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Miazzi MM, Babay E, De Vita P, Montemurro C, Chaabane R, Taranto F, Mangini G. Comparative Genetic Analysis of Durum Wheat Landraces and Cultivars Widespread in Tunisia. Front Plant Sci 2022; 13:939609. [PMID: 35909756 PMCID: PMC9326505 DOI: 10.3389/fpls.2022.939609] [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: 05/09/2022] [Accepted: 06/06/2022] [Indexed: 06/15/2023]
Abstract
The durum wheat (Triticum turgidum L. ssp. durum Desf.) landraces constitute a useful natural germplasm to increase the genetic diversity in the modern durum cultivars. The Tunisian durum germplasm constitutes 28 accessions conserved in Genebank of Tunisia, which are still unexplored. In this study, a comparative genetic analysis was performed to investigate the relationships between the Tunisian durum lines and the modern cultivars and detect divergent loci involved in breeding history. The genetic diversity analyses carried out using nine morphological descriptors and the 25K single-nucleotide polymorphism (SNP) array allowed us to distinguish two groups of Tunisian landraces and one of durum cultivars. The analysis of molecular variance and diversity indices confirmed the genetic variability among the groups. A total of 529 SNP loci were divergent between Tunisian durum landraces and modern cultivars. Candidate genes related to plant and spike architecture, including FLOWERING LOCUS T (FT-B1), zinc finger CONSTANS, and AP2/EREBPs transcription factors, were identified. In addition, divergent genes involved in grain composition and biotic stress nucleotide-binding site and leucine-reach repeats proteins and disease resistance proteins (NBS-LRR and RPM) were found, suggesting that the Tunisian durum germplasm may represent an important source of favorable alleles to be used in future durum breeding programs for developing well-adapted and resilient cultivars.
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Affiliation(s)
- Monica Marilena Miazzi
- Department of Soil, Plant and Food Sciences (DiSSPA), Section Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
| | - Elyes Babay
- National Gene Bank of Tunisia (BNG), Tunis, Tunisia
- Agricultural Applied Biotechnology Laboratory (LR16INRAT06), Institut National de la Recherche Agronomique de Tunisie (INRAT), University of Carthage, Tunis, Tunisia
| | - Pasquale De Vita
- Research Centre for Cereal and Industrial Crops (CREA-CI), Foggia, Italy
| | - Cinzia Montemurro
- Department of Soil, Plant and Food Sciences (DiSSPA), Section Genetics and Plant Breeding, University of Bari Aldo Moro, Bari, Italy
- Spin Off Sinagri s.r.l., University of Bari Aldo Moro, Bari, Italy
- Support Unit Bari, Institute for Sustainable Plant Protection, National Research Council of Italy (IPSP-CNR), Bari, Italy
| | - Ramzi Chaabane
- National Gene Bank of Tunisia (BNG), Tunis, Tunisia
- Agricultural Applied Biotechnology Laboratory (LR16INRAT06), Institut National de la Recherche Agronomique de Tunisie (INRAT), University of Carthage, Tunis, Tunisia
| | - Francesca Taranto
- Institute of Biosciences and Bioresources, National Research Council of Italy (IBBR-CNR), Bari, Italy
| | - Giacomo Mangini
- Institute of Biosciences and Bioresources, National Research Council of Italy (IBBR-CNR), Bari, Italy
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Zhang J, Xiong H, Guo H, Li Y, Xie X, Xie Y, Zhao L, Gu J, Zhao S, Ding Y, Liu L. Identification of the Q Gene Playing a Role in Spike Morphology Variation in Wheat Mutants and Its Regulatory Network. Front Plant Sci 2022; 12:807731. [PMID: 35087560 PMCID: PMC8787668 DOI: 10.3389/fpls.2021.807731] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/13/2021] [Indexed: 05/27/2023]
Abstract
The wheat AP2 family gene Q controls domestication traits, including spike morphology and threshability, which are critical for the widespread cultivation and yield improvement of wheat. Although many studies have investigated the molecular mechanisms of the Q gene, its direct target genes, especially those controlling spike morphology, are not clear, and its regulatory pathways are not well established. In this study, we conducted gene mapping of a wheat speltoid spike mutant and found that a new allele of the Q gene with protein truncation played a role in spike morphology variation in the mutant. Dynamic expression levels of the Q gene throughout the spike development process suggested that the transcript abundances of the mutant were decreased at the W6 and W7 scales compared to those of the WT. We identified several mutation sites on the Q gene and showed that mutations in different domains resulted in distinct phenotypes. In addition, we found that the Q gene produced three transcripts via alternative splicing and that they exhibited differential expression patterns in nodes, internodes, flag leaves, and spikes. Finally, we identified several target genes directly downstream of Q, including TaGRF1-2D and TaMGD-6B, and proposed a possible regulatory network. This study uncovered the target genes of Q, and the results can help to clarify the mechanism of wheat spike morphology and thereby improve wheat grain yield.
