bims-plasge 2018-12-02 papers

on Plastid genes

Issue of 2018‒12‒02
ten papers selected by
Vera S. Bogdanova
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences

RNA Sequencing-Based Bulked Segregant Analysis Facilitates Efficient D-genome Marker Development for a Specific Chromosomal Region of Synthetic Hexaploid Wheat.
Hybrid durum wheat: heterosis of grain yield and quality traits and genetic architecture of anther extrusion.
Fine mapping and molecular marker development of the Sm gene conferring resistance to gray leaf spot (Stemphylium spp.) in tomato.
Purine nucleotide biosynthetic gene GARS controls early chloroplast development in rice (Oryza sativa L.).
Comparative proteomic investigation of drought responses in foxtail millet.
Identification of expressed R-genes associated with leaf spot diseases in cultivated peanut.
Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.).
miRNomes involved in imparting thermotolerance to crop plants.
Screening of Mutants Related to the C4 Photosynthetic Kranz Structure in Foxtail Millet.
Anther culture in rice proportionally rescues microspores according to gametophytic gene effect and enhances genetic study of hybrid sterility.

Int J Mol Sci. 2018 Nov 26. pii: E3749. [Epub ahead of print]19(12):

RNA Sequencing-Based Bulked Segregant Analysis Facilitates Efficient D-genome Marker Development for a Specific Chromosomal Region of Synthetic Hexaploid Wheat.

Ryo Nishijima, Kentaro Yoshida, Kohei Sakaguchi, Shin-Ichi Yoshimura, Kazuhiro Sato, Shigeo Takumi.

  Common wheat originated from interspecific hybridization between cultivated tetraploid wheat and its wild diploid relative Aegilops tauschii followed by amphidiploidization. This evolutionary process can be reproduced artificially, resulting in synthetic hexaploid wheat lines. Here we performed RNA sequencing (RNA-seq)-based bulked segregant analysis (BSA) using a bi-parental mapping population of two synthetic hexaploid wheat lines that shared identical A and B genomes but included with D-genomes of distinct origins. This analysis permitted identification of D-genome-specific polymorphisms around the Net2 gene, a causative locus to hybrid necrosis. The resulting single nucleotide polymorphisms (SNPs) were classified into homoeologous polymorphisms and D-genome allelic variations, based on the RNA-seq results of a parental tetraploid and two Ae. tauschii accessions. The difference in allele frequency at the D-genome-specific SNP sites between the contrasting bulks (ΔSNP-index) was higher on the target chromosome than on the other chromosomes. Several SNPs with the highest ΔSNP-indices were converted into molecular markers and assigned to the Net2 chromosomal region. These results indicated that RNA-seq-based BSA can be applied efficiently to a synthetic hexaploid wheat population to permit molecular marker development in a specific chromosomal region of the D genome.

Keywords:  allohexaploid; homoeolog; hybrid necrosis; molecular marker; wheat

DOI:  https://doi.org/10.3390/ijms19123749
Theor Appl Genet. 2018 Nov 29.

Hybrid durum wheat: heterosis of grain yield and quality traits and genetic architecture of anther extrusion.

Wessam Akel, Matthias Rapp, Patrick Thorwarth, Tobias Würschum, C Friedrich H Longin.

KEY MESSAGE: Hybrid durum has a promising yield potential coupled with good quality, but the efficiency of hybrid seed production must be improved. Hybrid breeding is a tremendous success story in many crops, but has not yet made a breakthrough in wheat, mainly due to inefficient hybrid seed production. In this study, we investigated the heterosis for grain yield and important quality traits in durum wheat of 33 hybrids built up from 24 parental lines, as well as the variation in anther extrusion and its genetic architecture in a vast collection of Central European elite durum lines. Average mid-parent heterosis for grain yield was 5.8%, and the best hybrids had a more than one ton per hectare higher grain yield than the best line cultivars. Furthermore, hybrids had a higher grain yield than lines at a given level of protein content or sedimentation value, underpinning their potential for a sustainable agriculture. However, seed set in our experimental hybrid seed production was low. We therefore evaluated 315 elite durum lines for visual anther extrusion, which revealed a large genetic variance and a heritability of 0.66. Results from association mapping suggest a mainly quantitative inheritance of visual anther extrusion with few putative QTL being identified, the largest one explaining less than 20% of the genotypic variance. Genome-wide prediction taking the four largest putative QTL into account yielded a mean cross-validated prediction ability of 0.55. Consequently, breeding for improved male floral characteristics is feasible in durum wheat, but should be mainly based on phenotypic selection.

