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Parker T, Bolt T, Williams T, Penmetsa RV, Mulube M, Celebioglu B, Palkovic A, Jochua CN, Del Mar Rubio Wilhelmi M, Lo S, Bornhorst G, Tian L, Kamfwa K, Farmer A, Diepenbrock C, Gepts P. Seed color patterns in domesticated common bean are regulated by MYB-bHLH-WD40 transcription factors and temperature. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39152711 DOI: 10.1111/tpj.16947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 07/03/2024] [Accepted: 07/09/2024] [Indexed: 08/19/2024]
Abstract
Seed colors and color patterns are critical for the survival of wild plants and the consumer appeal of crops. In common bean, a major global staple, these patterns are also essential in determining market classes, yet the genetic and environmental control of many pigmentation patterns remains unresolved. In this study, we genetically mapped variation for several important seed pattern loci, including T, Bip, phbw, and Z, which co-segregated with candidate genes PvTTG1, PvMYC1, PvTT8, and PvTT2, respectively. Proteins encoded by these genes are predicted to work together in MYB-bHLH-WD40 (MBW) complexes, propagating flavonoid biosynthesis across the seed coat as observed in Arabidopsis. Whole-genome sequencing of 37 accessions identified mutations, including seven unique parallel mutations in T (PvTTG1) and non-synonymous SNPs in highly conserved residues in bipana (PvMYC1) and z (PvTT2). A 612 bp intron deletion in phbw (PvTT8) eliminated motifs conserved since the Papilionoideae origin and corresponded to a 20-fold reduction in transcript abundance. In multi-location field trials of seven varieties with partial seed coat pigmentation patterning, the pigmented seed coat area correlated positively with ambient temperature, with up to 11-fold increases in the pigmented area from the coolest to the warmest environments. In controlled growth chamber conditions, an increase of 4°C was sufficient to cause pigmentation on an average additional 21% of the seed coat area. Our results shed light on key steps of flavonoid biosynthesis in common bean. They will inform breeding efforts for seed coat color/patterning to improve consumer appeal in this nutritious staple crop.
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Affiliation(s)
- Travis Parker
- Department of Plant Sciences, University of California, Davis, California, USA
| | - Tayah Bolt
- Department of Plant Sciences, University of California, Davis, California, USA
| | - Troy Williams
- Department of Plant Sciences, University of California, Davis, California, USA
| | - R Varma Penmetsa
- Department of Plant Sciences, University of California, Davis, California, USA
| | - Mwiinga Mulube
- Department of Plant Sciences, School of Agricultural Sciences, University of Zambia, Lusaka, Zambia
| | - Burcu Celebioglu
- Department of Plant Sciences, University of California, Davis, California, USA
| | - Antonia Palkovic
- Department of Plant Sciences, University of California, Davis, California, USA
| | | | | | - Sassoum Lo
- Department of Plant Sciences, University of California, Davis, California, USA
| | - Gail Bornhorst
- Department of Biological and Agricultural Engineering, University of California, Davis, California, USA
| | - Li Tian
- Department of Plant Sciences, University of California, Davis, California, USA
| | - Kelvin Kamfwa
- Department of Plant Sciences, School of Agricultural Sciences, University of Zambia, Lusaka, Zambia
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, New Mexico, USA
| | | | - Paul Gepts
- Department of Plant Sciences, University of California, Davis, California, USA
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Celebioglu B, Hart JP, Porch T, Griffiths P, Myers JR. Genome-Wide Association Study to Identify Possible Candidate Genes of Snap Bean Leaf and Pod Color. Genes (Basel) 2023; 14:2234. [PMID: 38137056 PMCID: PMC10742591 DOI: 10.3390/genes14122234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2023] [Revised: 12/11/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023] Open
Abstract
Color can be an indicator of plant health, quality, and productivity, and is useful to researchers to understand plant nutritional content in their studies. Color may be related to chlorophyll content and photosynthetic activity and provides information for those studying diseases and mineral nutrition because every nutrient deficiency and many diseases produce symptoms that affect color. In order to identify significant loci related to both leaf and pod color in a snap bean (Phaseolus vulgaris L.) diversity panel, a genome-wide association study (GWAS) was carried out. Leaf color in one and pod traits in multiple environments were characterized using a colorimeter. L*a*b* color data were recorded and used to calculate chroma (C*) and hue angle (H°). Leaves were evaluated at three positions (lower, middle, and upper) in the canopy and both pod exterior and interior colors were obtained. GWAS was conducted using two reference genomes that represent the Andean (G19833) and Middle American (5-593) domestication centers. Narrow sense heritabilities were calculated using the mixed linear model (MLM) method in genome association and prediction integrated tool (GAPIT), and significant single nucleotide polymorphisms (SNPs) for each color parameter were obtained using the Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) GWAS model with two principal components (PCAs). In comparison to pod color traits, narrow sense heritabilities of leaf traits were low and similar for both reference genomes. Generally, narrow sense heritability for all traits was highest in the lower, followed by middle, and then upper leaf positions. Heritability for both pod interior and exterior color traits was higher using the G19833 reference genome compared to 5-593 when evaluated by year and means across years. Forty-five significant SNPs associated with leaf traits and 872 associated with pods, totaling 917 significant SNPs were identified. Only one SNP was found in common for both leaf and pod traits on Pv03 in the 5-593 reference genome. One-hundred thirteen significant SNPs, 30 in leaves and 83 in pods had phenotypic variation explained (PVE) of 10% or greater. Fourteen SNPs (four from G19833 and ten from 5-593) with ≥10 PVE%, large SNP effect, and largest p-value for L* and H° pod exterior was identified on Pv01, Pv02, Pv03, and Pv08. More SNPs were associated with pod traits than with leaf traits. The pod interior did not exhibit colors produced by anthocyanins or flavonols which allowed the differentiation of potential candidate genes associated with chloroplast and photosynthetic activity compared to the pod exterior where candidate genes related to both flavonoids and photosynthesis affected color. Several SNPs were associated with known qualitative genes including the wax pod locus (y), persistent color (pc), purple pods (V), and two genes expressed in seeds but not previously reported to affect other plant tissues (B and J). An evaluation of significant SNPs within annotated genes found a number, within a 200 kb window, involved in both flavonoid and photosynthetic biosynthetic pathways.
