1
|
Wang H, Fang T, Li X, Xie Y, Wang W, Hu T, Kudrna D, Amombo E, Yin Y, Fan S, Gong Z, Huang Y, Xia C, Zhang J, Wu Y, Fu J. Whole-genome sequencing of allotetraploid bermudagrass reveals the origin of Cynodon and candidate genes for salt tolerance. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2068-2084. [PMID: 38531629 DOI: 10.1111/tpj.16729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 02/06/2024] [Accepted: 03/09/2024] [Indexed: 03/28/2024]
Abstract
Bermudagrass (Cynodon dactylon) is a globally distributed, extensively used warm-season turf and forage grass with high tolerance to salinity and drought stress in alkaline environments. However, the origin of the species and genetic mechanisms for salinity tolerance in the species are basically unknown. Accordingly, we set out to study evolution divergence events in the Cynodon genome and to identify genes for salinity tolerance. We developed a 604.0 Mb chromosome-level polyploid genome sequence for bermudagrass 'A12359' (n = 18). The C. dactylon genome comprises 2 complete sets of homoeologous chromosomes, each with approximately 30 000 genes, and most genes are conserved as syntenic pairs. Phylogenetic study showed that the initial Cynodon species diverged from Oropetium thomaeum approximately 19.7-25.4 million years ago (Mya), the A and B subgenomes of C. dactylon diverged approximately 6.3-9.1 Mya, and the bermudagrass polyploidization event occurred 1.5 Mya on the African continent. Moreover, we identified 82 candidate genes associated with seven agronomic traits using a genome-wide association study, and three single-nucleotide polymorphisms were strongly associated with three salt resistance genes: RAP2-2, CNG channels, and F14D7.1. These genes may be associated with enhanced bermudagrass salt tolerance. These bermudagrass genomic resources, when integrated, may provide fundamental insights into evolution of diploid and tetraploid genomes and enhance the efficacy of comparative genomics in studying salt tolerance in Cynodon.
Collapse
Affiliation(s)
- Huan Wang
- College of Grassland Science, Qingdao Agricultural University, Qingdao City, Shandong Province, 266109, China
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Tilin Fang
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, Oklahoma, 74078, USA
| | - Xiaoning Li
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
| | - Yan Xie
- Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei Province, 430074, China
| | - Wei Wang
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
| | - Tao Hu
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou City, Gansu Province, 730020, China
| | - David Kudrna
- School of Plant Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - Erick Amombo
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
| | - Yanling Yin
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
| | - Shugao Fan
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
| | - Zhiyun Gong
- Agricultural Department, Yangzhou University, Yangzhou, Jiangsu Province, 225009, China
| | - Yicheng Huang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Chunjiao Xia
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Jianwei Zhang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei Province, 430070, China
| | - Yanqi Wu
- Department of Plant and Soil Sciences, Oklahoma State University, Stillwater, Oklahoma, 74078, USA
| | - Jinmin Fu
- College of Grassland Science, Qingdao Agricultural University, Qingdao City, Shandong Province, 266109, China
- Coastal Salinity Tolerant Grass Engineering and Research Center, Ludong University, Yantai, Shandong Province, 264025, China
| |
Collapse
|
2
|
Spychała J, Tomkowiak A, Noweiska A, Bobrowska R, Bocianowski J, Sobiech A, Kwiatek MT. Diversity of Expression Patterns of Lr34, Lr67, and Candidate Genes towards Lr46 with Analysis of Associated miRNAs in Common Wheat Hybrids in Response to Puccinia triticina Fungus. Curr Issues Mol Biol 2024; 46:5511-5529. [PMID: 38921001 PMCID: PMC11201949 DOI: 10.3390/cimb46060329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 05/21/2024] [Accepted: 05/29/2024] [Indexed: 06/27/2024] Open
Abstract
Leaf rust caused by Puccinia triticina (Pt) is one of the most dangerous diseases causing significant losses in common wheat crops. In adult plants resistant to rust, a horizontal adult plant resistance (APR) type is observed, which protects the plant against multiple pathogen races and is distinguished by greater persistence under production conditions. Crucial pleiotropic slow-rust genes such as Lr34, Lr46, Lr67, and Lr68, in combination with other genes of lesser influence, continue to increase durable resistance to rust diseases. Based on our previous results, we selected four candidate genes for Lr46 out of ten candidates and analysed them for expression before and after inoculation by P. triticina. As part of our study, we also investigated the expression patterns of miRNA molecules complementary to Lr34 and the candidate genes. The aim of the study was to analyse the expression profiles of candidate genes for the Lr46 gene and the Lr34 and Lr67 genes responsible for the differential leaf-rust resistance of hybrid forms of the F1 generation resulting from crosses between the Glenlea cultivar and cultivars from Polish breeding companies. In addition, the expression of five miRNAs (tae-miR9653b, tae-miR5384-3p, tae-miR9780, tae-miR9775 and tae-miR164), complementary to Lr34, and selected candidate genes were analysed using stem-loop RT-PCR and ddPCR. Biotic stress was induced in adult plants by inoculation with Pt fungal spores, under controlled conditions. Plant material was collected before and 6, 12, 24, and 48 h after inoculation (hpi). Differences in expression patterns of Lr34, Lr67, and candidate genes (for Lr46) were analysed by qRT-PCR and showed that gene expression changed at the analysed time points. Identification of molecular markers coupled to the Lr genes studied was also carried out to confirm the presence of these genes in wheat hybrids. qRT-PCR was used to examine the expression levels of the resistance genes. The highest expression of Lr46/Yr29 genes (Lr46-Glu2, Lr46-RLK1, Lr46-RLK2, and Lr46-RLK3) occurred at 12 and 24 hpi, and such expression profiles were obtained for only one candidate gene among the four genes analysed (Lr46-Glu2), indicating that it may be involved in resistance mechanisms of response to Pt infection.
Collapse
Affiliation(s)
- Julia Spychała
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (J.S.); (A.N.); (R.B.); (A.S.); (M.T.K.)
| | - Agnieszka Tomkowiak
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (J.S.); (A.N.); (R.B.); (A.S.); (M.T.K.)
| | - Aleksandra Noweiska
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (J.S.); (A.N.); (R.B.); (A.S.); (M.T.K.)
| | - Roksana Bobrowska
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (J.S.); (A.N.); (R.B.); (A.S.); (M.T.K.)
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, 60-637 Poznań, Poland
| | - Aleksandra Sobiech
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (J.S.); (A.N.); (R.B.); (A.S.); (M.T.K.)
| | - Michał Tomasz Kwiatek
- Department of Genetics and Plant Breeding, Faculty of Agronomy, Horticulture and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-632 Poznań, Poland; (J.S.); (A.N.); (R.B.); (A.S.); (M.T.K.)
- Plant Breeding and Acclimatization Institute—National Research Institute in Radzików, 05-870 Błonie, Poland
| |
Collapse
|
3
|
Liu X, Sukumaran S, Viitanen E, Naik N, Hassan S, Aronsson H. An Accurate Representation of the Number of bZIP Transcription Factors in the Triticum aestivum (Wheat) Genome and the Regulation of Functional Genes during Salt Stress. Curr Issues Mol Biol 2024; 46:4417-4436. [PMID: 38785536 PMCID: PMC11120151 DOI: 10.3390/cimb46050268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/24/2024] [Accepted: 04/28/2024] [Indexed: 05/25/2024] Open
Abstract
Climate change is dramatically increasing the overall area of saline soils around the world, which is increasing by approximately two million hectares each year. Soil salinity decreases crop yields and, thereby, makes farming less profitable, potentially causing increased poverty and hunger in many areas. A solution to this problem is increasing the salt tolerance of crop plants. Transcription factors (TFs) within crop plants represent a key to understanding salt tolerance, as these proteins play important roles in the regulation of functional genes linked to salt stress. The basic leucine zipper (bZIP) TF has a well-documented role in the regulation of salt tolerance. To better understand how bZIP TFs are linked to salt tolerance, we performed a genome-wide analysis in wheat using the Chinese spring wheat genome, which has been assembled by the International Wheat Genome Sequencing Consortium. We identified 89 additional bZIP gene sequences, which brings the total of bZIP gene sequences in wheat to 237. The majority of these 237 sequences included a single bZIP protein domain; however, different combinations of five other domains also exist. The bZIP proteins are divided into ten subfamily groups. Using an in silico analysis, we identified five bZIP genes (ABF2, ABF4, ABI5, EMBP1, and VIP1) that were involved in regulating salt stress. By scrutinizing the binding properties to the 2000 bp upstream region, we identified putative functional genes under the regulation of these TFs. Expression analyses of plant tissue that had been treated with or without 100 mM NaCl revealed variable patterns between the TFs and functional genes. For example, an increased expression of ABF4 was correlated with an increased expression of the corresponding functional genes in both root and shoot tissues, whereas VIP1 downregulation in root tissues strongly decreased the expression of two functional genes. Identifying strategies to sustain the expression of the functional genes described in this study could enhance wheat's salt tolerance.
Collapse
Affiliation(s)
- Xin Liu
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden; (X.L.); (S.S.); (E.V.); (N.N.); (S.H.)
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang 611130, China
| | - Selvakumar Sukumaran
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden; (X.L.); (S.S.); (E.V.); (N.N.); (S.H.)
| | - Esteri Viitanen
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden; (X.L.); (S.S.); (E.V.); (N.N.); (S.H.)
| | - Nupur Naik
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden; (X.L.); (S.S.); (E.V.); (N.N.); (S.H.)
| | - Sameer Hassan
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden; (X.L.); (S.S.); (E.V.); (N.N.); (S.H.)
| | - Henrik Aronsson
- Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 405 30 Gothenburg, Sweden; (X.L.); (S.S.); (E.V.); (N.N.); (S.H.)
| |
Collapse
|
4
|
Mascher M, Marone MP, Schreiber M, Stein N. Are cereal grasses a single genetic system? NATURE PLANTS 2024; 10:719-731. [PMID: 38605239 DOI: 10.1038/s41477-024-01674-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 03/17/2024] [Indexed: 04/13/2024]
Abstract
In 1993, a passionate and provocative call to arms urged cereal researchers to consider the taxon they study as a single genetic system and collaborate with each other. Since then, that group of scientists has seen their discipline blossom. In an attempt to understand what unity of genetic systems means and how the notion was borne out by later research, we survey the progress and prospects of cereal genomics: sequence assemblies, population-scale sequencing, resistance gene cloning and domestication genetics. Gene order may not be as extraordinarily well conserved in the grasses as once thought. Still, several recurring themes have emerged. The same ancestral molecular pathways defining plant architecture have been co-opted in the evolution of different cereal crops. Such genetic convergence as much as cross-fertilization of ideas between cereal geneticists has led to a rich harvest of genes that, it is hoped, will lead to improved varieties.
Collapse
Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
| | - Marina Püpke Marone
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mona Schreiber
- University of Marburg, Department of Biology, Marburg, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany.
- Martin Luther University Halle-Wittenberg, Halle (Saale), Germany.
| |
Collapse
|
5
|
Kaushik M, Mulani E, Kumar A, Chauhan H, Saini MR, Bharati A, Gayatri, Iyyappan Y, Madhavan J, Sevanthi AM, Mandal PK. Starch and storage protein dynamics in the developing and matured grains of durum wheat and diploid progenitor species. Int J Biol Macromol 2024; 267:131177. [PMID: 38583842 DOI: 10.1016/j.ijbiomac.2024.131177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 03/18/2024] [Accepted: 03/26/2024] [Indexed: 04/09/2024]
Abstract
Durum wheat, less immunogenically intolerant than bread wheat, originates from diploid progenitors known for nutritional quality and stress tolerance. Present study involves the analysis of major grain parameters, viz. size, weight, sugar, starch, and protein content of Triticum durum (AABB genome) and its diploid progenitors, Triticum monococcum (AA genome) and Aegilops speltoides (BB genome). Samples were collected during 2-5 weeks after anthesis (WAA), and at maturity. The investigation revealed that T. durum displayed the maximum grain size and weight. Expression analysis of Grain Weight 2 (GW2) and Glutamine Synthase (GS2), negative and positive regulators of grain weight and size, respectively, revealed higher GW2 expression in Ae. speltoides and higher GS2 expression in T. durum. Further we explored total starch, sugar and protein content, observing higher levels of starch and sugar in durum wheat while AA genome species exhibited higher protein content dominated by the fractions of albumin/globulin. HPLC profiling revealed unique sub-fractions in all three genome species. Additionally, a comparative transcriptome analysis also corroborated with the starch and protein content in the grains. This study provides valuable insights into the genetic and biochemical distinctions among durum wheat and its diploid progenitors, offering a foundation for their nutritional composition.
