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Zamorski R, Baba K, Noda T, Sawada R, Miyata K, Itoh T, Kaku H, Shibuya N. Variety-dependent accumulation of glucomannan in the starchy endosperm and aleurone cell walls of rice grains and its possible genetic basis. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:321-336. [PMID: 38434111 PMCID: PMC10905567 DOI: 10.5511/plantbiotechnology.23.0809a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 08/09/2023] [Indexed: 03/05/2024]
Abstract
Plant cell wall plays important roles in the regulation of plant growth/development and affects the quality of plant-derived food and industrial materials. On the other hand, genetic variability of cell wall structure within a plant species has not been well understood. Here we show that the endosperm cell walls, including both starchy endosperm and aleurone layer, of rice grains with various genetic backgrounds are clearly classified into two groups depending on the presence/absence of β-1,4-linked glucomannan. All-or-none distribution of the glucomannan accumulation among rice varieties is very different from the varietal differences of arabinoxylan content in wheat and barley, which showed continuous distributions. Immunoelectron microscopic observation suggested that the glucomannan was synthesized in the early stage of endosperm development, but the synthesis was down-regulated during the secondary thickening process associated with the differentiation of aleurone layer. Significant amount of glucomannan in the cell walls of the glucomannan-positive varieties, i.e., 10% or more of the starchy endosperm cell walls, and its close association with the cellulose microfibril suggested possible effects on the physicochemical/biochemical properties of these cell walls. Comparative genomic analysis indicated the presence of striking differences between OsCslA12 genes of glucomannan-positive and negative rice varieties, Kitaake and Nipponbare, which seems to explain the all-or-none glucomannan cell wall trait in the rice varieties. Identification of the gene responsible for the glucomannan accumulation could lead the way to clarify the effect of the accumulation of glucomannan on the agronomic traits of rice by using genetic approaches.
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Affiliation(s)
- Ryszard Zamorski
- National Institute of Agrobiological Resources, Ministry of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-8634, Japan
- National Food Research Institute, Ministry of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-8642, Japan
- Faculty of Agriculture and Biotechnology, University of Science and Technology, Bydgoszcz 85-796, Poland
| | - Kei’ichi Baba
- Wood Research Institute, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Takahiro Noda
- National Institute of Agrobiological Resources, Ministry of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-8634, Japan
- Hokkaido Agricultural Research Center, NARO, Memuro, Hokkaido 082-0081, Japan
| | - Rimpei Sawada
- National Institute of Agrobiological Resources, Ministry of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-8634, Japan
- Plant Biotechnology Laboratory, Life Science Institute, Mitsui Toatsu Chemicals Inc., Mobara, Chiba 297-0017, Japan
| | - Kana Miyata
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Takao Itoh
- Wood Research Institute, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Hanae Kaku
- National Institute of Agrobiological Resources, Ministry of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-8634, Japan
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
| | - Naoto Shibuya
- National Institute of Agrobiological Resources, Ministry of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-8634, Japan
- National Food Research Institute, Ministry of Agriculture, Forestry and Fisheries, Tsukuba, Ibaraki 305-8642, Japan
- Department of Life Sciences, School of Agriculture, Meiji University, Kawasaki, Kanagawa 214-8571, Japan
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Study on Characteristics and Lignification Mechanism of Postharvest Banana Fruit during Chilling Injury. Foods 2023; 12:foods12051097. [PMID: 36900614 PMCID: PMC10000439 DOI: 10.3390/foods12051097] [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: 12/15/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 03/08/2023] Open
Abstract
The banana is prone to chilling injury (CI) at low temperature and showing a series of chilling symptoms, such as peel browning, etc. Lignification is a response to abiotic stress and senescence, which is an important manifestation of fruits and vegetables during chilling exposure. However, little is known about the lignification of bananas during low-temperature storage. Our study explored the characteristics and lignification mechanism of banana fruits during low-temperature storage by analyzing the changes of chilling symptoms, oxidative stress, cell wall metabolism, microstructures, and gene expression related to lignification. The results showed that CI inhibited post-ripening by effecting the degradation of the cell wall and starch and accelerated senescence by increasing O2- and H2O2 content. For lignification, Phenylalanine ammonia-lyase (PAL) might start the phenylpropanoid pathway of lignin synthesis. Cinnamoyl-CoA reductase 4 (CCR4), cinnamyl alcohol dehydrogenase 2 (CAD2), and 4-coumarate--CoA ligase like 7 (4CL7) were up-regulated to promote the lignin monomer's synthesis. Peroxidase 1 (POD1) and Laccase 3 (LAC3) were up-regulated to promote the oxidative polymerization of lignin monomers. These results suggest that changes of the cell wall structure and cell wall metabolism, as well as lignification, are involved in the senescence and quality deterioration of the banana after chilling injury.
