bims-plasge 2018-12-23 papers

on Plastid genes

Issue of 2018‒12‒23
twenty papers selected by
Vera S. Bogdanova
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences

Analysis of genes encoding seed storage proteins (SSPs) in chickpea (Cicer arietinum L.) reveals co-expressing transcription factors and a seed-specific promoter.
Genome-wide analysis of the pentatricopeptide repeat gene family in different maize genomes and its important role in kernel development.
Toward the sequence-based breeding in legumes in the post-genome sequencing era.
PISTILLATA paralogs in Tarenaya hassleriana have diverged in interaction specificity.
Extreme variation in rates of evolution in the plastid Clp protease complex.
QTL analysis of domestication syndrome in zombi pea (Vigna vexillata), an underutilized legume crop.
Origin and evolution of qingke barley in Tibet.
Genomewide identification of PPR gene family and prediction analysis on restorer gene in Gossypium.
QTL Mapping Combined With Bulked Segregant Analysis Identify SNP Markers Linked to Leaf Shape Traits in Pisum sativum Using SLAF Sequencing.
Genome-Wide Transcription During Early Wheat Meiosis Is Independent of Synapsis, Ploidy Level, and the Ph1 Locus.
Genetic Mapping of Loci for Resistance to Stem Rust in a Tetraploid Wheat Collection.
Transcriptome-based gene expression profiling of diploid radish (Raphanus sativus L.) and the corresponding autotetraploid.
Control of plastidial metabolism by the Clp protease complex.
Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice.
A genetic system on chromosome arm 1BL of wild emmer causes distorted segregation in common wheat.
Evolution of the S-Genomes in Triticum-Aegilops Alliance: Evidences From Chromosome Analysis.
Proline synthesis in developing microspores is required for pollen development and fertility.
Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies Japonica and Indica.
A novel discovery of an LTR retrotransposon-induced hybrid weakness in rice.
Repeats of Unusual Size in Plant Mitochondrial Genomes: Identification, Incidence and Evolution.

Funct Integr Genomics. 2018 Dec 17.

Analysis of genes encoding seed storage proteins (SSPs) in chickpea (Cicer arietinum L.) reveals co-expressing transcription factors and a seed-specific promoter.

Subodh Verma, Sabhyata Bhatia.

  Improvement of the quality and quantity of chickpea seed protein can be greatly facilitated by an understanding of the genic organization and the genetic architecture of the genes encoding seed storage proteins (SSPs). The aim of this study was to provide a comprehensive analysis of the chickpea SSP genes, putative co-expressing transcription factors (TFs), and to identify a seed-specific SSP gene promoter. A genome-wide identification of SSP genes in chickpea led to the identification of 21 non-redundant SSP encoding genes located on 6 chromosomes. Phylogenetic analysis grouped SSP genes into 3 subgroups where members within the same clade demonstrated similar motif composition and intron-exon organization. Tandem duplications were identified to be the major contributors to the expansion of the SSP gene family in chickpea. Co-expression analysis revealed 14 TFs having expression profiles similar to the SSP genes that included members of important TF families that are known to regulate seed development. Expression analysis of SSP genes and TFs revealed significantly higher expression in late stages of seed development as well as in high seed protein content (HPC) genotypes. In silico analysis of the promoter regions of the SSP encoding genes revealed several seed-specific cis-regulatory elements such as RY repeats, ACGT motifs, CAANTG, and GCN4. A candidate promoter was analyzed for seed specificity by generating stable transgenics in Arabidopsis. Overall, this study provides a useful resource to explore the regulatory networks involved in SSP synthesis and/or accumulation for utilization in developing nutritionally improved chickpea genotypes.

Keywords:  Chickpea; Co-expression analysis; Promoter analysis; Seed storage proteins (SSPs)

DOI:  https://doi.org/10.1007/s10142-018-0650-8
BMC Plant Biol. 2018 Dec 19. 18(1): 366

Genome-wide analysis of the pentatricopeptide repeat gene family in different maize genomes and its important role in kernel development.

Lin Chen, Yong-Xiang Li, Chunhui Li, Yunsu Shi, Yanchun Song, Dengfeng Zhang, Yu Li, Tianyu Wang.

  BACKGROUND: The pentatricopeptide repeat (PPR) gene family is one of the largest gene families in land plants (450 PPR genes in Arabidopsis, 477 PPR genes in rice and 486 PPR genes in foxtail millet) and is important for plant development and growth. Most PPR genes are encoded by plastid and mitochondrial genomes, and the gene products regulate the expression of the related genes in higher plants. However, the functions remain largely unknown, and systematic analysis and comparison of the PPR gene family in different maize genomes have not been performed.RESULTS: In this study, systematic identification and comparison of PPR genes from two elite maize inbred lines, B73 and PH207, were performed. A total of 491 and 456 PPR genes were identified in the B73 and PH207 genomes, respectively. Basic bioinformatics analyses, including of the classification, gene structure, chromosomal location and conserved motifs, were conducted. Examination of PPR gene duplication showed that 12 and 15 segmental duplication gene pairs exist in the B73 and PH207 genomes, respectively, with eight duplication events being shared between the two genomes. Expression analysis suggested that 53 PPR genes exhibit qualitative variations in the different genetic backgrounds. Based on analysis of the correlation between PPR gene expression in kernels and kernel-related traits, four PPR genes are significantly negatively correlated with hundred kernel weight, 12 are significantly negatively correlated with kernel width, and eight are significantly correlated with kernel number. Eight of the 24 PPR genes are also located in metaQTL regions associated with yield and kernel-related traits in maize. Two important PPR genes (GRMZM2G353195 and GRMZM2G141202) might be regarded as important candidate genes associated with maize kernel-related traits.
CONCLUSIONS: Our results provide a more comprehensive understanding of PPR genes in different maize inbred lines and identify important candidate genes related to kernel development for subsequent functional validation in maize.

