1
|
Liu Q, Zhao Y, Rahman S, She M, Zhang J, Yang R, Islam S, O'Hara G, Varshney RK, Liu H, Ma H, Ma W. The putative vacuolar processing enzyme gene TaVPE3cB is a candidate gene for wheat stem pith-thickness. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:138. [PMID: 37233825 DOI: 10.1007/s00122-023-04372-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 04/27/2023] [Indexed: 05/27/2023]
Abstract
KEY MESSAGE The vacuolar processing enzyme gene TaVPE3cB is identified as a candidate gene for a QTL of wheat pith-thickness on chromosome 3B by BSR-seq and differential expression analyses. The high pith-thickness (PT) of the wheat stem could greatly enhance stem mechanical strength, especially the basal internodes which support the heavier upper part, such as upper stems, leaves and spikes. A QTL for PT in wheat was previously discovered on 3BL in a double haploid population of 'Westonia' × 'Kauz'. Here, a bulked segregant RNA-seq analysis was applied to identify candidate genes and develop associated SNP markers for PT. In this study, we aimed at screening differentially expressed genes (DEGs) and SNPs in the 3BL QTL interval. Sixteen DEGs were obtained based on BSR-seq and differential expression analyses. Twenty-four high-probability SNPs in eight genes were identified by comparing the allelic polymorphism in mRNA sequences between the high PT and low PT samples. Among them, six genes were confirmed to be associated with PT by qRT-PCR and sequencing. A putative vacuolar processing enzyme gene TaVPE3cB was screened out as a potential PT candidate gene in Australian wheat 'Westonia'. A robust SNP marker associated with TaVPE3cB was developed, which can assist in the introgression of TaVPE3cB.b in wheat breeding programs. In addition, we also discussed the function of other DEGs which may be related to pith development and programmed cell death (PCD). A five-level hierarchical regulation mechanism of stem pith PCD in wheat was proposed.
Collapse
Affiliation(s)
- Qier Liu
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
- Provincial Key Laboratory of Agrobiology, and Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Yun Zhao
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences, Shijiazhuang, 050035, People's Republic of China
| | - Shanjida Rahman
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Maoyun She
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Jingjuan Zhang
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Rongchang Yang
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Shahidul Islam
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Graham O'Hara
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Rajeev K Varshney
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Hang Liu
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia
| | - Hongxiang Ma
- Provincial Key Laboratory of Agrobiology, and Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, People's Republic of China
| | - Wujun Ma
- Centre for Crop and Food Innovation, Food Futures Institute and College of Science, Health, Engineering and Education, Murdoch University, Perth, WA, 6150, Australia.
- College of Agronomy, Qingdao Agriculture University, Qingdao, 266109, People's Republic of China.
| |
Collapse
|
2
|
Xiong H, Li Y, Guo H, Xie Y, Zhao L, Gu J, Zhao S, Ding Y, Liu L. Genetic Mapping by Integration of 55K SNP Array and KASP Markers Reveals Candidate Genes for Important Agronomic Traits in Hexaploid Wheat. FRONTIERS IN PLANT SCIENCE 2021; 12:628478. [PMID: 33708233 PMCID: PMC7942297 DOI: 10.3389/fpls.2021.628478] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/29/2021] [Indexed: 06/12/2023]
Abstract
Agronomic traits such as heading date (HD), plant height (PH), thousand grain weight (TGW), and spike length (SL) are important factors affecting wheat yield. In this study, we constructed a high-density genetic linkage map using the Wheat55K SNP Array to map quantitative trait loci (QTLs) for these traits in 207 recombinant inbred lines (RILs). A total of 37 QTLs were identified, including 9 QTLs for HD, 7 QTLs for PH, 12 QTLs for TGW, and 9 QTLs for SL, which explained 3.0-48.8% of the phenotypic variation. Kompetitive Allele Specific PCR (KASP) markers were developed based on sequencing data and used for validation of the stably detected QTLs on chromosomes 3A, 4B and 6A using 400 RILs. A QTL cluster on chromosome 4B for PH and TGW was delimited to a 0.8 Mb physical interval explaining 12.2-22.8% of the phenotypic variation. Gene annotations and analyses of SNP effects suggested that a gene encoding protein Photosynthesis Affected Mutant 68, which is essential for photosystem II assembly, is a candidate gene affecting PH and TGW. In addition, the QTL for HD on chromosome 3A was narrowed down to a 2.5 Mb interval, and a gene encoding an R3H domain-containing protein was speculated to be the causal gene influencing HD. The linked KASP markers developed in this study will be useful for marker-assisted selection in wheat breeding, and the candidate genes provide new insight into genetic study for those traits in wheat.