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Affiliation(s)
- Burcu Celebioglu
- Department of Horticulture, Oregon State University, 4017 Ag & Life Science Bldg., Corvallis, OR 97331, USA;
| | - John P. Hart
- USDA-ARS, Tropical Agriculture Research Station (TARS), 2200 P. A. Campos Ave., Suite 201, Mayagüez, PR 00680, USA; (J.P.H.); (T.P.)
| | - Timothy Porch
- USDA-ARS, Tropical Agriculture Research Station (TARS), 2200 P. A. Campos Ave., Suite 201, Mayagüez, PR 00680, USA; (J.P.H.); (T.P.)
| | - Phillip Griffiths
- School of Integrated Plant Sciences, Horticulture Section, Cornell Agritech, 635 W. North St., Geneva, NY 14456, USA;
| | - James R. Myers
- Department of Horticulture, Oregon State University, 4017 Ag & Life Science Bldg., Corvallis, OR 97331, USA;
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Campa A, Rodríguez Madrera R, Jurado M, García-Fernández C, Suárez Valles B, Ferreira JJ. Genome-wide association study for the extractable phenolic profile and coat color of common bean seeds (Phaseolus vulgaris L.). BMC PLANT BIOLOGY 2023; 23:158. [PMID: 36959530 PMCID: PMC10035135 DOI: 10.1186/s12870-023-04177-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 03/17/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND A large variation in seed coat colors and seed phenolic metabolites is present in common bean (Phaseolus vulgaris L.). The study of the relationships between seed coat color phenotype and the phenolic profile is an important step in the elucidation of the gene network involved in the phenylpropanoid biosynthetic pathway. However, this relationship is still poorly understood in this species. RESULTS A genome-wide association study (GWAS) was used to investigate the genomic regions associated with the synthesis of 10 flavonoids (5 anthocyanins and 5 flavonols) and with 10 seed coat color traits using a set of 308 common bean lines of the Spanish Diversity Panel (SDP) which have been genotyped with 11,763 SNP markers.. A total of 31 significant SNP-trait associations (QTNs) were identified, grouped in 20 chromosome regions: 6 for phenolic metabolites on chromosomes Pv01, Pv02, Pv04, Pv08, and Pv09, 13 for seed coat color on chromosomes Pv01, Pv02, Pv06, Pv07, and Pv10, and 1 including both types of traits located on chromosome Pv08. In all, 58 candidate genes underlying these regions have been proposed, 31 of them previously described in the phenylpropanoid pathway in common bean, and 27 of them newly proposed in this work based on the association study and their homology with Arabidopsis anthocyanin genes. CONCLUSIONS Chromosome Pv08 was identified as the main chromosome involved in the phenylpropanoid pathway and in consequence in the common bean seed pigmentation, with three independent chromosome regions identified, Phe/C_Pv08(2.7) (expanding from 2.71 to 4.04 Mbp), C_Pv08(5.8) (5.89-6.59 Mbp), and Phe_Pv08(62.5) (62.58 to 63.28 Mbp). Candidate genes previously proposed by other authors for the color genes V and P were validated in this GWAS. Candidate genes have been tentatively proposed from this study for color genes B and Rk on Pv02, Asp on Pv07, and complex C on Pv08. These results help to clarify the complex network of genes involved in the genetic control of phenolic compounds and seed color in common bean and provide the opportunity for future validation studies.
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Affiliation(s)
- Ana Campa
- Regional Service for Agrofood Research and Development (SERIDA), Ctra AS-267 PK 19, 33300, Villaviciosa, Asturias, Spain.
| | - Roberto Rodríguez Madrera
- Regional Service for Agrofood Research and Development (SERIDA), Ctra AS-267 PK 19, 33300, Villaviciosa, Asturias, Spain
| | - María Jurado
- Regional Service for Agrofood Research and Development (SERIDA), Ctra AS-267 PK 19, 33300, Villaviciosa, Asturias, Spain
| | - Carmen García-Fernández
- Regional Service for Agrofood Research and Development (SERIDA), Ctra AS-267 PK 19, 33300, Villaviciosa, Asturias, Spain
| | - Belén Suárez Valles
- Regional Service for Agrofood Research and Development (SERIDA), Ctra AS-267 PK 19, 33300, Villaviciosa, Asturias, Spain
| | - Juan José Ferreira
- Regional Service for Agrofood Research and Development (SERIDA), Ctra AS-267 PK 19, 33300, Villaviciosa, Asturias, Spain
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Hellinger J, Kim H, Ralph J, Karlen SD. p-Coumaroylation of lignin occurs outside of commelinid monocots in the eudicot genus Morus (mulberry). PLANT PHYSIOLOGY 2023; 191:854-861. [PMID: 36269202 PMCID: PMC9922387 DOI: 10.1093/plphys/kiac485] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 10/04/2022] [Indexed: 06/16/2023]
Abstract
The presence of p-coumarate (pCA) in plant cell walls is generally considered to be a trait present only in commelinid monocots. Here, we show that this long-held overgeneralizing assumption is incorrect and that mulberry trees (Morus) are eudicot plants that have lignins derived in part from monolignol pCA esters. As in commelinid monocots, the lignin-bound pCA acylates the sidechain γ-hydroxyl of both coniferyl and syringyl units. This discovery expands mulberry's potential applications to include being a source of p-coumaric acid, a supplier of nutritious berries, a forage crop, a decorative plant, and the main food source for silkworms.
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Affiliation(s)
- Jan Hellinger
- Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin–Madison, Madison, Wisconsin 53726, USA
| | - Hoon Kim
- Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin–Madison, Madison, Wisconsin 53726, USA
| | - John Ralph
- Department of Energy, Great Lakes Bioenergy Research Center, Wisconsin Energy Institute, University of Wisconsin–Madison, Madison, Wisconsin 53726, USA
- Department of Biochemistry, University of Wisconsin–Madison, Madison, Wisconsin 53706, USA
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5
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McClean PE, Lee R, Howe K, Osborne C, Grimwood J, Levy S, Haugrud AP, Plott C, Robinson M, Skiba RM, Tanha T, Zamani M, Thannhauser TW, Glahn RP, Schmutz J, Osorno JM, Miklas PN. The Common Bean V Gene Encodes Flavonoid 3'5' Hydroxylase: A Major Mutational Target for Flavonoid Diversity in Angiosperms. FRONTIERS IN PLANT SCIENCE 2022; 13:869582. [PMID: 35432409 PMCID: PMC9009181 DOI: 10.3389/fpls.2022.869582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
The classic V (violet, purple) gene of common bean (Phaseolus vulgaris) functions in a complex genetic network that controls seed coat and flower color and flavonoid content. V was cloned to understand its role in the network and the evolution of its orthologs in the Viridiplantae. V mapped genetically to a narrow interval on chromosome Pv06. A candidate gene was selected based on flavonoid analysis and confirmed by recombinational mapping. Protein and domain modeling determined V encodes flavonoid 3'5' hydroxylase (F3'5'H), a P450 enzyme required for the expression of dihydromyricetin-derived flavonoids in the flavonoid pathway. Eight recessive haplotypes, defined by mutations of key functional domains required for P450 activities, evolved independently in the two bean gene pools from a common ancestral gene. V homologs were identified in Viridiplantae orders by functional domain searches. A phylogenetic analysis determined F3'5'H first appeared in the Streptophyta and is present in only 41% of Angiosperm reference genomes. The evolutionarily related flavonoid pathway gene flavonoid 3' hydroxylase (F3'H) is found nearly universally in all Angiosperms. F3'H may be conserved because of its role in abiotic stress, while F3'5'H evolved as a major target gene for the evolution of flower and seed coat color in plants.
