1
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Liu P, Feng W, Wang T, Zhang H, Mao S, Zhang H, Huang W, Liu H, Feng S, Chu Z. Investigation of Imidazolinone Herbicide Resistance Gene with KASP Markers for Japonica/ Geng Rice Varieties in the Huanghuaihai Region of China. PLANTS (BASEL, SWITZERLAND) 2024; 13:1097. [PMID: 38674507 PMCID: PMC11053791 DOI: 10.3390/plants13081097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 04/08/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024]
Abstract
Rice is a staple food for more than half of the global population due to its food security and sustainable development. Weeds compete with crops for sunlight and indispensable nutrients, affecting the yield and quality of crops. Breeding herbicide-tolerant rice varieties paired with herbicide application is expected to help with weed control. In this study, 194 Japonica/Geng rice varieties or lines collected from the Huanghuaihai region of China were screened by Kompetitive Allele-Specific PCR (KASP) markers based on four mutation sites within OsALS1 (LOC_Os02g30630), which is the target of imidazolinone (IMI) herbicides. Only the OsALS1627N haplotype was identified in 18 varieties, including the previously reported Jingeng818 (JG818), and its herbicide resistance was validated by treatment with three IMIs. To investigate the origin of the OsALS1627N haplotype in the identified varieties, six codominant PCR-based markers tightly linked with OsALS1 were developed. PCR analysis revealed that the other 17 IMI-tolerant varieties were derived from JG818. We randomly selected three IMI-tolerant varieties for comparative whole-genome resequencing with known receptor parent varieties. Sequence alignment revealed that more loci from JG818 have been introduced into IMI-tolerant varieties. However, all three IMI-tolerant varieties carried clustered third type single nucleotide polymorphism (SNP) sites from unknown parents, indicating that these varieties were not directly derived from JG818, whereas those from different intermediate improved lines were crossed with JG818. Overall, we found that only OsALS1627N from JG818 has been broadly introduced into the Huanghuaihai region of China. Additionally, the 17 identified IMI-tolerant varieties provide alternative opportunities for improving such varieties along with other good traits.
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Affiliation(s)
- Peng Liu
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory, College of Life Science, Wuhan University, Wuhan 430072, China; (P.L.); (T.W.); (H.Z.); (S.M.); (W.H.)
| | - Wenjie Feng
- Jining Academy of Agricultural Sciences, Jining 272031, China;
| | - Tao Wang
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory, College of Life Science, Wuhan University, Wuhan 430072, China; (P.L.); (T.W.); (H.Z.); (S.M.); (W.H.)
| | - Huadong Zhang
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory, College of Life Science, Wuhan University, Wuhan 430072, China; (P.L.); (T.W.); (H.Z.); (S.M.); (W.H.)
| | - Shuaige Mao
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory, College of Life Science, Wuhan University, Wuhan 430072, China; (P.L.); (T.W.); (H.Z.); (S.M.); (W.H.)
| | - Hua Zhang
- Tancheng Jinghua Seed Co., Ltd., Linyi 276100, China;
| | - Wenchao Huang
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory, College of Life Science, Wuhan University, Wuhan 430072, China; (P.L.); (T.W.); (H.Z.); (S.M.); (W.H.)
| | - Haifeng Liu
- College of Agronomy, Shandong Agricultural University, Taian 271018, China;
| | - Shangzong Feng
- Agro-Technical Popularization Centre of Linyi City, Linyi 276000, China
| | - Zhaohui Chu
- State Key Laboratory of Hybrid Rice, Hongshan Laboratory, College of Life Science, Wuhan University, Wuhan 430072, China; (P.L.); (T.W.); (H.Z.); (S.M.); (W.H.)
- College of Agronomy, Shandong Agricultural University, Taian 271018, China;
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2
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Povkhova LV, Pushkova EN, Rozhmina TA, Zhuchenko AA, Frykin RI, Novakovskiy RO, Dvorianinova EM, Gryzunov AA, Borkhert EV, Sigova EA, Vladimirov GN, Snezhkina AV, Kudryavtseva AV, Krasnov GS, Dmitriev AA, Melnikova NV. Development and Complex Application of Methods for the Identification of Mutations in the FAD3A and FAD3B Genes Resulting in the Reduced Content of Linolenic Acid in Flax Oil. PLANTS (BASEL, SWITZERLAND) 2022; 12:95. [PMID: 36616223 PMCID: PMC9824437 DOI: 10.3390/plants12010095] [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: 10/11/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Flax is grown worldwide for seed and fiber production. Linseed varieties differ in their oil composition and are used in pharmaceutical, food, feed, and industrial production. The field of application primarily depends on the content of linolenic (LIN) and linoleic (LIO) fatty acids. Inactivating mutations in the FAD3A and FAD3B genes lead to a decrease in the LIN content and an increase in the LIO content. For the identification of the three most common low-LIN mutations in flax varieties (G-to-A in exon 1 of FAD3A substituting tryptophan with a stop codon, C-to-T in exon 5 of FAD3A leading to arginine to a stop codon substitution, and C-to-T in exon 2 of FAD3B resulting in histidine to tyrosine substitution), three approaches were proposed: (1) targeted deep sequencing, (2) high resolution melting (HRM) analysis, (3) cleaved amplified polymorphic sequences (CAPS) markers. They were tested on more than a thousand flax samples of various types and showed promising results. The proposed approaches can be used in marker-assisted selection to choose parent pairs for crosses, separate heterogeneous varieties into biotypes, and select genotypes with desired homozygous alleles of the FAD3A and FAD3B genes at the early stages of breeding for the effective development of varieties with a particular LIN and LIO content, as well as in basic studies of the molecular mechanisms of fatty acid synthesis in flax seeds to select genotypes adequate to the tasks.
