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Balážová Ž, Čišecká L, Gálová Z, Hromadová Z, Chňapek M, Pipan B, Meglič V. Characterization of Genetic Variability of Common and Tartary Buckwheat Genotypes Using Microsatellite Markers. PLANTS (BASEL, SWITZERLAND) 2024; 13:2147. [PMID: 39124265 PMCID: PMC11313801 DOI: 10.3390/plants13152147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Revised: 07/24/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024]
Abstract
Buckwheat is a highly nutritional pseudocereal with antioxidant potential. The aim of this study was to analyze the genetic variability of 21 varieties of common buckwheat (Fagopyrum esculentum Moench.) and 14 varieties of Tartary buckwheat (Fagopyrum tataricum Gaertn.) using microsatellite markers. By analyzing 21 SSR markers, an average of 11.6 alleles per locus were amplified and an average PIC value of 0.711 was determined. We determined the heterozygous status of the individuals and variability in the set using the SSR analysis on the basis of expected heterozygosity (He, 0.477), observed heterozygosity (Ho, 0.675), Shannon's index (I, 0.820), and fixation indices (FST, FIS, FIT). Based on the SSR analyses, the lower level of expected heterozygosity in the analyzed set of Tartary buckwheat genotypes was observed compared to common buckwheat. With the help of a hierarchical cluster analysis using the UPGMA algorithm, Structure analysis, and PCoA analysis for the SSR markers, we divided the buckwheat varieties in the dendrogram into two main clusters according to the species. The AMOVA analysis showed that genetic variability between the individuals prevails in the analyzed set. The SSR technique proved to be a suitable tool for the determination of intra- and inter-varietal genetic variability and for analysis of diversity.
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Affiliation(s)
- Želmíra Balážová
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (L.Č.); (Z.G.); (Z.H.); (M.C.)
| | - Lucia Čišecká
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (L.Č.); (Z.G.); (Z.H.); (M.C.)
| | - Zdenka Gálová
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (L.Č.); (Z.G.); (Z.H.); (M.C.)
| | - Zuzana Hromadová
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (L.Č.); (Z.G.); (Z.H.); (M.C.)
| | - Milan Chňapek
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (L.Č.); (Z.G.); (Z.H.); (M.C.)
| | - Barbara Pipan
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetocva Ulica 17, SI-1000 Ljubljana, Slovenia; (B.P.); (V.M.)
| | - Vladimir Meglič
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetocva Ulica 17, SI-1000 Ljubljana, Slovenia; (B.P.); (V.M.)
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Pipan B, Sinkovič L, Neji M, Janovská D, Zhou M, Meglič V. Agro-Morphological and Molecular Characterization Reveal Deep Insights in Promising Genetic Diversity and Marker-Trait Associations in Fagopyrum esculentum and Fagopyrum tataricum. PLANTS (BASEL, SWITZERLAND) 2023; 12:3321. [PMID: 37765484 PMCID: PMC10534386 DOI: 10.3390/plants12183321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 09/08/2023] [Accepted: 09/18/2023] [Indexed: 09/29/2023]
Abstract
Characterisation of genetic diversity is critical to adequately exploit the potential of germplasm collections and identify important traits for breeding programs and sustainable crop improvement. Here, we characterised the phenotypic and genetic diversity of a global collection of the two cultivated buckwheat species Fagopyrum esculentum and Fagopyrum tataricum (190 and 51 accessions, respectively) using 37 agro-morphological traits and 24 SSR markers. A wide range of variation was observed in both species for most of the traits analysed. The two species differed significantly in most traits, with traits related to seeds and flowering contributing most to differentiation. The accessions of each species were divided into three major phenoclusters with no clear geographic clustering. At the molecular level, the polymorphic SSR markers were highly informative, with an average polymorphic information content (PIC) of over 0.65 in both species. Genetic diversity, as determined by Nei's expected heterozygosity (He), was high (He = 0.77 and He = 0.66, respectively) and differed significantly between species (p = 0.03) but was homogeneously distributed between regions, confirming the lack of genetic structure as determined by clustering approaches. The weak genetic structure revealed by the phenotypic and SSR data and the low fixation indices in both species suggested frequent seed exchange and extensive cultivation and selection. In addition, 93 and 140 significant (p < 0.05) marker-trait associations (MTAs) were identified in both species using a general linear model and a mixed linear model, most of which explained >20% of the phenotypic variation in associated traits. Core collections of 23 and 13 phenotypically and genetically diverse accessions, respectively, were developed for F. esculentum and F. tataricum. Overall, the data analysed provided deep insights into the agro-morphological and genetic diversity and genetic relationships among F. esculentum and F. tataricum accessions and pointed to future directions for genomics-based breeding programs and germplasm management.
