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Song B, Ning W, Wei D, Jiang M, Zhu K, Wang X, Edwards D, Odeny DA, Cheng S. Plant genome resequencing and population genomics: Current status and future prospects. MOLECULAR PLANT 2023; 16:1252-1268. [PMID: 37501370 DOI: 10.1016/j.molp.2023.07.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 05/30/2023] [Accepted: 07/25/2023] [Indexed: 07/29/2023]
Abstract
Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.
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Affiliation(s)
- Bo Song
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
| | - Weidong Ning
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; Huazhong Agricultural University, College of Informatics, Hubei Key Laboratory of Agricultural Bioinformatics, Wuhan, Hubei, China
| | - Di Wei
- Biotechnology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 53007, China
| | - Mengyun Jiang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Kun Zhu
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - Xingwei Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China; State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng 475004, China; Shenzhen Research Institute of Henan University, Shenzhen 518000, China
| | - David Edwards
- School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT) - Eastern and Southern Africa, Nairobi, Kenya
| | - Shifeng Cheng
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China.
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Bokaei AS, Sofalian O, Sorkhilalehloo B, Asghari A, Pour-Aboughadareh A. Deciphering the level of genetic diversity in some aegilops species using CAAT box-derived polymorphism (CBDP) and start codon target polymorphism (SCoT) markers. Mol Biol Rep 2023:10.1007/s11033-023-08488-0. [PMID: 37219668 DOI: 10.1007/s11033-023-08488-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 04/26/2023] [Indexed: 05/24/2023]
Abstract
BACKGROUND Maintaining genetic diversity is of the most essential principle for a long-term conservation of plant genetic resources and could play a crucial role in their management. The genus Aegilops is one important member of wheat germplasm, and there are evidences that novel genes of this genus' species can be studied/utilized as ideal sources for the wheat cultivar improvement. The objective of this study was to dissect the genetic diversity and population structure among a set of Iranian Aegilops using two gene-based molecular markers. METHODS AND RESULTS This study investigated the level of genetic diversity among 157 Aegilops accessions consisting of Ae. tauschii Coss. (DD genome), Ae. crassa Boiss. (DDMM genome), and Ae. cylindrica Host. (CCDD genome) belonging to NPGBI using two sets of CBDP and SCoT markers. The SCoT and CBDP primers yielded 171 and 174 fragments, out of which 145 (90.23%) and 167 (97.66%) fragments were polymorphic, respectively. The average of polymorphism information content (PIC)/ marker index (MI)/resolving power (Rp) for SCoT and CBDP markers were 0.32/3.59/16.03 and 0.29/3.01/16.26, respectively. Results of AMOVA revealed the genetic variability within species was greater than the variation observed among them (SCoT: 88% vs. 12%; CBDP: 72% vs. 28%; SCoT + CBDP: 80% vs. 20%). Based on the information obtained from both markers, the higher level of genetic diversity was found in Ae. tauschii as compared to other species. The grouping patterns obtained by Neighbor-joining algorithms, principal coordinate analysis (PCoA), and Bayesian-model-based structure were consistent with each other and resulted in grouping all studied accessions according to their genomic constitutions. CONCLUSION The results of this study revealed a high level of genetic diversity among Iranian Aegilops germplasm. Moreover, SCoT and CBDP marker systems were efficient in deciphering DNA polymorphism and classification of Aegilops germplasm.
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Affiliation(s)
- Ali Sajjad Bokaei
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Omid Sofalian
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Behzad Sorkhilalehloo
- Seed and Plant Improvement Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran
| | - Ali Asghari
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Alireza Pour-Aboughadareh
- Seed and Plant Improvement Institute, Agricultural Research Education and Extension Organization (AREEO), Karaj, Iran.