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Affiliation(s)
- Liubov V. Povkhova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elena N. Pushkova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Tatiana A. Rozhmina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia
| | - Alexander A. Zhuchenko
- Federal Research Center for Bast Fiber Crops, 172002 Torzhok, Russia
- All-Russian Horticultural Institute for Breeding, Agrotechnology and Nursery, 115598 Moscow, Russia
| | - Roman I. Frykin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Roman O. Novakovskiy
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Ekaterina M. Dvorianinova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | - Aleksey A. Gryzunov
- All-Russian Scientific Research Institute of Refrigeration Industry—Branch of V.M. Gorbatov Federal Research Center for Food Systems of Russian Academy of Sciences, 127422 Moscow, Russia
| | - Elena V. Borkhert
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Elizaveta A. Sigova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
- Moscow Institute of Physics and Technology, 141701 Moscow, Russia
| | | | - Anastasiya V. Snezhkina
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - George S. Krasnov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Alexey A. Dmitriev
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Nataliya V. Melnikova
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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3
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Lu G, Pan YB, Wang Z, Xu F, Cheng W, Huang X, Ren H, Pang C, Que Y, Xu L. Utilization of a Sugarcane100K Single Nucleotide Polymorphisms Microarray-Derived High-Density Genetic Map in Quantitative Trait Loci Mapping and Function Role Prediction of Genes Related to Chlorophyll Content in Sugarcane. FRONTIERS IN PLANT SCIENCE 2021; 12:817875. [PMID: 35027918 PMCID: PMC8750863 DOI: 10.3389/fpls.2021.817875] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 11/30/2021] [Indexed: 06/14/2023]
Abstract
Chlorophyll is the most important pigment for plant photosynthesis that plays an important role in crop growth and production. In this study, the chlorophyll content trait was explored to improve sugarcane yield. Two hundred and eighty-five F1 progenies from the cross YT93-159 × ROC22 with significantly different chlorophyll contents were included as test materials. The chlorophyll content of the +1 leaves during elongation phase was measured using a SPAD-502 meter through a three-crop cycle (plant cane, first ratoon, and second ratoon). Linkage analysis was conducted on a high-density genetic map constructed based on the sugarcane 100K SNP chip. In addition, Fv/Fm, plant height, stalk diameter, brix data were collected on plant cane during the elongation and maturation phases. The results showed that the +1 leaf SPAD values, which can be used as an important reference to evaluate the growth potential of sugarcane, were significantly and positively correlated with the Fv/Fm during elongation phase, as well as with plant height, stalk diameter, and brix during maturity phase (P < 0.01). The broad sense heritability (H 2) of the chlorophyll content trait was 0.66 for plant cane crop, 0.67 for first ratoon crop, and 0.73 for second ratoon crop, respectively, indicating that this trait was mainly controlled by genetic factors. Thirty-one quantitative trait loci (QTL) were detected by QTL mapping. Among them, a major QTL, qCC-R1, could account for 12.95% of phenotypic variation explained (PVE), and the other 30 minor QTLs explained 2.37-7.99% PVE. Twenty candidate genes related to chlorophyll content were identified in the QTLs plus a 200-Kb extension region within either sides, of which four were homologous genes involved in the chlorophyll synthesis process and the remaining 16 played a certain role in chlorophyll catabolic pathway, chloroplast organization, or photosynthesis. These results provide a theoretical reference for analyzing the genetic mechanism of chlorophyll synthesis and subsequent improvement of photosynthetic characteristics in sugarcane.
