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Maximum likelihood phylogeny of the bristle clade, showing provisional placement of six partial sequences, indicated by arrows and boldface. Numbers above branches are parsimony bootstrap values. Clade numbers as in figure 1.
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The genus Setaria is the largest genus in the so-called bristle clade, a monophyletic group of panicoid grasses distinguished by the presence of sterile branches, or bristles, in their inflorescences. The clade includes both foxtail millet and pearl millet, the latter an important cereal crop in dry parts of the world. Other members of the clade ar...
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Context 1
... ML trees were recovered with the provisional sequences included; these were largely congruent with trees from the other analyses ( fig. 2). The likelihood score was 7507.69467. Analysis of the modified data set with the parsimony ratchet retrieved 3809 trees of 434 steps, with CI ¼ 0:4988 and RI ¼ ...
Context 2
... atrata fell in a weakly supported position sister to clade III, whereas S. appendiculata and S. grandis were in a larger group including clades II and III plus S. cernua and Pseudoraphis paradoxa in some of the trees; this group col- lapses in the consensus of the four trees (asterisk in fig. 2). Setaria orthosticha fell in clade IV with the other African taxa, as expected, and S. nicorae fell with the South American species of clade X. Paspalidium udum was sister to clade XII, but without bootstrap support, within the larger unsupported clade that included P. geminatum plus ...
Context 3
... inability to amplify large fragments presumably points to degradation of the DNA. The small number of informative characters, combined with the possibility of error, means that the placement of some taxa, particularly those in boldface in figure 2, should be considered provisional until confirmed by additional genes and accessions. ...
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Key message
An efficient and improved transformation method for functional genetics studies in S. italica, being a boon for the Setaria scientific community and for crop improvement.
Abstract
Foxtail millet (Setaria italica) is a short life cycle C4 plant, with sequenced genome, and a potential model plant for C4 species. S. italica is also import...
Citations
... The most complete phylogeny of Setaria and its related genera lacks the resolution of the backbone of the tree [15,29]. It is based on the plastid marker ndhF and shows the genus to be para-or polyphyletic, with a number of well-supported clades corresponding largely to geography [15,29]. ...
... The most complete phylogeny of Setaria and its related genera lacks the resolution of the backbone of the tree [15,29]. It is based on the plastid marker ndhF and shows the genus to be para-or polyphyletic, with a number of well-supported clades corresponding largely to geography [15,29]. The absence of a well-resolved phylogeny along with the difficult morphological delimitation of some species means that Setaria requires further in-depth research. ...
... The aim of this study was to increase the knowledge of taxa of the Cenchrinae through: (a) solving the systematic position of Panicum antidotale in the Cenchrinae, excluding the species from Panicum and establishing a new genus; (b) adding American Setaria species, not tested before, of subgenera Paurochaetium and Reverchoniae, discussing the position of these taxa in actual phylogeny of the genus; (c) analysing Old World species of Setaria and other genera of Cenchrinae from Genbank not considered in previous phylogenies [29]; and (d) presenting new accessions of some other New World species of Setaria (not Paurochaetium and Reverchoniae), in order to confirm their placement in the phylogenetic tree, and more vouchers of some species that were imprecisely located in [29], as they were represented by partial, not fully double-stranded and/or poor-quality accessions. In addition, we are including a new key to recognize all genera of the Cenchrinae. ...
Subtribe Cenchrinae, so-called as the “bristle clade”, is a monophyletic group of panicoid grasses characterized by having sterile branches or bristles on the inflorescences in most of its species. Within this subtribe is also placed Panicum antidotale Retz., an “incertae sedis” species of Panicum L. which lacks bristles along the inflorescence. In this study, we present an update of the subtribe Cenchrinae based on molecular, morphological, and anatomical evidence to clarify the systematic position of P. antidotale in the Cenchrinae, excluding it from Panicum and establishing it in a new genus (i.e., Janochloa Zuloaga & Delfini); the morphological features distinguishing the new genus from other closely related taxa are properly discussed and an identification key to the 24 genera recognized within Cenchrinae is presented. We also add American Setaria species, not tested before, of subgenera Paurochaetium and Reverchoniae, discussing the position of these taxa in actual phylogeny of the genus as well as defining placements in the tree of Setaria species that were imprecisely located in previous analyses. A comparison with the results from other studies, comments on Stenotaphrum Trin. and a brief discussion on conflicting placements in Cenchrus and related taxa, and of Acritochaete Pilg. are also included.
