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Peters Haugrud AR, Achilli AL, Martínez-Peña R, Klymiuk V. Future of durum wheat research and breeding: Insights from early career researchers. THE PLANT GENOME 2024:e20453. [PMID: 38760906 DOI: 10.1002/tpg2.20453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/26/2024] [Accepted: 04/02/2024] [Indexed: 05/20/2024]
Abstract
Durum wheat (Triticum turgidum ssp. durum) is globally cultivated for pasta, couscous, and bulgur production. With the changing climate and growing world population, the need to significantly increase durum production to meet the anticipated demand is paramount. This review summarizes recent advancements in durum research, encompassing the exploitation of existing and novel genetic diversity, exploration of potential new diversity sources, breeding for climate-resilient varieties, enhancements in production and management practices, and the utilization of modern technologies in breeding and cultivar development. In comparison to bread wheat (T. aestivum), the durum wheat community and production area are considerably smaller, often comprising many small-family farmers, notably in African and Asian countries. Public breeding programs such as the International Maize and Wheat Improvement Center (CIMMYT) and the International Center for Agricultural Research in the Dry Areas (ICARDA) play a pivotal role in providing new and adapted cultivars for these small-scale growers. We spotlight the contributions of these and others in this review. Additionally, we offer our recommendations on key areas for the durum research community to explore in addressing the challenges posed by climate change while striving to enhance durum production and sustainability. As part of the Wheat Initiative, the Expert Working Group on Durum Wheat Genomics and Breeding recognizes the significance of collaborative efforts in advancing toward a shared objective. We hope the insights presented in this review stimulate future research and deliberations on the trajectory for durum wheat genomics and breeding.
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Affiliation(s)
- Amanda R Peters Haugrud
- Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Agricultural Research Service, United States Department of Agriculture, Fargo, North Dakota, USA
| | - Ana Laura Achilli
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Raquel Martínez-Peña
- Regional Institute of Agri-Food and Forestry Research and Development of Castilla-La Mancha (IRIAF), Agroenvironmental Research Center El Chaparrillo, Ciudad Real, Spain
| | - Valentyna Klymiuk
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
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Wang F, Sun T, Yu S, Liu C, Cheng Z, Xia J, Han L. Ethnobotanical studies on rice landraces under on-farm conservation in Xishuangbanna of Yunnan Province, China. JOURNAL OF ETHNOBIOLOGY AND ETHNOMEDICINE 2024; 20:45. [PMID: 38685098 DOI: 10.1186/s13002-024-00683-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Accepted: 04/01/2024] [Indexed: 05/02/2024]
Abstract
BACKGROUND A complex interaction and mutual influence exists among landscapes, cultures, and landraces, with rice culture being a typical embodiment of this relationship. The conservation of landraces operates alongside preserving traditional practices. The Xishuangbanna region stands out as a hub for the genetic diversity of landraces, boasting rich genetic resources. Despite the diverse rice resources in this region, a comprehensive and systematic study has not been undertaken. METHODS From October to November 2023, we collected rice landraces under the on-farm conservation in 18 townships including Menghai, Mengla and Jinghong in Xishuangbanna. Employing semi-structured interviews and various methods, we investigated factors influencing the preservation and loss of rice landraces in the region. Statistical analysis was applied to the agronomic traits of collected local rice, encompassing indica or japonica, glutinous or non-glutinous, grain shape, and hull color as second category traits. The second category included quantitative traits like thousand grain weight and grain length. Rice diversity among different regions, traits, and ethnic groups was assessed using the Shannon-Wiener index. Additionally, clustering analysis via the UPGMA method depicted the distribution characteristics of the resources. RESULTS A total of 70 rice landraces were collected in the Xishuangbanna region, each exhibiting distinct characteristics. Differences were observed across regions, trait, naming, and ethnic groups. Diversity analysis revealed that Mengla had the highest diversity, followed by Menghai, while Jinghong exhibited the lowest diversity. The second category of traits displayed broader diversity than the first, with the Dai people's glutinous rice showcasing greater diversity than other ethnic groups. Cluster analysis categorized the 70 samples into seven groups at a genetic distance of 1.15. Ethnobotanical interviews emphasized the rapid loss of rice landraces resources in Xishuangbanna, with indigenous ethnic cultures playing a vital role in the conservation of rice landraces. Dai traditions, in particular, played a crucial role in protecting glutinous rice resources, showcasing a mutual dependence between Dai culture and glutinous rice. CONCLUSIONS The rich natural environment and diverse ethnic cultures in Xishuangbanna have given rise to various rice landraces. The Dai, primary cultivators of glutinous rice with higher diversity, intertwine their traditional ethnic culture with the conservation of glutinous rice resources. At the same time, the preserving glutinous rice resources promotes the inheritance of Dai ethnic culture. However, rice landraces are facing the risk of loss. Hence, collecting and documenting rice landraces is crucial. Encourage local communities to sustain and expand their cultivation, promoting on-farm conservation. These measures contribute valuable germplasm and genes for rice breeding and serve as a means of cultural preservation.