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Affiliation(s)
- Guilong Lu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Vegetables, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Yong-Bao Pan
- Sugarcane Research Unit, United States Department of Agriculture (USDA), Agricultural Research Service (ARS), Houma, LA, United States
| | - Zhoutao Wang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fu Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei Cheng
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xinge Huang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Hui Ren
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chao Pang
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Youxiong Que
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liping Xu
- Key Laboratory of Sugarcane Biology and Genetic Breeding, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, China
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4
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Mehnaz M, Dracatos P, Pham A, March T, Maurer A, Pillen K, Forrest K, Kulkarni T, Pourkheirandish M, Park RF, Singh D. Discovery and fine mapping of Rph28: a new gene conferring resistance to Puccinia hordei from wild barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:2167-2179. [PMID: 33774682 DOI: 10.1007/s00122-021-03814-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
A new gene Rph28 conferring resistance to barley leaf rust was discovered and fine-mapped on chromosome 5H from wild barley. Leaf rust is a highly destructive disease of barley caused by the fungal pathogen Puccinia hordei. Genetic resistance is considered to be the most effective, economical and eco-friendly approach to minimize losses caused by this disease. A study was undertaken to characterize and fine map a seedling resistance gene identified in a Hordeum vulgare ssp. spontaneum-derived barley line, HEB-04-101, that is broadly effective against a diverse set of Australian P. hordei pathotypes. Genetic analysis of an F3 population derived from a cross between HEB-04-101 and the H. vulgare cultivar Flagship (seedling susceptible) confirmed the presence of a single dominant gene for resistance in HEB-04-101. Selective genotyping was performed on representative plants from non-segregating homozygous resistant and homozygous susceptible F3 families using the targeted genotyping-by-sequencing (tGBS) assay. Putatively linked SNP markers with complete fixation were identified on the long arm of chromosome 5H spanning a physical interval between 622 and 669 Mb based on the 2017 Morex barley reference genome assembly. Several CAPS (cleaved amplified polymorphic sequences) markers were designed from the pseudomolecule sequence of the Morex assembly (v1.0 and v2.0), and 16 polymorphic markers were able to delineate the RphHEB locus to a 0.05 cM genetic interval spanning 98.6 kb. Based on its effectiveness and wild origin, RphHEB is distinct from all other designated Rph genes located on chromosome 5H and therefore the new locus symbol Rph28 is recommended for RphHEB in accordance with the rules and cataloguing system of barley gene nomenclature.
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Affiliation(s)
- M Mehnaz
- Plant Breeding Institute Cobbitty, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW, Australia
| | - P Dracatos
- Plant Breeding Institute Cobbitty, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW, Australia
| | - A Pham
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - T March
- School of Agriculture, Food and Wine, University of Adelaide, Waite Campus, Urrbrae, SA, 5064, Australia
| | - A Maurer
- Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120, Halle/Saale, Germany
| | - K Pillen
- Martin-Luther-University Halle-Wittenberg, Betty-Heimann-Str. 3, 06120, Halle/Saale, Germany
| | - K Forrest
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, 3083, Australia
| | - T Kulkarni
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, Victoria, 3083, Australia
| | - M Pourkheirandish
- Faculty of Veterinary and Agriculture, The University of Melbourne, Parkville, 3010, Australia
| | - R F Park
- Plant Breeding Institute Cobbitty, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW, Australia
| | - D Singh
- Plant Breeding Institute Cobbitty, School of Life and Environmental Sciences, University of Sydney, Narellan, NSW, Australia.
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5
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Survey of Drought-Associated TAWRKY2-D1 Gene Diversity in Bread Wheat and Wheat Relatives. Mol Biotechnol 2021; 63:953-962. [PMID: 34131856 DOI: 10.1007/s12033-021-00350-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 06/03/2021] [Indexed: 10/21/2022]
Abstract
Recent advances in plant genomics revealed numerous factors related to drought tolerance, including a family of WRKY transcription factors. The aim of this study was to evaluate polymorphism of the TaWRKY2-D1 across a range of bread wheat cultivars, interspecific hybrids, and wild wheat relatives within the Triticum genus as a potential molecular target for marker-assistant selection. The initial sequencing of the TaWRKY2-D1 gene in six Ukrainian commercial cultivars detected some sequence variations along the ~ 1.8 kb of gene promoter and the followed coding region composed of four exons and three introns. Based on the gained sequence information, five sets of primers covering different gene regions were designed to annotate theTaWRKY2-D1 genetic diversity in 202 wheat cultivars, including 77 accessions from the CIMMYT collection, 72 commercial varieties cultivated in Ukraine, and 53 hybrids and wild wheat species. The combination of developed DNA markers enabled effective and reproducible annotation of cultivars genetic diversity. The primers set targeting introns adjusted to the gene's exon 3, turned out to be the most informative for screening heterogeneity of the TaWRKY2-D1. The developed molecular markers represent effective, informative means for selecting drought tolerance germplasm donors to promote wheat breeding programs.
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6
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Lyubimova A, Eremin D, Loskutov I, Levshtanov S, Trifuntova I. Analysis of the genetic diversity of Russian common oat varieties using alleles of avenin-coding loci. BIO WEB OF CONFERENCES 2021. [DOI: 10.1051/bioconf/20213601015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Alleles of avenin-coding loci were identified in 24 varieties of common oat origin from 6 different breeding centers of the Russian Federation. It was found that 33% of the studied varieties are homogeneous. Heterogeneous varieties contain from 2 to 10 biotypes. The analysis revealed 67 different genotypes, ten of which are found in the spectra of several varieties at once. Despite the presence of matching genotypes, all the studied varieties differ in the genetic formulas of avenin, the number and frequency of occurrence of biotypes. This makes it possible to effectively identify and distinguish oat varieties sown by Russian breeding using the method of prolamin electrophoresis. The analyzed groups of varieties are characterized by high values of genetic (0.54-0.79) and intra-population diversity, which indicates the stability of populations. The exception is varieties originating from the Irkutsk region, low values of genetic and intra-population diversity in the population of which may indicate the process of genetic erosion. Analysis of the frequency distribution of alleles of avenin-coding loci does not allow to determine whether oat varieties belong to certain breeding centers, which is associated with the introduction of the same genotypes into the breeding programs of different regions.