... For example, Setaria also appears to be polyphyletic (Fig. 3). Polyphyly of the genus has also been suggested in molecular phylogenetic analyses and inflorescence differentiation pattern studies (Doust and Kellogg, 2002;Doust et al., 2007;Kellogg et al., 2009). Korean Setaria species are divided into two groups; the first is an annual, with highly condensed panicle and spikelets with bristles (S. chondrachne, S. pycnocoma, S. verticillata, S. italica, S. viridis); the second group is an annual or perennial, with loose panicles, narrow spikelets, and wrinkled leaves (S. pumila). ...
... Korean Setaria species are divided into two groups; the first is an annual, with highly condensed panicle and spikelets with bristles (S. chondrachne, S. pycnocoma, S. verticillata, S. italica, S. viridis); the second group is an annual or perennial, with loose panicles, narrow spikelets, and wrinkled leaves (S. pumila). This is consistent with the results reported by Kellogg et al. (2009). ...
This study was conducted to clarify the phylogenetic position and relationships of Korean Poaceae taxa. A total of 438 taxa including 155 accessions of Korean Poaceae (representing 92% and 72% of Korean Poaceous genera and species, respectively) were employed for phylogeny reconstruction. Sequence data of eight chloroplast DNA markers were used for molecular phylogenetic analyses. The resulted phylogeny was mostly concordant with previous phylogenetic hypotheses, especially in terms of subfamilial and tribal relationships. Several taxa-specific indels were detected in the molecular phylogeny, including a 45 bp deletion in rps3 (PACMAD [Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, Danthonioideae] clade), a 15 bp deletion in ndhF (Oryzeae + Phyllorachideae), a 6 bp deletion in trnLF (Poeae s.l.), and two (17 bp and 378 bp) deletions in atpF-H (Pooideae). The Korean Poaceae members were classified into 23 tribes, representing eight subfamilies. The subfamilial and tribal classifications of the Korean taxa were generally congruent with a recently published system, whereas some subtribes and genera were found to be non-monophyletic. The taxa included in the PACMAD clade (especially Andropogoneae) showed very weak and uncertain phylogenetic relationships, presumably to be due to evolutionary radiation and polyploidization. The reconstructed phylogeny can be utilized to update the taxonomic positions of the newly examined grass accessions.
... gen/alel antara aksesi dari wilayah berbeda cukup tinggi yang dideteksi menggunakan marka Random Amplified Polymorphic DNA (RAPD) dan Inter Simple Sequence Repeat (ISSR). Namun, pada hasil penelitian Vetriventhan et. al. (2012), keragaman genetik dari jewawut berkorelasi cukup baik berdasarkan klasifikasi wilayah, begitu pula pada hasil penelitian Kellogg et. al. (2009) yang menunjukkan bahwa spesies Setaria lebih terkelompok oleh wilayah dari pada klasifikasi sub-generiknya, serta pada hasil penelitian Benabdelmouna et al. (2001) yang menggunakan sekuens gen tertentu yang menunjukkan bahwa jewawut yang berkerabat dekat dapat berkelompok berdasarkan geografis lokasi pertumbuhan tanaman. Hal ini berbeda ...
Keragaman genetik sangat penting dalam pengembangan tanaman, oleh karena itu informasi genetik sangat dibutuhkan dalam kegiatan pemuliaan untuk seleksi. Teknologi molekuler dengan menggunakan marka SSR saat ini banyak digunakan untuk penelitian diversitas genetik karena keakuratan informasi yang tinggi dan sangat polimorfik bahkan untuk spesies atau galur yang berkerabat dekat. Penelitian ini dilakukan untuk mengidentifikasi keragaman genetik dari 14 koleksi plasmanutfah jewawut berkerabat dekat dengan menggunakan 27 marka SSR yang menyebar pada semua kromosom jewawut. Hasil penelitian menunjukkan bahwa koleksi plasmanutfah jewawut berkerabat dekat mengelompok pada klaster yang sama, kecuali pada koleksi aksesi Wete yang menyebar pada kelompok yang berbeda pada kisaran nilai koefisien kemiripan genetik 0.28-0.85 dengan nilai matriks korelasi (r) sebesar 0.954. Koleksi Jewawut yang memiliki koefisien kemiripan genetik yang tinggi (0.85) ditunjukkan pada koleksi ICE-276-11A dengan ICE-276-12A dan yang memiliki koefisien kemiripan terkecil (0.61) ditujukkan pada koleksi 2007-ICE-1335 dan 2007-ICE-1335B. Koleksi jewawut yang berasal dari NTT (WeteGha dan WeteWolowea) dan Introduksi (2007-ICE-1335B dan 2007-ICE-1335) memiliki tingkat variasi genetik yang tinggi yang ditunjukkan oleh penyebaran aksesi pada klaster yang berbeda dengan nilai jarak genetik rata-rata yang cukup tinggi terhadap aksesi koleksi. Adanya keragaman yang tinggi memberikan peluang untuk pemuliaan tanaman jewawut dalam menghasilkan variasi yang lebih banyak dari persilangan aksesi-aksesi tersebut.