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Affiliation(s)
- Phillip E. McClean
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
- Genomics, Phenomics, and Bioinformatic Program, North Dakota State University, Fargo, ND, United States
| | - Rian Lee
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Kevin Howe
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, United States
| | - Caroline Osborne
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Shawn Levy
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Amanda Peters Haugrud
- Genomics, Phenomics, and Bioinformatic Program, North Dakota State University, Fargo, ND, United States
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Melanie Robinson
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Ryan M. Skiba
- Genomics, Phenomics, and Bioinformatic Program, North Dakota State University, Fargo, ND, United States
| | - Tabassum Tanha
- Genomics, Phenomics, and Bioinformatic Program, North Dakota State University, Fargo, ND, United States
| | - Mariam Zamani
- Genomics, Phenomics, and Bioinformatic Program, North Dakota State University, Fargo, ND, United States
| | - Theodore W. Thannhauser
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, United States
| | - Raymond P. Glahn
- USDA-ARS, Robert W. Holley Center for Agriculture and Health, Cornell University, Ithaca, NY, United States
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, United States
| | - Juan M. Osorno
- Department of Plant Sciences, North Dakota State University, Fargo, ND, United States
| | - Phillip N. Miklas
- USDA-ARS, Grain Legumes Genetics and Physiology Research Unit, Prosser, WA, United States
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García-Fernández C, Campa A, Ferreira JJ. Dissecting the genetic control of seed coat color in a RIL population of common bean (Phaseolus vulgaris L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:3687-3698. [PMID: 34328529 DOI: 10.1007/s00122-021-03922-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 07/20/2021] [Indexed: 06/13/2023]
Abstract
Three genes associated with the seed coat color in a TU/Musica RIL population were located on a genetic map, and two candidate genes proposed to control black seed coat in the TU genotype were characterized. Seed coat color is an important characteristic of common bean (Phaseolus vulgaris L.) associated with the marketability of dry bean cultivars, quality and nutritional characteristics of seed, as well as response to pathogens. In this study, the genetic control of seed coat color in a recombinant inbred line population (175 lines) obtained from the cross 'TU' × 'Musica' was investigated. Phenotypic segregation fitted 1:1 for white vs. nonwhite, and 3:1 for brown versus black, indicating the involvement of three independent genes, one controlling white color and two (with epistatic interaction) controlling black color. Using a genetic map built with 842 SNPs, the gene responsible for the white seed coat was mapped on the linkage group Pv07, in the position previously described for the P gene. For the black seed coat phenotype, two genes were mapped to the beginning of chromosomes Pv06 and Pv08, in the positions estimated for the V gene and the complex C locus, respectively, by classical studies. The involvement of these two genomic regions was verified through two crosses between three selected RILs exhibiting complementary and dominant inheritance, in which the TU alleles for both genes resulted in a black phenotype. Two genes involved in the anthocyanin biosynthesis pathway were proposed as candidate genes: Phvul.006G018800 encoding a flavonoid 3'5'hydroxylase and Phvul.008G038400 encoding MYB113 transcription factor. These findings add knowledge to the complex network of genes controlling seed coat color in common bean as well as providing genetic markers to be used in future genetic analysis or plant breeding.
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Affiliation(s)
- Carmen García-Fernández
- 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
| | - Juan Jose Ferreira
- Plant Genetic Group, Regional Service for Agrofood Research and Development (SERIDA), 33300, Villaviciosa, Asturias, Spain
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Qiao F, Yang X, Xu F, Huang Y, Zhang J, Song M, Zhou S, Zhang M, He D. TMT-based quantitative proteomic analysis reveals defense mechanism of wheat against the crown rot pathogen Fusarium pseudograminearum. BMC PLANT BIOLOGY 2021; 21:82. [PMID: 33557748 PMCID: PMC7869478 DOI: 10.1186/s12870-021-02853-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 01/24/2021] [Indexed: 05/24/2023]
Abstract
BACKGROUND Fusarium crown rot is major disease in wheat. However, the wheat defense mechanisms against this disease remain poorly understood. RESULTS Using tandem mass tag (TMT) quantitative proteomics, we evaluated a disease-susceptible (UC1110) and a disease-tolerant (PI610750) wheat cultivar inoculated with Fusarium pseudograminearum WZ-8A. The morphological and physiological results showed that the average root diameter and malondialdehyde content in the roots of PI610750 decreased 3 days post-inoculation (dpi), while the average number of root tips increased. Root vigor was significantly increased in both cultivars, indicating that the morphological, physiological, and biochemical responses of the roots to disease differed between the two cultivars. TMT analysis showed that 366 differentially expressed proteins (DEPs) were identified by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment in the two comparison groups, UC1110_3dpi/UC1110_0dpi (163) and PI610750_3dpi/PI610750_0dpi (203). It may be concluded that phenylpropanoid biosynthesis (8), secondary metabolite biosynthesis (12), linolenic acid metabolites (5), glutathione metabolism (8), plant hormone signal transduction (3), MAPK signaling pathway-plant (4), and photosynthesis (12) contributed to the defense mechanisms in wheat. Protein-protein interaction network analysis showed that the DEPs interacted in both sugar metabolism and photosynthesis pathways. Sixteen genes were validated by real-time quantitative polymerase chain reaction and were found to be consistent with the proteomics data. CONCLUSION The results provided insight into the molecular mechanisms of the interaction between wheat and F. pseudograminearum.