Collapse
Affiliation(s)
- Megha Kaushik
- Indian Council of Agricultural Research - National Institute for Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi 110012, India
| | - Ekta Mulani
- Indian Council of Agricultural Research - National Institute for Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi 110012, India
| | - Amit Kumar
- Indian Council of Agricultural Research - National Institute for Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi 110012, India
| | - Harsh Chauhan
- Indian Council of Agricultural Research - National Institute for Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi 110012, India
| | - Manish Ranjan Saini
- Indian Council of Agricultural Research - National Institute for Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi 110012, India
| | - Alka Bharati
- Indian Council of Agricultural Research - National Institute for Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi 110012, India
| | - Gayatri
- Indian Council of Agricultural Research - National Institute for Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi 110012, India
| | - Yuvaraj Iyyappan
- Indian Council of Agricultural Research - National Institute for Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi 110012, India
| | - Jayanthi Madhavan
- Division of Genetics, ICAR - Indian Agriculture Research Institute, Pusa Campus, New Delhi 110012, India
| | - Amitha Mithra Sevanthi
- Indian Council of Agricultural Research - National Institute for Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi 110012, India
| | - Pranab Kumar Mandal
- Indian Council of Agricultural Research - National Institute for Plant Biotechnology (ICAR-NIPB), LBS Building, Pusa Campus, New Delhi 110012, India.
| |
Collapse
|
6
|
Sobrino-Mengual G, Alvarez D, Twyman RM, Gerrish C, Fraser PD, Capell T, Christou P. Activation of the native PHYTOENE SYNTHASE 1 promoter by modifying near-miss cis-acting elements induces carotenoid biosynthesis in embryogenic rice callus. PLANT CELL REPORTS 2024; 43:118. [PMID: 38632121 PMCID: PMC11024007 DOI: 10.1007/s00299-024-03199-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 03/13/2024] [Indexed: 04/19/2024]
Abstract
KEY MESSAGE Modification of silent latent endosperm-enabled promoters (SLEEPERs) allows the ectopic activation of non-expressed metabolic genes in rice callus Metabolic engineering in plants typically involves transgene expression or the mutation of endogenous genes. An alternative is promoter modification, where small changes in the promoter sequence allow genes to be switched on or off in particular tissues. To activate silent genes in rice endosperm, we screened native promoters for near-miss cis-acting elements that can be converted to endosperm-active regulatory motifs. We chose rice PHYTOENE SYNTHASE 1 (PSY1), encoding the enzyme responsible for the first committed step in the carotenoid biosynthesis pathway, because it is not expressed in rice endosperm. We identified six motifs within a 120-bp region, upstream of the transcriptional start site, which differed from endosperm-active elements by up to four nucleotides. We mutated four motifs to match functional elements in the endosperm-active BCH2 promoter, and this promoter was able to drive GFP expression in callus and in seeds of regenerated plants. The 4 M promoter was not sufficient to drive PSY1 expression, so we mutated the remaining two elements and used the resulting 6 M promoter to drive PSY1 expression in combination with a PDS transgene. This resulted in deep orange callus tissue indicating the accumulation of carotenoids, which was subsequently confirmed by targeted metabolomics analysis. PSY1 expression driven by the uncorrected or 4 M variants of the promoter plus a PDS transgene produced callus that lacked carotenoids. These results confirm that the adjustment of promoter elements can facilitate the ectopic activation of endogenous plant promoters in rice callus and endosperm and most likely in other tissues and plant species.
Collapse
Affiliation(s)
- Guillermo Sobrino-Mengual
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Derry Alvarez
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
- Division of Biological and Environmental Sciences and Engineering, Center for Desert Agriculture, BioActives Lab, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | | | - Christopher Gerrish
- Department of Biological Sciences, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Paul D Fraser
- Department of Biological Sciences, Royal Holloway University of London, Egham Hill, Egham, Surrey, TW20 0EX, UK
| | - Teresa Capell
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain
| | - Paul Christou
- Applied Plant Biotechnology Group, Department of Agricultural and Forest Sciences and Engineering, University of Lleida-Agrotecnio CERCA Center, Lleida, Spain.
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona, Spain.
| |
Collapse
|
7
|
Sun W, Lu C, Wen L, Liu Y, Zhou X, Xiao X, Guo X, Wang Z, Sun Z, Zhang Z, Zhang Y. Low sucrose availability reduces basal spikelet fertility by inducing abscisic acid and jasmonic acid synthesis in wheat. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1967-1981. [PMID: 38069503 DOI: 10.1093/jxb/erad484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/02/2023] [Indexed: 03/28/2024]
Abstract
Within a spike of wheat, the central spikelets usually generate three to four fertile florets, while the basal spikelets generate zero to one fertile floret. The physiological and transcriptional mechanism behind the difference in fertility between the basal and central spikelets is unclear. This study reports a high temporal resolution investigation of transcriptomes, number and morphology of floret primordia, and physiological traits. The W6.5-W7.5 stage was regarded as the boundary to distinguish between fertile and abortive floret primordia; those floret primordia reaching the W6.5-W7.5 stage during the differentiation phase (3-9 d after terminal spikelet stage) usually developed into fertile florets in the next dimorphism phase (12-27 d after terminal spikelet stage), whereas the others aborted. The central spikelets had a greater number of fertile florets than the basal spikelets, which was associated with more floret primordia reaching the W6.5-W7.5 stage. Physiological and transcriptional results demonstrated that the central spikelets had a higher sucrose content and lower abscisic acid (ABA) and jasmonic acid (JA) accumulation than the basal spikelets due to down-regulation of genes involved in ABA and JA synthesis. Collectively, we propose a model in which ABA and JA accumulation is induced under limiting sucrose availability (basal spikelet) through the up-regulation of genes involved in ABA and JA synthesis; this leads to floret primordia in the basal spikelets failing to reach their fertile potential (W6.5-W7.5 stage) during the differentiation phase and then aborting. This fertility repression model may also regulate spikelet fertility in other cereal crops and potentially provides genetic resources to improve spikelet fertility.
Collapse
Affiliation(s)
- Wan Sun
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Chongjing Lu
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Liangyun Wen
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yaqun Liu
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xiaohan Zhou
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xuechen Xiao
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Xiaolei Guo
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Zhimin Wang
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
- Engineering Technology Research Center for Agriculture in Low Plain Areas, Hebei Province, 061800, China
| | - Zhencai Sun
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
- Engineering Technology Research Center for Agriculture in Low Plain Areas, Hebei Province, 061800, China
| | - Zhen Zhang
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
| | - Yinghua Zhang
- College of Agronomy and Biotechnology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, China
- Engineering Technology Research Center for Agriculture in Low Plain Areas, Hebei Province, 061800, China
| |
Collapse
|
8
|
Gao Y, Qiao L, Mei C, Nong L, Li Q, Zhang X, Li R, Gao W, Chen F, Chang L, Zhang S, Guo H, Cheng T, Wen H, Chang Z, Li X. Mapping of a Major-Effect Quantitative Trait Locus for Seed Dormancy in Wheat. Int J Mol Sci 2024; 25:3681. [PMID: 38612492 PMCID: PMC11011268 DOI: 10.3390/ijms25073681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2024] [Revised: 03/21/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
The excavation and utilization of dormancy loci in breeding are effective endeavors for enhancing the resistance to pre-harvest sprouting (PHS) of wheat varieties. CH1539 is a wheat breeding line with high-level seed dormancy. To clarify the dormant loci carried by CH1539 and obtain linked molecular markers, in this study, a recombinant inbred line (RIL) population derived from the cross of weak dormant SY95-71 and strong dormant CH1539 was genotyped using the Wheat17K single-nucleotide polymorphism (SNP) array, and a high-density genetic map covering 21 chromosomes and consisting of 2437 SNP markers was constructed. Then, the germination percentage (GP) and germination index (GI) of the seeds from each RIL were estimated. Two QTLs for GP on chromosomes 5A and 6B, and four QTLs for GI on chromosomes 5A, 6B, 6D and 7A were identified. Among them, the QTL on chromosomes 6B controlling both GP and GI, temporarily named QGp/Gi.sxau-6B, is a major QTL for seed dormancy with the maximum phenotypic variance explained of 17.66~34.11%. One PCR-based diagnostic marker Ger6B-3 for QGp/Gi.sxau-6B was developed, and the genetic effect of QGp/Gi.sxau-6B on the RIL population and a set of wheat germplasm comprising 97 accessions was successfully confirmed. QGp/Gi.sxau-6B located in the 28.7~30.9 Mbp physical position is different from all the known dormancy loci on chromosomes 6B, and within the interval, there are 30 high-confidence annotated genes. Our results revealed a novel QTL QGp/Gi.sxau-6B whose CH1539 allele had a strong and broad effect on seed dormancy, which will be useful in further PHS-resistant wheat breeding.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Xin Li
- College of Agronomy, Shanxi Key Laboratory of Crop Genetics and Molecular Improvement, Shanxi Agricultural University, Taiyuan 030031, China; (Y.G.)
| |
Collapse
|
9
|
Aliprandi E, Demaria S, Colpo A, Brestič M, Živčak M, Martina A, Pancaldi S, Baldisserotto C, Ferroni L. Thylakoid ultrastructural variations in chlorophyll-deficient wheat: aberrations or structural acclimation? PLANTA 2024; 259:90. [PMID: 38478121 PMCID: PMC10937782 DOI: 10.1007/s00425-024-04362-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 02/06/2024] [Indexed: 03/17/2024]
Abstract
MAIN CONCLUSION A structural re-modeling of the thylakoid system, including granum size and regularity, occurs in chlorophyll-deficient wheat mutants affected by photosynthetic membrane over-reduction. In the chloroplast of land plants, the thylakoid system is defined by appressed grana stacks and unstacked stroma lamellae. This study focuses on the variations of the grana organization occurring in outdoor-grown wheat mutants characterized by low chlorophyll content and a tendency for photosynthetic membrane over-reduction. Triticum aestivum ANK-32A and Triticum durum ANDW-7B were compared to their corresponding WT lines, NS67 and LD222, respectively. Electron micrographs of chloroplasts were used to calculate grana ultrastructural parameters. Photosynthetic parameters were obtained by modulated chlorophyll fluorescence and applying Light Curves (LC) and Rapid Light Curves (RLC) protocols. For each photosynthetic parameter, the difference Δ(RLC-LC) was calculated to evaluate the flexible response to light in the examined lines. In the mutants, fewer and smaller disks formed grana stacks characterized by a marked increase in lateral and cross-sectional irregularity, both negatively correlated with the number of layers per granum. A relationship was found between membrane over-reduction and granum structural irregularity. The possible acclimative significance of a greater proportion of stroma-exposed grana domains in relieving the excess electron pressure on PSI is discussed.
Collapse
Affiliation(s)
- Elisabetta Aliprandi
- Department of Environmental and Prevention Sciences, University of Ferrara, Corso Ercole I D'Este 32, 44121, Ferrara, Italy
| | - Sara Demaria
- Department of Environmental and Prevention Sciences, University of Ferrara, Corso Ercole I D'Este 32, 44121, Ferrara, Italy
| | - Andrea Colpo
- Department of Environmental and Prevention Sciences, University of Ferrara, Corso Ercole I D'Este 32, 44121, Ferrara, Italy
| | - Marian Brestič
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, Trieda A. Hlinku 2, 949 76, Nitra, Slovakia
| | - Marek Živčak
- Institute of Plant and Environmental Sciences, Faculty of Agrobiology and Food Resources, Slovak University of Agriculture, Trieda A. Hlinku 2, 949 76, Nitra, Slovakia
| | - Angela Martina
- Department of Environmental and Prevention Sciences, University of Ferrara, Corso Ercole I D'Este 32, 44121, Ferrara, Italy
| | - Simonetta Pancaldi
- Department of Environmental and Prevention Sciences, University of Ferrara, Corso Ercole I D'Este 32, 44121, Ferrara, Italy
| | - Costanza Baldisserotto
- Department of Environmental and Prevention Sciences, University of Ferrara, Corso Ercole I D'Este 32, 44121, Ferrara, Italy
| | - Lorenzo Ferroni
- Department of Environmental and Prevention Sciences, University of Ferrara, Corso Ercole I D'Este 32, 44121, Ferrara, Italy.
| |
Collapse
|
10
|
Liu J, Wei L, Wu Y, Wang Z, Wang H, Xiao J, Wang X, Sun L. Characterization of sucrose nonfermenting-1-related protein kinase 2 (SnRK2) gene family in Haynaldia villosa demonstrated SnRK2.9-V enhances drought and salt stress tolerance of common wheat. BMC Genomics 2024; 25:209. [PMID: 38408894 PMCID: PMC10895793 DOI: 10.1186/s12864-024-10114-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 02/12/2024] [Indexed: 02/28/2024] Open
Abstract
BACKGROUND The sucrose nonfermenting-1-related protein kinase 2 (SnRK2) plays a crucial role in responses to diverse biotic/abiotic stresses. Currently, there are reports on these genes in Haynaldia villosa, a diploid wild relative of wheat. RESULTS To understand the evolution of SnRK2-V family genes and their roles in various stress conditions, we performed genome-wide identification of the SnRK2-V gene family in H. villosa. Ten SnRK2-V genes were identified and characterized for their structures, functions and spatial expressions. Analysis of gene exon/intron structure further revealed the presence of evolutionary paths and replication events of SnRK2-V gene family in the H. villosa. In addition, the features of gene structure, the chromosomal location, subcellular localization of the gene family were investigated and the phylogenetic relationship were determined using computational approaches. Analysis of cis-regulatory elements of SnRK2-V gene members revealed their close correlation with different phytohormone signals. The expression profiling revealed that ten SnRK2-V genes expressed at least one tissue (leave, stem, root, or grain), or in response to at least one of the biotic (stripe rust or powdery mildew) or abiotic (drought or salt) stresses. Moreover, SnRK2.9-V was up-regulated in H. villosa under the drought and salt stress and overexpressing of SnRK2.9-V in wheat enhanced drought and salt tolerances via enhancing the genes expression of antioxidant enzymes, revealing a potential value of SnRK2.9-V in wheat improvement for salt tolerance. CONCLUSION Our present study provides a basic genome-wide overview of SnRK2-V genes in H. villosa and demonstrates the potential use of SnRK2.9-V in enhancing the drought and salt tolerances in common wheat.
Collapse
Affiliation(s)
- Jia Liu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
- Jinhua Academy, Zhejiang Chinese Medical University, Jinhua, 321000, China
| | - Luyang Wei
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Yirong Wu
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Zongkuan Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Haiyan Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Jin Xiao
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China
| | - Xiue Wang
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China.
| | - Li Sun
- National Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Cytogenetics Institute, Zhongshan Biological Breeding Laboratory, Nanjing Agricultural University/JCIC-MCP, Nanjing, 210095, China.
| |
Collapse
|
11
|
Boehm J, Cai X. Enrichment and Diversification of the Wheat Genome via Alien Introgression. PLANTS (BASEL, SWITZERLAND) 2024; 13:339. [PMID: 38337872 PMCID: PMC10857235 DOI: 10.3390/plants13030339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/08/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
Wheat, including durum and common wheat, respectively, is an allopolyploid with two or three homoeologous subgenomes originating from diploid wild ancestral species. The wheat genome's polyploid origin consisting of just three diploid ancestors has constrained its genetic variation, which has bottlenecked improvement. However, wheat has a large number of relatives, including cultivated crop species (e.g., barley and rye), wild grass species, and ancestral species. Moreover, each ancestor and relative has many other related subspecies that have evolved to inhabit specific geographic areas. Cumulatively, they represent an invaluable source of genetic diversity and variation available to enrich and diversify the wheat genome. The ancestral species share one or more homologous genomes with wheat, which can be utilized in breeding efforts through typical meiotic homologous recombination. Additionally, genome introgressions of distant relatives can be moved into wheat using chromosome engineering-based approaches that feature induced meiotic homoeologous recombination. Recent advances in genomics have dramatically improved the efficacy and throughput of chromosome engineering for alien introgressions, which has served to boost the genetic potential of the wheat genome in breeding efforts. Here, we report research strategies and progress made using alien introgressions toward the enrichment and diversification of the wheat genome in the genomics era.
