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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. JOURNAL OF EXPERIMENTAL BOTANY 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] [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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Taranto F, Esposito S, De Vita P. Genomics for Yield and Yield Components in Durum Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:2571. [PMID: 37447132 DOI: 10.3390/plants12132571] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
In recent years, many efforts have been conducted to dissect the genetic basis of yield and yield components in durum wheat thanks to linkage mapping and genome-wide association studies. In this review, starting from the analysis of the genetic bases that regulate the expression of yield for developing new durum wheat varieties, we have highlighted how, currently, the reductionist approach, i.e., dissecting the yield into its individual components, does not seem capable of ensuring significant yield increases due to diminishing resources, land loss, and ongoing climate change. However, despite the identification of genes and/or chromosomal regions, controlling the grain yield in durum wheat is still a challenge, mainly due to the polyploidy level of this species. In the review, we underline that the next-generation sequencing (NGS) technologies coupled with improved wheat genome assembly and high-throughput genotyping platforms, as well as genome editing technology, will revolutionize plant breeding by providing a great opportunity to capture genetic variation that can be used in breeding programs. To date, genomic selection provides a valuable tool for modeling optimal allelic combinations across the whole genome that maximize the phenotypic potential of an individual under a given environment.
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Affiliation(s)
- Francesca Taranto
- Institute of Biosciences and Bioresources (CNR-IBBR), 70126 Bari, Italy
| | - Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA-Council for Agricultural Research and Economics, 71122 Foggia, Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA-Council for Agricultural Research and Economics, 71122 Foggia, Italy
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Esposito S, Taranto F, Vitale P, Ficco DBM, Colecchia SA, Stevanato P, De Vita P. Unlocking the molecular basis of wheat straw composition and morphological traits through multi-locus GWAS. BMC PLANT BIOLOGY 2022; 22:519. [PMID: 36344939 PMCID: PMC9641881 DOI: 10.1186/s12870-022-03900-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 10/21/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Rapid reductions in emissions from fossil fuel burning are needed to curb global climate change. Biofuel production from crop residues can contribute to reducing the energy crisis and environmental deterioration. Wheat is a renewable source for biofuels owing to the low cost and high availability of its residues. Thus, identifying candidate genes controlling these traits is pivotal for efficient biofuel production. Here, six multi-locus genome-wide association (ML-GWAS) models were applied using 185 tetraploid wheat accessions to detect quantitative trait nucleotides (QTNs) for fifteen traits associated with biomass composition. RESULTS Among the 470 QTNs, only 72 identified by at least two models were considered as reliable. Among these latter, 16 also showed a significant effect on the corresponding trait (p.value < 0.05). Candidate genes survey carried out within 4 Mb flanking the QTNs, revealed putative biological functions associated with lipid transfer and metabolism, cell wall modifications, cell cycle, and photosynthesis. Four genes encoded as Cellulose Synthase (CeSa), Anaphase promoting complex (APC/C), Glucoronoxylan 4-O Methyltransferase (GXM) and HYPONASTIC LEAVES1 (HYL1) might be responsible for an increase in cellulose, and natural and acid detergent fiber (NDF and ADF) content in tetraploid wheat. In addition, the SNP marker RFL_Contig3228_2154 associated with the variation in stem solidness (Q.Scsb-3B) was validated through two molecular methods (High resolution melting; HRM and RNase H2-dependent PCR; rhAMP). CONCLUSIONS The study provides new insights into the genetic basis of biomass composition traits on tetraploid wheat. The application of six ML-GWAS models on a panel of diverse wheat genotypes represents an efficient approach to dissect complex traits with low heritability such as wheat straw composition. The discovery of genes/genomic regions associated with biomass production and straw quality parameters is expected to accelerate the development of high-yielding wheat varieties useful for biofuel production.
