Evolution and dispersal of emmer wheat (Triticum sp.) from novel haplotypes of Ppd-1 (photoperiod response) genes and their surrounding DNA sequences

Takenaka, Shotaro; Kawahara, Takuji

doi:10.1007/s00122-012-1890-y

Cited by 21 publications

(17 citation statements)

References 34 publications

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“…5.1 (Librado and Rozas 2009) and Median-Joining (MJ) networks (Bandelt et al 1999) were constructed with the Network 4.610 program (Fluxus Technology Ltd, Clare, Suffolk, UK). GenBank sequencing accessions analyzed in this study were AB691782-AB691938, AB693038, AB692786-AB692942, AB693039 (Takenaka and Kawahara 2012), and AB745510-AB745620 (sequenced in this study).…”

Section: Data Analysesmentioning

confidence: 99%

“…), and 5 domesticated einkorn wheat (T. monococcum L.) were used (Table S). A total of 158 accessions had been analyzed by Takenaka and Kawahara (2012), of which were wild emmer wheat accessions, 45 hulled emmer wheat accessions, and 94 FT emmer wheat accessions. Sixty-seven wild emmer accessions had been analyzed by Özkan et al (2011).…”

Section: Plant Materialsmentioning

confidence: 99%

“…Extracted DNA was stored in 100 μL of TE buffer at 4°C. DNA was amplified by PCR using specific primers for Type AI and Type AII, which corresponded to Type AI and Type AII and produced a band (Takenaka and Kawahara 2012). PCR amplification involved 50 ng of template DNA, 1 μM each primer, 1.5 mM MgCl2, 0.2 mM dNTPs, 1.5 μL of 10×PCR Buffer (TaKaRa, Japan), and 0.5 U of Taq Polymerase (TaKaRa, Japan) in a total volume of 15 μL.…”

Section: Plant Materialsmentioning

confidence: 99%

“…The primers used for PCR amplification and sequencing, designed for use with primer 3 (Rozen and Skaletsky 2000), were based on sequence data from the DDBJ website (http://www.ddbj.nig.ac.jp/). The sequence data from Ppd-A1, Ppd-B1, and Ppd-G1 and their adjacent regions were obtained from a total of 77 accessions (5 wild emmer wheat, 9 hulled emmer wheat, 2 FT emmer wheat, 10 wild timopheevii wheat, 5 domesticated timopheevii wheat, 43 wild einkorn wheat, and 3 domesticated einkorn wheat, table S) according to a previous study (Takenaka and Kawahara 2012).…”

Section: Dna Sequencingmentioning

confidence: 99%

“…Our previous study shows that emmer wheat is divided into two groups (Type AI and Type AII) based on about 200 bp sequences, which are around 1 kbp upstream of the Ppd-A1 gene and include insertion/deletion mutations (Fig. 1, Takenaka and Kawahara 2012). Some hulled emmer wheat of Type AII are devoid of about 100 bp of MITE-like sequences (Type AIIa).…”

Section: Introductionmentioning

confidence: 99%

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Evolution of tetraploid wheat based on variations in 5′ UTR regions of Ppd-A1: evidence of gene flow between emmer and timopheevi wheat

Takenaka

Kawahara

2013

Genet Resour Crop Evol

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Previous study showed that tetraploid wheat was divided into two groups (Type AI and Type AII) based on sequences around Ppd-A1 gene (Takenaka and Kawahara 2012). That study focused on domesticated emmer wheat and used only 19 wild emmer wheat, so could not be clear the evolutional relationship between Type AI and Type AII. Here, a total of 669 accessions comprising 65 einkorn wheat, 185 wild emmer wheat, 107 hulled emmer wheat, 204 free-threshing (FT) emmer wheat, and 108 timopheevii wheat were studied by PCR assay and DNA sequencing for Type AI/AII. Type AII was an older type than Type AI because all einkorn accessions had Type AII. In wild emmer, Type AI was distributed in the northeast regions of its distribution and Type AII was found to be centered on Israel. A total of 37.4% of hulled emmer accessions were Type AI, while 92.2% of FT emmer accessions were Type AI. Differences in the proportion of Type AI/AII in domesticated emmer suggested a strong bottleneck effect. We also found two MITE-like sequence deletion patterns from a part of Type AII accessions (dic-del and ara-del). Dic-del was found from only Israeli wild emmer accessions and ara-del was found from almost all timopheevii wheat accessions. Only three timopheevii accessions did not have ara-del, and one wild emmer accession and ten hulled emmer accessions had ara-del. These accessions suggested gene flow between emmer and timopheevii wheat.

