Novel alleles of the VERNALIZATION1 genes in wheat are associated with modulation of DNA curvature and flexibility in the promoter region

Muterko, Alexandr; Kalendar, Ruslan; Салина, Е. А.

doi:10.1186/s12870-015-0691-2

Cited by 47 publications

(82 citation statements)

References 79 publications

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“…В нашем предыдущем исследовании участка промотора гена VRN-A1 были оптимизированы условия для на-блюдения конформационного полиморфизма ДНК, что позволило дискриминировать аллельные варианты, разли-чающиеся между собой по ОНП в пределах аденинового тракта (Muterko et al, 2016). В настоящем исследовании модуляция кривизны молекул ДНК, обусловленная по-лиморфизмом А-трактов, взята за основу для разработки особого типа кодоминантных ДНК-маркеров, позволя-ющих в ходе одной реакции качественно различить аль-тернативные аллели, представленные в различных копиях данного гена.…”

Section: Discussionunclassified

“…В нашем предыдущем исследовании генов VRN1 в гек-саплоидных и тетраплоидных видах пшеницы, согласно результатам ДНК-маркерного анализа, аллель Vrn-A1a.3 был ошибочно идентифицирован в образцах T. dicoccum PI 191091 и PI 276015 (Muterko et al, 2016). Однако уста-новленные в этой работе ассоциации между гаплотипами и аллелями гена VRN-A1 поставили под сомнение ранее полученные результаты.…”

Section: Discussionunclassified

“…Электрофорез продуктов амплификации проведен в неденатурирующих полиакриламидных гелях (ПААГ) в оптимизированных ранее условиях (Muterko et al, 2016), усиливающих аномально медленную миграцию искрив-ленных молекул ДНК. Агарозный гель-электрофорез выполнен с использованием 1.5 % агарозных гелей в 1× ТБЭ буфере.…”

Section: материалы и методыunclassified

“…Согласно данным ДНК-маркерного анализа, образцы T. dicoccum (PI 191091 и PI 276015) несут доминантный аллель Vrn-A1a.3 (Muterko et al, 2016), который содержит инсерцию мобильного генетического элемента в области промотора. Однако в настоящем исследовании установлено, что гаплотип Ex4C, идентифицированный в образцах PI 191091 и PI 276015 (GenBank: KU844093), не присущ аллелю Vrn-A1a, который характеризуется гаплотипом Ex4C.f.…”

Section: Vrn-a1i 713unclassified

“…Согласно паспортным данным, образцы PI 191091 и PI 276015 характеризуются яровым типом развития. Кроме того, ДНК-маркерный анализ не выявил в данных образцах доминантных аллелей генов VRN-B1 и VRN-B3 (Muterko et al, 2016). В связи с этим предполага-ется, что инсерция размером 42 п. н. в промоторе Vrn-A1k может быть ассоциирована со снижением потребности в яровизации и яровым типом развития пшеницы.…”

Section: Vrn-a1i 713unclassified

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Analysis of the VERNALIZATION-A1 exon-4 polymorphism in polyploid wheat

Muterko¹,

Салина²

2017

Vestn. VOGiS

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One of the key genes that influence the adaptability of wheat to environments and yield are the VRN1 genes. In recent studies, an association of missense mutations within VERNALIZATION-A1 exon-4 with modulation of quantitative values of such agronomically valuable traits as frost tolerance, vernalization requirement duration and flowering time of wheat was shown. However, these investigations were carried out exclusively in T. aestivum varieties and have not covered other species of polyploid wheat and different VRN-A1 alleles. The earlier studies did not consider more than one copy of VRN-A1 per genome. Furthermore, only recently it was shown that only several SNPs distinguish the VRN-D4 and VRN-A1 genes. In the present study, VRN-A1 exon-4 polymorphism was investigated in 158 accessions of 6 tetraploid and 5 hexaploid wheat species carrying the different VRN-A1 alleles. To identify the VRN-A1 exon-4 haplotypes, a co-dominant marker was designed, based on modulation of the curvature of the DNA molecule. Polymorphism of the VRN-A1 exon-4 was revealed only in hexaploid wheat accessions and was associated with the presence of not less than two copies of VRN-A1 per genome. With the exception of one accession, the mutant type of exon-4 was identified only in combination with the wild type. Furthermore, allele-specific primers were designed to identify the VRN-D4 gene or in order to exclude its impact on the results during analysis of the VRN-A1 haplotypes. By expanding the region being analyzed, additional haplotypes, which are associated with polymorphism of adenine tracts within intron-4, were identified. Haplotype segregation was attained among accessions carrying only intact exon-4 of VRN-A1 and among dominant alleles of this gene. Finally, based on the associations revealed between the VRN-A1 alleles and haplotypes, the new putative dominant VRN-A1 allele (designated Vrn-A1k) carrying a 42-bp insertion within the promoter region was identified in tetraploid wheat of Triticum dicoccum.Key words: wheat; VRN-A1; exon 4 polymorphism; haplotypes.Одними из ключевых генов в селекции пшеницы, влияющих на адаптивность и урожайность культуры, являются гены VRN1. В недавних исследованиях установлена ассоциация полимор-физма нуклеотидной последовательности четвертого экзона гена VRN-A1 с вариабельностью количественных показателей ряда агрономически ценных признаков озимой пшеницы, таких как чувствительность к продолжительности яровизации, морозостойкость, время выхода в трубку и время колошения. Однако эти исследования были выполнены на ограниченном количестве сортов T. aestivum и не охватывали другие виды по-липлоидной пшеницы. В ранних исследованиях не предпола-галось наличия более чем одной копии гена VRN-A1 на геном. Кроме того, только недавно было показано, что ген VRN-D4 отличается от VRN-A1 всего по нескольким однонуклеотидным мутациям. В настоящей работе проанализировано распреде-ление гаплотипов экзона-4 гена VRN-A1 в 158 образцах 6 видов тетраплоидной и 5 видов гексаплоидной пшеницы, несущих различные аллели этог...