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7
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Rychel-Bielska S, Nazzicari N, Plewiński P, Bielski W, Annicchiarico P, Książkiewicz M. Development of PCR-based markers and whole-genome selection model for anthracnose resistance in white lupin (Lupinus albus L.). J Appl Genet 2020; 61:531-545. [PMID: 32968972 PMCID: PMC7652745 DOI: 10.1007/s13353-020-00585-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 09/07/2020] [Accepted: 09/14/2020] [Indexed: 12/15/2022]
Abstract
White lupin (Lupinus albus L.) is a high-protein grain legume crop, grown since ancient Greece and Rome. Despite long domestication history, its cultivation remains limited, partly because of susceptibility to anthracnose. Only some late-flowering, bitter, low-yielding landraces from Ethiopian mountains displayed resistance to this devastating disease. The resistance is controlled by various genes, thereby complicating the breeding efforts. The objective of this study was developing tools for molecular tracking of Ethiopian resistance genes based on genotyping-by-sequencing (GBS) data, envisaging linkage mapping and genomic selection approaches. Twenty GBS markers from two major quantitative trait loci (QTLs), antr04_1/antr05_1 and antr04_2/antr05_2, were converted to PCR-based markers using assigned transcriptome sequences. Newly developed markers improved mapping resolution around both anthracnose resistance loci, providing more precise QTL estimation. PCR-based screening of diversified domesticated and primitive germplasm revealed the high specificity of two markers for the antr04_1/antr05_1 locus (TP222136 and TP47110) and one for the antr04_2/antr05_2 locus (TP338761), highlighted by simple matching coefficients of 0.96 and 0.89, respectively. Moreover, a genomic selection approach based on GBS data of a recombinant inbred line mapping population was assessed, providing an average predictive ability of 0.56. These tools can be used for preselection of candidate white lupin germplasm for anthracnose resistance assays.
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Affiliation(s)
- Sandra Rychel-Bielska
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 24A, 50-363, Wrocław, Poland.,Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Nelson Nazzicari
- CREA-FLC, Council for Agricultural Research and Economics, Research Centre for Fodder Crops and Dairy Production, Viale Piacenza 29, 26900, Lodi, Italy
| | - Piotr Plewiński
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Wojciech Bielski
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Paolo Annicchiarico
- CREA-FLC, Council for Agricultural Research and Economics, Research Centre for Fodder Crops and Dairy Production, Viale Piacenza 29, 26900, Lodi, Italy
| | - Michał Książkiewicz
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
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Lyubimova AV, Tobolova GV, Eremin DI, Loskutov IG. Dynamics of the genetic diversity of oat varieties in the Tyumen region at avenin-coding loci. Vavilovskii Zhurnal Genet Selektsii 2020; 24:123-130. [PMID: 33659791 PMCID: PMC7716543 DOI: 10.18699/vj20.607] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Molecular and biochemical markers are used to analyze the intraspecific genetic diversity of crops.
Prolamin-coding
loci are highly effective for assessing this indicator. On the basis of the Laboratory of Varietal
Seed Identification of the State Agrarian University of the Northern Trans-Urals, 18 varieties of common oat
included in the State Register of Selection Achievements in the Tyumen Region from the 1930s to 2019 were
studied
by electrophoresis in 2018–2019. The aim of the work was to study the dynamics of the genetic diversity
of oat varieties
at avenin-coding loci. For the analysis, 100 grains of each variety were used. Electrophoresis was
carried out in vertical plates of 13.2 % polyacrylamide gel at a constant voltage
of 500 V for 4.0–4.5 h. It was found
that 44.4 % of the varieties are heterogeneous, each consisting of two biotypes. For three loci, 20 alleles were
identified, 10 of which were detected for the first time. The allele frequency of avenin-coding loci varied with
time. In the process of variety exchange, alleles that are characteristic of varieties of non-Russian origin were replaced
by alleles present in domestic varieties and then in the varieties developed by local breeding institutions.
The following alleles had the highest frequency in Tyumen varieties: Avn A4 (50.0 %), A2 (25.0 %), Avn B4 (50.0 %),
Bnew6 (37.5 %), Avn C1 (37.5 %), C2 and C5 (25.0 %). These alleles are of great value as markers of agronomically
and adaptively important characters for the region in question. The amount of genetic diversity of oats varied
with time from 0.33 in 1929–1950 to up to 0.75 in 2019. The high value of genetic diversity in modern breeding
varieties of the Scientific Research Institute of Agriculture of the Northern Trans-Urals and an increase in this
indicator over the past 20 years are associated with the use of genetically heterogeneous source material in the
breeding process. This allowed obtaining varieties with high adaptive potentials in the natural climatic conditions
of the region.