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Zhan N, Li L, Zhang L, He W, Yang Q, Bi F, Deng G, Kiggundu A, Yi G, Sheng O. Transcriptome and metabolome profiling provide insights into hormone-mediated enhanced growth in autotetraploid seedlings of banana (Musa spp.). FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2023. [DOI: 10.3389/fsufs.2022.1070108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
IntroductionReconstructive breeding based on autotetraploids to generate triploid varieties is a promising breeding strategy in banana (Musa spp.). Therefore understanding the molecular mechanisms underlying the phenotypic differences between the original diploid and its autopolyploid derivatives is of significant importance in such breeding programs of banana.MethodsIn this study, a number of non-chimeric autotetraploid plants, confirmed by flow cytometry and chromosome counting were obtained using colchicine treatment of ‘Pisang Berlin' (AA Group), a diploid banana cultivar highly resistant to Fusarium wilt Tropical Race 4 (Foc TR4) and widely cultivated in Asia.Results and discussionThe autotetraploids showed significant increase in plant height, pseudostem diameter, root length, leaf thickness, leaf area, and leaf chlorophyll content. Transcriptomic analysis indicated that differentially expressed genes were mainly enriched in plant hormone signal transduction, mitogen-activated protein kinase (MAPK) signaling pathway, and carbon fixation in photosynthetic organelles. The genes related to the metabolism, transport or signaling of auxin, abscisic acid (ABA), cytokinin (CTK) and gibberellin (GA), as well as the genes encoding essential enzymes in photosynthetic CO2 fixation were differentially expressed in leaves of autotetraploids and most of them were up-regulated. Metabolomic analysis revealed that the differentially accumulated metabolites were mainly involved in plant hormone signal transduction, porphyrin and chlorophyll metabolism, indole alkaloid biosynthesis, and carbon fixation in photosynthetic organelles. The results therefore, demonstrate that the hormones IAA, ABA, and photosynthetic regulation may play a vital role in the observed enhancement in the autotetraploids. These could be used as molecular and biochemical markers to facilitate the generation of triploid progenies as suitable new varieties for cultivation.
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Panahabadi R, Ahmadikhah A, McKee LS, Ingvarsson PK, Farrokhi N. Genome-wide association study for lignocellulosic compounds and fermentable sugar in rice straw. THE PLANT GENOME 2022; 15:e20174. [PMID: 34806838 DOI: 10.1002/tpg2.20174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
Cellulose and lignin are the two main components of secondary plant cell walls with substantial impact on stalk in the field and on straw during industrial processing. The amount of fermentable sugar that can be accessed is another important parameter affecting various industrial applications. In the present study, genetic variability of rice (Oryza sativa L.) genotypes for cellulose, lignin, and fermentable sugars contents was analyzed in rice straw. A genome-wide association study of 33,484 single nucleotide polymorphisms (SNPs) with a minor allele frequency (MAF) >0.05 was performed. The genome-wide association study identified seven, three, and three genomic regions to be significantly associated with cellulose, lignin, and fermentable sugar contents, respectively. Candidate genes in the associated genomic regions were enzymes mainly involved in cell wall metabolism. Novel SNP markers associated with cellulose were tagged to GH16, peroxidase, GT6, GT8, and CSLD2. For lignin content, Villin protein, OsWAK1/50/52/53, and GH16 were identified. For fermentable sugar content, UTP-glucose-1-phosphate uridylyltransferase, BRASSINOSTEROID INSENSITIVE 1, and receptor-like protein kinase 5 were found. The results of this study should improve our understanding of the genetic basis of the factors that might be involved in biosynthesis, turnover, and modification of major cell wall components and saccharides in rice straw.
