Decoupling the molecular regulation of perenniality and flowering in bulbous barley (Hordeum bulbosum)

Global crop production is being challenged by rapid population growth, declining natural resources, and dramatic climatic turnovers. These challenges have prompted plant breeders to explore new ventures to enhance adaptation and sustainability in crops. One intriguing approach to make agriculture more sustainable is by turning annual systems into perennial which offers many economic and biodiversity-friendly benefits. Previous attempts to develop a perennial cereal crop employed a classical breeding approach and extended over a long period with limited success. Thus, elucidating the genetic basis of perenniality at the molecular level can accelerate the breeding process. Here, we investigated the genetic basis of bulb formation in the barley congener species Hordeum bulbosum by elucidating the transcripts presence/absence variation compared with other annual species in the Poaceae, and a differential expression analysis of meristem tissues. The PAV analysis recaptured the expected phylogeny and indicated that H. bulbosum is enriched with developmental and disease responsive genes that are absent among annual species. Next, the abundance of transcripts was quantified and allowed to identify differentially expressed genes that are associated with bulb formation pathways in addition to major circadian clock genes that regulate flowering. A first model for the bulb formation pathway is suggested and include developmental and starch biosynthesis genes. To the best of our knowledge this is the first transcriptome developed for H. bulbosum and the first attempt to describe the regulation of bulb initiation in cereals at the molecular level.

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Identification of the Genetic Basis of Response to de-Acclimation in Winter Barley

International Journal of Molecular Sciences ◽

10.3390/ijms22031057 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1057

Author(s):

Magdalena Wójcik-Jagła ◽

Agata Daszkowska-Golec ◽

Anna Fiust ◽

Przemysław Kopeć ◽

Marcin Rapacz

Keyword(s):

Enzyme Activity ◽

Stress Response ◽

Genetic Basis ◽

Differential Expression Analysis ◽

Winter Barley ◽

Developmental Changes ◽

Molecular Regulation ◽

Quantitative Real Time Pcr ◽

Breeding Lines ◽

Functionally Diverse

Mechanisms involved in the de-acclimation of herbaceous plants caused by warm periods during winter are poorly understood. This study identifies the genes associated with this mechanism in winter barley. Seedlings of eight accessions (four tolerant and four susceptible to de-acclimation cultivars and advanced breeding lines) were cold acclimated for three weeks and de-acclimated at 12 °C/5 °C (day/night) for one week. We performed differential expression analysis using RNA sequencing. In addition, reverse-transcription quantitative real-time PCR and enzyme activity analyses were used to investigate changes in the expression of selected genes. The number of transcripts with accumulation level changed in opposite directions during acclimation and de-acclimation was much lower than the number of transcripts with level changed exclusively during one of these processes. The de-acclimation-susceptible accessions showed changes in the expression of a higher number of functionally diverse genes during de-acclimation. Transcripts associated with stress response, especially oxidoreductases, were the most abundant in this group. The results provide novel evidence for the distinct molecular regulation of cold acclimation and de-acclimation. Upregulation of genes controlling developmental changes, typical for spring de-acclimation, was not observed during mid-winter de-acclimation. Mid-winter de-acclimation seems to be perceived as an opportunity to regenerate after stress. Unfortunately, it is competitive to remain in the cold-acclimated state. This study shows that the response to mid-winter de-acclimation is far more expansive in de-acclimation-susceptible cultivars, suggesting that a reduced response to the rising temperature is crucial for de-acclimation tolerance.