Keywords:  Expression variation; Gene structure; Kernel development; Maize; Pentatricopeptide repeat (PPR) proteins

DOI:  https://doi.org/10.1186/s12870-018-1572-2
Theor Appl Genet. 2018 Dec 17.

Toward the sequence-based breeding in legumes in the post-genome sequencing era.

Rajeev K Varshney, Manish K Pandey, Abhishek Bohra, Vikas K Singh, Mahendar Thudi, Rachit K Saxena.

Efficiency of breeding programs of legume crops such as chickpea, pigeonpea and groundnut has been considerably improved over the past decade through deployment of modern genomic tools and technologies. For instance, next-generation sequencing technologies have facilitated availability of genome sequence assemblies, re-sequencing of several hundred lines, development of HapMaps, high-density genetic maps, a range of marker genotyping platforms and identification of markers associated with a number of agronomic traits in these legume crops. Although marker-assisted backcrossing and marker-assisted selection approaches have been used to develop superior lines in several cases, it is the need of the hour for continuous population improvement after every breeding cycle to accelerate genetic gain in the breeding programs. In this context, we propose a sequence-based breeding approach which includes use of independent or combination of parental selection, enhancing genetic diversity of breeding programs, forward breeding for early generation selection, and genomic selection using sequencing/genotyping technologies. Also, adoption of speed breeding technology by generating 4-6 generations per year will be contributing to accelerate genetic gain. While we see a huge potential of the sequence-based breeding to revolutionize crop improvement programs in these legumes, we anticipate several challenges especially associated with high-quality and precise phenotyping at affordable costs, data analysis and management related to improving breeding operation efficiency. Finally, integration of improved seed systems and better agronomic packages with the development of improved varieties by using sequence-based breeding will ensure higher genetic gains in farmers' fields.

DOI: https://doi.org/10.1007/s00122-018-3252-x
BMC Plant Biol. 2018 Dec 22. 18(1): 368

PISTILLATA paralogs in Tarenaya hassleriana have diverged in interaction specificity.

Suzanne de Bruijn, Tao Zhao, Jose M Muiño, Eric M Schranz, Gerco C Angenent, Kerstin Kaufmann.

  BACKGROUND: Floral organs are specified by MADS-domain transcription factors that act in a combinatorial manner, as summarized in the (A)BCE model. However, this evolutionarily conserved model is in contrast to a remarkable amount of morphological diversity in flowers. One of the mechanisms suggested to contribute to this diversity is duplication of floral MADS-domain transcription factors. Although gene duplication is often followed by loss of one of the copies, sometimes both copies are retained. If both copies are retained they will initially be redundant, providing freedom for one of the paralogs to change function. Here, we examine the evolutionary fate and functional consequences of a transposition event at the base of the Brassicales that resulted in the duplication of the floral regulator PISTILLATA (PI), using Tarenaya hassleriana (Cleomaceae) as a model system.RESULTS: The transposition of a genomic region containing a PI gene led to two paralogs which are located at different positions in the genome. The original PI copy is syntenic in position with most angiosperms, whereas the transposed copy is syntenic with the PI genes in Brassicaceae. The two PI paralogs of T. hassleriana have very similar expression patterns. However, they may have diverged in function, as only one of these PI proteins was able to act heterologously in the first whorl of A. thaliana flowers. We also observed differences in protein complex formation between the two paralogs, and the two paralogs exhibit subtle differences in DNA-binding specificity. Sequence analysis indicates that most of the protein sequence divergence between the two T. hassleriana paralogs emerged in a common ancestor of the Cleomaceae and the Brassicaceae.
CONCLUSIONS: We found that the PI paralogs in T. hassleriana have similar expression patterns, but may have diverged at the level of protein function. Data suggest that most protein sequence divergence occurred rapidly, prior to the origin of the Brassicaceae and Cleomaceae. It is tempting to speculate that the interaction specificities of the Brassicaceae-specific PI proteins are different compared to the PI found in other angiosperms. This could lead to PI regulating partly different genes in the Brassicaceae, and ultimately might result in change floral in morphology.

Keywords:  Cleomaceae; Flower development; Gene duplications; MADS; PISTILLATA; Paralogs; Tarenaya

DOI:  https://doi.org/10.1186/s12870-018-1574-0
Plant J. 2018 Dec 20.

Extreme variation in rates of evolution in the plastid Clp protease complex.

Alissa M Williams, Giulia Friso, Klaas J van Wijk, Daniel B Sloan.