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Section: Data Analysesmentioning

confidence: 99%

Section: Plant Materialsmentioning

confidence: 99%

Section: Plant Materialsmentioning

confidence: 99%

Section: Dna Sequencingmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Evolution of tetraploid wheat based on variations in 5′ UTR regions of Ppd-A1: evidence of gene flow between emmer and timopheevi wheat

Takenaka

Kawahara

2013

Genet Resour Crop Evol

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Novel PHOTOPERIOD-1 gene variants associate with yield-related and root-angle traits in European bread wheat

Makhoul,

Schlichtermann,

Ugwuanyi

et al. 2024

Theor Appl Genet

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Key message PHOTOPERIOD-1 homoeologous gene copies play a pivotal role in regulation of flowering time in wheat. Here, we show that their influence also extends to spike and shoot architecture and even impacts root development. Abstract The sequence diversity of three homoeologous copies of the PHOTOPERIOD-1 gene in European winter wheat was analyzed by Oxford Nanopore amplicon-based multiplex sequencing and molecular markers in a panel of 194 cultivars representing breeding progress over the past 5 decades. A strong, consistent association with an average 8% increase in grain yield was observed for the PpdA1-Hap1 haplotype across multiple environments. This haplotype was found to be linked in 51% of cultivars to the 2NS/2AS translocation, originally introduced from Aegilops ventricosa, which leads to an overestimation of its effect. However, even in cultivars without the 2NS/2AS translocation, PpdA1-Hap1 was significantly associated with increased grain yield, kernel per spike and kernel per m2 under optimal growth conditions, conferring a 4% yield advantage compared to haplotype PpdA1-Hap4. In contrast to Ppd-B1 and Ppd-D1, the Ppd-A1 gene exhibits novel structural variations and a high number of SNPs, highlighting the evolutionary changes that have occurred in this region over the course of wheat breeding history. Additionally, cultivars carrying the photoperiod-insensitive Ppd-D1a allele not only exhibit earlier heading, but also deeper roots compared to those with photoperiod-sensitive alleles under German conditions. PCR and KASP assays have been developed that can be effectively employed in marker-assisted breeding programs to introduce these favorable haplotypes.

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Allelic variation at the VERNALIZATION-A1, VRN-B1, VRN-B3, and PHOTOPERIOD-A1 genes in cultivars of Triticum durum Desf.

Muterko

Kalendar

Салина

2016

Planta

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The durum wheat varieties from Ukraine, Russia, and Kazakhstan are characterized by the specific allelic composition of the VRN genes that sharply distinguish them from the Triticum durum varieties from other countries. For numerous varieties, the VRN alleles which previously were not found in tetraploid wheat were identified. The ability of wheat to adapt to a wide range of environmental conditions is mostly determined by the allelic diversity within genes regulating the vernalization requirement (VRN) and photoperiod response (PPD). In the present study, allelic variation in the VRN1, VRN3, and PPD-A1 genes was investigated for 134 varieties of Triticum durum from different eco-geographic areas. It was shown that varieties from Russia and Ukraine have a specific allelic composition at the VRN genes, which in quantity and quality differed from European and American cultivars. A large number of varieties of T. durum from Russia carry the dominant Vrn-A1a.1 allele, previously identified mainly in hexaploid wheat. For some varieties from Eastern Europe and Asia, Vrn-A1i and vrn-A1b.3 recently revealed in wheat were also identified. Polymorphism of the VRN-B1 promoter region, distinguishing all three variants of this sequence (VRN-B1.f, VRN-B1.s, and VRN-B1.m), was detected. It was found that the dominant Vrn-B1c allele is commonly found in varieties of T. durum from Russia and Ukraine, but not Europe or USA. Furthermore, many Ukrainian and Russian varieties carry the dominant alleles of the both VRN-A1 and VRN-B1 genes simultaneously, while varieties from Europe and America carry the dominant allele of VRN-A1 alone. Finally, a high frequency of the Vrn-B3a allele, which previously was found only in some accessions of hexaploid wheat, was observed for varieties from Ukraine and Russia. It was revealed that the Ukrainian pool of T. durum varieties is currently the largest genetic source of the dominant Vrn-B3a allele in wheat in the worldwide.

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Evolution and dispersal of emmer wheat (Triticum sp.) from novel haplotypes of Ppd-1 (photoperiod response) genes and their surrounding DNA sequences

Cited by 21 publications

References 34 publications

Evolution of tetraploid wheat based on variations in 5′ UTR regions of Ppd-A1: evidence of gene flow between emmer and timopheevi wheat

Evolution of tetraploid wheat based on variations in 5′ UTR regions of Ppd-A1: evidence of gene flow between emmer and timopheevi wheat

Novel PHOTOPERIOD-1 gene variants associate with yield-related and root-angle traits in European bread wheat

Allelic variation at the VERNALIZATION-A1, VRN-B1, VRN-B3, and PHOTOPERIOD-A1 genes in cultivars of Triticum durum Desf.

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