Collapse
Affiliation(s)
- Jeffrey Boehm
- USDA-ARS, Wheat, Sorghum & Forage Research Unit, Lincoln, NE 68583, USA;
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| | - Xiwen Cai
- USDA-ARS, Wheat, Sorghum & Forage Research Unit, Lincoln, NE 68583, USA;
- Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68583, USA
| |
Collapse
|
12
|
Li F, Xi K, Li Y, Ming T, Huang Y, Zhang L. Genome-wide analysis of transmembrane 9 superfamily genes in wheat ( Triticum aestivum) and their expression in the roots under nitrogen limitation and Bacillus amyloliquefaciens PDR1 treatment conditions. FRONTIERS IN PLANT SCIENCE 2024; 14:1324974. [PMID: 38259936 PMCID: PMC10800943 DOI: 10.3389/fpls.2023.1324974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 12/19/2023] [Indexed: 01/24/2024]
Abstract
Introduction Transmembrane 9 superfamily (TM9SF) proteins play significant roles in plant physiology. However, these proteins are poorly characterized in wheat (Triticum aestivum). The present study aimed at the genome-wide analysis of putative wheat TM9SF (TraesTM9SF) proteins and their potential involvement in response to nitrogen limitation and Bacillus amyloliquefaciens PDR1 treatments. Methods TraesTM9SF genes were retrieved from the wheat genome, and their physiochemical properties, alignment, phylogenetic, motif structure, cis-regulatory element, synteny, protein-protein interaction (PPI), and transcription factor (TF) prediction analyses were performed. Transcriptome sequencing and quantitative real-time polymerase reaction (qRT-PCR) were performed to detect gene expression in roots under single or combined treatments with nitrogen limitation and B. amyloliquefaciens PDR1. Results and discussion Forty-seven TraesTM9SF genes were identified in the wheat genome, highlighting the significance of these genes in wheat. TraesTM9SF genes were absent on some wheat chromosomes and were unevenly distributed on the other chromosomes, indicating that potential regulatory functions and evolutionary events may have shaped the TraesTM9SF gene family. Fifty-four cis-regulatory elements, including light-response, hormone response, biotic/abiotic stress, and development cis-regulatory elements, were present in the TraesTM9SF promoter regions. No duplication of TraesTM9SF genes in the wheat genome was recorded, and 177 TFs were predicted to target the 47 TraesTM9SF genes in a complex regulatory network. These findings offer valued data for predicting the putative functions of uncharacterized TM9SF genes. Moreover, transcriptome analysis and validation by qRT-PCR indicated that the TraesTM9SF genes are expressed in the root system of wheat and are potentially involved in the response of this plant to single or combined treatments with nitrogen limitation and B. amyloliquefaciens PDR1, suggesting their functional roles in plant growth, development, and stress responses. Conclusion These findings may be vital in further investigation of the function and biological applications of TM9SF genes in wheat.
Collapse
Affiliation(s)
- Fei Li
- The Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Kuanling Xi
- The Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yuke Li
- The Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Tang Ming
- The Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Yufeng Huang
- The Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Lijun Zhang
- Science and Technology Division, Guizhou Normal University, Guiyang, China
| |
Collapse
|
13
|
Raza A, Tabassum J, Fakhar AZ, Sharif R, Chen H, Zhang C, Ju L, Fotopoulos V, Siddique KHM, Singh RK, Zhuang W, Varshney RK. Smart reprograming of plants against salinity stress using modern biotechnological tools. Crit Rev Biotechnol 2023; 43:1035-1062. [PMID: 35968922 DOI: 10.1080/07388551.2022.2093695] [Citation(s) in RCA: 41] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 05/08/2022] [Indexed: 01/19/2023]
Abstract
Climate change gives rise to numerous environmental stresses, including soil salinity. Salinity/salt stress is the second biggest abiotic factor affecting agricultural productivity worldwide by damaging numerous physiological, biochemical, and molecular processes. In particular, salinity affects plant growth, development, and productivity. Salinity responses include modulation of ion homeostasis, antioxidant defense system induction, and biosynthesis of numerous phytohormones and osmoprotectants to protect plants from osmotic stress by decreasing ion toxicity and augmented reactive oxygen species scavenging. As most crop plants are sensitive to salinity, improving salt tolerance is crucial in sustaining global agricultural productivity. In response to salinity, plants trigger stress-related genes, proteins, and the accumulation of metabolites to cope with the adverse consequence of salinity. Therefore, this review presents an overview of salinity stress in crop plants. We highlight advances in modern biotechnological tools, such as omics (genomics, transcriptomics, proteomics, and metabolomics) approaches and different genome editing tools (ZFN, TALEN, and CRISPR/Cas system) for improving salinity tolerance in plants and accomplish the goal of "zero hunger," a worldwide sustainable development goal proposed by the FAO.
Collapse
Affiliation(s)
- Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Javaria Tabassum
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Science (CAAS), Zhejiang, China
| | - Ali Zeeshan Fakhar
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Rahat Sharif
- Department of Horticulture, College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Hua Chen
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Chong Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Luo Ju
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Science (CAAS), Zhejiang, China
| | - Vasileios Fotopoulos
- Department of Agricultural Sciences, Biotechnology & Food Science, Cyprus University of Technology, Lemesos, Cyprus
| | - Kadambot H M Siddique
- The UWA Institute of Agriculture, The University of Western Australia, Crawley, Perth, Australia
| | - Rakesh K Singh
- Crop Diversification and Genetics, International Center for Biosaline Agriculture, Dubai, United Arab Emirates
| | - Weijian Zhuang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Rajeev K Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
- Murdoch's Centre for Crop and Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Murdoch, Australia
| |
Collapse
|
14
|
Sharma N, Raman H, Wheeler D, Kalenahalli Y, Sharma R. Data-driven approaches to improve water-use efficiency and drought resistance in crop plants. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 336:111852. [PMID: 37659733 DOI: 10.1016/j.plantsci.2023.111852] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 08/23/2023] [Accepted: 08/29/2023] [Indexed: 09/04/2023]
Abstract
With the increasing population, there lies a pressing demand for food, feed and fibre, while the changing climatic conditions pose severe challenges for agricultural production worldwide. Water is the lifeline for crop production; thus, enhancing crop water-use efficiency (WUE) and improving drought resistance in crop varieties are crucial for overcoming these challenges. Genetically-driven improvements in yield, WUE and drought tolerance traits can buffer the worst effects of climate change on crop production in dry areas. While traditional crop breeding approaches have delivered impressive results in increasing yield, the methods remain time-consuming and are often limited by the existing allelic variation present in the germplasm. Significant advances in breeding and high-throughput omics technologies in parallel with smart agriculture practices have created avenues to dramatically speed up the process of trait improvement by leveraging the vast volumes of genomic and phenotypic data. For example, individual genome and pan-genome assemblies, along with transcriptomic, metabolomic and proteomic data from germplasm collections, characterised at phenotypic levels, could be utilised to identify marker-trait associations and superior haplotypes for crop genetic improvement. In addition, these omics approaches enable the identification of genes involved in pathways leading to the expression of a trait, thereby providing an understanding of the genetic, physiological and biochemical basis of trait variation. These data-driven gene discoveries and validation approaches are essential for crop improvement pipelines, including genomic breeding, speed breeding and gene editing. Herein, we provide an overview of prospects presented using big data-driven approaches (including artificial intelligence and machine learning) to harness new genetic gains for breeding programs and develop drought-tolerant crop varieties with favourable WUE and high-yield potential traits.
Collapse
Affiliation(s)
- Niharika Sharma
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW 2800, Australia.
| | - Harsh Raman
- NSW Department of Primary Industries, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia
| | - David Wheeler
- NSW Department of Primary Industries, Orange Agricultural Institute, Orange, NSW 2800, Australia
| | - Yogendra Kalenahalli
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, Telangana 502324, India
| | - Rita Sharma
- Department of Biological Sciences, BITS Pilani, Pilani Campus, Rajasthan 333031, India
| |
Collapse
|
15
|
Tanade C, Rakestraw E, Ladd W, Draeger E, Randles A. Cloud Computing to Enable Wearable-Driven Longitudinal Hemodynamic Maps. INTERNATIONAL CONFERENCE FOR HIGH PERFORMANCE COMPUTING, NETWORKING, STORAGE AND ANALYSIS : [PROCEEDINGS]. SC (CONFERENCE : SUPERCOMPUTING) 2023; 2023:82. [PMID: 38939612 PMCID: PMC11210499 DOI: 10.1145/3581784.3607101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Tracking hemodynamic responses to treatment and stimuli over long periods remains a grand challenge. Moving from established single-heartbeat technology to longitudinal profiles would require continuous data describing how the patient's state evolves, new methods to extend the temporal domain over which flow is sampled, and high-throughput computing resources. While personalized digital twins can accurately measure 3D hemodynamics over several heartbeats, state-of-the-art methods would require hundreds of years of wallclock time on leadership scale systems to simulate one day of activity. To address these challenges, we propose a cloud-based, parallel-in-time framework leveraging continuous data from wearable devices to capture the first 3D patient-specific, longitudinal hemodynamic maps. We demonstrate the validity of our method by establishing ground truth data for 750 beats and comparing the results. Our cloud-based framework is based on an initial fixed set of simulations to enable the wearable-informed creation of personalized longitudinal hemodynamic maps.
Collapse
Affiliation(s)
| | | | | | - Erik Draeger
- Lawrence Livermore National Lab, Livermore, CA, USA
| | | |
Collapse
|
16
|
Zhong Y, Tian Y, Głazowska S, Blennow A, Shen L, Zhang A, Liu D, Liu X. Periodic changes in chain lengths distribution parameters of wheat starch during endosperm development. Food Chem 2023; 424:136455. [PMID: 37263096 DOI: 10.1016/j.foodchem.2023.136455] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 04/30/2023] [Accepted: 05/22/2023] [Indexed: 06/03/2023]
Abstract
This study analyzed the molecular structure of developing wheat endosperm starch at different stages after anthesis (DAA) using chain length distribution analysis by size exclusion chromatography (SEC) and fluorophore-assisted carbohydrate electrophoresis. Our results revealed periodic changes in the content of both amylose and amylopectin fractions. Specifically, the content of amylose chains with a degree of polymerization (DP) > 100 significantly decreased from 5 to 10 DAA (28% to 21%) and from 15 to 20 DAA (29% to 26%), but increased between 10 and 15 DAA (21% to 29%) and 20 to 25 DAA (30.0% to 33%). Conversely, the content of short amylopectin chains with DP ≤ 32 showed the opposite trend. Interestingly, mRNA expression levels of key starch biosynthesis genes did not exhibit periodic changes. These findings contribute to our understanding of starch biosynthesis and provide important insights for the development of starch-based products.
Collapse
Affiliation(s)
- Yuyue Zhong
- Lab of Food Soft Matter Structure and Advanced Manufacturing, College of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing University of Finance and Economics, Nanjing 210023, China; Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark
| | - Yu Tian
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark
| | - Sylwia Głazowska
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark
| | - Andreas Blennow
- Department of Plant and Environmental Sciences, Faculty of Science, University of Copenhagen, Denmark
| | - Lisha Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
| | - Aimin Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Chaoyang District, Beijing 100101, China
| | - Dongcheng Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding 071000, Hebei, China.
| | - Xingxun Liu
- Lab of Food Soft Matter Structure and Advanced Manufacturing, College of Food Science and Engineering/Collaborative Innovation Center for Modern Grain Circulation and Safety, Nanjing University of Finance and Economics, Nanjing 210023, China.
| |
Collapse
|
17
|
Licaj I, Felice D, Germinario C, Zanotti C, Fiorillo A, Marra M, Rocco M. An artificial intelligence-integrated analysis of the effect of drought stress on root traits of "modern" and "ancient" wheat varieties. FRONTIERS IN PLANT SCIENCE 2023; 14:1241281. [PMID: 37900753 PMCID: PMC10613089 DOI: 10.3389/fpls.2023.1241281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 09/25/2023] [Indexed: 10/31/2023]
Abstract
Due to drought stress, durum wheat production in the Mediterranean basin will be severely affected in the coming years. Durum wheat cultivation relies on a few genetically uniform "modern" varieties, more productive but less tolerant to stresses, and "traditional" varieties, still representing a source of genetic biodiversity for drought tolerance. Root architecture plasticity is crucial for plant adaptation to drought stress and the relationship linking root structures to drought is complex and still largely under-explored. In this study, we examined the effect of drought stress on the roots' characteristics of the "traditional" Saragolla cultivar and the "modern" Svevo. By means of "SmartRoot" software, we demonstrated that drought stress affected primary and lateral roots as well as root hair at different extents in Saragolla and Svevo cultivars. Indeed, we observed that under drought stress Saragolla possibly revamped its root architecture, by significantly increasing the length of lateral roots, and the length/density of root hairs compared to the Svevo cultivar. Scanning Electron Microscopy analysis of root anatomical traits demonstrated that under drought stress a greater stele area and an increase of the xylem lumen size vessel occurred in Saragolla, indicating that the Saragolla variety had a more efficient adaptive response to osmotic stress than the Svevo. Furthermore, for the analysis of root structural data, Artificial Intelligence (AI) algorithms have been used: Their application allowed to predict from root structural traits modified by the osmotic stress the type of cultivar observed and to infer the relationship stress-cultivar type, thus demonstrating that root structural traits are clear and incontrovertible indicators of the higher tolerance to osmotic stress of the Saragolla cultivar. Finally, to obtain an integrated view of root morphogenesis, phytohormone levels were investigated. According to the phenotypic effects, under drought stress,a larger increase in IAA and ABA levels, as well as a more pronounced reduction in GA levels occurred in Saragolla as compared to Svevo. In conclusion, these results show that the root growth and hormonal profile of Saragolla are less affected by osmotic stress than those of Svevo, demonstrating the great potential of ancient varieties as reservoirs of genetic variability for improving crop responses to environmental stresses.