  Eukaryotic cells represent an intricate collaboration between multiple genomes, even down to the level of multisubunit complexes in mitochondria and plastids. One such complex in plants is the caseinolytic protease (Clp), which plays an essential role in plastid protein turnover. The proteolytic core of Clp comprises subunits from one plastid-encoded gene (clpP1) and multiple nuclear genes. The clpP1 gene is highly conserved across most green plants, but it is by far the fastest evolving plastid-encoded gene in some angiosperms. To better understand these extreme and mysterious patterns of divergence, we investigated the history of clpP1 molecular evolution across green plants by extracting sequences from 988 published plastid genomes. We find that clpP1 has undergone remarkably frequent bouts of accelerated sequence evolution and architectural changes (e.g., loss of introns and RNA-editing sites) within seed plants. Although clpP1 is often assumed to be a pseudogene in such cases, multiple lines of evidence suggest that this is rarely true. We applied comparative native gel electrophoresis of chloroplast protein complexes followed by protein mass spectrometry in two species within the angiosperm genus Silene, which has highly elevated and heterogeneous rates of clpP1 evolution. We confirmed that clpP1 is expressed as a stable protein and forms oligomeric complexes with the nuclear-encoded Clp subunits, even in one of the most divergent Silene species. Additionally, there is a tight correlation between amino-acid substitution rates in clpP1 and the nuclear-encoded Clp subunits across a broad sampling of angiosperms, suggesting ongoing selection on interactions within this complex. This article is protected by copyright. All rights reserved.

Keywords:  Clp complex; caseinolytic protease; chloroplast; evolution; evolutionary rates

DOI:  https://doi.org/10.1111/tpj.14208
PLoS One. 2018 ;13(12): e0200116

QTL analysis of domestication syndrome in zombi pea (Vigna vexillata), an underutilized legume crop.

Sujinna Dachapak, Norihiko Tomooka, Prakit Somta, Ken Naito, Akito Kaga, Peerasak Srinives.

Zombi pea (Vigna vexillata (L.) A. Rich) is an underutilized crop belonging to the genus Vigna. Two domesticated forms of zombi pea are cultivated as crop plants; seed and tuber forms. The cultivated seed form is present in Africa, while the cultivated tuber form is present in a very limited part of Asia. Genetics of domestication have been investigated in most of cultivated Vigna crops by means of quantitative trait locus (QTL) mapping. In this study, we investigated genetics of domestication in zombi pea by QTL analysis using an F2 population of 139 plants derived from a cross between cultivated tuber form of V. vexillata (JP235863) and wild V. vexillata (AusTRCF66514). A linkage map with 11 linkage groups (LGs) was constructed from this F2 population using 145 SSR, 117 RAD-seq and 2 morphological markers. Many highly segregation distorted markers were found on LGs 5, 6, 7, 8, 10 and 11. Most of the distorted markers were clustered together and all the markers on LG8 were highly distorted markers. Comparing this V. vexillata linkage map with linkage maps of other four Vigna species demonstrated several genome rearrangements in V. vexillata. QTL analysis for 22 domestication-related traits was investigated by inclusive composite interval mapping in which 37 QTLs were identified for 18 traits; no QTL was detected for 4 traits. Number of QTLs detected in each trait ranged from 1 to 5 with an average of only 2.3. Five QTLs for tuber width and three QTLs for tuber weight. Interestingly, 2 QTLs each for tuber width and tuber weight detected on LG2 and LG4 were located at similar position and wild allele increased tuber width and weight. This indicated wild germplasm having small tuber have potential to increase yield of large tuber cultivated type. Large-effect QTLs (PVE > 20%) were on LG4 (pod length), LG5 (leaf size and seed thickness), and LG7 (for seed-related traits). Comparison of domestication-related QTLs of the zombi pea with those of cowpea (Vigna unguiculata), azuki bean (Vigna angularis), mungbean (Vigna radiata) and rice bean (Vigna umbellata) revealed that there was conservation of some QTLs for seed size, pod size and leaf size between zombi pea and cowpea and that QTLs associated with seed size (weight, length, width and thickness) in each species were clustered on same linkage.

DOI: https://doi.org/10.1371/journal.pone.0200116
Nat Commun. 2018 Dec 21. 9(1): 5433

Origin and evolution of qingke barley in Tibet.

Xingquan Zeng, Yu Guo, Qijun Xu, Martin Mascher, Ganggang Guo, Shuaicheng Li, Likai Mao, Qingfeng Liu, Zhanfeng Xia, Juhong Zhou, Hongjun Yuan, Shuaishuai Tai, Yulin Wang, Zexiu Wei, Li Song, Sang Zha, Shiming Li, Yawei Tang, Lijun Bai, Zhenhua Zhuang, Weiming He, Shancen Zhao, Xiaodong Fang, Qiang Gao, Ye Yin, Jian Wang, Huanming Yang, Jing Zhang, Robert J Henry, Nils Stein, Nyima Tashi.

Tibetan barley (Hordeum vulgare L., qingke) is the principal cereal cultivated on the Tibetan Plateau for at least 3,500 years, but its origin and domestication remain unclear. Here, based on deep-coverage whole-genome and published exome-capture resequencing data for a total of 437 accessions, we show that contemporary qingke is derived from eastern domesticated barley and it is introduced to southern Tibet most likely via north Pakistan, India, and Nepal between 4,500 and 3,500 years ago. The low genetic diversity of qingke suggests Tibet can be excluded as a center of origin or domestication for barley. The rapid decrease in genetic diversity from eastern domesticated barley to qingke can be explained by a founder effect from 4,500 to 2,000 years ago. The haplotypes of the five key domestication genes of barley support a feral or hybridization origin for Tibetan weedy barley and reject the hypothesis of native Tibetan wild barley.

