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García-Fernández C, Jurado M, Campa A, Bitocchi E, Papa R, Ferreira JJ. Genetic control of pod morphological traits and pod edibility in a common bean RIL population. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 137:6. [PMID: 38091106 PMCID: PMC10719158 DOI: 10.1007/s00122-023-04516-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2023] [Accepted: 11/30/2023] [Indexed: 12/17/2023]
Abstract
KEY MESSAGE QTL mapping, association analysis, and colocation study with previously reported QTL revealed three main regions controlling pod morphological traits and two loci for edible pod characteristics on the common bean chromosomes Pv01 and Pv06. Bean pod phenotype is a complex characteristic defined by the combination of different traits that determine the potential use of a genotype as a snap bean. In this study, the TUM RIL population derived from a cross between 'TU' (dry) and 'Musica' (snap) was used to investigate the genetic control of pod phenotype. The character was dissected into pod morphological traits (PMTs) and edible pod characteristics (EPC). The results revealed 35 QTL for PMTs located on seven chromosomes, suggesting a strong QTL colocation on chromosomes Pv01 and Pv06. Some QTL were colocated with previously reported QTL, leading to the mapping of 15 consensus regions associated with bean PMTs. Analysis of EPC of cooked beans revealed that two major loci with epistatic effect, located on chromosomes Pv01 and Pv06, are involved in the genetic control of this trait. An association study using a subset of the Spanish Diversity Panel (snap vs. non-snap) detected 23 genomic regions, with three regions being mapped at a position similar to those of two loci identified in the TUM population. The results demonstrated the relevant roles of Pv01 and Pv06 in the modulation of bean pod phenotype. Gene ontology enrichment analysis revealed a significant overrepresentation of genes regulating the phenylpropanoid metabolic process and auxin response in regions associated with PMTs and EPC, respectively. Both biological functions converged in the lignin biosynthetic pathway, suggesting the key role of the pathway in the genetic control of bean pod phenotype.
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Affiliation(s)
- Carmen García-Fernández
- Plant Genetic Group, Regional Service for Agrofood Research and Development (SERIDA), 33300, Villaviciosa, Asturias, Spain.
| | - Maria Jurado
- Plant Genetic Group, Regional Service for Agrofood Research and Development (SERIDA), 33300, Villaviciosa, Asturias, Spain
| | - Ana Campa
- Plant Genetic Group, Regional Service for Agrofood Research and Development (SERIDA), 33300, Villaviciosa, Asturias, Spain
| | - Elena Bitocchi
- Department of Agricultural, Food, and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, 60131, Ancona, Italy
| | - Roberto Papa
- Department of Agricultural, Food, and Environmental Sciences, Marche Polytechnic University, Via Brecce Bianche, 60131, Ancona, Italy
| | - Juan Jose Ferreira
- Plant Genetic Group, Regional Service for Agrofood Research and Development (SERIDA), 33300, Villaviciosa, Asturias, Spain
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2
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Zrig A, Yousif Sidahmed Elsheikh S, Hamouda F, Najar B, A. Alsherif E, Magdy Korany S, Hassan AHA, AbdElgawad H. Potassium Nitrate and Ascorbic Acid Priming Improved Tissue Chemical Composition and Antioxidant and Antimicrobial Activities of Linseed ( Linum usitatissimum L.) Sprouts. ACS OMEGA 2023; 8:35975-35987. [PMID: 37810652 PMCID: PMC10551915 DOI: 10.1021/acsomega.3c03002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 09/06/2023] [Indexed: 10/10/2023]
Abstract
Potassium nitrate (KNO3) and ascorbic acid (AsA) priming can effectively boost biomass accumulation and nutritional value of plants; nevertheless, few studies investigated their effects on seed sprouting. Thus, we aimed to explore the effects of KNO3 and AsA priming on linseed (Linum usitatissimum L.) sprout growth and assess the changes in bioactive compound levels, which provide valuable insights into the potential benefits of these priming treatments on sprout quality and nutritional value. To this end, germination, biomass accumulation, photosynthetic pigments, primary and secondary metabolites, and mineral profiles in the primed sprouts were evaluated. Moreover, to assess the impact on biological value, we determined the antioxidant and antimicrobial activities of the treated sprout extract. A marked enhancement was observed in germination and pigment levels of KNO3- and AsA-primed sprouts. These increases were in line with induced primary metabolites (e.g., carbohydrate and amino acid contents), particularly under KNO3 treatment. There was also an increase in amino acid metabolism (e.g., increased GS, GDH, and GOGAT enzyme activities), nitrogen level, and nitrate reductase (NR) activity. The linseed sprouts primed with AsA exhibited strong antioxidant and antibacterial activities. Consistently, high levels of polyphenols, flavonoids, total AsA, and tocopherols, as well as improved activity of antioxidant enzymes [peroxidase (POX), catalase (CAT), and superoxide dismutase (SOD)], were recorded. This study proposes KNO3 and AsA priming as an innovative approach to improving the nutritional and health-promoting properties of linseed sprouts. This knowledge will contribute to a better understanding of the biochemical processes involved in improving the nutritional quality and functional benefits of linseed sprouts.
