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Khazaei H, Carlson-Nilsson U, Schulman AH. The Jan Sjödin faba bean mutant collection: morphological and molecular characterization. Hereditas 2024; 161:37. [PMID: 39375815 PMCID: PMC11457391 DOI: 10.1186/s41065-024-00339-7] [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: 08/16/2024] [Accepted: 09/30/2024] [Indexed: 10/09/2024] Open
Abstract
BACKGROUND Plant mutagenesis creates novel alleles, thereby increasing genetic and phenotypic diversity. The availability of the faba bean (Vicia faba L.) reference genome and a growing set of additional genomic resources has increased the scientific and practical value of mutant collections. We aimed to genotype and morphologically phenotype a historical faba bean mutant collection developed and characterized by Jan Sjödin (1934-2023) over half a century ago in order to increase its value to researchers. The collection was genotyped using high-throughput single-primer enrichment technology (SPET) assays. RESULTS We used 11,073 informative single nucleotide polymorphism (SNP) markers spanning the faba bean genome to genotype 52 mutant lines along with the background line, cv. Primus. A range of flower, seed, leaf, and stipule mutations were observed. The analysis of population structure revealed a shallow structure with no major subpopulations. Principal component and cluster analyses revealed, to a minor extent, that the mutants clustered by their phenotype. CONCLUSIONS The mutants' phenotypic variation and shallow structure indicate that the Sjödin faba bean collection has the potential to play a significant role in faba bean breeding and in genetic and functional studies.
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Affiliation(s)
- Hamid Khazaei
- Production systems, Natural Resources Institute Finland, Helsinki, Finland.
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland.
| | | | - Alan H Schulman
- Production systems, Natural Resources Institute Finland, Helsinki, Finland
- Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland
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Chen J, Zhou H, Yuan X, He Y, Yan Q, Lin Y, Wu R, Liu J, Xue C, Chen X. Homolog of Pea SGR Controls Stay-Green in Faba Bean ( Vicia faba L.). Genes (Basel) 2023; 14:1030. [PMID: 37239389 PMCID: PMC10218623 DOI: 10.3390/genes14051030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/20/2023] [Accepted: 04/28/2023] [Indexed: 05/28/2023] Open
Abstract
Faba bean is an important legume crop consumed as a vegetable or snack food, and its green cotyledons could present an attractive color for consumers. A mutation in SGR causes stay-green in plants. In this study, vfsgr was identified from a green-cotyledon-mutant faba bean, SNB7, by homologous blast between the SGR of pea and the transcriptome of faba bean. Sequence analysis revealed that a SNP at position 513 of the CDS of VfSGR caused a pre-stop codon, resulting in a shorter protein in the green-cotyledon faba bean SNB7. A dCaps marker was developed according to the SNP that caused the pre-stop, and this marker was completely associated with the color of the cotyledon of faba bean. SNB7 stayed green during dark treatment, while the expression level of VfSGR increased during dark-induced senescence in the yellow-cotyledon faba bean HST. Transient expression of VfSGR in Nicotiana. benthamiana leaves resulted in chlorophyll degradation. These results indicate that vfsgr is the gene responsible for the stay-green of faba bean, and the dCaps marker developed in this study provides a molecular tool for the breeding of green-cotyledon faba beans.
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Affiliation(s)
- Jingbin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.C.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Huimin Zhou
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.C.)
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Xingxing Yuan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.C.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Yaming He
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.C.)
- College of Life Sciences, Nanjing Agricultural University, Nanjing 210095, China
| | - Qiang Yan
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.C.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Yun Lin
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.C.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Ranran Wu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.C.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Jinyang Liu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.C.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Chenchen Xue
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.C.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
| | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.C.)