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Li S, Li X, Li S, Liu Y, Zang T, Hao M, Zhang L, Huang L, Jiang B, Yuan Z, Chen X, Chen X, Liu D, Ning S. Variation in the tonoplast cadmium transporter heavy metal ATPase 3 (HMA3) homolog gene in Aegilops tauschii. PLoS One 2023; 18:e0279707. [PMID: 36867624 PMCID: PMC9983875 DOI: 10.1371/journal.pone.0279707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 12/13/2022] [Indexed: 03/04/2023] Open
Abstract
The functionality of HMA3 is a key determinant controlling Cd accumulation in the shoots and grains of plants. Wild relatives of modern crop plants can serve as sources of valuable genetic variation for various traits. Here, resequencing of HMA3 homoeologous genes from Aegilops tauschii (the donor of the wheat D genome) was carried out to identify natural variation at both the nucleotide and polypeptide levels. HMA3 homoeologs are highly conserved, and 10 haplotypes were revealed based on 19 single nucleotide polymorphisms (eight induced single amino acid residue substitutions, including 2 altered amino acids in transmembrane domains) in 80 widely distributed Ae. tauschii accessions. The results provide genetic resources for low/no Cd concentration wheat improvement.
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Affiliation(s)
- Shengke Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiao Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shijie Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yu’e Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Tianqing Zang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lin Huang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xuejiao Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xue Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, Sichuan, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Shunzong Ning
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
- * E-mail:
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Li Y, Zhang Y, Luo H, Lv D, Yi Z, Duan M, Deng M. WGCNA Analysis Revealed the Hub Genes Related to Soil Cadmium Stress in Maize Kernel ( Zea mays L.). Genes (Basel) 2022; 13:2130. [PMID: 36421805 PMCID: PMC9690088 DOI: 10.3390/genes13112130] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/07/2022] [Accepted: 11/13/2022] [Indexed: 01/12/2024] Open
Abstract
Soil contamination by heavy metals has become a prevalent topic due to their widespread release from industry, agriculture, and other human activities. Great progress has been made in elucidating the uptake and translocation of cadmium (Cd) accumulation in rice. However, there is still little known about corresponding progress in maize. In the current study, we performed a comparative RNA-Seq-based approach to identify differentially expressed genes (DEGs) of maize immature kernel related to Cd stress. In total, 55, 92, 22, and 542 DEGs responsive to high cadmium concentration soil were identified between XNY22-CHS-8 vs. XNY22-YA-8, XNY22-CHS-24 vs. XNY22-YA-24, XNY27-CHS-8 vs. XNY27-YA-8, and XNY27-CHS-24 vs. XNY27-YA-24, respectively. The weighted gene co-expression network analysis (WGCNA) categorized the 9599 Cd stress-responsive hub genes into 37 different gene network modules. Combining the hub genes and DEGs, we obtained 71 candidate genes. Gene Ontology (GO) enrichment analysis of genes in the greenyellow module in XNY27-YA-24 and connectivity genes of these 71 candidate hub genes showed that the responses to metal ion, inorganic substance, abiotic stimulus, hydrogen peroxide, oxidative stress, stimulus, and other processes were enrichment. Moreover, five candidate genes that were responsive to Cd stress in maize kernel were detected. These results provided the putative key genes and pathways to response to Cd stress in maize kernel, and a useful dataset for unraveling the underlying mechanism of Cd accumulation in maize kernel.
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Affiliation(s)
- Yongjin Li
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Ying Zhang
- College of Agronomy, Northwest A&F University, Xianyang 712100, China
| | - Hongbing Luo
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Maize Engineering Technology Research Center of Hunan Province, Changsha 410128, China
| | - Dan Lv
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Zhenxie Yi
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Meijuan Duan
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
| | - Min Deng
- College of Agronomy, Hunan Agricultural University, Changsha 410128, China
- Maize Engineering Technology Research Center of Hunan Province, Changsha 410128, China
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Minaei S, Mohammadi SA, Sabouri A, Dadras AR. High genetic diversity in Aegilops tauschii Coss. accessions from North Iran as revealed by IRAP and REMAP markers. J Genet Eng Biotechnol 2022; 20:86. [PMID: 35696009 PMCID: PMC9192835 DOI: 10.1186/s43141-022-00363-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 05/02/2022] [Indexed: 11/10/2022]
Abstract
BACKGROUND Aegilops tauschii Coss. as a donor of wheat D genome has an important role in wheat breeding programs. Genetic and phylogeographic diversity of 79 Ae. tauschii accessions collected from north and northwest of Iran were analyzed based on retroelement insertional polymorphisms using inter-retrotransposon amplified polymorphism (IRAP) and retrotransposon-microsatellite amplified polymorphism (REMAP) markers. RESULTS In total, 306 and 151 polymorphic bands were amplified in IRAP and REMAP analyses, respectively. As a result, a high level of polymorphism was observed among the studied accessions as revealed by an average of 25.5 bands per primer/primer combination and mean PIC value of 0.47 in IRAP and an average of 25.16 bands per primer combination and mean PIC value of 0.47 in REMAP. Genetic relationships of the accessions were analyzed using distance- and model-based cluster analyses. CONCLUSION The result showed that genetic distance did not seem to be related to geographic distribution, and the accessions could be divided into three groups, which was further supported by principal coordinate analysis. These results on genetic diversity and population structure of Ae. tauschii in Iran should provide important knowledge on genetic resources and their applications in wheat breeding programs.
