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Allele mining of TaGRF-2D gene 5'-UTR in Triticum aestivum and Aegilops tauschii genotypes.
PLoS One. 2020; 15(4):e0231704.Plos

Abstract

The low diversity of the D-subgenome of bread wheat requires the involvement of new alleles for breeding. In grasses, the allelic state of Growth Regulating Factor (GRF) gene is correlated with nitrogen uptake. In this study, we characterized the sequence of TaGRF-2D and assessed its diversity in bread wheat and goatgrass Aegilops tauschii (genome DD). In silico analysis was performed for reference sequence searching, primer pairs design and sequence assembly. The gene sequence was obtained using Illumina and Sanger sequencing. The complete sequences of TaGRF-2D were obtained for 18 varieties of wheat. The polymorphism in the presence/absence of two GCAGCC repeats in 5' UTR was revealed and the GRF-2D-SSR marker was developed. Our results showed that the alleles 5' UTR-250 and 5' UTR-238 were present in wheat varieties, 5' UTR-250 was presented in the majority of wheat varieties. In Ae. tauschii ssp. strangulata (likely donor of the D-subgenome of polyploid wheat), most accessions carried the 5' UTR-250 allele, whilst most Ae. tauschii ssp. tauschii have 5' UTR-244. The developed GRF-2D-SSR marker can be used to study the genetic diversity of wheat and Ae. tauschii.

Authors+Show Affiliations

Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia.Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia.Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia.Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia.Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia.Federal Research Center Vavilov All-Russian Institute of Plant Genetic Resources, Saint Petersburg, Russia.Laboratory of Applied Genomics and Crop Breeding, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia. Centre for Molecular Biotechnology, Russian State Agrarian University-Moscow Timiryazev Agricultural Academy, Moscow, Russia. Kurchatov Genomics Center-ARRIAB, All-Russia Research Institute of Agricultural Biotechnology, Moscow, Russia.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

32298343

Citation

Kroupin, Pavel Yu, et al. "Allele Mining of TaGRF-2D Gene 5'-UTR in Triticum Aestivum and Aegilops Tauschii Genotypes." PloS One, vol. 15, no. 4, 2020, pp. e0231704.
Kroupin PY, Chernook AG, Bazhenov MS, et al. Allele mining of TaGRF-2D gene 5'-UTR in Triticum aestivum and Aegilops tauschii genotypes. PLoS One. 2020;15(4):e0231704.
Kroupin, P. Y., Chernook, A. G., Bazhenov, M. S., Karlov, G. I., Goncharov, N. P., Chikida, N. N., & Divashuk, M. G. (2020). Allele mining of TaGRF-2D gene 5'-UTR in Triticum aestivum and Aegilops tauschii genotypes. PloS One, 15(4), e0231704. https://doi.org/10.1371/journal.pone.0231704
Kroupin PY, et al. Allele Mining of TaGRF-2D Gene 5'-UTR in Triticum Aestivum and Aegilops Tauschii Genotypes. PLoS One. 2020;15(4):e0231704. PubMed PMID: 32298343.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Allele mining of TaGRF-2D gene 5'-UTR in Triticum aestivum and Aegilops tauschii genotypes. AU - Kroupin,Pavel Yu, AU - Chernook,Anastasiya G, AU - Bazhenov,Mikhail S, AU - Karlov,Gennady I, AU - Goncharov,Nikolay P, AU - Chikida,Nadezhda N, AU - Divashuk,Mikhail G, Y1 - 2020/04/16/ PY - 2020/01/14/received PY - 2020/03/30/accepted PY - 2020/4/17/entrez PY - 2020/4/17/pubmed PY - 2020/7/17/medline SP - e0231704 EP - e0231704 JF - PloS one JO - PLoS One VL - 15 IS - 4 N2 - The low diversity of the D-subgenome of bread wheat requires the involvement of new alleles for breeding. In grasses, the allelic state of Growth Regulating Factor (GRF) gene is correlated with nitrogen uptake. In this study, we characterized the sequence of TaGRF-2D and assessed its diversity in bread wheat and goatgrass Aegilops tauschii (genome DD). In silico analysis was performed for reference sequence searching, primer pairs design and sequence assembly. The gene sequence was obtained using Illumina and Sanger sequencing. The complete sequences of TaGRF-2D were obtained for 18 varieties of wheat. The polymorphism in the presence/absence of two GCAGCC repeats in 5' UTR was revealed and the GRF-2D-SSR marker was developed. Our results showed that the alleles 5' UTR-250 and 5' UTR-238 were present in wheat varieties, 5' UTR-250 was presented in the majority of wheat varieties. In Ae. tauschii ssp. strangulata (likely donor of the D-subgenome of polyploid wheat), most accessions carried the 5' UTR-250 allele, whilst most Ae. tauschii ssp. tauschii have 5' UTR-244. The developed GRF-2D-SSR marker can be used to study the genetic diversity of wheat and Ae. tauschii. SN - 1932-6203 UR - https://www.unboundmedicine.com/medline/citation/32298343/Allele_mining_of_TaGRF_2D_gene_5'_UTR_in_Triticum_aestivum_and_Aegilops_tauschii_genotypes_ L2 - https://dx.plos.org/10.1371/journal.pone.0231704 DB - PRIME DP - Unbound Medicine ER -