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Samuels ME, Lapointe C, Halwas S, Worley AC. Genomic Sequence of Canadian Chenopodium berlandieri: A North American Wild Relative of Quinoa. PLANTS (BASEL, SWITZERLAND) 2023; 12:467. [PMID: 36771551 PMCID: PMC9920564 DOI: 10.3390/plants12030467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 01/06/2023] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Chenopodium berlandieri (pitseed goosefoot) is a widespread native North American plant, which was cultivated and consumed by indigenous peoples prior to the arrival of European colonists. Chenopodium berlandieri is closely related to, and freely hybridizes with the domesticated South American food crop C. quinoa. As such it is a potential source of wild germplasm for breeding with C. quinoa, for improved quinoa production in North America. The C. berlandieri genome sequence could also be a useful source of information for improving quinoa adaptation. To this end, we first optimized barcode markers in two chloroplast genes, rbcL and matK. Together these markers can distinguish C. berlandieri from the morphologically similar Eurasian invasive C. album (lamb's quarters). Second, we performed whole genome sequencing and preliminary assembly of a C. berlandieri accession collected in Manitoba, Canada. Our assembly, while fragmented, is consistent with the expected allotetraploid structure containing diploid Chenopodium sub-genomes A and B. The genome of our accession is highly homozygous, with only one variant site per 3-4000 bases in non-repetitive sequences. This is consistent with predominant self-fertilization. As previously reported for the genome of a partly domesticated Mexican accession of C. berlandieri, our genome assembly is similar to that of C. quinoa. Somewhat unexpectedly, the genome of our accession had almost as many variant sites when compared to the Mexican C. berlandieri, as compared to C. quinoa. Despite the overall similarity of our genome sequence to that of C. quinoa, there are differences in genes known to be involved in the domestication or genetics of other food crops. In one example, our genome assembly appears to lack one functional copy of the SOS1 (salt overly sensitive 1) gene. SOS1 is involved in soil salinity tolerance, and by extension may be relevant to the adaptation of C. berlandieri to the wet climate of the Canadian region where it was collected. Our genome assembly will be a useful tool for the improved cultivation of quinoa in North America.
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Affiliation(s)
- Mark E. Samuels
- Centre de Recherche du CHU Ste-Justine, Montréal, QC H3T 1C5, Canada
- Département de Biochimie, Université de Montréal, Montréal, QC H3T 1C5, Canada
- Département de Médecine, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Cassandra Lapointe
- Centre de Recherche du CHU Ste-Justine, Montréal, QC H3T 1C5, Canada
- Département de Biochimie, Université de Montréal, Montréal, QC H3T 1C5, Canada
| | - Sara Halwas
- Department of Anthropology, University of Manitoba, Winnipeg, MB R3T 2M8, Canada
| | - Anne C. Worley
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2M8, Canada
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Subedi M, Ghimire B, Bagwell JW, Buck JW, Mergoum M. Wheat end-use quality: State of art, genetics, genomics-assisted improvement, future challenges, and opportunities. Front Genet 2023; 13:1032601. [PMID: 36685944 PMCID: PMC9849398 DOI: 10.3389/fgene.2022.1032601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
Wheat is the most important source of food, feed, and nutrition for humans and livestock around the world. The expanding population has increasing demands for various wheat products with different quality attributes requiring the development of wheat cultivars that fulfills specific demands of end-users including millers and bakers in the international market. Therefore, wheat breeding programs continually strive to meet these quality standards by screening their improved breeding lines every year. However, the direct measurement of various end-use quality traits such as milling and baking qualities requires a large quantity of grain, traits-specific expensive instruments, time, and an expert workforce which limits the screening process. With the advancement of sequencing technologies, the study of the entire plant genome is possible, and genetic mapping techniques such as quantitative trait locus mapping and genome-wide association studies have enabled researchers to identify loci/genes associated with various end-use quality traits in wheat. Modern breeding techniques such as marker-assisted selection and genomic selection allow the utilization of these genomic resources for the prediction of quality attributes with high accuracy and efficiency which speeds up crop improvement and cultivar development endeavors. In addition, the candidate gene approach through functional as well as comparative genomics has facilitated the translation of the genomic information from several crop species including wild relatives to wheat. This review discusses the various end-use quality traits of wheat, their genetic control mechanisms, the use of genetics and genomics approaches for their improvement, and future challenges and opportunities for wheat breeding.