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Affiliation(s)
- Rahele Panahabadi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti Univ., Tehran, Iran
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, 106 91, Sweden
| | | | - Lauren S McKee
- Division of Glycoscience, School of Biotechnology, Royal Institute of Technology (KTH), AlbaNova University Centre, Stockholm, 106 91, Sweden
- Wallenberg Wood Science Centre, Teknikringen 56-58, Stockholm, 100 44, Sweden
| | - Pär K Ingvarsson
- Linnean Centre for Plant Biology, Dep. of Plant Biology, Swedish Univ. of Agricultural Sciences, Uppsala, Sweden
| | - Naser Farrokhi
- Faculty of Life Sciences and Biotechnology, Shahid Beheshti Univ., Tehran, Iran
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Wang J, Yu J, Lipka AE, Zhang Z. Interpretation of Manhattan Plots and Other Outputs of Genome-Wide Association Studies. Methods Mol Biol 2022; 2481:63-80. [PMID: 35641759 DOI: 10.1007/978-1-0716-2237-7_5] [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: 06/15/2023]
Abstract
With increasing marker density, estimation of recombination rate between a marker and a causal mutation using linkage analysis becomes less important. Instead, linkage disequilibrium (LD) becomes the major indicator for gene mapping through genome-wide association studies (GWAS). In addition to the linkage between the marker and the causal mutation, many other factors may contribute to the LD, including population structure and cryptic relationships among individuals. As statistical methods and software evolve to improve statistical power and computing speed in GWAS, the corresponding outputs must also evolve to facilitate the interpretation of input data, the analytical process, and final association results. In this chapter, our descriptions focus on (1) considerations in creating a Manhattan plot displaying the strength of LD and locations of markers across a genome; (2) criteria for genome-wide significance threshold and the different appearance of Manhattan plots in single-locus and multiple-locus models; (3) exploration of population structure and kinship among individuals; (4) quantile-quantile (QQ) plot; (5) LD decay across the genome and LD between the associated markers and their neighbors; (6) exploration of individual and marker information on Manhattan and QQ plots via interactive visualization using HTML. The ultimate objective of this chapter is to help users to connect input data to GWAS outputs to balance power and false positives, and connect GWAS outputs to the selection of candidate genes using LD extent.
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Affiliation(s)
- Jiabo Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu, Sichuan, China.
| | - Jianming Yu
- Department of Agronomy, Iowa State University, Ames, IA, USA
| | - Alexander E Lipka
- Department of Crop Sciences, University of Illinois, Urbana, IL, USA
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, USA
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Yang X, Li J, Lai JL, Zhang Y, Luo XG. Adsorption and enrichment of U in a cellulase-producing Trichoderma sp. and its physiological response mechanism. CHEMOSPHERE 2022; 287:132173. [PMID: 34509764 DOI: 10.1016/j.chemosphere.2021.132173] [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: 05/25/2021] [Revised: 08/21/2021] [Accepted: 09/03/2021] [Indexed: 06/13/2023]
Abstract
The cellulase produced by Trichoderma sp. was characterized by investigating the adsorption and enrichment of U and the physiological response to U exposure. The effects of U exposure (0 and 400 μM) on the growth, morphological characteristics, cellulase production, U adsorption, and U enrichment capacity of the Trichoderma strain were assessed. The effects of U exposure on the basic metabolism of this fungus were also analyzed by non-targeted metabolomics. Exposure to U (400 μM) for 24 h resulted in OD600 turbidity of 0.278, and activities of carboxymethyl cellulase (CMC), filter paper enzyme (FPA), and β-glucosidase of 12834 U·mL-1, 9285 U·mL-1, and 12574 U·mL-1, respectively. The measurement of the background α and β radioactivity showed an α activity concentration of 3.35 × 106 Bq·kg-1 in the fungus, a β activity concentration of 6.28 × 105 Bq·kg-1, and a U enrichment rate of 70.4 ± 4.5%. GC-MS metabolomics analysis identified a total of 319 metabolites (34 up-regulated and 30 down-regulated), which mainly caused the metabolic imbalance of organic acids and derivatives. The alanine, aspartate, and glutamate metabolic pathways were the most significantly enriched. Trichoderma sp. therefore has a strong ability to tolerate/accumulate U and continues to produce cellulase under U (400 μM) exposure. However, U interferes with the basic metabolism of this fungus.