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The Applications of Nanotechnology in Crop Production

Molecules ◽

10.3390/molecules26237070 ◽

2021 ◽

Vol 26 (23) ◽

pp. 7070

Author(s):

Chenxu Liu ◽

Hui Zhou ◽

Jie Zhou

Keyword(s):

Plant Growth ◽

Specific Surface ◽

Crop Production ◽

Molecular Level ◽

High Specific Surface Area ◽

Growth Stages ◽

Crop Tolerance ◽

Plant Growth Stages ◽

Global Agriculture ◽

Promote Plant Growth

With the frequent occurrence of extreme climate, global agriculture is confronted with unprecedented challenges, including increased food demand and a decline in crop production. Nanotechnology is a promising way to boost crop production, enhance crop tolerance and decrease the environmental pollution. In this review, we summarize the recent findings regarding innovative nanotechnology in crop production, which could help us respond to agricultural challenges. Nanotechnology, which involves the use of nanomaterials as carriers, has a number of diverse applications in plant growth and crop production, including in nanofertilizers, nanopesticides, nanosensors and nanobiotechnology. The unique structures of nanomaterials such as high specific surface area, centralized distribution size and excellent biocompatibility facilitate the efficacy and stability of agro-chemicals. Besides, using appropriate nanomaterials in plant growth stages or stress conditions effectively promote plant growth and increase tolerance to stresses. Moreover, emerging nanotools and nanobiotechnology provide a new platform to monitor and modify crops at the molecular level.

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Number of Candidate Effector Genes in Accessory Genomes Differentiates Pathogenic From Endophytic Fusarium oxysporum Strains

Frontiers in Plant Science ◽

10.3389/fpls.2021.761740 ◽

2021 ◽

Vol 12 ◽

Author(s):

Maria E. Constantin ◽

Like Fokkens ◽

Mara de Sain ◽

Frank L. W. Takken ◽

Martijn Rep

Keyword(s):

Fusarium Oxysporum ◽

Plant Species ◽

Genetic Basis ◽

Molecular Level ◽

Similar Amount ◽

Tomato Plants ◽

Grass Roots ◽

Effector Gene ◽

Effector Genes ◽

Potential Pathogen

The fungus Fusarium oxysporum (Fo) is widely known for causing wilt disease in over 100 different plant species. Endophytic interactions of Fo with plants are much more common, and strains pathogenic on one plant species can even be beneficial endophytes on another species. However, endophytic and beneficial interactions have been much less investigated at the molecular level, and the genetic basis that underlies endophytic versus pathogenic behavior is unknown. To investigate this, 44 Fo strains from non-cultivated Australian soils, grass roots from Spain, and tomato stems from United States were characterized genotypically by whole genome sequencing, and phenotypically by examining their ability to symptomlessly colonize tomato plants and to confer resistance against Fusarium Wilt. Comparison of the genomes of the validated endophytic Fo strains with those of 102 pathogenic strains revealed that both groups have similar genomes sizes, with similar amount of accessory DNA. However, although endophytic strains can harbor homologs of known effector genes, they have typically fewer effector gene candidates and associated non-autonomous transposons (mimps) than pathogenic strains. A pathogenic ‘lifestyle’ is associated with extended effector gene catalogs and a set of “host specific” effectors. No candidate effector genes unique to endophytic strains isolated from the same plant species were found, implying little or no host-specific adaptation. As plant-beneficial interactions were observed to be common for the tested Fo isolates, the propensity for endophytism and the ability to confer biocontrol appears to be a predominant feature of this organism. These findings allow prediction of the lifestyle of a Fo strain based on its genome sequence as a potential pathogen or as a harmless or even beneficial endophyte by determining its effectorome and mimp number.

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Sex-specific markers for waterhemp (Amaranthus tuberculatus) and Palmer amaranth (Amaranthus palmeri)

Weed Science ◽

10.1017/wsc.2019.27 ◽

2019 ◽

Vol 67 (4) ◽

pp. 412-418 ◽

Cited By ~ 6

Author(s):

Jacob S. Montgomery ◽

Ahmed Sadeque ◽

Darci A. Giacomini ◽

Patrick J. Brown ◽

Patrick J. Tranel

Keyword(s):