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Nanjing 210014, China
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Adhikari KN, Khazaei H, Ghaouti L, Maalouf F, Vandenberg A, Link W, O'Sullivan DM. Conventional and Molecular Breeding Tools for Accelerating Genetic Gain in Faba Bean ( Vicia Faba L.). FRONTIERS IN PLANT SCIENCE 2021; 12:744259. [PMID: 34721470 PMCID: PMC8548637 DOI: 10.3389/fpls.2021.744259] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 09/09/2021] [Indexed: 05/11/2023]
Abstract
Faba bean is a cool-season grain legume crop, which is grown worldwide for food and feed. Despite a decrease in area under faba bean in the past, the interest in growing faba bean is increasing globally due to its high seed protein content and its excellent ecological service. The crop is, however, exposed to diverse biotic and abiotic stresses causing unstable, low grain yield. Although, sources of resistance to main diseases, such as ascochyta blight (Ascochyta fabae Speg.), rust (Uromyces viciae-fabae (Pers.) Schroet.), chocolate spot (Botrytis fabae Sard.) and gall disease (Physioderma viciae), have been identified, their resistance is only partial and cannot prevent grain yield losses without agronomical practices. Tightly associated DNA markers for host plant resistance genes are needed to enhance the level of resistance. Less progress has been made for abiotic stresses. Different breeding methods are proposed, but until now line breeding, based on the pedigree method, is the dominant practice in breeding programs. Nonetheless, the low seed multiplication coefficient and the requirement for growing under insect-proof enclosures to avoid outcrossing hampers breeding, along with the lack of tools such as double haploid system and cytoplasmic male sterility. This reduces breeding population size and speed of breeding hence the chances of capturing rare combinations of favorable alleles. Availability and use of the DNA markers such as vicine-convicine (vc -) and herbicide tolerance in breeding programs have encouraged breeders and given confidence in marker assisted selection. Closely linked QTL for several biotic and abiotic stress tolerance are available and their verification and conversion in breeder friendly platform will enhance the selection process. Recently, genomic selection and speed breeding techniques together with genomics have come within reach to accelerate the genetic gains in faba bean. Advancements in genomic resources with other breeding tools, methods and platforms will enable to accelerate the breeding process for enhancing genetic gain in this species.
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Affiliation(s)
- Kedar N. Adhikari
- The University of Sydney, School of Life and Environmental Science, Plant Breeding Institute, Narrabri, NSW, Australia
| | | | - Lamiae Ghaouti
- Institute of Agronomy and Veterinary Medicine Hassan II, Department of Plant Production, Protection and Biotechnology, Rabat, Morocco
| | - Fouad Maalouf
- International Center for Agricultural Research in Dry Areas, Beirut, Lebanon
| | - Albert Vandenberg
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Wolfgang Link
- Department of Crop Sciences, Georg-August-Universität, Göttingen, Germany
| | - Donal M. O'Sullivan
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
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Khazaei H, O'Sullivan DM, Stoddard FL, Adhikari KN, Paull JG, Schulman AH, Andersen SU, Vandenberg A. Recent advances in faba bean genetic and genomic tools for crop improvement. LEGUME SCIENCE 2021; 3:e75. [PMID: 34977588 PMCID: PMC8700193 DOI: 10.1002/leg3.75] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 01/10/2021] [Accepted: 02/02/2021] [Indexed: 05/04/2023]
Abstract
Faba bean (Vicia faba L.), a member of the Fabaceae family, is one of the important food legumes cultivated in cool temperate regions. It holds great importance for human consumption and livestock feed because of its high protein content, dietary fibre, and nutritional value. Major faba bean breeding challenges include its mixed breeding system, unknown wild progenitor, and genome size of ~13 Gb, which is the largest among diploid field crops. The key breeding objectives in faba bean include improved resistance to biotic and abiotic stress and enhanced seed quality traits. Regarding quality traits, major progress on reduction of vicine-convicine and seed coat tannins, the main anti-nutritional factors limiting faba bean seed usage, have been recently achieved through gene discovery. Genomic resources are relatively less advanced compared with other grain legume species, but significant improvements are underway due to a recent increase in research activities. A number of bi-parental populations have been constructed and mapped for targeted traits in the last decade. Faba bean now benefits from saturated synteny-based genetic maps, along with next-generation sequencing and high-throughput genotyping technologies that are paving the way for marker-assisted selection. Developing a reference genome, and ultimately a pan-genome, will provide a foundational resource for molecular breeding. In this review, we cover the recent development and deployment of genomic tools for faba bean breeding.