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Affiliation(s)
- Ahlem Zrig
- Higher Institute of Preparatory Studies in Biology and Geology, University of Carthage, 1054 Tunis, Tunisia
- Laboratory of Engineering Processes and
Industrial Systems, Chemical Engineering Department, National School
of Engineers of Gabes, University of Gabes, 6072 Gabes, Tunisia
| | | | - Foued Hamouda
- Research Unit in Enterprise and Decisions, Higher Institute of Management, Road Jilani Habib, 6002 Gabes Tunis, Tunisia
| | - Basma Najar
- Department of Agricultural, Food and Agri-environmental Sciences, University of Pisa, Via del Borghetto, 80, 56124, Pisa, Italy
| | - Emad A. Alsherif
- Department
of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni Suef 62511, Egypt
| | - Shereen Magdy Korany
- Department of Biology, College of Science, Princess Nourah bint Abdulrahman University, P.O. Box 84428, Riyadh 11671, Saudi Arabia
| | | | - Hamada AbdElgawad
- Department
of Botany and Microbiology, Faculty of Science, Beni-Suef University, Beni Suef 62511, Egypt
- Integrated Molecular Plant
Physiology Research, Department of Biology, University of Antwerp, 2020 Antwerp, Belgium
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3
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Liu N, Wei Z, Min X, Yang L, Zhang Y, Li J, Yang Y. Genome-Wide Identification and Expression Analysis of the SWEET Gene Family in Annual Alfalfa ( Medicago polymorpha). PLANTS (BASEL, SWITZERLAND) 2023; 12:1948. [PMID: 37653865 PMCID: PMC10222687 DOI: 10.3390/plants12101948] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/03/2023] [Accepted: 05/06/2023] [Indexed: 09/02/2023]
Abstract
SWEET (Sugars will eventually be exported transporter) proteins are a group of sugar transporters that are involved in sugar efflux, phloem loading, reproductive development, plant senescence, and stress responses. In this study, 23 SWEET transporter members were identified in the Medicago polymorpha genome, heterogeneously distributed on seven chromosomes. These MpSWEET genes were divided into four subfamilies, which showed similar gene structure and motif composition within the same subfamily. Seventeen MpSWEET genes encode seven transmembrane helices (TMHs), and all MpSWEET proteins possess conserved membrane domains and putative serine phosphorylation sites. Four and three pairs of MpSWEET genes were predicted to be segmentally and tandemly duplicated, respectively, which may have contributed to their evolution of M. polymorpha. The results of microarray and RNA-Seq data showed that some MpSWEET genes were specifically expressed in disparate developmental stages (including seedling stage, early flowering stage, and late flowering stage) or tissues such as flower and large pod. Based on protein network interaction and expression patterns of MpSWEET genes, six MpSWEET genes were selected for further quantitative real-time PCR validation in different stress treatments. qRT-PCR results showed that MpSWEET05, MpSWEET07, MpSWEET12, MpSWEET15, and MpSWEET21 were significantly upregulated for at least two of the three abiotic stress treatments. These findings provide new insights into the complex transcriptional regulation of MpSWEET genes, which facilitates future research to elucidate the function of MpSWEET genes in M. polymorpha and other legume crops.
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Affiliation(s)
- Nana Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhenwu Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Institute of Grassland Science, Yangzhou University, Yangzhou 225009, China
| | - Xueyang Min
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Linghua Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Youxin Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Jiaqing Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yuwei Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
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Yang L, Min X, Wei Z, Liu N, Li J, Zhang Y, Yang Y. Genome-Wide Identification and Expression Analysis of the Dof Transcription Factor in Annual Alfalfa Medicago polymorpha. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12091831. [PMID: 37176890 PMCID: PMC10181442 DOI: 10.3390/plants12091831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 05/15/2023]
Abstract
The Dof transcription factor is a plant-specific transcription gene family that plays various biological functions in plant development and stress response. However, no relevant research has been conducted on Medicago polymorpha. Here, 36 MpDof genes were identified in the M. polymorpha genome and further divided into 10 groups based on the comparative phylogenetic analysis. The essential information of MpDof genes, such as chromosomal localization, gene structure, conserved motifs, and selective pressures were systematically analyzed. All 36 MpDof genes were predicted to contain more cis-acting elements related to hormone response. MpDof24 and MpDof25 were predicted to interact with MpDof11 and MpDof26 to involve in the photoperiod blooms process. The MpDof genes showed a diverse expression pattern in different tissues. Notably, MpDof29 and MpDof31 were specifically expressed in the large pod and root, respectively, suggesting their crucial role in the pod and root development. qRT-PCR analysis indicated that the expression levels of MpDof10, MpDof25, MpDof26, and MpDof29 were obviously up-regulated under drought, salt, and cold stress. Collectively, genome-wide identification, evolutionary, and expression analysis of the Dof transcription gene family in M. polymorpha will provide new information to further understand and utilize the function of these Dof genes in Medicago plants.