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Affiliation(s)
- Xu Yang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Jie Li
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
| | - Jin-Long Lai
- State Key Laboratory of NBC Protection for Civilian, Beijing, 102205, China; Engineering Research Center of Biomass Materials, Ministry of Education of SWUST, Mianyang, 621010, China.
| | - Yu Zhang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China.
| | - Xue-Gang Luo
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, 621010, China
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Alomari DZ, Alqudah AM, Pillen K, von Wirén N, Röder MS. Toward identification of a putative candidate gene for nutrient mineral accumulation in wheat grains for human nutrition purposes. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6305-6318. [PMID: 34145452 PMCID: PMC8483787 DOI: 10.1093/jxb/erab297] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 06/16/2021] [Indexed: 05/21/2023]
Abstract
A multilocus genome-wide association study of a panel of 369 diverse wheat (Triticum aestivum) genotypes was carried out in order to examine the genetic basis of variations in nutrient mineral concentrations in the grains. The panel was grown under field conditions for three consecutive years and the concentrations of Ca, K, Mg, Mn, P, and S were determined. Wide ranges of natural variation were detected among the genotypes. Strong positive correlations were found among the minerals except for K, which showed negative correlation trends with the other minerals. Genetic association analysis detected 86 significant marker-trait associations (MTAs) underlying the natural variations in mineral concentrations in grains. The major MTA was detected on the long arm of chromosome 5A and showed a pleiotropic effect on Ca, K, Mg, Mn, and S. Further significant MTAs were distributed among the whole genome except for chromosomes 3D and 6D. We identified putative candidate genes that are potentially involved in metal uptake, transport, and assimilation, including TraesCS5A02G542600 on chromosome 5A, which was annotated as a Major Facilitator Superfamily transporter and acted on all the minerals except K. TraesCS5A02G542600 was highly expressed in seed coat, and to a lesser extent in the peduncle, awns, and lemma. Our results provide important insights into the genetic basis of enhancement of nutrient mineral concentrations that can help to inform future breeding studies in order to improve human nutrition.
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Affiliation(s)
- Dalia Z Alomari
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D-06466 Stadt Seeland OT Gatersleben, Germany
- Correspondence: or
| | - Ahmad M Alqudah
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle/Saale, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120 Halle/Saale, Germany
| | - Nicolaus von Wirén
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D-06466 Stadt Seeland OT Gatersleben, Germany
| | - Marion S Röder
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, D-06466 Stadt Seeland OT Gatersleben, Germany
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Li C, Luo Y, Jin M, Sun S, Wang Z, Li Y. Response of Lignin Metabolism to Light Quality in Wheat Population. FRONTIERS IN PLANT SCIENCE 2021; 12:729647. [PMID: 34589105 PMCID: PMC8473876 DOI: 10.3389/fpls.2021.729647] [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: 06/23/2021] [Accepted: 08/13/2021] [Indexed: 06/02/2023]
Abstract
The low red/far-red (R/FR) light proportion at the base of the high-density wheat population leads to poor stem quality and increases lodging risk. We used Shannong 23 and Shannong 16 as the test materials. By setting three-light quality treatments: normal light (CK), red light (RL), and far-red light (FRL), we irradiated the base internodes of the stem with RL and FRL for 7h. Our results showed that RL irradiation enhanced stem quality, as revealed by increased breaking strength, stem diameter, wall thickness and, dry weight per unit length, and the total amount of lignin and related gene expression increased, at the same time. The composition of lignin subunits was related to the lodging resistance of wheat. The proportion of S+G subunits and H subunits played a key role in wheat lodging resistance. RL could increase the content of S subunits and G subunits and the proportion of S+G subunits, reduce the proportion of H subunits. We described here, to the best of our knowledge, the systematic study of the mechanism involved in the regulation of stem breaking strength by light quality, particularly the effect of light quality on lignin biosynthesis and its relationship with lodging resistance in wheat.
