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Gene Duplication and Its Contribution to Wheat Domestication and Improvement

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A special issue of Plants (ISSN 2223-7747). This special issue belongs to the section "Plant Genetics, Genomics and Biotechnology".

Deadline for manuscript submissions: closed (31 July 2023) | Viewed by 6126

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Special Issue Editors

Dr. Xiuying Kong

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Guest Editor

Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: genomic and functional genomic studies in wheat

Prof. Jizeng Jia

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Guest Editor

Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
Interests: wheat;genetics;genomics;gene cloning
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Special Issue Information

Dear Colleagues,

Gene duplication is a prevalent phenomenon in plants and a driving force for evolution and adaptation. Wheat is a worldwide allopolyploid crop and comprises A, B, and D subgenomes. Besides its economic importance, it is also considered to be a model plant to study gene duplication. However, due to the lack of a high-quality wheat reference genome sequence, genome-wide analysis of gene duplication is facing great challenges. In recent years, a batch of wheat genome sequences, specifically high-quality reference genomes and pan-genome, have become available. These resources give us the opportunity to gain insights into duplicate genes in wheat. This Special Issue of Plants will highlight gene duplication, evolution, divergence, and its impacts on wheat domestication and improvement. These insights will not only benefit wheat research but also accelerate the study of gene duplication in other crops.

Dr. Xiuying Kong
Prof. Jizeng Jia
Guest Editors

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Keywords

wheat
gene duplication
evolution
divergence
impacts

Published Papers (4 papers)

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Research

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22 pages, 6884 KiB

Open AccessFeature PaperArticle

Comparative Analysis Reveals Different Evolutionary Fates and Biological Functions in Wheat Duplicated Genes (Triticum aestivum L.)

by Licao Cui, Hao Cheng, Zhe Yang, Chuan Xia, Lichao Zhang and Xiuying Kong

Plants 2023, 12(17), 3021; https://doi.org/10.3390/plants12173021 - 22 Aug 2023

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Abstract

Wheat (Triticum aestivum L.) is a staple food crop that provides 20% of total human calorie consumption. Gene duplication has been considered to play an important role in evolution by providing new genetic resources. However, the evolutionary fates and biological functions of the duplicated genes in wheat remain to be elucidated. In this study, the resulting data showed that the duplicated genes evolved faster with shorter gene lengths, higher codon usage bias, lower expression levels, and higher tissue specificity when compared to non-duplicated genes. Our analysis further revealed functions of duplicated genes in various biological processes with significant enrichment to environmental stresses. In addition, duplicated genes derived from dispersed, proximal, tandem, transposed, and whole-genome duplication differed in abundance, evolutionary rate, gene compactness, expression pattern, and genetic diversity. Tandem and proximal duplicates experienced stronger selective pressure and showed a more compact gene structure with diverse expression profiles than other duplication modes. Moreover, genes derived from different duplication modes showed an asymmetrical evolutionary pattern for wheat A, B, and D subgenomes. Several candidate duplication hotspots associated with wheat domestication or polyploidization were characterized as potential targets for wheat molecular breeding. Our comprehensive analysis revealed the evolutionary trajectory of duplicated genes and laid the foundation for future functional studies on wheat. Full article

(This article belongs to the Special Issue Gene Duplication and Its Contribution to Wheat Domestication and Improvement)

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25 pages, 5458 KiB

Open AccessArticle

Insights into the Bioinformatics and Transcriptional Analysis of the Elongator Complexes (ELPs) Gene Family of Wheat: TaELPs Contribute to Wheat Abiotic Stress Tolerance and Leaf Senescence

by Feng Guo, Md Ashraful Islam, Chenxu Lv, Xiujuan Jin, Lili Sun, Kai Zhao, Juan Lu, Rongyue Yan, Wenjun Zhang, Yugang Shi, Ning Li and Daizhen Sun