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Affiliation(s)
- Linghua Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Institution of Grassland Science, Yangzhou University, Yangzhou 225009, China
| | - Xueyang Min
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Institution of Grassland Science, Yangzhou University, Yangzhou 225009, China
| | - Zhenwu Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Institution of Grassland Science, Yangzhou University, Yangzhou 225009, China
| | - Nana Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Institution of Grassland Science, Yangzhou University, Yangzhou 225009, China
| | - Jiaqing Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Institution of Grassland Science, Yangzhou University, Yangzhou 225009, China
| | - Youxin Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Institution of Grassland Science, Yangzhou University, Yangzhou 225009, China
| | - Yuwei Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
- Institution of Grassland Science, Yangzhou University, Yangzhou 225009, China
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5
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Chen Y, Fang T, Su H, Duan S, Ma R, Wang P, Wu L, Sun W, Hu Q, Zhao M, Sun L, Dong X. A reference-grade genome assembly for Astragalus mongholicus and insights into the biosynthesis and high accumulation of triterpenoids and flavonoids in its roots. PLANT COMMUNICATIONS 2023; 4:100469. [PMID: 36307985 PMCID: PMC10030368 DOI: 10.1016/j.xplc.2022.100469] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 09/18/2022] [Accepted: 10/23/2022] [Indexed: 05/04/2023]
Abstract
Astragalus membranaceus var. mongholicus (AMM), a member of the Leguminosae, is one of the most important medicinal plants worldwide. The dried roots of AMM have a wide range of pharmacological effects and are a traditional Chinese medicine. Here, we report the first chromosome-level reference genome of AMM, comprising nine pseudochromosomes with a total size of 1.47 Gb and 27 868 protein-encoding genes. Comparative genomic analysis reveals that AMM has not experienced an independent whole-genome duplication (WGD) event after the WGD event shared by the Papilionoideae species. Analysis of long terminal repeat retrotransposons suggests a recent burst of these elements at approximately 0.13 million years ago, which may explain the large size of the AMM genome. Multiple gene families involved in the biosynthesis of triterpenoids and flavonoids were expanded, and our data indicate that tandem duplication has been the main driver for expansion of these families. Among the expanded families, the phenylalanine ammonia-lyase gene family was primarily expressed in the roots of AMM, suggesting their roles in the biosynthesis of phenylpropanoid compounds. The functional versatility of 2,3-oxidosqualene cyclase genes in cluster III may play a critical role in the diversification of triterpenoids in AMM. Our findings provide novel insights into triterpenoid and flavonoid biosynthesis and can facilitate future research on the genetics and medical applications of AMM.
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Affiliation(s)
- Yi Chen
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ting Fang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - He Su
- The Second Clinical Medical College of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou 510120, China
| | - Sifei Duan
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ruirui Ma
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Ping Wang
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Lin Wu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Wenbin Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Qichen Hu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Meixia Zhao
- Department of Microbiology and Cell Science, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL 32611, USA
| | - Lianjun Sun
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
| | - Xuehui Dong
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China.
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6
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Sun M, Zhang Y, Bai H, Sun G, Zhang J, Shi L. Population diversity analyses provide insights into key horticultural traits of Chinese native thymes. HORTICULTURE RESEARCH 2023; 10:uhac262. [PMID: 36778183 PMCID: PMC9907056 DOI: 10.1093/hr/uhac262] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Revised: 12/02/2022] [Accepted: 11/25/2022] [Indexed: 06/18/2023]
Abstract
Chinese native thymes (CNTs) in the genus Thymus (family Lamiaceae) are rich in bioactive terpenes, which exert antiviral, anti-inflammatory, antioxidation, immunological, and antimicrobial effects. Plants exhibit morphological variation, including erect-type and creeping-type growth forms; however, the molecular mechanisms underlying important horticultural traits have not been determined. Here, we collected 39 CNTs providing strategic plant resources for studies of lignin, terpenoids, and glandular trichomes of thymes. Using resequencing data as well as phenotypic, metabonomic, phylogenetic, population genetic, and transcriptomic analyses, we identified and characterized key genes involved in lignin biosynthesis, terpenoid biosynthesis, and glandular trichome formation. We found many regulatory genes or transcription factors related to these three important horticultural traits, including genes encoding caffeic acid O-methyltransferase (COMT), terpene synthase (TPS), v-myb avian myeloblastosis viral oncogene homolog (MYB), and homeodomain-leucine zipper (HD-ZIP). Population diversity analyses provided insights into growth form, terpenoid, and glandular trichome evolution in CNTs. Furthermore, our results revealed that T. mongolicus accessions might be wild ancestors, and T. quinquecostatus, T. quinquecostatus var. asiaticus, and T. quinquecostatus var. przewalskii might be transitional accessions that derived from T. mongolicus accessions. Finally, T. nervulosus, T. inaequalis, T. mandschuricus, T. curtus, T. amurensis, T. proximus, T. altaicus, T. roseus, and T. marschallianus showed high divergence. We found evidence for introgression between erect-type European cultivated thymes and CNTs. These findings improve our understanding of the determinants of variation in horticultural traits and provide candidate loci for research and breeding.
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Affiliation(s)
| | | | - Hongtong Bai
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
- China National Botanical Garden, Beijing 100093, China
| | - Guofeng Sun
- China National Botanical Garden, Beijing 100093, China
| | | | - Lei Shi
- Corresponding author. E-mail: ,
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Ren H, Wei Z, Zhou B, Chen X, Gao Q, Zhang Z. Molecular marker development and genetic diversity exploration in Medicago polymorpha. PeerJ 2023; 11:e14698. [PMID: 36684677 PMCID: PMC9851046 DOI: 10.7717/peerj.14698] [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: 04/26/2022] [Accepted: 12/14/2022] [Indexed: 01/17/2023] Open
Abstract
Medicago polymorpha L. (bur clover), an invasive plant species of the genus Medicago, has been traditionally used in China as an edible vegetable crop because of its high nutritive value. However, few molecular markers for M. polymorpha have been identified. Using the recently published high-quality reference genome of M. polymorpha, we performed a specific-locus amplified fragment sequencing (SLAF-seq) analysis of 10 M. polymorpha accessions to identify molecular markers and explore genetic diversity. A total of 52,237 high-quality single nucleotide polymorphisms (SNPs) were developed. These SNPs were mostly distributed on pseudochromosome 3, least distributed on pseudochromosome 7, and relatively evenly distributed on five other pseudochromosomes of M. polymorpha. Phenotypic analysis showed that there was a great difference in phenotypic traits among different M. polymorpha accessions. Moreover, clustering all M. polymorpha accessions based on their phenotypic traits revealed three groups. Both phylogenetic analysis and principal component analysis (PCA) of all M. polymorpha accessions based on SNP markers consistently indicated that all M. polymorpha accessions could be divided into three distinct groups (I, II, and III). Subsequent genetic diversity analysis for the 10 M. polymorpha accessions validated the effectiveness of the M. polymorpha germplasm molecular markers in China. Additionally, SSR mining analysis was also performed to identify polymorphic SSR motifs, which could provide valuable candidate markers for the further breeding of M. polymorpha. Since M. polymorpha genetics have not been actively studied, the molecular markers generated from our research will be useful for further research on M. polymorpha resource utilization and marker-assisted breeding.