DOI: https://doi.org/10.1038/s41467-018-07920-5
J Genet. 2018 Dec;97(5): 1083-1095

Genomewide identification of PPR gene family and prediction analysis on restorer gene in Gossypium.

Nan Zhao, Yumei Wang, Jinping Hua.

Pentatricopeptide repeat (PPR) gene family plays an essential role in the regulation of plant growth and organelle gene expression. Some PPR genes are related to fertility restoration in plant, but there is no detailed information in Gossypium. In the present study, we identified 482 and 433 PPR homologues in Gossypium raimondii (D5) and G. arboreum (A2) genomes, respectively. Most PPR homologues showed an even distribution on the whole chromosomes. Given an evolutionary analysis to PPR genes from G. raimondii (D5), G. arboreum (A2) and G. hirsutum genomes, eight PPR genes were clustered together with restoring genes of other species. Most cotton PPR genes were qualified with no intron, high proportion of α-helix and classical tertiary structure of PPR protein. Based on bioinformatics analyses, eight PPR genes were targeted in mitochondrion, encoding typical P subfamily protein with protein binding activity and organelle RNA metabolism in function. Further verified by RNA-seq and quantitative real-time PCR (qRT-PCR) analyses, two PPR candidate genes, Gorai.005G0470 (D5) and Cotton_A_08373 (A2), were upregulated in fertile line than sterile line. These results reveal new insights into PPR gene evolution in Gossypium.
Front Genet. 2018 ;9 615

QTL Mapping Combined With Bulked Segregant Analysis Identify SNP Markers Linked to Leaf Shape Traits in Pisum sativum Using SLAF Sequencing.

Yuanting Zheng, Fei Xu, Qikai Li, Gangjun Wang, Na Liu, Yaming Gong, Lulu Li, Zhong-Hua Chen, Shengchun Xu.

  Leaf shape is an important trait that influences the utilization rate of light, and affects quality and yield of pea (Pisum sativum). In the present study, a joint method of high-density genetic mapping using specific locus amplified fragment sequencing (SLAF-seq) and bulked segregant analysis (BSA) was applied to rapidly detect loci with leaf shape traits. A total of 7,146 polymorphic SLAFs containing 12,213 SNP markers were employed to construct a high-density genetic map for pea. We conducted quantitative trait locus (QTL) mapping on an F2 population to identify QTLs associated with leaf shape traits. Moreover, SLAF-BSA was conducted on the same F2 population to identify the single nucleotide polymorphism (SNP) markers linked to leaf shape in pea. Two QTLs (qLeaf_or-1, qLeaf_or-2) were mapped on linkage group 7 (LG7) for pea leaf shape. Through alignment of SLAF markers with Cicer arietinum, Medicago truncatula, and Glycine max, the pea LGs were assigned to their corresponding homologous chromosomal groups. The comparative genetic analysis showed that pea is more closely related to M. truncatula. Based on the sequencing results of two pools with different leaf shape, 179 associated markers were obtained after association analysis. The joint analysis of SLAF-seq and BSA showed that the QTLs obtained from mapping on a high-density genetic map are convincing due to the closely associated map region with the BSA results, which provided more potential markers related to leaf shape. Thus, the identified QTLs could be used in marker-assisted selection for pea breeding in the future. Our study revealed that joint analysis of QTL mapping on a high-density genetic map and BSA-seq is a cost-effective and accurate method to reveal genetic architecture of target traits in plant species without a reference genome.

Keywords:  Pisum sativum; bulked segregant analysis; high-density genetic map; leaf shape; specific locus amplified fragment sequencing

DOI:  https://doi.org/10.3389/fgene.2018.00615
Front Plant Sci. 2018 ;9 1791

Genome-Wide Transcription During Early Wheat Meiosis Is Independent of Synapsis, Ploidy Level, and the Ph1 Locus.

Azahara Carmen Martín, Philippa Borrill, Janet Higgins, Abdulkader Alabdullah, Ricardo H Ramírez-González, David Swarbreck, Cristobal Uauy, Peter Shaw, Graham Moore.

  Polyploidization is a fundamental process in plant evolution. One of the biggest challenges faced by a new polyploid is meiosis, particularly discriminating between multiple related chromosomes so that only homologous chromosomes synapse and recombine to ensure regular chromosome segregation and balanced gametes. Despite its large genome size, high DNA repetitive content and similarity between homoeologous chromosomes, hexaploid wheat completes meiosis in a shorter period than diploid species with a much smaller genome. Therefore, during wheat meiosis, mechanisms additional to the classical model based on DNA sequence homology, must facilitate more efficient homologous recognition. One such mechanism could involve exploitation of differences in chromosome structure between homologs and homoeologs at the onset of meiosis. In turn, these chromatin changes, can be expected to be linked to transcriptional gene activity. In this study, we present an extensive analysis of a large RNA-seq data derived from six different genotypes: wheat, wheat-rye hybrids and newly synthesized octoploid triticale, both in the presence and absence of the Ph1 locus. Plant material was collected at early prophase, at the transition leptotene-zygotene, when the telomere bouquet is forming and synapsis between homologs is beginning. The six genotypes exhibit different levels of synapsis and chromatin structure at this stage; therefore, recombination and consequently segregation, are also different. Unexpectedly, our study reveals that neither synapsis, whole genome duplication nor the absence of the Ph1 locus are associated with major changes in gene expression levels during early meiotic prophase. Overall wheat transcription at this meiotic stage is therefore highly resilient to such alterations, even in the presence of major chromatin structural changes. Further studies in wheat and other polyploid species will be required to reveal whether these observations are specific to wheat meiosis.

