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Zaïm M, Sanchez-Garcia M, Belkadi B, Filali-Maltouf A, Al Abdallat A, Kehel Z, Bassi FM. Genomic regions of durum wheat involved in water productivity. J Exp Bot 2024; 75:316-333. [PMID: 37702385 PMCID: PMC10735558 DOI: 10.1093/jxb/erad357] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 09/11/2023] [Indexed: 09/14/2023]
Abstract
Durum wheat is a staple food in the Mediterranean Basin, mostly cultivated under rainfed conditions. As such, the crop is often exposed to moisture stress. Therefore, the identification of genetic factors controlling the capacity of genotypes to convert moisture into grain yield (i.e., water productivity) is quintessential to stabilize production despite climatic variations. A global panel of 384 accessions was tested across 18 Mediterranean environments (in Morocco, Lebanon, and Jordan) representing a vast range of moisture levels. The accessions were assigned to water responsiveness classes, with genotypes 'Responsive to Low Moisture' reaching an average +1.5 kg ha-1 mm-1 yield advantage. Genome wide association studies revealed that six loci explained most of this variation. A second validation panel tested under moisture stress confirmed that carrying the positive allele at three loci on chromosomes 1B, 2A, and 7B generated an average water productivity gain of +2.2 kg ha-1 mm-1. These three loci were tagged by kompetitive allele specific PCR (KASP) markers, and these were used to screen a third independent validation panel composed of elites tested across moisture stressed sites. The three KASP combined predicted up to 10% of the variation for grain yield at 60% accuracy. These loci are now ready for molecular pyramiding and transfer across cultivars to improve the moisture conversion of durum wheat.
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Affiliation(s)
- Meryem Zaïm
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, University Mohammed V in Rabat, Morocco
- ICARDA, Biodiversity and Integrated Gene Management, P.O. Box 6299, Rabat Institutes, Rabat, Morocco
| | - Miguel Sanchez-Garcia
- ICARDA, Biodiversity and Integrated Gene Management, P.O. Box 6299, Rabat Institutes, Rabat, Morocco
| | - Bouchra Belkadi
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, University Mohammed V in Rabat, Morocco
| | - Abdelkarim Filali-Maltouf
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, University Mohammed V in Rabat, Morocco
| | - Ayed Al Abdallat
- Faculty of Agriculture, The University of Jordan, Amman 11942, Jordan
| | - Zakaria Kehel
- ICARDA, Biodiversity and Integrated Gene Management, P.O. Box 6299, Rabat Institutes, Rabat, Morocco
| | - Filippo M Bassi
- ICARDA, Biodiversity and Integrated Gene Management, P.O. Box 6299, Rabat Institutes, Rabat, Morocco
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Tadesse W, Gataa ZE, Rachdad FE, Baouchi AE, Kehel Z, Alemu A. Single- and multi-trait genomic prediction and genome-wide association analysis of grain yield and micronutrient-related traits in ICARDA wheat under drought environment. Mol Genet Genomics 2023; 298:1515-1526. [PMID: 37851098 PMCID: PMC10657311 DOI: 10.1007/s00438-023-02074-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Accepted: 09/28/2023] [Indexed: 10/19/2023]
Abstract
Globally, over 2 billion people suffer from malnutrition due to inadequate intake of micronutrients. Genomic-assisted breeding is identified as a valuable method to facilitate developing new improved plant varieties targeting grain yield and micronutrient-related traits. In this study, a genome-wide association study (GWAS) and single- and multi-trait-based genomic prediction (GP) analysis was conducted using a set of 252 elite wheat genotypes from the International Center for Agricultural Research in Dry Areas (ICARDA). The objective was to identify linked SNP markers, putative candidate genes and to evaluate the genomic estimated breeding values (GEBVs) of grain yield and micronutrient-related traits.. For this purpose, a field trial was conducted at a drought-prone station, Merchouch, Morocco for 2 consecutive years (2018 and 2019) followed by GWAS and genomic prediction analysis with 10,173 quality SNP markers. The studied genotypes exhibited a significant genotypic variation in grain yield and micronutrient-related traits. The GWAS analysis identified highly significantly associated markers and linked putative genes on chromosomes 1B and 2B for zinc (Zn) and iron (Fe) contents, respectively. The genomic predictive ability of selenium (Se) and Fe traits with the multi-trait-based GP GBLUP model was 0.161 and 0.259 improving by 6.62 and 4.44%, respectively, compared to the corresponding single-trait-based models. The identified significantly linked SNP markers, associated putative genes, and developed GP models could potentially facilitate breeding programs targeting to improve the overall genetic gain of wheat breeding for grain yield and biofortification of micronutrients via marker-assisted (MAS) and genomic selection (GS) methods.
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Affiliation(s)
- Wuletaw Tadesse
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Zakaria El Gataa
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Fatima Ezzahra Rachdad
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Adil El Baouchi
- AgroBioSciences, Mohammed VI Polytechnic University (UM6P), Ben Guerir, Morocco
| | - Zakaria Kehel
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Admas Alemu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden.
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Elouadi F, Amri A, El-Baouchi A, Kehel Z, Jilal A, Ibriz M. Genotypic and environmental effects on quality and nutritional attributes of Moroccan barley cultivars and elite breeding lines. Front Nutr 2023; 10:1204572. [PMID: 37899827 PMCID: PMC10602734 DOI: 10.3389/fnut.2023.1204572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 09/12/2023] [Indexed: 10/31/2023] Open
Abstract
Although barley is mainly used for livestock feed and beverages, its use as human feed can enrich human diets with some health benefits. The development of new hulless varieties rich in β-glucans and micronutrients can enhance the use of barley as food, but little is known about the effects of the environment on these nutritional traits. In this study, we evaluated five Moroccan varieties and two elite breeding lines of barley at four locations in Morocco during the 2016-2017 and 2017-2018 cropping seasons. The results showed highly significant differences between genotypes for β-glucan, protein, iron, and selenium contents, as well as 1000 kernel weight, but not zinc content; significant to highly significant differences between environments for all traits except β-glucan content; and significant to highly significant interactions for all traits. The highest level of β-glucan content has reached 11.57% observed at the Sidi El Aydi site during the growing season 2017-2018 for the hulless variety Chifaa. This variety has shown the highest content of β-glucan (6.2-11.57%) over all environments except at Tassaout during the 2016-2017 seasons. The breeding line M9V5 has achieved significantly higher protein content at all the locations during the two growing seasons, ranging from 12.38 to 20.14%. Most hulless lines had significantly higher β-glucan and protein contents, but lower 1000 kernel weight. For micronutrients, the content ranges were 28.94 to 38.23 ppm for Fe, 28.78 to 36.49 ppm for Zn, and 0.14 to 0.18 ppm for Se, with the highest content for Fe and Zn shown by the breeding line M9V5 and Chifaa showing average contents of 33.39 ppm, 35.34 ppm, and 0.18 ppm for Fe, Zn, and Se, respectively. The GGE biplot confirmed the high and relatively stable content of β-glucan and acceptable micronutrient contents of the Chifaa variety and identified Marchouch as the most discriminant site to breed for biofortified barley varieties.
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Affiliation(s)
- Fadwa Elouadi
- Plant Animal Productions and Agro-Industry Laboratory, Ibn Tofail University, Kenitra, Morocco
| | - Ahmed Amri
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Adil El-Baouchi
- AgroBioSciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Abderrazek Jilal
- National Institute for Agricultural Research, Regional Center of Rabat, Rabat Institutes, Rabat, Morocco
| | - Mohammed Ibriz
- Plant Animal Productions and Agro-Industry Laboratory, Ibn Tofail University, Kenitra, Morocco
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Alsamman AM, El Allali A, Mokhtar MM, Al-Sham’aa K, Nassar AE, Mousa KH, Kehel Z. AlignStatPlot: An R package and online tool for robust sequence alignment statistics and innovative visualization of big data. PLoS One 2023; 18:e0291204. [PMID: 37729135 PMCID: PMC10511070 DOI: 10.1371/journal.pone.0291204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Accepted: 08/23/2023] [Indexed: 09/22/2023] Open
Abstract
Multiple sequence alignment (MSA) is essential for understanding genetic variations controlling phenotypic traits in all living organisms. The post-analysis of MSA results is a difficult step for researchers who do not have programming skills. Especially those working with large scale data and looking for potential variations or variable sample groups. Generating bi-allelic data and the comparison of wild and alternative gene forms are important steps in population genetics. Customising MSA visualisation for a single page view is difficult, making viewing potential indels and variations challenging. There are currently no bioinformatics tools that permit post-MSA analysis, in which data on gene and single nucleotide scales could be combined with gene annotations and used for cluster analysis. We introduce "AlignStatPlot," a new R package and online tool that is well-documented and easy-to use for MSA and post-MSA analysis. This tool performs both traditional and cutting-edge analyses on sequencing data and generates new visualisation methods for MSA results. When compared to currently available tools, AlignStatPlot provides a robust ability to handle and visualise diversity data, while the online version will save time and encourage researchers to focus on explaining their findings. It is a simple tool that can be used in conjunction with population genetics software.