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Affiliation(s)
- Hailong Ren
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China,Guangzhou Academy of Agricultural Sciences, Guangzhou, Guangdong, China,Hainan Sanya Test Center of Crop Breeding, Xinjiang Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Zhenwu Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Bo Zhou
- Hainan Sanya Test Center of Crop Breeding, Xinjiang Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Xiang Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Qiang Gao
- Hainan Sanya Test Center of Crop Breeding, Xinjiang Academy of Agricultural Sciences, Sanya, Hainan, China
| | - Zhibin Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, Henan, China
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Kapazoglou A, Gerakari M, Lazaridi E, Kleftogianni K, Sarri E, Tani E, Bebeli PJ. Crop Wild Relatives: A Valuable Source of Tolerance to Various Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12020328. [PMID: 36679041 PMCID: PMC9861506 DOI: 10.3390/plants12020328] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 05/27/2023]
Abstract
Global climate change is one of the major constraints limiting plant growth, production, and sustainability worldwide. Moreover, breeding efforts in the past years have focused on improving certain favorable crop traits, leading to genetic bottlenecks. The use of crop wild relatives (CWRs) to expand genetic diversity and improve crop adaptability seems to be a promising and sustainable approach for crop improvement in the context of the ongoing climate challenges. In this review, we present the progress that has been achieved towards CWRs exploitation for enhanced resilience against major abiotic stressors (e.g., water deficiency, increased salinity, and extreme temperatures) in crops of high nutritional and economic value, such as tomato, legumes, and several woody perennial crops. The advances in -omics technologies have facilitated the elucidation of the molecular mechanisms that may underlie abiotic stress tolerance. Comparative analyses of whole genome sequencing (WGS) and transcriptomic profiling (RNA-seq) data between crops and their wild relative counterparts have unraveled important information with respect to the molecular basis of tolerance to abiotic stressors. These studies have uncovered genomic regions, specific stress-responsive genes, gene networks, and biochemical pathways associated with resilience to adverse conditions, such as heat, cold, drought, and salinity, and provide useful tools for the development of molecular markers to be used in breeding programs. CWRs constitute a highly valuable resource of genetic diversity, and by exploiting the full potential of this extended allele pool, new traits conferring abiotic-stress tolerance may be introgressed into cultivated varieties leading to superior and resilient genotypes. Future breeding programs may greatly benefit from CWRs utilization for overcoming crop production challenges arising from extreme environmental conditions.
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Affiliation(s)
- Aliki Kapazoglou
- Institute of Olive Tree, Subtropical Crops and Viticulture (IOSV), Department of Vitis, Hellenic Agricultural Organization-Dimitra (ELGO-Dimitra), Sofokli Venizelou 1, Lykovrysi, 14123 Athens, Greece
| | - Maria Gerakari
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Efstathia Lazaridi
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Konstantina Kleftogianni
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Efi Sarri
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Eleni Tani
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
| | - Penelope J. Bebeli
- Laboratory of Plant Breeding and Biometry, Department of Crop Science, Agricultural University of Athens, Iera Odos 75, 11855 Athens, Greece
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Yang S, Sun Z, Zhang G, Wang L, Zhong Q. Identification of the key metabolites and related genes network modules highly associated with the nutrients and taste components among different Pepino (Solanum muricatum) cultivars. Food Res Int 2023; 163:112287. [PMID: 36596193 DOI: 10.1016/j.foodres.2022.112287] [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: 04/15/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 12/12/2022]
Abstract
There is considerable knowledge about plant compounds that produce flavor, scent, and aroma. Aside from the similarities, however, groups of plant-produced nutrients and taste components have little in common with each other. Network analysis holds promise for metabolic gene discovery, which is especially important in plant systems where metabolic networks are not yet fully resolved. To bridge this gap, we propose a joint model of gene regulation and metabolic reactions in two different pepino varieties. Differential metabolomics analysis is carried out for detection of eventual interaction of compound. We adopted a multi-omics approach to profile the transcriptome and metabolome analyze differences in phenolic acids, flavonoids, organic acids, lipids, alkaloids, and sugars between LOF and SRF. The two most predominant classes of metabolites are phenolic acids and lipids in pepino. Overall results show enrichment in most DEGs was carbohydrate and biosynthesis of secondary metabolites pathway. Results of DEMs predominantly comprised N-p-coumaroyl agmatine and tryptamine, and significant differences were observed in their expression between LOF and SRF. Integrated DEMs and DEGs specific networks were constructed by combining two types of networks: transcriptional regulatory networks composed of interactions between DEMs and the regulated genes, and pepino metabolite-metabolite interaction networks. Newly discovered features, such as DEGs (USPA, UBE2 and DELLA) involved in the production of secondary metabolites are found in coregulated gene clusters. Moreover, lipid metabolites were most involved in DEMs correlations by OPLS-DA while identifying a significant number of DEGs co-regulated by SENP1, HMGCS et al. These results further that the metabolite discrepancies result from characterized the nutrients and taste components between two pepino genotype. Among the possible causes of the differences between species in pepino metabolite concentrations is co-regulated by these DEGs, continue to suggest that novel features of metabolite biosynthetic pathway remain to be uncovered. Finally, the integrated metabolome and transcriptome analyses have revealed that many important metabolic pathways are regulated at the transcriptional level. The metabolites content differences observed among varieties of the same species mainly originates from different regulated genes and enzymes expression. Overall, this study provides new insights into the underlying causes of differences in the plant metabolites and suggests that genetic data can be used to improve its nutrients and taste components.