Collapse
|
3
|
Zhong Y, Lu X, Deng Z, Lu Z, Fu M. A 1232 bp upstream sequence of glutamine synthetase 1b from Eichhornia crassipes is a root-preferential promoter sequence. BMC PLANT BIOLOGY 2021; 21:66. [PMID: 33514320 PMCID: PMC7845104 DOI: 10.1186/s12870-021-02832-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/11/2021] [Indexed: 06/12/2023]
Abstract
BACKGROUND Glutamine synthetase (GS) acts as a key enzyme in plant nitrogen (N) metabolism. It is important to understand the regulation of GS expression in plant. Promoters can initiate the transcription of its downstream gene. Eichhornia crassipes is a most prominent aquatic invasive plant, which has negative effects on environment and economic development. It also can be used in the bioremediation of pollutants present in water and the production of feeding and energy fuel. So identification and characterization of GS promoter in E. crassipes can help to elucidate its regulation mechanism of GS expression and further to control its N metabolism. RESULTS A 1232 bp genomic fragment upstream of EcGS1b sequence from E. crassipes (EcGS1b-P) has been cloned, analyzed and functionally characterized. TSSP-TCM software and PlantCARE analysis showed a TATA-box core element, a CAAT-box, root specific expression element, light regulation elements including chs-CMA1a, Box I, and Sp1 and other cis-acting elements in the sequence. Three 5'-deletion fragments of EcGS1b upstream sequence with 400 bp, 600 bp and 900 bp length and the 1232 bp fragment were used to drive the expression of β-glucuronidase (GUS) in tobacco. The quantitative test revealed that GUS activity decreased with the decreasing of the promoter length, which indicated that there were no negative regulated elements in the EcGS1-P. The GUS expressions of EcGS1b-P in roots were significantly higher than those in leaves and stems, indicating EcGS1b-P to be a root-preferential promoter. Real-time Quantitative Reverse Transcription-Polymerase Chain Reaction (qRT-PCR) analysis of EcGS1b gene also showed higher expression in the roots of E.crassipes than in stems and leaves. CONCLUSIONS EcGS1b-P is a root-preferential promoter sequence. It can specifically drive the transcription of its downstream gene in root. This study will help to elucidate the regulatory mechanisms of EcGS1b tissue-specific expression and further study its other regulatory mechanisms in order to utilize E.crassipes in remediation of eutrophic water and control its overgrowth from the point of nutrient metabolism.
Collapse
Affiliation(s)
- Yanshan Zhong
- Bioengineering Department, Biological and Pharmaceutical College, Guangdong University of Technology, Guangzhou, Guangdong, P.R. China, 510006
| | - Xiaodan Lu
- Bioengineering Department, Biological and Pharmaceutical College, Guangdong University of Technology, Guangzhou, Guangdong, P.R. China, 510006
| | - Zhiwei Deng
- Bioengineering Department, Biological and Pharmaceutical College, Guangdong University of Technology, Guangzhou, Guangdong, P.R. China, 510006
| | - Ziqing Lu
- Bioengineering Department, Biological and Pharmaceutical College, Guangdong University of Technology, Guangzhou, Guangdong, P.R. China, 510006
| | - Minghui Fu
- Bioengineering Department, Biological and Pharmaceutical College, Guangdong University of Technology, Guangzhou, Guangdong, P.R. China, 510006.