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Affiliation(s)
- Hamid Khazaei
- Department of Plant SciencesUniversity of SaskatchewanSaskatoonSaskatchewanCanada
| | | | - Frederick L. Stoddard
- Department of Agricultural Sciences, Viikki Plant Science Centre, and Helsinki Sustainability Science CentreUniversity of HelsinkiHelsinkiFinland
| | - Kedar N. Adhikari
- Plant Breeding Institute, Faculty of ScienceThe University of SydneyNarrabriNew South WalesAustralia
| | - Jeffrey G. Paull
- School of Agriculture, Food and WineThe University of AdelaideAdelaideSouth AustraliaAustralia
| | - Alan H. Schulman
- Production SystemsNatural Resources Institute Finland (Luke)HelsinkiFinland
- Institute of Biotechnology and Viikki Plant Science CentreUniversity of HelsinkiHelsinkiFinland
| | - Stig U. Andersen
- Department of Molecular Biology and GeneticsAarhus UniversityAarhusDenmark
| | - Albert Vandenberg
- Department of Plant SciencesUniversity of SaskatchewanSaskatoonSaskatchewanCanada
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Meng Z, Liu Q, Zhang Y, Chen J, Sun Z, Ren C, Zhang Z, Cheng X, Huang Y. Nutritive value of faba bean ( Vicia faba L.) as a feedstuff resource in livestock nutrition: A review. Food Sci Nutr 2021; 9:5244-5262. [PMID: 34532032 PMCID: PMC8441412 DOI: 10.1002/fsn3.2342] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 04/18/2021] [Accepted: 04/19/2021] [Indexed: 11/25/2022] Open
Abstract
The review evaluates faba bean (Vicia faba L.; FB) seeds relative to their nutritional composition, their content of antinutritional factors, and their impact on animal performance. The literature indicates that FB plant is a cool-season, annual grain legume that grows the best in cool and humid conditions. Its seeds are rich in protein, energy, and mineral compounds and have particularly high unsaturated fatty acid levels. However, FB seeds also contain various proportions of antinutritional factors (ANFs) that can interfere with nutrient utilization in nonruminants. The various processing methods are efficient in either reducing or inactivating the ANFs of FB seeds, with extrusion treatment offering the most effective method of improving apparent nutrient and energy digestibility of nonruminants. In vivo studies on ruminants, pigs, poultry, and fishes reveal that FB seeds have the potential to be used as a substitute for soybean meal and/or cereal seeds in livestock diets in order to support milk, meat, and/or egg production.
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Affiliation(s)
- Zhu Meng
- Department of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
| | - Qingqing Liu
- Department of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
| | - Yan Zhang
- Department of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
| | - Jiahong Chen
- Center of Agriculture Technology Cooperation and Promotion of Dingyuan CountyChuzhouChina
| | - Zhipeng Sun
- Department of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
| | - Chunhuan Ren
- Department of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
- Center of Agriculture Technology Cooperation and Promotion of Dingyuan CountyChuzhouChina
| | - Zijun Zhang
- Department of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
- Center of Agriculture Technology Cooperation and Promotion of Dingyuan CountyChuzhouChina
| | - Xiao Cheng
- Department of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
- Center of Agriculture Technology Cooperation and Promotion of Dingyuan CountyChuzhouChina
| | - Yafeng Huang
- Department of Animal Science and TechnologyAnhui Agricultural UniversityHefeiChina
- Center of Agriculture Technology Cooperation and Promotion of Dingyuan CountyChuzhouChina
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Kaldate S, Patel A, Modha K, Parekh V, Kale B, Vadodariya G, Patel R. Allelic characterization and protein structure analysis reveals the involvement of splice site mutation for growth habit differences in Lablab purpureus (L.) Sweet. J Genet Eng Biotechnol 2021; 19:34. [PMID: 33619637 PMCID: PMC7900342 DOI: 10.1186/s43141-021-00136-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 02/14/2021] [Indexed: 11/10/2022]
Abstract
BACKGROUND Interrelationship between growth habit and flowering played a key role in the domestication history of pulses; however, the actual genes responsible for these traits have not been identified in Indian bean. Determinate growth habit is desirable due to its early flowering, photo-insensitivity, synchronous pod maturity, ease in manual harvesting and short crop duration. The present study aimed to identify, characterize and validate the gene responsible for growth habit by using a candidate gene approach coupled with sequencing, multiple sequence alignment, protein structure prediction and binding pocket analysis. RESULTS Terminal flowering locus was amplified from GPKH 120 (indeterminate) and GNIB-21 (determinate) using the primers designed from PvTFL1y locus of common bean. Gene prediction revealed that the length of the third and fourth exons differed between the two alleles. Allelic sequence comparison indicated a transition from guanine to adenine at the end of the third exon in GNIB 21. This splice site single-nucleotide polymorphism (SNP) was validated in germplasm lines by sequencing. Protein structure analysis indicated involvement of two binding pockets for interaction of terminal flowering locus (TFL) protein with other proteins. CONCLUSION The splice site SNP present at the end of the third exon of TFL locus is responsible for the transformation of shoot apical meristem into a reproductive fate in the determinate genotype GNIB 21. The splice site SNP leads to absence of 14 amino acids in mutant TFL protein of GNIB 21, rendering the protein non-functional. This deletion disturbed previously reported anion-binding pocket and secondary binding pocket due to displacement of small β-sheet away from an external loop. This finding may enable the modulation of growth habit in Indian bean and other pulse crops through genome editing.