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Affiliation(s)
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Morad M. Mokhtar
- Agricultural Genetic Engineering Research Institute, Giza, Egypt
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Khaled Al-Sham’aa
- International Center for Agriculture Research in the Dry Areas, Giza, Egypt
| | - Ahmed E. Nassar
- Agricultural Genetic Engineering Research Institute, Giza, Egypt
- International Center for Agriculture Research in the Dry Areas, Giza, Egypt
| | - Khaled H. Mousa
- Agricultural Genetic Engineering Research Institute, Giza, Egypt
- International Center for Agriculture Research in the Dry Areas, Giza, Egypt
| | - Zakaria Kehel
- International Center for Agriculture Research in the Dry Areas, Giza, Egypt
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El Hanafi S, Jiang Y, Kehel Z, Schulthess AW, Zhao Y, Mascher M, Haupt M, Himmelbach A, Stein N, Amri A, Reif JC. Genomic predictions to leverage phenotypic data across genebanks. Front Plant Sci 2023; 14:1227656. [PMID: 37701801 PMCID: PMC10493331 DOI: 10.3389/fpls.2023.1227656] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/07/2023] [Indexed: 09/14/2023]
Abstract
Genome-wide prediction is a powerful tool in breeding. Initial results suggest that genome-wide approaches are also promising for enhancing the use of the genebank material: predicting the performance of plant genetic resources can unlock their hidden potential and fill the information gap in genebanks across the world and, hence, underpin prebreeding programs. As a proof of concept, we evaluated the power of across-genebank prediction for extensive germplasm collections relying on historical data on flowering/heading date, plant height, and thousand kernel weight of 9,344 barley (Hordeum vulgare L.) plant genetic resources from the German Federal Ex situ Genebank for Agricultural and Horticultural Crops (IPK) and of 1,089 accessions from the International Center for Agriculture Research in the Dry Areas (ICARDA) genebank. Based on prediction abilities for each trait, three scenarios for predictive characterization were compared: 1) a benchmark scenario, where test and training sets only contain ICARDA accessions, 2) across-genebank predictions using IPK as training and ICARDA as test set, and 3) integrated genebank predictions that include IPK with 30% of ICARDA accessions as a training set to predict the rest of ICARDA accessions. Within the population of ICARDA accessions, prediction abilities were low to moderate, which was presumably caused by a limited number of accessions used to train the model. Interestingly, ICARDA prediction abilities were boosted up to ninefold by using training sets composed of IPK plus 30% of ICARDA accessions. Pervasive genotype × environment interactions (GEIs) can become a potential obstacle to train robust genome-wide prediction models across genebanks. This suggests that the potential adverse effect of GEI on prediction ability was counterbalanced by the augmented training set with certain connectivity to the test set. Therefore, across-genebank predictions hold the promise to improve the curation of the world's genebank collections and contribute significantly to the long-term development of traditional genebanks toward biodigital resource centers.
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Affiliation(s)
- Samira El Hanafi
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Yong Jiang
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Zakaria Kehel
- International Center for Agricultural Research in Dry Areas (ICARDA), Rabat, Morocco
| | - Albert W. Schulthess
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Yusheng Zhao
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Max Haupt
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany
| | - Ahmed Amri
- International Center for Agricultural Research in Dry Areas (ICARDA), Rabat, Morocco
| | - Jochen C. Reif
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
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Alsamman AM, Mousa KH, Nassar AE, Faheem MM, Radwan KH, Adly MH, Hussein A, Istanbuli T, Mokhtar MM, Elakkad TA, Kehel Z, Hamwieh A, Abdelsattar M, El Allali A. Identification, characterization, and validation of NBS-encoding genes in grass pea. Front Genet 2023; 14:1187597. [PMID: 37408775 PMCID: PMC10318170 DOI: 10.3389/fgene.2023.1187597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/01/2023] [Indexed: 07/07/2023] Open
Abstract
Grass pea is a promising crop with the potential to provide food and fodder, but its genomics has not been adequately explored. Identifying genes for desirable traits, such as drought tolerance and disease resistance, is critical for improving the plant. Grass pea currently lacks known R-genes, including the nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family, which plays a key role in protecting the plant from biotic and abiotic stresses. In our study, we used the recently published grass pea genome and available transcriptomic data to identify 274 NBS-LRR genes. The evolutionary relationships between the classified genes on the reported plants and LsNBS revealed that 124 genes have TNL domains, while 150 genes have CNL domains. All genes contained exons, ranging from 1 to 7. Ten conserved motifs with lengths ranging from 16 to 30 amino acids were identified. We found TIR-domain-containing genes in 132 LsNBSs, with 63 TIR-1 and 69 TIR-2, and RX-CCLike in 84 LsNBSs. We also identified several popular motifs, including P-loop, Uup, kinase-GTPase, ABC, ChvD, CDC6, Rnase_H, Smc, CDC48, and SpoVK. According to the gene enrichment analysis, the identified genes undergo several biological processes such as plant defense, innate immunity, hydrolase activity, and DNA binding. In the upstream regions, 103 transcription factors were identified that govern the transcription of nearby genes affecting the plant excretion of salicylic acid, methyl jasmonate, ethylene, and abscisic acid. According to RNA-Seq expression analysis, 85% of the encoded genes have high expression levels. Nine LsNBS genes were selected for qPCR under salt stress conditions. The majority of the genes showed upregulation at 50 and 200 μM NaCl. However, LsNBS-D18, LsNBS-D204, and LsNBS-D180 showed reduced or drastic downregulation compared to their respective expression levels, providing further insights into the potential functions of LsNBSs under salt stress conditions. They provide valuable insights into the potential functions of LsNBSs under salt stress conditions. Our findings also shed light on the evolution and classification of NBS-LRR genes in legumes, highlighting the potential of grass pea. Further research could focus on the functional analysis of these genes, and their potential use in breeding programs to improve the salinity, drought, and disease resistance of this important crop.
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Affiliation(s)
- Alsamman M. Alsamman
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Khaled H. Mousa
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Ahmed E. Nassar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Mostafa M. Faheem
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Khaled H. Radwan
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Monica H. Adly
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Ahmed Hussein
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Tawffiq Istanbuli
- International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol, Lebanon
| | - Morad M. Mokhtar
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Tamer Ahmed Elakkad
- Department of Genetics and Genetic Engineering, Faculty of Agriculture at Moshtohor, Benha University, Benha, Egypt
- Moshtohor Research Park, Molecular Biology Lab, Benha University, Benha, Egypt
| | - Zakaria Kehel
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Aladdin Hamwieh
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Mohamed Abdelsattar
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
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Alsamman AM, Abdelsattar M, El Allali A, Radwan KH, Nassar AE, Mousa KH, Hussein A, Mokhtar MM, Abd El-Maksoud MM, Istanbuli T, Kehel Z, Hamwieh A. Genome-wide identification, characterization, and validation of the bHLH transcription factors in grass pea. Front Genet 2023; 14:1128992. [PMID: 37021003 PMCID: PMC10067732 DOI: 10.3389/fgene.2023.1128992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 03/02/2023] [Indexed: 03/22/2023] Open
Abstract
Background: The basic helix-loop-helix (bHLH) transcription factor is a vital component in plant biology, with a significant impact on various aspects of plant growth, cell development, and physiological processes. Grass pea is a vital agricultural crop that plays a crucial role in food security. However, the lack of genomic information presents a major challenge to its improvement and development. This highlights the urgency for deeper investigation into the function of bHLH genes in grass pea to improve our understanding of this important crop.Results: The identification of bHLH genes in grass pea was performed on a genome-wide scale using genomic and transcriptomic screening. A total of 122 genes were identified as having conserved bHLH domains and were functionally and fully annotated. The LsbHLH proteins could be classified into 18 subfamilies. There were variations in intron-exon distribution, with some genes lacking introns. The cis-element and gene enrichment analyses showed that the LsbHLHs were involved in various plant functions, including response to phytohormones, flower and fruit development, and anthocyanin synthesis. A total of 28 LsbHLHs were found to have cis-elements associated with light response and endosperm expression biosynthesis. Ten conserved motifs were identified across the LsbHLH proteins. The protein-protein interaction analysis showed that all LsbHLH proteins interacted with each other, and nine of them displayed high levels of interaction. RNA-seq analysis of four Sequence Read Archive (SRA) experiments showed high expression levels of LsbHLHs across a range of environmental conditions. Seven highly expressed genes were selected for qPCR validation, and their expression patterns in response to salt stress showed that LsbHLHD4, LsbHLHD5, LsbHLHR6, LsbHLHD8, LsbHLHR14, LsbHLHR68, and LsbHLHR86 were all expressed in response to salt stress.Conclusion: The study provides an overview of the bHLH family in the grass pea genome and sheds light on the molecular mechanisms underlying the growth and evolution of this crop. The report covers the diversity in gene structure, expression patterns, and potential roles in regulating plant growth and response to environmental stress factors in grass pea. The identified candidate LsbHLHs could be utilized as a tool to enhance the resilience and adaptation of grass pea to environmental stress.
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Affiliation(s)
- Alsamman M. Alsamman
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Mohamed Abdelsattar
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Achraf El Allali
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- *Correspondence: Achraf El Allali, ; Aladdin Hamwieh,
| | - Khaled H. Radwan
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- National Biotechnology Network of Expertise, ASRT, Cairo, Egypt
| | - Ahmed E. Nassar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Khaled H. Mousa
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
| | - Ahmed Hussein
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Morad M. Mokhtar
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | | | - Tawffiq Istanbuli
- International Center for Agricultural Research in the Dry Areas (ICARDA), Terbol, Lebanon
| | - Zakaria Kehel
- Biodiversity and Crop Improvement Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Aladdin Hamwieh
- International Center for Agricultural Research in the Dry Areas (ICARDA), Giza, Egypt
- *Correspondence: Achraf El Allali, ; Aladdin Hamwieh,
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Willcox MC, Burgueño JA, Jeffers D, Rodriguez-Chanona E, Guadarrama-Espinoza A, Kehel Z, Chepetla D, Shrestha R, Swarts K, Buckler ES, Hearne S, Chen C. Mining alleles for tar spot complex resistance from CIMMYT's maize Germplasm Bank. Front Sustain Food Syst 2022. [DOI: 10.3389/fsufs.2022.937200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The tar spot complex (TSC) is a devastating disease of maize (Zea mays L.), occurring in 17 countries throughout Central, South, and North America and the Caribbean, and can cause grain yield losses of up to 80%. As yield losses from the disease continue to intensify in Central America, Phyllachora maydis, one of the causal pathogens of TSC, was first detected in the United States in 2015, and in 2020 in Ontario, Canada. Both the distribution and yield losses due to TSC are increasing, and there is a critical need to identify the genetic resources for TSC resistance. The Seeds of Discovery Initiative at CIMMYT has sought to combine next-generation sequencing technologies and phenotypic characterization to identify valuable alleles held in the CIMMYT Germplasm Bank for use in germplasm improvement programs. Individual landrace accessions of the “Breeders' Core Collection” were crossed to CIMMYT hybrids to form 918 unique accessions topcrosses (F1 families) which were evaluated during 2011 and 2012 for TSC disease reaction. A total of 16 associated SNP variants were identified for TSC foliar leaf damage resistance and increased grain yield. These variants were confirmed by evaluating the TSC reaction of previously untested selections of the larger F1 testcross population (4,471 accessions) based on the presence of identified favorable SNPs. We demonstrated the usefulness of mining for donor alleles in Germplasm Bank accessions for newly emerging diseases using genomic variation in landraces.