... Moreover, the use of the chloroplast gene ndhF, alone or in combination with rbcL and matK, has been proposed 32,36 . Additionally, the use of the ndhF region may also increase the resolution level when used to discern between grass species 37,38 . Unfortunately, the use of trnH-psbA for differentiating Panicum species has not proven useful, as the existence of inversions or mononucleotide repeats at this locus can result in incorrect alignments or additional difficulties in sequencing 39 . ...
Australia has over 30 Panicum spp. (panic grass) including several non-native species that cause crop and pasture loss and hepatogenous photosensitisation in livestock. It is critical to correctly identify them at the species level to facilitate the development of appropriate management strategies for efficacious control of Panicum grasses in crops, fallows and pastures. Currently, identification of Panicum spp. relies on morphological examination of the reproductive structures, but this approach is only useful for flowering specimens and requires significant taxonomic expertise. To overcome this limitation, we used multi-locus DNA barcoding for the identification of ten selected Panicum spp. found in Australia. With the exception of P. buncei , other native Australian Panicum were genetically separated at the species level and distinguished from non-native species. One nuclear ( ITS ) and two chloroplast regions ( matK and trnL intron -trnF ) were identified with varying facility for DNA barcode separation of the Panicum species. Concatenation of sequences from ITS, matK and trnL intron -trnF regions provided clear separation of eight regionally collected species, with a maximum intraspecific distance of 0.22% and minimum interspecific distance of 0.33%. Two of three non-native Panicum species exhibited a smaller genome size compared to native species evaluated, and we speculate that this may be associated with biological advantages impacting invasion of non-native Panicum species in novel locations. We conclude that multi-locus DNA barcoding, in combination with traditional taxonomic identification, provides an accurate and cost-effective adjunctive tool for further distinguishing Panicum spp. at the species level.
... The characteristics, such as degree of fusion of the bristles, the presence of pedicellate spikelets, and type of bristles (flat or stiff), are commonly used to separate Pennisetum from Cenchrus (Clayton & Renvoize., 1982Watson & Dallwitz, 1992); however, none of them can be effectively used to segregate the two genera (Webster, 1988). Kellogg, Aliscioni, Morrone, Pensiero, and Zuloaga (2009) also placed the genus Odontelytrum, harboring only a single species, O. abyssinicum, in this clade along with two genera: Pennisetum and Cenchrus. A study based on a combined nuclear, plastid, and morphological analysis proposed the unification of three genera Pennisetum, Cenchrus, and Odontelytrum (Chemisquy, Giussani, Scataglini, Kellogg, & Morrone, 2010). ...
Pearl millet [Pennisetum glaucum (L.) R. Br.] is one of the world's hardiest warm‐season cereal crop and is cultivated mainly in the semi‐arid tropics of Asia and Africa for food, feed, fodder, and brewing. It is mainly cultivated for its gluten‐free grains with high content and better quality of nutrients. Pearl millet is a resilient crop that can produce grain and biomass under harsh conditions like low fertility, erratic rainfall, acidic and saline soils, and the hottest climates. However, biotic stresses such as downy mildew and blast diseases and abiotic stresses, especially drought and seedling‐ and flowering‐stage heat stress, pose constant threat to the realization of yield potential of this crop. To make further improvement in threshold level of abiotic and biotic stress tolerance, breeders are looking for novel genes in diverse germplasm sources. Crop wild relatives (CWRs) could be a source of novel genes that are important for diversification of the genetic base of pearl millet. A stage‐gate process is proposed for the efficient management of prebreeding programs using CWRs as a source of germplasm diversity and improvement. This article explains the various strategies for capturing and using alleles for climate resilience traits improvement. This article covers breeders’ perspectives on importance of using CWRs as germplasm source for crop improvement. This article also describes the availability of CWRs, characterization of new traits and the strategies to be applied for the identification and introduction of genes of interest in elite breeding lines and commercial varieties and hybrids of pearl millet.