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Affiliation(s)
- Supriya Kaldate
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, 396 450, India
| | - Apexa Patel
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, 396 450, India
| | - Kaushal Modha
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, 396 450, India.
| | - Vipulkumar Parekh
- Department of Basic Science and Humanities, ASPEE College of Horticulture and Forestry, NAU, Navsari, Gujarat, 396 450, India
| | - Bhushan Kale
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, 396 450, India
| | - Gopal Vadodariya
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, 396 450, India
| | - Ritesh Patel
- Department of Genetics and Plant Breeding, N. M. College of Agriculture, Navsari Agricultural University, Navsari, Gujarat, 396 450, India
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Afzal M, Alghamdi SS, Migdadi HH, Khan MA, Nurmansyah, Mirza SB, El-Harty E. Legume genomics and transcriptomics: From classic breeding to modern technologies. Saudi J Biol Sci 2019; 27:543-555. [PMID: 31889880 PMCID: PMC6933173 DOI: 10.1016/j.sjbs.2019.11.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/16/2019] [Accepted: 11/17/2019] [Indexed: 02/06/2023] Open
Abstract
Legumes are essential and play a significant role in maintaining food standards and augmenting physiochemical soil properties through the biological nitrogen fixation process. Biotic and abiotic factors are the main factors limiting legume production. Classical breeding methodologies have been explored extensively about the problem of truncated yield in legumes but have not succeeded at the desired rate. Conventional breeding improved legume genotypes but with more resources and time. Recently, the invention of next-generation sequencing (NGS) and high-throughput methods for genotyping have opened new avenues for research and developments in legume studies. During the last decade, genome sequencing for many legume crops documented. Sequencing and re-sequencing of important legume species have made structural variation and functional genomics conceivable. NGS and other molecular techniques such as the development of markers; genotyping; high density genetic linkage maps; quantitative trait loci (QTLs) identification, expressed sequence tags (ESTs), single nucleotide polymorphisms (SNPs); and transcription factors incorporated into existing breeding technologies have made possible the accurate and accelerated delivery of information for researchers. The application of genome sequencing, RNA sequencing (transcriptome sequencing), and DNA sequencing (re-sequencing) provide considerable insights for legume development and improvement programs. Moreover, RNA-Seq helps to characterize genes, including differentially expressed genes, and can be applied for functional genomics studies, especially when there is limited information available for the studied genomes. Genome-based crop development studies and the availability of genomics data as well as decision-making gears look be specific for breeding programs. This review mainly presents an overview of the path from classical breeding to new emerging genomics tools, which will trigger and accelerate genomics-assisted breeding for recognition of novel genes for yield and quality characters for sustainable legume crop production.
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Affiliation(s)
- Muhammad Afzal
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Salem S Alghamdi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Hussein H Migdadi
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Altaf Khan
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Nurmansyah
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
| | - Shaher Bano Mirza
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey.,Department of Biosciences, COMSATS Institute of Information Technology (CIIT), Chak Shahzad, Islamabad, Pakistan
| | - Ehab El-Harty
- Department of Plant Production, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
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Gutierrez N, Torres AM. Characterization and diagnostic marker for TTG1 regulating tannin and anthocyanin biosynthesis in faba bean. Sci Rep 2019; 9:16174. [PMID: 31700069 PMCID: PMC6838129 DOI: 10.1038/s41598-019-52575-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/11/2019] [Indexed: 02/07/2023] Open
Abstract
Condensed tannins, found in coloured-flowering varieties of faba bean (Vicia faba L) are, after vicine and convicine, one of the major anti-nutritional factors for monogastric animals. The development of tannin-free cultivars is a key goal in breeding to broaden the use of this legume in the animal feed industry. Two recessive genes, zt-1 and zt-2, control the zero-tannin content and promote white-flowered plants. Previous studies exploiting synteny with the model Medicago truncatula reported a mutation in TTG1, a gene encoding a WD40 transcription factor located in chromosome II, as the responsible for the zt-1 phenotypes. Here a comprehensive analysis of VfTTG1 (including phylogenetic relationships, gene structure and gene expression) has been conducted to confirm the identity of the gene and to reveal structural changes that may result in different functional alleles. The results confirmed the identity of the candidate and revealed the existence of two different alleles responsible for the phenotype: ttg1-a, probably due to a mutation in the promoter region, and ttg1-b caused by a deletion at the 5′end of VfTTG1. Based on the sequencing results, an allele-specific diagnostic marker was designed that differentiate zt-1 from wild and zt-2 genotypes and facilitates its deployment in faba bean breeding programs.