Crop Production ◽

Genetic Basis ◽

The United States ◽

Palmer Amaranth ◽

Amaranthus Palmeri ◽

Data Set ◽

Amaranthus Tuberculatus ◽

Primer Sets ◽

Male Specific ◽

Specific Sequences

AbstractWaterhemp [Amaranthus tuberculatus (Moq.) J. D. Sauer] and Palmer amaranth (Amaranthus palmeri S. Watson) are troublesome weeds of row-crop production in the United States. Their dioecious reproductive systems ensure outcrossing, facilitating rapid evolution and distribution of resistances to multiple herbicides. Little is known, however, about the genetic basis of dioecy in Amaranthus species. In this work, we use restriction site–associated DNA sequencing (RAD-Seq) to investigate the genetic basis of sex determination in A. tuberculatus and A. palmeri. For each species, approximately 200 plants of each sex were sampled and used to create RAD-Seq libraries. The resulting libraries were separately bar-coded and then pooled for sequencing with the Illumina platform, yielding millions of 64-bp reads. These reads were analyzed to identify sex-specific and sex-biased sequences. We identified 345 male-specific sequences from the A. palmeri data set and 2,754 male-specific sequences in A. tuberculatus. An unexpected 723 female-specific sequences were identified in a subset of the A. tuberculatus females; subsequent research, however, indicated female specificity of these markers was limited to the population from which they were identified. Primer sets designed to specifically amplify male-specific sequences were tested for accuracy on multiple, geographically distinct populations of A. tuberculatus and A. palmeri, as well as other Amaranthus species. Two primer sets for A. palmeri and four primer sets for A. tuberculatus were each able to distinguish between male and female plants with at least 95% accuracy. In the near term, sex-specific markers will be useful to the A. tuberculatus and A. palmeri research communities (e.g., to predict sex for crossing experiments). In the long-term, this research will provide the foundational tools for detailed investigations into the molecular biology and evolution of dioecy in weedy Amaranthus species.

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The genetic basis of seed set in barley genotypes varying in compatibility with Hordeum bulbosum

Genome ◽

10.1139/g92-122 ◽

1992 ◽

Vol 35 (5) ◽

pp. 799-805 ◽

Cited By ~ 2

Author(s):

F. Q. Chen ◽

P. M. Hayes

Keyword(s):

Doubled Haploid ◽

Segregation Analysis ◽

Production Efficiency ◽

Genetic Basis ◽

Seed Set ◽

Hordeum Bulbosum ◽

Hordeum Vulgare L ◽

Wide Crosses ◽

Haploid Production ◽

Barley Genotypes

Low seed set, owing to partial incompatibility, can limit sexual gene transfer and haploid production efficiency in wide crosses. The inheritance of partial incompatibility in barley Hordeum vulgare L. × H. bulbosum L. crosses and its effect on gamete sampling in doubled haploid production were studied by doubled haploid progeny analysis. The dominant, monogenic control of partial incompatibility in 'Vada' was confirmed. Partial incompatibility in 'Harrington' is also monogenic but appears to be controlled by a different gene. An association between the Inc gene and a deficiency in a stigma–stylodium specific high pI protein was found in the co-segregation analysis of doubled haploid progeny. Segregation analysis of Mendelian markers in doubled haploid progeny showed that there is no evidence that the compatibility status of the parents has an effect on gamete sampling by the bulbosum technique.Key words: barley, haploids, Hordeum bulbosum, incompatibility.

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Genomic divergence during feralization reveals both conserved and distinct mechanisms of parallel weediness evolution

Communications Biology ◽

10.1038/s42003-021-02484-5 ◽

2021 ◽

Vol 4 (1) ◽

Author(s):

Toshiyuki Imaizumi ◽

Kaworu Ebana ◽

Yoshihiro Kawahara ◽

Chiaki Muto ◽

Hiroyuki Kobayashi ◽

...

Keyword(s):

