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Li R, Nie S, Zhang N, Tian M, Zhang L. Transcriptome Analysis Reveals a Major Gene Expression Pattern and Important Metabolic Pathways in the Control of Heterosis in Chinese Cabbage. PLANTS (BASEL, SWITZERLAND) 2023; 12:1195. [PMID: 36904055 PMCID: PMC10005390 DOI: 10.3390/plants12051195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
Although heterosis is commonly used in Chinese cabbage, its molecular basis is poorly understood. In this study, 16Chinese cabbage hybrids were utilized as test subjects to explore the potential molecular mechanism of heterosis. RNA sequencing revealed 5815-10,252 differentially expressed genes (DEGs) (female parent vs. male parent), 1796-5990 DEGs (female parent-vs-hybrid), and 2244-7063 DEGs (male parent vs. hybrid) in 16 cross combinations at the middle stage of heading. Among of them, 72.83-84.20% DEGs conformed to the dominant expression pattern, which is the predominant expression pattern in hybrids. There were 13 pathways in which DEGs were significantly enriched in most cross combinations. Among them, the plant-pathogen interaction (ko04626) and circadian rhythm-plant (ko04712)were significantly enriched by DEGs in strong heterosis hybrids. WGCNA also proved that the two pathways were significantly related to heterosis in Chinese cabbage.
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Mbebi AJ, Breitler JC, Bordeaux M, Sulpice R, McHale M, Tong H, Toniutti L, Castillo JA, Bertrand B, Nikoloski Z. A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids. G3 GENES|GENOMES|GENETICS 2022; 12:6632664. [PMID: 35792875 PMCID: PMC9434219 DOI: 10.1093/g3journal/jkac170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 06/14/2022] [Indexed: 11/14/2022]
Abstract
Abstract
Genomic prediction has revolutionized crop breeding despite remaining issues of transferability of models to unseen environmental conditions and environments. Usage of endophenotypes rather than genomic markers leads to the possibility of building phenomic prediction models that can account, in part, for this challenge. Here, we compare and contrast genomic prediction and phenomic prediction models for 3 growth-related traits, namely, leaf count, tree height, and trunk diameter, from 2 coffee 3-way hybrid populations exposed to a series of treatment-inducing environmental conditions. The models are based on 7 different statistical methods built with genomic markers and ChlF data used as predictors. This comparative analysis demonstrates that the best-performing phenomic prediction models show higher predictability than the best genomic prediction models for the considered traits and environments in the vast majority of comparisons within 3-way hybrid populations. In addition, we show that phenomic prediction models are transferrable between conditions but to a lower extent between populations and we conclude that chlorophyll a fluorescence data can serve as alternative predictors in statistical models of coffee hybrid performance. Future directions will explore their combination with other endophenotypes to further improve the prediction of growth-related traits for crops.
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Affiliation(s)
- Alain J Mbebi
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam , Potsdam-Golm 14476, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology , Potsdam-Golm 14476, Germany
| | - Jean-Christophe Breitler
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier 34398, France
| | - Mélanie Bordeaux
- Fundación Nicafrance , Finca La Cumplida Km. 147 Carretera Matagalpa - La Dalia, 3 Km al Noreste, Matagalpa, Nicaragua
| | - Ronan Sulpice
- National University Ireland Galway, Plant Systems Biology Laboratory, Ryan Institute, School of Natural Sciences , Galway H91 TK33, Ireland
| | - Marcus McHale
- National University Ireland Galway, Plant Systems Biology Laboratory, Ryan Institute, School of Natural Sciences , Galway H91 TK33, Ireland
| | - Hao Tong
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam , Potsdam-Golm 14476, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology , Potsdam-Golm 14476, Germany
- Center for Plant Systems Biology and Biotechnology , Plovdiv 4000, Bulgaria
| | - Lucile Toniutti
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier 34398, France
| | - Jonny Alonso Castillo
- Fundación Nicafrance , Finca La Cumplida Km. 147 Carretera Matagalpa - La Dalia, 3 Km al Noreste, Matagalpa, Nicaragua
| | - Benoît Bertrand
- Centre de Coopération Internationale en Recherche Agronomique pour le Développement, Montpellier 34398, France
| | - Zoran Nikoloski
- Bioinformatics Group, Institute of Biochemistry and Biology, University of Potsdam , Potsdam-Golm 14476, Germany
- Systems Biology and Mathematical Modeling Group, Max Planck Institute of Molecular Plant Physiology , Potsdam-Golm 14476, Germany
- Center for Plant Systems Biology and Biotechnology , Plovdiv 4000, Bulgaria
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Description of an Arabica Coffee Ideotype for Agroforestry Cropping Systems: A Guideline for Breeding More Resilient New Varieties. PLANTS 2022; 11:plants11162133. [PMID: 36015436 PMCID: PMC9414076 DOI: 10.3390/plants11162133] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 08/01/2022] [Accepted: 08/08/2022] [Indexed: 11/17/2022]
Abstract