Collapse
Affiliation(s)
- Ilva Licaj
- Department of Science and Technology, University of Sannio, Benevento, Italy
| | - Domenico Felice
- Department of Management Engineering, Polytechnic of Milan, Milan, Italy
| | - Chiara Germinario
- Department of Science and Technology, University of Sannio, Benevento, Italy
| | | | - Anna Fiorillo
- Department of Biology, University of Tor Vergata, Rome, Italy
| | - Mauro Marra
- Department of Biology, University of Tor Vergata, Rome, Italy
| | - Mariapina Rocco
- Department of Science and Technology, University of Sannio, Benevento, Italy
| |
Collapse
|
18
|
Mao H, Jiang C, Tang C, Nie X, Du L, Liu Y, Cheng P, Wu Y, Liu H, Kang Z, Wang X. Wheat adaptation to environmental stresses under climate change: Molecular basis and genetic improvement. MOLECULAR PLANT 2023; 16:1564-1589. [PMID: 37671604 DOI: 10.1016/j.molp.2023.09.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 08/19/2023] [Accepted: 09/01/2023] [Indexed: 09/07/2023]
Abstract
Wheat (Triticum aestivum) is a staple food for about 40% of the world's population. As the global population has grown and living standards improved, high yield and improved nutritional quality have become the main targets for wheat breeding. However, wheat production has been compromised by global warming through the more frequent occurrence of extreme temperature events, which have increased water scarcity, aggravated soil salinization, caused plants to be more vulnerable to diseases, and directly reduced plant fertility and suppressed yield. One promising option to address these challenges is the genetic improvement of wheat for enhanced resistance to environmental stress. Several decades of progress in genomics and genetic engineering has tremendously advanced our understanding of the molecular and genetic mechanisms underlying abiotic and biotic stress responses in wheat. These advances have heralded what might be considered a "golden age" of functional genomics for the genetic improvement of wheat. Here, we summarize the current knowledge on the molecular and genetic basis of wheat resistance to abiotic and biotic stresses, including the QTLs/genes involved, their functional and regulatory mechanisms, and strategies for genetic modification of wheat for improved stress resistance. In addition, we also provide perspectives on some key challenges that need to be addressed.
Collapse
Affiliation(s)
- Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Cong Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chunlei Tang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaojun Nie
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Linying Du
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Life Science, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuling Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peng Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yunfeng Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Huiquan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Xiaojie Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China.
| |
Collapse
|
19
|
Chen H, Zhang X, Xu S, Song C, Mao H. TaSPL17s act redundantly with TaSPL14s to control spike development and their elite haplotypes may improve wheat grain yield. FRONTIERS IN PLANT SCIENCE 2023; 14:1229827. [PMID: 37745997 PMCID: PMC10514913 DOI: 10.3389/fpls.2023.1229827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 08/21/2023] [Indexed: 09/26/2023]
Abstract
Wheat is a staple crop for the world's population, and there is constant pressure to improve grain yield, which is largely determined by plant architecture. SQUAMOSA promotor-binding protein-like (SPL) genes have been widely studied in rice, including their effects on plant architecture, grain development, and grain yield. However, the function of SPL homologous genes in wheat has not been well investigated. In this study, TaSPL14s and TaSPL17s, wheat's closest orthologous of OsSPL14, were functionally investigated using gene-editing assays, revealing that these genes redundantly influence plant height, tiller number, spike length, and thousand-grain weight (TGW). Bract outgrowth was frequently observed in the hexa-mutant, occasionally in the quintuple mutant but never in the wild type. Transcriptome analysis revealed that the expression of many spike development-associated genes was altered in taspl14taspl17 hexa-mutants compared to that in the wild type. In addition, we analyzed the sequence polymorphisms of TaSPL14s and TaSPL17s among wheat germplasm and found superior haplotypes of TaSPL17-A and TaSPL17-D with significantly higher TGW, which had been positively selected during wheat breeding. Accordingly, dCAPS and KASP markers were developed for TaSPL17-A and TaSPL17-D, respectively, providing a novel insight for molecular marker-assisted breeding in wheat. Overall, our results highlight the role of TaSPLs in regulating plant architecture and their potential application for wheat grain yield improvement through molecular breeding.
Collapse
Affiliation(s)
| | | | | | | | - Hailiang Mao
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| |
Collapse
|
20
|
Chaudhary N, Salgotra RK, Chauhan BS. Genetic Enhancement of Cereals Using Genomic Resources for Nutritional Food Security. Genes (Basel) 2023; 14:1770. [PMID: 37761910 PMCID: PMC10530810 DOI: 10.3390/genes14091770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Advances in genomics resources have facilitated the evolution of cereal crops with enhanced yield, improved nutritional values, and heightened resistance to various biotic and abiotic stresses. Genomic approaches present a promising avenue for the development of high-yielding varieties, thereby ensuring food and nutritional security. Significant improvements have been made within the omics domain, specifically in genomics, transcriptomics, and proteomics. The advent of Next-Generation Sequencing (NGS) techniques has yielded an immense volume of data, accompanied by substantial progress in bioinformatic tools for proficient analysis. The synergy between genomics and computational tools has been acknowledged as pivotal for unravelling the intricate mechanisms governing genome-wide gene regulation. Within this review, the essential genomic resources are delineated, and their harmonization in the enhancement of cereal crop varieties is expounded upon, with a paramount focus on fulfilling the nutritional requisites of humankind. Furthermore, an encompassing compendium of the available genomic resources for cereal crops is presented, accompanied by an elucidation of their judicious utilization in the advancement of crop attributes.
Collapse
Affiliation(s)
- Neeraj Chaudhary
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu 180009, Jammu and Kashmir, India; (N.C.); (R.K.S.)
| | - Romesh Kumar Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Chatha, Jammu 180009, Jammu and Kashmir, India; (N.C.); (R.K.S.)
| | - Bhagirath Singh Chauhan
- Queensland Alliance for Agriculture and Food Innovation (QAAFI), The University of Queensland, Gatton, QLD 4343, Australia
| |
Collapse
|
21
|
Liu Y, Chen J, Yin C, Wang Z, Wu H, Shen K, Zhang Z, Kang L, Xu S, Bi A, Zhao X, Xu D, He Z, Zhang X, Hao C, Wu J, Gong Y, Yu X, Sun Z, Ye B, Liu D, Zhang L, Shen L, Hao Y, Ma Y, Lu F, Guo Z. A high-resolution genotype-phenotype map identifies the TaSPL17 controlling grain number and size in wheat. Genome Biol 2023; 24:196. [PMID: 37641093 PMCID: PMC10463835 DOI: 10.1186/s13059-023-03044-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Accepted: 08/21/2023] [Indexed: 08/31/2023] Open
Abstract
BACKGROUND Large-scale genotype-phenotype association studies of crop germplasm are important for identifying alleles associated with favorable traits. The limited number of single-nucleotide polymorphisms (SNPs) in most wheat genome-wide association studies (GWASs) restricts their power to detect marker-trait associations. Additionally, only a few genes regulating grain number per spikelet have been reported due to sensitivity of this trait to variable environments. RESULTS We perform a large-scale GWAS using approximately 40 million filtered SNPs for 27 spike morphology traits. We detect 132,086 significant marker-trait associations and the associated SNP markers are located within 590 associated peaks. We detect additional and stronger peaks by dividing spike morphology into sub-traits relative to GWAS results of spike morphology traits. We propose that the genetic dissection of spike morphology is a powerful strategy to detect signals for grain yield traits in wheat. The GWAS results reveal that TaSPL17 positively controls grain size and number by regulating spikelet and floret meristem development, which in turn leads to enhanced grain yield per plant. The haplotypes at TaSPL17 indicate geographical differentiation, domestication effects, and breeding selection. CONCLUSION Our study provides valuable resources for genetic improvement of spike morphology and a fast-forward genetic solution for candidate gene detection and cloning in wheat.
Collapse
Affiliation(s)
- Yangyang Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jun Chen
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Changbin Yin
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Ziying Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - He Wu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kuocheng Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiliang Zhang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Lipeng Kang
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Song Xu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Aoyue Bi
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Xuebo Zhao
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Daxing Xu
- University of Chinese Academy of Sciences, Beijing, 100049, China
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China
| | - Zhonghu He
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT) China Office, c/o CAAS, Beijing, 100081, China
| | - Xueyong Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Chenyang Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Jianhui Wu
- State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Yan Gong
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China
| | - Xuchang Yu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhiwen Sun
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Botao Ye
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Danni Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Lili Zhang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Liping Shen
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuanfeng Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Youzhi Ma
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, 100081, China.
| | - Fei Lu
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, 10011, China.
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100093, China.
| | - Zifeng Guo
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
22
|
Gao Z, Bian J, Lu F, Jiao Y, He H. Triticeae crop genome biology: an endless frontier. FRONTIERS IN PLANT SCIENCE 2023; 14:1222681. [PMID: 37546276 PMCID: PMC10399237 DOI: 10.3389/fpls.2023.1222681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 07/04/2023] [Indexed: 08/08/2023]
Abstract
Triticeae, the wheatgrass tribe, includes several major cereal crops and their wild relatives. Major crops within the Triticeae are wheat, barley, rye, and oat, which are important for human consumption, animal feed, and rangeland protection. Species within this tribe are known for their large genomes and complex genetic histories. Powered by recent advances in sequencing technology, researchers worldwide have made progress in elucidating the genomes of Triticeae crops. In addition to assemblies of high-quality reference genomes, pan-genome studies have just started to capture the genomic diversities of these species, shedding light on our understanding of the genetic basis of domestication and environmental adaptation of Triticeae crops. In this review, we focus on recent signs of progress in genome sequencing, pan-genome analyses, and resequencing analysis of Triticeae crops. We also propose future research avenues in Triticeae crop genomes, including identifying genome structure variations, the association of genomic regions with desired traits, mining functions of the non-coding area, introgression of high-quality genes from wild Triticeae resources, genome editing, and integration of genomic resources.
Collapse
Affiliation(s)
- Zhaoxu Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
| | - Jianxin Bian
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
| | - Fei Lu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science (CEPAMS), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Yuling Jiao
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
- University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory for Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing, China
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing, China
- Peking University Institute of Advanced Agricultural Sciences, Shandong Laboratory of Advanced Agricultural Sciences in Weifang, Shandong, China
| |
Collapse
|
23
|
Ning S, Li S, Xu K, Liu D, Ma L, Ma C, Hao M, Zhang L, Chen W, Zhang B, Jiang Y, Huang L, Chen X, Jiang B, Yuan Z, Liu D. Development and Characterization of Near-Isogenic Lines Derived from Synthetic Wheat Revealing the 2 kb Insertion in the PPD-D1 Gene Responsible for Heading Delay and Grain Number Improvement. Int J Mol Sci 2023; 24:10834. [PMID: 37446014 DOI: 10.3390/ijms241310834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/24/2023] [Accepted: 06/26/2023] [Indexed: 07/15/2023] Open
Abstract
Spikelet number and grain number per spike are two crucial and correlated traits for grain yield in wheat. Photoperiod-1 (Ppd-1) is a key regulator of inflorescence architecture and spikelet formation in wheat. In this study, near-isogenic lines derived from the cross of a synthetic hexaploid wheat and commercial cultivars generated by double top-cross and two-phase selection were evaluated for the number of days to heading and other agronomic traits. The results showed that heading time segregation was conferred by a single incomplete dominant gene PPD-D1, and the 2 kb insertion in the promoter region was responsible for the delay in heading. Meanwhile, slightly delayed heading plants and later heading plants obviously have advantages in grain number and spikelet number of the main spike compared with early heading plants. Utilization of PPD-D1 photoperiod sensitivity phenotype as a potential means to increase wheat yield potential.
Collapse
Affiliation(s)
- Shunzong Ning
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Shengke Li
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Kai Xu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Dongmei Liu
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Li Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Chunfang Ma
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Ming Hao
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Lianquan Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Wenjie Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Bo Zhang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining 810008, China
| | - Yun Jiang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610061, China
| | - Lin Huang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Xuejiao Chen
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Jiang
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Zhongwei Yuan
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| | - Dengcai Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu 611130, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu 611130, China
| |
Collapse
|
24
|
Cabral AL, Ruan Y, Cuthbert RD, Li L, Zhang W, Boyle K, Berraies S, Henriquez MA, Burt A, Kumar S, Fobert P, Piche I, Bokore FE, Meyer B, Sangha J, Knox RE. Multi-locus genome-wide association study of fusarium head blight in relation to days to anthesis and plant height in a spring wheat association panel. FRONTIERS IN PLANT SCIENCE 2023; 14:1166282. [PMID: 37457352 PMCID: PMC10346453 DOI: 10.3389/fpls.2023.1166282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/03/2023] [Indexed: 07/18/2023]
Abstract
Fusarium head blight (FHB) is a highly destructive fungal disease of wheat to which host resistance is quantitatively inherited and largely influenced by the environment. Resistance to FHB has been associated with taller height and later maturity; however, a further understanding of these relationships is needed. An association mapping panel (AMP) of 192 predominantly Canadian spring wheat was genotyped with the wheat 90K single-nucleotide polymorphism (SNP) array. The AMP was assessed for FHB incidence (INC), severity (SEV) and index (IND), days to anthesis (DTA), and plant height (PLHT) between 2015 and 2017 at three Canadian FHB-inoculated nurseries. Seven multi-environment trial (MET) datasets were deployed in a genome-wide association study (GWAS) using a single-locus mixed linear model (MLM) and a multi-locus random SNP-effect mixed linear model (mrMLM). MLM detected four quantitative trait nucleotides (QTNs) for INC on chromosomes 2D and 3D and for SEV and IND on chromosome 3B. Further, mrMLM identified 291 QTNs: 50 (INC), 72 (SEV), 90 (IND), 41 (DTA), and 38 (PLHT). At two or more environments, 17 QTNs for FHB, DTA, and PLHT were detected. Of these 17, 12 QTNs were pleiotropic for FHB traits, DTA, and PLHT on chromosomes 1A, 1D, 2D, 3B, 5A, 6B, 7A, and 7B; two QTNs for DTA were detected on chromosomes 1B and 7A; and three PLHT QTNs were located on chromosomes 4B and 6B. The 1B DTA QTN and the three pleiotropic QTNs on chromosomes 1A, 3B, and 6B are potentially identical to corresponding quantitative trait loci (QTLs) in durum wheat. Further, the 3B pleiotropic QTN for FHB INC, SEV, and IND co-locates with TraesCS3B02G024900 within the Fhb1 region on chromosome 3B and is ~3 Mb from a cloned Fhb1 candidate gene TaHRC. While the PLHT QTN on chromosome 6B is putatively novel, the 1B DTA QTN co-locates with a disease resistance protein located ~10 Mb from a Flowering Locus T1-like gene TaFT3-B1, and the 7A DTA QTN is ~5 Mb away from a maturity QTL QMat.dms-7A.3 of another study. GWAS and QTN candidate genes enabled the characterization of FHB resistance in relation to DTA and PLHT. This approach should eventually generate additional and reliable trait-specific markers for breeding selection, in addition to providing useful information for FHB trait discovery.