Keywords:  Ph1 gene; RNA-seq analysis; ZIP4; chromosomal rearrangements; polyploidy; triticale; wheat–rye hybrid; whole-genome duplication

DOI:  https://doi.org/10.3389/fpls.2018.01791
Int J Mol Sci. 2018 Dec 06. pii: E3907. [Epub ahead of print]19(12):

Genetic Mapping of Loci for Resistance to Stem Rust in a Tetraploid Wheat Collection.

Antonietta Saccomanno, Oadi Matny, Daniela Marone, Giovanni Laidò, Giuseppe Petruzzino, Elisabetta Mazzucotelli, Francesca Desiderio, Antonio Blanco, Agata Gadaleta, Nicola Pecchioni, Pasquale De Vita, Brian Steffenson, Anna Maria Mastrangelo.

  Stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is a major biotic constraint to wheat production worldwide. Disease resistant cultivars are a sustainable means for the efficient control of this disease. To identify quantitative trait loci (QTLs) conferring resistance to stem rust at the seedling stage, an association mapping panel consisting of 230 tetraploid wheat accessions were evaluated for reaction to five Pgt races under greenhouse conditions. A high level of phenotypic variation was observed in the panel in response to all of the races, allowing for genome-wide association mapping of resistance QTLs in wild, landrace, and cultivated tetraploid wheats. Twenty-two resistance QTLs were identified, which were characterized by at least two marker-trait associations. Most of the identified resistance loci were coincident with previously identified rust resistance genes/QTLs; however, six regions detected on chromosomes 1B, 5A, 5B, 6B, and 7B may be novel. Availability of the reference genome sequence of wild emmer wheat accession Zavitan facilitated the search for candidate resistance genes in the regions where QTLs were identified, and many of them were annotated as NOD (nucleotide binding oligomerization domain)-like receptor (NLR) genes or genes related to broad spectrum resistance.

Keywords:  resistant loci; stem rust; tetraploid wheat

DOI:  https://doi.org/10.3390/ijms19123907
Mol Biol Rep. 2018 Dec 17.

Transcriptome-based gene expression profiling of diploid radish (Raphanus sativus L.) and the corresponding autotetraploid.

Wanwan Cheng, Mingjia Tang, Yang Xie, Liang Xu, Yan Wang, Xiaobo Luo, Lianxue Fan, Liwang Liu.

  Polyploidy is an important evolutionary factor in most land plant lineages which possess more than two complete sets of chromosomes. Radish (Raphanus sativus L.) is an economically annual/biennial root vegetable crop worldwide. However, the expression patterns of duplicated homologs involved in the autopolyploidization remains unclear. In present study, the autotetraploid radish plants (2n = 4x = 36) were produced with colchicine and exhibited an increase in the size of flowers, leaves, stomata and pollen grains. The differential gene expression (DGE) profiling was performed to investigate the differences in gene expression patterns between diploid and its corresponding autotetraploid by RNA-Sequencing (RNA-Seq). Totally, 483 up-regulated differentially expressed genes (DEGs) and 408 down-regulated DEGs were detected in diploid and autotetraploid radishes, which majorly involved in the pathways of hormones, photosynthesis and stress response. Moreover, the xyloglucan endotransglucosylase/hydrolase (XTH) and pectin methylesterases (PME) family members related to cell enlargement and cell wall construction were found to be enriched in GO enrichment analysis, of which XTH family members enriched in "apoplast" and "cell wall" terms, while PME family members enriched in "cell wall" term. Reverse-transcription quantitative PCR (RT-qPCR) analysis indicated that the expression profile of DEGs were consistent with results from the RNA-Seq analysis. The DEGs involved in cell wall construction and auxin metabolism were predicted to be associated with organs size increase of autotetraploid radishes in the present study. These results could provide valuable information for elucidating the molecular mechanism underlying polyploidization and facilitating further genetic improvements of important traits in radish breeding programs.

Keywords:  Autotetraploid; DEGs; Radish (Raphanus sativus L.); Reverse-transcription quantitative PCR (RT-qPCR); Transcriptome sequencing

DOI:  https://doi.org/10.1007/s11033-018-4549-1
J Exp Bot. 2018 Dec 21.

Control of plastidial metabolism by the Clp protease complex.

Manuel Rodriguez-Concepcion, Lucio D'Andrea, Pablo Pulido.