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Sakai Y, Cao L, Funata R, Shiraishi T, Yoshikawa K, Maeno K, Miura H, Onishi K. QTLs for agronomic traits detected in recombinant inbred lines derived from a bread wheat × spelt cross. Breed Sci 2018; 68:587-595. [PMID: 30697120 PMCID: PMC6345227 DOI: 10.1270/jsbbs.18046] [Citation(s) in RCA: 2] [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] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 09/06/2018] [Indexed: 06/09/2023]
Abstract
Spelt wheat (Triticum aestivum subsp. spelta), a subspecies of common wheat, is a genetic resource for the breeding of bread wheat (T. aestivum subsp. aestivum); however, genetic analyses of agronomic traits in bread wheat × spelt crosses are insufficient. Here, we conducted QTL analysis in the recombinant inbred lines from a bread wheat × spelt cross. In addition to the major Q locus, QSpd.obu-4D was detected with the spelt allele conferring a higher spikelet density than the bread wheat allele. The effect of QSpd.obu-4D was evident in the presence of the Q allele of bread wheat, suggesting that this variation might be cryptic in spelt wheat with the q allele. Two QTLs with stable effects were identified for grain length, one of which (QGl.obu-1A) has never been detected in a bread wheat × spelt cross. The spelt wheat allele at QHt.obu-7B conferring later heading was identified in the Vrn-B3 region and could be a novel gene source for modifying heading time. Furthermore, QGi.obu-2B, responsible for low grain dormancy of spelt wheat, was detected. Further exploration and identification of useful QTLs could accelerate the utilization of spelt wheat as a genetic resource for bread wheat breeding programs.
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Affiliation(s)
- Yuki Sakai
- Obihiro University of Agriculture and Veterinary Medicine,
Hokkaido 080-8555,
Japan
| | - Liangzi Cao
- Obihiro University of Agriculture and Veterinary Medicine,
Hokkaido 080-8555,
Japan
- The United Graduate School of Agricultural Sciences, Iwate University,
Iwate 020-8550,
Japan
- Institute of Crop Cultivation and Tillage, Heilongjiang Academy of Agricultural Sciences,
Heilongjiang 150086,
China
| | - Ryosuke Funata
- Obihiro University of Agriculture and Veterinary Medicine,
Hokkaido 080-8555,
Japan
| | - Takatou Shiraishi
- Obihiro University of Agriculture and Veterinary Medicine,
Hokkaido 080-8555,
Japan
| | - Koki Yoshikawa
- Obihiro University of Agriculture and Veterinary Medicine,
Hokkaido 080-8555,
Japan
| | - Kohei Maeno
- Obihiro University of Agriculture and Veterinary Medicine,
Hokkaido 080-8555,
Japan
| | - Hideho Miura
- Obihiro University of Agriculture and Veterinary Medicine,
Hokkaido 080-8555,
Japan
| | - Kazumitsu Onishi
- Obihiro University of Agriculture and Veterinary Medicine,
Hokkaido 080-8555,
Japan
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Guo Z, Chen D, Alqudah AM, Röder MS, Ganal MW, Schnurbusch T. Genome-wide association analyses of 54 traits identified multiple loci for the determination of floret fertility in wheat. New Phytol 2017; 214:257-270. [PMID: 27918076 DOI: 10.1111/nph.14342] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/17/2016] [Indexed: 05/18/2023]
Abstract
Increasing grain yield is still the main target of wheat breeding; yet today's wheat plants utilize less than half of their yield potential. Owing to the difficulty of determining grain yield potential in a large population, few genetic factors regulating floret fertility (i.e. the difference between grain yield potential and grain number) have been reported to date. In this study, we conducted a genome-wide association study (GWAS) by quantifying 54 traits (16 floret fertility traits and 38 traits for assimilate partitioning and spike morphology) in 210 European winter wheat accessions. The results of this GWAS experiment suggested potential associations between floret fertility, assimilate partitioning and spike morphology revealed by shared quantitative trait loci (QTLs). Several candidate genes involved in carbohydrate metabolism, phytohormones or floral development colocalized with such QTLs, thereby providing potential targets for selection. Based on our GWAS results we propose a genetic network underlying floret fertility and related traits, nominating determinants for improved yield performance.