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Ramirez-Villegas J, Khoury CK, Achicanoy HA, Diaz MV, Mendez AC, Sosa CC, Kehel Z, Guarino L, Abberton M, Aunario J, Awar BA, Alarcon JC, Amri A, Anglin NL, Azevedo V, Aziz K, Capilit GL, Chavez O, Chebotarov D, Costich DE, Debouck DG, Ellis D, Falalou H, Fiu A, Ghanem ME, Giovannini P, Goungoulou AJ, Gueye B, Hobyb AIE, Jamnadass R, Jones CS, Kpeki B, Lee JS, McNally KL, Muchugi A, Ndjiondjop MN, Oyatomi O, Payne TS, Ramachandran S, Rossel G, Roux N, Ruas M, Sansaloni C, Sardos J, Setiyono TD, Tchamba M, van den Houwe I, Velazquez JA, Venuprasad R, Wenzl P, Yazbek M, Zavala C. State of ex situ conservation of landrace groups of 25 major crops. Nat Plants 2022; 8:491-499. [PMID: 35534721 PMCID: PMC9122826 DOI: 10.1038/s41477-022-01144-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Crop landraces have unique local agroecological and societal functions and offer important genetic resources for plant breeding. Recognition of the value of landrace diversity and concern about its erosion on farms have led to sustained efforts to establish ex situ collections worldwide. The degree to which these efforts have succeeded in conserving landraces has not been comprehensively assessed. Here we modelled the potential distributions of eco-geographically distinguishable groups of landraces of 25 cereal, pulse and starchy root/tuber/fruit crops within their geographic regions of diversity. We then analysed the extent to which these landrace groups are represented in genebank collections, using geographic and ecological coverage metrics as a proxy for genetic diversity. We find that ex situ conservation of landrace groups is currently moderately comprehensive on average, with substantial variation among crops; a mean of 63% ± 12.6% of distributions is currently represented in genebanks. Breadfruit, bananas and plantains, lentils, common beans, chickpeas, barley and bread wheat landrace groups are among the most fully represented, whereas the largest conservation gaps persist for pearl millet, yams, finger millet, groundnut, potatoes and peas. Geographic regions prioritized for further collection of landrace groups for ex situ conservation include South Asia, the Mediterranean and West Asia, Mesoamerica, sub-Saharan Africa, the Andean mountains of South America and Central to East Asia. With further progress to fill these gaps, a high degree of representation of landrace group diversity in genebanks is feasible globally, thus fulfilling international targets for their ex situ conservation.
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Affiliation(s)
- Julian Ramirez-Villegas
- International Center for Tropical Agriculture (CIAT), Cali, Colombia.
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), Cali, Colombia.
- Wageningen University & Research (WUR), Plant Production Systems Group, Wageningen, The Netherlands.
| | - Colin K Khoury
- International Center for Tropical Agriculture (CIAT), Cali, Colombia.
- San Diego Botanic Garden, Encinitas, CA, USA.
| | | | | | - Andres C Mendez
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Chrystian C Sosa
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
- Pontificia Universidad Javeriana Cali, Cali, Colombia
- Universidad del Quindío, Armenia, Colombia
| | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | | | - Michael Abberton
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Jorrel Aunario
- International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Bashir Al Awar
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
| | | | - Ahmed Amri
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Noelle L Anglin
- International Potato Center (CIP), Lima, Peru
- United States Department of Agriculture (USDA), Agricultural Research Service, Aberdeen, ID, USA
| | - Vania Azevedo
- International Potato Center (CIP), Lima, Peru
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Hyderabad, India
| | - Khadija Aziz
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Grace Lee Capilit
- International Rice Research Institute (IRRI), Los Baños, Philippines
| | | | - Dmytro Chebotarov
- International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Denise E Costich
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México
| | - Daniel G Debouck
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - David Ellis
- International Potato Center (CIP), Lima, Peru
| | - Hamidou Falalou
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Niamey, Niger
| | - Albert Fiu
- Centre for Pacific Crops and Trees (CePaCT), Narere, Fiji
| | | | | | | | - Badara Gueye
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Amal Ibn El Hobyb
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | | | - Chris S Jones
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | | | - Jae-Sung Lee
- International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Kenneth L McNally
- International Rice Research Institute (IRRI), Los Baños, Philippines
| | - Alice Muchugi
- International Livestock Research Institute (ILRI), Addis Ababa, Ethiopia
| | | | - Olaniyi Oyatomi
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Thomas S Payne
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México
| | - Senthil Ramachandran
- International Crops Research Institute for the Semi-arid Tropics (ICRISAT), Hyderabad, India
| | | | | | - Max Ruas
- Bioversity International, Montpellier, France
| | - Carolina Sansaloni
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México
| | | | - Tri Deri Setiyono
- International Rice Research Institute (IRRI), Los Baños, Philippines
- Louisiana State University, Baton Rouge, LA, USA
| | - Marimagne Tchamba
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | | | | | | | - Peter Wenzl
- International Center for Tropical Agriculture (CIAT), Cali, Colombia
| | - Mariana Yazbek
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
| | - Cristian Zavala
- International Maize and Wheat Improvement Center (CIMMYT), Texcoco, México
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Alo F, Rani AR, Baum M, Singh S, Kehel Z, Rani U, Udupa S, Al-Sham’aa K, Alsamman AM, Istanbuli T, Attar B, Hamwieh A, Amri A. Novel Genomic Regions Linked to Ascochyta Blight Resistance in Two Differentially Resistant Cultivars of Chickpea. Front Plant Sci 2022; 13:762002. [PMID: 35548283 PMCID: PMC9083910 DOI: 10.3389/fpls.2022.762002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Accepted: 02/10/2022] [Indexed: 06/15/2023]
Abstract
Ascochyta blight (AB), caused by the fungal pathogen Ascochyta rabiei, is a devastating foliar disease of chickpea (Cicer arietinum L.). The genotyping-by-sequencing (GBS)-based approach was deployed for mapping QTLs associated with AB resistance in chickpea in two recombinant inbred line populations derived from two crosses (AB3279 derived from ILC 1929 × ILC 3279 and AB482 derived from ILC 1929 × ILC 482) and tested in six different environments. Twenty-one different genomic regions linked to AB resistance were identified in regions CalG02 and CalG04 in both populations AB3279 and AB482. These regions contain 1,118 SNPs significantly associated with AB resistance (p ≤ 0.001), which explained 11.2-39.3% of the phenotypic variation (PVE). Nine of the AB resistance-associated genomic regions were newly detected in this study, while twelve regions were known from previous AB studies. The proposed physical map narrows down AB resistance to consistent genomic regions identified across different environments. Gene ontology (GO) assigned these QTLs to 319 genes, many of which were associated with stress and disease resistance, and with most important genes belonging to resistance gene families such as leucine-rich repeat (LRR) and transcription factor families. Our results indicate that the flowering-associated gene GIGANTEA is a possible key factor in AB resistance in chickpea. The results have identified AB resistance-associated regions on the physical genetic map of chickpea and allowed for the identification of associated markers that will help in breeding of AB-resistant varieties.
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Affiliation(s)
- Fida Alo
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
| | - Anupalli Roja Rani
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, India
| | - Michael Baum
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
| | - Sarvjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
| | - Upasana Rani
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Sripada Udupa
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
| | - Khaled Al-Sham’aa
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
| | - Alsamman M. Alsamman
- African Genome Center, Mohammed VI Polytechnic University, Ben Guerir, Morocco
- Agriculture Genetic Engineering Research Institute, Giza, Egypt
| | - Tawffiq Istanbuli
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
| | - Basem Attar
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, United Kingdom
| | - Aladdin Hamwieh
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
| | - Ahmed Amri
- International Center for Agricultural Research in the Dry Areas (ICARDA), Beirut, Lebanon
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11
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Badaeva ED, Konovalov FA, Knüpffer H, Fricano A, Ruban AS, Kehel Z, Zoshchuk SA, Surzhikov SA, Neumann K, Graner A, Hammer K, Filatenko A, Bogaard A, Jones G, Özkan H, Kilian B. Genetic diversity, distribution and domestication history of the neglected GGA tA t genepool of wheat. Theor Appl Genet 2022; 135:755-776. [PMID: 34283259 PMCID: PMC8942905 DOI: 10.1007/s00122-021-03912-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/07/2021] [Indexed: 05/03/2023]
Abstract
We present a comprehensive survey of cytogenetic and genomic diversity of the GGAtAt genepool of wheat, thereby unlocking these plant genetic resources for wheat improvement. Wheat yields are stagnating around the world and new sources of genes for resistance or tolerances to abiotic traits are required. In this context, the tetraploid wheat wild relatives are among the key candidates for wheat improvement. Despite its potential huge value for wheat breeding, the tetraploid GGAtAt genepool is largely neglected. Understanding the population structure, native distribution range, intraspecific variation of the entire tetraploid GGAtAt genepool and its domestication history would further its use for wheat improvement. The paper provides the first comprehensive survey of genomic and cytogenetic diversity sampling the full breadth and depth of the tetraploid GGAtAt genepool. According to the results obtained, the extant GGAtAt genepool consists of three distinct lineages. We provide detailed insights into the cytogenetic composition of GGAtAt wheats, revealed group- and population-specific markers and show that chromosomal rearrangements play an important role in intraspecific diversity of T. araraticum. The origin and domestication history of the GGAtAt lineages is discussed in the context of state-of-the-art archaeobotanical finds. We shed new light on the complex evolutionary history of the GGAtAt wheat genepool and provide the basis for an increased use of the GGAtAt wheat genepool for wheat improvement. The findings have implications for our understanding of the origins of agriculture in southwest Asia.