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Affiliation(s)
| | | | | | | | | | - Yong Li
- State Key Laboratory of Crop Biology, Agronomy College of Shandong Agricultural University, Tai’an, China
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Malik P, Kumar J, Sharma S, Sharma R, Sharma S. Multi-locus genome-wide association mapping for spike-related traits in bread wheat (Triticum aestivum L.). BMC Genomics 2021; 22:597. [PMID: 34353288 PMCID: PMC8340506 DOI: 10.1186/s12864-021-07834-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 06/23/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Bread wheat (Triticum aestivum L.) is one of the most important cereal food crops for the global population. Spike-layer uniformity (the consistency of the spike distribution in the vertical space)-related traits (SLURTs) are quantitative and have been shown to directly affect yield potential by modifying the plant architecture. Therefore, these parameters are important breeding targets for wheat improvement. The present study is the first genome-wide association study (GWAS) targeting SLURTs in wheat. In this study, a set of 225 diverse spring wheat accessions were used for multi-locus GWAS to evaluate SLURTs, including the number of spikes per plant (NSPP), spike length (SL), number of spikelets per spike (NSPS), grain weight per spike (GWPS), lowest tiller height (LTH), spike-layer thickness (SLT), spike-layer number (SLN) and spike-layer uniformity (SLU). RESULTS In total, 136 significant marker trait associations (MTAs) were identified when the analysis was both performed individually and combined for two environments. Twenty-nine MTAs were detected in environment one, 48 MTAs were discovered in environment two and 59 MTAs were detected using combined data from the two environments. Altogether, 15 significant MTAs were found for five traits in one of the two environments, and four significant MTAs were detected for the two traits, LTH and SLU, in both environments i.e. E1, E2 and also in combined data from the two environments. In total, 279 candidate genes (CGs) were identified, including Chaperone DnaJ, ABC transporter-like, AP2/ERF, SWEET sugar transporter, as well as genes that have previously been associated with wheat spike development, seed development and grain yield. CONCLUSIONS The MTAs detected through multi-locus GWAS will be useful for improving SLURTs and thus yield in wheat production through marker-assisted and genomic selection.
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Affiliation(s)
- Parveen Malik
- Department of Genetics and Plant Breeding, ChaudharyCharan Singh University (CCSU), Meerut, 250 004, India
| | - Jitendra Kumar
- Department of Genetics and Plant Breeding, ChaudharyCharan Singh University (CCSU), Meerut, 250 004, India.,National Agri-Food Biotechnology Institute (NABI), Sector 81(Knowledge City), SahibzadaAjit Singh Nagar, Punjab, 140306, India
| | - Shiveta Sharma
- Department of Genetics and Plant Breeding, ChaudharyCharan Singh University (CCSU), Meerut, 250 004, India
| | - Rajiv Sharma
- Scotland's Rural College (SRUC), Peter Wilson Building, West Mains Road, Edinburgh, EH9 3JG, UK
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, ChaudharyCharan Singh University (CCSU), Meerut, 250 004, India.