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Affiliation(s)
- Shipeng Yang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China; College of Life Sciences, Northwest A&F University, Shaanxi, Yangling 712100, China
| | - Zhu Sun
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China
| | - Guangnan Zhang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China
| | - Lihui Wang
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China
| | - Qiwen Zhong
- Laboratory for Research and Utilization of Germplasm Resources in Qinghai Tibet Plateau, Agriculture and Forestry Sciences, Institute of Qinghai University, Qinghai, Xining 810016, China.
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10
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Zhang XX, Ren XL, Qi XT, Yang ZM, Feng XL, Zhang T, Wang HJ, Liang P, Jiang QY, Yang WJ, Fu Y, Chen M, Fu ZX, Xu B. Evolution of the CBL and CIPK gene families in Medicago: genome-wide characterization, pervasive duplication, and expression pattern under salt and drought stress. BMC PLANT BIOLOGY 2022; 22:512. [PMID: 36324083 PMCID: PMC9632064 DOI: 10.1186/s12870-022-03884-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Accepted: 10/17/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND Calcineurin B-like proteins (CBLs) are ubiquitous Ca2+ sensors that mediate plant responses to various stress and developmental processes by interacting with CBL-interacting protein kinases (CIPKs). CBLs and CIPKs play essential roles in acclimatization of crop plants. However, evolution of these two gene families in the genus Medicago is poorly understood. RESULTS A total of 68 CBL and 135 CIPK genes have been identified in five genomes from Medicago. Among these genomes, the gene number of CBLs and CIPKs shows no significant difference at the haploid genome level. Phylogenetic and comprehensive characteristic analyses reveal that CBLs and CIPKs are classified into four clades respectively, which is validated by distribution of conserved motifs. The synteny analysis indicates that the whole genome duplication events (WGDs) have contributed to the expansion of both families. Expression analysis demonstrates that two MsCBLs and three MsCIPKs are specifically expressed in roots, mature leaves, developing flowers and nitrogen fixing nodules of Medicago sativa spp. sativa, the widely grown tetraploid species. In particular, the expression of these five genes was highly up-regulated in roots when exposed to salt and drought stress, indicating crucial roles in stress responses. CONCLUSIONS Our study leads to a comprehensive understanding of evolution of CBL and CIPK gene families in Medicago, but also provides a rich resource to further address the functions of CBL-CIPK complexes in cultivated species and their closely related wild relatives.
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Affiliation(s)
- Xiao-Xia Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiao-Long Ren
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao-Tong Qi
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhi-Min Yang
- Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou, 075000, China
| | - Xiao-Lei Feng
- Zhangjiakou Academy of Agricultural Sciences, Zhangjiakou, 075000, China
| | - Tian Zhang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui-Jie Wang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Peng Liang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Qi-Ying Jiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen-Jun Yang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuan Fu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Min Chen
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing, 210014, China
| | - Zhi-Xi Fu
- College of Life Sciences, Sichuan Normal University, Chengdu, 610101, China
| | - Bo Xu
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
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11
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Liu B, Zhang D, Pan X. Nodules of wild legumes as unique natural hotspots of antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156036. [PMID: 35597353 DOI: 10.1016/j.scitotenv.2022.156036] [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: 04/15/2022] [Revised: 05/13/2022] [Accepted: 05/14/2022] [Indexed: 06/15/2023]
Abstract
Root nodules (RN) of legumes have distinct microenvironment from their symbiotic roots and surrounding soils. The rhizobia can withstand the host-produced phytoalexins and antimicrobial compounds. We thus hypothesize that the wild legume RN may develop unique natural resistome and be antibiotic resistance gene (ARG) hotspots. In this study, in comparison with rhizosphere soil (RS) and bulk soil (BS), we characterized the feature of antibiotic resistance in the RN of two wild legumes, Medicago polymorpha and Astragalus sinicus, by metagenomics. It was shown that the total relative abundance of ARGs followed the order of RN > RS > BS for both legumes. ARGs encoding antibiotic efflux pump predominated in all samples with increased proportion from BS to RN samples for both legumes. Totally 275 ARG subtypes were detected, and diversity of ARGs in RN was significantly lower than in BS samples for both legumes. 32 and 25 unique ARGs subtypes were detected in RN of both legumes. Bacterial community played a key role in shaping nodule-associated resistome because both ARG profiles and bacterial community differed greatly among BS, RS and RN. Rhizobia potentially hosted 10 and 15 ARGs subtypes for both legumes. The number and proportion of plasmid- and ARG-carrying contigs (ACCs) were higher in RN than in BS. Host tracking analysis of plasmid-ACCs suggests that proportion of rhizobial bacteria identified as their hosts decreased from BS to RN samples. No plasmid-ACCs with multiple ARGs were observed in BS samples, whereas they were detected in RN samples of both legumes. Our study showed that even wild legume nodules are unique natural ARG hotspots and enough attention should be paid to the dissemination risk of ARGs posed by globally produced legume crops.