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Affiliation(s)
- Fei Wang
- Key Laboratory of Ecological Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Tao Sun
- Institute of Agricultural Sciences, Xishuangbanna Prefecture, Jinghong, 666100, China
| | - Shuai Yu
- Institute of Agricultural Sciences, Xishuangbanna Prefecture, Jinghong, 666100, China
| | - Chunhui Liu
- College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China
| | - Zhuo Cheng
- Key Laboratory of Ecological Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China
| | - Jianxin Xia
- Key Laboratory of Ecological Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, 100081, China.
- College of Life and Environmental Sciences, Minzu University of China, Beijing, 100081, China.
| | - Longzhi Han
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
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Haber Z, Sharma D, Selvaraj KSV, Sade N. Is CRISPR/Cas9-based multi-trait enhancement of wheat forthcoming? PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 341:112021. [PMID: 38311249 DOI: 10.1016/j.plantsci.2024.112021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 02/09/2024]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) technologies have been implemented in recent years in the genome editing of eukaryotes, including plants. The original system of knocking out a single gene by causing a double-strand break (DSB), followed by non-homologous end joining (NHEJ) or Homology-directed repair (HDR) has undergone many adaptations. These adaptations include employing CRISPR/Cas9 to upregulate gene expression or to cause specific small changes to the DNA sequence of the gene-of-interest. In plants, multiplexing, i.e., inducing multiple changes by CRISPR/Cas9, is extremely relevant due to the redundancy of many plant genes, and the time- and labor-consuming generation of stable transgenic plant lines via crossing. Here we discuss relevant examples of various traits, such as yield, biofortification, gluten content, abiotic stress tolerance, and biotic stress resistance, which have been successfully manipulated using CRISPR/Cas9 in plants. While existing studies have primarily focused on proving the impact of CRISPR/Cas9 on a single trait, there is a growing interest among researchers in creating a multi-stress tolerant wheat cultivar 'super wheat', to commercially and sustainably enhance wheat yields under climate change. Due to the complexity of the technical difficulties in generating multi-target CRISPR/Cas9 lines and of the interactions between stress responses, we propose enhancing already commercial local landraces with higher yield traits along with stress tolerances specific to the respective localities, instead of generating a general 'super wheat'. We hope this will serve as the sustainable solution to commercially enhancing crop yields under both stable and challenging environmental conditions.
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Affiliation(s)
- Zechariah Haber
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - Davinder Sharma
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel
| | - K S Vijai Selvaraj
- Vegetable Research Station, Tamil Nadu Agricultural University, Palur 607102, Tamil Nadu, India
| | - Nir Sade
- School of Plant Sciences and Food Security, Tel Aviv University, Tel Aviv 69978, Israel.
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Shorinola O, Marks R, Emmrich P, Jones C, Odeny D, Chapman MA. Integrative and inclusive genomics to promote the use of underutilised crops. Nat Commun 2024; 15:320. [PMID: 38191605 PMCID: PMC10774273 DOI: 10.1038/s41467-023-44535-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 12/14/2023] [Indexed: 01/10/2024] Open
Abstract
Underutilised crops or orphan crops are important for diversifying our food systems towards food and nutrition security. Here, the authors discuss how the development of underutilised crop genomic resource should align with their breeding and capacity building strategies, and leverage advances made in major crops.
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Affiliation(s)
- Oluwaseyi Shorinola
- International Livestock Research Institute, Naivasha Road, Nairobi, Kenya.
- School of Bioscience, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK.