Plant metabolism is strongly dependent on plastids. Besides hosting the photosynthetic machinery, these endosymbiotic organelles synthesize starch, fatty acids, amino acids, nucleotides, tetrapyrroles, and isoprenoids. Virtually all enzymes involved in plastid-localized metabolic pathways are encoded by the nuclear genome and imported into plastids. Once there, protein quality control systems ensure proper folding of the mature forms and remove irreversibly damaged proteins. The Clp protease is the main machinery for protein degradation in the plastid stroma. Recent work has unveiled an increasing number of client proteins of this proteolytic complex in plants. Notably, a substantial proportion of these substrates are required for normal chloroplast metabolism, including enzymes involved in the production of essential tetrapyrroles and isoprenoids such as chlorophylls and carotenoids. The Clp protease complex acts in coordination with nuclear-encoded plastidial chaperones for the control of both enzyme levels and proper folding (i.e. activity). This communication involves a retrograde signaling pathway, similarly to the unfolded protein response previously characterized in mitochondria and endoplasmic reticulum. Coordinated Clp protease and chaperone activities appear to further influence other plastid processes, such as the differentiation of chloroplasts into carotenoid-accumulating chromoplasts during fruit ripening.

DOI: https://doi.org/10.1093/jxb/ery441
Theor Appl Genet. 2018 Dec 21.

Comparisons of molecular diversity indices, selective sweeps and population structure of African rice with its wild progenitor and Asian rice.

Marie Noelle Ndjiondjop, Nikolaos Alachiotis, Pavlos Pavlidis, Alphonse Goungoulou, Sèdjro Bienvenu Kpeki, Dule Zhao, Kassa Semagn.

KEY MESSAGE: The extent of molecular diversity parameters across three rice species was compared using large germplasm collection genotyped with genomewide SNPs and SNPs that fell within selective sweep regions. Previous studies conducted on limited number of accessions have reported very low genetic variation in African rice (Oryza glaberrima Steud.) as compared to its wild progenitor (O. barthii A. Chev.) and to Asian rice (O. sativa L.). Here, we characterized a large collection of African rice and compared its molecular diversity indices and population structure with the two other species using genomewide single nucleotide polymorphisms (SNPs) and SNPs that mapped within selective sweeps. A total of 3245 samples representing African rice (2358), Asian rice (772) and O. barthii (115) were genotyped with 26,073 physically mapped SNPs. Using all SNPs, the level of marker polymorphism, average genetic distance and nucleotide diversity in African rice accounted for 59.1%, 63.2% and 37.1% of that of O. barthii, respectively. SNP polymorphism and overall nucleotide diversity of the African rice accounted for 20.1-32.1 and 16.3-37.3% of that of the Asian rice, respectively. We identified 780 SNPs that fell within 37 candidate selective sweeps in African rice, which were distributed across all 12 rice chromosomes. Nucleotide diversity of the African rice estimated from the 780 SNPs was 8.3 × 10-4, which is not only 20-fold smaller than the value estimated from all genomewide SNPs (π = 1.6 × 10-2), but also accounted for just 4.1%, 0.9% and 2.1% of that of O. barthii, lowland Asian rice and upland Asian rice, respectively. The genotype data generated for a large collection of rice accessions conserved at the AfricaRice genebank will be highly useful for the global rice community and promote germplasm use.

DOI: https://doi.org/10.1007/s00122-018-3268-2
J Genet. 2018 Dec;97(5): 1421-1431

A genetic system on chromosome arm 1BL of wild emmer causes distorted segregation in common wheat.

Yunzheng Miao, Siqing Yang, Yurong Jiang, Junkang Rong, Jinsheng Yu.

Nonrandom segregation ratios of alleles 'segregation distortion' can have a striking impact on transmission genetics, and with widespread availability of genetic markers has been shown to be a frequent phenomenon. To investigate the possible effect of genetic interaction on segregation distortion and genetic map construction, the segregation and mapping of genetic markers locatedon wheat chromosomes 1A and 1B were followed in four recombinant substitution line (RSL) populations, produced using four chromosome-arm substitution lines (CASLs 1AS, 1AL, 1BS and 1BL) of wild emmer (Triticum turgidum var. dicoccoides, accession TTD140) in the background of the common wheat (T. aestivum) cultivar Bethlehem (BLH), each crossed to BLH itself. Using these four RSL populations, four genetic maps of chromosome 1 arms were constructed. A total of 22 genetic markers representing 19 loci were assigned to chromosome 1A, and 32 markers representing 30 loci were assigned to 1B. For chromosome 1B, two linkage maps were also constructed using RFLP data of an F2 population derived from the same cross combination as the RSLs. The RSL and F2 maps varied in genetic distances, but showed the same linear order of DNA markers. Segregation analysis revealed strong selection against BLH alleles on chromosome 1B, skewing the allelic frequency distribution in favour of TTD in both F2 and RSL populations at all marker loci. On the contrary, strong selection against TTD alleles on chromosome 1A was detected for some loci in the BLH × CASL1AL RSLs, and their distribution was significantly skewed to BLH. F2 populations always showed more segregation distortion than the corresponding RSLs. More markers near the region of chromosome 1B shared by both CASL1BS and 1BL (∼55 cM on chromosome 1B across the centromere) showed significantly distorted segregation in the BLH × CASL1BL population than in thecorresponding BLH × CASL1BS populations. Six markers located on chromosome 1A region shared by CASL1AS and 1AL showed significantly distorted segregation in 1AL-RSL, while no marker showed distorted segregation in 1AS-RSL. These results indicated that genetic factor(s) in the centromere region cause the distorted segregation of genetic markers on wheat chromosome 1B.
Front Plant Sci. 2018 ;9 1756

Evolution of the S-Genomes in Triticum-Aegilops Alliance: Evidences From Chromosome Analysis.