Collapse
Affiliation(s)
- Adrian L. Cabral
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Yuefeng Ruan
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Richard D. Cuthbert
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Lin Li
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Wentao Zhang
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, SK, Canada
| | - Kerry Boyle
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Saskatoon, SK, Canada
| | - Samia Berraies
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Maria Antonia Henriquez
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Andrew Burt
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Santosh Kumar
- Brandon Research and Development Centre, Agriculture and Agri-Food Canada, Brandon, MB, Canada
| | - Pierre Fobert
- Aquatic and Crop Resource Development Research Centre, National Research Council of Canada, Ottawa, ON, Canada
| | - Isabelle Piche
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Firdissa E. Bokore
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Brad Meyer
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Jatinder Sangha
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| | - Ron E. Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Swift Current, SK, Canada
| |
Collapse
|
25
|
Hasanpour K, Aalami A, Seraj RGM, Hosseini R, Naeimi S, Esmaeilzadeh-Salestani K. Identification of drought-tolerant hub genes in Iranian KC-2226 genotype of Aegilops tauschii using transcriptomic analysis. Sci Rep 2023; 13:9499. [PMID: 37308505 DOI: 10.1038/s41598-023-36133-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 05/30/2023] [Indexed: 06/14/2023] Open
Abstract
Aegilops tauschii, as a donor of D genome to the bread wheat with a valuable source of resistance to different biotic and abiotic stresses, is used to improve the quality of wheat cultivars. Every genotype has a specific genetic content, the investigation of which can lead to the identification of useful genes such as stress tolerance genes, including drought. Therefore, 23 genotypes of Ae. tauschii were selected to evaluate their morphological and physiological traits under greenhouse conditions. Among them, a superior tolerant genotype (KC-2226) was chosen for transcriptomic analysis. Our result showed that 5007 and 3489 genes were deferentially up- and downregulated, respectively. Upregulated genes were involved in photosynthesis, glycolysis/gluconeogenesis, and amino acid biosynthesis whereas downregulated genes were often engaged in DNA synthesis, replication, repair and topological changes. The result of protein-protein interaction network analysis showed that AT1G76550 (1.46), AT1G20950 (1.42), IAR4 (1.19), and PYD2 (1.16) among upregulated genes and THY-1 (44), PCNA1 (41) and TOPII (22) among down-regulated genes had the highest interactions with other genes. In conclusion, Ae. tauschii employs elevated transcription of specific genes involved in photosynthesis, glycolysis and gluconeogenesis and amino acid biosynthesis pathways rather than genes active in DNA synthesis and repair to provide the energy needed for the plant to survive under stress conditions.
Collapse
Affiliation(s)
- Keyvan Hasanpour
- Department of Agricultural Biotechnology, University of Guilan, University Campus 2, Rasht, Iran
| | - Ali Aalami
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.
| | - Rahele Ghanbari Moheb Seraj
- Department of Horticultural Sciences, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Ramin Hosseini
- Department of Biotechnology, Faculty of Agriculture and Natural Resource, Imam Khomeini International University, Qazvin, Iran
| | - Shahram Naeimi
- Department of Biological Control Research, Iranian Research Institute of Plant Protection, Agricultural Research, Education and Extension Organization (AREEO), Tehran, 19858-13111, Iran
| | - Keyvan Esmaeilzadeh-Salestani
- Chair of Crop Science and Plant Biology, Institute of Agricultural and Environmental Sciences, Estonian University of Life Sciences, Kreutzwaldi 1, 51006, Tartu, Estonia
| |
Collapse
|
26
|
Thakur N, Chaturvedi S, Tiwari S. Wheat derived glucuronokinase as a potential target for regulating ascorbic acid and phytic acid content with increased root length under drought and ABA stresses in Arabidopsis thaliana. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 331:111671. [PMID: 36931562 DOI: 10.1016/j.plantsci.2023.111671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 02/20/2023] [Accepted: 03/10/2023] [Indexed: 06/18/2023]
Abstract
Glucuronokinase (GlcAK) converts glucuronic acid into glucuronic acid-1-phosphate, which is then converted into UDP-glucuronic acid (UDP-GlcA) via myo-inositol oxygenase (MIOX) pathway. UDP-GlcA acts as a precursor in the synthesis of nucleotide-sugar moieties forming cell wall biomass. GlcAK being present at the bifurcation point between UDP-GlcA and ascorbic acid (AsA) biosyntheses, makes it necessary to study its role in plants. In this study, the three homoeologs of GlcAK gene from hexaploid wheat were overexpressed in Arabidopsis thaliana. The GlcAK overexpressing transgenic lines showed decreased contents of AsA and phytic acid (PA) as compared to control plants. Root length and seed germination analyses under abiotic stress (drought and abscisic acid) conditions revealed enhanced root length in transgenic lines as compared to control plants. These results indicate that the MIOX pathway might be contributing towards AsA biosynthesis as evident by the decreased AsA content in the GlcAK overexpressing transgenic Arabidopsis thaliana plants. Findings of the present study will enhance the understanding of the involvement of GlcAK gene in MIOX pathway and subsequent physiological effects in plants.
Collapse
Affiliation(s)
- Neha Thakur
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector-81, Mohali 140306, Punjab, India; Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Siddhant Chaturvedi
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector-81, Mohali 140306, Punjab, India; Department of Biotechnology, Panjab University, Chandigarh 160014, India
| | - Siddharth Tiwari
- Plant Tissue Culture and Genetic Engineering Lab, National Agri-Food Biotechnology Institute (NABI), Department of Biotechnology, Ministry of Science and Technology (Government of India), Sector-81, Mohali 140306, Punjab, India.
| |
Collapse
|
27
|
Adel S, Carels N. Plant Tolerance to Drought Stress with Emphasis on Wheat. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112170. [PMID: 37299149 DOI: 10.3390/plants12112170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/16/2023] [Accepted: 03/29/2023] [Indexed: 06/12/2023]
Abstract
Environmental stresses, such as drought, have negative effects on crop yield. Drought is a stress whose impact tends to increase in some critical regions. However, the worldwide population is continuously increasing and climate change may affect its food supply in the upcoming years. Therefore, there is an ongoing effort to understand the molecular processes that may contribute to improving drought tolerance of strategic crops. These investigations should contribute to delivering drought-tolerant cultivars by selective breeding. For this reason, it is worthwhile to review regularly the literature concerning the molecular mechanisms and technologies that could facilitate gene pyramiding for drought tolerance. This review summarizes achievements obtained using QTL mapping, genomics, synteny, epigenetics, and transgenics for the selective breeding of drought-tolerant wheat cultivars. Synthetic apomixis combined with the msh1 mutation opens the way to induce and stabilize epigenomes in crops, which offers the potential of accelerating selective breeding for drought tolerance in arid and semi-arid regions.
Collapse
Affiliation(s)
- Sarah Adel
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Nicolas Carels
- Laboratory of Biological System Modeling, Center of Technological Development for Health (CDTS), Oswaldo Cruz Foundation (Fiocruz), Rio de Janeiro 21040-361, Brazil
| |
Collapse
|
28
|
Türkoğlu A, Haliloğlu K, Mohammadi SA, Öztürk A, Bolouri P, Özkan G, Bocianowski J, Pour-Aboughadareh A, Jamshidi B. Genetic Diversity and Population Structure in Türkiye Bread Wheat Genotypes Revealed by Simple Sequence Repeats (SSR) Markers. Genes (Basel) 2023; 14:1182. [PMID: 37372362 DOI: 10.3390/genes14061182] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/19/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023] Open
Abstract
Wheat genotypes should be improved through available germplasm genetic diversity to ensure food security. This study investigated the molecular diversity and population structure of a set of Türkiye bread wheat genotypes using 120 microsatellite markers. Based on the results, 651 polymorphic alleles were evaluated to determine genetic diversity and population structure. The number of alleles ranged from 2 to 19, with an average of 5.44 alleles per locus. Polymorphic information content (PIC) ranged from 0.031 to 0.915 with a mean of 0.43. In addition, the gene diversity index ranged from 0.03 to 0.92 with an average of 0.46. The expected heterozygosity ranged from 0.00 to 0.359 with a mean of 0.124. The unbiased expected heterozygosity ranged from 0.00 to 0.319 with an average of 0.112. The mean values of the number of effective alleles (Ne), genetic diversity of Nei (H) and Shannon's information index (I) were estimated at 1.190, 1.049 and 0.168, respectively. The highest genetic diversity (GD) was estimated between genotypes G1 and G27. In the UPGMA dendrogram, the 63 genotypes were grouped into three clusters. The three main coordinates were able to explain 12.64, 6.38 and 4.90% of genetic diversity, respectively. AMOVA revealed diversity within populations at 78% and between populations at 22%. The current populations were found to be highly structured. Model-based cluster analyses classified the 63 genotypes studied into three subpopulations. The values of F-statistic (Fst) for the identified subpopulations were 0.253, 0.330 and 0.244, respectively. In addition, the expected values of heterozygosity (He) for these sub-populations were recorded as 0.45, 0.46 and 0.44, respectively. Therefore, SSR markers can be useful not only in genetic diversity and association analysis of wheat but also in its germplasm for various agronomic traits or mechanisms of tolerance to environmental stresses.
Collapse
Affiliation(s)
- Aras Türkoğlu
- Department of Field Crops, Faculty of Agriculture, Necmettin Erbakan University, 42310 Konya, Turkey
| | - Kamil Haliloğlu
- Department of Field Crops, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
| | - Seyyed Abolgahasem Mohammadi
- Department of Plant Breeding and Biotechnology, Faculty of Agriculture, University of Tabriz, Tabriz 5166616471, Iran
| | - Ali Öztürk
- Department of Field Crops, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
| | - Parisa Bolouri
- Department of Field Crops, Faculty of Agriculture, Ataturk University, 25240 Erzurum, Turkey
| | - Güller Özkan
- Department of Biology, Faculty of Science, Ankara University, 06100 Ankara, Turkey
| | - Jan Bocianowski
- Department of Mathematical and Statistical Methods, Poznań University of Life Sciences, Wojska Polskiego 28, 60-637 Poznań, Poland
| | - Alireza Pour-Aboughadareh
- Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization (AREEO), Karaj 31585-854, Iran
| | - Bita Jamshidi
- Department of Food Security and Public Health, Khabat Technical Institute, Erbil Polytechnic University, Erbil 44001, Iraq
| |
Collapse
|
29
|
Chen K, Yang H, Peng Y, Liu D, Zhang J, Zhao Z, Wu L, Lin T, Bai L, Wang L. Genomic analyses provide insights into the polyploidization-driven herbicide adaptation in Leptochloa weeds. PLANT BIOTECHNOLOGY JOURNAL 2023. [PMID: 37154437 PMCID: PMC10363762 DOI: 10.1111/pbi.14065] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Revised: 02/21/2023] [Accepted: 04/14/2023] [Indexed: 05/10/2023]
Abstract
Polyploidy confers a selective advantage under stress conditions; however, whether polyploidization mediates enhanced herbicide adaptation remains largely unknown. Tetraploid Leptochloa chinensis is a notorious weed in the rice ecosystem, causing severe yield loss in rice. In China, L. chinensis has only one sister species, the diploid L. panicea, whose damage is rarely reported. To gain insights into the effects of polyploidization on herbicide adaptation, we first assembled a high-quality genome of L. panicea and identified genome structure variations with L. chinensis. Moreover, we identified herbicide-resistance genes specifically expanded in L. chinensis, which may confer a greater herbicide adaptability in L. chinensis. Analysis of gene retention and loss showed that five herbicide target-site genes and several herbicide nontarget-site resistance gene families were retained during polyploidization. Notably, we identified three pairs of polyploidization-retained genes including LcABCC8, LcCYP76C1 and LcCYP76C4 that may enhance herbicide resistance. More importantly, we found that both copies of LcCYP76C4 were under herbicide selection during the spread of L. chinensis in China. Furthermore, we identified another gene potentially involved in herbicide resistance, LcCYP709B2, which is also retained during polyploidization and under selection. This study provides insights into the genomic basis of the enhanced herbicide adaptability of Leptochloa weeds during polyploidization and provides guidance for the precise and efficient control of polyploidy weeds.