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Affiliation(s)
- Sona Minaei
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Seyyed Abolghasem Mohammadi
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz, Iran. .,Center of Excellence in Cereal Molecular Breeding, University of Tabriz, Tabriz, Iran. .,Department of Life Sciences, Center for Cell Pathology, Khazar University, Baku, AZ1096, Azerbaijan.
| | - Atefeh Sabouri
- Department of Agronomy and Plant Breeding, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Ahmad Reza Dadras
- Department of Crop and Horticultural Research, Zanjan Agricultural and Natural Resource Research and Education, AREEO, Zanjan, Iran
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Wei J, Liao S, Li M, Zhu B, Wang H, Gu L, Yin H, Du X. AetSRG1 contributes to the inhibition of wheat Cd accumulation by stabilizing phenylalanine ammonia lyase. JOURNAL OF HAZARDOUS MATERIALS 2022; 428:128226. [PMID: 35032956 DOI: 10.1016/j.jhazmat.2022.128226] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/24/2021] [Accepted: 01/04/2022] [Indexed: 06/14/2023]
Abstract
Cadmium (Cd) is a toxic heavy metal that poses a serious threat to crop safety, productivity, and human health. Aegilops tauschii is the D genome donor of common wheat and shows abundant genetic variation. However, the tolerance of Ae. tauschii toward Cd at the molecular level is poorly understood. In this study, key factors involved in the Cd stress response of Ae. tauschii were investigated by RNA sequencing. Differentially expressed genes (DEGs) under Cd stress were identified in Ae. tauschii roots and shoots. A Fe(II)/2-oxoglutarate dependent dioxygenase (designated as AetSRG1), with an unknown function in Cd stress, was of particular interest. The open reading frame of AetSRG1 was cloned and overexpressed in wheat, which resulted in reduced Cd accumulation along with a lower Cd2+ flux, decreased electrolyte leakage, and higher reactive oxygen species production. The protein of AetSRG1 interacted with phenylalanine ammonia lyase (PAL). Finally, we found that AetSRG1 stabilizes PAL and promotes the synthesis of endogenous salicylic acid. This study provides novel insights into the molecular mechanisms underlying the response of Ae. tauschii toward Cd stress. The key genes identified in this work serve as potential targets for developing low cadmium wheat.
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Affiliation(s)
- Jialian Wei
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou Province, China
| | - Sisi Liao
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou Province, China
| | - Muzi Li
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou Province, China
| | - Bin Zhu
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou Province, China
| | - Hongcheng Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou Province, China
| | - Lei Gu
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou Province, China
| | - Huayan Yin
- College of Agronomy, Qingdao Agricultural University, Qingdao, Shandong Province, China.
| | - Xuye Du
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou Province, China.