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Affiliation(s)
- Ekaterina D Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Fedor A Konovalov
- Independent Clinical Bioinformatics Laboratory, Moscow, Russia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Helmut Knüpffer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Agostino Fricano
- Council for Agricultural Research and Economics - Research Centre for Genomics & Bioinformatics, Fiorenzuola d'Arda (PC), Italy
| | - Alevtina S Ruban
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | - Zakaria Kehel
- International Center for the Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Svyatoslav A Zoshchuk
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergei A Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Karl Hammer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Anna Filatenko
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Independent Researcher, St. Petersburg, Russia
| | | | - Glynis Jones
- Department of Archaeology, University of Sheffield, Sheffield, UK
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Global Crop Diversity Trust, Bonn, Germany
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12
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Tsivelikas AL, Ben Ghanem H, El-Baouchi A, Kehel Z. Single-Plant Selection at Ultra-Low Density Enhances Buffering Capacity of Barley Varieties and Landraces to Unpredictable Environments and Improves Their Agronomic Performance. Front Plant Sci 2022; 13:838536. [PMID: 35251108 PMCID: PMC8895306 DOI: 10.3389/fpls.2022.838536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 01/24/2022] [Indexed: 06/14/2023]
Abstract
Rainfall and temperature are unpredictable factors in Mediterranean environments that result in irregular environmental conditions for crop growth, thus being a critical source of uncertainty for farmers. This study applied divergent single-plant selection for high and low yield within five barley varieties and two Tunisian landraces under semi-arid conditions at an ultra-low density of 1.2 plants/m2 for two consecutive years. Progeny evaluation under dense stands following farmers' practices was conducted in two semi-arid locations in Tunisia during one cropping season and in one location during a second season, totalling three environments. The results revealed significant genotypic effects for all recorded agronomic and physiological traits. No genotype × environment interaction was shown for biological yield, implying a biomass buffering capacity for selected lines under different environmental conditions. However, genotype × environment interaction was present in terms of grain yield since plasticity for biomass production under drought stress conditions was not translated directly to yield compensation for some of the lines. Nevertheless, several lines selected for high yield were identified to surpass their source material and best checks in each environment, while one line (IH4-4) outperformed consistently by 62.99% on average, in terms of grain yield, the best check across all environments. In addition, improved agronomic performance under drought conditions induced an indirect effect on some grain quality traits. Most of the lines selected for high yield maintained or even improved their grain protein content in comparison to their source material (average increase by 2.33%). On the other hand, most of the lines selected for low yield indicated a poor agronomic performance, further confirming the coherence between selection under ultra-low density and performance under dense stand.
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Affiliation(s)
- Athanasios L. Tsivelikas
- Genetic Resources Section, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Hajer Ben Ghanem
- Field Crop Laboratory, National Institute of Agricultural Research, University of Carthage, Tunis, Tunisia
| | - Adil El-Baouchi
- African Integrated Plant and Soil Research Group (AiPlaS), AgroBioSciences, Mohammed VI Polytechnic University, Ben Guerir, Morocco
| | - Zakaria Kehel
- Genetic Resources Section, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
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13
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El Hanafi S, Cherkaoui S, Kehel Z, Sanchez-Garcia M, Sarazin JB, Baenziger S, Tadesse W. Hybrid Seed Set in Relation with Male Floral Traits, Estimation of Heterosis and Combining Abilities for Yield and Its Components in Wheat ( Triticum aestivum L.). Plants (Basel) 2022; 11:508. [PMID: 35214841 PMCID: PMC8880032 DOI: 10.3390/plants11040508] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Breeding hybrids with maximum heterosis requires efficient cross-pollination and an improved male sterility system. Renewed efforts have been made to dissect the phenotypic variation and genetic basis of hybrid floral traits, although the potential of tailoring the appropriate flower design on seed setting is less known. To this end, elite wheat genotypes were crossed using a chemical hybridizing agent at different doses. A total of 23 hybrids were developed from a partial diallel design; and planted in an alpha lattice design with their parents at two locations in Morocco, for two years, to evaluate for yield components, heterosis and combining abilities. The 13.5 L ha-1 dose induced a maximum level of sterility (95%) and seed set showed large phenotypic variation and high heritability. In parallel, seed set showed tight correlation with pollen mass (0.97), visual anther extrusion (0.94) and pollen shedding (0.91) (p < 0.001), allowing direct selection of the associated traits. Using the combined data, mid-parent heterosis ranges were -7.64-14.55% for biomass (BM), -8.34-12.51% for thousand kernel weight (TKW) and -5.29-26.65% for grain yield (YLD); while best-parent heterosis showed ranges of -11.18-7.20%, -11.35-11.26% and -8.27-24.04% for BM, TKW and YLD, respectively. The magnitude of general combining ability (GCA) variance was greater than the specific combining ability (SCA) variance suggesting a greater additive gene action for BM, TKW and YLD. The favorable GCA estimates showed a simple method to predict additive effects contributing to high heterosis and thus could be an effective approach for the selection of promising parents in early generations.
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Affiliation(s)
- Samira El Hanafi
- International Center for Agricultural Research in the Dry Areas, Rue Hafiane Cherkaoui, Rabat-Institutes, Rabat B.P. 6299, Morocco; (Z.K.); (M.S.-G.); (W.T.)
- Physiology Plant Biotechnology Unit, Bio-Bio Center, Faculty of Sciences, Mohammed V University of Rabat, 4 Avenue Ibn Battouta, Rabat B.P. 1014, Morocco;
| | - Souad Cherkaoui
- Physiology Plant Biotechnology Unit, Bio-Bio Center, Faculty of Sciences, Mohammed V University of Rabat, 4 Avenue Ibn Battouta, Rabat B.P. 1014, Morocco;
| | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas, Rue Hafiane Cherkaoui, Rabat-Institutes, Rabat B.P. 6299, Morocco; (Z.K.); (M.S.-G.); (W.T.)
| | - Miguel Sanchez-Garcia
- International Center for Agricultural Research in the Dry Areas, Rue Hafiane Cherkaoui, Rabat-Institutes, Rabat B.P. 6299, Morocco; (Z.K.); (M.S.-G.); (W.T.)
| | | | - Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68588, USA;
| | - Wuletaw Tadesse
- International Center for Agricultural Research in the Dry Areas, Rue Hafiane Cherkaoui, Rabat-Institutes, Rabat B.P. 6299, Morocco; (Z.K.); (M.S.-G.); (W.T.)
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14
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Abed A, Kehel Z. Preparation and Curation of Multiyear, Multilocation, Multitrait Datasets. Methods Mol Biol 2022; 2481:83-104. [PMID: 35641760 DOI: 10.1007/978-1-0716-2237-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Genome-wide association studies (GWAS) are a powerful approach to dissect genotype-phenotype associations and identify causative regions. However, this power is highly influenced by the accuracy of the phenotypic data. To obtain accurate phenotypic values, the phenotyping should be achieved through multienvironment trials (METs). In order to avoid any technical errors, the required time needs to be spent on exploring, understanding, curating and adjusting the phenotypic data in each trial before combining them using an appropriate linear mixed model (LMM). The LMM is chosen to minimize as much as possible any effect that can lead to misestimation of the phenotypic values. The purpose of this chapter is to explain a series of important steps to explore and analyze data from METs used to characterize an association panel. Two datasets are used to illustrate two different scenarios.
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Affiliation(s)
- Amina Abed
- Consortium de recherche sur la pomme de terre du Québec (CRPTQ), Québec, Canada.
| | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco.
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15
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El Fakhouri K, Sabraoui A, Kehel Z, El Bouhssini M. Population Dynamics and Yield Loss Assessment for Pea Aphid, Acyrthosiphon pisum (Harris) (Homoptera: Aphididae), on Lentil in Morocco. Insects 2021; 12:insects12121080. [PMID: 34940168 PMCID: PMC8707183 DOI: 10.3390/insects12121080] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 10/05/2021] [Accepted: 10/14/2021] [Indexed: 11/16/2022]
Abstract
Simple Summary In Morocco, lentil is being grown under rainfed conditions and plays an important role in cereal-based cropping systems. Pea aphid (Acyrthosiphon pisum Harris) is one of the most important constraints limiting the yield of lentil in several countries; however, the extent of yield loss it causes in Morocco is unknown. Pea aphid weakens the plant directly by sucking its sap, and can also spread viruses from infected plants to healthy ones. Currently, there are no effective tools available for A. pisum control, with most farmers being reliant on chemical insecticides. The aim of this study is to investigate the population fluctuation of pea aphid over different seasons and their effects on yield loss in Morocco. Correlation analysis was performed to find out the extent of influence of weather parameters on the population dynamics of an aphid population over different seasons. The results demonstrated that the avoidable losses due to aphid infestation were in the range of 4.56–12.51%. The pea aphid populations increased rapidly between March and April when climate factors and the plants became more suitable for aphid development. The maximum temperature, relative humidity, and wind speed influenced pea aphid infestation on different lentil varieties. Abstract Pea aphid (Acyrthosiphon pisum Harris) is the major insect pest of lentil in Morocco. We investigated pea aphid mean numbers and yield losses on three lentil varieties at one location during three successive cropping seasons during 2015–2018. The effects of several weather factors on pea aphid population dynamics were investigated. Population density increased in early spring followed by several peaks during March–April and then steeply declined during the late spring. Aphid populations peaked at different times during the three years of the study. In 2016, higher populations occurred during the second and third weeks of April for Abda and Zaria varieties with averages of 27 and 28 aphids/20 twigs, respectively. In 2017, higher populations occurred on the 12th and 13th standard meteorological weeks (SMWs) for Zaria with averages of 24.7 and 27.03 aphids/20 twigs, respectively. In 2018, the population peaked for all varieties at three different times, 11th, 13th, and 17th SMW, with the highest for Zaria being 26.00, 47.41, and 32.33 aphids/20 twigs. Pea aphid population dynamics changed with weather conditions. The number of aphids significantly and positively correlated with maximum temperature, but significantly negatively correlated with relative humidity and wind speed. The minimum temperature and rainfall had non-significant correlations. Pea aphid infestation resulted in losses of total seed weight for all lentil varieties, with the highest avoidable losses for Bakria being 12.51% followed by Zaria with 7.72% and Abda with 4.56%. These losses may justify the development of integrated management options for control of this pest.