Collapse
Affiliation(s)
- Ke Chen
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha, China
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
- Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
- Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Haona Yang
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha, China
- Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China
- Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Yajun Peng
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha, China
- Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Ducai Liu
- Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | | | - Zhenghong Zhao
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha, China
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
- Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
| | - Lamei Wu
- Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Tao Lin
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory of Growth and Developmental Regulation for Protected Vegetable Crops, College of Horticulture, China Agricultural University, Beijing, China
| | - Lianyang Bai
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha, China
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
- Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
- Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| | - Lifeng Wang
- State Key Laboratory of Hybrid Rice, Hunan Academy of Agricultural Sciences, Changsha, China
- Key Laboratory of Indica Rice Genetics and Breeding in the Middle and Lower Reaches of Yangtze River Valley, Ministry of Agriculture and Rural Affairs, Hunan Rice Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
- Huangpu Research Institute of Longping Agricultural Science and Technology, Guangzhou, China
- Longping Branch, College of Biology, Hunan University, Changsha, China
- Hunan Weed Science Key Laboratory, Hunan Agricultural Biotechnology Research Institute, Hunan Academy of Agricultural Sciences, Changsha, China
| |
Collapse
|
30
|
Chang C, Zhang H, Lu J, Si H, Ma C. Genetic Improvement of Wheat with Pre-Harvest Sprouting Resistance in China. Genes (Basel) 2023; 14:genes14040837. [PMID: 37107595 PMCID: PMC10137347 DOI: 10.3390/genes14040837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 04/03/2023] Open
Abstract
Wheat pre-harvest sprouting (PHS) refers to the germination of seeds directly on the spike due to rainy weather before harvest, which often results in yield reduction, quality deterioration, and seed value loss. In this study, we reviewed the research progress in the quantitative trait loci (QTL) detection and gene excavation related to PHS resistance in wheat. Simultaneously, the identification and creation of germplasm resources and the breeding of wheat with PHS resistance were expounded in this study. Furthermore, we also discussed the prospect of molecular breeding during genetic improvement of PHS-resistant wheat.
Collapse
|
31
|
Zhang P, Ni Y, Jiao Z, Li J, Wang T, Yao Z, Jiang Y, Yang X, Sun Y, Li H, He D, Niu J. The wheat leaf delayed virescence of mutant dv4 is associated with the abnormal photosynthetic and antioxidant systems. Gene X 2023; 856:147134. [PMID: 36586497 DOI: 10.1016/j.gene.2022.147134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/29/2022] Open
Abstract
Chlorophyll (Chl) is a key pigment for wheat (Triticum aestivum L.) photosynthesis, consequently impacts grain yield. A wheat mutant named as delayed virescence 4 (dv4) was obtained from cultivar Guomai 301 (wild type, WT) treated with ethyl methane sulfonate (EMS). The seedling leaves of dv4 were shallow yellow, apparently were chlorophyll deficient. They started to turn green at the jointing stage and returned to almost ordinary green at the heading stage. Leaf transcriptome comparison of Guomai 301 and dv4 at the jointing stage showed that most differentially expressed genes (DEGs) of transcription and translation were highly expressed in dv4, one key gene nicotianamine aminotransferase A (NAAT-A) involved in the synthesis and metabolism pathways of tyrosine, methionine and phenylalanine was significantly lowly expressed. The expression levels of the most photosynthesis related genes, such as photosystem I (PS I), ATPase and light-harvesting chlorophyll protein complex-related homeotypic genes, and protochlorophyllide reductase A (PORA) were lower; but macromolecule degradation and hypersensitivity response (HR) related gene heat shock protein 82 (HSP82) was highly expressed. Compared to WT, the contents of macromolecules such as proteins and sugars were reduced; the contents of Chl a, Chl b, total Chl, and carotenoids in leaves of dv4 were significantly less at the jointing stage, while the ratio of Chl a / Chl b was the same as that of WT. The net photosynthetic rate, stomatal conductance and transpiration rate of dv4 were significantly lower. The H2O2 content were higher, while the contents of total phenol and malondialdehyde (MDA), antioxidant enzyme activities were lower in leaves of dv4. In conclusion, the reduced contents of macromolecules and photosynthetic pigments, the abnormal photosynthetic and antioxidant systems were closely related to the phenotype of dv4.
Collapse
Affiliation(s)
- Peipei Zhang
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Yongjing Ni
- Shangqiu Academy of Agricultural and Forestry Sciences, Shangqiu 476000, Henan, China
| | - Zhixin Jiao
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Junchang Li
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Ting Wang
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Ziping Yao
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Yumei Jiang
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Xiwen Yang
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Yulong Sun
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Huijuan Li
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China
| | - Dexian He
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| | - Jishan Niu
- Henan Technology Innovation Centre of Wheat / National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, Henan, China.
| |
Collapse
|
32
|
Liu M, Wang C, Xu Q, Pan Y, Jiang B, Zhang L, Zhang Y, Tian Z, Lu J, Ma C, Chang C, Zhang H. Genome-wide identification of the CPK gene family in wheat (Triticum aestivum L.) and characterization of TaCPK40 associated with seed dormancy and germination. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:608-623. [PMID: 36780723 DOI: 10.1016/j.plaphy.2023.02.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 02/01/2023] [Accepted: 02/07/2023] [Indexed: 06/18/2023]
Abstract
Calcium-dependent protein kinases (CPKs), important sensors of calcium signals, play an essential role in plant growth, development, and stress responses. Although the CPK gene family has been characterized in many plants, the functions of the CPK gene family in wheat, including their relationship to seed dormancy and germination, remain unclear. In this study, we identified 84 TaCPK genes in wheat (TaCPK1-84). According to their phylogenetic relationship, they were divided into four groups (I-IV). TaCPK genes in the same group were found to have similar gene structures and motifs. Chromosomal localization indicated that TaCPK genes were unevenly distributed across 21 wheat chromosomes. TaCPK gene expansion occurred through segmental duplication events and underwent strong negative selection. A large number of cis-regulatory elements related to light response, phytohormone response, and abiotic stress response were identified in the upstream promoter sequences of TaCPK genes. TaCPK gene expression was found to be tissue- and growth-stage-diverse. Analysis of the expression patterns of several wheat varieties with contrasting seed dormancy and germination phenotypes resulted in the identification of 11 candidate genes (TaCPK38/-40/-43/-47/-50/-60/-67/-70/-75/-78/-80) which are likely associated with seed dormancy and germination. The ectopic expression of TaCPK40 in Arabidopsis promoted seed germination and reduced abscisic acid (ABA) sensitivity during germination, indicating that TaCPK40 negatively regulates seed dormancy and positively regulates seed germination. These findings advance our understanding of the multifaceted functions of CPK genes in seed dormancy and germination, and provide potential candidate genes for controlling wheat seed dormancy and germination.
Collapse
Affiliation(s)
- Mingli Liu
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Afairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Chenchen Wang
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Afairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Qing Xu
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Afairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Yonghao Pan
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Afairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Bingli Jiang
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Afairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Litian Zhang
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Afairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Yue Zhang
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Afairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Zhuangbo Tian
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Afairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Jie Lu
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Afairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Chuanxi Ma
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Afairs, Anhui Agricultural University, Hefei, 230036, Anhui, China
| | - Cheng Chang
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Afairs, Anhui Agricultural University, Hefei, 230036, Anhui, China.
| | - Haiping Zhang
- College of Agronomy, Key Laboratory of Wheat Biology and Genetic Improvement on Southern Yellow & Huai River Valley, Ministry of Agriculture and Rural Afairs, Anhui Agricultural University, Hefei, 230036, Anhui, China.
| |
Collapse
|
33
|
Bilal Tufail M, Yasir M, Zuo D, Cheng H, Ali M, Hafeez A, Soomro M, Song G. Identification and Characterization of Phytocyanin Family Genes in Cotton Genomes. Genes (Basel) 2023; 14:genes14030611. [PMID: 36980883 PMCID: PMC10048054 DOI: 10.3390/genes14030611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 03/04/2023] Open
Abstract
Phytocyanins (PCs) are a class of plant-specific blue copper proteins that have been demonstrated to play a role in electron transport and plant development. Through analysis of the copper ligand residues, spectroscopic properties, and domain architecture of the protein, PCs have been grouped into four subfamilies: uclacyanins (UCs), stellacyanins (SCs), plantacyanins (PLCs), and early nodulin-like proteins (ENODLs). The present study aimed to identify and characterise the PCs present in three distinct cotton species (Gossypium hirsutum, Gossyium arboreum, and Gossypium raimondii) through the identification of 98, 63, and 69 genes respectively. We grouped PCs into four clades by using bioinformatics analysis and sequence alignment, which exhibit variations in gene structure and motif distribution. PCs are distributed across all chromosomes in each of the three species, with varying numbers of exons per gene and multiple conserved motifs, and with a minimum of 1 and maximum of 11 exons found on one gene. Transcriptomic data and qRT-PCR analysis revealed that two highly differentiated PC genes were expressed at the fibre initiation stage, while three highly differentiated PCs were expressed at the fibre elongation stage. These findings serve as a foundation for further investigations aimed at understanding the contribution of this gene family in cotton fibre production.
Collapse
Affiliation(s)
- Muhammad Bilal Tufail
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Muhammad Yasir
- The Key Laboratory for Quality Improvement of Agricultural Products of Zhejiang Province, College of Advanced Agricultural Sciences, Zhejiang A&F University, Hangzhou 311300, China
| | - Dongyun Zuo
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Hailiang Cheng
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Mushtaque Ali
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Abdul Hafeez
- Department of Agronomy, Sindh Agriculture University Campus Umerkot, Sindh 69100, Pakistan
| | - Mahtab Soomro
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Guoli Song
- State Key Laboratory of Cotton Biology, Institute of Cotton Research of the Chinese Academy of Agricultural Sciences, Anyang 455000, China
- Correspondence: ; Tel.: +86-037-2256-2377
| |
Collapse
|
34
|
Liu G, Zhang R, Li S, Ullah R, Yang F, Wang Z, Guo W, You M, Li B, Xie C, Wang L, Liu J, Ni Z, Sun Q, Liang R. TaMADS29 interacts with TaNF-YB1 to synergistically regulate early grain development in bread wheat. SCIENCE CHINA. LIFE SCIENCES 2023:10.1007/s11427-022-2286-0. [PMID: 36802319 DOI: 10.1007/s11427-022-2286-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Accepted: 01/18/2023] [Indexed: 02/23/2023]
Abstract
Grain development is a crucial determinant of yield and quality in bread wheat (Triticum aestivum L.). However, the regulatory mechanisms underlying wheat grain development remain elusive. Here we report how TaMADS29 interacts with TaNF-YB1 to synergistically regulate early grain development in bread wheat. The tamads29 mutants generated by CRISPR/Cas9 exhibited severe grain filling deficiency, coupled with excessive accumulation of reactive oxygen species (ROS) and abnormal programmed cell death that occurred in early developing grains, while overexpression of TaMADS29 increased grain width and 1,000-kernel weight. Further analysis revealed that TaMADS29 interacted directly with TaNF-YB1; null mutation in TaNF-YB1 caused grain developmental deficiency similar to tamads29 mutants. The regulatory complex composed of TaMADS29 and TaNF-YB1 exercises its possible function that inhibits the excessive accumulation of ROS by regulating the genes involved in chloroplast development and photosynthesis in early developing wheat grains and prevents nucellar projection degradation and endosperm cell death, facilitating transportation of nutrients into the endosperm and wholly filling of developing grains. Collectively, our work not only discloses the molecular mechanism of MADS-box and NF-Y TFs in facilitating bread wheat grain development, but also indicates that caryopsis chloroplast might be a central regulator of grain development rather than merely a photosynthesis organelle. More importantly, our work offers an innovative way to breed high-yield wheat cultivars by controlling the ROS level in developing grains.
Collapse
Affiliation(s)
- Guoyu Liu
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Runqi Zhang
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Sen Li
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Rehmat Ullah
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Fengping Yang
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zihao Wang
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Mingshan You
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Baoyun Li
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Chaojie Xie
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Liangsheng Wang
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Jie Liu
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China
| | - Rongqi Liang
- Frontiers Science Center for Molecular Design Breeding (MOE), State Key Laboratory for Agrobiotechnology, State Key Laboratory of Plant Physiology and Biochemistry, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China.
| |
Collapse
|
35
|
Abstract
Wheat grain development is an important biological process to determine grain yield and quality, which is controlled by the interplay of genetic, epigenetic, and environmental factors. Wheat grain development has been extensively characterized at the phenotypic and genetic levels. The advent of innovative molecular technologies allows us to characterize genes, proteins, and regulatory factors involved in wheat grain development, which have enhanced our understanding of the wheat seed development process. However, wheat is an allohexaploid with a large genome size, the molecular mechanisms underlying the wheat grain development have not been well understood as those in diploids. Understanding grain development, and how it is regulated, is of fundamental importance for improving grain yield and quality through conventional breeding or genetic engineering. Herein, we review the current discoveries on the molecular mechanisms underlying wheat grain development. Notably, only a handful of genes that control wheat grain development have, thus far, been well characterized, their interplay underlying the grain development remains elusive. The synergistic network-integrated genomics and epigenetics underlying wheat grain development and how the subgenome divergence dynamically and precisely regulates wheat grain development are unknown.
Collapse
Affiliation(s)
- Yiling Wang
- College of Life Science, Shanxi Normal University, Taiyuan, China
| | - Genlou Sun
- Biology Department, Saint Mary's University, Halifax, Canada
| |
Collapse
|
36
|
Pan Y, Surendra A, Liu Z, Ouellet T, Foroud NA. Differential Expression Feature Extraction (DEFE): A Case Study in Wheat FHB RNA-Seq Data Analysis. Methods Mol Biol 2023; 2659:137-159. [PMID: 37249891 DOI: 10.1007/978-1-0716-3159-1_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In differential gene expression data analysis, one objective is to identify groups of co-expressed genes from a large dataset in order to detect the association between such a group of genes and an experimental condition. This is often done through a clustering approach, such as k-means or bipartition hierarchical clustering, based on particular similarity measures in the grouping process. In such a dataset, the gene differential expression itself is an innate attribute that can be used in the feature extraction process. For example, in a dataset consisting of multiple treatments versus their controls, the expression of a gene in each treatment would have three possible behaviors, upregulated, downregulated, or unchanged. We present in this chapter, a differential expression feature extraction (DEFE) method by using a string consisting of three numerical values at each character to denote such behavior, i.e., 1 = up, 2 = down, and 0 = unchanged, which results in up to 3B differential expression patterns across all B comparisons. This approach has been successfully applied in many research projects, and among these, we demonstrate the strength of DEFE in a case study on RNA-sequencing (RNA-seq) data analysis of wheat challenged with the phytopathogenic fungus, Fusarium graminearum. Combinations of multiple schemes of DEFE patterns revealed groups of genes putatively associated with resistance or susceptibility to FHB.
Collapse
Affiliation(s)
- Youlian Pan
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada.
| | - Anuradha Surendra
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Ziying Liu
- Digital Technologies Research Centre, National Research Council Canada, Ottawa, ON, Canada
| | - Thérèse Ouellet
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, Ottawa, ON, Canada
| | - Nora A Foroud
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada
| |
Collapse
|
37
|
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.