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Malik P, Kumar J, Singh S, Sharma S, Meher PK, Sharma MK, Roy JK, Sharma PK, Balyan HS, Gupta PK, Sharma S. Single-trait, multi-locus and multi-trait GWAS using four different models for yield traits in bread wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2021; 41:46. [PMID: 37309385 PMCID: PMC10236106 DOI: 10.1007/s11032-021-01240-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 06/30/2021] [Indexed: 06/14/2023]
Abstract
A genome-wide association study (GWAS) for 10 yield and yield component traits was conducted using an association panel comprising 225 diverse spring wheat genotypes. The panel was genotyped using 10,904 SNPs and evaluated for three years (2016-2019), which constituted three environments (E1, E2 and E3). Heritability for different traits ranged from 29.21 to 97.69%. Marker-trait associations (MTAs) were identified for each trait using data from each environment separately and also using BLUP values. Four different models were used, which included three single trait models (CMLM, FarmCPU, SUPER) and one multi-trait model (mvLMM). Hundreds of MTAs were obtained using each model, but after Bonferroni correction, only 6 MTAs for 3 traits were available using CMLM, and 21 MTAs for 4 traits were available using FarmCPU; none of the 525 MTAs obtained using SUPER could qualify after Bonferroni correction. Using BLUP, 20 MTAs were available, five of which also figured among MTAs identified for individual environments. Using mvLMM model, after Bonferroni correction, 38 multi-trait MTAs, for 15 different trait combinations were available. Epistatic interactions involving 28 pairs of MTAs were also available for seven of the 10 traits; no epistatic interactions were available for GNPS, PH, and BYPP. As many as 164 putative candidate genes (CGs) were identified using all the 50 MTAs (CMLM, 3; FarmCPU, 9; mvLMM, 6, epistasis, 21 and BLUP, 11 MTAs), which ranged from 20 (CMLM) to 66 (epistasis) CGs. In-silico expression analysis of CGs was also conducted in different tissues at different developmental stages. The information generated through the present study proved useful for developing a better understanding of the genetics of each of the 10 traits; the study also provided novel markers for marker-assisted selection (MAS) to be utilized for the development of wheat cultivars with improved agronomic traits. Supplementary Information The online version contains supplementary material available at 10.1007/s11032-021-01240-1.
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Affiliation(s)
- Parveen Malik
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Jitendra Kumar
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
- National Agri-Food Biotechnology Institute (NABI), Sector 81, Sahibzada Ajit Singh Nagar, 140306 Punjab India
| | - Sahadev Singh
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Shiveta Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Prabina Kumar Meher
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi 110012, India
| | - Mukesh Kumar Sharma
- Department of Mathematics, Chaudhary Charan Singh University, Meerut 250004, India
| | - Joy Kumar Roy
- National Agri-Food Biotechnology Institute (NABI), Sector 81, Sahibzada Ajit Singh Nagar, 140306 Punjab India
| | - Pradeep Kumar Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Harindra Singh Balyan
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Pushpendra Kumar Gupta
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut 250004, India
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Liu W, Li S, Zhang C, Jin F, Li W, Li X. Identification of Candidate Genes for Drought Tolerance at Maize Seedlings Using Genome-Wide Association. IRANIAN JOURNAL OF BIOTECHNOLOGY 2021; 19:e2637. [PMID: 34825009 PMCID: PMC8590722 DOI: 10.30498/ijb.2021.209324.2637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
BACKGROUND Drought stress is a serious threat that limit maize growth and production. OBJECTIVES The assessment tolerance level of maize by measuring changes in the main biochemical and physiological indicators under drought stress. MATERIAL AND METHODS We performed a genome-wide association analysis of biochemical and physiological indicators using an elite association panel. RESULTS The results revealed that eight significant SNPs (p<0.05/N) located in eight genes that are distributed on different chromosomes were associated with drought resistance indices under drought stress. Among these genes, four genes were linked via the associated SNPs with drought-resistance indices of the malondialdehyde activity (MDA), three genes were linked with drought resistance indexes of the superoxide dismutase activity (SOD), and one gene was linked with drought resistance indexes of relative conductivity (REC). The candidate genes functioned as transcription factors, enzymes, and transporters, which included trehalase, the AP2/EREB160 transcription factor, and glutathione S-transferase and also encoded a gene of unknown function. These genes may be directly or indirectly involved in drought resistance. The expression levels of ZmEREB160 responded to ABA and drought stress. CONCLUSIONS These results provided good information to understand the genetic basis of variation in drought resistance indices of biochemical and physiological indicators during drought stress.