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Affiliation(s)
- Natalia Gutierrez
- Área de Genómica y Biotecnología, IFAPA-Centro Alameda del Obispo, Apdo 3092, E-14080, Córdoba, Spain.
| | - Ana M Torres
- Área de Genómica y Biotecnología, IFAPA-Centro Alameda del Obispo, Apdo 3092, E-14080, Córdoba, Spain
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Nurmansyah, Alghamdi SS, Migdadi HM, Farooq M. Novel inflorescence architecture in gamma radiation-induced faba bean mutant populations. Int J Radiat Biol 2019; 95:1744-1751. [PMID: 31486707 DOI: 10.1080/09553002.2019.1665205] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Purpose: Inflorescence architecture is an important trait in the seed production of grain legumes. As several genes are responsible for this trait, any mutation, on these genes, may cause change in the inflorescence architecture. This study was conducted to evaluate inflorescence architecture in faba bean exposed to gamma radiation and to characterize the inflorescence architecture mutants phenotypically.Materials and methods: Faba bean M2 seeds (4898) generated from M1 generation of cultivars Hassawi 2 and ILB4347 were used in this study. M1 seeds were produced by irradiation treatments at two doses of gamma radiations (25 and 50 Gy). Faba bean M2 seeds were planted under field conditions. A total of 4032 mutant plants out of 4898 M2 seeds were evaluated for their inflorescence architecture.Results: A total of 20 determinate mutants were found and classified into four different types. Determinate type 1 was characterized by the formation of single terminal inflorescence on shoot apical meristem (SAM), type 2 by the formation of multiple inflorescences on SEM and generated upper branches that act as indeterminate type. Type 3 was characterized by the formation of a panicle-like inflorescence. While type 4 was characterized by the formation of primary and secondary panicle-like inflorescence. All of the determinate mutant types had shorter plant height and earlier maturity than control indeterminate type but had lower biological yield and seed yield. Among the determinate mutant types, determinate type 1 was only mutant that had a higher harvest index than the control indeterminate type. This promising mutant can be used to further breeding program to increase biological yield and seed yield.Conclusions: This study indicated potential of gamma radiation in inducing novel inflorescence architecture in faba bean. The mutants developed are valuable resources to study genes related to inflorescence architecture through forward genetics approach.
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Affiliation(s)
- Nurmansyah
- Plant Production Department, College of Food and Agriculture Sciences, Legume Research Group, King Saud University, Riyadh, Saudi Arabia
| | - Salem S Alghamdi
- Plant Production Department, College of Food and Agriculture Sciences, Legume Research Group, King Saud University, Riyadh, Saudi Arabia
| | - Hussein M Migdadi
- Plant Production Department, College of Food and Agriculture Sciences, Legume Research Group, King Saud University, Riyadh, Saudi Arabia.,National Agricultural Research Center, Baq'a', Jordan
| | - Muhammad Farooq
- Plant Production Department, College of Food and Agriculture Sciences, Legume Research Group, King Saud University, Riyadh, Saudi Arabia.,Department of Crop Sciences, College of Agricultural and Marine Science, Sultan Qaboos University, Muscat, Oman.,Department of Agronomy, University of Agriculture, Faisalabad, Pakistan
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10
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Zhang Y, Wang L, Gao Y, Li D, Yu J, Zhou R, Zhang X. Genetic dissection and fine mapping of a novel dt gene associated with determinate growth habit in sesame. BMC Genet 2018; 19:38. [PMID: 29902971 PMCID: PMC6003200 DOI: 10.1186/s12863-018-0614-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 04/18/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND As an important oil crop, growth habit of sesame (Sesamum indicum L.) is naturally indeterminate, which brings about asynchronous maturity of capsules and causes loss of yield. RESULTS The genetic basis of determinate growth habit in sesame was investigated by classical genetic analysis through multiple populations, results revealed that it was controlled by an unique recessive gene. The genotyping by sequencing (GBS) approach was employed for high-throughput SNP identification and genotyping in the F2 population, then a high density bin map was constructed, the map was 1086.403 cM in length, which consisted of 1184 bins (13,679 SNPs), with an average of 0.918 cM between adjacent bins. Based on bin mapping in conjunction with SSR markers analysis in targeted region, the novel sesame determinacy gene was mapped on LG09 in a genome region of 41 kb. CONCLUSIONS This study dissected genetic basis of determinate growth habit in sesame, constructed a new high-density bin map and mapped a novel determinacy gene. Results of this study demonstrate that we employed an optimized approach to get fine-accuracy, high-resolution and high-efficiency mapping result in sesame. The findings provided important foundation for sesame determinacy gene cloning and were expected to be applied in breeding for cultivars suited to mechanized production.