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Affiliation(s)
- Barbara Pipan
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetocva ulica 17, SI-1000 Ljubljana, Slovenia; (L.S.); (M.N.); (V.M.)
| | - Lovro Sinkovič
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetocva ulica 17, SI-1000 Ljubljana, Slovenia; (L.S.); (M.N.); (V.M.)
| | - Mohamed Neji
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetocva ulica 17, SI-1000 Ljubljana, Slovenia; (L.S.); (M.N.); (V.M.)
| | - Dagmar Janovská
- Gene Bank, Crop Research Institute, Drnovská 507, 161 06 Prague, Czech Republic;
| | - Meiliang Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Room 420, National Crop Genebank Building, Zhongguancun South Street No. 12, Haidian District, Beijing 100081, China;
| | - Vladimir Meglič
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetocva ulica 17, SI-1000 Ljubljana, Slovenia; (L.S.); (M.N.); (V.M.)
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Zargar SM, Manzoor M, Bhat B, Wani AB, Sofi PA, Sudan J, Ebinezer LB, Dall'Acqua S, Peron G, Masi A. Metabolic-GWAS provides insights into genetic architecture of seed metabolome in buckwheat. BMC PLANT BIOLOGY 2023; 23:373. [PMID: 37501129 PMCID: PMC10375682 DOI: 10.1186/s12870-023-04381-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 07/13/2023] [Indexed: 07/29/2023]
Abstract
BACKGROUND Buckwheat (Fagopyrum spp.), belonging to the Polygonaceae family, is an ancient pseudo-cereal with high nutritional and nutraceutical properties. Buckwheat proteins are gluten-free and show balanced amino acid and micronutrient profiles, with higher content of health-promoting bioactive flavonoids that make it a golden crop of the future. Plant metabolome is increasingly gaining importance as a crucial component to understand the connection between plant physiology and environment and as a potential link between the genome and phenome. However, the genetic architecture governing the metabolome and thus, the phenome is not well understood. Here, we aim to obtain a deeper insight into the genetic architecture of seed metabolome in buckwheat by integrating high throughput metabolomics and genotyping-by-sequencing applying an array of bioinformatics tools for data analysis. RESULTS High throughput metabolomic analysis identified 24 metabolites in seed endosperm of 130 diverse buckwheat genotypes. The genotyping-by-sequencing (GBS) of these genotypes revealed 3,728,028 SNPs. The Genome Association and Prediction Integrated Tool (GAPIT) assisted in the identification of 27 SNPs/QTLs linked to 18 metabolites. Candidate genes were identified near 100 Kb of QTLs, providing insights into several metabolic and biosynthetic pathways. CONCLUSIONS We established the metabolome inventory of 130 germplasm lines of buckwheat, identified QTLs through marker trait association and positions of potential candidate genes. This will pave the way for future dissection of complex economic traits in buckwheat.