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Affiliation(s)
- Fangfang Qiao
- College of Agronomy, Henan Agricultural University/ National Engineering Research Center for Wheat/ Co-construction State Key Laboratory of Wheat and Maize Crop Science/ Collaborative Innovation Center of Henan Grain Crops, 15 Longzihu College District, Zhengzhou, 450046, China
| | - Xiwen Yang
- College of Agronomy, Henan Agricultural University/ National Engineering Research Center for Wheat/ Co-construction State Key Laboratory of Wheat and Maize Crop Science/ Collaborative Innovation Center of Henan Grain Crops, 15 Longzihu College District, Zhengzhou, 450046, China
| | - Fengdan Xu
- College of Agronomy, Henan Agricultural University/ National Engineering Research Center for Wheat/ Co-construction State Key Laboratory of Wheat and Maize Crop Science/ Collaborative Innovation Center of Henan Grain Crops, 15 Longzihu College District, Zhengzhou, 450046, China
| | - Yuan Huang
- College of Agronomy, Henan Agricultural University/ National Engineering Research Center for Wheat/ Co-construction State Key Laboratory of Wheat and Maize Crop Science/ Collaborative Innovation Center of Henan Grain Crops, 15 Longzihu College District, Zhengzhou, 450046, China
| | - Jiemei Zhang
- College of Agronomy, Henan Agricultural University/ National Engineering Research Center for Wheat/ Co-construction State Key Laboratory of Wheat and Maize Crop Science/ Collaborative Innovation Center of Henan Grain Crops, 15 Longzihu College District, Zhengzhou, 450046, China
| | - Miao Song
- College of Agronomy, Henan Agricultural University/ National Engineering Research Center for Wheat/ Co-construction State Key Laboratory of Wheat and Maize Crop Science/ Collaborative Innovation Center of Henan Grain Crops, 15 Longzihu College District, Zhengzhou, 450046, China
| | - Sumei Zhou
- College of Agronomy, Henan Agricultural University/ National Engineering Research Center for Wheat/ Co-construction State Key Laboratory of Wheat and Maize Crop Science/ Collaborative Innovation Center of Henan Grain Crops, 15 Longzihu College District, Zhengzhou, 450046, China
| | - Meng Zhang
- College of Plant Protection, Henan Agricultural University, Zhengzhou, 450002, Henan, China.
| | - Dexian He
- College of Agronomy, Henan Agricultural University/ National Engineering Research Center for Wheat/ Co-construction State Key Laboratory of Wheat and Maize Crop Science/ Collaborative Innovation Center of Henan Grain Crops, 15 Longzihu College District, Zhengzhou, 450046, China.
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Lei P, Han B, Wang Y, Zhu X, Xuan Y, Liu X, Fan H, Chen L, Duan Y. Identification of MicroRNAs That Respond to Soybean Cyst Nematode Infection in Early Stages in Resistant and Susceptible Soybean Cultivars. Int J Mol Sci 2019; 20:E5634. [PMID: 31718001 PMCID: PMC6888636 DOI: 10.3390/ijms20225634] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 11/06/2019] [Accepted: 11/09/2019] [Indexed: 02/06/2023] Open
Abstract
Soybean cyst nematode (SCN) causes heavy losses to soybean yield. In order to investigate the roles of soybean miRNAs during the early stages of infection (1 and 5 dpi), 24 small RNA libraries were constructed from SCN resistant cultivar Huipizhi (HPZ) and the susceptible Williams 82 (W82) cultivar for high-throughput sequencing. By sequencing the small RNA libraries, a total of 634 known miRNAs were identified, and 252 novel miRNAs were predicted. Altogether, 14 known miRNAs belonging to 13 families, and 26 novel miRNAs were differentially expressed and may respond to SCN infection in HPZ and W82. Similar expression results were also confirmed by qRT-PCR. Further analysis of the biological processes that these potential target genes of differentially expressed miRNAs regulate found that they may be strongly related to plant-pathogen interactions. Overall, soybean miRNAs experience profound changes in early stages of SCN infection in both HPZ and W82. The findings of this study can provide insight into miRNAome changes in both HPZ and W82 at the early stages of infection, and may provide a stepping stone for future SCN management.
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Affiliation(s)
- Piao Lei
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Bing Han
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuanyuan Wang
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Biological Science and Technology, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaofeng Zhu
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuanhu Xuan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaoyu Liu
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Sciences, Shenyang Agricultural University, Shenyang 110866, China
| | - Haiyan Fan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Lijie Chen
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuxi Duan
- Nematology Institute of Northern China, Shenyang Agricultural University, Shenyang 110866, China; (P.L.); (B.H.); (Y.W.); (X.Z.); (Y.X.); (H.F.); (L.C.)
- College of Plant Protection, Shenyang Agricultural University, Shenyang 110866, China
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Myers JR, Wallace LT, Mafi Moghaddam S, Kleintop AE, Echeverria D, Thompson HJ, Brick MA, Lee R, McClean PE. Improving the Health Benefits of Snap Bean: Genome-Wide Association Studies of Total Phenolic Content. Nutrients 2019; 11:E2509. [PMID: 31635241 PMCID: PMC6835575 DOI: 10.3390/nu11102509] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 10/04/2019] [Accepted: 10/05/2019] [Indexed: 01/09/2023] Open
Abstract
Snap beans are a significant source of micronutrients in the human diet. Among the micronutrients present in snap beans are phenolic compounds with known beneficial effects on human health, potentially via their metabolism by the gut-associated microbiome. The genetic pathways leading to the production of phenolics in snap bean pods remain uncertain. In this study, we quantified the level of total phenolic content (TPC) in the Bean Coordinated Agriculture Program (CAP) snap bean diversity panel of 149 accessions. The panel was characterized spectrophotometrically for phenolic content with a Folin-Ciocalteu colorimetric assay. Flower, seed and pod color were also quantified, as red, purple, yellow and brown colors are associated with anthocyanins and flavonols in common bean. Genotyping was performed through an Illumina Infinium Genechip BARCBEAN6K_3 single nucleotide polymorphism (SNP) array. Genome-Wide Association Studies (GWAS) analysis identified 11 quantitative trait nucleotides (QTN) associated with TPC. An SNP was identified for TPC on Pv07 located near the P gene, which is a major switch in the flavonoid biosynthetic pathway. Candidate genes were identified for seven of the 11 TPC QTN. Five regulatory genes were identified and represent novel sources of variation for exploitation in developing snap beans with higher phenolic levels for greater health benefits to the consumer.
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Affiliation(s)
- James R Myers
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA.
| | - Lyle T Wallace
- Department of Horticulture, University of Wisconsin at Madison, Madison, WI 53706, USA.
| | - Samira Mafi Moghaddam
- Plant Resilience Institute, Department of Plant Biology, Michigan State University, East Lansing, MI 48824, USA.
| | - Adrienne E Kleintop
- Department of Plant Science, Delaware Valley University, Doylestown, PA 18901, USA.
| | - Dimas Echeverria
- RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Henry J Thompson
- Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO 80523, USA.
| | - Mark A Brick
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA.
| | - Rian Lee
- Department of Plant Science, North Dakota State University, Fargo, ND 58105, USA.
| | - Phillip E McClean
- Department of Plant Science, North Dakota State University, Fargo, ND 58105, USA.
