Chromosome-Level Genome Assembly Provides New Insights into Genome Evolution and Tuberous Root Formation of .

is a perennial stoloniferous plant with edible tuberous roots in Rosaceae, served as important food and medicine sources for Tibetans in the Qinghai-Tibetan Plateau (QTP), China, over thousands of years. However, a lack of genome information hindered the genetic study. Here, we presented a chromosome-level genome assembly using single-molecule long-read sequencing, and the Hi-C technique.

Transcriptome Assembly and Comparative Analysis Highlight the Primary Mechanism Regulating the Response to Selenium Stimuli in Oats ( L.).

Selenium is an essential microelement for humans and animals. The specific processing technique of oats can maximize the preservation of its nutrients. In this study, to understand the genetic response of oats in a high-selenium environment, oats were treated with sodium selenate for 24 h, and transcriptome analysis was performed.

Molecular Marker Based Design for Breeding Wheat Lines with Multiple Resistance and Superior Quality.

There has not been a major wheat stem rust epidemic worldwide since the 1970s, but the emergence of race TTKSK of f. sp. in 1998 presented a great threat to the world wheat production.

Mapping Quantitative Trait Loci for 1000-Grain Weight in a Double Haploid Population of Common Wheat.

Thousand-grain weight (TGW) is a very important yield trait of crops. In the present study, we performed quantitative trait locus (QTL) analysis of TGW in a doubled haploid population obtained from a cross between the bread wheat cultivar "Superb" and the breeding line "M321" using the wheat 55-k single-nucleotide polymorphism (SNP) genotyping assay. A genetic map containing 15,001 SNP markers spanning 2209.

A fructan: the fructan 1-fructosyl-transferase gene from Helianthus tuberosus increased the PEG-simulated drought stress tolerance of tobacco.

Background: Jerusalem artichoke (Helianthus tuberosus) is a fructan-accumulating plant, and an industrial source of raw material for fructan production, but the crucial enzymes involved in fructan biosynthesis remain poorly understood in this plant.

Results: In this study, a fructan: fructan 1-fructosyl-transferase (1-FFT) gene, Ht1-FFT, was isolated from Jerusalem artichoke. The coding sequence of Ht1-FFT was 2025 bp in length, encoding 641 amino acids.

A bHLH transcription factor TsMYC2 is associated with the blue grain character in triticale (Triticum × Secale).

RNA-Seq was employed to compare the transcriptome differences between the triticale lines and to identify the key gene responsible for the blue aleurone trait. The accumulation of anthocyanins in the aleurone of triticale results in the formation of the blue-grained trait, but the identity of the genes associated with anthocyanin biosynthesis in the aleurone has not yet been reported. In this manuscript, RNA-Seq was employed to compare the transcriptome differences between the triticale lines HM13 (blue aleurone) and HM5 (white aleurone), and to identify the key genes responsible for the blue aleurone trait.

A breeding strategy targeting the secondary gene pool of bread wheat: introgression from a synthetic hexaploid wheat.

Introgressing one-eighth of synthetic hexaploid wheat genome through a double top-cross plus a two-phase selection is an effective strategy to develop high-yielding wheat varieties. The continued expansion of the world population and the likely onset of climate change combine to form a major crop breeding challenge. Genetic advances in most crop species to date have largely relied on recombination and reassortment within a relatively narrow gene pool.

Transcriptome Analysis Identifies Key Genes Responsible for Red Coleoptiles in .

Red coleoptiles can help crops to cope with adversity and the key genes that are responsible for this trait have previously been isolated from , , and . This report describes the use of transcriptome analysis to determine the candidate gene that controls the trait for white coleoptiles in by screening three cultivars with white coleoptiles and two with red coleoptiles. Fifteen structural genes and two transcription factors that are involved in anthocyanin biosynthesis were identified from the assembled UniGene database through BLAST analysis and their transcript levels were then compared in white and red coleoptiles.

Comparative transcriptome analysis of two selenium-accumulating genotypes of Aegilops tauschii Coss. in response to selenium.

Background: Selenium (Se), an essential micronutrient in both animals and humans, has various biological functions, and its deficiency can lead to various diseases. The most common method for increasing Se uptake is the consumption of Se-rich plants, which transform inorganic Se into organic forms. Wheat is eaten daily by many people.

The transfer to and functional annotation of alien alleles in advanced wheat lines derived from synthetic hexaploid wheat.

The abundant genetic diversity in synthetic hexaploid wheat (SHW) can achieve breakthroughs in wheat genetic improvement, but little is known of the genetic mechanisms involved. In this study, three populations of advanced lines (totaling 284 individuals), derived from three top-crosses of SHW-L1 with different common wheat cultivars, followed by ten generations of artificial selection, were used to evaluate the transfer of alien alleles with 24872 Diversity Arrays Technology (DArT) markers. Only 1824, 1786 and 1514 DArT markers were needed to distinguish the alleles from SHW-L1 and the other common wheat parent in the populations SCPD, SS7M and SSYZ, respectively.

AetMYC1, the Candidate Gene Controlling the Red Coleoptile Trait in Aegilops tauschii Coss. Accession As77.

The red coleoptile trait can help monocotyledonous plants withstand stresses, and key genes responsible for the trait have been isolated from , , and , but no corresponding research has been reported for . In this research, transcriptome analysis was performed to isolate the candidate gene controlling the white coleoptile trait in . There were 5348 upregulated, differentially-expressed genes (DEGs) and 4761 downregulated DEGs in red coleoptile vs.

Genetic diversity of avenin-like b genes in Aegilops tauschii Coss.