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Affiliation(s)
- A V Lyubimova
- Scientific Research Institute of Agriculture of the Northern Trans-Ural Region - Branch of the Tyumen Scientific Center of Siberian Branch of the Russian Academy of Sciences, Moskowsky village, Tyumen district, Tyumen region, Russia Northern Trans-Ural State Agricultural University, Tyumen, Russia
| | - G V Tobolova
- Northern Trans-Ural State Agricultural University, Tyumen, Russia
| | - D I Eremin
- Northern Trans-Ural State Agricultural University, Tyumen, Russia
| | - I G Loskutov
- Federal Research Center the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), St. Petersburg, Russia
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9
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Zhang J, Yang J, Zhang L, Luo J, Zhao H, Zhang J, Wen C. A new SNP genotyping technology Target SNP-seq and its application in genetic analysis of cucumber varieties. Sci Rep 2020; 10:5623. [PMID: 32221398 PMCID: PMC7101363 DOI: 10.1038/s41598-020-62518-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 03/11/2020] [Indexed: 01/18/2023] Open
Abstract
To facilitate the utility of SNP-based genotyping, we developed a new method called target SNP-seq which combines the advantages of multiplex PCR amplification and high throughput sequencing. Compared with KASP, Microarrays, GBS and other SNP genotyping methods, target SNP-seq is flexible both in SNPs and samples, yields high accuracy, especially when genotyping genome wide perfect SNPs with high polymorphism and conserved flanking sequences, and is cost-effective, requiring 3 days and $7 for per DNA sample to genotype hundreds of SNP loci. The present study established a DNA fingerprint of 261 cucumber varieties by target SNP-seq with 163 perfect SNPs from 4,612,350 SNPs based on 182 cucumber resequencing datasets. Four distinct subpopulations were found in 261 Chinese cucumber varieties: the north China type, the south China type, the Europe type, and the Xishuangbanna type. The north China type and Xishuangbanna type harbored lower genetic diversity, indicating greater risk of genetic erosion in these two subpopulations. Furthermore, a core set of 24 SNPs was able to distinguish 99% of the 261 cucumber varieties. 29 core cucumber backbone varieties in China were identified. Therefore, target SNP-seq provides a new way to screen out core SNP loci from the whole genome for DNA fingerprinting of crop varieties. The high efficiency and low cost of target SNP-seq is more competitive than the current SNP genotyping methods, and it has excellent application prospects in genetic research, as well as in promoting plant breeding processes in the near future.
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Affiliation(s)
- Jian Zhang
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China.,Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Jingjing Yang
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China.,Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Like Zhang
- National Agricultural Technology Extension and Service Center, Ministry of Agriculture and Rural Affairs, Beijing, China
| | - Jiang Luo
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China.,Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Hong Zhao
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China.,Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China
| | - Jianan Zhang
- Molbreeding Biotechnology Company, Shijiazhuang, 050000, China
| | - Changlong Wen
- Beijing Vegetable Research Center, Beijing Academy of Agricultural and Forestry Sciences, National Engineering Research Center for Vegetables, Beijing, 100097, China. .,Beijing Key Laboratory of Vegetable Germplasms Improvement, Beijing, 100097, China.
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Rychel S, Książkiewicz M. Development of gene-based molecular markers tagging low alkaloid pauper locus in white lupin (Lupinus albus L.). J Appl Genet 2019; 60:269-281. [PMID: 31410824 PMCID: PMC6803572 DOI: 10.1007/s13353-019-00508-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/02/2019] [Accepted: 07/18/2019] [Indexed: 12/20/2022]
Abstract
White lupin (Lupinus albus L.) is a legume grain crop cultivated since ancient Greece and Egypt. Modern white lupin cultivars are appreciated as a source of protein with positive nutraceutical impact. However, white lupins produce anti-nutritional compounds, quinolizidine alkaloids, which provide bitter taste and have a negative influence on human health. During domestication of this species, several recessive alleles at unlinked loci controlling low alkaloid content were selected. One of these loci, pauper, was exploited worldwide providing numerous low-alkaloid cultivars. However, molecular tracking of pauper has been hampered due to the lack of diagnostic markers. In the present study, the synteny-based approach was harnessed to target pauper locus. Single-nucleotide polymorphisms flanking pauper locus on white lupin linkage map as well as candidate gene sequences elucidated from the narrow-leafed lupin (L. angustifolius L.) chromosome segment syntenic to the pauper linkage group region were transformed to PCR-based molecular markers. These markers were analyzed both in the mapping population and world germplasm collection. From fourteen markers screened, eleven were localized at a distance below 1.5 cM from this locus, including five co-segregating with pauper. The linkage of these markers was confirmed by high LOD values (up to 58.4). Validation performed in the set of 127 bitter and 23 sweet accessions evidenced high applicability of one marker, LAGI01_35805_F1_R1, for pauper locus selection, highlighted by the low ratio of false-positive scores (2.5%). LAGI01_35805 represents a homolog of L. angustifolius acyltransferase-like (LaAT) gene which might hypothetically participate in the alkaloid biosynthesis process in lupins.
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Affiliation(s)
- Sandra Rychel
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland
| | - Michał Książkiewicz
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479, Poznań, Poland.