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10
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Paauw M, Koes R, Quattrocchio FM. Alteration of flavonoid pigmentation patterns during domestication of food crops. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3719-3735. [PMID: 30949670 DOI: 10.1093/jxb/erz141] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 03/15/2019] [Indexed: 05/20/2023]
Abstract
Flavonoids are plant pigments that provide health benefits for human and animal consumers. Understanding why domesticated crops have altered pigmentation patterns and unraveling the molecular/genetic mechanisms that underlie this will facilitate the breeding of new (healthier) varieties. We present an overview of changes in flavonoid pigmentation patterns that have occurred during crop domestication and, where possible, link them to the molecular changes that brought about the new phenotypes. We consider species that lost flavonoid pigmentation in the edible part of the plant at some point during domestication (like cereals). We also consider the converse situation, for example eggplant (aubergine), which instead gained strong anthocyanin accumulation in the skin of the fruit during domestication, and some varieties of citrus and apple that acquired anthocyanins in the fruit flesh. Interestingly, the genes responsible for such changes are sometimes closely linked to, or have pleiotropic effects on, important domestication genes, suggesting accidental and perhaps inevitable changes of anthocyanin patterning during domestication. In other cases, flavonoid pigmentation patterns in domesticated crops are the result of cultural preferences, with examples being found in varieties of citrus, barley, wheat, and maize. Finally, and more recently, in some species, anthocyanins seem to have been the direct target of selection in a second wave of domestication that followed the introduction of industrial food processing.
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Affiliation(s)
- Misha Paauw
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park, XH, Amsterdam, Netherlands
| | - Ronald Koes
- Plant Development and (Epi)Genetics, Swammerdam Institute for Life Sciences, University of Amsterdam, Science Park, XH, Amsterdam, Netherlands
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11
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Erfatpour M, Navabi A, Pauls KP. Mapping the non-darkening trait from 'Wit-rood boontje' in bean (Phaseolus vulgaris). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:1331-1343. [PMID: 29502138 DOI: 10.1007/s00122-018-3081-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 02/24/2018] [Indexed: 05/28/2023]
Abstract
A QTL for non-darkening seed coat from 'Wit-rood boontje' was mapped in pinto bean population on chromosome Pv10, comprising 40 candidate genes. The seed coat colour darkens with age in some market classes of dry beans (Phaseolus vulgaris), including pinto bean. Beans with darkened seed coats are discounted in the market place, since they are believed to be associated with lower nutritional quality, increased cooking time, and decreased palatability. The objective of this research was to map a non-darkening gene from a cranberry-like bean 'Wit-rood boontje' using a recombinant inbred line population, derived from a cross between 'Wit-rood boontje' and a slow-darkening pinto bean (1533-15). The population was characterized for seed phenotype and genotyped with an Illumina BeadChip. A genetic linkage map was constructed with 1327 informative SNP markers plus an STS marker (OL4S500) and an SSR marker (Pvsd-0028), previously associated with the J gene and Sd gene, respectively, as well as non-darkening and slow-darkening phenotypes. The linkage map spanned 1253.2 cM over 11 chromosomes. A major QTL for the non-darkening trait was flanked by SNP 715646341 and SNP 715646348 on chromosome Pv10. The region, which spanned 13.2 cM, explained 48% of the phenotypic variation for seed coat darkening. Forty candidate genes were identified in the QTL interval. This information can be used to develop a gene-based marker to facilitate breeding non-darkening pinto beans and may lead to a better understanding of the molecular mechanism for the postharvest darkening phenomenon in pinto bean.
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Affiliation(s)
- M Erfatpour
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - A Navabi
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - K P Pauls
- Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2W1, Canada.
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12
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Leonetti P, Accotto GP, Hanafy MS, Pantaleo V. Viruses and Phytoparasitic Nematodes of Cicer arietinum L.: Biotechnological Approaches in Interaction Studies and for Sustainable Control. FRONTIERS IN PLANT SCIENCE 2018; 9:319. [PMID: 29599788 PMCID: PMC5862823 DOI: 10.3389/fpls.2018.00319] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 02/27/2018] [Indexed: 05/31/2023]
Abstract
Cicer arietinum L. (chickpea) is the world's fourth most widely grown pulse. Chickpea seeds are a primary source of dietary protein for humans, and chickpea cultivation contributes to biological nitrogen fixation in the soil, given its symbiotic relationship with rhizobia. Therefore, chickpea cultivation plays a pivotal role in innovative sustainable models of agro-ecosystems inserted in crop rotation in arid and semi-arid environments for soil improvement and the reduction of chemical inputs. Indeed, the arid and semi-arid tropical zones of Africa and Asia have been primary areas of cultivation and diversification. Yet, nowadays, chickpea is gaining prominence in Canada, Australia, and South America where it constitutes a main ingredient in vegetarian and vegan diets. Viruses and plant parasitic nematodes (PPNs) have been considered to be of minor and local impact in primary areas of cultivation. However, the introduction of chickpea in new environments exposes the crop to these biotic stresses, compromising its yields. The adoption of high-throughput genomic technologies, including genome and transcriptome sequencing projects by the chickpea research community, has provided major insights into genome evolution as well as genomic architecture and domestication. This review summarizes the major viruses and PPNs that affect chickpea cultivation worldwide. We also present an overview of the current state of chickpea genomics. Accordingly, we explore the opportunities that genomics, post-genomics and novel editing biotechnologies are offering in order to understand chickpea diseases and stress tolerance and to design innovative control strategies.
