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Merchuk-Ovnat L, Barak V, Fahima T, Ordon F, Lidzbarsky GA, Krugman T, Saranga Y. Ancestral QTL Alleles from Wild Emmer Wheat Improve Drought Resistance and Productivity in Modern Wheat Cultivars. FRONTIERS IN PLANT SCIENCE 2016; 7:452. [PMID: 27148287 PMCID: PMC4832586 DOI: 10.3389/fpls.2016.00452] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 03/22/2016] [Indexed: 05/21/2023]
Abstract
Wild emmer wheat (Triticum turgidum ssp. dicoccoides) is considered a promising source for improving stress resistances in domesticated wheat. Here we explored the potential of selected quantitative trait loci (QTLs) from wild emmer wheat, introgressed via marker-assisted selection, to enhance drought resistance in elite durum (T. turgidum ssp. durum) and bread (T. aestivum) wheat cultivars. The resultant near-isogenic lines (BC3F3 and BC3F4) were genotyped using SNP array to confirm the introgressed genomic regions and evaluated in two consecutive years under well-watered (690-710 mm) and water-limited (290-320 mm) conditions. Three of the introgressed QTLs were successfully validated, two in the background of durum wheat cv. Uzan (on chromosomes 1BL and 2BS), and one in the background of bread wheat cvs. Bar Nir and Zahir (chromosome 7AS). In most cases, the QTL x environment interaction was validated in terms of improved grain yield and biomass-specifically under drought (7AS QTL in cv. Bar Nir background), under both treatments (2BS QTL), and a greater stability across treatments (1BL QTL). The results provide a first demonstration that introgression of wild emmer QTL alleles can enhance productivity and yield stability across environments in domesticated wheat, thereby enriching the modern gene pool with essential diversity for the improvement of drought resistance.
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Affiliation(s)
- Lianne Merchuk-Ovnat
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
| | - Vered Barak
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
| | - Tzion Fahima
- Institute of Evolution and Department of Evolutionary and Environmental Biology, University of HaifaHaifa, Israel
| | - Frank Ordon
- Federal Research Centre for Cultivated Plants, Julius Kuehn-Institute, Institute for Resistance Research and Stress ToleranceQuedlinburg, Germany
| | - Gabriel A. Lidzbarsky
- Institute of Evolution and Department of Evolutionary and Environmental Biology, University of HaifaHaifa, Israel
| | - Tamar Krugman
- Institute of Evolution and Department of Evolutionary and Environmental Biology, University of HaifaHaifa, Israel
| | - Yehoshua Saranga
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of JerusalemRehovot, Israel
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Maccaferri M, El-Feki W, Nazemi G, Salvi S, Canè MA, Colalongo MC, Stefanelli S, Tuberosa R. Prioritizing quantitative trait loci for root system architecture in tetraploid wheat. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:1161-78. [PMID: 26880749 PMCID: PMC4753857 DOI: 10.1093/jxb/erw039] [Citation(s) in RCA: 101] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Optimization of root system architecture (RSA) traits is an important objective for modern wheat breeding. Linkage and association mapping for RSA in two recombinant inbred line populations and one association mapping panel of 183 elite durum wheat (Triticum turgidum L. var. durum Desf.) accessions evaluated as seedlings grown on filter paper/polycarbonate screening plates revealed 20 clusters of quantitative trait loci (QTLs) for root length and number, as well as 30 QTLs for root growth angle (RGA). Divergent RGA phenotypes observed by seminal root screening were validated by root phenotyping of field-grown adult plants. QTLs were mapped on a high-density tetraploid consensus map based on transcript-associated Illumina 90K single nucleotide polymorphisms (SNPs) developed for bread and durum wheat, thus allowing for an accurate cross-referencing of RSA QTLs between durum and bread wheat. Among the main QTL clusters for root length and number highlighted in this study, 15 overlapped with QTLs for multiple RSA traits reported in bread wheat, while out of 30 QTLs for RGA, only six showed co-location with previously reported QTLs in wheat. Based on their relative additive effects/significance, allelic distribution in the association mapping panel, and co-location with QTLs for grain weight and grain yield, the RSA QTLs have been prioritized in terms of breeding value. Three major QTL clusters for root length and number (RSA_QTL_cluster_5#, RSA_QTL_cluster_6#, and RSA_QTL_cluster_12#) and nine RGA QTL clusters (QRGA.ubo-2A.1, QRGA.ubo-2A.3, QRGA.ubo-2B.2/2B.3, QRGA.ubo-4B.4, QRGA.ubo-6A.1, QRGA.ubo-6A.2, QRGA.ubo-7A.1, QRGA.ubo-7A.2, and QRGA.ubo-7B) appear particularly valuable for further characterization towards a possible implementation of breeding applications in marker-assisted selection and/or cloning of the causal genes underlying the QTLs.