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Zulfiqar U, Jiang W, Xiukang W, Hussain S, Ahmad M, Maqsood MF, Ali N, Ishfaq M, Kaleem M, Haider FU, Farooq N, Naveed M, Kucerik J, Brtnicky M, Mustafa A. Cadmium Phytotoxicity, Tolerance, and Advanced Remediation Approaches in Agricultural Soils; A Comprehensive Review. FRONTIERS IN PLANT SCIENCE 2022; 13:773815. [PMID: 35371142 PMCID: PMC8965506 DOI: 10.3389/fpls.2022.773815] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 02/02/2022] [Indexed: 05/03/2023]
Abstract
Cadmium (Cd) is a major environmental contaminant due to its widespread industrial use. Cd contamination of soil and water is rather classical but has emerged as a recent problem. Cd toxicity causes a range of damages to plants ranging from germination to yield suppression. Plant physiological functions, i.e., water interactions, essential mineral uptake, and photosynthesis, are also harmed by Cd. Plants have also shown metabolic changes because of Cd exposure either as direct impact on enzymes or other metabolites, or because of its propensity to produce reactive oxygen species, which can induce oxidative stress. In recent years, there has been increased interest in the potential of plants with ability to accumulate or stabilize Cd compounds for bioremediation of Cd pollution. Here, we critically review the chemistry of Cd and its dynamics in soil and the rhizosphere, toxic effects on plant growth, and yield formation. To conserve the environment and resources, chemical/biological remediation processes for Cd and their efficacy have been summarized in this review. Modulation of plant growth regulators such as cytokinins, ethylene, gibberellins, auxins, abscisic acid, polyamines, jasmonic acid, brassinosteroids, and nitric oxide has been highlighted. Development of plant genotypes with restricted Cd uptake and reduced accumulation in edible portions by conventional and marker-assisted breeding are also presented. In this regard, use of molecular techniques including identification of QTLs, CRISPR/Cas9, and functional genomics to enhance the adverse impacts of Cd in plants may be quite helpful. The review's results should aid in the development of novel and suitable solutions for limiting Cd bioavailability and toxicity, as well as the long-term management of Cd-polluted soils, therefore reducing environmental and human health hazards.
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Affiliation(s)
- Usman Zulfiqar
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Wenting Jiang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Wang Xiukang
- College of Life Sciences, Yan’an University, Yan’an, China
| | - Saddam Hussain
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Muhammad Ahmad
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | | | - Nauman Ali
- Agronomic Research Institute, Ayub Agricultural Research Institute, Faisalabad, Pakistan
| | - Muhammad Ishfaq
- Department of Agronomy, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Muhammad Kaleem
- Department of Botany, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Fasih Ullah Haider
- College of Resources and Environmental Sciences, Gansu Agricultural University, Lanzhou, China
| | - Naila Farooq
- Department of Soil and Environmental Science, College of Agriculture, University of Sargodha, Sargodha, Pakistan
| | - Muhammad Naveed
- Institute of Soil and Environmental Science, University of Agriculture Faisalabad, Faisalabad, Pakistan
| | - Jiri Kucerik
- Institute of Chemistry and Technology of Environmental Protection, Faculty of Chemistry, Brno University of Technology, Brno, Czechia
| | - Martin Brtnicky
- Institute of Chemistry and Technology of Environmental Protection, Faculty of Chemistry, Brno University of Technology, Brno, Czechia
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
| | - Adnan Mustafa
- Institute of Chemistry and Technology of Environmental Protection, Faculty of Chemistry, Brno University of Technology, Brno, Czechia
- Department of Agrochemistry, Soil Science, Microbiology and Plant Nutrition, Faculty of AgriSciences, Mendel University in Brno, Brno, Czechia
- Institute for Environmental Studies, Faculty of Science, Charles University in Prague, Prague, Czechia
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Genome-Wide Association Study of Morpho-Physiological Traits in Aegilops tauschii to Broaden Wheat Genetic Diversity. PLANTS 2021; 10:plants10020211. [PMID: 33499189 PMCID: PMC7911611 DOI: 10.3390/plants10020211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 11/16/2022]
Abstract
Aegilops tauschii, the D-genome donor of bread wheat, is a storehouse of genetic diversity that can be used for wheat improvement. This species consists of two main lineages (TauL1 and TauL2) and one minor lineage (TauL3). Its morpho-physiological diversity is large, with adaptations to a wide ecological range. Identification of allelic diversity in Ae. tauschii is of utmost importance for efficient breeding and widening of the genetic base of wheat. This study aimed at identifying markers or genes associated with morpho-physiological traits in Ae. tauschii, and at understanding the difference in genetic diversity between the two main lineages. We performed genome-wide association studies of 11 morpho-physiological traits of 343 Ae. tauschii accessions representing the entire range of habitats using 34,829 DArTseq markers. We observed a wide range of morpho-physiological variation among all accessions. We identified 23 marker-trait associations (MTAs) in all accessions, 15 specific to TauL1 and eight specific to TauL2, suggesting independent evolution in each lineage. Some of the MTAs could be novel and have not been reported in bread wheat. The markers or genes identified in this study will help reveal the genes controlling the morpho-physiological traits in Ae. tauschii, and thus in bread wheat even if the plant morphology is different.