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Affiliation(s)
- Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, India.
| | - Madhiya Manzoor
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, India
| | - Basharat Bhat
- Division of Animal Biotechnology, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Amir Bashir Wani
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, India
| | - Parvaze Ahmad Sofi
- Division of Genetics and Plant Breeding, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
| | - Jebi Sudan
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-E-Kashmir University of Agricultural Sciences and Technology of Kashmir, Shalimar, Srinagar, Jammu and Kashmir, India
| | - Leonard Barnabas Ebinezer
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy
| | - Stefano Dall'Acqua
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, Padua, Italy
| | - Gregorio Peron
- Department of Molecular and Translational Medicine (DMMT), University of Brescia, Brescia, Italy
| | - Antonio Masi
- Department of Agronomy, Food, Natural Resources, Animals, and Environment, University of Padova, Padua, Italy.
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Tak AM, Hami A, Bhat B, Bhat SA, Masoodi KZ, Bhat MA, Shah MD, Khan MK, Zargar SM. Unravelling rutin content of tartary buckwheat of north western Himalayas and insights into nucleotide polymorphisms in PAL gene to infer the associations with rutin biosynthesis. 3 Biotech 2022; 12:156. [PMID: 35791410 PMCID: PMC9250572 DOI: 10.1007/s13205-022-03218-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 06/14/2022] [Indexed: 11/25/2022] Open
Abstract
Buckwheat (Fagopyrum spp.) has immense nutritional and nutraceutical potential. All the plant parts of buckwheat possess various metabolites, such as rutin, quercetin, vitexin etc. The high content of rutin in this pseudo cereal crop strongly adapts it to grow under adverse environments. In the present study 50 germplasm lines of Fagopyrum tataricum were used for estimation of seed endosperm rutin content through HPLC. Furthermore, molecular analysis of PAL gene (Phenylalanine Ammonia Lyase), an upstream gene in rutin biosynthesis pathway was targeted for detection of SNPs to understand the variations in the concentrations of seed endosperm rutin content, among tartary buckwheat genotypes with highest and lowest seed endosperm rutin content. Three primer pairs were employed for amplification of PAL gene for F. tartaricum (covering whole gene) followed by sequencing. Rutin concentration in seed endosperm of F. tartaricum ranged from 194.86 to 1403.22 ppm with an average of 617.06 ppm. Highest rutin concentration was found in genotype BWZ90 and lowest in BWZ16. Significant variations were observed in the seed endosperm rutin content among the genotypes of tartary buckwheat. Furthermore, alignment of PAL gene sequences of genotypes with high seed endosperm rutin content and low seed endosperm rutin content revealed variations at 21 polymorphic sites. The amino acid sequences obtained from the nucleotide sequences were also aligned and the variations were detected at 19 positions. The putative protein structure showed conformational changes among predicted proteins from two contrasting genotypes for endosperm rutin content. We here established an inventory of seed endosperm rutin content of tartary buckwheat. This study also provided insights about role of these SNPs in rutin biosynthesis. Furthermore, this information can be used for breeding buckwheat for high metabolite contents. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03218-y.
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Mudau FN, Chimonyo VGP, Modi AT, Mabhaudhi T. Neglected and Underutilised Crops: A Systematic Review of Their Potential as Food and Herbal Medicinal Crops in South Africa. Front Pharmacol 2022; 12:809866. [PMID: 35126143 PMCID: PMC8811033 DOI: 10.3389/fphar.2021.809866] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 12/23/2021] [Indexed: 12/16/2022] Open
Abstract
The African continent harbours many native species with nutraceutical and pharmaceutical potential. This study reviewed underutilised crops in South Africa to determine their potential as food and herbal medicinal crops. Over 5,000 species have been identified and earmarked for their medical attributes in formal and informal setups. Researchers, plant breeders and policymakers have mostly ignored the development potential of these crops. Consequently, their value chains are poorly developed. In South Africa, there is a wide range of neglected and underutilised crops, which were historically popular and used by communities; however, over the years, they have lost their status within farming systems and been relegated to the status of neglected and underutilised. Recently, driven by the need to transition to more sustainable and resilient food systems, there has been renewed interest in their potential as food and herbal medicinal crops to establish new value chains that include vulnerable groups. They are now gaining global attention, and their conservation and sustainable utilisation are now being prioritized. The review confirmed that several of these crops possess nutraceutical and pharmaceutical properties, highlighting their potential for development as food and herbal medicines. However, current production levels are too low to meet the requirements for industrial development; research and development should focus on all aspects of their value chain, from crop improvement to utilisation. A transdisciplinary approach involving a wide range of actors is needed to develop the identified neglected and underutilised crops' potential as food and herbal medicinal crops and support the development of new and inclusive value chains.