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Affiliation(s)
- Yanxin Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Rd, Wuhan, 430062, China
| | - Linhai Wang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Rd, Wuhan, 430062, China
| | - Yuan Gao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Rd, Wuhan, 430062, China
| | - Donghua Li
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Rd, Wuhan, 430062, China
| | - Jingyin Yu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Rd, Wuhan, 430062, China
| | - Rong Zhou
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Rd, Wuhan, 430062, China
| | - Xiurong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, No.2 Xudong 2nd Rd, Wuhan, 430062, China.
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O'Sullivan DM, Angra D. Advances in Faba Bean Genetics and Genomics. Front Genet 2016; 7:150. [PMID: 27597858 PMCID: PMC4993074 DOI: 10.3389/fgene.2016.00150] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 08/03/2016] [Indexed: 12/21/2022] Open
Abstract
Vicia faba L, is a globally important grain legume whose main centers of diversity are the Fertile Crescent and Mediterranean basin. Because of its small number (six) of exceptionally large and easily observed chromosomes it became a model species for plant cytogenetics the 70s and 80s. It is somewhat ironic therefore, that the emergence of more genomically tractable model plant species such as Arabidopsis and Medicago coincided with a marked decline in genome research on the formerly favored plant cytogenetic model. Thus, as ever higher density molecular marker coverage and dense genetic and even complete genome sequence maps of key crop and model species emerged through the 1990s and early 2000s, genetic and genome knowledge of Vicia faba lagged far behind other grain legumes such as soybean, common bean and pea. However, cheap sequencing technologies have stimulated the production of deep transcriptome coverage from several tissue types and numerous distinct cultivars in recent years. This has permitted the reconstruction of the faba bean meta-transcriptome and has fueled development of extensive sets of Simple Sequence Repeat and Single Nucleotide Polymorphism (SNP) markers. Genetics of faba bean stretches back to the 1930s, but it was not until 1993 that DNA markers were used to construct genetic maps. A series of Random Amplified Polymorphic DNA-based genetic studies mainly targeted at quantitative loci underlying resistance to a series of biotic and abiotic stresses were conducted during the 1990's and early 2000s. More recently, SNP-based genetic maps have permitted chromosome intervals of interest to be aligned to collinear segments of sequenced legume genomes such as the model legume Medicago truncatula, which in turn opens up the possibility for hypotheses on gene content, order and function to be translated from model to crop. Some examples of where knowledge of gene content and function have already been productively exploited are discussed. The bottleneck in associating genes and their functions has therefore moved from locating gene candidates to validating their function and the last part of this review covers mutagenesis and genetic transformation, two complementary routes to validating gene function and unlocking novel trait variation for the improvement of this important grain legume.
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Affiliation(s)
- Donal M. O'Sullivan
- School of Agriculture, Policy and Development, University of ReadingReading, UK
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Webb A, Cottage A, Wood T, Khamassi K, Hobbs D, Gostkiewicz K, White M, Khazaei H, Ali M, Street D, Duc G, Stoddard FL, Maalouf F, Ogbonnaya FC, Link W, Thomas J, O'Sullivan DM. A SNP-based consensus genetic map for synteny-based trait targeting in faba bean (Vicia faba L.). PLANT BIOTECHNOLOGY JOURNAL 2016; 14:177-85. [PMID: 25865502 PMCID: PMC4973813 DOI: 10.1111/pbi.12371] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 02/12/2015] [Accepted: 03/03/2015] [Indexed: 05/20/2023]
Abstract
Faba bean (Vicia faba L.) is a globally important nitrogen-fixing legume, which is widely grown in a diverse range of environments. In this work, we mine and validate a set of 845 SNPs from the aligned transcriptomes of two contrasting inbred lines. Each V. faba SNP is assigned by BLAST analysis to a single Medicago orthologue. This set of syntenically anchored polymorphisms were then validated as individual KASP assays, classified according to their informativeness and performance on a panel of 37 inbred lines, and the best performing 757 markers used to genotype six mapping populations. The six resulting linkage maps were merged into a single consensus map on which 687 SNPs were placed on six linkage groups, each presumed to correspond to one of the six V. faba chromosomes. This sequence-based consensus map was used to explore synteny with the most closely related crop species, lentil and the most closely related fully sequenced genome, Medicago. Large tracts of uninterrupted colinearity were found between faba bean and Medicago, making it relatively straightforward to predict gene content and order in mapped genetic interval. As a demonstration of this, we mapped a flower colour gene to a 2-cM interval of Vf chromosome 2 which was highly colinear with Mt3. The obvious candidate gene from 78 gene models in the collinear Medicago chromosome segment was the previously characterized MtWD40-1 gene controlling anthocyanin production in Medicago and resequencing of the Vf orthologue showed a putative causative deletion of the entire 5' end of the gene.