DOI: https://doi.org/10.1007/s00122-018-3248-6
Theor Appl Genet. 2018 Nov 26.

Fine mapping and molecular marker development of the Sm gene conferring resistance to gray leaf spot (Stemphylium spp.) in tomato.

Xiaomei Su, Guangtao Zhu, Zejun Huang, Xiaoxuan Wang, Yanmei Guo, Baoju Li, Yongchen Du, Wencai Yang, Jianchang Gao.

KEY MESSAGE: The tomato gray leaf spot resistance gene Sm was fine-mapped in a 185-kb region through a map-based cloning strategy and genome-wide association study; a candidate gene was proved to be involved in Sm-mediated resistance through transient gene silencing. Gray leaf spot, caused by Stemphylium spp., is a warm weather foliar disease in tomato (Solanum lycopersicum L). Resistance against gray leaf spot is conferred by a single incompletely dominant gene (Sm) located on chromosome 11. This study aimed to map and identify molecular marker tightly linked to the Sm gene for the use of marker-assisted selection in breeding. Using an F2 population derived from a cross between the resistant line '9706' and the susceptible line 'Heinz 1706', the Sm gene was mapped to a 185-kb interval between two markers, InDel343 and InDel-FT-32 on chromosome 11, which was consistent with the result of a genome-wide association study using 289 diverse accessions. An ORF predicted in this region was proved to be involved in Sm-mediated resistance through transient gene silencing and seems to be a good candidate of the Sm locus. To clone the Sm gene, a bacterial artificial chromosome (BAC) library was screened and one BAC clone B80B15 containing the predicted ORF was identified. The analysis of sequence and structure characteristics demonstrated that the candidate gene was not a typical type resistance gene. Additionally, a co-dominant marker Sm-InDel, which produced a 122-bp or 140-bp fragment for resistant or susceptible alleles, respectively, was developed. This marker was validated in 289 germplasm and could be used in marker-assisted selection for gray leaf spot resistance.

DOI: https://doi.org/10.1007/s00122-018-3242-z
Plant Cell Rep. 2018 Nov 29.

Purine nucleotide biosynthetic gene GARS controls early chloroplast development in rice (Oryza sativa L.).

Penghui Cao, Yakun Ren, Xi Liu, Tianyu Zhang, Ping Zhang, Lianjie Xiao, Fulin Zhang, Shijia Liu, Ling Jiang, Jianmin Wan.

  KEY MESSAGE: GARS encodes an enzyme catalyzing the second step of purine nucleotide biosynthesis and plays an important role to maintain the development of chloroplasts in juvenile plants by affecting the expression of plastid-encoded genes. A series of rice white striped mutants were previously described. In this research, we characterized a novel gars mutant with white striped leaves at the seedling stage. By positional cloning, we identified the mutated gene, which encodes a glycinamide ribonucleotide synthetase (GARS) that catalyzes the second step of purine nucleotide biosynthesis. Thylakoid membranes were less abundant in the albinic sectors of mutant seedling leaves compared to the wild type. The expression levels of genes involved in chlorophyll synthesis and photosynthesis were changed. Contents of ATP, ADP, AMP, GTP and GDP, which are crucial for plant growth and development, were decreased in the mutant seedlings. Complementation and CrispR tests confirmed the role of the GARS allele, which was expressed in all rice tissues, especially in the leaves. GARS protein displayed a typical chloroplast location pattern in rice protoplasts. Our results indicated that GARS was involved in chloroplast development at early leaf development by affecting the expression of plastid-encoded genes.