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Affiliation(s)
- Wenping Liu
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, Jilin, China
| | - Shufang Li
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, Jilin, China
| | - Chunxiao Zhang
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, Jilin, China
| | - Fengxue Jin
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, Jilin, China
| | - Wanjun Li
- Taonan Research Center, Jilin Academy of Agricultural Sciences, Taonan 137100, Jilin, China
| | - Xiaohui Li
- Crop Germplasm Resources Institute, Jilin Academy of Agricultural Sciences, Gongzhuling 136100, Jilin, China
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Su J, Zhang C, Zhu L, Yang N, Yang J, Ma B, Ma F, Li M. MdFRK2-mediated sugar metabolism accelerates cellulose accumulation in apple and poplar. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:137. [PMID: 34130710 PMCID: PMC8204578 DOI: 10.1186/s13068-021-01989-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 06/08/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Cellulose is not only a common component in vascular plants, but also has great economic benefits for paper, wood, and industrial products. In addition, its biosynthesis is highly regulated by carbohydrate metabolism and allocation in plant. MdFRK2, which encodes a key fructokinase (FRK) in apple, showed especially high affinity to fructose and regulated carbohydrate metabolism. RESULTS It was observed that overexpression of MdFRK2 in apple decreased sucrose (Suc) and fructose (Fru) with augmented FRK activity in stems, and caused the alterations of many phenotypic traits that include increased cellulose content and an increase in thickness of the phloem region. To further investigate the involved mechanisms, we generated FRK2-OE poplar lines OE#1, OE#4 and OE#9 and discovered (1) that overexpression of MdFRK2 resulted in the huge increased cellulose level by shifting the fructose 6-phosphate or glucose 6-phsophate towards UDPG formation, (2) a direct metabolic pathway for the biosynthesis of cellulose is that increased cleavage of Suc into UDP-glucose (UDPG) for cellulose synthesis via the increased sucrose synthase (SUSY) activity and transcript levels of PtrSUSY1, (3) that the increased FRK activity increases the sink strength overall so there is more carbohydrate available to fuel increased cambial activity and that resulted in more secondary phloem. These results demonstrated that MdFRK2 overexpression would significantly changes the photosynthetic carbon flux from sucrose and hexose to UDPG for increased cellulose synthesis. CONCLUSIONS The present data indicated that MdFRK2 overexpression in apple and poplar changes the photosynthetic carbon flux from sucrose and hexose to UDPG for stem cellulose synthesis. A strategy is proposed to increase cellulose production by regulating sugar metabolism as a whole.
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Affiliation(s)
- Jing Su
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Chunxia Zhang
- College of Forestry, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Lingcheng Zhu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Nanxiang Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Jingjing Yang
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Baiquan Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Mingjun Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100 Shaanxi China
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Ageeva EV, Leonova IN, Likhenko IE. [Lodging in wheat: genetic and environmental factors and ways of overcoming]. Vavilovskii Zhurnal Genet Selektsii 2021; 24:356-362. [PMID: 33659818 PMCID: PMC7716515 DOI: 10.18699/vj20.628] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Lodging is one of the main factors in reducing the yield and grain quality of winter and spring wheat varieties. The resistance of wheat cultivars to lodging largely depends on environmental factors, biological and morphological features of the stem and root systems. Selection of the varieties for resistance to lodging is relevant in many countries of the world and has a number of achievements. Plant height is one of the most important morphological characters associated with lodging resistance. Breeding of the varieties carrying the dwarfing genes (Rht) is the main direction to reduce the risk of lodging. The Rht-B1b, Rht-D1b, Rht8 and Rht11 genes are widely used throughout the world due to their significant influence on agronomically valuable traits, including lodging. It turned out to be important to study the anatomical and morphological features and chemical composition of stem tissues, which complement the assessment of resistance to lodging and allow the varietal material to be more fully characterized. The thickness of stem internodes and their anatomical structure play an important role in the stem strength. The diameter of the stem, its thickness and weight, a large number of vascular bundles and a wide ring of mechanical tissues correlate with resistance to lodging. The content of lignin, silicon and cellulose are important structural components and provide the stem strength of wheat plants. Molecular genetic analysis and mapping of genes and quantitative trait loci are of great importance in identifying the genetic basis of the relationship between the anatomical and morphophysiological characters of the stem and root system and lodging. Genetic factors reflecting correlations between the lodging and the thickness of the stem wall, the number of vascular bundles and other characters were mapped to chromosomes 1A, 1B, 2A, 2D, 3A, 4B, 4D, 5A, 5D, 6D and 7D. It has been found that loci with high phenotypic effects on lodging tolerance are colocalized with loci responsible for plant height, stem diameter and stem strength. To increase resistance to lodging, it is necessary to develop a set of agrotechnical methods that reduce the influence of soil and climatic factors and create wheat varieties tolerant to lodging.