Crop Production ◽

Genetic Basis ◽

Whole Genome Sequence ◽

Weedy Rice ◽

Cultivated Rice ◽

Tropical Japonica ◽

Adaptive Introgression ◽

Genomic Signatures ◽

Genomic Divergence ◽

Genetic Mechanisms

AbstractAgricultural weeds are the most important biotic constraints to global crop production, and chief among these is weedy rice. Despite increasing yield losses from weedy rice in recent years worldwide, the genetic basis of weediness evolution remains unclear. Using whole-genome sequence analyses, we examined the origins and adaptation of Japanese weedy rice. We find evidence for a weed origin from tropical japonica crop ancestry, which has not previously been documented in surveys of weedy rice worldwide. We further show that adaptation occurs largely through different genetic mechanisms between independently-evolved temperate japonica- and tropical japonica-derived strains; most genomic signatures of positive selection are unique within weed types. In addition, some weedy rice strains have evolved through hybridization between weedy and cultivated rice with adaptive introgression from the crop. Surprisingly, introgression from cultivated rice confers not only crop-like adaptive traits (such as shorter plant height, facilitating crop mimicry) but also weedy-like traits (such as seed dormancy). These findings reveal how hybridization with cultivated rice can promote persistence and proliferation of weedy rice.

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Coloring inside the lines: genomic architecture and evolution of a widespread color pattern in frogs

10.1101/2021.10.28.466315 ◽

2021 ◽

Author(s):

Sandra Goutte ◽

Imtiyaz Hariyani ◽

Kole Deroy Utzinger ◽

Yann Bourgeois ◽

Stephane Boissinot

Keyword(s):

Evolutionary History ◽

Genetic Basis ◽

Molecular Level ◽

Parallel Evolution ◽

Color Pattern ◽

Evolutionary Dynamic ◽

Ideal System ◽

Terrestrial Habitats ◽

History Of ◽

Repeated Evolution

Traits shared among distantly related lineages are indicators of common evolutionary constraints, at the ecological, physiological or molecular level. The vertebral stripe is a color pattern that is widespread across the anuran phylogeny. Despite its prevalence in the order, surprisingly little is known about the genetic basis and evolutionary dynamic of this color pattern. Here we combine histology, genome- and transcriptome-wide analyses with order-scale phylogenetic comparative analyses to investigate this common phenotype. We show that the vertebral stripe has evolved hundreds of times in the evolutionary history of anurans and is selected for in terrestrial habitats. Using the Ethiopian Ptychadena radiation as a model system, we demonstrate that variation at the ASIP gene is responsible for the different vertebral stripe phenotypes. Alleles associated to these phenotypes are younger than the split between closely related Ptychadena species, thus indicating that the vertebral stripe results from parallel evolution within the group. Our findings demonstrate that this widespread color pattern evolves rapidly and recurrently in terrestrial anurans, and therefore constitute an ideal system to study repeated evolution.

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Interaction of Gibberellin With Photoinduction in the Initiation of the Dormant Phase in Vernalized Hordeum bulbosum L

Functional Plant Biology ◽

10.1071/pp9760827 ◽

1976 ◽

Vol 3 (6) ◽

pp. 827 ◽

Cited By ~ 5

Author(s):

M Ofir

Keyword(s):

Gibberellic Acid ◽

Hordeum Bulbosum ◽

Bulb Formation ◽

Short Days ◽

Do So

Vernalized plants of H. bulbosum growing in short (8-h) photoperiods may be induced to form bulbs after exposure to a number of long (16-h) photoperiods. This response was enhanced significantly by application of gibberellic acid (GA3) just before, concurrently with, or at the end of the photoinductive treatment. Exogenous GA3 induced bulb formation even with subthreshold photoinductive treatment but failed to do so without it (i.e. in short days throughout). Thus, induction of bulb initiation under long days may involve both a gibberellin-like factor and one that is unlike gibberellin. Plants treated with GA3 before, or concurrently with, photoinductive treatments produced the bulb at a lower internode than those treated later or not at all. Gibberellin may affect bulb initiation by sensitizing a receptive internode. The non-gibberellin-like factor also produced under long days is required for expression of bulb formation.

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Assembly and characterisation of a unique onion diversity set identifies resistance to Fusarium basal rot and improved seedling vigour

Theoretical and Applied Genetics ◽

10.1007/s00122-019-03422-0 ◽

2019 ◽

Vol 132 (12) ◽

pp. 3245-3264 ◽

Cited By ~ 1

Author(s):

Andrew Taylor ◽

Graham R. Teakle ◽

Peter G. Walley ◽

William E. Finch-Savage ◽

Alison C. Jackson ◽

...