Keywords:  Chloroplast development; GARS; Purine nucleotide biosynthesis; Rice (Oryza sativa L.)

DOI:  https://doi.org/10.1007/s00299-018-2360-z
BMC Plant Biol. 2018 Nov 29. 18(1): 315

Comparative proteomic investigation of drought responses in foxtail millet.

Jiaowen Pan, Zhen Li, Qingguo Wang, Anna K Garrell, Min Liu, Yanan Guan, Wenqing Zhou, Wei Liu.

  BACKGROUND: Foxtail millet (Setaria italica L. P. Beauv) has been considered as a tractable model crop in recent years due to its short growing cycle, lower amount of repetitive DNA, inbreeding nature, small diploid genome, and outstanding abiotic stress-tolerance characteristics. With modern agriculture facing various adversities, it's urgent to dissect the mechanisms of how foxtail millet responds and adapts to drought and stress on the proteomic-level.RESULTS: In this research, a total of 2474 differentially expressed proteins were identified by quantitative proteomic analysis after subjecting foxtail millet seedlings to drought conditions. 321 of these 2474 proteins exhibited significant expression changes, including 252 up-regulated proteins and 69 down-regulated proteins. The resulting proteins could then be divided into different categories, such as stress and defense responses, photosynthesis, carbon metabolism, ROS scavenging, protein synthesis, etc., according to Gene Ontology annotation. Proteins implicated in fatty acid and amino acid metabolism, polyamine biosynthesis, hormone metabolism, and cell wall modifications were also identified. These obtained differential proteins and their possible biological functions under drought stress all suggested that various physiological and metabolic processes might function cooperatively to configure a new dynamic homeostasis in organisms. The expression patterns of five drought-responsive proteins were further validated using western blot analysis. The qRT-PCR was also carried out to analyze the transcription levels of 21 differentially expressed proteins. The results showed large inconsistency in the variation between proteins and the corresponding mRNAs, which showed once again that post-transcriptional modification performs crucial roles in regulating gene expression.
CONCLUSION: The results offered a valuable inventory of proteins that may be involved in drought response and adaption, and provided a regulatory network of different metabolic pathways under stress stimulation. This study will illuminate the stress tolerance mechanisms of foxtail millet, and shed some light on crop germplasm breeding and innovation.

Keywords:  Comparative proteomics; Drought stress; Expression pattern; Foxtail millet (Setaria italica L.); Western blot; qRT-PCR

DOI:  https://doi.org/10.1186/s12870-018-1533-9
Mol Biol Rep. 2018 Nov 30.

Identification of expressed R-genes associated with leaf spot diseases in cultivated peanut.

Phat M Dang, Marshall C Lamb, Kira L Bowen, Charles Y Chen.

  Peanut (Arachis hypogaea L.) is an important food and oilseed crop worldwide. Yield and quality can be significantly reduced by foliar fungal diseases, such as early and late leaf spot diseases. Acceptable levels of leaf spot resistance in cultivated peanut have been elusive due to environmental interactions and the proper combination of QTLs in any particular peanut genotype. Resistance gene analogs, as potential resistance (R)-genes, have unique roles in the recognition and activation of disease resistance responses. Novel R-genes can be identified by searches for conserved domains such as nucleotide binding site, leucine rich repeat, receptor like kinase, and receptor like protein from expressed genes or through genomic sequences. Expressed R-genes represent necessary plant signals in a disease response. The goals of this research are to identify expressed R-genes from cultivated peanuts that are naturally infected by early and late spot pathogens, compare these to the closest diploid progenitors, and evaluate specific gene expression in cultivated peanuts. Putative peanut R-genes (381) were available from a public database (NCBI). Primers were designed and PCR products were sequenced. A total of 214 sequences were produced which matched to proteins with the corresponding R-gene motifs. These R-genes were mapped to the genome sequences of Arachis duranensis and Arachis ipaensis, which are the closest diploid progenitors for tetraploid cultivated peanut, A. hypogaea. Identification and association of specific gene-expression will elucidate potential disease resistance mechanism in peanut and may facilitate the selection of breeding lines with high levels of leaf spot resistance.