Collapse
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:
| |
Collapse
|
38
|
Zia MAB, Yousaf MF, Asim A, Naeem M. An overview of genome-wide association mapping studies in Poaceae species (model crops: wheat and rice). Mol Biol Rep 2022; 49:12077-12090. [DOI: 10.1007/s11033-022-08036-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 10/17/2022] [Indexed: 11/06/2022]
|
39
|
Olivera PD, Szabo LJ, Kokhmetova A, Morgounov A, Luster DG, Jin Y. Puccinia graminis f. sp. tritici Population Causing Recent Wheat Stem Rust Epidemics in Kazakhstan Is Highly Diverse and Includes Novel Virulence Pathotypes. PHYTOPATHOLOGY 2022; 112:2403-2415. [PMID: 35671480 DOI: 10.1094/phyto-08-21-0320-r] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a reemerging disease that caused severe epidemics in northern Kazakhstan and western Siberia in the period of 2015 to 2019. We analyzed 51 stem rust samples collected between 2015 and 2017 in five provinces in Kazakhstan. A total of 112 Pgt races were identified from 208 single-pustule isolates. These races are phenotypically and genotypically diverse, and most of them are likely of sexual origin. No differentiation of phenotypes and single-nucleotide polymorphism genotypes was observed between isolates from Akmola and North Kazakhstan provinces, supporting the idea of a wide dispersal of inoculum in the northern regions of the country. Similarities in virulence profiles with Pgt races previously reported in Siberia, Russia, suggest that northern Kazakhstan and western Siberia constitute a single stem rust epidemiological region. In addition to the races of sexual origin, six races reported in Europe, the Caucasus, and East Africa were detected in Kazakhstan, indicating that this epidemiological region is not isolated, and spore inflow from the west occurs. Virulence alone or in combination to several genes effective against the Ug99 race group was detected, including novel virulence on Sr32 + Sr40 and Sr47. The occurrence of a highly diverse Pgt population with virulence to an important group of Sr genes demonstrated the importance of the pathogen's sexual cycle in generating new and potentially damaging virulence combinations.
Collapse
Affiliation(s)
- P D Olivera
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - L J Szabo
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN 55108, U.S.A
| | - A Kokhmetova
- Institute of Plant Biology and Biotechnology, Almaty, Kazakhstan
| | - A Morgounov
- International Maize and Wheat Improvement Center (CIMMYT), Ankara, Turkey
| | - D G Luster
- USDA-ARS Foreign Disease-Weed Science Research Unit, Ft. Detrick, MD 21702, U.S.A
| | - Y Jin
- USDA-ARS Cereal Disease Laboratory, University of Minnesota, St. Paul, MN 55108, U.S.A
| |
Collapse
|
40
|
Iqbal M, Semagn K, Jarquin D, Randhawa H, McCallum BD, Howard R, Aboukhaddour R, Ciechanowska I, Strenzke K, Crossa J, Céron-Rojas JJ, N’Diaye A, Pozniak C, Spaner D. Identification of Disease Resistance Parents and Genome-Wide Association Mapping of Resistance in Spring Wheat. PLANTS (BASEL, SWITZERLAND) 2022; 11:2905. [PMID: 36365358 PMCID: PMC9658635 DOI: 10.3390/plants11212905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/03/2022] [Accepted: 10/25/2022] [Indexed: 06/16/2023]
Abstract
The likelihood of success in developing modern cultivars depend on multiple factors, including the identification of suitable parents to initiate new crosses, and characterizations of genomic regions associated with target traits. The objectives of the present study were to (a) determine the best economic weights of four major wheat diseases (leaf spot, common bunt, leaf rust, and stripe rust) and grain yield for multi-trait restrictive linear phenotypic selection index (RLPSI), (b) select the top 10% cultivars and lines (hereafter referred as genotypes) with better resistance to combinations of the four diseases and acceptable grain yield as potential parents, and (c) map genomic regions associated with resistance to each disease using genome-wide association study (GWAS). A diversity panel of 196 spring wheat genotypes was evaluated for their reaction to stripe rust at eight environments, leaf rust at four environments, leaf spot at three environments, common bunt at two environments, and grain yield at five environments. The panel was genotyped with the Wheat 90K SNP array and a few KASP SNPs of which we used 23,342 markers for statistical analyses. The RLPSI analysis performed by restricting the expected genetic gain for yield displayed significant (p < 0.05) differences among the 3125 economic weights. Using the best four economic weights, a subset of 22 of the 196 genotypes were selected as potential parents with resistance to the four diseases and acceptable grain yield. GWAS identified 37 genomic regions, which included 12 for common bunt, 13 for leaf rust, 5 for stripe rust, and 7 for leaf spot. Each genomic region explained from 6.6 to 16.9% and together accounted for 39.4% of the stripe rust, 49.1% of the leaf spot, 94.0% of the leaf rust, and 97.9% of the common bunt phenotypic variance combined across all environments. Results from this study provide valuable information for wheat breeders selecting parental combinations for new crosses to develop improved germplasm with enhanced resistance to the four diseases as well as the physical positions of genomic regions that confer resistance, which facilitates direct comparisons for independent mapping studies in the future.
Collapse
Affiliation(s)
- Muhammad Iqbal
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4–10 Agriculture-Forestry Centre, Edmonton, AB T6G 2P5, Canada
| | - Kassa Semagn
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4–10 Agriculture-Forestry Centre, Edmonton, AB T6G 2P5, Canada
| | - Diego Jarquin
- Agronomy Department, University of Florida, Gainesville, FL 32611, USA
| | - Harpinder Randhawa
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada
| | - Brent D. McCallum
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, MB R6M 1Y5, Canada
| | - Reka Howard
- Department of Statistics, University of Nebraska—Lincoln, Lincoln, NE 68583, USA
| | - Reem Aboukhaddour
- Lethbridge Research and Development Centre, Agriculture and Agri-Food Canada, 5403 1st Avenue South, Lethbridge, AB T1J 4B1, Canada
| | - Izabela Ciechanowska
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4–10 Agriculture-Forestry Centre, Edmonton, AB T6G 2P5, Canada
| | - Klaus Strenzke
- Department of Agricultural, Food and Nutritional Science, University of Alberta, 4–10 Agriculture-Forestry Centre, Edmonton, AB T6G 2P5, Canada
| | - José Crossa
- Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), Km 45 Carretera, Veracruz 52640, Mexico
| | - J. Jesus Céron-Rojas
- Biometrics and Statistics Unit, International Maize and Wheat Improvement Center (CIMMYT), Km 45 Carretera, Veracruz 52640, Mexico
| | - Amidou N’Diaye
- Crop Development Centre and Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, 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, University of Alberta, 4–10 Agriculture-Forestry Centre, Edmonton, AB T6G 2P5, Canada
| |
Collapse
|
41
|
Rakkammal K, Priya A, Pandian S, Maharajan T, Rathinapriya P, Satish L, Ceasar SA, Sohn SI, Ramesh M. Conventional and Omics Approaches for Understanding the Abiotic Stress Response in Cereal Crops-An Updated Overview. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11212852. [PMID: 36365305 PMCID: PMC9655223 DOI: 10.3390/plants11212852] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/19/2022] [Accepted: 10/22/2022] [Indexed: 05/22/2023]
Abstract
Cereals have evolved various tolerance mechanisms to cope with abiotic stress. Understanding the abiotic stress response mechanism of cereal crops at the molecular level offers a path to high-yielding and stress-tolerant cultivars to sustain food and nutritional security. In this regard, enormous progress has been made in the omics field in the areas of genomics, transcriptomics, and proteomics. Omics approaches generate a massive amount of data, and adequate advancements in computational tools have been achieved for effective analysis. The combination of integrated omics and bioinformatics approaches has been recognized as vital to generating insights into genome-wide stress-regulation mechanisms. In this review, we have described the self-driven drought, heat, and salt stress-responsive mechanisms that are highlighted by the integration of stress-manipulating components, including transcription factors, co-expressed genes, proteins, etc. This review also provides a comprehensive catalog of available online omics resources for cereal crops and their effective utilization. Thus, the details provided in the review will enable us to choose the appropriate tools and techniques to reduce the negative impacts and limit the failures in the intensive crop improvement study.
Collapse
Affiliation(s)
- Kasinathan Rakkammal
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India
| | - Arumugam Priya
- Department of Biological Sciences, North Carolina State University, Raleigh, NC 27606, USA
| | - Subramani Pandian
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea
| | - Theivanayagam Maharajan
- Department of Biosciences, Rajagiri College of Social Sciences, Cochin 683104, Kerala, India
| | - Periyasamy Rathinapriya
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India
| | - Lakkakula Satish
- Applied Phycology and Biotechnology Division, Marine Algal Research Station, Mandapam Camp, CSIR—Central Salt and Marine Chemicals Research Institute, Bhavnagar 623519, Tamil Nadu, India
| | | | - Soo-In Sohn
- Department of Agricultural Biotechnology, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Korea
| | - Manikandan Ramesh
- Department of Biotechnology, Science Campus, Alagappa University, Karaikudi 630003, Tamil Nadu, India
- Correspondence:
| |
Collapse
|
42
|
Park SY, Jung WJ, Bang G, Hwang H, Kim JY. Transcriptome and Proteome Co-Profiling Offers an Understanding of Pre-Harvest Sprouting (PHS) Molecular Mechanisms in Wheat ( Triticum aestivum). PLANTS (BASEL, SWITZERLAND) 2022; 11:2807. [PMID: 36365261 PMCID: PMC9657071 DOI: 10.3390/plants11212807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 10/17/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
While wheat (Triticum aestivum L.) is a widely grown and enjoyed crop, the diverse and complex global situation and climate are exacerbating the instability of its supply. In particular, pre-harvest sprouting (PHS) is one of the major abiotic stresses that frequently occurs due to irregular climate conditions, causing serious damage to wheat and its quality. In this study, transcriptomic analysis with RNA-seq and proteomic analysis with LC-MS/MS were performed in PHS-treated spikes from two wheat cultivars presenting PHS sensitivity and tolerance, respectively. A total of 13,154 differentially expressed genes (DEGs) and 706 differentially expressed proteins (DEPs) were identified in four comparison groups between the susceptible/tolerant cultivars. Gene function and correlation analysis were performed to determine the co-profiled genes and proteins affected by PHS treatment. In the functional annotation of each comparative group, similar functions were confirmed in each cultivar under PHS treatment; however, in Keumgang PHS+7 (K7) vs. Woori PHS+7 (W7), functional annotations presented clear differences in the "spliceosome" and "proteasome" pathways. In addition, our results indicate that alternative splicing and ubiquitin-proteasome support the regulation of germination and seed dormancy. This study provides an advanced understanding of the functions involved in transcription and translation related to PHS mechanisms, thus enabling specific proposals for the further analysis of germination and seed dormancy mechanisms and pathways in wheat.
Collapse
Affiliation(s)
- Sang Yong Park
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea
| | - Woo Joo Jung
- Institute of Life Science and Natural Resources, Korea University, Seoul 02841, Korea
| | - Geul Bang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju 28119, Korea
| | - Heeyoun Hwang
- Research Center for Bioconvergence Analysis, Korea Basic Science Institute, Cheongju 28119, Korea
| | - Jae Yoon Kim
- Department of Plant Resources, College of Industrial Science, Kongju National University, Yesan 32439, Korea
| |
Collapse
|
43
|
Gohar S, Sajjad M, Zulfiqar S, Liu J, Wu J, Rahman MU. Domestication of newly evolved hexaploid wheat—A journey of wild grass to cultivated wheat. Front Genet 2022; 13:1022931. [PMID: 36263418 PMCID: PMC9574122 DOI: 10.3389/fgene.2022.1022931] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Domestication of wheat started with the dawn of human civilization. Since then, improvement in various traits including resistance to diseases, insect pests, saline and drought stresses, grain yield, and quality were improved through selections by early farmers and then planned hybridization after the discovery of Mendel’s laws. In the 1950s, genetic variability was created using mutagens followed by the selection of superior mutants. Over the last 3 decades, research was focused on developing superior hybrids, initiating marker-assisted selection and targeted breeding, and developing genetically modified wheat to improve the grain yield, tolerance to drought, salinity, terminal heat and herbicide, and nutritive quality. Acceptability of genetically modified wheat by the end-user remained a major hurdle in releasing into the environment. Since the beginning of the 21st century, changing environmental conditions proved detrimental to achieving sustainability in wheat production particularly in developing countries. It is suggested that high-tech phenotyping assays and genomic procedures together with speed breeding procedures will be instrumental in achieving food security beyond 2050.
Collapse
Affiliation(s)
- Sasha Gohar
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Muhammad Sajjad
- Department of Biosciences, COMSATS University Islamabad, Islamabad, Pakistan
| | - Sana Zulfiqar
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
| | - Jiajun Liu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, Shandong, China
- *Correspondence: Jiajie Wu, ; Mehboob-ur- Rahman,
| | - Mehboob-ur- Rahman
- Plant Genomics and Molecular Breeding Laboratory, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan
- Department of Biotechnology, Pakistan Institute of Engineering and Applied Sciences (PIEAS), Islamabad, Pakistan
- *Correspondence: Jiajie Wu, ; Mehboob-ur- Rahman,
| |
Collapse
|
44
|
Singh A, Basnal N, Shukla G, Chaudhary N, Singh S, Gaurav SS. Evaluation of efficacy of Phyto-synthesized iron oxide nanoparticles in contributing drought resilience in wheat ( Triticum aestivumL.). NANOTECHNOLOGY 2022; 33:485101. [PMID: 36001941 DOI: 10.1088/1361-6528/ac8c48] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 08/24/2022] [Indexed: 06/15/2023]
Abstract
Wheat is the majorly cultivated staple crop worldwide. The world witnesses a great percentage of yield loss of wheat due to drought stress. The present study aimed at evaluating the efficacy of phytosynthesized iron oxide nanoparticles (FeONPs) in contributing to drought resilience in wheat (Triticum aestivumL.) under rain-fed conditions. FeONPs were biosynthesized by using leaf extract ofProsopis cinerariaas a reducing and capping agent. The synthesized nanoparticles were characterized to evaluate the structural and biochemical aspects. The FeONPs were found to be irregularly spherical in shape with a mean size of 42.6 nm. The concentration of nanoparticles in the sample was found to be 164.01 mg l-1. An experimental setup was laid out in a randomized-plot design with 3 replications for Rabi season 2020-2021. Five dosages of nanoparticles were prepared as 12.5, 25, 50, 75 and 100 ppm from the stock solution. The wheat crop varieties grown in the field were subjected to a total of 3 treatments; Nanopriming, foliar application of FeONPs at seedling development stage (20 DAS), and tillering stage (30 DAS). Plants that were not treated with NPs were considered as control. No irrigation regime was followed as the effect of NPs on the crop was to be assessed under rain-fed conditions only. Plant growth parameters were recorded. The obtained results revealed that the application of FeONPs positively affected all the morphological and yield attributes in the wheat crop. The highest concentrations used were found to be most effective and showed a significantly pronounced effect as compared to the control atp≤ 0.05. The study concluded that the FeONPs can contribute to drought resilience in wheat.