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Affiliation(s)
- Karim El Fakhouri
- International Center for Agricultural Research in the Dry Areas (ICARDA), Entomology Laboratory, Rabat Institutes, Rabat P.O. Box 6299, Morocco;
- Correspondence:
| | - Abdelhadi Sabraoui
- International Center for Agricultural Research in the Dry Areas (ICARDA), Entomology Laboratory, Rabat Institutes, Rabat P.O. Box 6299, Morocco;
| | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas (ICARDA), Genetic Resources Program, Rabat Institutes, Rabat P.O. Box 6299, Morocco;
| | - Mustapha El Bouhssini
- AgroBioSciences Research Division, Mohammed VI Polytechnic University, Lot 660, Hay Moulay Rachid, Ben Guerir P.O. Box 43150, Morocco;
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16
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Badaeva ED, Konovalov FA, Knüpffer H, Fricano A, Ruban AS, Kehel Z, Zoshchuk SA, Surzhikov SA, Neumann K, Graner A, Hammer K, Filatenko A, Bogaard A, Jones G, Özkan H, Kilian B. Correction to: Genetic diversity, distribution and domestication history of the neglected GGA tA t genepool of wheat. Theor Appl Genet 2021; 134:3493. [PMID: 34379147 PMCID: PMC8440298 DOI: 10.1007/s00122-021-03931-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Affiliation(s)
- Ekaterina D Badaeva
- N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia.
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
| | - Fedor A Konovalov
- Independent Clinical Bioinformatics Laboratory, Moscow, Russia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Helmut Knüpffer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Agostino Fricano
- Council for Agricultural Research and Economics - Research Centre for Genomics & Bioinformatics, Fiorenzuola d'Arda (PC), Italy
| | - Alevtina S Ruban
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- KWS SAAT SE & Co. KGaA, Einbeck, Germany
| | - Zakaria Kehel
- International Center for the Agricultural Research in the Dry Areas (ICARDA), Rabat, Morocco
| | - Svyatoslav A Zoshchuk
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Sergei A Surzhikov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Kerstin Neumann
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Karl Hammer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Anna Filatenko
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Independent Researcher, St. Petersburg, Russia
| | | | - Glynis Jones
- Department of Archaeology, University of Sheffield, Sheffield, UK
| | - Hakan Özkan
- Department of Field Crops, Faculty of Agriculture, University of Çukurova, Adana, Turkey
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
- Global Crop Diversity Trust, Bonn, Germany
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17
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El Gataa Z, El Hanafi S, El Messoadi K, Samir K, Kehel Z, Tadesse W. Genome wide association and prediction studies of agronomic and quality traits in spring beard wheat (Triticum aestivum L.) under rain-fed environment with terminal moisture stress. J Cereal Sci 2021. [DOI: 10.1016/j.jcs.2021.103278] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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18
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El Hanafi S, Cherkaoui S, Kehel Z, Al-Abdallat A, Tadesse W. Genome-Wide Association and Prediction of Male and Female Floral Hybrid Potential Traits in Elite Spring Bread Wheat Genotypes. Plants (Basel) 2021; 10:plants10050895. [PMID: 33946624 PMCID: PMC8145198 DOI: 10.3390/plants10050895] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/31/2021] [Accepted: 04/09/2021] [Indexed: 11/26/2022]
Abstract
Hybrid wheat breeding is one of the most promising technologies for further sustainable yield increases. However, the cleistogamous nature of wheat displays a major bottleneck for a successful hybrid breeding program. Thus, an optimized breeding strategy by developing appropriate parental lines with favorable floral trait combinations is the best way to enhance the outcrossing ability. This study, therefore, aimed to dissect the genetic basis of various floral traits using genome-wide association study (GWAS) and to assess the potential of genome-wide prediction (GP) for anther extrusion (AE), visual anther extrusion (VAE), pollen mass (PM), pollen shedding (PSH), pollen viability (PV), anther length (AL), openness of the flower (OPF), duration of floret opening (DFO) and stigma length. To this end, we employed 196 ICARDA spring bread wheat lines evaluated for three years and genotyped with 10,477 polymorphic SNP. In total, 70 significant markers were identified associated to the various assessed traits at FDR ≤ 0.05 contributing a minor to large proportion of the phenotypic variance (8–26.9%), affecting the traits either positively or negatively. GWAS revealed multi-marker-based associations among AE, VAE, PM, OPF and DFO, most likely linked markers, suggesting a potential genomic region controlling the genetic association of these complex traits. Of these markers, Kukri_rep_c103359_233 and wsnp_Ex_rep_c107911_91350930 deserve particular attention. The consistently significant markers with large effect could be useful for marker-assisted selection. Genomic selection revealed medium to high prediction accuracy ranging between 52% and 92% for the assessed traits with the least and maximum value observed for stigma length and visual anther extrusion, respectively. This indicates the feasibility to implement genomic selection to predict the performance of hybrid floral traits with high reliability.
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Affiliation(s)
- Samira El Hanafi
- International Center for Agricultural Research in the Dry Areas, B.P. 6299, Rue Hafiane Cherkaoui, Rabat-Institutes, Rabat 10100, Morocco; (Z.K.); (W.T.)
- Bio-Bio Center, Physiology Plant Biotechnology Unit, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, B.P. 1014, Rabat 10100, Morocco;
- Correspondence:
| | - Souad Cherkaoui
- Bio-Bio Center, Physiology Plant Biotechnology Unit, Faculty of Sciences, Mohammed V University in Rabat, 4 Avenue Ibn Battouta, B.P. 1014, Rabat 10100, Morocco;
| | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas, B.P. 6299, Rue Hafiane Cherkaoui, Rabat-Institutes, Rabat 10100, Morocco; (Z.K.); (W.T.)
| | - Ayed Al-Abdallat
- Department of Horticulture and Crop Science, School of Agriculture, The University of Jordan, Amman 11942, Jordan;
| | - Wuletaw Tadesse
- International Center for Agricultural Research in the Dry Areas, B.P. 6299, Rue Hafiane Cherkaoui, Rabat-Institutes, Rabat 10100, Morocco; (Z.K.); (W.T.)
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Tehseen MM, Kehel Z, Sansaloni CP, Lopes MDS, Amri A, Kurtulus E, Nazari K. Comparison of Genomic Prediction Methods for Yellow, Stem, and Leaf Rust Resistance in Wheat Landraces from Afghanistan. Plants (Basel) 2021; 10:plants10030558. [PMID: 33809650 PMCID: PMC8001917 DOI: 10.3390/plants10030558] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/28/2021] [Accepted: 03/13/2021] [Indexed: 11/16/2022]
Abstract
Wheat rust diseases, including yellow rust (Yr; also known as stripe rust) caused by Puccinia striiformis Westend. f. sp. tritici, leaf rust (Lr) caused by Puccinia triticina Eriks. and stem rust (Sr) caused by Puccinia graminis Pres f. sp. tritici are major threats to wheat production all around the globe. Durable resistance to wheat rust diseases can be achieved through genomic-assisted prediction of resistant accessions to increase genetic gain per unit time. Genomic prediction (GP) is a promising technology that uses genomic markers to estimate genomic-assisted breeding values (GBEVs) for selecting resistant plant genotypes and accumulating favorable alleles for adult plant resistance (APR) to wheat rust diseases. To evaluate GP we compared the predictive ability of nine different parametric, semi-parametric and Bayesian models including Genomic Unbiased Linear Prediction (GBLUP), Ridge Regression (RR), Least Absolute Shrinkage and Selection Operator (LASSO), Elastic Net (EN), Bayesian Ridge Regression (BRR), Bayesian A (BA), Bayesian B (BB), Bayesian C (BC) and Reproducing Kernel Hilbert Spacing model (RKHS) to estimate GEBV’s for APR to yellow, leaf and stem rust of wheat in a panel of 363 bread wheat landraces of Afghanistan origin. Based on five-fold cross validation the mean predictive abilities were 0.33, 0.30, 0.38, and 0.33 for Yr (2016), Yr (2017), Lr, and Sr, respectively. No single model outperformed the rest of the models for all traits. LASSO and EN showed the lowest predictive ability in four of the five traits. GBLUP and RR gave similar predictive abilities, whereas Bayesian models were not significantly different from each other as well. We also investigated the effect of the number of genotypes and the markers used in the analysis on the predictive ability of the GP model. The predictive ability was highest with 1000 markers and there was a linear trend in the predictive ability and the size of the training population. The results of the study are encouraging, confirming the feasibility of GP to be effectively applied in breeding programs for resistance to all three wheat rust diseases.
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Affiliation(s)
| | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas (ICARDA), ICARDA-PreBreeding & Genebank Operations, Biodiversity and Crop Improvement Program, P.O. Box 10000 Rabat, Morocco; (Z.K.); (A.A.)
| | - Carolina P. Sansaloni
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco C.P. 56237, Mexico;
| | - Marta da Silva Lopes
- Sustainable Field Crops Programme, IRTA (Institute for Food and Agricultural Research and Technology), 25198 Lleida, Spain;
| | - Ahmed Amri
- International Center for Agricultural Research in the Dry Areas (ICARDA), ICARDA-PreBreeding & Genebank Operations, Biodiversity and Crop Improvement Program, P.O. Box 10000 Rabat, Morocco; (Z.K.); (A.A.)