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Affiliation(s)
- Anne Webb
- National Institute of Agricultural Botany, Cambridge, UK
| | - Amanda Cottage
- National Institute of Agricultural Botany, Cambridge, UK
| | - Thomas Wood
- National Institute of Agricultural Botany, Cambridge, UK
| | | | - Douglas Hobbs
- National Institute of Agricultural Botany, Cambridge, UK
| | | | | | - Hamid Khazaei
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | - Mohamed Ali
- Department of Crop Sciences, Georg-August-Universität, Göttingen, Germany
| | | | - Gérard Duc
- INRA, UMR1347 Agroécologie, Dijon, France
| | - Fred L Stoddard
- Department of Agricultural Sciences, University of Helsinki, Helsinki, Finland
| | | | | | - Wolfgang Link
- Department of Crop Sciences, Georg-August-Universität, Göttingen, Germany
| | - Jane Thomas
- National Institute of Agricultural Botany, Cambridge, UK
| | - Donal M O'Sullivan
- National Institute of Agricultural Botany, Cambridge, UK
- School of Agriculture, Policy and Development, University of Reading, Whiteknights, UK
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Benlloch R, Berbel A, Ali L, Gohari G, Millán T, Madueño F. Genetic control of inflorescence architecture in legumes. FRONTIERS IN PLANT SCIENCE 2015; 6:543. [PMID: 26257753 PMCID: PMC4508509 DOI: 10.3389/fpls.2015.00543] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 07/06/2015] [Indexed: 05/18/2023]
Abstract
The architecture of the inflorescence, the shoot system that bears the flowers, is a main component of the huge diversity of forms found in flowering plants. Inflorescence architecture has also a strong impact on the production of fruits and seeds, and on crop management, two highly relevant agronomical traits. Elucidating the genetic networks that control inflorescence development, and how they vary between different species, is essential to understanding the evolution of plant form and to being able to breed key architectural traits in crop species. Inflorescence architecture depends on the identity and activity of the meristems in the inflorescence apex, which determines when flowers are formed, how many are produced and their relative position in the inflorescence axis. Arabidopsis thaliana, where the genetic control of inflorescence development is best known, has a simple inflorescence, where the primary inflorescence meristem directly produces the flowers, which are thus borne in the main inflorescence axis. In contrast, legumes represent a more complex inflorescence type, the compound inflorescence, where flowers are not directly borne in the main inflorescence axis but, instead, they are formed by secondary or higher order inflorescence meristems. Studies in model legumes such as pea (Pisum sativum) or Medicago truncatula have led to a rather good knowledge of the genetic control of the development of the legume compound inflorescence. In addition, the increasing availability of genetic and genomic tools for legumes is allowing to rapidly extending this knowledge to other grain legume crops. This review aims to describe the current knowledge of the genetic network controlling inflorescence development in legumes. It also discusses how the combination of this knowledge with the use of emerging genomic tools and resources may allow rapid advances in the breeding of grain legume crops.