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Affiliation(s)
- Fhatuwani Nixwell Mudau
- School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Vimbayi Grace Petrova Chimonyo
- Centre for Transformative Agricultural and Food Systems, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- International Maize and Wheat Improvement Center (CIMMYT), Harare, Zimbabwe
| | - Albert Thembinkosi Modi
- Centre for Transformative Agricultural and Food Systems, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Tafadzwanashe Mabhaudhi
- Centre for Transformative Agricultural and Food Systems, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
- International Water Management Institute (IWMI-GH), West Africa Office, Kumasi, Ghana
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Sabreena, Nazir M, Mahajan R, Hashim MJ, Iqbal J, Alyemeni MN, Ganai BA, Zargar SM. Deciphering allelic variability and population structure in buckwheat: An analogy between the efficiency of ISSR and SSR markers. Saudi J Biol Sci 2021; 28:6050-6056. [PMID: 34764738 PMCID: PMC8568815 DOI: 10.1016/j.sjbs.2021.07.061] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/26/2021] [Accepted: 07/21/2021] [Indexed: 12/03/2022] Open
Abstract
Food and nutritional security continue to be the issues of concern in developing countries like ours. Exploring the reservoir of high potential unexplored genetic resources could address the world's food and nutritional insecurity. The availability of diverse data and the population structure of any crop germplasm is a valuable genetic resource for discovering genes that can help achieve food and nutritional stability. We used seven ISSR and seven SSR markers to investigate diversity among 63 buckwheat genotypes, including landraces from India's northwestern Himalayas. Various parameters such as percent polymorphism, PIC, resolving power, and marker index was used to evaluate the inequitable efficacy of these markers. We foundthat both marker systems are effective in detecting polymorphism in buckwheat germplasm. Seven ISSRs produced 55 polymorphic bands, while seven SSRs produced 32bands. When compared to ISSRs, SSRs had a greater average PIC value (0.43) than that of (0.36). ISSRs, on the other hand, had a resolving power of (4.38) compared to (1.42) for SSRs. The hierarchical cluster analysis dendrogram divided genotypes into three major clusters. We found that both marker systems were equally accurate in grouping buckwheat genotypes according to their geographical origins. Using 7 ISSR and 7 SSR markers, the model-based STRUCTURE analysis established a population with two sub-populations that correspond to species-based groupings. Within the population, there was a high level of genetic diversity. These results have consequences for both buckwheat breeding and conservation efforts.
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Affiliation(s)
- Sabreena
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, India
- Department of Environmental Sciences, University of Kashmir, Hazratbal, Srinagar, Jammu & Kashmir, India
| | - Muslima Nazir
- CORD, University of Kashmir, Hazratbal, Srinagar, Jammu & Kashmir, India
| | - Reetika Mahajan
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, India
| | - Maha J. Hashim
- School of Life Sciences, The University of Nottingham, Nottingham NG7 2TQ, United Kingdom
| | - Javed Iqbal
- Department of Botany, Bacha Khan University, Charsadda, Khyber Pakhtunkhwa, Pakistan
| | | | - Bashir Ahmad Ganai
- CORD, University of Kashmir, Hazratbal, Srinagar, Jammu & Kashmir, India
| | - Sajad Majeed Zargar
- Proteomics Laboratory, Division of Plant Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Kashmir, Shalimar, Srinagar, Jammu & Kashmir, India
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