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Affiliation(s)
- Madhav Subedi
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - Bikash Ghimire
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - John White Bagwell
- Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - James W. Buck
- Department of Plant Pathology, University of Georgia, Griffin Campus, Griffin, GA, United States
| | - Mohamed Mergoum
- Department of Crop and Soil Sciences, University of Georgia, Griffin Campus, Griffin, GA, United States
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Gutierrez-Larruscain D, Krüger M, Abeyawardana OAJ, Belz C, Dobrev PI, Vaňková R, Eliášová K, Vondráková Z, Juříček M, Štorchová H. The high concentrations of abscisic, jasmonic, and salicylic acids produced under long days do not accelerate flowering in Chenopodium ficifolium 459. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 320:111279. [PMID: 35643618 DOI: 10.1016/j.plantsci.2022.111279] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/28/2022] [Accepted: 03/30/2022] [Indexed: 06/15/2023]
Abstract
The survival and adaptation of angiosperms depends on the proper timing of flowering. The weedy species Chenopodium ficifolium serves as a useful diploid model for comparing the transition to flowering with the important tetraploid crop Chenopodium quinoa due to the close phylogenetic relationship. The detailed transcriptomic and hormonomic study of the floral induction was performed in the short-day accession C. ficifolium 459. The plants grew more rapidly under long days but flowered later than under short days. The high levels of abscisic, jasmonic, and salicylic acids at long days were accompanied by the elevated expression of the genes responding to oxidative stress. The increased concentrations of stress-related phytohormones neither inhibited the plant growth nor accelerated flowering in C. ficifolium 459 at long photoperiods. Enhanced content of cytokinins and the stimulation of cytokinin and gibberellic acid signaling pathways under short days may indicate the possible participation of these phytohormones in floral initiation. The accumulation of auxin metabolites suggests the presence of a dynamic regulatory network in C. ficifolium 459.
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Affiliation(s)
- David Gutierrez-Larruscain
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | - Manuela Krüger
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | - Oushadee A J Abeyawardana
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | - Claudia Belz
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | - Petre I Dobrev
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | - Radomíra Vaňková
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | - Kateřina Eliášová
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | - Zuzana Vondráková
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | - Miloslav Juříček
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic
| | - Helena Štorchová
- Institute of Experimental Botany, Czech Academy of Sciences, Rozvojová 263, 16502 Prague, Czech Republic.
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Nolen H, Smith C, Davis TM, Poleatewich A. Evaluation of Disease Severity and Molecular Relationships Between Peronospora variabilis Isolates on Chenopodium Species in New Hampshire. PLANT DISEASE 2022; 106:564-571. [PMID: 34633235 DOI: 10.1094/pdis-06-21-1150-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Quinoa is a potential new crop for New England; however, its susceptibility to downy mildew, caused by Peronospora variabilis, is a key obstacle for cultivation. The objectives of this study were to evaluate differential resistance within the Chenopodium genus, identify novel sources of resistance for use in future genetic studies or breeding programs, and investigate phylogenetic relationships of P. variabilis isolates from different Chenopodium hosts. The long-term goal of this research is to develop a resistant variety of quinoa to be grown in New England. Field trials conducted at the University of New Hampshire evaluated downy mildew disease severity on 10 Chenopodium accessions representing four species. Disease severity for each treatment was compared and significant differences in disease severity were observed between accessions. C. berlandieri var. macrocalycium ecotypes collected from Rye Beach, New Hampshire and Appledore Island, Maine exhibited the lowest disease severity over the growing season. P. variabilis was isolated from each accession, and COX2 sequences were compared. Phylogenetic analyses suggest no effect of host species on P. variabilis sequence similarity; however, isolates are shown to cluster by geographic location. This research provides the first step in identifying potential New England native sources of resistance to downy mildew within the genus Chenopodium and provides preliminary information needed to further investigate resistance at the genomic level in Chenopodium spp.
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Affiliation(s)
- Haley Nolen
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, NH 03824
| | - Cheryl Smith
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824
| | - Thomas M Davis
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824
| | - Anissa Poleatewich
- Department of Agriculture, Nutrition, and Food Systems, University of New Hampshire, Durham, NH 03824
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