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Affiliation(s)
- Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, 71122 Foggia, Italy
| | - Francesca Taranto
- Institute of Biosciences and Bioresources, (CNR-IBBR), 70126 Bari, Italy
| | - Paolo Vitale
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, 71122 Foggia, Italy
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, 71122 Foggia, Italy
| | - Donatella Bianca Maria Ficco
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, 71122 Foggia, Italy
| | - Salvatore Antonio Colecchia
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, 71122 Foggia, Italy
| | - Piergiorgio Stevanato
- Department of Agronomy, Food, Natural Resources, Animals and Environment, University of Padova, 35020 Padova, Legnaro Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA - Council for Agricultural Research and Economics, 71122 Foggia, Italy
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High-Density Linkage Mapping of Agronomic Trait QTLs in Wheat under Water Deficit Condition using Genotyping by Sequencing (GBS). PLANTS 2022; 11:plants11192533. [PMID: 36235399 PMCID: PMC9571144 DOI: 10.3390/plants11192533] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/05/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022]
Abstract
Improvement of grain yield is the ultimate goal for wheat breeding under water-limited environments. In the present study, a high-density linkage map was developed by using genotyping-by-sequencing (GBS) of a recombinant inbred line (RIL) population derived from the cross between Iranian landrace #49 and cultivar Yecora Rojo. The population was evaluated in three locations in Iran during two years under irrigated and water deficit conditions for the agronomic traits grain yield (GY), plant height (PH), spike number per square meter (SM), 1000 kernel weight (TKW), grain number per spike (GNS), spike length (SL), biomass (BIO) and harvest index (HI). A linkage map was constructed using 5831 SNPs assigned to 21 chromosomes, spanning 3642.14 cM of the hexaploid wheat genome with an average marker density of 0.62 (markers/cM). In total, 85 QTLs were identified on 19 chromosomes (all except 5D and 6D) explaining 6.06–19.25% of the traits phenotypic variance. We could identify 20 novel QTLs explaining 8.87–19.18% of phenotypic variance on chromosomes 1A, 1B, 1D, 2B, 3A, 3B, 6A, 6B and 7A. For 35 out of 85 mapped QTLs functionally annotated genes were identified which could be related to a potential role in drought stress.
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Esposito S, D'Agostino N, Taranto F, Sonnante G, Sestili F, Lafiandra D, De Vita P. Whole-exome sequencing of selected bread wheat recombinant inbred lines as a useful resource for allele mining and bulked segregant analysis. Front Genet 2022; 13:1058471. [PMID: 36482886 PMCID: PMC9723387 DOI: 10.3389/fgene.2022.1058471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 11/07/2022] [Indexed: 03/22/2023] Open
Abstract
Although wheat (Triticum aestivum L.) is the main staple crop in the world and a major source of carbohydrates and proteins, functional genomics and allele mining are still big challenges. Given the advances in next-generation sequencing (NGS) technologies, the identification of causal variants associated with a target phenotype has become feasible. For these reasons, here, by combining sequence capture and target-enrichment methods with high-throughput NGS re-sequencing, we were able to scan at exome-wide level 46 randomly selected bread wheat individuals from a recombinant inbred line population and to identify and classify a large number of single nucleotide polymorphisms (SNPs). For technical validation of results, eight randomly selected SNPs were converted into Kompetitive Allele-Specific PCR (KASP) markers. This resource was established as an accessible and reusable molecular toolkit for allele data mining. The dataset we are making available could be exploited for novel studies on bread wheat genetics and as a foundation for starting breeding programs aimed at improving different key agronomic traits.
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Affiliation(s)
- Salvatore Esposito
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA-Council for Agricultural Research and Economics, Foggia, Italy
| | - Nunzio D'Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | | | | | - Francesco Sestili
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Viterbo, Italy
| | - Domenico Lafiandra
- Department of Agriculture and Forest Sciences (DAFNE), University of Tuscia, Viterbo, Italy
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), CREA-Council for Agricultural Research and Economics, Foggia, Italy
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