Alevtina S Ruban, Ekaterina D Badaeva.

  Five diploid Aegilops species of the Sitopsis section: Ae. speltoides, Ae. longissima, Ae. sharonensis, Ae. searsii, and Ae. bicornis, two tetraploid species Ae. peregrina (= Ae. variabilis) and Ae. kotschyi (Aegilops section) and hexaploid Ae. vavilovii (Vertebrata section) carry the S-genomes. The B- and G-genomes of polyploid wheat are also the derivatives of the S-genome. Evolution of the S-genome species was studied using Giemsa C-banding and fluorescence in situ hybridization (FISH) with DNA probes representing 5S (pTa794) and 18S-5.8S-26S (pTa71) rDNAs as well as nine tandem repeats: pSc119.2, pAesp_SAT86, Spelt-1, Spelt-52, pAs1, pTa-535, and pTa-s53. To correlate the C-banding and FISH patterns we used the microsatellites (CTT)10 and (GTT)9, which are major components of the C-banding positive heterochromatin in wheat. According to the results obtained, diploid species split into two groups corresponding to Emarginata and Truncata sub-sections, which differ in the C-banding patterns, distribution of rDNA and other repeats. The B- and G-genomes of polyploid wheat are most closely related to the S-genome of Ae. speltoides. The genomes of allopolyploid wheat have been evolved as a result of different species-specific chromosome translocations, sequence amplification, elimination and re-patterning of repetitive DNA sequences. These events occurred independently in different wheat species and in Ae. speltoides . The 5S rDNA locus of chromosome 1S was probably lost in ancient Ae. speltoides prior to formation of Timopheevii wheat, but after the emergence of ancient emmer. Evolution of Emarginata species was associated with an increase of C-banding and (CTT)10-positive heterochromatin, amplification of Spelt-52, re-pattering of the pAesp_SAT86, and a gradual decrease in the amount of the D-genome-specific repeats pAs1, pTa-535, and pTa-s53. The emergence of Ae. peregrina and Ae. kotschyi did not lead to significant changes of the S*-genomes. However, partial elimination of 45S rDNA repeats from 5S* and 6S* chromosomes and alterations of C-banding and FISH-patterns have been detected. Similarity of the Sv-genome of Ae. vavilovii with the Ss genome of diploid Ae. searsii confirmed the origin of this hexaploid. A model of the S-genome evolution is suggested.

Keywords:  Aegilops; C-banding; FISH; S*-genome of other Aegilops species; S-genome of Ae. speltoides; chromosome; karyotype evolution; wheat

DOI:  https://doi.org/10.3389/fpls.2018.01756
BMC Plant Biol. 2018 Dec 17. 18(1): 356

Proline synthesis in developing microspores is required for pollen development and fertility.

Roberto Mattioli, Marco Biancucci, Amira El Shall, Luciana Mosca, Paolo Costantino, Dietmar Funck, Maurizio Trovato.

  BACKGROUND: In many plants, the amino acid proline is strongly accumulated in pollen and disruption of proline synthesis caused abortion of microspore development in Arabidopsis. So far, it was unclear whether local biosynthesis or transport of proline determines the success of fertile pollen development.RESULTS: We analyzed the expression pattern of the proline biosynthetic genes PYRROLINE-5-CARBOXYLATE SYNTHETASE 1 & 2 (P5CS1 & 2) in Arabidopsis anthers and both isoforms were strongly expressed in developing microspores and pollen grains but only inconsistently in surrounding sporophytic tissues. We introduced in a p5cs1/p5cs1 p5cs2/P5CS2 mutant background an additional copy of P5CS2 under the control of the Cauliflower Mosaic Virus (CaMV) 35S promoter, the tapetum-specific LIPID TRANSFER PROTEIN 12 (Ltp12) promoter or the pollen-specific At5g17340 promoter to determine in which site proline biosynthesis can restore the fertility of proline-deficient microspores. The specificity of these promoters was confirmed by β-glucuronidase (GUS) analysis, and by direct proline measurement in pollen grains and stage-9/10 anthers. Expression of P5CS2 under control of the At5g17340 promoter fully rescued proline content and normal morphology and fertility of mutant pollen. In contrast, expression of P5CS2 driven by either the Ltp12 or CaMV35S promoter caused only partial restoration of pollen development with little effect on pollen fertility.
CONCLUSIONS: Overall, our results indicate that proline transport is not able to fulfill the demand of the cells of the male germ line. Pollen development and fertility depend on local proline biosynthesis during late stages of microspore development and in mature pollen grains.

Keywords:  Anthers; Arabidopsis; Pollen development; Proline biosynthesis; Tissue specificity

DOI:  https://doi.org/10.1186/s12870-018-1571-3
Plant J. 2018 Dec 20.

Differential alternative polyadenylation contributes to the developmental divergence between two rice subspecies Japonica and Indica.

Qian Zhou, Haihui Fu, Dewei Yang, Congting Ye, Sheng Zhu, Juncheng Lin, Wenbin Ye, Guoli Ji, Xinfu Ye, Xiaohui Wu, Qingshun Quinn Li.