... The characteristics, such as degree of fusion of the bristles, the presence of pedicellate spikelets, and type of bristles (flat or stiff), are commonly used to separate Pennisetum from Cenchrus (Clayton & Renvoize., 1982Watson & Dallwitz, 1992); however, none of them can be effectively used to segregate the two genera (Webster, 1988). Kellogg, Aliscioni, Morrone, Pensiero, and Zuloaga (2009) also placed the genus Odontelytrum, harboring only a single species, O. abyssinicum, in this clade along with two genera: Pennisetum and Cenchrus. A study based on a combined nuclear, plastid, and morphological analysis proposed the unification of three genera Pennisetum, Cenchrus, and Odontelytrum (Chemisquy, Giussani, Scataglini, Kellogg, & Morrone, 2010). ...
Pearl millet [Pennisetum glaucum (L.) R. Br.] is one of the world's hardiest warm-season cereal crop and is cultivated mainly in the semi-arid tropics of Asia and Africa for food, feed, fodder, and brewing. It is mainly cultivated for its gluten-free grains with high content and better quality of nutrients. Pearl millet is a resilient crop that can produce grain and biomass under harsh conditions like low fertility, erratic rainfall , acidic and saline soils, and the hottest climates. However, biotic stresses such as downy mildew and blast diseases and abiotic stresses, especially drought and seedling-and flowering-stage heat stress, pose constant threat to the realization of yield potential of this crop. To make further improvement in threshold level of abiotic and biotic stress tolerance, breeders are looking for novel genes in diverse germplasm sources. Crop wild relatives (CWRs) could be a source of novel genes that are important for diversification of the genetic base of pearl millet. A stage-gate process is proposed for the efficient management of prebreeding programs using CWRs as a source of germplasm diversity and improvement. This article explains the various strategies for capturing and using alleles for climate resilience traits improvement. This article covers breeders' perspectives on importance of using CWRs as germplasm source for crop improvement. This article also describes the availability of CWRs, characterization of new traits and the strategies to be applied for the identification and introduction of genes of interest in elite breeding lines and commercial varieties and hybrids of pearl millet.
... Bipolaris sivanesaniana has been isolated from Paspalidium distans and Setaria sphacelata which possibly suggests a co-evolutionary relationship as these hosts are closely related (Kellogg et al. 2009;Morrone et al. 2012). This is the only Bipolaris species described on Paspalidium distans. ...
Bipolaris species are important plant pathogens with a worldwide distribution in tropical and temperate environments. Species recognition in Bipolaris has been problematic due to a lack of molecular data from ex-type cultures, the use of few gene regions for species resolution and overlapping morphological characters. In this study, we evaluate the efficiency of different DNA barcodes in species delimitation in Bipolaris by phylogenetic analyses, Automatic Barcode Gap Discovery and Objective Clustering. GAPDH is determined to be the best single marker for the genus. These approaches are used to clarify the taxonomic placement of all sequences currently named as Bipolaris in GenBank based on ITS and GAPDH gene sequence data. In checking various publications, we found that the majority of new host records of fungal species published in the Plant Disease journal from 2010 to 2019 were based on BLAST searches of the ITS sequences and up to 82% of those records could be erroneous. Therefore, relying on BLAST searches from GenBank to name species is not recommended. Editorial boards of journals and reviewers of new record papers should be aware of this problem. In naming Bipolaris species, whether new or known, it is recommended to perform phylogenetic analyses based on GAPDH using the correct taxon sampling for accurate results and the species relationship should have reliable statistical support. At least two new species are represented by molecular data in GenBank and we provide an updated taxonomic revision of Bipolaris. We accept 45 species in Bipolaris and notes are provided for all the species including hosts and geographic distribution.