Keywords:  Cultivated peanut; Disease resistance; Genetic diversity; Leaf spot; Markers; R-genes; RGAs; Resistance gene analogs

DOI:  https://doi.org/10.1007/s11033-018-4464-5
BMC Plant Biol. 2018 Nov 29. 18(1): 314

Effects of ploidy variation on promoter DNA methylation and gene expression in rice (Oryza sativa L.).

Hongyu Zhang, Asif Ali, Feixue Hou, Tingkai Wu, Daiming Guo, Xiufeng Zeng, Fangfang Wang, Huixia Zhao, Xiaoqiong Chen, Peizhou Xu, Xianjun Wu.

  BACKGROUND: Polyploidy, or whole-genome duplication (WGD) promotes genetic diversification in plants. However, whether WGD is accompanied by epigenetic regulation especially DNA methylation remains yet elusive. Methylation of different region in genomic DNA play discrete role in gene regulation and developmental processes in plants.RESULTS: In our study, we used an apomictic rice line (SARII-628) that produces twin seedlings of different ploidy for methylated DNA immunoprecipitation sequencing (MeDIP-seq). We compared the level of methylation and mRNA expression in three different (CG, CHG, and CHH) sequence contexts of promoter region among haploid (1X), diploid (2X), and triploid (3X) seedling. We used MeDIP-Seq analysis of 14 genes to investigate whole genome DNA methylation and found that relative level of DNA methylation across different ploidy was in following order e.g. diploid > triploid > haploid. GO functional classification of differentially methylated genes into 9 comparisons group of promoter, intergenic and intragenic region discovered, these genes were mostly enriched for cellular component, molecular function, and biological process. By the comparison of methylome data, digital gene expression (DGE), mRNA expression profile, and Q-PCR findings LOC_ Os07g31450 and LOC_ Os01g59320 were analyzed for BS-Seq (Bisulphite sequencing).
CONCLUSIONS: We found that (1) The level of the promoter DNA methylation is negatively correlated with gene expression within each ploidy level. (2) Among all ploidy levels, CG sequence context had highest methylation frequency, and demonstrated that the high CG methylation did reduce gene expression change suggesting that DNA methylation exert repressive function and ensure genome stability during WGD. (3) Alteration in ploidy (from diploid to haploid, or diploid to triploid) reveals supreme changes in methylation frequency of CHH sequence context. Our finding will contribute an understanding towards lower stability of CHH sequence context and educate the effect of promoter region methylation during change in ploidy state in rice.

Keywords:  DNA methylation; Digital gene expression; MeDIP sequencing; Sodium bisulfite sequencing; WGD; mRNA expression

DOI:  https://doi.org/10.1186/s12870-018-1553-5
3 Biotech. 2018 Dec;8(12): 497

miRNomes involved in imparting thermotolerance to crop plants.

Vijay Gahlaut, Vinay Kumar Baranwal, Paramjit Khurana.

  Thermal stress is one of the challenges to crop plants that negatively impacts crop yield. To overcome this ever-growing problem, utilization of regulatory mechanisms, especially microRNAs (miRNAs), that provide efficient and precise regulation in a targeted manner have been found to play determining roles. Besides their roles in plant growth and development, many recent studies have shown differential regulation of several miRNAs during abiotic stresses including heat stress (HS). Thus, understanding the underlying mechanism of miRNA-mediated gene expression during HS will enable researchers to exploit this regulatory mechanism to address HS responses. This review focuses on the miRNAs and regulatory networks that were involved in physiological, metabolic and morphological adaptations during HS in plant, specifically in crops. Illustrated examples including, the miR156-SPL, miR169-NF-YA5, miR395-APS/AST, miR396-WRKY, etc., have been discussed in specific relation to the crop plants. Further, we have also discussed the available plant miRNA databases and bioinformatics tools useful for miRNA identification and study of their regulatory role in response to HS. Finally, we have briefly discussed the future prospects about the miRNA-related mechanisms of HS for improving thermotolerance in crop plants.