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11
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Utebayev M, Dashkevich S, Bome N, Bulatova K, Shavrukov Y. Genetic diversity of gliadin-coding alleles in bread wheat ( Triticum aestivum L.) from Northern Kazakhstan. PeerJ 2019; 7:e7082. [PMID: 31223532 PMCID: PMC6571009 DOI: 10.7717/peerj.7082] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/02/2019] [Indexed: 11/20/2022] Open
Abstract
Background Spring bread wheat (Triticum aestivum L.) represents the main cereal crop in Northern Kazakhstan. The quality of wheat grain and flour strongly depends on the structure of gluten, comprised of gliadin and glutenin proteins. Electrophoresis spectra of gliadins are not altered by environmental conditions or plant growth, are easily reproducible and very useful for wheat germplasm identification in addition to DNA markers. Genetic polymorphism of two Gli loci encoding gliadins can be used for selection of preferable genotypes of wheat with high grain quality. Methods Polyacrylamide gel electrophoresis was used to analyse genetic diversity of gliadins in a germplasm collection of spring bread wheat from Northern Kazakhstan. Results The highest frequencies of gliadin alleles were found as follows, in Gli1: -A1f (39.3%), -B1e (71.9%), and -D1a (41.0%); and in Gli-2: -A2q (17.8%), -B2t (13.5%), and -D2q (20.4%). The combination of these alleles in a single genotype may be associated with higher quality of grain as well as better adaptation to the dry environment of Northern Kazakhstan; preferable for wheat breeding in locations with similar conditions.
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Affiliation(s)
- Maral Utebayev
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan.,Institute of Biology, University of Tyumen, Tyumen, Russia
| | - Svetlana Dashkevich
- A.I. Barayev Research and Production Centre of Grain Farming, Shortandy, Kazakhstan
| | - Nina Bome
- Institute of Biology, University of Tyumen, Tyumen, Russia
| | - Kulpash Bulatova
- Kazakh Research Institute of Agriculture and Plant Growing, Almaty region, Kazakhstan
| | - Yuri Shavrukov
- College of Science and Engineering, School of Biological Sciences, Flinders University, Bedford Park, SA, Australia
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12
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Fazlikhani L, Keilwagen J, Kopahnke D, Deising H, Ordon F, Perovic D. High Resolution Mapping of Rph MBR1012 Conferring Resistance to Puccinia hordei in Barley ( Hordeum vulgare L.). FRONTIERS IN PLANT SCIENCE 2019; 10:640. [PMID: 31191570 PMCID: PMC6541035 DOI: 10.3389/fpls.2019.00640] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/29/2019] [Indexed: 06/01/2023]
Abstract
Isolation of disease resistance genes in barley was hampered by the large genome size, but has become easy due to the availability of the reference genome sequence. During the last years, many genomic resources, e.g., the Illumina 9K iSelect, the 50K Infinium arrays, the Barley Genome Zipper, POPSEQ, and genotyping by sequencing (GBS), were developed that enable enhanced gene isolation in combination with the barley genome sequence. In the present study, we developed a fine map of the barley leaf rust resistance gene Rph MBR1012. 537 segmental homozygous recombinant inbred lines (RILs) derived from 4775 F2-plants were used to construct a high-resolution mapping population (HRMP). The Barley Genome Zipper, the 9K iSelect chip, the 50K Infinium chip and GBS were used to develop 56 molecular markers located in the target interval of 8 cM. This interval was narrowed down to about 0.07 cM corresponding to 0.44 Mb of the barley reference genome. Eleven low-confidence and 18 high-confidence genes were identified in this interval. Five of these are putative disease resistance genes and were subjected to allele-specific sequencing. In addition, comparison of the genetic map and the reference genome revealed an inversion of 1.34 Mb located distally to the resistance locus. In conclusion, the barley reference sequence and the respective gene annotation delivered detailed information about the physical size of the target interval, the genes located in the target interval and facilitated the efficient development of molecular markers for marker-assisted selection for RphMBR1012.
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Affiliation(s)
- Leila Fazlikhani
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
- Department of Phytopathology and Plant Protection, Institute of Agricultural and Nutrition Sciences, Faculty of Natural Sciences III, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Jens Keilwagen
- Institute for Biosafety in Plant Biotechnology, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | - Doris Kopahnke
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | - Holger Deising
- Department of Phytopathology and Plant Protection, Institute of Agricultural and Nutrition Sciences, Faculty of Natural Sciences III, Martin Luther University of Halle-Wittenberg, Halle, Germany
| | - Frank Ordon
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
| | - Dragan Perovic
- Institute for Resistance Research and Stress Tolerance, Federal Research Centre for Cultivated Plants, Julius Kühn-Institute (JKI), Quedlinburg, Germany
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13
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Protein Disulfide Isomerase (PDI1-1) differential expression and modification in Mexican malting barley cultivars. PLoS One 2018; 13:e0206470. [PMID: 30427898 PMCID: PMC6235301 DOI: 10.1371/journal.pone.0206470] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 10/12/2018] [Indexed: 12/30/2022] Open
Abstract
Barley malting quality depends on seed characteristics achieved during grain development and germination. One important parameter is protein accumulation in the mature seed, which may vary between cultivars. Here we conducted a protein pattern analysis in the range of pI 4–7 of mature grains from five Mexican barley cultivars, commonly used for malt and beer production. Reproducibly distinct protein spots, separated by 2D SDS PAGE, were identified by mass spectrometry and considered as potential markers for cultivars with distinct seed protein accumulation. The expression patterns of glutamate decarboxylase (GAD) and protein disulfide isomerase (PDI1-1) were followed at transcript level during grain development for three independent growth cycles to establish whether differences between cultivars were reproducible. Quantitative determination of PDI1-1 protein levels by ELISA confirmed a reproducibly, distinctive accumulation and post-translational modifications between cultivars, which were independent of plant growth regimes. According to its impact on differential storage protein accumulation, we propose the PDI1-1 protein as potential biomarker for Mexican malting barley cultivars.