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Affiliation(s)
- Paola Leonetti
- Institute for Sustainable Plant Protection, Research Unit of Bari, National Research Council, Bari, Italy
| | - Gian Paolo Accotto
- Institute for Sustainable Plant Protection, Research Unit of Turin, National Research Council, Turin, Italy
| | - Moemen S. Hanafy
- Department of Plant Biotechnology, National Research Centre, Cairo, Egypt
| | - Vitantonio Pantaleo
- Institute for Sustainable Plant Protection, Research Unit of Bari, National Research Council, Bari, Italy
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13
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Tohge T, de Souza LP, Fernie AR. Current understanding of the pathways of flavonoid biosynthesis in model and crop plants. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4013-4028. [PMID: 28922752 DOI: 10.1093/jxb/erx177] [Citation(s) in RCA: 238] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Flavonoids are a signature class of secondary metabolites formed from a relatively simple collection of scaffolds. They are extensively decorated by chemical reactions including glycosylation, methylation, and acylation. They are present in a wide variety of fruits and vegetables and as such in Western populations it is estimated that 20-50 mg of flavonoids are consumed daily per person. In planta they have demonstrated to contribute to both flower color and UV protection. Their consumption has been suggested to presenta wide range of health benefits. Recent technical advances allowing affordable whole genome sequencing, as well as a better inventory of species-by-species chemical diversity, have greatly advanced our understanding as to how flavonoid biosynthesis pathways vary across species. In parallel, reverse genetics combined with detailed molecular phenotyping is currently allowing us to elucidate the functional importance of individual genes and metabolites and by this means to provide further mechanistic insight into their biological roles. Here we provide an inventory of current knowledge of pathways of flavonoid biosynthesis in both the model plant Arabidopsis thaliana and a range of crop species, including tomato, maize, rice, and bean.
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Affiliation(s)
- Takayuki Tohge
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm
| | | | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm
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14
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Xie W, Perry G, Martin CJ, Shim YS, Navabi A, Pauls KP. Molecular characterization of dihydroneopterin aldolase and aminodeoxychorismate synthase in common bean—genes coding for enzymes in the folate synthesis pathway. Genome 2017; 60:588-600. [DOI: 10.1139/gen-2016-0227] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Common beans (Phaseolus vulgaris) are excellent sources of dietary folates, but different varieties contain different amounts of these compounds. Genes coding for dihydroneopterin aldolase (DHNA) and aminodeoxychorismate synthase (ADCS) of the folate synthesis pathway were characterized by PCR amplification, BAC clone sequencing, and whole genome sequencing. All DHNA and ADCS genes in the Mesoamerican cultivar OAC Rex were isolated and compared with those genes in the genome of Andean genotype G19833. Both genotypes have two functional DHNA genes and one pseudo gene. PvDHNA1 and PvDHNA2 proteins have similar secondary structures and conserved residues as DHNA homologs in Staphylococcus aureus and Arabidopsis. Sequence analysis and synteny mapping indicated that PvDHNA1 might be a duplicated and transposed copy of PvDHNA2. There is only one ADCS gene (PvADCS) identified in the bean genome and it is identical in OAC Rex and G19833. PvADCS has the conserved motifs required for catalytic activity similar to other plant ADCS homologs. DHNA and ADCS gene-specific markers were developed, mapped, and compared to their physical locations on chromosomes 1 and 7, respectively. The gene-specific markers developed in this study should be useful for detection and selection of varieties with enhanced folate contents in bean breeding programs.
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Affiliation(s)
- Weilong Xie
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
| | - Gregory Perry
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
| | - C. Joe Martin
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
| | - Youn-Seb Shim
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
| | - Alireza Navabi
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
| | - K. Peter Pauls
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
- Crop Science Building, Department of Plant Agriculture, University of Guelph, 50 Stone Road, Guelph, ON N1G 2W1, Canada
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15
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Mirali M, Purves RW, Vandenberg A. Profiling the Phenolic Compounds of the Four Major Seed Coat Types and Their Relation to Color Genes in Lentil. JOURNAL OF NATURAL PRODUCTS 2017; 80:1310-1317. [PMID: 28448137 DOI: 10.1021/acs.jnatprod.6b00872] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Phenolic compounds can provide antioxidant health benefits for humans, and foods such as lentils can be valuable dietary sources of different subclasses of these secondary metabolites. This study used LC-MS analyses to compare the phenolic profiles of lentil genotypes with four seed coat background colors (green, gray, tan, and brown) and two cotyledon colors (red and yellow) grown at two locations. The mean area ratio per mg sample (MARS) values of various phenolic compounds in lentil seeds varied with the different seed coat colors conferred by specific genotypes. Seed coats of lentil genotypes with the homozygous recessive tgc allele (green and gray seed coats) had higher MARS values of flavan-3-ols, proanthocyanidins, and some flavonols. This suggests lentils featuring green and gray seed coats might be more promising as health-promoting foods.
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Affiliation(s)
- Mahla Mirali
- Plant Sciences Department, University of Saskatchewan , Saskatoon, SK, Canada S7N 5A8
| | - Randy W Purves
- Plant Sciences Department, University of Saskatchewan , Saskatoon, SK, Canada S7N 5A8
| | - Albert Vandenberg
- Plant Sciences Department, University of Saskatchewan , Saskatoon, SK, Canada S7N 5A8
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16
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Rispail N, Rubiales D. Genome-wide identification and comparison of legume MLO gene family. Sci Rep 2016; 6:32673. [PMID: 27596925 PMCID: PMC5011691 DOI: 10.1038/srep32673] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 08/09/2016] [Indexed: 12/15/2022] Open
Abstract
MLO proteins are highly conserved proteins with seven trans-membrane domains. Specific MLO genes have been linked to plant disease susceptibility. Others are involved in plant reproduction and in root thigmomorphogenesis. Functions of the remaining MLOs are still unknown. Here we performed a genome-wide survey of the MLO family in eight legume species from different clades of the Papillionoideae sub-family. A total of 118 MLO sequences were identified and characterized. Their deduced protein sequences shared the characteristics of MLO proteins. The total number of MLO genes per legume species varied from 13 to 20 depending on the species. Legume MLOs were evenly distributed over their genomes and tended to localize within syntenic blocks conserved across legume genomes. Phylogenetic analysis indicated that these sequences clustered in seven well-defined clades. Comparison of MLO protein sequences revealed 34 clade-specific motifs in the variable regions of the proteins. Comparative analyses of the MLO family between legume species also uncovered several evolutionary differences between the tropical legume species from the Phaseoloid clades and the other legume species. Altogether, this study provides interesting new features on the evolution of the MLO family. It also provides valuable clues to identify additional MLO genes from non-sequenced species.
