Phylogeny and genetic diversity of D-genome species of Aegilops and Triticum (Triticeae, Poaceae) from Iran based on microsatellites, ITS, and trnL-F

Bordbar, Firouzeh; Rahiminejad, Mohammad Reza; Saeidi, Hojjatollah; Blattner, Frank R.

doi:10.1007/s00606-010-0375-1

Cited by 26 publications

(12 citation statements)

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“…In this work we aimed for a molecular phylogeny of the chloroplast lineages in Triticeae. The results from ndh F and whole chloroplast genome phylogenetic analyses are mainly in agreement with hypotheses previously published for groups within the tribe [ 9 , 26 , 83 ] and with respect to the domesticated wheats and their close relatives [ 30 , 31 , 84 ]. Compared to these latter publications a better understanding was obtained, particularly because of the comprehensive taxon sampling, the usage of whole chloroplast genomes, and the inclusion of multiple individuals per species.…”

Section: Discussionsupporting

confidence: 90%

“…Yet, plastid sequence data is limited for Triticeae. Studies based on a tribe-wide taxon sampling are rare and focused on single or few plastid markers [ 9 , 26 – 28 ]. To date, the number of whole plastid genome sequences is increasing [ 29 – 34 ], however, entire chloroplast genomes are mainly available for the domesticated taxa and their closest relatives.…”

Section: Introductionmentioning

confidence: 99%

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Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae

et al. 2017

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BackgroundTriticeae, the tribe of wheat grasses, harbours the cereals barley, rye and wheat and their wild relatives. Although economically important, relationships within the tribe are still not understood. We analysed the phylogeny of chloroplast lineages among nearly all monogenomic Triticeae taxa and polyploid wheat species aiming at a deeper understanding of the tribe’s evolution. We used on- and off-target reads of a target-enrichment experiment followed by Illumina sequencing.ResultsThe read data was used to assemble the plastid locus ndhF for 194 individuals and the whole chloroplast genome for 183 individuals, representing 53 Triticeae species and 15 genera. We conducted Bayesian and multispecies coalescent analyses to infer relationships and estimate divergence times of the taxa. We present the most comprehensive dated Triticeae chloroplast phylogeny and review previous hypotheses in the framework of our results. Monophyly of Triticeae chloroplasts could not be confirmed, as either Bromus or Psathyrostachys captured a chloroplast from a lineage closely related to a Bromus-Triticeae ancestor. The most recent common ancestor of Triticeae occurred approximately between ten and 19 million years ago.ConclusionsThe comparison of the chloroplast phylogeny with available nuclear data in several cases revealed incongruences indicating past hybridizations. Recent events of chloroplast capture were detected as individuals grouped apart from con-specific accessions in otherwise monopyhletic groups.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0989-9) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 90%

Section: Introductionmentioning

confidence: 99%

Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae

et al. 2017

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“…monococcum, which are closely related to T. urartu. Triticeae species probably originated in the Fertile Crescent, which includes Iran, Iraq, south-east Turkey, Syria, Lebanon, Jordan and Israel (Kihara, 1944;Feldman et al, 1995;Devos et al, 2005;Kilian et al, 2007a;Bordbar et al, 2011). However, the divergence times and phylogenetic relationships, especially between bread wheat and closely related taxa, is not fully understood.…”

Section: Introductionmentioning

confidence: 99%

“…dicoccon was further complemented by the addition of the D genome from Ae. tauschii approximately 8000 years ago to form the hexaploid T. aestivum (Kihara, 1944;McFadden and Sears, 1946;Feldman et al, 1995;Devos et al, 2005;Dubcovsky and Dvorak, 2007;Kilian et al, 2007b;Bordbar et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Comparative analysis of genome composition in Triticeae reveals strong variation in transposable element dynamics and nucleotide diversity

et al. 2012

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SUMMARYA 454 sequencing snapshot was utilised to investigate the genome composition and nucleotide diversity of transposable elements (TEs) for several Triticeae taxa, including Triticum aestivum, Hordeum vulgare, Hordeum spontaneum and Secale cereale together with relatives of the A, B and D genome donors of wheat, Triticum urartu (A), Aegilops speltoides (S) and Aegilops tauschii (D). Additional taxa containing the A genome, Triticum monococcum and its wild relative Triticum boeoticum, were also included. The main focus of the analysis was on the genomic composition of TEs as these make up at least 80% of the overall genome content. Although more than 200 TE families were identified in each species, approximately 50% of the overall genome comprised 12-15 TE families. The BARE1 element was the largest contributor to all genomes, contributing more than 10% to the overall genome. We also found that several TE families differ strongly in their abundance between species, indicating that TE families can thrive extremely successfully in one species while going virtually extinct in another. Additionally, the nucleotide diversity of BARE1 populations within individual genomes was measured. Interestingly, the nucleotide diversity in the domesticated barley H. vulgare cv. Barke was found to be twice as high as in its wild progenitor H. spontaneum, suggesting that the domesticated barley gained nucleotide diversity from the addition of different genotypes during the domestication and breeding process. In the rye/wheat lineage, sequence diversity of BARE1 elements was generally higher, suggesting that factors such as geographical distribution and mating systems might play a role in intragenomic TE diversity.

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“…The B genome is still unclear and may be extinct, but cytological evidence suggests that the S genome of Aegilops speltoides is a closely related species or an ancestral progenitor to the B genome of wheat [6,7]. The second hybridization event resulted in the complete form of the hexaploid genome T. aestivum (2n = 6x = 42), which occurred between the domesticated Triticum dicoccum or T. durum, a wild goatgrass, and Aegilops Tauschii about 8000-10,000 years ago [8][9][10]. Like most allopolyploid plants, wheat also has the diploid-like chromosome pairing behavior during meiosis, preventing multivalent formation created by multiple homologous or homoeologous chromosomes [11].…”

Section: Introductionmentioning

confidence: 99%

Past, Present and Future Molecular Approaches to Improve Yield in Wheat

Kim¹,

Kim²,

Jang³

2017

Wheat Improvement, Management and Utilization

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This chapter addresses the development and use of molecular markers for yield enhancement in wheat. Since their key goal for breeding is to maximize yield, extensive eforts have been made toward the improvement of yield. Agronomic traits related to yield, yield-related, disease resistance, and abiotic stresses are considered to be quantitative traits (QTLs), also known as complex traits, because they are controlled by numerous genes and are afected by environmental factors. Researchers have been studying such traits in the past decades for the development of molecular markers which can be used in various wheat breeding studies mainly involving restriction fragment length polymorphism (RFLP), simple sequence repeat (SSR), single nucleotide polymorphism (SNP), random ampliied polymorphic DNA (RAPD), and ampliied fragment length polymorphism (AFLP). Furthermore, the advent of next-generation sequencing (NGS) has accelerated the discovery of agronomically important genes. All of the technologies have enabled great advances for increasing the productivity of wheat. Here, the past history of irst-generation sequencing, present status of second-generation sequencing, and future potential of translational genomics linked to the yield will be discussed.

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Phylogeny and genetic diversity of D-genome species of Aegilops and Triticum (Triticeae, Poaceae) from Iran based on microsatellites, ITS, and trnL-F

Cited by 26 publications

References 51 publications

Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae

Dated tribe-wide whole chloroplast genome phylogeny indicates recurrent hybridizations within Triticeae

Comparative analysis of genome composition in Triticeae reveals strong variation in transposable element dynamics and nucleotide diversity

Past, Present and Future Molecular Approaches to Improve Yield in Wheat

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