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Affiliation(s)
- Bingshen Liu
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Daoyong Zhang
- Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China
| | - Xiangliang Pan
- Xinjiang Key Laboratory of Environmental Pollution and Bioremediation, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; Key Laboratory of Microbial Technology for Industrial Pollution Control of Zhejiang Province, College of Environment, Zhejiang University of Technology, Hangzhou 310014, China.
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12
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Bai G, Chen C, Zhao C, Zhou T, Li D, Zhou T, Li W, Lu Y, Cong X, Jia Y, Li S. The chromosome-level genome for Toxicodendron vernicifluum provides crucial insights into Anacardiaceae evolution and urushiol biosynthesis. iScience 2022; 25:104512. [PMID: 35733792 PMCID: PMC9207680 DOI: 10.1016/j.isci.2022.104512] [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] [Revised: 04/21/2022] [Accepted: 05/27/2022] [Indexed: 12/04/2022] Open
Abstract
The lacquer tree (Toxicodendron vernicifluum (Stokes) F.A. Barkley) is an important tree with economic, industrial, and medicinal values. Here, we generated the reference genome of T. vernicifluum at the chromosome level with 491.93 Mb in size, in which 98.26% of the assembled contigs were anchored onto 15 pseudochromosomes with the scaffold N50 of 32.97 Mb. Comparative genomic analysis revealed the gene families related to urushiol biosynthesis were expanded, contributing to the ecological fitness and biological adaptability of the lacquer tree. We combined multi-omics data to identify genes that encode key enzymes in the T. vernicifluum urushiol and lignin biosynthetic pathways. Furthermore, the unique active metabolites, such as butin and fisetin, in cultivar lacquers were identified by metabolism profiling. Our work would provide crucial insights into metabolite synthesis such as urushiol and lignin, meanwhile offer a basis for further exploration of the cultivation and breeding of T. vernicifluum and other Anacardiaceae members. We provide the first chromosome-level genome for Toxicodendron vernicifluum We explore the phylogenetic position of lacquer tree We identify genes involved in the urushiol and lignin biosynthetic pathways Analysis of the unique active metabolites in cultivar lacquers by LC-MS/MS is reported
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Affiliation(s)
- Guoqing Bai
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Chen Chen
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Chenxi Zhao
- BGI Genomics, BGI-Shenzhen, Shenzhen 518083, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tao Zhou
- School of Pharmacy, Xi’an Jiaotong University, Xi’an 710061, China
| | - Dan Li
- SDIC Biotech Investment Co., Ltd., Shanghai 200082, China
| | - Tianhua Zhou
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China
| | - Weimin Li
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Yuan Lu
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Xiaofeng Cong
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Yun Jia
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
| | - Sifeng Li
- Xi’an Botanical Garden of Shaanxi Province, Shaanxi Province Qinling-Bashan Mountains Engineering Research Centre of Conservation and Utilization of Biological Resources, Xi’an 710061, China
- Corresponding author
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13
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Jha UC, Nayyar H, Parida SK, Bakır M, von Wettberg EJB, Siddique KHM. Progress of Genomics-Driven Approaches for Sustaining Underutilized Legume Crops in the Post-Genomic Era. Front Genet 2022; 13:831656. [PMID: 35464848 PMCID: PMC9021634 DOI: 10.3389/fgene.2022.831656] [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: 12/08/2021] [Accepted: 02/24/2022] [Indexed: 12/22/2022] Open
Abstract
Legume crops, belonging to the Fabaceae family, are of immense importance for sustaining global food security. Many legumes are profitable crops for smallholder farmers due to their unique ability to fix atmospheric nitrogen and their intrinsic ability to thrive on marginal land with minimum inputs and low cultivation costs. Recent progress in genomics shows promise for future genetic gains in major grain legumes. Still it remains limited in minor legumes/underutilized legumes, including adzuki bean, cluster bean, horse gram, lathyrus, red clover, urd bean, and winged bean. In the last decade, unprecedented progress in completing genome assemblies of various legume crops and resequencing efforts of large germplasm collections has helped to identify the underlying gene(s) for various traits of breeding importance for enhancing genetic gain and contributing to developing climate-resilient cultivars. This review discusses the progress of genomic resource development, including genome-wide molecular markers, key breakthroughs in genome sequencing, genetic linkage maps, and trait mapping for facilitating yield improvement in underutilized legumes. We focus on 1) the progress in genomic-assisted breeding, 2) the role of whole-genome resequencing, pangenomes for underpinning the novel genomic variants underlying trait gene(s), 3) how adaptive traits of wild underutilized legumes could be harnessed to develop climate-resilient cultivars, 4) the progress and status of functional genomics resources, deciphering the underlying trait candidate genes with putative function in underutilized legumes 5) and prospects of novel breeding technologies, such as speed breeding, genomic selection, and genome editing. We conclude the review by discussing the scope for genomic resources developed in underutilized legumes to enhance their production and play a critical role in achieving the "zero hunger" sustainable development goal by 2030 set by the United Nations.