Keywords:  Crops; Heat stress; MicroRNA; Regulatory mechanisms; Target genes

DOI:  https://doi.org/10.1007/s13205-018-1521-7
Front Plant Sci. 2018 ;9 1650

Screening of Mutants Related to the C4 Photosynthetic Kranz Structure in Foxtail Millet.

Mingzhao Luo, Shuo Zhang, Chanjuan Tang, Guanqing Jia, Sha Tang, Hui Zhi, Xianmin Diao.

  C4 plants exhibit significantly higher photosynthetic, water and nutrient use efficiency compared with C3 plants. Kranz anatomy is associated with many C4 plants in which bundle sheath cells surround the veins and are themselves surrounded by mesophyll cells. This specialized Kranz anatomy is elucidated as an important contributor to C4 photosynthetic activities in C4 plant. Characterizing the molecular basis of Kranz structure formation has become a key objective for studies of C4 photosynthesis. However, severe mutants that specifically disrupt Kranz anatomy have not been identified. In this study, we detected 549 stable ethyl methane sulfonate-induced foxtail millet (cultivar Yugu1) mutants related to leaf development and photosynthesis among 2,709 mutants screened (M3/M4 generation). The identified mutants included 52 that had abnormal leaf veins (with abnormal starch accumulation based on iodine staining). Each of the 52 mutants was characterized through an analysis of leaf morphology, and through microscopic observations of leaf tissue sections embedded in resin and paraffin. In total, 14 mutants were identified with abnormal Kranz structures exemplified by small bundle sheath cell size. Additional phenotypes of the mutants included poorly differentiated mesophyll and bundle sheath cells, increased vein density and the absence of chloroplasts in the bundle sheath cells. Kranz structure mutations were accompanied by varying leaf thickness, implying these mutations induced complex effects. We identified mutations related to Kranz structure development in this trial, which may be useful for the mapping and cloning of genes responsible for mediating Kranz structure development.

Keywords:  C4 photosynthesis; EMS mutant; Kranz structure; foxtail millet; leaf mutant

DOI:  https://doi.org/10.3389/fpls.2018.01650
Plant Methods. 2018 ;14 102

Anther culture in rice proportionally rescues microspores according to gametophytic gene effect and enhances genetic study of hybrid sterility.

Yoshitaka Kanaoka, Daichi Kuniyoshi, Eri Inada, Yohei Koide, Yoshihiro Okamoto, Hideshi Yasui, Yuji Kishima.

  Background: To investigate plant hybrid sterility, we studied interspecific hybrids of two cultivated rice species, Asian rice (Oryza sativa) and African rice (O. glaberrima). Male gametes of these hybrids display complete sterility owing to a dozen of hybrid sterility loci, termed HS loci, but this complicated genetic system remains poorly understood.Results: Microspores from these interspecific hybrids form sterile pollen but are viable at the immature stage. Application of the anther culture (AC) method caused these immature microspores to induce callus. The segregation distortion of 11 among 13 known HS loci was assessed in the callus population. Using many individual calli, fine mapping of the HS loci was attempted based on heterozygotes produced from chromosome segment substitution lines (CSSLs). Transmission ratio distortion (TRD) from microspores was detected at 6 of 11 HS loci in the callus population. The fine mapping of S 1 and S 19 loci using CSSLs revealed precise distances of markers from the positions of HS loci exhibiting excessive TRD.
Conclusions: We demonstrated that AC to generate callus populations derived from immature microspores is a useful methodology for genetic study. The callus population facilitated detection of TRD at multiple HS loci and dramatically shortened the process for mapping hybrid sterility genes.

Keywords:  Anther culture; Callus; Hybrid sterility; Mapping; Microspore; O. glaberrima; Oryza sativa; Rice

DOI:  https://doi.org/10.1186/s13007-018-0370-z