Plants 2023, 12(4), 952; https://doi.org/10.3390/plants12040952 - 20 Feb 2023

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Abstract

Elongator complexes (ELPs) are the protein complexes that promote transcription through histone acetylation in eukaryotic cells and interact with elongating RNA polymerase II (RNAPII). ELPs’ role in plant growth and development, signal transduction, and response to biotic and abiotic stresses have been confirmed in model plants. However, the functions of the wheat ELP genes are not well documented. The present study identified 18 members of the ELPs from the wheat genome with a homology search. Further, bioinformatics and transcription patterns in response to different stress conditions were analyzed to dissect their potential regulatory mechanisms in wheat. Gene duplication analysis showed that 18 pairs of ELP paralogous genes were derived from segmental duplication, which was divided into six clades by protein phylogenetic and cluster analysis. The orthologous analysis of wheat TaELP genes showed that TaELP genes may have evolved from orthologous genes of other plant species or closely related plants. Moreover, a variety of cis-acting regulatory elements (CAREs) related to growth and development, hormone response, and biotic and abiotic stresses were identified in the TaELPs’ promoter regions. The qRT-PCR analysis showed that the transcription of TaELPs was induced under hormone, salt, and drought stress and during leaf senescence. The TaELP2 gene was silenced with BSMV-VIGS, and TaELP2 was preliminarily verified to be involved in the regulation of wheat leaf senescence. Overall, TaELP genes might be regulated by hormone signaling pathways and response to abiotic stress and leaf senescence, which could be investigated further as potential candidate genes for wheat abiotic stress tolerance and yield improvement. Full article

(This article belongs to the Special Issue Gene Duplication and Its Contribution to Wheat Domestication and Improvement)

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Review

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13 pages, 1151 KiB

Open AccessReview

Contribution of Duplicated Nucleotide-Binding Leucine-Rich Repeat (NLR) Genes to Wheat Disease Resistance

by Yongchao Hao, Yinghua Pan, Wuying Chen, Muhammad Abdul Rehman Rashid, Mengyao Li, Naixiu Che, Xu Duan and Yan Zhao

Plants 2023, 12(15), 2794; https://doi.org/10.3390/plants12152794 - 27 Jul 2023

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Abstract

Wheat has a large and diverse repertoire of NLRs involved in disease resistance, with over 1500 NLRs detected in some studies. These NLR genes occur as singletons or clusters containing copies of NLRs from different phylogenetic clades. The number of NLRs and cluster size can differ drastically among ecotypes and cultivars. Primarily, duplication has led to the evolution and diversification of NLR genes. Among the various mechanisms, whole genome duplication (WGD) is the most intense and leading cause, contributing to the complex evolutionary history and abundant gene set of hexaploid wheat. Tandem duplication or recombination is another major mechanism of NLR gene expansion in wheat. The diversity and divergence of duplicate NLR genes are responsible for the broad-spectrum resistance of most plant species with limited R genes. Understanding the mechanisms underlying the rapid evolution and diversification of wheat NLR genes will help improve disease resistance in crops. The present review focuses on the diversity and divergence of duplicate NLR genes and their contribution to wheat disease resistance. Moreover, we provide an overview of disease resistance-associated gene duplication and the underlying strategies in wheat. Full article

(This article belongs to the Special Issue Gene Duplication and Its Contribution to Wheat Domestication and Improvement)

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Graphical abstract

21 pages, 1092 KiB

Open AccessReview

Duplicate Genes Contribute to Variability in Abiotic Stress Resistance in Allopolyploid Wheat

by Linying Du, Zhenbing Ma and Hude Mao

Plants 2023, 12(13), 2465; https://doi.org/10.3390/plants12132465 - 28 Jun 2023

Cited by 1 | Viewed by 1459

Abstract

Gene duplication is a universal biological phenomenon that drives genomic variation and diversity, plays a crucial role in plant evolution, and contributes to innovations in genetic engineering and crop development. Duplicated genes participate in the emergence of novel functionality, such as adaptability to new or more severe abiotic stress resistance. Future crop research will benefit from advanced, mechanistic understanding of the effects of gene duplication, especially in the development and deployment of high-performance, stress-resistant, elite wheat lines. In this review, we summarize the current knowledge of gene duplication in wheat, including the principle of gene duplication and its effects on gene function, the diversity of duplicated genes, and how they have functionally diverged. Then, we discuss how duplicated genes contribute to abiotic stress response and the mechanisms of duplication. Finally, we have a future prospects section that discusses the direction of future efforts in the short term regarding the elucidation of replication and retention mechanisms of repetitive genes related to abiotic stress response in wheat, excellent gene function research, and practical applications. Full article

(This article belongs to the Special Issue Gene Duplication and Its Contribution to Wheat Domestication and Improvement)

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