Avenin-like storage proteins influence the rheological properties and processing quality in common wheat, and the discovery of new alleles will benefit wheat quality improvement. In this study, 13 avenin-like b alleles (TaALPb7D-A-M) were discovered in 108 Aegilops tauschii Coss. accessions.

Allelic Variation and Transcriptional Isoforms of Wheat Gene Regulating Anthocyanin Synthesis in Pericarp.

Recently the gene encoding bHLH transcription factor has been isolated from the bread wheat ( L.) genome and shown to co-locate with the gene conferring purple pericarp color. As a functional evidence of and being the same, higher transcriptional activity of the gene in colored pericarp compared to uncolored one has been demonstrated.

ThMYC4E, candidate Blue aleurone 1 gene controlling the associated trait in Triticum aestivum.

Blue aleurone is a useful and interesting trait in common wheat that was derived from related species. Here, transcriptomes of blue and white aleurone were compared for isolating Blue aleurone 1 (Ba1) transferred from Thinopyrum ponticum. In the genes involved in anthocyanin biosynthesis, only a basic helix-loop-helix (bHLH) transcription factor, ThMYC4E, had a higher transcript level in blue aleurone phenotype, and was homologous to the genes on chromosome 4 of Triticum aestivum.

The abundance of homoeologue transcripts is disrupted by hybridization and is partially restored by genome doubling in synthetic hexaploid wheat.

Background: The formation of an allopolyploid is a two step process, comprising an initial wide hybridization event, which is later followed by a whole genome doubling. Both processes can affect the transcription of homoeologues. Here, RNA-Seq was used to obtain the genome-wide leaf transcriptome of two independent Triticum turgidum × Aegilops tauschii allotriploids (F1), along with their spontaneous allohexaploids (S1) and their parental lines.

The characteristics and functions of a miniature inverted-repeat transposable element TaMITE81 in the 5' UTR of TaCHS7BL from Triticum aestivum.

Miniature inverted-repeat transposable elements (MITEs) are truncated derivatives of autonomous DNA transposons, and are dispersed abundantly in eukaryotic and prokaryotic genomes. In this article, a MITE, TaMITE81, was isolated from the 5' untranslated region (UTR) of TaCHS7BL, chalcone synthase (CHS) catalyzing the first committed step of anthocyanin biosynthesis, in the wheat cultivar 'Opata' with white grain. TaMITE81 was only 81 nucleotides, including a terminal inverted repeat with 39 nucleotides and was flanked by two nucleotides, "TA", target site duplications that were typical features of stowaway-like MITEs.

Transcriptome Analysis of Purple Pericarps in Common Wheat (Triticum aestivum L.).

Wheat (Triticum aestivum L.) cultivars possessing purple grain arethought to be more nutritious because of high anthocyanin contents in the pericarp. Comparative transcriptome analysis of purple (cv Gy115) and white pericarps was carried out using next-generation sequencing technology.

[PS II photochemical efficiency in flag leaf of wheat varieties and its adaptation to strong sun- light intensity on farmland of Xiangride in Qinghai Province, Northwest China].

Taking four wheat varieties developed by Northwest Institute of Plateau Biology, Chinese Academy of Sciences, as test materials, with the measurement of content of photosynthetic pigments, leaf area, fresh and dry mass of flag leaf, the PS II photochemistry efficiency of abaxial and adaxial surface of flag leaf and its adaptation to strong solar radiation during the period of heading stage in Xiangride region were investigated with the pulse-modulated in-vivo chlorophyll fluorescence technique. The results indicated that flag leaf angle mainly grew in horizontal state in Gaoyuan 314, Gaoyuan 363 and Gaoyuan 584, and mainly in vertical state in Gaoyuan 913 because of its smaller leaf area and larger width. Photosynthetic pigments were different among the 4 varieties, and positively correlated with intrinsic PS II photochemistry efficiencies (Fv/Fm).

Genetic variation in cultivated Rheum tanguticum populations.

To examine whether cultivation reduced genetic variation in the important Chinese medicinal plant Rheum tanguticum, the levels and distribution of genetic variation were investigated using ISSR markers. Fifty-eight R. tanguticum individuals from five cultivated populations were studied.

QTug.sau-3B is a major quantitative trait locus for wheat hexaploidization.

Meiotic nonreduction resulting in unreduced gametes is thought to be the predominant mechanism underlying allopolyploid formation in plants. Until now, however, its genetic base was largely unknown. The allohexaploid crop common wheat (Triticum aestivum L.

In situ hybridization analysis indicates that 4AL-5AL-7BS translocation preceded subspecies differentiation of Triticum turgidum.

The important cyclic translocation 4AL-5AL-7BS is an evolutionary signature of polyploidy in wheat. This study aimed to determine its distribution within the subspecies of Triticum turgidum L., using genomic in situ hybridization and fluorescence in situ hybridization.

The genetic study utility of a hexaploid wheat DH population with non-recombinant A- and B-genomes.

To study the D-genome of the wild wheat relative Aegilops tauschii Cosson at the hexaploid level, we developed a synthetic doubled-haploid (DH) hexaploid wheat population, SynDH3. This population was derived from the spontaneous chromosome doubling of triploid F1 hybrid plants obtained from a cross between Triticum turgidum ssp. dicoccon PI377655 and A.

Microsatellite mutation rate during allohexaploidization of newly resynthesized wheat.

Simple sequence repeats (SSRs, also known as microsatellites) are known to be mutational hotspots in genomes. DNA rearrangements have also been reported to accompany allopolyploidization. A study of the effect of allopolyploidization on SSR mutation is therefore important for understanding the origin and evolutionary dynamics of SSRs in allopolyploids.