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Affiliation(s)
- Nicolas Rispail
- Institute for Sustainable Agriculture, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Avda. Menéndez Pidal s/n, 14004 Córdoba, Spain
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17
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Wyrwa K, Książkiewicz M, Szczepaniak A, Susek K, Podkowiński J, Naganowska B. Integration of Lupinus angustifolius L. (narrow-leafed lupin) genome maps and comparative mapping within legumes. Chromosome Res 2016; 24:355-78. [PMID: 27168155 PMCID: PMC4969343 DOI: 10.1007/s10577-016-9526-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 04/14/2016] [Accepted: 04/24/2016] [Indexed: 11/30/2022]
Abstract
Narrow-leafed lupin (Lupinus angustifolius L.) has recently been considered a reference genome for the Lupinus genus. In the present work, genetic and cytogenetic maps of L. angustifolius were supplemented with 30 new molecular markers representing lupin genome regions, harboring genes involved in nitrogen fixation during the symbiotic interaction of legumes and soil bacteria (Rhizobiaceae). Our studies resulted in the precise localization of bacterial artificial chromosomes (BACs) carrying sequence variants for early nodulin 40, nodulin 26, nodulin 45, aspartate aminotransferase P2, asparagine synthetase, cytosolic glutamine synthetase, and phosphoenolpyruvate carboxylase. Together with previously mapped chromosomes, the integrated L. angustifolius map encompasses 73 chromosome markers, including 5S ribosomal DNA (rDNA) and 45S rDNA, and anchors 20 L. angustifolius linkage groups to corresponding chromosomes. Chromosomal identification using BAC fluorescence in situ hybridization identified two BAC clones as narrow-leafed lupin centromere-specific markers, which served as templates for preliminary studies of centromere composition within the genus. Bioinformatic analysis of these two BACs revealed that centromeric/pericentromeric regions of narrow-leafed lupin chromosomes consisted of simple sequence repeats ordered into tandem repeats containing the trinucleotide and pentanucleotide simple sequence repeats AGG and GATAC, structured into long arrays. Moreover, cross-genus microsynteny analysis revealed syntenic patterns of 31 single-locus BAC clones among several legume species. The gene and chromosome level findings provide evidence of ancient duplication events that must have occurred very early in the divergence of papilionoid lineages. This work provides a strong foundation for future comparative mapping among legumes and may facilitate understanding of mechanisms involved in shaping legume chromosomes.
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Affiliation(s)
- Katarzyna Wyrwa
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, Poznań, 60-479, Poland.
| | - Michał Książkiewicz
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, Poznań, 60-479, Poland
| | - Anna Szczepaniak
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, Poznań, 60-479, Poland
| | - Karolina Susek
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, Poznań, 60-479, Poland
| | - Jan Podkowiński
- Institute of Bioorganic Chemistry of the Polish Academy of Sciences, Z. Noskowskiego 12/14, Poznań, 61-704, Poland
| | - Barbara Naganowska
- Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, Poznań, 60-479, Poland
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18
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Li MW, Muñoz NB, Wong CF, Wong FL, Wong KS, Wong JWH, Qi X, Li KP, Ng MS, Lam HM. QTLs Regulating the Contents of Antioxidants, Phenolics, and Flavonoids in Soybean Seeds Share a Common Genomic Region. FRONTIERS IN PLANT SCIENCE 2016; 7:854. [PMID: 27379137 PMCID: PMC4906965 DOI: 10.3389/fpls.2016.00854] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2016] [Accepted: 05/31/2016] [Indexed: 05/21/2023]
Abstract
Soybean seeds are a rich source of phenolic compounds, especially isoflavonoids, which are important nutraceuticals. Our study using 14 wild- and 16 cultivated-soybean accessions shows that seeds from cultivated soybeans generally contain lower total antioxidants compared to their wild counterparts, likely an unintended consequence of domestication or human selection. Using a recombinant inbred population resulting from a wild and a cultivated soybean parent and a bin map approach, we have identified an overlapping genomic region containing major quantitative trait loci (QTLs) that regulate the seed contents of total antioxidants, phenolics, and flavonoids. The QTL for seed antioxidant content contains 14 annotated genes based on the Williams 82 reference genome (Gmax1.01). None of these genes encodes functions that are related to the phenylpropanoid pathway of soybean. However, we found three putative Multidrug And Toxic Compound Extrusion (MATE) transporter genes within this QTL and one adjacent to it (GmMATE1-4). Moreover, we have identified non-synonymous changes between GmMATE1 and GmMATE2, and that GmMATE3 encodes an antisense transcript that expresses in pods. Whether the polymorphisms in GmMATE proteins are major determinants of the antioxidant contents, or whether the antisense transcripts of GmMATE3 play important regulatory roles, awaits further functional investigations.
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Affiliation(s)
- Man-Wah Li
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong KongHong Kong, China
| | - Nacira B. Muñoz
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong KongHong Kong, China
- Instituto de Fisiología y Recursos Genéticos Vegetales, Centro de Investigaciones Agropecuarias–INTACórdoba, Argentina
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de CórdobaCórdoba, Argentina
| | - Chi-Fai Wong
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong KongHong Kong, China
| | - Fuk-Ling Wong
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong KongHong Kong, China
| | - Kwong-Sen Wong
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong KongHong Kong, China
| | - Johanna Wing-Hang Wong
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong KongHong Kong, China
| | - Xinpeng Qi
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong KongHong Kong, China
| | - Kwan-Pok Li
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong KongHong Kong, China
| | - Ming-Sin Ng
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong KongHong Kong, China
| | - Hon-Ming Lam
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong KongHong Kong, China
- *Correspondence: Hon-Ming Lam,
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Hu J, Chen G, Zhang Y, Cui B, Yin W, Yu X, Zhu Z, Hu Z. Anthocyanin composition and expression analysis of anthocyanin biosynthetic genes in kidney bean pod. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2015; 97:304-312. [PMID: 26512970 DOI: 10.1016/j.plaphy.2015.10.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 10/14/2015] [Accepted: 10/14/2015] [Indexed: 06/05/2023]
Abstract
Kidney bean (Phaseolus vulgaris L.) is an important dietary legume crop cultivated and consumed worldwide. A purple cultivar (Zi Bawang) and a green cultivar (Chun Qiu), the main difference of which is in the pod skin color, were selected for the study. Malvidin 3, 5-diglucoside is identified as the major anthocyanin in the pod skin of Zi Bawang by HPLC-ESI-MS/MS. Three regulatory genes PvMYB1, PvMYB2, PvTT8-1 and most structural genes are dramatically up-regulated in purple pod skin compared to those in other materials. Significantly decreased expression levels of all regulatory genes and most biosynthetic genes are also detected in the purple skin of pods covered with bags compared to non-covered ones. All the results suggest that PvMYB1, PvMYB2 and PvTT8-1 might play a critical role in transcriptional activation of most anthocyanin biosynthetic genes in purple kidney bean pod.