Climate change (CC) is already impacting Arabica coffee cultivation in the intertropical zone. To deal with this situation, it is no longer possible to manage this crop using industrial agriculture techniques, which has been the main strategy implemented since the Green Revolution. Developing a more sustainable agriculture system that respects people and the environment is essential to guarantee future generations’ access to natural resources. In the case of Arabica coffee, the solution has been found. Agroforestry is proposed as an ecosystem-based strategy to mitigate and adapt to CC. At least 60% of Arabica coffee is produced in agroforestry systems (AFSs), which are the most sustainable way to produce coffee. Nevertheless, AFS coffee cultivation is currently uncompetitive partly because all modern varieties, selected for full-sun intensive cropping systems, have low yields in shaded environments. Here we review the reasons why agroforestry is part of the solution to CC, and why no breeding work has been undertaken for this cropping system. Based on the literature data, for breeding purposes we also define for the first time one possible coffee ideotype required for AFS coffee cultivation. The four main traits are: (1) productivity based on F1 hybrid vigor, tree volume and flowering intensity under shade; (2) beverage quality by using wild Ethiopian accessions as female progenitors and selecting for this criterion using specific biochemical and molecular predictors; (3) plant health to ensure good tolerance to stress, especially biotic; and (4) low fertilization to promote sustainable production. For each of these traits, numerous criteria with threshold values to be achieved per trait were identified. Through this research, an ecosystem-based breeding strategy was defined to help create new F1 hybrid varieties within the next 10 years.
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Koutouleas A, Sarzynski T, Bordeaux M, Bosselmann AS, Campa C, Etienne H, Turreira-García N, Rigal C, Vaast P, Ramalho JC, Marraccini P, Ræbild A. Shaded-Coffee: A Nature-Based Strategy for Coffee Production Under Climate Change? A Review. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2022. [DOI: 10.3389/fsufs.2022.877476] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Coffee is deemed to be a high-risk crop in light of upcoming climate changes. Agroforestry practices have been proposed as a nature-based strategy for coffee farmers to mitigate and adapt to future climates. However, with agroforestry systems comes shade, a highly contentious factor for coffee production in terms of potential yield reduction, as well as additional management needs and interactions between shade trees and pest and disease. In this review, we summarize recent research relating to the effects of shade on (i) farmers' use and perceptions, (ii) the coffee microenvironment, (iii) pest and disease incidence, (iv) carbon assimilation and phenology of coffee plants, (v) coffee quality attributes (evaluated by coffee bean size, biochemical compounds, and cup quality tests), (vi) breeding of new Arabica coffee F1 hybrids and Robusta clones for future agroforestry systems, and (vii) coffee production under climate change. Through this work, we begin to decipher whether shaded systems are a feasible strategy to improve the coffee crop sustainability in anticipation of challenging climate conditions. Further research is proposed for developing new coffee varieties adapted to agroforestry systems (exhibiting traits suitable for climate stressors), refining extension tools by selecting locally-adapted shade trees species and developing policy and economic incentives enabling the adoption of sustainable agroforestry practices.
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José Luis SC, Paulino PR, Bello-Bello JJ, Esteban EP, Víctor Heber AR, Tarsicio CT, Gabino GDLS, Victorino MR. SNP markers identification by genome wide association study for chemical quality traits of coffee (Coffea spp.) Germplasm. Mol Biol Rep 2022; 49:4849-4859. [PMID: 35474051 DOI: 10.1007/s11033-022-07339-8] [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: 08/24/2021] [Revised: 01/18/2022] [Accepted: 03/04/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Coffee quality is an important selection criterion for coffee breeding. Metabolite profiling and Genome-Wide Association Studies (GWAS) effectively dissect the genetic background of complex traits such as metabolites content (caffeine, trigonelline, and 5-caffeoylquinic acid (5-CQA)) in coffee that affect quality. Therefore, it is important to determine the metabolic profiles of Coffea spp. genotypes. This study aimed to identify Single Nucleotide Polymorphisms (SNPs) within Coffea spp. genotypes through GWAS and associate these significant SNPs to the metabolic profiles of the different genotypes. METHODS AND RESULTS A total of 1,739 SNP markers were obtained from 80 genotypes using the DArTseq™ method. Caffeine, trigonelline, and 5-CQA content were determined in coffee leaves using Ultra-Performance Liquid Chromatography/tandem mass spectrometry (UPLC-MS/MS) analyses. The GWAS was carried out using the Genome Association and Prediction Integrated Tool (GAPIT) software and a compressed mixed linear model. Finally, a total of three significant SNP markers out of ten were identified. One SNP, located in the coffee chromosome (Chr) 8, was significantly associated with caffeine. The two remaining SNPs, located in Chr 4 and 5, were significantly associated with trigonelline and six SNPs markers were associated with 5-CQA in Chr 1, 5 and 10, but these six markers were not significant. CONCLUSIONS These significant SNP sequences were associated with protein ubiquitination, assimilation, and wall receptor kinases. Therefore, these SNPs might be useful hits in subsequent quality coffee breeding programs.