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Lin Y, Zhou K, Hu H, Jiang X, Yu S, Wang Q, Li C, Ma J, Chen G, Yang Z, Liu Y. Multi-Locus Genome-Wide Association Study of Four Yield-Related Traits in Chinese Wheat Landraces. FRONTIERS IN PLANT SCIENCE 2021; 12:665122. [PMID: 34484253 PMCID: PMC8415402 DOI: 10.3389/fpls.2021.665122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 07/20/2021] [Indexed: 05/13/2023]
Abstract
Wheat (Triticum aestivum L.) is one of the most important crops in the world. Here, four yield-related traits, namely, spike length, spikelets number, tillers number, and thousand-kernel weight, were evaluated in 272 Chinese wheat landraces in multiple environments. Five multi-locus genome-wide association studies (FASTmrEMMA, ISIS EN-BLASSO, mrMLM, pKWmEB, and pLARmEB) were performed using 172,711 single-nucleotide polymorphisms (SNPs) to identify yield-related quantitative trait loci (QTL). A total of 27 robust QTL were identified by more than three models. Nine of these QTL were consistent with those in previous studies. The remaining 18 QTL may be novel. We identified a major QTL, QTkw.sicau-4B, with up to 18.78% of phenotypic variation explained. The developed kompetitive allele-specific polymerase chain reaction marker for QTkw.sicau-4B was validated in two recombinant inbred line populations with an average phenotypic difference of 16.07%. After combined homologous function annotation and expression analysis, TraesCS4B01G272300 was the most likely candidate gene for QTkw.sicau-4B. Our findings provide new insights into the genetic basis of yield-related traits and offer valuable QTL to breed wheat cultivars via marker-assisted selection.
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Affiliation(s)
- Yu Lin
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Kunyu Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Haiyan Hu
- School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Xiaojun Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Shifan Yu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Qing Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Caixia Li
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Guangdeng Chen
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Zisong Yang
- College of Resources and Environment, Aba Teachers University, Wenchuan, China
| | - Yaxi Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
- *Correspondence: Yaxi Liu, , orcid.org/0000-0001-6814-7218
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Safdar LB, Almas F, Sarfraz S, Ejaz M, Ali Z, Mahmood Z, Yang L, Tehseen MM, Ikram M, Liu S, Quraishi UM. Genome-wide association study identifies five new cadmium uptake loci in wheat. THE PLANT GENOME 2020; 13:e20030. [PMID: 33016603 DOI: 10.1002/tpg2.20030] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 05/28/2023]
Abstract
Cadmium (Cd) toxicity is a serious threat to future food security and health safety. To identify genetic factors contributing to Cd uptake in wheat, we conducted a genome-wide association study with genotyping from 90K SNP array. A spring wheat diversity panel was planted under normal conditions and Cd stress (50 mg Cd/kg soil). The impact of Cd stress on agronomic traits ranged from a reduction of 16% in plant height to 93% in grain iron content. Individual genotypes showed a considerable variation for Cd uptake and translocation subdividing the panel into three groups: (1) hyper-accumulators (i.e. high Leaf_Cd and low Seed_Cd ), (2) hyper-translocators (i.e. low Leaf_Cd and high Seed_Cd ), and (3) moderate lines (i.e. low Leaf_Cd and low Seed_Cd ). Two lines (SKD-1 and TD-1) maintained an optimum grain yield under Cd stress and were therefore considered as Cd resistant lines. Genome-wide association identified 179 SNP-trait associations for various traits including 16 for Cd uptake at a significance level of P < .001. However, only five SNPs were significant after applying multiple testing correction. These loci were associated with seed-cadmium, grain-iron, and grain-zinc: qSCd-1A, qSCd-1D, qZn-2B1, qZn-2B2, and qFe-6D. These five loci had not been identified in the previously reported studies for Cd uptake in wheat. These loci and the underlying genes should be further investigated using molecular biology techniques to identify Cd resistant genes in wheat.