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Affiliation(s)
- Reyes Benlloch
- Molecular Genetics Department, Center for Research in Agricultural Genomics, Consortium CSIC-IRTA-UAB-UB, Parc de Recerca Universitat Autònoma de BarcelonaBarcelona, Spain
| | - Ana Berbel
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas – Universidad Politécnica de ValenciaValencia, Spain
| | - Latifeh Ali
- Departamento de Genética, Universidad de CórdobaCórdoba, Spain
| | - Gholamreza Gohari
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas – Universidad Politécnica de ValenciaValencia, Spain
| | - Teresa Millán
- Departamento de Genética, Universidad de CórdobaCórdoba, Spain
| | - Francisco Madueño
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas – Universidad Politécnica de ValenciaValencia, Spain
- *Correspondence: Francisco Madueño, Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas – Universidad Politécnica de Valencia, Avenida Los Naranjos s/n, Valencia 46022, Spain,
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Bohra A, Pandey MK, Jha UC, Singh B, Singh IP, Datta D, Chaturvedi SK, Nadarajan N, Varshney RK. Genomics-assisted breeding in four major pulse crops of developing countries: present status and prospects. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:1263-91. [PMID: 24710822 PMCID: PMC4035543 DOI: 10.1007/s00122-014-2301-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Accepted: 03/17/2014] [Indexed: 05/08/2023]
Abstract
KEY MESSAGE Given recent advances in pulse molecular biology, genomics-driven breeding has emerged as a promising approach to address the issues of limited genetic gain and low productivity in various pulse crops. The global population is continuously increasing and is expected to reach nine billion by 2050. This huge population pressure will lead to severe shortage of food, natural resources and arable land. Such an alarming situation is most likely to arise in developing countries due to increase in the proportion of people suffering from protein and micronutrient malnutrition. Pulses being a primary and affordable source of proteins and minerals play a key role in alleviating the protein calorie malnutrition, micronutrient deficiencies and other undernourishment-related issues. Additionally, pulses are a vital source of livelihood generation for millions of resource-poor farmers practising agriculture in the semi-arid and sub-tropical regions. Limited success achieved through conventional breeding so far in most of the pulse crops will not be enough to feed the ever increasing population. In this context, genomics-assisted breeding (GAB) holds promise in enhancing the genetic gains. Though pulses have long been considered as orphan crops, recent advances in the area of pulse genomics are noteworthy, e.g. discovery of genome-wide genetic markers, high-throughput genotyping and sequencing platforms, high-density genetic linkage/QTL maps and, more importantly, the availability of whole-genome sequence. With genome sequence in hand, there is a great scope to apply genome-wide methods for trait mapping using association studies and to choose desirable genotypes via genomic selection. It is anticipated that GAB will speed up the progress of genetic improvement of pulses, leading to the rapid development of cultivars with higher yield, enhanced stress tolerance and wider adaptability.
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Affiliation(s)
- Abhishek Bohra
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | - Manish K. Pandey
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
| | - Uday C. Jha
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | - Balwant Singh
- National Research Centre on Plant Biotechnology (NRCPB), New Delhi, 110012 India
| | - Indra P. Singh
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | - Dibendu Datta
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | | | - N. Nadarajan
- Indian Institute of Pulses Research (IIPR), Kanpur, 208024 India
| | - Rajeev K. Varshney
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, 502324 India
- The University of Western Australia (UWA), Crawley, 6009 Australia
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Cruz-Izquierdo S, Avila CM, Satovic Z, Palomino C, Gutierrez N, Ellwood SR, Phan HTT, Cubero JI, Torres AM. Comparative genomics to bridge Vicia faba with model and closely-related legume species: stability of QTLs for flowering and yield-related traits. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 125:1767-82. [PMID: 22864387 DOI: 10.1007/s00122-012-1952-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Accepted: 07/21/2012] [Indexed: 05/20/2023]
Abstract
This study presents the development of an enhanced map in faba bean. The map contains 258 loci, mostly gene-based markers, organized in 16 linkage groups that expand 1,875 cM, with an average inter-marker distance of 7.26 cM. The combination of EST-derived markers with a number of markers physically located or previously ascribed to chromosomes by trisomic segregation, allowed the allocation of eight linkage groups (229 markers), to specific chromosomes. Moreover, this approach provided anchor points to establish a global homology among the faba bean chromosomes and those of closely-related legumes species. The map was used to identify and validate, for the first time, QTLs controlling five flowering and reproductive traits: days to flowering, flowering length, pod length, number of seeds per pod and number of ovules per pod. Twelve QTLs stable in the 2 years of evaluation were identified in chromosomes II, V and VI. Comparative mapping suggested the conservation of one of the faba bean genomic regions controlling the character days to flowering in other five legume species (Medicago, Lotus, pea, lupine, chickpea). Additional syntenic co-localizations of QTLs controlling pod length and number of seeds per pod between faba bean and Lotus japonicus are likely. The new genetic map opens the way for further translational studies between faba bean and related legume species, and provides an efficient tool for breeding applications such as QTL analysis and marker-assisted selection.
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Affiliation(s)
- S Cruz-Izquierdo
- Área de Mejora y Biotecnología, IFAPA, Centro Alameda del Obispo, Apdo. 3092, 14080 Córdoba, Spain
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Impact of Molecular Technologies on Faba Bean (Vicia faba L.) Breeding Strategies. AGRONOMY-BASEL 2012. [DOI: 10.3390/agronomy2030132] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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