| | - Ezgi Kurtulus
- International Center for Agricultural Research in the Dry Areas (ICARDA), Biodiversity and Crop Improvement Program, Regional Cereal Rust Research Center (RCRRC), P.O. Box 35661 Menemen, Izmir, Turkey;
| | - Kumarse Nazari
- International Center for Agricultural Research in the Dry Areas (ICARDA), Biodiversity and Crop Improvement Program, Regional Cereal Rust Research Center (RCRRC), P.O. Box 35661 Menemen, Izmir, Turkey;
- Correspondence:
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20
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Tehseen MM, Istipliler D, Kehel Z, Sansaloni CP, da Silva Lopes M, Kurtulus E, Muazzam S, Nazari K. Genetic Diversity and Population Structure Analysis of Triticum aestivum L. Landrace Panel from Afghanistan. Genes (Basel) 2021; 12:genes12030340. [PMID: 33668962 PMCID: PMC7996569 DOI: 10.3390/genes12030340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/18/2021] [Accepted: 02/20/2021] [Indexed: 11/27/2022] Open
Abstract
Landraces are a potential source of genetic diversity and provide useful genetic resources to cope with the current and future challenges in crop breeding. Afghanistan is located close to the centre of origin of hexaploid wheat. Therefore, understanding the population structure and genetic diversity of Afghan wheat landraces is of enormous importance in breeding programmes for the development of high-yielding cultivars as well as broadening the genetic base of bread wheat. Here, a panel of 363 bread wheat landraces collected from seven north and north-eastern provinces of Afghanistan were evaluated for population structure and genetic diversity using single nucleotide polymorphic markers (SNPs). The genotyping-by-sequencing of studied landraces after quality control provided 4897 high-quality SNPs distributed across the genomes A (33.75%), B (38.73%), and D (27.50%). The population structure analysis was carried out by two methods using model-based STRUCTURE analysis and cluster-based discriminant analysis of principal components (DAPC). The analysis of molecular variance showed a higher proportion of variation within the sub-populations compared with the variation observed as a whole between sub-populations. STRUCTURE and DAPC analysis grouped the majority of the landraces from Badakhshan and Takhar together in one cluster and the landraces from Baghlan and Kunduz in a second cluster, which is in accordance with the micro-climatic conditions prevalent within the north-eastern agro-ecological zone. Genetic distance analysis was also studied to identify differences among the Afghan regions; the strongest correlation was observed for the Badakhshan and Takhar (0.003), whereas Samangan and Konarha (0.399) showed the highest genetic distance. The population structure and genetic diversity analysis highlighted the complex genetic variation present in the landraces which were highly correlated to the geographic origin and micro-climatic conditions within the agro-climatic zones of the landraces. The higher proportions of admixture could be attributed to historical unsupervised exchanges of seeds between the farmers of the central and north-eastern provinces of Afghanistan. The results of this study will provide useful information for genetic improvement in wheat and is essential for association mapping and genomic prediction studies to identify novel sources for resistance to abiotic and biotic stresses.
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Affiliation(s)
| | - Deniz Istipliler
- Department of Field Crops, Ege University, Bornova, Izmir 35100, Turkey; (M.M.T.); (D.I.)
| | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas (ICARDA), ICARDA-PreBreeding & Genebank Operations, Rabat 10000, Morocco;
| | - Carolina P. Sansaloni
- International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45, El Batán, Texcoco C.P. 56237, Mexico;
| | - Marta da Silva Lopes
- IRTA (Institute for Food and Agricultural Research and Technology), 25198 Lleida, Spain;
| | - Ezgi Kurtulus
- International Center for Agricultural Research in the Dry Areas (ICARDA), Turkey-ICARDA Regional Cereal Rust Research Center (RCRRC), Menemen, Izmir 35661, Turkey;
| | - Sana Muazzam
- Department of Plant Breeding and Genetics, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan;
| | - Kumarse Nazari
- International Center for Agricultural Research in the Dry Areas (ICARDA), Turkey-ICARDA Regional Cereal Rust Research Center (RCRRC), Menemen, Izmir 35661, Turkey;
- Correspondence:
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21
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Farouk I, Alsaleh A, Motowaj J, Gaboun F, Belkadi B, Filali Maltouf A, Kehel Z, Elouafi I, Nsarellah N, M Nachit M. Detection of grain yield QTLs in the durum population Lahn/Cham1 tested in contrasting environments. ACTA ACUST UNITED AC 2021; 45:65-78. [PMID: 33597823 PMCID: PMC7877719 DOI: 10.3906/biy-2008-41] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 11/19/2020] [Indexed: 11/03/2022]
Abstract
Durum wheat (Triticum turgidum L. var durum) is tetraploid wheat (AABB); it is the main source of semolina and other pasta products. Grain yield in wheat is quantitatively inherited and influenced by the environment. The genetic map construction constitutes the essential step in identifying quantitative trait loci (QTLs) linked to complex traits, such as grain yield. The study aimed to construct a genetic linkage map of two parents that are widely grown durum cultivars (Lahn and Cham1) in the Mediterranean basin, which is characterized by varying climate changes. The genetic linkage map of Lahn/Cham1 population consisted of 112 recombinant inbred lines (RILs) and was used to determine QTLs linked to the grain yield in 11 contrasting environments (favorable, cold, dry, and hot). Simple sequence repeat (SSR) molecular markers were used to construct an anchor map, which was later enriched with single nucleotide polymorphisms (SNPs). The map was constructed with 247 SSRs and enriched with 1425 SNPs. The map covered 6122.22 cM. One hundred and twenty-six QTLs were detected on different chromosomes. Chromosomes 2A and 4B harbored the most significant grain yield QTLs. Furthermore, by comparison with several wheat mapping populations, all the A and B chromosomes of Lahn/Cham1 QTLs contributed to grain yield. The results showed that the detected QTLs can be used as a potential candidate for marker-assisted selection in durum breeding programs.
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Affiliation(s)
- Issame Farouk
- Laboratory of Microbiology and Molecular Biology, Department of Biology, Med V University, Rabat Morocco
| | - Ahmad Alsaleh
- Department of Science and Technology Bozok University, Yozgat Turkey
| | - Jihan Motowaj
- ICARDA, The International Center for Agricultural Research in the Dry Areas, Rabat Morocco
| | - Fatima Gaboun
- INRA, National Institute of Agronomical Research, Unity of Biotechnology Research, Rabat Morocco
| | - Bouchra Belkadi
- Laboratory of Microbiology and Molecular Biology, Department of Biology, Med V University, Rabat Morocco
| | - Abdelkarim Filali Maltouf
- Laboratory of Microbiology and Molecular Biology, Department of Biology, Med V University, Rabat Morocco
| | - Zakaria Kehel
- ICARDA, The International Center for Agricultural Research in the Dry Areas, Rabat Morocco
| | - Ismahane Elouafi
- ICBA, International Center for Biosaline Agriculture, Dubai United Arab Emirates
| | - Nasserelhaq Nsarellah
- INRA, National Institute of Agronomical Research, Unity of Biotechnology Research, Rabat Morocco
| | - Miloudi M Nachit
- ICARDA, The International Center for Agricultural Research in the Dry Areas, Rabat Morocco
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22
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McCouch S, Navabi ZK, Abberton M, Anglin NL, Barbieri RL, Baum M, Bett K, Booker H, Brown GL, Bryan GJ, Cattivelli L, Charest D, Eversole K, Freitas M, Ghamkhar K, Grattapaglia D, Henry R, Valadares Inglis MC, Islam T, Kehel Z, Kersey PJ, King GJ, Kresovich S, Marden E, Mayes S, Ndjiondjop MN, Nguyen HT, Paiva SR, Papa R, Phillips PWB, Rasheed A, Richards C, Rouard M, Amstalden Sampaio MJ, Scholz U, Shaw PD, Sherman B, Staton SE, Stein N, Svensson J, Tester M, Montenegro Valls JF, Varshney R, Visscher S, von Wettberg E, Waugh R, Wenzl P, Rieseberg LH. Mobilizing Crop Biodiversity. Mol Plant 2020; 13:1341-1344. [PMID: 32835887 DOI: 10.1016/j.molp.2020.08.011] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 08/19/2020] [Accepted: 08/19/2020] [Indexed: 05/10/2023]
Affiliation(s)
- Susan McCouch
- Plant Breeding and Genetics, School of Integrated Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Zahra Katy Navabi
- DivSeek, Global Institute for Food Security, 110 Gymnasium Place, University of Saskatchewan, Saskatoon, SK, S7N 0W9, Canada; Global Institute for Food Security, 110 Gymnasium Place, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Michael Abberton
- International Institute of Tropical Agriculture (IITA), PMB 5320, Oyo Rd, Ibadan, Nigeria
| | - Noelle L Anglin
- International Potato Center (CIP) 1895 Avenida La Molina, Lima Peru 12, Lima 15023, Peru
| | - Rosa Lia Barbieri
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Michael Baum
- International Center for Agricultural Research in the Dry Areas (ICARDA), Station Exp. INRA-Quich. Rue Hafiane Cherkaoui. Agdal. Rabat - Instituts, 10111, Rabat, Morocco
| | - Kirstin Bett
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK S7N 5A8, Canada
| | - Helen Booker
- Department of Plant Agriculture, University of Guelph, Rm 316, Crop Science Bldg, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada
| | - Gerald L Brown
- Genome Prairie, 111 Research Drive, Suite 101, Saskatoon, SK, S7N 3R2, Canada
| | - Glenn J Bryan
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Luigi Cattivelli
- CREA, Research Centre for Genomics and Bioinformatics, via San Protaso 302, Fiorenzuola d'Arda, 29017, Italy
| | - David Charest
- Genome British Columbia, 400-575 West 8th Avenue, Vancouver, BC, V5Z 0C4, Canada
| | - Kellye Eversole
- International Wheat Genome Sequencing Consortium, 2841 NE Marywood Ct, Lee's Summit, MO, 64086, USA
| | - Marcelo Freitas
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Kioumars Ghamkhar
- Forage Science, Grasslands Research Centre, AgResearch, Palmerston North, 4410, New Zealand
| | - Dario Grattapaglia
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Robert Henry
- Queensland Alliance for Agriculture and Food Innovation, University of Queensland, Brisbane, QLD 4072, Australia
| | - Maria Cleria Valadares Inglis
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Tofazzal Islam