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Affiliation(s)
- E V Ageeva
- Siberian Research Institute of Plant Production and Breeding - Branch of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I N Leonova
- Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - I E Likhenko
- Siberian Research Institute of Plant Production and Breeding - Branch of the Institute of Cytology and Genetics of Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
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Xu D, Xie Y, Guo H, Zeng W, Xiong H, Zhao L, Gu J, Zhao S, Ding Y, Liu L. Transcriptome Analysis Reveals a Potential Role of Benzoxazinoid in Regulating Stem Elongation in the Wheat Mutant qd. Front Genet 2021; 12:623861. [PMID: 33633784 PMCID: PMC7900560 DOI: 10.3389/fgene.2021.623861] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 01/14/2021] [Indexed: 11/13/2022] Open
Abstract
The stems of cereal crops provide both mechanical support for lodging resistance and a nutrient supply for reproductive organs. Elongation, which is considered a critical phase for yield determination in winter wheat (Triticum aestivum L.), begins from the first node detectable to anthesis. Previously, we characterized a heavy ion beam triggered wheat mutant qd, which exhibited an altered stem elongation pattern without affecting mature plant height. In this study, we further analyzed mutant stem developmental characteristics by using transcriptome data. More than 40.87 Mb of clean reads including at least 36.61 Mb of unique mapped reads were obtained for each biological sample in this project. We utilized our transcriptome data to identify 124,971 genes. Among these genes, 4,340 differentially expressed genes (DEG) were identified between the qd and wild-type (WT) plants. Compared to their WT counterparts, qd plants expressed 2,462 DEGs with downregulated expression levels and 1878 DEGs with upregulated expression levels. Using DEXSeq, we identified 2,391 counting bins corresponding to 1,148 genes, and 289 of them were also found in the DEG analysis, demonstrating differences between qd and WT. The 5,199 differentially expressed genes between qd and WT were employed for GO and KEGG analyses. Biological processes, including protein-DNA complex subunit organization, protein-DNA complex assembly, nucleosome organization, nucleosome assembly, and chromatin assembly, were significantly enriched by GO analysis. However, only benzoxazinoid biosynthesis pathway-associated genes were enriched by KEGG analysis. Genes encoding the benzoxazinoid biosynthesis enzymes Bx1, Bx3, Bx4, Bx5, and Bx8_9 were confirmed to be differentially expressed between qd and WT. Our results suggest that benzoxazinoids could play critical roles in regulating the stem elongation phenotype of qd.
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Affiliation(s)
- Daxing Xu
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Yongdun Xie
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Huijun Guo
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Weiwei Zeng
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Hongchun Xiong
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Linshu Zhao
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Jiayu Gu
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Shirong Zhao
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Yuping Ding
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
| | - Luxiang Liu
- National Engineering Laboratory for Crop Molecular Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, National Center of Space Mutagenesis for Crop Improvement, Beijing, China
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