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14
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Ferreira JR, Faria BF, Comar M, Delatorre CA, Minella E, Pereira JF. Is a non-synonymous SNP in the HvAACT1 coding region associated with acidic soil tolerance in barley? Genet Mol Biol 2017; 40:480-490. [PMID: 28486573 PMCID: PMC5488463 DOI: 10.1590/1678-4685-gmb-2016-0225] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 12/19/2016] [Indexed: 11/22/2022] Open
Abstract
The barley HvAACT1 gene codes for a citrate transporter associated with tolerance to acidic soil. In this report, we describe a single nucleotide polymorphism (SNP) in the HvAACT1 coding region that was detected as T-1,198 (in genotypes with lower root growth on acidic soil) or G-1,198 (greater root growth) and resulted in a single amino acid change (L/V-172). Molecular dynamic analysis predicted that HvAACT1 proteins with L or V-172 were stable, although the substitution led to structural changes within the protein. To evaluate the effect of the SNP on tolerance to acidic soil, barley accessions were separated into haplotypes based on the presence of a 1 kb insertion in the HvAACT1 promoter and a 21 bp insertion/deletion. These markers and the SNP-1,198 allowed the identification of five haplotypes. Short-term soil experiments showed no difference in root growth for most of the accessions containing the 21 bp insertion and T or G-1,198. In contrast, genotypes showing both the 21 bp deletion and G-1,198, with one of them having the 1 kb insertion, showed greater root growth. These results indicate that the SNP was not advantageous or deleterious when genotypes from the same haplotype were compared. The occurrence of the SNP was highly correlated with the 21 bp insertion/deletion that, together with the 1 kb insertion, explained most of the barley tolerance to acidic soil.
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Affiliation(s)
- Jéssica Rosset Ferreira
- Departamento de Plantas de Lavoura, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil
| | - Bruna Franciele Faria
- Programa Multicêntrico de Pós-Graduação em Bioquímica e Biologia Molecular, Universidade Federal de São João del-Rey, 35501-296, Divinópolis, MG, Brazil
| | - Moacyr Comar
- Programa Multicêntrico de Pós-Graduação em Bioquímica e Biologia Molecular, Universidade Federal de São João del-Rey, 35501-296, Divinópolis, MG, Brazil
| | - Carla Andréa Delatorre
- Departamento de Plantas de Lavoura, Faculdade de Agronomia, Universidade Federal do Rio Grande do Sul, 91501-970, Porto Alegre, RS, Brazil
| | | | - Jorge Fernando Pereira
- Embrapa Trigo, 99001-970, Passo Fundo, RS, Brazil.,Embrapa Gado de Leite, 36038-330, Juiz de Fora, MG, Brazil
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Ren J, Chen L, Jin X, Zhang M, You FM, Wang J, Frenkel V, Yin X, Nevo E, Sun D, Luo MC, Peng J. Solar Radiation-Associated Adaptive SNP Genetic Differentiation in Wild Emmer Wheat, Triticum dicoccoides. FRONTIERS IN PLANT SCIENCE 2017; 8:258. [PMID: 28352272 PMCID: PMC5348526 DOI: 10.3389/fpls.2017.00258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 02/10/2017] [Indexed: 05/06/2023]
Abstract
Whole-genome scans with large number of genetic markers provide the opportunity to investigate local adaptation in natural populations and identify candidate genes under positive selection. In the present study, adaptation genetic differentiation associated with solar radiation was investigated using 695 polymorphic SNP markers in wild emmer wheat originated in a micro-site at Yehudiyya, Israel. The test involved two solar radiation niches: (1) sun, in-between trees; and (2) shade, under tree canopy, separated apart by a distance of 2-4 m. Analysis of molecular variance showed a small (0.53%) but significant portion of overall variation between the sun and shade micro-niches, indicating a non-ignorable genetic differentiation between sun and shade habitats. Fifty SNP markers showed a medium (0.05 ≤ FST ≤ 0.15) or high genetic differentiation (FST > 0.15). A total of 21 outlier loci under positive selection were identified by using four different FST -outlier testing algorithms. The markers and genome locations under positive selection are consistent with the known patterns of selection. These results suggested that genetic differentiation between sun and shade habitats is substantial, radiation-associated, and therefore ecologically determined. Hence, the results of this study reflected effects of natural selection through solar radiation on EST-related SNP genetic diversity, resulting presumably in different adaptive complexes at a micro-scale divergence. The present work highlights the evolutionary theory and application significance of solar radiation-driven natural selection in wheat improvement.