... 2012)では，イネ科は大きく BOP(Bambusoideae, Ehrhartoideae ( 旧 Oryzoideae), Pooideae) クレードと PACMAD (Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, Danthonioideae)クレードに分けられるが，エノ コログサ属は後者に分類され(GPWG II 2012; Kellogg 2002, 2016) ，キビ亜科 Panicoideae，キビ連 Paniceae のエノコログ サ属である(第 1 図) 。亜科内の分子系統学的な研究もなさ れており(Giussani et al. 2001;Kellogg et al. 2009) ，クリノイ ガ属やチカラシバ属とともに小花が退化して刺毛(bristle) となる "bristle-clade" 別名 Cenchrinae 亜連に分類されている(Doust et al. 2007;Kellogg 2016) 。エノコログサ属植物，倍数性種， アワとエノコログサエノコログサ属植物は多くの雑草種を含み(Hubbard 1915;Rominger 1962;Dekker 2003Dekker , 2004) ，世界に約 100 種以上ある とされており，世界中に広く分布している(Zhao et al. . viridis (L.) P. Beauv.)は，作物であるアワ(S. ...
... The phylogeny of Paniceae. Previous studies have established the phylogeny in the grass subfamily Panicoideae, although the genetic information may be limited to have an exact estimation of the evolutionary timeline 23,50 . Furthermore, as a model species in Paniceae, the timing of the tetraploidization in the lineage of broomcorn millet remained unresolved. ...
Broomcorn millet (Panicum miliaceum L.) has strong tolerance to abiotic stresses, and is probably one of the oldest crops, with its earliest cultivation that dated back to ca. ~10,000 years. We report here its genome assembly through a combination of PacBio sequencing, BioNano, and Hi-C (in vivo) mapping. The 18 super scaffolds cover ~95.6% of the estimated genome (~887.8 Mb). There are 63,671 protein-coding genes annotated in this tetraploid genome. About ~86.2% of the syntenic genes in foxtail millet have two homologous copies in broomcorn millet, indicating rare gene loss after tetraploidization in broomcorn millet. Phylogenetic analysis reveals that broomcorn millet and foxtail millet diverged around ~13.1 Million years ago (Mya), while the lineage specific tetraploidization of broomcorn millet may be happened within ~5.91 million years. The genome is not only beneficial for the genome assisted breeding of broomcorn millet, but also an important resource for other Panicum species.
... Foxtail millet is an annual grass and self-pollinating species with a relatively short life cycle, small plant stature, abundant seed production, diploidy (2n = 2x = 18) with a small genome (~515 Mb), and high genetic diversity [5][6][7][8]. Because foxtail millet and its wild progenitor, green foxtail, are easy to grow under low-input conditions and transformable as well, they have recently become a potential C 4 model for polyploid relatives such as switchgrass (Panicum virgatum L.) and to address biological questions related to abiotic stress tolerance and the evolution of C 4 photosynthesis [5,[9][10][11][12]. ...
Foxtail millet (Setaria italica (L.) P. Beauv.), the second most cultivated millet species, is well adapted to diverse environments and remains an important cereal food and forage crop in arid and semiarid regions worldwide. A symbolic crop for indigenous Austronesian peoples, foxtail millet has been cultivated in Taiwan for more than 5,000 years, and landraces reflect diversifying selection for various food applications. A total of 124 accessions collected within Taiwan were assessed for Wx genotypes. Four identified Wx alleles, I, III, IV, and IX were caused by insertion of various transposable elements (TEs) and resulted in endosperm with non-waxy, low amylose content (AC), and waxy, respectively. A total of 16.9%, 4.0%, 49.2%, and 29.8% of accessions were classified as type I, III, IV, and IX, respectively; approximately half of the accessions belonged to the waxy type, indicating that glutinous grains were favored for making traditional food and wine. The TE insertion affected splicing efficiency rather than accuracy, leading to significantly reduced expression of wx in types III, IV, and IX, although their transcripts were the same as wild-type, type I. Consequently, the granule-bound starch synthase I (GBSSI) contents of the three mutated genotypes were relatively low, leading to waxy or low AC endosperm, and the Wx genotypes could explain 78% of variance in AC. The geographic distribution of Wx genotypes are associated with culinary preferences and migration routes of Taiwanese indigenous peoples—in particular, the genotype of landraces collected from Orchid Island was distinct from those from Taiwan Island. This information on the major gene regulating starch biosynthesis in foxtail millet endosperm can be applied to breeding programs for grain quality, and contributes to knowledge of Austronesian cultures.