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Affiliation(s)
- Uday Chand Jha
- ICAR-Indian Institute of Pulses Research (IIPR), Kanpur, India
| | | | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Melike Bakır
- Department of Agricultural Biotechnology, Faculty of Agriculture, Erciyes University, Kayseri, Turkey
| | - Eric J. B. von Wettberg
- Plant and Soil Science and Gund Institute for the Environment, The University of Vermont, Burlington, VT, United States
- Peter the Great St. Petersburg Polytechnic University, St. Petersburg, Russia
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14
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Choi IS, Wojciechowski MF, Steele KP, Hunter SG, Ruhlman TA, Jansen RK. Born in the mitochondrion and raised in the nucleus: evolution of a novel tandem repeat family in Medicago polymorpha (Fabaceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:389-406. [PMID: 35061308 DOI: 10.1111/tpj.15676] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Plant nuclear genomes harbor sequence elements derived from the organelles (mitochondrion and plastid) through intracellular gene transfer (IGT). Nuclear genomes also show a dramatic range of repeat content, suggesting that any sequence can be readily amplified. These two aspects of plant nuclear genomes are well recognized but have rarely been linked. Through investigation of 31 Medicago taxa we detected exceptionally high post-IGT amplification of mitochondrial (mt) DNA sequences containing rps10 in the nuclear genome of Medicago polymorpha and closely related species. The amplified sequences were characterized as tandem arrays of five distinct repeat motifs (2157, 1064, 987, 971, and 587 bp) that have diverged from the mt genome (mitogenome) in the M. polymorpha nuclear genome. The mt rps10-like arrays were identified in seven loci (six intergenic and one telomeric) of the nuclear chromosome assemblies and were the most abundant tandem repeat family, representing 1.6-3.0% of total genomic DNA, a value approximately three-fold greater than the entire mitogenome in M. polymorpha. Compared to a typical mt gene, the mt rps10-like sequence coverage level was 691.5-7198-fold higher in M. polymorpha and closely related species. In addition to the post-IGT amplification, our analysis identified the canonical telomeric repeat and the species-specific satellite arrays that are likely attributable to an ancestral chromosomal fusion in M. polymorpha. A possible relationship between chromosomal instability and the mt rps10-like tandem repeat family in the M. polymorpha clade is discussed.
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Affiliation(s)
- In-Su Choi
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287, USA
| | | | - Kelly P Steele
- Division of Science and Mathematics, Arizona State University, Mesa, AZ, 85212, USA
| | - Sarah G Hunter
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Tracey A Ruhlman
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
| | - Robert K Jansen
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, 78712, USA
- Centre of Excellence in Bionanoscience Research, Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia
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15
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Sakurai N. Recent applications of metabolomics in plant breeding. BREEDING SCIENCE 2022; 72:56-65. [PMID: 36045891 PMCID: PMC8987846 DOI: 10.1270/jsbbs.21065] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 12/19/2021] [Indexed: 05/27/2023]
Abstract
Metabolites play a central role in maintaining organismal life and in defining crop phenotypes, such as nutritional value, fragrance, color, and stress resistance. Among the 'omes' in biology, the metabolome is the closest to the phenotype. Consequently, metabolomics has been applied to crop improvement as method for monitoring changes in chemical compositions, clarifying the mechanisms underlying cellular functions, discovering markers and diagnostics, and phenotyping for mQTL, mGWAS, and metabolite-genome predictions. In this review, 359 reports of the most recent applications of metabolomics to plant breeding-related studies were examined. In addition to the major crops, more than 160 other crops including rare medicinal plants were considered. One bottleneck associated with using metabolomics is the wide array of instruments that are used to obtain data and the ambiguity associated with metabolite identification and quantification. To further the application of metabolomics to plant breeding, the features and perspectives of the technology are discussed.
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Affiliation(s)
- Nozomu Sakurai
- Bioinformation and DDBJ Center, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan
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16
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Medicago truncatula (model legume), Medicago sativa (alfalfa), Medicago polymorpha (bur clover), and Medicago ruthenica. Trends Genet 2022; 38:782-783. [DOI: 10.1016/j.tig.2022.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/07/2022] [Accepted: 03/07/2022] [Indexed: 11/22/2022]
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17
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Zhong Y, Chen Y, Zheng D, Pang J, Liu Y, Luo S, Meng S, Qian L, Wei D, Dai S, Zhou R. Chromosomal-level genome assembly of the orchid tree Bauhinia variegata (Leguminosae; Cercidoideae) supports the allotetraploid origin hypothesis of Bauhinia. DNA Res 2022; 29:6570587. [PMID: 35438173 PMCID: PMC9052405 DOI: 10.1093/dnares/dsac012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 04/14/2022] [Indexed: 11/20/2022] Open
Abstract
Cercidoideae, one of the six subfamilies of Leguminosae, contains one genus Cercis with its chromosome number 2n = 14 and all other genera with 2n = 28. An allotetraploid origin hypothesis for the common ancestor of non-Cercis genera in this subfamily has been proposed; however, no chromosome-level genomes from Cercidoideae have been available to test this hypothesis. Here, we conducted a chromosome-level genome assembly of Bauhinia variegata to test this hypothesis. The assembled genome is 326.4 Mb with the scaffold N50 of 22.1 Mb and contains 37,996 protein-coding genes. The Ks distribution between gene pairs in the syntenic regions indicates two whole-genome duplications (WGDs): one is B. variegata-specific, and the other is shared among core eudicots. Although Ks between gene pairs generated by the recent WGD in Bauhinia is greater than that between Bauhinia and Cercis, the WGD was not detected in Cercis, which can be explained by an accelerated evolutionary rate in Bauhinia after divergence from Cercis. Ks distribution and phylogenetic analysis for gene pairs generated by the recent WGD in Bauhinia and their corresponding orthologs in Cercis support the allopolyploidy origin hypothesis of Bauhinia. The genome of B. variegata also provides a genomic resource for dissecting genetic basis of its ornamental traits.