| | - Rose Marks
- Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
- Plant Resilience Institute, Michigan State University, East Lansing, MI, 48824, USA
| | - Peter Emmrich
- Norwich Institute for Sustainable Development, School of Global Development, University of East Anglia, England, NR4 7TJ, UK
| | - Chris Jones
- International Livestock Research Institute, Naivasha Road, Nairobi, Kenya
| | - Damaris Odeny
- Center of Excellence in Genomics and Systems Biology, ICRISAT, Patancheru, 502324, Telangana, India
| | - Mark A Chapman
- Biological Sciences, University of Southampton, Life Sciences Building 85, Highfield Campus, Southampton, SO17 1BJ, UK
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Dagnaw T, Mulugeta B, Haileselassie T, Geleta M, Ortiz R, Tesfaye K. Genetic Diversity of Durum Wheat ( Triticum turgidum L. ssp. durum, Desf) Germplasm as Revealed by Morphological and SSR Markers. Genes (Basel) 2023; 14:1155. [PMID: 37372335 DOI: 10.3390/genes14061155] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 05/21/2023] [Accepted: 05/23/2023] [Indexed: 06/29/2023] Open
Abstract
Ethiopia is considered a center of origin and diversity for durum wheat and is endowed with many diverse landraces. This research aimed to estimate the extent and pattern of genetic diversity in Ethiopian durum wheat germplasm. Thus, 104 durum wheat genotypes representing thirteen populations, three regions, and four altitudinal classes were investigated for their genetic diversity, using 10 grain quality- and grain yield-related phenotypic traits and 14 simple sequence repeat (SSR) makers. The analysis of the phenotypic traits revealed a high mean Shannon diversity index (H' = 0.78) among the genotypes and indicated a high level of phenotypic variation. The principal component analysis (PCA) classified the genotypes into three groups. The SSR markers showed a high mean value of polymorphic information content (PIC = 0.50) and gene diversity (h = 0.56), and a moderate number of alleles per locus (Na = 4). Analysis of molecular variance (AMOVA) revealed a high level of variation within populations, regions, and altitudinal classes, accounting for 88%, 97%, and 97% of the total variation, respectively. Pairwise genetic differentiation and Nei's genetic distance analyses identified that the cultivars are distinct from the landrace populations. The distance-based (Discriminant Analysis of Principal Component (DAPC) and Minimum Spanning Network (MSN)) and model-based population stratification (STRUCTURE) methods of clustering grouped the genotypes into two clusters. Both the phenotypic data-based PCA and the molecular data-based DAPC and MSN analyses defined distinct groupings of cultivars and landraces. The phenotypic and molecular diversity analyses highlighted the high genetic variation in the Ethiopian durum wheat gene pool. The investigated SSRs showed significant associations with one or more target phenotypic traits. The markers identify landraces with high grain yield and quality traits. This study highlights the usefulness of Ethiopian landraces for cultivar development, contributing to food security in the region and beyond.
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Affiliation(s)
- Temesgen Dagnaw
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia
| | - Behailu Mulugeta
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, SE-23422 Lomma, Sweden
| | | | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, SE-23422 Lomma, Sweden
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, SE-23422 Lomma, Sweden
| | - Kassahun Tesfaye
- Department of Microbial, Cellular and Molecular Biology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia
- Ethiopian Bio and Emerging Technology Institute, Addis Ababa P.O. Box 5954, Ethiopia
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de Sousa K, Brown D, Steinke J, van Etten J. gosset: An R package for analysis and synthesis of ranking data in agricultural experimentation. SOFTWAREX 2023; 22:None. [PMID: 37250590 PMCID: PMC10212778 DOI: 10.1016/j.softx.2023.101402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2022] [Revised: 04/10/2023] [Accepted: 05/03/2023] [Indexed: 05/31/2023]
Abstract
To derive insights from data, researchers working on agricultural experiments need appropriate data management and analysis tools. To ensure that workflows are reproducible and can be applied on a routine basis, programmatic tools are needed. Such tools are increasingly necessary for rank-based data, a type of data that is generated in on-farm experimentation and data synthesis exercises, among others. To address this need, we developed the R package gosset, which provides functionality for rank-based data and models. The gosset package facilitates data preparation, modeling and results presentation stages. It introduces novel functions not available in existing R packages for analyzing ranking data. This paper demonstrates the package functionality using the case study of a decentralized on-farm trial of common bean (Phaseolus vulgaris L.) varieties in Nicaragua.
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Affiliation(s)
- Kauê de Sousa
- Department of Agricultural Sciences, Inland Norway University of Applied Sciences, 2318 Hamar, Norway
- Digital Inclusion, Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 5, France
| | - David Brown
- Laboratory of Geo-Information Science and Remote Sensing, Wageningen University & Research, Droevendaalsesteeg 3, 6708 PB, Wageningen, The Netherlands
- Digital Inclusion, Bioversity International, 30501, Turrialba, Costa Rica
- College of Agriculture and Life Sciences, Cornell University, 14853 Ithaca, NY, United States of America
| | - Jonathan Steinke
- Digital Inclusion, Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 5, France
- Thaer Institute of Agricultural and Horticultural Sciences, Humboldt University Berlin, Unter den Linden 6, 10099 Berlin, Germany
| | - Jacob van Etten
- Digital Inclusion, Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier Cedex 5, France
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