- Institute of Biotechnology and Genetic Engineering (IBGE), Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas (ICARDA), Station Exp. INRA-Quich. Rue Hafiane Cherkaoui. Agdal. Rabat - Instituts, 10111, Rabat, Morocco
| | - Paul J Kersey
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
| | - Graham J King
- Southern Cross University, PO Box 157, Lismore, NSW 2480, Australia
| | - Stephen Kresovich
- Feed the Future Innovation Lab for Crop Improvement, 431 Weill Hall, Cornell University, Ithaca, NY, 14853, USA
| | - Emily Marden
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6R 2A5, Canada
| | - Sean Mayes
- Crops For the Future (UK) CIC 76-80 Baddow Road, Chelmsford, Essex, CM2 7PJ, UK
| | - Marie Noelle Ndjiondjop
- Africa Rice Center (AfricaRice), Mbe Research Station, Bouaké, 01 BP 2511 Bouaké, Côte d'Ivoire
| | - Henry T Nguyen
- University of Missouri, Division of Plant Sciences, 25 Agriculture Lab Bldg, College of Agriculture, Food and Natural Resources, University of Missouri, Columbia, MO 65211, USA
| | - Samuel Rezende Paiva
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Roberto Papa
- Università Politecnica delle Marche, D3A-Dipartimento di Scienze Agrarie, Alimentari e Ambientali, Via Brecce Bianche, 60131, Ancona, Italy
| | - Peter W B Phillips
- Johnson Shoyama Graduate School of Public Policy, University of Saskatchewan, 101 Diefenbaker Place, Saskatoon, S7N 5B8, Canada
| | - Awais Rasheed
- CIMMYT-China office, Beijing 100081, Beijing, P.R. China
| | - Christopher Richards
- USDA-ARS National Laboratory for Genetic Resources Preservation, 1111 South Mason St, Fort Collins, CO, 80521, USA
| | - Mathieu Rouard
- Bioversity International, Parc Scientifique Agropolis II, 34397, Montpellier, Cedex 5, France
| | - Maria Jose Amstalden Sampaio
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany
| | - Paul D Shaw
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK
| | - Brad Sherman
- Law School, University of Queensland, St Lucia, QLD, 4072, Australia
| | - S Evan Staton
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6R 2A5, Canada
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Corrensstr. 3, D-06466 Seeland, Germany; CiBreed - Center for Integrated Breeding Research, Department of Crop Sciences, Georg-August University Göttingen, Von Siebold Straße 8, D-37075 Göttingen, Germany
| | | | - Mark Tester
- King Abdullah University of Science & Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Jose Francisco Montenegro Valls
- Embrapa Genetic Resources and Biotechnology, Parque Estação Biológica, Final Av W5 Norte, Caixa Postal 02372, 70770-917 - Brasília DF, Brazil
| | - Rajeev Varshney
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru - 502 324, Telangana State, India
| | - Stephen Visscher
- Global Institute for Food Security, 110 Gymnasium Place, University of Saskatchewan, Saskatoon, SK, S7N 4J8, Canada
| | - Eric von Wettberg
- University of Vermont, 63 Carrigan Drive, Jeffords Hall, Burlington, VT, 05405, USA
| | - Robbie Waugh
- The James Hutton Institute, Errol Road, Invergowrie, Dundee, DD2 5DA, UK; School of Agriculture and Wine & Waite Research Institute, University of Adelaide, Waite Campus, Glen Osmond, SA, 5064, Australia
| | - Peter Wenzl
- Centro Internacional de Agricultura Tropical (CIAT), Km 17 Recta Cali-Palmira, 763537 Cali, Colombia
| | - Loren H Rieseberg
- Department of Botany and Biodiversity Research Centre, University of British Columbia, Vancouver, BC V6R 2A5, Canada.
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Sansaloni C, Franco J, Santos B, Percival-Alwyn L, Singh S, Petroli C, Campos J, Dreher K, Payne T, Marshall D, Kilian B, Milne I, Raubach S, Shaw P, Stephen G, Carling J, Pierre CS, Burgueño J, Crosa J, Li H, Guzman C, Kehel Z, Amri A, Kilian A, Wenzl P, Uauy C, Banziger M, Caccamo M, Pixley K. Diversity analysis of 80,000 wheat accessions reveals consequences and opportunities of selection footprints. Nat Commun 2020; 11:4572. [PMID: 32917907 PMCID: PMC7486412 DOI: 10.1038/s41467-020-18404-w] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 08/16/2020] [Indexed: 11/09/2022] Open
Abstract
Undomesticated wild species, crop wild relatives, and landraces represent sources of variation for wheat improvement to address challenges from climate change and the growing human population. Here, we study 56,342 domesticated hexaploid, 18,946 domesticated tetraploid and 3,903 crop wild relatives in a massive-scale genotyping and diversity analysis. Using DArTseqTM technology, we identify more than 300,000 high-quality SNPs and SilicoDArT markers and align them to three reference maps: the IWGSC RefSeq v1.0 genome assembly, the durum wheat genome assembly (cv. Svevo), and the DArT genetic map. On average, 72% of the markers are uniquely placed on these maps and 50% are linked to genes. The analysis reveals landraces with unexplored diversity and genetic footprints defined by regions under selection. This provides fertile ground to develop wheat varieties of the future by exploring specific gene or chromosome regions and identifying germplasm conserving allelic diversity missing in current breeding programs. Genebanks hold comprehensive collections of wild species, wild relatives, and landraces that are useful for genetic improvement. Here, the authors report the genotype of nearly 80,000 wheat accessions using DArTseq technology to show the less explored genetic diversity.
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Affiliation(s)
- Carolina Sansaloni
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico.
| | - Jorge Franco
- Departamento de Biometria y Estadística, Facultad de agronomía, Universidad de la República, Ruta 3, km 363, Paysandú, C.P., 60000, Uruguay
| | - Bruno Santos
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | | | - Sukhwinder Singh
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico.,Geneshifters, 222 Mary Jena Lane, Pullman, WA, 99163, USA
| | - Cesar Petroli
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - Jaime Campos
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - Kate Dreher
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - Thomas Payne
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - David Marshall
- Information and Computational Science, The James Hutton Institute, Invergowrie Dundee, DD2 5DA, Scotland
| | - Benjamin Kilian
- Global Crop Diversity Trust, Platz Der Vereinten Nationen 7, Bonn, 53113, Germany
| | - Iain Milne
- Information and Computational Science, The James Hutton Institute, Invergowrie Dundee, DD2 5DA, Scotland
| | - Sebastian Raubach
- Information and Computational Science, The James Hutton Institute, Invergowrie Dundee, DD2 5DA, Scotland
| | - Paul Shaw
- Information and Computational Science, The James Hutton Institute, Invergowrie Dundee, DD2 5DA, Scotland
| | - Gordon Stephen
- Information and Computational Science, The James Hutton Institute, Invergowrie Dundee, DD2 5DA, Scotland
| | - Jason Carling
- Diversity Arrays Technology, Building 3, Level D, University of Canberra, Monana St., Bruce, ACT, 2617, Australia
| | - Carolina Saint Pierre
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - Juan Burgueño
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - José Crosa
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - HuiHui Li
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - Carlos Guzman
- Departamento de Genética Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Universidad de Córdoba, Córdoba, Spain
| | - Zakaria Kehel
- Genetic Resouces Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Rabat-Salé-Zemmour-Zaër, Morocco
| | - Ahmed Amri
- Genetic Resouces Program, International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat, Rabat-Salé-Zemmour-Zaër, Morocco
| | - Andrzej Kilian
- Diversity Arrays Technology, Building 3, Level D, University of Canberra, Monana St., Bruce, ACT, 2617, Australia
| | - Peter Wenzl
- Genetic Resouces Program, International Center for Tropical Agriculture (CIAT), Km 17 Recta Cali-Palmira CP 763537 Apartado Aéreo 6713, Cali, Colombia
| | - Cristobal Uauy
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Marianne Banziger
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
| | - Mario Caccamo
- NIAB, 93 Lawrence Weaver Road, Cambridge, CB3 0LE, UK
| | - Kevin Pixley
- Genetic Resources Program, International Maize and Wheat Improvement Center (CIMMYT), Carretera México-Veracruz Km. 45 El Batán, Texcoco, C.P., 56237, Mexico
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24
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Zaïm M, Kabbaj H, Kehel Z, Gorjanc G, Filali-Maltouf A, Belkadi B, Nachit MM, Bassi FM. Combining QTL Analysis and Genomic Predictions for Four Durum Wheat Populations Under Drought Conditions. Front Genet 2020; 11:316. [PMID: 32435259 PMCID: PMC7218065 DOI: 10.3389/fgene.2020.00316] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Accepted: 03/16/2020] [Indexed: 11/28/2022] Open
Abstract
Durum wheat is an important crop for the human diet and its consumption is gaining popularity. In order to ensure that durum wheat production maintains the pace with the increase in demand, it is necessary to raise productivity by approximately 1.5% per year. To deliver this level of annual genetic gain the incorporation of molecular strategies has been proposed as a key solution. Here, four RILs populations were used to conduct QTL discovery for grain yield (GY) and 1,000 kernel weight (TKW). A total of 576 individuals were sown at three locations in Morocco and one in Lebanon. These individuals were genotyped by sequencing with 3,202 high-confidence polymorphic markers, to derive a consensus genetic map of 2,705.7 cM, which was used to impute any missing data. Six QTLs were found to be associated with GY and independent from flowering time on chromosomes 2B, 4A, 5B, 7A and 7B, explaining a phenotypic variation (PV) ranging from 4.3 to 13.4%. The same populations were used to train genomic prediction models incorporating the relationship matrix, the genotype by environment interaction, and marker by environment interaction, to reveal significant advantages for models incorporating the marker effect. Using training populations (TP) in full sibs relationships with the validation population (VP) was shown to be the only effective strategy, with accuracies reaching 0.35–0.47 for GY. Reducing the number of markers to 10% of the whole set, and the TP size to 20% resulted in non-significant changes in accuracies. The QTLs identified were also incorporated in the models as fixed effects, showing significant accuracy gain for all four populations. Our results confirm that the prediction accuracy depends considerably on the relatedness between TP and VP, but not on the number of markers and size of TP used. Furthermore, feeding the model with information on markers associated with QTLs increased the overall accuracy.