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Affiliation(s)
- Jingtao Hu
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Campus B, Room 515, 174 Shapingba Main Street, Chongqing 400044, PR China
| | - Guoping Chen
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Campus B, Room 515, 174 Shapingba Main Street, Chongqing 400044, PR China
| | - Yanjie Zhang
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Campus B, Room 515, 174 Shapingba Main Street, Chongqing 400044, PR China
| | - Baolu Cui
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Campus B, Room 515, 174 Shapingba Main Street, Chongqing 400044, PR China
| | - Wencheng Yin
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Campus B, Room 515, 174 Shapingba Main Street, Chongqing 400044, PR China
| | - Xiaohui Yu
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Campus B, Room 515, 174 Shapingba Main Street, Chongqing 400044, PR China
| | - Zhiguo Zhu
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Campus B, Room 515, 174 Shapingba Main Street, Chongqing 400044, PR China
| | - Zongli Hu
- Key Laboratory of Biorheological Science and Technology (Chongqing University), Ministry of Education, Bioengineering College, Chongqing University, Campus B, Room 515, 174 Shapingba Main Street, Chongqing 400044, PR China.
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Książkiewicz M, Zielezinski A, Wyrwa K, Szczepaniak A, Rychel S, Karlowski W, Wolko B, Naganowska B. Remnants of the Legume Ancestral Genome Preserved in Gene-Rich Regions: Insights from Lupinus angustifolius Physical, Genetic, and Comparative Mapping. PLANT MOLECULAR BIOLOGY REPORTER 2015; 33:84-101. [PMID: 25620837 PMCID: PMC4295026 DOI: 10.1007/s11105-014-0730-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The narrow-leafed lupin (Lupinus angustifolius) was recently considered as a legume reference species. Genetic resources have been developed, including a draft genome sequence, linkage maps, nuclear DNA libraries, and cytogenetic chromosome-specific landmarks. Here, we used a complex approach, involving DNA fingerprinting, sequencing, genetic mapping, and molecular cytogenetics, to localize and analyze L. angustifolius gene-rich regions (GRRs). A L. angustifolius genomic bacterial artificial chromosome (BAC) library was screened with short sequence repeat (SSR)-based probes. Selected BACs were fingerprinted and assembled into contigs. BAC-end sequence (BES) annotation allowed us to choose clones for sequencing, targeting GRRs. Additionally, BESs were aligned to the scaffolds of the genome sequence. The genetic map was supplemented with 35 BES-derived markers, distributed in 14 linkage groups and tagging 37 scaffolds. The identified GRRs had an average gene density of 19.6 genes/100 kb and physical-to-genetic distance ratios of 11 to 109 kb/cM. Physical and genetic mapping was supported by multi-BAC-fluorescence in situ hybridization (FISH), and five new linkage groups were assigned to the chromosomes. Syntenic links to the genome sequences of five legume species (Medicago truncatula, Glycine max, Lotus japonicus, Phaseolus vulgaris, and Cajanus cajan) were identified. The comparative mapping of the two largest lupin GRRs provides novel evidence for ancient duplications in all of the studied species. These regions are conserved among representatives of the main clades of Papilionoideae. Furthermore, despite the complex evolution of legumes, some segments of the nuclear genome were not substantially modified and retained their quasi-ancestral structures. Cytogenetic markers anchored in these regions constitute a platform for heterologous mapping of legume genomes.
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Affiliation(s)
- Michał Książkiewicz
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
| | - Andrzej Zielezinski
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Katarzyna Wyrwa
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
| | - Anna Szczepaniak
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
| | - Sandra Rychel
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
| | - Wojciech Karlowski
- Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, 61-614 Poznan, Poland
| | - Bogdan Wolko
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
| | - Barbara Naganowska
- Department of Genomics, Institute of Plant Genetics of the Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznan, Poland
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Valdés-López O, Hernández G. Phenylpropanoids as master regulators: state of the art and perspectives in common bean (Phaseolus vulgaris). FRONTIERS IN PLANT SCIENCE 2014; 5:336. [PMID: 25101096 PMCID: PMC4102167 DOI: 10.3389/fpls.2014.00336] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 06/24/2014] [Indexed: 05/14/2023]
Affiliation(s)
- Oswaldo Valdés-López
- Unidad de Morfología y Función, Laboratorio de Bioquímica, Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de MéxicoTlalnepantla, Mexico
- *Correspondence:
| | - Georgina Hernández
- Genómica Funcional de Eucariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de MéxicoCuernavaca, México
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Smýkal P, Vernoud V, Blair MW, Soukup A, Thompson RD. The role of the testa during development and in establishment of dormancy of the legume seed. FRONTIERS IN PLANT SCIENCE 2014; 5:351. [PMID: 25101104 PMCID: PMC4102250 DOI: 10.3389/fpls.2014.00351] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Accepted: 06/30/2014] [Indexed: 05/19/2023]
Abstract
Timing of seed germination is one of the key steps in plant life cycles. It determines the beginning of plant growth in natural or agricultural ecosystems. In the wild, many seeds exhibit dormancy and will only germinate after exposure to certain environmental conditions. In contrast, crop seeds germinate as soon as they are imbibed usually at planting time. These domestication-triggered changes represent adaptations to cultivation and human harvesting. Germination is one of the common sets of traits recorded in different crops and termed the "domestication syndrome." Moreover, legume seed imbibition has a crucial role in cooking properties. Different seed dormancy classes exist among plant species. Physical dormancy (often called hardseededness), as found in legumes, involves the development of a water-impermeable seed coat, caused by the presence of phenolics- and suberin-impregnated layers of palisade cells. The dormancy release mechanism primarily involves seed responses to temperature changes in the habitat, resulting in testa permeability to water. The underlying genetic controls in legumes have not been identified yet. However, positive correlation was shown between phenolics content (e.g., pigmentation), the requirement for oxidation and the activity of catechol oxidase in relation to pea seed dormancy, while epicatechin levels showed a significant positive correlation with soybean hardseededness. myeloblastosis family of transcription factors, WD40 proteins and enzymes of the anthocyanin biosynthesis pathway were involved in seed testa color in soybean, pea and Medicago, but were not tested directly in relation to seed dormancy. These phenolic compounds play important roles in defense against pathogens, as well as affecting the nutritional quality of products, and because of their health benefits, they are of industrial and medicinal interest. In this review, we discuss the role of the testa in mediating legume seed germination, with a focus on structural and chemical aspects.
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Affiliation(s)
- Petr Smýkal
- Department of Botany, Faculty of Sciences, Palacký University in OlomoucOlomouc, Czech Republic
- *Correspondence: Petr Smýkal, Department of Botany, Faculty of Sciences, Palacký University in Olomouc, Šlechtitelů 11, 783 71 Olomouc, Czech Republic e-mail:
| | | | - Matthew W. Blair
- Department of Agricultural and Environmental Sciences, Tennessee State UniversityNashville, TN, USA
| | - Aleš Soukup
- Department of Experimental Plant Biology, Charles UniversityPrague, Czech Republic
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