  Alternative polyadenylation (APA) is a widespread post-transcriptional mechanism that regulates gene expression through mRNA metabolism, playing a pivotal role in modulating rice (Oryza sativa L.) phenotypic traits. However, little is known about APA-mediated regulations underlying the distinct characteristics between two major rice subspecies, Indica and Japonica. Using poly(A)-tag sequencing approach, polyadenylation (poly(A)) site profiles were investigated and compared pairwise from germinating to mature stage between Indica and Japonica, and extensive differentiation in APA profiles were detected genome-wide. Genes with subspecies-specific poly(A) sites were found to contribute to subspecies characteristics particularly in disease resistance of Indica and cold-stress tolerance of Japonica. In most tissues, differential usages of APA sites exhibited apparent impact on the gene expression profiles between subspecies, and were significantly enriched in quantitative trait loci (QTL) related to yield traits, such as spikelet number and 1000-seed weight. In leaves of booting stage, APA site switching genes displayed global 3' UTR shortening with increased expression in Indica compared with Japonica, and they were overrepresented in the porphyrin and chlorophyll metabolism pathway. This phenomenon may lead to higher chlorophyll contents and photosynthesis in Indica than in Japonica, being associated with their differential growth rates and yield potentials. We further constructed an online website for querying and visualizing the poly(A) atlas in these two rice subspecies. Our results suggest that APA may largely involve in developmental differentiations between two rice subspecies, especially in leaf characteristics and stress response, broadening our knowledge of the post-transcriptional genetic basis underlying the divergence of rice traits. This article is protected by copyright. All rights reserved.

Keywords:  3’ end formation; Alternative polyadenylation; Environmental adaptation; Post-transcriptional regulation; RNA processing; Rice subspecies; Transcriptome analysis

DOI:  https://doi.org/10.1111/tpj.14209
J Exp Bot. 2018 Dec 20.

A novel discovery of an LTR retrotransposon-induced hybrid weakness in rice.

Sadia Nadir, Wei Li, Qian Zhu, Sehroon Khan, Xiao-Ling Zhang, Hui Zhang, Zhen-Fei Wei, Meng-Ting Li, Li Zhou, Cheng-Yun Li, Li-Juan Chen, Dong-Sun Lee.

Hybrid weakness is a post-zygotic hybridization barrier frequently observed in plants, including rice. In this study, we describe the genomic variation among three temperate japonica rice (Oryza sativa ssp. japonica) varieties 'Aranghyangchalbyeo' ('CH7'), 'Sanghaehyangheolua' ('CH8') and 'Shinseonchalbyeo' ('CH9'), carrying different hybrid weakness genes. The reciprocal progenies obtained from crossing any two varieties displayed characteristic hybrid weakness traits. We mapped and cloned a new locus, Hwc3 (hybrid weakness 3), on chromosome 4. Sequence analysis identified that an LTR retrotransposon was inserted into the promoter region of the Hwc3 gene in CH7. A 4-kb DNA fragment from CH7 containing the Hwc3 gene with the inserted LTR retrotransposon was able to induce hybrid weakness in hybrids with CH8 plants carrying the Hwc1 gene by genetic complementation. We investigated the differential gene expression profile of F1 plants exhibiting hybrid weakness and detected that the genes associated with energy metabolism were significantly down-regulated compared to the parents. Based on our results, we propose that LTR retrotransposons could be a potential cause of hybrid weakness in intra-subspecific hybrids in japonica rice. Understanding the molecular mechanisms underlying intra-subspecific hybrid weakness has significance for increasing our knowledge on reproductive isolation and could have significant implications for rice improvement and hybrid breeding.

DOI: https://doi.org/10.1093/jxb/ery442
G3 (Bethesda). 2018 Dec 18. pii: g3.200948.2018. [Epub ahead of print]

Repeats of Unusual Size in Plant Mitochondrial Genomes: Identification, Incidence and Evolution.

Emily L Wynn, Alan C Christensen.

  Plant mitochondrial genomes have excessive size relative to coding capacity, a low mutation rate in genes and a high rearrangement rate. They also have abundant non-tandem repeats often including pairs of large repeats which cause isomerization of the genome by recombination, and numerous repeats of up to several hundred base pairs that recombine only when the genome is stressed by DNA damaging agents or mutations in DNA repair pathway genes. Early work on mitochondrial genomes led to the suggestion that repeats in the size range from several hundred to a few thousand base pair are underrepresented. The repeats themselves are not well-conserved between species, and are not always annotated in mitochondrial sequence assemblies. We systematically identified and compared these repeats, which are important clues to mechanisms of DNA maintenance in mitochondria. We developed a tool to find and curate non-tandem repeats larger than 50bp and analyzed the complete mitochondrial sequences from 157 plant species. We observed an interesting difference between taxa: the repeats are larger and more frequent in the vascular plants. Analysis of closely related species also shows that plant mitochondrial genomes evolve in dramatic bursts of breakage and rejoining, complete with DNA sequence gain and loss. We suggest an adaptive explanation for the existence of the repeats and their evolution.

Keywords:  genome rearrangement; organelle genome evolution; plant mitochondrial genomes; repeated sequence

DOI:  https://doi.org/10.1534/g3.118.200948