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Affiliation(s)
- Meryem Zaïm
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco.,ICARDA, Biodiversity and Integrated Gene Management, Rabat, Morocco
| | - Hafssa Kabbaj
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco.,ICARDA, Biodiversity and Integrated Gene Management, Rabat, Morocco
| | - Zakaria Kehel
- ICARDA, Biodiversity and Integrated Gene Management, Rabat, Morocco
| | - Gregor Gorjanc
- The Roslin Institute, The University of Edinburgh, Edinburgh, United Kingdom
| | - Abdelkarim Filali-Maltouf
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Bouchra Belkadi
- Laboratory of Microbiology and Molecular Biology, Faculty of Sciences, Mohammed V University, Rabat, Morocco
| | - Miloudi M Nachit
- ICARDA, Biodiversity and Integrated Gene Management, Rabat, Morocco
| | - Filippo M Bassi
- ICARDA, Biodiversity and Integrated Gene Management, Rabat, Morocco
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25
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Kehel Z, Sanchez-Garcia M, El Baouchi A, Aberkane H, Tsivelikas A, Charles C, Amri A. Predictive Characterization for Seed Morphometric Traits for Genebank Accessions Using Genomic Selection. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00032] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
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26
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Ramirez‐Villegas J, Khoury CK, Achicanoy HA, Mendez AC, Diaz MV, Sosa CC, Debouck DG, Kehel Z, Guarino L. A gap analysis modelling framework to prioritize collecting for ex situ conservation of crop landraces. DIVERS DISTRIB 2020. [DOI: 10.1111/ddi.13046] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Julian Ramirez‐Villegas
- International Center for Tropical Agriculture (CIAT) Cali Colombia
- CGIAR Research Program on Climate Change, Agriculture and Food Security (CCAFS), c/o CIAT Cali Colombia
| | - Colin K. Khoury
- International Center for Tropical Agriculture (CIAT) Cali Colombia
- United States Department of Agriculture Agricultural Research Service National Laboratory for Genetic Resources Preservation Fort Collins CO USA
- Department of Biology Saint Louis University St. Louis MO USA
| | | | - Andres C. Mendez
- International Center for Tropical Agriculture (CIAT) Cali Colombia
| | | | | | | | - Zakaria Kehel
- International Center for Agricultural Research in the Dry Areas (ICARDA) Rabat Morocco
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27
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Singh PK, Singh S, Deng Z, He X, Kehel Z, Singh RP. Characterization of QTLs for Seedling Resistance to Tan Spot and Septoria Nodorum Blotch in the PBW343/Kenya Nyangumi Wheat Recombinant Inbred Lines Population. Int J Mol Sci 2019; 20:E5432. [PMID: 31683619 PMCID: PMC6862150 DOI: 10.3390/ijms20215432] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 11/25/2022] Open
Abstract
Tan spot (TS) and Septoria nodorum blotch (SNB) induced by Pyrenophora tritici-repentis and Parastagonospora nodorum, respectively, cause significant yield losses and adversely affect grain quality. The objectives of this study were to decipher the genetics and map the resistance to TS and SNB in the PBW343/Kenya Nyangumi (KN) population comprising 204 F6 recombinant inbred lines (RILs). Disease screening was performed at the seedling stage under greenhouse conditions. TS was induced by P. tritici-repentis isolate MexPtr1 while SNB by P. nodorum isolate MexSN1. Segregation pattern of the RILs indicated that resistance to TS and SNB in this population was quantitative. Diversity Array Technology (DArTs) and simple sequence repeats (SSRs) markers were used to identify the quantitative trait loci (QTL) for the diseases using inclusive composite interval mapping (ICIM). Seven significant additive QTLs for TS resistance explaining 2.98 to 23.32% of the phenotypic variation were identified on chromosomes 1A, 1B, 5B, 7B and 7D. For SNB, five QTLs were found on chromosomes 1A, 5A, and 5B, explaining 5.24 to 20.87% of the phenotypic variation. The TS QTL on 1B chromosome coincided with the pleiotropic adult plant resistance (APR) gene Lr46/Yr29/Pm39. This is the first report of the APR gene Lr46/Yr29/Pm39 contributing to TS resistance.
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Affiliation(s)
- Pawan Kumar Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México 06600, D.F., Mexico.
| | - Sukhwinder Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México 06600, D.F., Mexico.
| | - Zhiying Deng
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México 06600, D.F., Mexico.
- State Key Laboratory of Crop Biology, Cooperation Innovation Center of Efficient Production with High Annual Yield of Wheat and Corn, Shandong Agricultural University, Taian 271018, China.
| | - Xinyao He
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México 06600, D.F., Mexico.
| | - Zakaria Kehel
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México 06600, D.F., Mexico.
| | - Ravi Prakash Singh
- International Maize and Wheat Improvement Center (CIMMYT), Apdo. Postal 6-641, México 06600, D.F., Mexico.
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28
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Abstract
Genebanks are responsible for collecting, maintaining, characterizing, documenting, and distributing plant genetic resources for research, education, and breeding purposes. The rationale for requests of plant materials varies highly from areas of anthropology, social science, small-holder farmers, the commercial sector, rehabilitation of degraded systems, all the way to crop improvement and basic research. Matching "the right" accessions to a particular request is not always a straightforward process especially when genetic resource collections are large and the user does not already know which accession or even which species they want to study. Some requestors have limited knowledge of the crop; therefore, they do not know where to begin and thus, initiate the search by consultation with crop curators to help direct their request to the most suitable germplasm. One way to enhance the use of genebank material and aid in the selection of genetic resources is to have thoroughly cataloged agronomic, biochemical, genomic, and other traits linked to genebank accessions. In general, traits of importance to most users include genotypes that thrive under various biotic and abiotic stresses, morphological traits (color, shape, size of fruits), plant architecture, disease resistance, nutrient content, yield, and crop specific quality traits. In this review, we discuss methods for linking traits to genebank accessions, examples of linked traits, and some of the complexities involved, while reinforcing why it is critical to have well characterized accessions with clear trait data publicly available.
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Affiliation(s)
| | - Ahmed Amri
- ICARDA-International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Zakaria Kehel
- ICARDA-International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Dave Ellis
- CIP-International Potato Center, Lima, Peru
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29
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Visioni A, Gyawali S, Selvakumar R, Gangwar OP, Shekhawat PS, Bhardwaj SC, Al-Abdallat AM, Kehel Z, Verma RPS. Genome Wide Association Mapping of Seedling and Adult Plant Resistance to Barley Stripe Rust ( Puccinia striiformis f. sp. hordei) in India. Front Plant Sci 2018; 9:520. [PMID: 29740461 PMCID: PMC5928535 DOI: 10.3389/fpls.2018.00520] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 04/04/2018] [Indexed: 05/08/2023]
Abstract
Barley stripe rust is caused by Puccinia striiformis f.sp. hordei, (Psh), occurs worldwide, and is a major disease in South Asia. The aim of this work was to identify and estimate effects of loci underlying quantitative resistance to rust at seedling and adult plant stages. HI-AM panel of 261 barley genotypes consisting of released cultivars from North and South America, Europe, Australia, advanced breeding lines, and local landraces from ICARDA barley program were screened at seedling and adult plant stages for resistance to Psh. Seedling resistance was evaluated with the five prevalent Psh races in India. Screening for the adult plant stage resistance was also performed in two different locations by inoculating with a mixture of the five races used for seedling screeing. The panel was genotyped using DaRT-Seq high-throughput genotyping platform. The genome-wide association mapping (GWAM) showed a total of 45 QTL located across the seven barley chromosomes for seedling resistance to the five races and 18 QTL for adult plant stage resistance. Common QTL for different races at seedling stage were found on all chromosomes except on chromosome 1H. Four common QTL associated with seedling and adult plant stage resistance were found on chromosomes 2, 5, and 6H. Moreover, one of the QTL located on the long arm of chromosome 5H showed stable effects across environments for adult plant stage resistance. Several QTL identified in this study were also reported before in bi-parental and association mapping populations studies validating current GWAM. However 15 new QTL were found at adult plant stage on all chromosomes except the 4H, explaining up to 36.79% of the variance. The promising QTL detected at both stages, once validated, can be used for MAS in Psh resistance breeding program globally.
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Affiliation(s)
- Andrea Visioni
- Biodiversity and Integrated Gene Management, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
- *Correspondence: Andrea Visioni
| | - Sanjaya Gyawali
- Biodiversity and Integrated Gene Management, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
- Department of Plant Science, University of Manitoba, Winnipeg, MB, Canada
| | - Rajan Selvakumar
- Indian Institute of Wheat and Barley Research, Indian Council of Agricultural Research, Karnal, India
| | - Om P. Gangwar
- Indian Institute of Wheat and Barley Research, Indian Council of Agricultural Research, Karnal, India
| | | | - Subhash C. Bhardwaj
- Indian Institute of Wheat and Barley Research, Indian Council of Agricultural Research, Karnal, India
| | - Ayed M. Al-Abdallat
- Biodiversity and Integrated Gene Management, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
- Department of Horticulture and Crop Science, Faculty of Agriculture, The University of Jordan, Amman, Jordan
| | - Zakaria Kehel
- Biodiversity and Integrated Gene Management, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
| | - Ramesh P. S. Verma
- Biodiversity and Integrated Gene Management, International Center for Agricultural Research in the Dry Areas, Rabat, Morocco
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30
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Abstract
Climate change is projected to have a significant impact on temperature and precipitation profiles in the Mediterranean basin. The incidence and severity of drought will become commonplace and this will reduce the productivity of rain-fed crops such as durum wheat. Genetic diversity is the material basis for crop improvement and plant breeding has exploited naturally occurring variation to deliver cultivars with improved resistance to abiotic stresses. The coupling of new genomic tools, technologies, and resources with genetic approaches is essential to underpin wheat breeding through marker-assisted selection and hence mitigate climate change. Improvements in crop performance under abiotic stresses have primarily targeted yield-related traits and it is anticipated that the application of genomic technologies will introduce new target traits for consideration in wheat breeding for resistance to drought. Many traits relating to the plant's response and adaptation to drought are complex and multigenic, and quantitative genetics coupled with genomic technologies have the potential to dissect complex genetic traits and to identify regulatory loci, genes and networks. Full realization of our abilities to manipulate metabolism, transduction pathways, and transcription factors for crop improvement ultimately relies on our basic understanding of the regulation of plant networks at all levels of function.
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Affiliation(s)
- D Z Habash
- Plant Science Department, Centre for Crop Genetic Improvement, Rothamsted Research, Harpenden, Hertfordshire AL5 2JQ, UK.
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