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Affiliation(s)
- Yan Zhong
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Yong Chen
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Danjing Zheng
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Jingyi Pang
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Ying Liu
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Shukai Luo
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Shiyuan Meng
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Lei Qian
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Dan Wei
- Guangdong Academy of Forestry, Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangzhou 510520, China
| | - Seping Dai
- Guangzhou Institute of Forestry and Landscape Architecture, Guangzhou 510405, China
| | - Renchao Zhou
- State Key Laboratory of Biocontrol and Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
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18
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Rubiales D, Annicchiarico P, Vaz Patto MC, Julier B. Legume Breeding for the Agroecological Transition of Global Agri-Food Systems: A European Perspective. FRONTIERS IN PLANT SCIENCE 2021; 12:782574. [PMID: 34868184 PMCID: PMC8637196 DOI: 10.3389/fpls.2021.782574] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Wider and more profitable legume crop cultivation is an indispensable step for the agroecological transition of global agri-food systems but represents a challenge especially in Europe. Plant breeding is pivotal in this context. Research areas of key interest are represented by innovative phenotypic and genome-based selection procedures for crop yield, tolerance to abiotic and biotic stresses enhanced by the changing climate, intercropping, and emerging crop quality traits. We see outmost priority in the exploration of genomic selection (GS) opportunities and limitations, to ease genetic gains and to limit the costs of multi-trait selection. Reducing the profitability gap of legumes relative to major cereals will not be possible in Europe without public funding devoted to crop improvement research, pre-breeding, and, in various circumstances, public breeding. While most of these activities may profit of significant public-private partnerships, all of them can provide substantial benefits to seed companies. A favorable institutional context may comprise some changes to variety registration tests and procedures.
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Affiliation(s)
- Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
| | | | | | - Bernadette Julier
- Institut National de Recherche Pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), URP3F, Lusignan, France
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19
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Oluwole OO, Aworunse OS, Aina AI, Oyesola OL, Popoola JO, Oyatomi OA, Abberton MT, Obembe OO. A review of biotechnological approaches towards crop improvement in African yam bean ( Sphenostylis stenocarpa Hochst. Ex A. Rich.). Heliyon 2021; 7:e08481. [PMID: 34901510 PMCID: PMC8642607 DOI: 10.1016/j.heliyon.2021.e08481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/11/2021] [Accepted: 11/19/2021] [Indexed: 11/29/2022] Open
Abstract
Globally, climate change is a major factor that contributes significantly to food and nutrition insecurity, limiting crop yield and availability. Although efforts are being made to curb food insecurity, millions of people still suffer from malnutrition. For the United Nations (UN) Sustainable Development Goal of Food Security to be achieved, diverse cropping systems must be developed instead of relying mainly on a few staple crops. Many orphan legumes have untapped potential that can be of significance for developing improved cultivars with enhanced tolerance to changing climatic conditions. One typical example of such an orphan crop is Sphenostylis stenocarpa Hochst. Ex A. Rich. Harms, popularly known as African yam bean (AYB). The crop is an underutilised tropical legume that is climate-resilient and has excellent potential for smallholder agriculture in sub-Saharan Africa (SSA). Studies on AYB have featured morphological characterisation, assessment of genetic diversity using various molecular markers, and the development of tissue culture protocols for rapidly multiplying propagules. However, these have not translated into varietal development, and low yields remain a challenge. The application of suitable biotechnologies to improve AYB is imperative for increased yield, sustainable utilisation and conservation. This review discusses biotechnological strategies with prospective applications for AYB improvement. The potential risks of these strategies are also highlighted.
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Affiliation(s)
- Olubusayo O. Oluwole
- Department of Biological Sciences, Covenant University, Canaan Land, Ota, Nigeria
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Oluwadurotimi S. Aworunse
- Department of Biological Sciences, Covenant University, Canaan Land, Ota, Nigeria
- UNESCO Chair on Plant Biotechnology, Plant Science Research Cluster, Covenant University, Canaan Land, Ota, Nigeria
| | - Ademola I. Aina
- Department of Crop Protection and Environmental Biology, University of Ibadan, Oyo State, Nigeria
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Olusola L. Oyesola
- Department of Biological Sciences, Covenant University, Canaan Land, Ota, Nigeria
- UNESCO Chair on Plant Biotechnology, Plant Science Research Cluster, Covenant University, Canaan Land, Ota, Nigeria
| | - Jacob O. Popoola
- Department of Biological Sciences, Covenant University, Canaan Land, Ota, Nigeria
- UNESCO Chair on Plant Biotechnology, Plant Science Research Cluster, Covenant University, Canaan Land, Ota, Nigeria
| | - Olaniyi A. Oyatomi
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Michael T. Abberton
- Genetic Resources Centre, International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Olawole O. Obembe
- Department of Biological Sciences, Covenant University, Canaan Land, Ota, Nigeria
- UNESCO Chair on Plant Biotechnology, Plant Science Research Cluster, Covenant University, Canaan Land, Ota, Nigeria
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