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Affiliation(s)
- Marco Maccaferri
- Department of Agricultural Sciences (DipSA), University of Bologna, 40127 Bologna, Italy
| | - Walid El-Feki
- Department of Agricultural Sciences (DipSA), University of Bologna, 40127 Bologna, Italy Department of Crop Sciences, Faculty of Agriculture, Alexandria University, 23714 Alexandria, Egypt
| | - Ghasemali Nazemi
- Department of Agricultural Sciences (DipSA), University of Bologna, 40127 Bologna, Italy Department of Agriculture, Hajiabad Branch, Islamic Azad University, 21100 Hajiabad, Iran
| | - Silvio Salvi
- Department of Agricultural Sciences (DipSA), University of Bologna, 40127 Bologna, Italy
| | - Maria Angela Canè
- Department of Agricultural Sciences (DipSA), University of Bologna, 40127 Bologna, Italy
| | - Maria Chiara Colalongo
- Department of Agricultural Sciences (DipSA), University of Bologna, 40127 Bologna, Italy
| | - Sandra Stefanelli
- Department of Agricultural Sciences (DipSA), University of Bologna, 40127 Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural Sciences (DipSA), University of Bologna, 40127 Bologna, Italy
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Perez-Lara E, Semagn K, Chen H, Iqbal M, N'Diaye A, Kamran A, Navabi A, Pozniak C, Spaner D. QTLs Associated with Agronomic Traits in the Cutler × AC Barrie Spring Wheat Mapping Population Using Single Nucleotide Polymorphic Markers. PLoS One 2016. [PMID: 27513976 DOI: 10.1371/journalpone0160623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023] Open
Abstract
We recently reported three earliness per se quantitative trait loci (QTL) associated with flowering and maturity in a recombinant inbred lines (RILs) population derived from a cross between the spring wheat (Triticum aestivum L.) cultivars 'Cutler' and 'AC Barrie' using 488 microsatellite and diversity arrays technology (DArT) markers. Here, we present QTLs associated with flowering time, maturity, plant height, and grain yield using high density single nucleotide polymorphic (SNP) markers in the same population. A mapping population of 158 RILs and the two parents were evaluated at five environments for flowering, maturity, plant height and grain yield under field conditions, at two greenhouse environments for flowering, and genotyped with a subset of 1809 SNPs out of the 90K SNP array and 2 functional markers (Ppd-D1 and Rht-D1). Using composite interval mapping on the combined phenotype data across all environments, we identified a total of 19 QTLs associated with flowering time in greenhouse (5), and field (6) conditions, maturity (5), grain yield (2) and plant height (1). We mapped these QTLs on 8 chromosomes and they individually explained between 6.3 and 37.8% of the phenotypic variation. Four of the 19 QTLs were associated with multiple traits, including a QTL on 2D associated with flowering, maturity and grain yield; two QTLs on 4A and 7A associated with flowering and maturity, and another QTL on 4D associated with maturity and plant height. However, only the QTLs on both 2D and 4D had major effects, and they mapped adjacent to well-known photoperiod response Ppd-D1 and height reducing Rht-D1 genes, respectively. The QTL on 2D reduced flowering and maturity time up to 5 days with a yield penalty of 436 kg ha-1, while the QTL on 4D reduced plant height by 13 cm, but increased maturity by 2 days. The high density SNPs allowed us to map eight moderate effect, two major effect, and nine minor effect QTLs that were not identified in our previous study using microsatellite and DArT markers. Results from this study provide additional information to wheat researchers developing early maturing and short stature spring wheat cultivars.
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Affiliation(s)
- Enid Perez-Lara
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Kassa Semagn
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Hua Chen
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Muhammad Iqbal
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
- National Institute for Genomics and Advanced Biotechnology, National Agricultural Research Centre, Park Road, Islamabad 45500, Pakistan
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Atif Kamran
- Seed Centre, Department of Botany, The University of Punjab, New Campus, Lahore, 54590, Pakistan
| | - Alireza Navabi
- Department of Plant Agriculture, Crop Science Building, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada
| | - Dean Spaner
- Department of Agricultural, Food and Nutritional Science, 4-10 Agriculture-Forestry Centre, University of Alberta, Edmonton, AB T6G 2P5, Canada
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Maccaferri M, Ricci A, Salvi S, Milner SG, Noli E, Martelli PL, Casadio R, Akhunov E, Scalabrin S, Vendramin V, Ammar K, Blanco A, Desiderio F, Distelfeld A, Dubcovsky J, Fahima T, Faris J, Korol A, Massi A, Mastrangelo AM, Morgante M, Pozniak C, N'Diaye A, Xu S, Tuberosa R. A high-density, SNP-based consensus map of tetraploid wheat as a bridge to integrate durum and bread wheat genomics and breeding. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:648-63. [PMID: 25424506 DOI: 10.1111/pbi.12288] [Citation(s) in RCA: 179] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/26/2014] [Accepted: 10/03/2014] [Indexed: 05/20/2023]
Abstract
Consensus linkage maps are important tools in crop genomics. We have assembled a high-density tetraploid wheat consensus map by integrating 13 data sets from independent biparental populations involving durum wheat cultivars (Triticum turgidum ssp. durum), cultivated emmer (T. turgidum ssp. dicoccum) and their ancestor (wild emmer, T. turgidum ssp. dicoccoides). The consensus map harboured 30 144 markers (including 26 626 SNPs and 791 SSRs) half of which were present in at least two component maps. The final map spanned 2631 cM of all 14 durum wheat chromosomes and, differently from the individual component maps, all markers fell within the 14 linkage groups. Marker density per genetic distance unit peaked at centromeric regions, likely due to a combination of low recombination rate in the centromeric regions and even gene distribution along the chromosomes. Comparisons with bread wheat indicated fewer regions with recombination suppression, making this consensus map valuable for mapping in the A and B genomes of both durum and bread wheat. Sequence similarity analysis allowed us to relate mapped gene-derived SNPs to chromosome-specific transcripts. Dense patterns of homeologous relationships have been established between the A- and B-genome maps and between nonsyntenic homeologous chromosome regions as well, the latter tracing to ancient translocation events. The gene-based homeologous relationships are valuable to infer the map location of homeologs of target loci/QTLs. Because most SNP and SSR markers were previously mapped in bread wheat, this consensus map will facilitate a more effective integration and exploitation of genes and QTL for wheat breeding purposes.