| |
Collapse
|
4
|
Bazhenov MS, Chernook AG, Goncharov NP, Chikida NN, Belousova MK, Karlov GI, Divashuk MG. The Allelic Diversity of the Gibberellin Signaling Pathway Genes in Aegilops tauschii Coss. PLANTS 2020; 9:plants9121696. [PMID: 33276632 PMCID: PMC7761575 DOI: 10.3390/plants9121696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 11/27/2020] [Accepted: 11/30/2020] [Indexed: 11/16/2022]
Abstract
Gibberellin-insensitive reduced height genes are widely spread in modern wheat varieties, making them resistant to lodging under conditions of intensive farming. However, the limited diversity of these genes present in wheat germplasm can limit the adaptability of newly created cultivars to the changing climate. The diversity of the gibberellin signaling pathway genes involved in plant height control- Reduced height 1 (Rht-D1), Gibberellin-insensitive dwarf 1 (Gid1‑D) and Gibberellin-insensitive dwarf 2 (Gid2-D)-was studied in the diploid wild goatgrass Aegilops tauschii Coss., one of the ancestral species of the bread wheat (Triticum aestivum L.) and the donor of its D subgenome, using high-throughput sequencing. The examination of 24 Ae. tauschii accessions of different geographical origins revealed a large number of new alleles (haplotypes) not found in bread wheat varieties. Some of the detected polymorphisms lead to changes in the amino acid sequence of proteins. Four isoforms (amino acid sequence variants) were found for the RHT-D1 protein, and two isoforms-for the GID1 and GID2 proteins, each. An analysis of the co-occurrence frequencies of various isoforms of the three proteins showed that their combinations were not random in Ae. tauschii, which may indicate the functional significance of their differences. New alleles of the Rht-D1, Gid1-D, and Gid2-D genes are promising for introgression into bread wheat and studying their effect on plant height and adaptability.
Collapse
Affiliation(s)
- Mikhail S. Bazhenov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia; (A.G.C.); (G.I.K.); (M.G.D.)
- Correspondence:
| | - Anastasiya G. Chernook
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia; (A.G.C.); (G.I.K.); (M.G.D.)
| | - Nikolay P. Goncharov
- Wheat Genetics Laboratory, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Akademika Lavrentieva Avenue, 10, 630090 Novosibirsk, Russia;
| | - Nadezhda N. Chikida
- Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), 190000 Saint Petersburg, Russia;
| | - Mariya Kh. Belousova
- Dagestan Experimental Station—The Branch of the Federal Research Center N. I. Vavilov All-Russian Institute of Plant Genetic Resources, Vavilovo Village, Derbent District, 368600 Dagestan, Russia;
| | - Gennady I. Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia; (A.G.C.); (G.I.K.); (M.G.D.)
| | - Mikhail G. Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia; (A.G.C.); (G.I.K.); (M.G.D.)