Collapse
Affiliation(s)
- Amardeep Singh
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut (UP), India
| | - Namita Basnal
- Department of Biotechnology, Chaudhary Charan Singh University, Meerut (UP), India
| | - Gyanika Shukla
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut (UP), India
| | - Neha Chaudhary
- Department of Biotechnology, Chaudhary Charan Singh University, Meerut (UP), India
| | - Swati Singh
- Department of Biotechnology, Chaudhary Charan Singh University, Meerut (UP), India
| | - Shailendra Singh Gaurav
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University, Meerut (UP), India
| |
Collapse
|
45
|
Wheat genomic study for genetic improvement of traits in China. SCIENCE CHINA. LIFE SCIENCES 2022; 65:1718-1775. [PMID: 36018491 DOI: 10.1007/s11427-022-2178-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/10/2022] [Indexed: 01/17/2023]
Abstract
Bread wheat (Triticum aestivum L.) is a major crop that feeds 40% of the world's population. Over the past several decades, advances in genomics have led to tremendous achievements in understanding the origin and domestication of wheat, and the genetic basis of agronomically important traits, which promote the breeding of elite varieties. In this review, we focus on progress that has been made in genomic research and genetic improvement of traits such as grain yield, end-use traits, flowering regulation, nutrient use efficiency, and biotic and abiotic stress responses, and various breeding strategies that contributed mainly by Chinese scientists. Functional genomic research in wheat is entering a new era with the availability of multiple reference wheat genome assemblies and the development of cutting-edge technologies such as precise genome editing tools, high-throughput phenotyping platforms, sequencing-based cloning strategies, high-efficiency genetic transformation systems, and speed-breeding facilities. These insights will further extend our understanding of the molecular mechanisms and regulatory networks underlying agronomic traits and facilitate the breeding process, ultimately contributing to more sustainable agriculture in China and throughout the world.
Collapse
|
46
|
Structural and Functional Characterization at the Molecular Level of the MATE Gene Family in Wheat in Silico. CONTRAST MEDIA & MOLECULAR IMAGING 2022. [DOI: 10.1155/2022/9289007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A series of multidrug extransporters known as the multidrug and potentially toxic extrusion (MATE) genes are found in all living things and are crucial for the removal of heavy metal ions, metalloids, exogenous xenobiotics, endogenous secondary metabolites, and other toxic substances from the cells. However, there has only been a small amount of them in silico analysis of the MATE family of genes in plant species. In the current study, the MATE gene family was characterized in silico where two families and seven subfamilies based on their evolutionary relationships were proposed. Plant breeders may use TraesCS1D02G030400, TraesCS4B02G244400, and TraesCS1A02G029900 genes for marker-assisted or transgenic breeding to develop novel cultivars since these genes have been hypothesized from protein-protein interaction study to play a critical role in the transport of toxic chemicals across cells. The exon number varies from 01 to 14. One exon has TraesCS1A02G188100, TraesCS5B02G562500, TraesCS6A02G256400, and TraesCS6D02G384300 genes, while 14 exons have only two genes that are TraesCS6A02G418800 and TraesCS6D02G407900. Biological stress (infestations of disease) affects the expression of most of the MATE genes, with the gene TraesCS5D02G355500 having the highest expression level in the wheat expression browser tool. Using the Grain interpretation search engine tool, it is found that the vast bulk of MATE genes are voiced throughout biotic environmental stresses caused by disease pests, with the genotype TraesCS5B02G326600.1 from family 1 exhibiting the greatest level of expression throughout Fusarium head blight infection by Fusarium graminearum after 4 days of infection. The researchers constructed 39 ternary plots, each with a distinct degree of expression under biotic and abiotic stress settings, and observed that 44% of the triplets have imbalanced outputs (extreme values) due to their higher tissue specificity and increased intensity.
Collapse
|
47
|
Khan H, Krishnappa G, Kumar S, Mishra CN, Krishna H, Devate NB, Rathan ND, Parkash O, Yadav SS, Srivastava P, Biradar S, Kumar M, Singh GP. Genome-wide association study for grain yield and component traits in bread wheat (Triticum aestivum L.). Front Genet 2022; 13:982589. [PMID: 36092913 PMCID: PMC9458894 DOI: 10.3389/fgene.2022.982589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022] Open
Abstract
Genomic regions governing days to heading (DH), grain filling duration (GFD), grain number per spike (GNPS), grain weight per spike (GWPS), plant height (PH), and grain yield (GY) were investigated in a set of 280 diverse bread wheat genotypes. The genome-wide association studies (GWAS) panel was genotyped using a 35K Axiom Array and phenotyped in five environments. The GWAS analysis showed a total of 27 Bonferroni-corrected marker-trait associations (MTAs) on 15 chromosomes representing all three wheat subgenomes. The GFD showed the highest MTAs (8), followed by GWPS (7), GY (4), GNPS (3), PH (3), and DH (2). Furthermore, 20 MTAs were identified with more than 10% phenotypic variation. A total of five stable MTAs (AX-95024590, AX-94425015, AX-95210025 AX-94539354, and AX-94978133) were identified in more than one environment and associated with the expression of DH, GFD, GNPS, and GY. Similarly, two novel pleiotropic genomic regions with associated MTAs i.e. AX-94978133 (4D) and AX-94539354 (6A) harboring co-localized QTLs governing two or more traits were also identified. In silico analysis revealed that the SNPs were located on important putative candidate genes such as F-box-like domain superfamily, Lateral organ boundaries, LOB, Thioredoxin-like superfamily Glutathione S-transferase, RNA-binding domain superfamily, UDP-glycosyltransferase family, Serine/threonine-protein kinase, Expansin, Patatin, Exocyst complex component Exo70, DUF1618 domain, Protein kinase domain involved in the regulation of grain size, grain number, growth and development, grain filling duration, and abiotic stress tolerance. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection (MAS).
Collapse
Affiliation(s)
- Hanif Khan
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Gopalareddy Krishnappa
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
- ICAR-Sugarcane Breeding Institute, Coimbatore, India
- *Correspondence: Gopalareddy Krishnappa, ; Gyanendra Pratap Singh,
| | - Satish Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | | | - Hari Krishna
- ICAR-Indian Agricultural Research Institute, New Delhi, India
| | | | | | - Om Parkash
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | - Sonu Singh Yadav
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
| | | | - Suma Biradar
- University of Agricultural Sciences, Dharwad, India
| | - Monu Kumar
- ICAR-Indian Agricultural Research Institute, Jharkhand, India
| | - Gyanendra Pratap Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, India
- *Correspondence: Gopalareddy Krishnappa, ; Gyanendra Pratap Singh,
| |
Collapse
|
48
|
Triticale doubled haploid plant regeneration factors linked by structural equation modeling. J Appl Genet 2022; 63:677-690. [PMID: 36018540 PMCID: PMC9637073 DOI: 10.1007/s13353-022-00719-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/26/2022]
Abstract
Triticale regeneration via anther culture faces many difficulties, e.g., a low percentage of regenerated plants and the presence of albinos. Plant regeneration may be affected by abiotic stresses and by ingredients added to the induction medium. The latter influences biochemical pathways and plant regeneration efficiency. Among such ingredients, copper and silver ions acting as cofactors for enzymatic reactions are of interest. However, their role in plant tissue cultures and relationships with biochemical pathways has not been studied yet. The study evaluated relationships between DNA methylation, changes in DNA sequence variation, and green plant regeneration efficiency influenced by copper and silver ions during triticale plant regeneration. For this purpose, a biological model based on donor plants and their regenerants, a methylation-sensitive amplified fragment length polymorphism, and structural equation modeling were employed. The green plant regeneration efficiency varied from 0.71 to 6.06 green plants per 100 plated anthers. The values for the components of tissue culture-induced variation related to cytosine methylation in a CHH sequence context (where H is A, C, or T) were 8.65% for sequence variation, 0.76% for DNA demethylation, and 0.58% for de novo methylation. The proposed model states that copper ions affect the regeneration efficiency through cytosine methylation and may induce mutations through, e.g., oxidative processes, which may interfere with the green plant regeneration efficiency. The linear regression confirms that the plant regeneration efficiency rises with increasing copper ion concentration in the absence of Ag ions in the induction medium. The least absolute shrinkage and selection operator regression shows that de novo methylation, demethylation, and copper ions may be involved in the green plant regeneration efficiency. According to structural equation modeling, copper ions play a central role in the model determining the regeneration efficiency.
Collapse
|
49
|
Pathirana R, Carimi F. Management and Utilization of Plant Genetic Resources for a Sustainable Agriculture. PLANTS 2022; 11:plants11152038. [PMID: 35956515 PMCID: PMC9370719 DOI: 10.3390/plants11152038] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/27/2022] [Accepted: 08/01/2022] [Indexed: 12/02/2022]
Abstract
Despite the dramatic increase in food production thanks to the Green Revolution, hunger is increasing among human populations around the world, affecting one in nine people. The negative environmental and social consequences of industrial monocrop agriculture is becoming evident, particularly in the contexts of greenhouse gas emissions and the increased frequency and impact of zoonotic disease emergence, including the ongoing COVID-19 pandemic. Human activity has altered 70–75% of the ice-free Earth’s surface, squeezing nature and wildlife into a corner. To prevent, halt, and reverse the degradation of ecosystems worldwide, the UN has launched a Decade of Ecosystem Restoration. In this context, this review describes the origin and diversity of cultivated species, the impact of modern agriculture and other human activities on plant genetic resources, and approaches to conserve and use them to increase food diversity and production with specific examples of the use of crop wild relatives for breeding climate-resilient cultivars that require less chemical and mechanical input. The need to better coordinate in situ conservation efforts with increased funding has been highlighted. We emphasise the need to strengthen the genebank infrastructure, enabling the use of modern biotechnological tools to help in genotyping and characterising accessions plus advanced ex situ conservation methods, identifying gaps in collections, developing core collections, and linking data with international databases. Crop and variety diversification and minimising tillage and other field practices through the development and introduction of herbaceous perennial crops is proposed as an alternative regenerative food system for higher carbon sequestration, sustaining economic benefits for growers, whilst also providing social and environmental benefits.
Collapse
Affiliation(s)
- Ranjith Pathirana
- Plant & Food Research Australia Pty Ltd., Waite Campus Research Precinct—Plant Breeding WT46, University of Adelaide, Waite Rd, Urrbrae, SA 5064, Australia
- School of Agriculture, Food and Wine, Waite Campus Research Precinct—Plant Breeding WT46, University of Adelaide, Waite Rd, Urrbrae, SA 5064, Australia
- Correspondence:
| | - Francesco Carimi
- Istituto di Bioscienze e BioRisorse (IBBR), C.N.R., Corso Calatafimi 414, 90129 Palermo, Italy
| |
Collapse
|
50
|
Molinari C, Talbot NJ. A Basic Guide to the Growth and Manipulation of the Blast Fungus,
Magnaporthe oryzae. Curr Protoc 2022; 2:e523. [PMID: 35997707 PMCID: PMC9542439 DOI: 10.1002/cpz1.523] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The blast fungus, Magnaporthe oryzae, is a devastating plant pathogen that threatens global food security. The social and economic importance of blast disease has contributed to this filamentous fungus becoming a model organism for the study of host‐pathogen interactions. Availability of the complete genome sequences of many strains of the pathogen, as well as rice and wheat cultivars, coupled with the tractability of M. oryzae to classical and molecular genetic manipulation have contributed to its widespread study. Although M. oryzae has been extensively investigated for the past two decades, procedures for storing, maintaining, and manipulating the blast fungus in the laboratory had not been compiled and updated. As a consequence, there is considerable disparity in how the fungus is stored and manipulated between studies. In this article, we present a collection of protocols providing clear explanations of how to preserve filter stocks of M. oryzae; how to grow the fungus in both liquid and solid media; how to extract genomic DNA from fungal mycelium; how to induce appressorium formation on coverslips for visualization and tissue collection; and how to perform two distinct types of plant infection assay for virulence assessment. By sharing our most used laboratory procedures, we aim to address some of the knowledge gaps in current M. oryzae protocols and contribute to uniformity and robustness in studies by the Magnaporthe research community. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Storage of M. oryzae strains Basic Protocol 2: Revival and regular maintenance of M. oryzae cultures in solid medium Alternate Protocol 1: Regular maintenance of M. oryzae cultures in liquid medium Basic Protocol 3: Genomic DNA extraction from M. oryzae mycelium Alternate Protocol 2: Quick DNA extraction from M. oryzae mycelium Basic Protocol 4: M. oryzae induction of appressorium development on glass coverslips for microscopy Alternate Protocol 3: M. oryzae induction of appressorium development on glass coverslips for tissue collection Basic Protocol 5: M. oryzae rice infection assay through spray inoculation Alternate Protocol 4: M. oryzae leaf‐drop plant infection assay
Collapse
Affiliation(s)
- Camilla Molinari
- The Sainsbury Laboratory, Norwich Research Park University of East Anglia Norwich United Kingdom
| | - Nicholas J. Talbot
- The Sainsbury Laboratory, Norwich Research Park University of East Anglia Norwich United Kingdom
| |
Collapse
|