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Affiliation(s)
- Jing Ren
- Shandong Provincial Key Laboratory of Biophysics, Institute of Biophysics, Dezhou UniversityDezhou, China
| | - Liang Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of SciencesWuhan, China
| | - Xiaoli Jin
- Department of Agronomy and the Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang UniversityHangzhou, China
| | - Miaomiao Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Chinese Academy of SciencesWuhan, China
| | - Frank M. You
- Cereal Research Centre, Agriculture and Agri-Food CanadaWinnipeg, MB, Canada
| | - Jirui Wang
- Department of Plant Sciences, University of CaliforniaDavis, CA, USA
| | - Vladimir Frenkel
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of HaifaHaifa, Israel
| | - Xuegui Yin
- Department of Biotechnology, College of Agriculture, Guangdong Ocean UniversityZhanjiang, China
| | - Eviatar Nevo
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of HaifaHaifa, Israel
| | - Dongfa Sun
- Department of Agronomy, College of Plant Science and Technology, Huazhong Agricultural UniversityWuhan, China
| | - Ming-Cheng Luo
- Department of Plant Sciences, University of CaliforniaDavis, CA, USA
| | - Junhua Peng
- Department of Biotechnology, College of Agriculture, Guangdong Ocean UniversityZhanjiang, China
- The State Key Lab of Crop Breeding Technology Innovation and Integration, China National Seed Group Co. Ltd.Wuhan, China
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16
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Shavrukov Y, Zhumalin A, Serikbay D, Botayeva M, Otemisova A, Absattarova A, Sereda G, Sereda S, Shvidchenko V, Turbekova A, Jatayev S, Lopato S, Soole K, Langridge P. Expression Level of the DREB2-Type Gene, Identified with Amplifluor SNP Markers, Correlates with Performance, and Tolerance to Dehydration in Bread Wheat Cultivars from Northern Kazakhstan. FRONTIERS IN PLANT SCIENCE 2016; 7:1736. [PMID: 27917186 PMCID: PMC5114286 DOI: 10.3389/fpls.2016.01736] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2016] [Accepted: 11/03/2016] [Indexed: 05/18/2023]
Abstract
A panel of 89 local commercial cultivars of bread wheat was tested in field trials in the dry conditions of Northern Kazakhstan. Two distinct groups of cultivars (six cultivars in each group), which had the highest and the lowest grain yield under drought were selected for further experiments. A dehydration test conducted on detached leaves indicated a strong association between rates of water loss in plants from the first group with highest grain yield production in the dry environment relative to the second group. Modern high-throughput Amplifluor Single Nucleotide Polymorphism (SNP) technology was applied to study allelic variations in a series of drought-responsive genes using 19 SNP markers. Genotyping of an SNP in the TaDREB5 (DREB2-type) gene using the Amplifluor SNP marker KATU48 revealed clear allele distribution across the entire panel of wheat accessions, and distinguished between the two groups of cultivars with high and low yield under drought. Significant differences in expression levels of TaDREB5 were revealed by qRT-PCR. Most wheat plants from the first group of cultivars with high grain yield showed slight up-regulation in the TaDREB5 transcript in dehydrated leaves. In contrast, expression of TaDREB5 in plants from the second group of cultivars with low grain yield was significantly down-regulated. It was found that SNPs did not alter the amino acid sequence of TaDREB5 protein. Thus, a possible explanation is that alternative splicing and up-stream regulation of TaDREB5 may be affected by SNP, but these hypotheses require additional analysis (and will be the focus of future studies).
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Affiliation(s)
- Yuri Shavrukov
- School of Agriculture, Food and Wine, Faculty of Sciences, University of AdelaideUrrbrae, SA, Australia
- School of Biological Sciences, Flinders University, Bedford ParkSA, Australia
- *Correspondence: Yuri Shavrukov, ;
| | - Aibek Zhumalin
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Dauren Serikbay
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Makpal Botayeva
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Ainur Otemisova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | | | - Grigoriy Sereda
- Karaganda Research Institute of Plant Industry and BreedingKaraganda, Kazakhstan
| | - Sergey Sereda
- Karaganda Research Institute of Plant Industry and BreedingKaraganda, Kazakhstan
| | - Vladimir Shvidchenko
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Arysgul Turbekova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical UniversityAstana Kazakhstan
| | - Sergiy Lopato
- School of Agriculture, Food and Wine, Faculty of Sciences, University of AdelaideUrrbrae, SA, Australia
| | - Kathleen Soole
- School of Biological Sciences, Flinders University, Bedford ParkSA, Australia
| | - Peter Langridge
- School of Agriculture, Food and Wine, Faculty of Sciences, University of AdelaideUrrbrae, SA, Australia
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