- Kurchatov Genomics Center–ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya Street, 42, 127550 Moscow, Russia
| |
Collapse
|
5
|
Kroupin PY, Karlov GI, Bespalova LA, Salina EA, Chernook AG, Watanabe N, Bazhenov MS, Panchenko VV, Nazarova LA, Kovtunenko VY, Divashuk MG. Effects of Rht17 in combination with Vrn-B1 and Ppd-D1 alleles on agronomic traits in wheat in black earth and non-black earth regions. BMC PLANT BIOLOGY 2020; 20:304. [PMID: 33050878 PMCID: PMC7556923 DOI: 10.1186/s12870-020-02514-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Accepted: 06/22/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Plant height is an important wheat trait that is regulated by multiple genes, among which Rht is of the utmost value. In wheat, Rht-B1p (=Rht17) is a mutant allele of the Rht gene that encodes for a DELLA-protein and results in the development of gibberellin-insensitive plants with a dwarfing phenotype. The pleiotropic effects of dwarfing genes on yield are highly dependent on both the genetic background and the environmental conditions. In Russia, the Central Non-Black Earth Region and Krasnodar Krai are two economically important regions that require differing management for sustainable wheat production for food, feed and industry. The purpose of our study was to compare the pleiotropic effects of Rht-B1p on the main valuable agronomic traits in the F3:4 families of the spring bread wheat Chris Mutant/Novosibirskaya 67 in the genetic background of Vrn-B1a/vrn-B1 (spring/winter phenotype) and Ppd-D1a/Ppd-D1b (insensitivity/sensitivity to photoperiod) alleles in a field experiment in Moscow and Krasnodar Krai. RESULTS Plant height was reduced on average by 21 cm (28%) and 25 cm (30%), respectively; Ppd-D1a slightly strengthened the dwarfing effect in Moscow and mitigated it in Krasnodar Krai. Grain weight of the main spike was reduced by Rht-B1p in Moscow and to lesser extent in Krasnodar; Ppd-D1a and Vrn-B1a tended to partially compensate for this loss in Krasnodar Krai. Thousand grain weight was reduced on average by 5.3 g (16%) and 2.9 g (10%) in Moscow and Krasnodar Krai, respectively, but was partially compensated for by Ppd-D1a in Krasnodar Krai. Harvest index was increased due to Rht-B1p by 6 and 10% in Moscow and Krasnodar Krai, respectively. Rht-B1p resulted in a delay of heading by 1-2 days in Moscow. Ppd-D1a accelerated heading by 1 day and 6 days in Moscow and in Krasnodar Krai, respectively. CONCLUSIONS Rht-B1p could be introduced into wheat breeding along with dwarfing genes such as Rht-B1b and Rht-D1b. Special attention should be paid to its combination with Ppd-D1a and Vrn-B1a as regulators of developmental rates, compensators of adverse effects of Rht-B1p on productivity and enhancers of positive effect of Rht-B1p on harvest index.
Collapse
Affiliation(s)
- Pavel Yu Kroupin
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow, 127550, Russia
- Centre for Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow, 127550, Russia
| | - Gennady I Karlov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow, 127550, Russia
- Centre for Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow, 127550, Russia
| | - Ludmila A Bespalova
- Department of Breeding and Seed Production of Wheat and Triticale, National center of grain named after P.P. Lukyanenko, Central Estate of KNIISH, Krasnodar, 350012, Russia
| | - Elena A Salina
- Kurchatov Genomics Center, Institute of Cytology and Genetics SB RAS, Prospekt Lavrentyeva 10, Novosibirsk, 630090, Russia
| | - Anastasiya G Chernook
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow, 127550, Russia
- Centre for Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow, 127550, Russia
| | - Nobuyoshi Watanabe
- College of Agriculture, Ibaraki University, 3-21-1 Chuo, Ami, Inashiki, Ibaraki, 300-0393, Japan
| | - Mikhail S Bazhenov
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow, 127550, Russia
- Centre for Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow, 127550, Russia
| | - Vladimir V Panchenko
- Department of Breeding and Seed Production of Wheat and Triticale, National center of grain named after P.P. Lukyanenko, Central Estate of KNIISH, Krasnodar, 350012, Russia
| | - Lubov A Nazarova
- Kurchatov Genomics Center-ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow, 127550, Russia
| | - Victor Ya Kovtunenko
- Department of Breeding and Seed Production of Wheat and Triticale, National center of grain named after P.P. Lukyanenko, Central Estate of KNIISH, Krasnodar, 350012, Russia
| | - Mikhail G Divashuk
- Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow, 127550, Russia.
- Centre for Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Timiryazevskaya street, 49, Moscow, 127550, Russia.
- Kurchatov Genomics Center-ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Timiryazevskaya str. 42, Moscow, 127550, Russia.
| |
Collapse
|