changes in the same standard unit of RUE and Ei produce increases on GY of 0.20 and 0.19 standard units, respectively. RUE, Ei, and HI exhibited better environmental stability than GY, although changes associated with year and location showed a moderate effect in Ei and RUE, respectively. This study brings insight into a group of traits involving A, iWUE, and RL to be prioritized during the breeding process for high-yielding cultivars.
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Affiliation(s)
| | | | - Katy Martin Rainey
- Department of Agronomy, Purdue University, West Lafayette, IN, United States
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Zan Y, Carlborg Ö. Dissecting the Genetic Regulation of Yeast Growth Plasticity in Response to Environmental Changes. Genes (Basel) 2020; 11:genes11111279. [PMID: 33137976 PMCID: PMC7693874 DOI: 10.3390/genes11111279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 10/26/2020] [Accepted: 10/27/2020] [Indexed: 11/16/2022] Open
Abstract
Variable individual responses to environmental changes, such as phenotype plasticity, are heritable, with some genotypes being robust and others plastic. This variation for plasticity contributes to variance in complex traits as genotype-by-environment interactions (G × E). However, the genetic basis of this variability in responses to the same external stimuli is still largely unknown. In an earlier study of a large haploid segregant yeast population, genotype-by-genotype-by-environment interactions were found to make important contributions to the release of genetic variation in growth responses to alterations of the growth medium. Here, we explore the genetic basis for heritable variation of different measures of phenotype plasticity in the same dataset. We found that the central loci in the environmentally dependent epistatic networks were associated with overall measures of plasticity, while the specific measures of plasticity identified a more diverse set of loci. Based on this, a rapid one-dimensional genome-wide association (GWA) approach to overall plasticity is proposed as a strategy to efficiently identify key epistatic loci contributing to the phenotype plasticity. The study thus provided both analytical strategies and a deeper understanding of the complex genetic regulation of phenotype plasticity in yeast growth.
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Affiliation(s)
- Yanjun Zan
- Department of Forestry Genetics and Plant Physiology, Swedish University of Agricultural Sciences, 90736 Umeå, Sweden
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75123 Uppsala, Sweden;
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Correspondence:
| | - Örjan Carlborg
- Department of Medical Biochemistry and Microbiology, Uppsala University, 75123 Uppsala, Sweden;
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