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Affiliation(s)
- Luqman Bin Safdar
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Fakhrah Almas
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Sidra Sarfraz
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Muhammad Ejaz
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Zeshan Ali
- Plant Physiology Program, Crop Sciences Institute, National Agricultural Research Centre, Park Road, Islamabad, PO 45500, Pakistan
| | - Zahid Mahmood
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
- Wheat Programme, Crop Sciences Institute, National Agricultural Research Centre, Park Road, Islamabad, PO 45500, Pakistan
| | - Li Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | | | - Muhammad Ikram
- Statistical Genomics Lab, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Umar Masood Quraishi
- Department of Plant Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
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Arora S, Singh N, Kaur S, Bains NS, Uauy C, Poland J, Chhuneja P. Genome-Wide Association Study of Grain Architecture in Wild Wheat Aegilops tauschii. FRONTIERS IN PLANT SCIENCE 2017; 8:886. [PMID: 28620398 PMCID: PMC5450224 DOI: 10.3389/fpls.2017.00886] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Accepted: 05/11/2017] [Indexed: 05/18/2023]
Abstract
Aegilops tauschii, the D-genome progenitor of Triticum aestivum, encompasses huge diversity for various traits of potential economic importance such as yield, biotic and abiotic stress tolerance, quality and nutrition. In the present study, variation for grain size in Ae. tauschii germplasm was studied and its genetic basis dissected using genome-wide association study (GWAS). Grain length, width, and weight evaluated in 177 Ae. tauschii accessions over 3 years showed near normal distribution with 1.74-, 1.75-, and 2.82-fold variation, respectively. These lines were genetically characterized using genotyping-by-sequencing (GBS) protocol that produced 11,489 single nucleotide polymorphic (SNP) markers. Genetic diversity analysis revealed the presence of two distinct subgroups (designated as lineage 1 and 2) in Ae. tauschii. Based on GBS markers, the genetic similarity was calculated between the accessions and GWAS was conducted using 114 non-redundant accessions and 5,249 SNP markers. A total of 17 SNPs associated with grain size traits distributed over all the seven chromosomes were revealed with 6D, 5D, and 2D harboring most significant marker-trait associations. Some of the chromosomal regions such as 6D_66.4-71.1 cM, 1D_143.5-156.7 cM, and 2D_89.9-92.5 cM had associations with multiple traits. Candidate genes associated with cell division and differentiation were identified for some of the associated SNP markers. Further efforts to validate these loci will help to understand their role in determining grain size and allelic diversity in current germplasm and its effect on grain size upon transfer to bread wheat background.
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Affiliation(s)
- Sanu Arora
- School of Agricultural Biotechnology, Punjab Agricultural UniversityLudhiana, India
- Crop Genetics, John Innes CentreNorwich, United Kingdom
| | - Narinder Singh
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, ManhattanKS, United States
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural UniversityLudhiana, India
| | - Navtej S. Bains
- School of Agricultural Biotechnology, Punjab Agricultural UniversityLudhiana, India
- Department of Plant Breeding and Genetics, Punjab Agricultural UniversityLudhiana, India
| | | | - Jesse Poland
- Wheat Genetics Resource Center, Department of Plant Pathology, Kansas State University, ManhattanKS, United States
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural UniversityLudhiana, India
- *Correspondence: Parveen Chhuneja,
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