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Affiliation(s)
- Spinoso-Castillo José Luis
- Colegio de Postgraduados Campus Montecillo, Carretera Federal México-Texcoco km 36.5, 56230, Texcoco, Estado de México, México.
| | - Pérez-Rodríguez Paulino
- Colegio de Postgraduados Campus Montecillo, Carretera Federal México-Texcoco km 36.5, 56230, Texcoco, Estado de México, México
| | - Jericó Jabín Bello-Bello
- CONACYT-Colegio de Postgraduados Campus Córdoba, Carretera Federal Córdoba-Veracruz km 348, Amatlán de los Reyes 94946, Veracruz, México
| | - Escamilla-Prado Esteban
- Universidad Autónoma Chapingo, Centro Regional Universitario Oriente, Carretera Huatusco-Xalapa Km 6, 94100, Huatusco, Veracruz, México
| | - Aguilar-Rincón Víctor Heber
- Colegio de Postgraduados Campus Montecillo, Carretera Federal México-Texcoco km 36.5, 56230, Texcoco, Estado de México, México
| | - Corona-Torres Tarsicio
- Colegio de Postgraduados Campus Montecillo, Carretera Federal México-Texcoco km 36.5, 56230, Texcoco, Estado de México, México
| | - García-de Los Santos Gabino
- Colegio de Postgraduados Campus Montecillo, Carretera Federal México-Texcoco km 36.5, 56230, Texcoco, Estado de México, México
| | - Morales-Ramos Victorino
- Colegio de Postgraduados Campus Córdoba, Carretera Federal Córdoba-Veracruz km 348, Amatlán de los Reyes, 94946, Veracruz, México
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Li Y, Lu Y, Zhou Y, Wei X, Peng Y, Dai Y, Zhang L, Zhu Z. Diurnal transcriptomics analysis reveals the regulatory role of the circadian rhythm in super-hybrid rice LY2186. Genomics 2021; 113:1281-1290. [PMID: 33705889 DOI: 10.1016/j.ygeno.2020.12.046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Revised: 11/23/2020] [Accepted: 12/09/2020] [Indexed: 12/13/2022]
Abstract
Heterosis, an important biological phenomenon wherein F1 hybrids exhibit better performance than any of their parents, has been widely applied; however, its underlying mechanism remains largely unknown. Here, we studied and compared the dynamic transcriptional profiles of super-hybrid rice LY2186 and its parents at 17 time points during 2 day/night cycles and identified 1552 rhythmic differentially expressed genes (RDGs). Cluster and functional enrichment analyses revealed that the day- and night-phased RDGs were mainly enriched in the photosynthesis and stress response categories, respectively. Regulatory network analysis indicated that circadian-related RDGs are core components in both the day and night phases and extensively regulate downstream genes involved in photosynthesis, starch synthesis, plant hormone signal transduction, and other pathways. Furthermore, among the 282 RDGs mapped onto the quantitative tract loci of small intervals (≤100 genes), 72.3% were significantly enriched in the yield, vigor, and anatomy categories. These findings provide valuable information for exploring heterosis mechanisms further and guiding breeding practices.
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Affiliation(s)
- Yue Li
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yufei Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yun Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiaoli Wei
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yonggang Peng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Yan Dai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Lei Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Zhen Zhu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
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McClung CR. Circadian Clock Components Offer Targets for Crop Domestication and Improvement. Genes (Basel) 2021; 12:genes12030374. [PMID: 33800720 PMCID: PMC7999361 DOI: 10.3390/genes12030374] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 03/01/2021] [Accepted: 03/04/2021] [Indexed: 12/31/2022] Open
Abstract
During plant domestication and improvement, farmers select for alleles present in wild species that improve performance in new selective environments associated with cultivation and use. The selected alleles become enriched and other alleles depleted in elite cultivars. One important aspect of crop improvement is expansion of the geographic area suitable for cultivation; this frequently includes growth at higher or lower latitudes, requiring the plant to adapt to novel photoperiodic environments. Many crops exhibit photoperiodic control of flowering and altered photoperiodic sensitivity is commonly required for optimal performance at novel latitudes. Alleles of a number of circadian clock genes have been selected for their effects on photoperiodic flowering in multiple crops. The circadian clock coordinates many additional aspects of plant growth, metabolism and physiology, including responses to abiotic and biotic stresses. Many of these clock-regulated processes contribute to plant performance. Examples of selection for altered clock function in tomato demonstrate that with domestication, the phasing of the clock is delayed with respect to the light–dark cycle and the period is lengthened; this modified clock is associated with increased chlorophyll content in long days. These and other data suggest the circadian clock is an attractive target during breeding for crop improvement.
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Affiliation(s)
- C Robertson McClung
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
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