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Affiliation(s)
- Marco Maccaferri
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Andrea Ricci
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Silvio Salvi
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Sara Giulia Milner
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | - Enrico Noli
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
| | | | - Rita Casadio
- Biocomputing Group, University of Bologna, Bologna, Italy
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, Manhattan, KS, USA
| | - Simone Scalabrin
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | - Vera Vendramin
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | | | - Antonio Blanco
- Dipartimento di Biologia e Chimica Agro-forestale ed ambientale, Università di Bari, Aldo Moro, Bari, Italy
| | - Francesca Desiderio
- Consiglio per la ricerca e la sperimentazione in agricoltura, Genomics Research Centre, Fiorenzuola d'Arda, Italy
| | - Assaf Distelfeld
- Faculty of Life Sciences, Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, Israel
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA
- Howard Hughes Medical Institute, Chevy Chase, MD, USA
| | - Tzion Fahima
- Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel
| | - Justin Faris
- USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA
| | - Abraham Korol
- Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Haifa, Israel
| | - Andrea Massi
- Società Produttori Sementi Bologna (PSB), Argelato, Italy
| | - Anna Maria Mastrangelo
- Consiglio per la ricerca e la sperimentazione in agricoltura, Cereal Research Centre, Foggia, Italy
| | - Michele Morgante
- Istituto di Genomica Applicata, Udine, Italy
- Dipartimento di Scienze Agrarie e Ambientali, University of Udine, Udine, Italy
| | - Curtis Pozniak
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Amidou N'Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
| | - Steven Xu
- USDA-ARS Cereal Crops Research Unit, Fargo, ND, USA
| | - Roberto Tuberosa
- Department of Agricultural Sciences (DipSA), University of Bologna, Bologna, Italy
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Canè MA, Maccaferri M, Nazemi G, Salvi S, Francia R, Colalongo C, Tuberosa R. Association mapping for root architectural traits in durum wheat seedlings as related to agronomic performance. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2014; 34:1629-1645. [PMID: 25506257 PMCID: PMC4257993 DOI: 10.1007/s11032-014-0177-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 10/08/2014] [Indexed: 05/18/2023]
Abstract
Association mapping provides useful insights on the genetic architecture of quantitative traits across a large number of unrelated genotypes, which in turn allows an informed choice of the lines to be crossed for a more accurate characterization of major QTLs in a biparental genetic background. In this study, seedlings of 183 durum wheat elite accessions were evaluated in order to identify QTLs for root system architecture (RSA). The QTLs identified were compared with QTLs detected for grain yield and its component traits, plant height and peduncle length measured in a previous study where the same accessions were evaluated in 15 field trials with a broad range of soil moisture availability and productivity (Maccaferri et al. in J Exp Bot 62:409-438, 2011). The following RSA features were investigated in seedlings at the four-leaf stage: seminal root angle, primary root length, total root length, average root length, root number and shoot length. Highly significant differences among accessions were detected for all traits. The highest repeatability (h2 = 0.72) was observed for seminal root angle. Out of the 48 QTLs detected for RSA, 15 overlapped with QTLs for agronomic traits and/or grain yield in two or more environments. The congruency of the effects of RSA traits and agronomic traits was evaluated. Seminal root angle and root number appear the most promising traits for further studies on the adaptive role of RSA plasticity on field performance in environments differing for water availability. Our results provide novel insights on the genetic control of RSA and its implications on field performance of durum wheat.
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Affiliation(s)
- Maria Angela Canè
- Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Marco Maccaferri
- Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Ghasemali Nazemi
- Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
- Department of Plant Production, I.A.U. Haji abad Branch, Haji abad, Iran
| | - Silvio Salvi
- Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Rossella Francia
- Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Chiara Colalongo
- Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
| | - Roberto Tuberosa
- Department of Agricultural Sciences (DipSA), University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
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