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Affiliation(s)
- Zifeng Guo
- Independent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Stadt Seeland, OT Gatersleben, Germany
| | - Dijun Chen
- Research Group Image Analysis, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Stadt Seeland, OT Gatersleben, Germany
| | - Ahmad M Alqudah
- Independent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Stadt Seeland, OT Gatersleben, Germany
| | - Marion S Röder
- Research Group Gene and Genome Mapping, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Stadt Seeland, OT Gatersleben, Germany
| | - Martin W Ganal
- TraitGenetics GmbH, 06466, Stadt Seeland, OT Gatersleben, Germany
| | - Thorsten Schnurbusch
- Independent HEISENBERG Research Group Plant Architecture, Leibniz Institute of Plant Genetics and Crop Plant Research, 06466, Stadt Seeland, OT Gatersleben, Germany
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Zhai H, Feng Z, Li J, Liu X, Xiao S, Ni Z, Sun Q. QTL Analysis of Spike Morphological Traits and Plant Height in Winter Wheat ( Triticum aestivum L.) Using a High-Density SNP and SSR-Based Linkage Map. Front Plant Sci 2016; 7:1617. [PMID: 27872629 PMCID: PMC5097907 DOI: 10.3389/fpls.2016.01617] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2016] [Accepted: 10/12/2016] [Indexed: 05/18/2023]
Abstract
Wheat yield can be enhanced by modifying the spike morphology and the plant height. In this study, a population of 191 F9 recombinant inbred lines (RILs) was developed from a cross between two winter cultivars Yumai 8679 and Jing 411. A dense genetic linkage map with 10,816 markers was constructed by incorporating single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) marker information. Five spike morphological traits and plant height were evaluated under nine environments for the RILs and parental lines, and the number of detected environmentally stable QTLs were 18 and three, respectively. The 1RS/1BL (rye) translocation increased both spike length and spikelet number with constant spikelet compactness. The QPht.cau-2D.1 was identical to gene Rht8, which decreased spike length without modifying spikelet number. Notably, four novel QTLs locating on chromosomes 1AS (QSc.cau-1A.1), 2DS (QSc.cau-2D.1), and 7BS (QSl.cau-7B.1 and QSl.cau-7B.2) were firstly identified in this study, which provide further insights into the genetic factors that shaped the spike morphology in wheat. Moreover, SNP markers tightly linked to previously reported QTLs will eventually facilitate future studies including their positional cloning or marker-assisted selection.
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Affiliation(s)
- Huijie Zhai
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Plant Gene Research CentreBeijing, China
| | - Zhiyu Feng
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Plant Gene Research CentreBeijing, China
| | - Jiang Li
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Plant Gene Research CentreBeijing, China
| | - Xinye Liu
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Plant Gene Research CentreBeijing, China
| | - Shihe Xiao
- Institute of Crop Science, Chinese Academy of Agricultural SciencesBeijing, China
| | - Zhongfu Ni
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Plant Gene Research CentreBeijing, China
- *Correspondence: Zhongfu Ni
| | - Qixin Sun
- State Key Laboratory for Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityBeijing, China
- National Plant Gene Research CentreBeijing, China
- Qixin Sun
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