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Section: Discussionunclassified

Section: материалы и методыunclassified

Section: Vrn-a1i 713unclassified

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Analysis of the VERNALIZATION-A1 exon-4 polymorphism in polyploid wheat

Muterko¹,

Салина²

2017

Vestn. VOGiS

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Genomic Insights on Global Journeys of Adaptive Wheat Genes that Brought Us to Modern Wheat

Sehgal,

Dixon,

Pequeno

et al. 2023

Compendium of Plant Genomes

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Since its first cultivation, hexaploid wheat has evolved, allowing for its widespread cultivation and contributing to global food security. The identification of adaptive genes, such as vernalization and photoperiod response genes, has played a crucial role in optimizing wheat production, being instrumental in fine-tuning flowering and reproductive cycles in response to changing climates and evolving agricultural practices. While these adaptive genes have expanded the range of variation suitable for adaptation, further research is needed to understand their mechanisms, dissect the pathways involved, and expedite their implementation in breeding programs. By analyzing data across different environments and over time, Meta-QTL analysis can help identify novel genomic regions and facilitate the discovery of new candidate genes. This chapter reports on two previously unknown Meta-QTL regions, highlighting the potential for further exploration in this field. Moving forward, it will be increasingly important to expand our understanding of how genetic regions influence not only flowering time but also other developmental traits and their responses to environmental factors. Advances in gene-based modeling hold promise for describing growth and development processes using QTL and other genomic loci analysis. Integrating these findings into process-based crop models can provide valuable insights for future research. Overall, the study of adaptive genes and their impact on wheat production represents a vital area of research that continues to contribute to global food security.

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Development and characterization of a spring hexaploid wheat line with no functional VRN2 genes

et al. 2016

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Key message The combination of three non-functional alleles of the flowering repressor VRN2 results in a spring growth habit in wheat. AbstractIn temperate cereals with a winter growth habit, a prolonged exposure to low temperatures (vernalization) accelerates flowering. Before vernalization, the VRN2 locus plays a central role in maintaining flowering repression. Non-functional VRN2 alleles result in spring growth habit and are frequent in diploid wheat and barley. However, in hexaploid wheat, the effect of these non-functional VRN2 alleles is masked by gene redundancy. In this study, we developed a triple VRN2 mutant (synthetic vrn2-null) in hexaploid wheat by combining the non-functional VRN-A2 allele present in most polyploid wheats with a VRN-B2 deletion from tetraploid wheat, and a non-functional VRN-D2 allele from Aegilops tauschii (Ae. tauschii) (the donor of hexaploid wheat D genome). Non-vernalized vrn2-null plants flowered 118 days (P < 2.8E−07) earlier than the winter control, and showed a limited vernalization response. The functional VRN-B2 allele is expressed at higher levels than the functional VRN-D2 allele and showed a stronger repressive effect under partial vernalization (4 °C for 4 weeks), and also in non-vernalized plants carrying only a functional VRN-B2 or VRN-D2 in heterozygous state. These results suggest that different combinations of VRN-B2 and VRN-D2 alleles can be a used to modulate the vernalization response in regions with mild winters. Spring vrn2-null mutants have been selected repeatedly in diploid wheat and barley, suggesting that they may have an adaptative value and that may be useful in hexaploid wheat. Spring wheat breeders can use these new alleles to improve wheat adaptation to different or changing environments.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-016-2713-3) contains supplementary material, which is available to authorized users.

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Novel alleles of the VERNALIZATION1 genes in wheat are associated with modulation of DNA curvature and flexibility in the promoter region

Cited by 47 publications

References 79 publications

Analysis of the VERNALIZATION-A1 exon-4 polymorphism in polyploid wheat

Analysis of the VERNALIZATION-A1 exon-4 polymorphism in polyploid wheat

Genomic Insights on Global Journeys of Adaptive Wheat Genes that Brought Us to Modern Wheat

Development and characterization of a spring hexaploid wheat line with no functional VRN2 genes

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