Keyword(s):

Crop Production ◽

Principal Component ◽

Snp Markers ◽

Seedling Vigour ◽

Bulb Formation ◽

Basal Rot ◽

Fusarium Basal Rot ◽

Sib Families ◽

Beneficial Traits ◽

High Level

Abstract Key message A unique, global onion diversity set was assembled, genotyped and phenotyped for beneficial traits. Accessions with strong basal rot resistance and increased seedling vigour were identified along with associated markers. Abstract Conserving biodiversity is critical for safeguarding future crop production. Onion (Allium cepa L.) is a globally important crop with a very large (16 Gb per 1C) genome which has not been sequenced. While onions are self-fertile, they suffer from severe inbreeding depression and as such are highly heterozygous as a result of out-crossing. Bulb formation is driven by daylength, and accessions are adapted to the local photoperiod. Onion seed is often directly sown in the field, and hence seedling establishment is a critical trait for production. Furthermore, onion yield losses regularly occur worldwide due to Fusarium basal rot caused by Fusarium oxysporum f. sp. cepae. A globally relevant onion diversity set, consisting of 10 half-sib families for each of 95 accessions, was assembled and genotyping carried out using 892 SNP markers. A moderate level of heterozygosity (30–35%) was observed, reflecting the outbreeding nature of the crop. Using inferred phylogenies, population structure and principal component analyses, most accessions grouped according to local daylength. A high level of intra-accession diversity was observed, but this was less than inter-accession diversity. Accessions with strong basal rot resistance and increased seedling vigour were identified along with associated markers, confirming the utility of the diversity set for discovering beneficial traits. The onion diversity set and associated trait data therefore provide a valuable resource for future germplasm selection and onion breeding.

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Transcriptome Profiling, Biochemical and Physiological Analyses Provide New Insights towards Drought Tolerance in Nicotiana tabacum L.

Genes ◽

10.3390/genes10121041 ◽

2019 ◽

Vol 10 (12) ◽

pp. 1041 ◽

Cited By ~ 1

Author(s):

Rayyan Khan ◽

Peilu Zhou ◽

Xinghua Ma ◽

Lei Zhou ◽

Yuanhua Wu ◽

...

Keyword(s):

Drought Stress ◽

Nicotiana Tabacum ◽

Leaf Anatomy ◽

Crop Production ◽

Molecular Mechanisms ◽

Molecular Level ◽

Transcriptome Profiling ◽

Dry Weight ◽

Antioxidant Defense System ◽

Nicotiana Tabacum L

Drought stress is one of the main factors limiting crop production, which provokes a number of changes in plants at physiological, anatomical, biochemical and molecular level. To unravel the various mechanisms underpinning tobacco (Nicotiana tabacum L.) drought stress tolerance, we conducted a comprehensive physiological, anatomical, biochemical and transcriptome analyses of three tobacco cultivars (i.e., HongHuaDaJinYuan (H), NC55 (N) and Yun Yan-100 (Y)) seedlings that had been exposed to drought stress. As a result, H maintained higher growth in term of less reduction in plant fresh weight, dry weight and chlorophyll content as compared with N and Y. Anatomical studies unveiled that drought stress had little effect on H by maintaining proper leaf anatomy while there were significant changes in the leaf anatomy of N and Y. Similarly, H among the three varieties was the least affected variety under drought stress, with more proline content accumulation and a powerful antioxidant defense system, which mitigates the negative impacts of reactive oxygen species. The transcriptomic analysis showed that the differential genes expression between HongHuaDaJinYuan, NC55 and Yun Yan-100 were enriched in the functions of plant hormone signal transduction, starch and sucrose metabolism, and arginine and proline metabolism. Compared to N and Y, the differentially expressed genes of H displayed enhanced expression in the corresponding pathways under drought stress. Together, our findings offer insights that H was more tolerant than the other two varieties, as evidenced at physiological, biochemical, anatomical and molecular level. These findings can help us to enhance our understanding of the molecular mechanisms through the networks of various metabolic pathways mediating drought stress adaptation in tobacco.

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