bims-plasge 2018-12-16 papers

bims-plasge

Biomed News

on Plastid genes

Issue of 2018–12–16
twelve papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Comparative Mapping Combined With Map-Based Cloning of the Brassica juncea Genome Reveals a Candidate Gene for Multilocular Rapeseed.
Effects of Chilling on the Structure, Function and Development of Chloroplasts.
Discovery of genomic regions and candidate genes controlling shelling percentage using QTL-seq approach in cultivated peanut (Arachis hypogaea L.).
Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.).
Transcriptome and Hormone Comparison of Three Cytoplasmic Male Sterile Systems in Brassica napus.
Divergence between bread wheat and Triticum militinae in the powdery mildew resistance QPm.tut-4A locus and its implications for cloning of the resistance gene.
Genetic Contribution of Emmer Wheat (Triticum dicoccon Schrank) to Heat Tolerance of Bread Wheat.
Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants.
Convergent evolution of a metabolic switch between aphid and caterpillar resistance in cereals.
Mapping resistance to Phytophthora root rot identifies independent loci from cultivated (Cicer arietinum L.) and wild (Cicer echinospermum P.H. Davis) chickpea.
The mitochondrial pentatricopeptide repeat protein EMP12 is involved in the splicing of three nad2 introns and seed development in maize.
Identification of New Sources of Resistance to Wheat Stem Rust in Aegilops spp. in the Tertiary Genepool of Wheat.

Front Plant Sci. 2018 ;9 1744

Comparative Mapping Combined With Map-Based Cloning of the Brassica juncea Genome Reveals a Candidate Gene for Multilocular Rapeseed.

Cuiping Chen, Lu Xiao, Xin Li, Dezhi Du.

  Multilocular traits exist in a variety of plants and exert important effects on plant yield. Previous genetic studies have shown that multilocular trait of the Brassica juncea cultivar Duoshi is controlled by two recessive genes, Bjln1 and Bjln2. In previous studies, the Bjln1 gene is located on chromosome A07, and the Bjln1 candidate gene is BjuA07.CLV1. In this study, a BC4 mapping population for the Bjln2 gene was generated. This population was used to construct genetic linkage maps of the Bjln2 gene using amplified fragment length polymorphism (AFLP), intron length polymorphism (IP) and simple sequence repeat (SSR) methodology. The results showed that the Bjln2 gene was restricted to a 0.63 cM interval. BLAST alignment with B. juncea revealed the Bjln2 gene was located within a 11.81-16.65 Mb region on chromosome B07. Moreover, the candidate gene BjuB07.CLV1 (equivalent to Bjln2) was cloned by comparing mapping and map-based cloning, and BjuB07.CLV1 gene was shown to have the ability to restore the bilocular traits in a genetic complementation experiment. The sequencing revealed that a 4961 bp insertion interrupted the coding sequence of the BjuB07.CLV1 gene, resulting in an increase in locule number. Expression analysis revealed that BjuB07.CLV1 was expressed in all tissues and the expression level in bilocular plants was significantly higher than that in multilocular plants. In addition, markers closely linked to the Bjln2 gene were developed and used for molecular marker-assisted breeding of multilocular traits.

Keywords:  Brassica juncea; CLV1; fine mapping; map-based cloning; multilocular

DOI:  https://doi.org/10.3389/fpls.2018.01744
Front Plant Sci. 2018 ;9 1715

Effects of Chilling on the Structure, Function and Development of Chloroplasts.

Xiaomin Liu, Yunlin Zhou, Jianwei Xiao, Fei Bao.

  Chloroplasts are the organelles that perform energy transformation in plants. The normal physiological functions of chloroplasts are essential for plant growth and development. Chilling is a common environmental stress in nature that can directly affect the physiological functions of chloroplasts. First, chilling can change the lipid membrane state and enzyme activities in chloroplasts. Then, the efficiency of photosynthesis declines, and excess reactive oxygen species (ROS) are produced. On one hand, excess ROS can damage the chloroplast lipid membrane; on the other hand, ROS also represent a stress signal that can alter gene expression in both the chloroplast and nucleus to help regenerate damaged proteins, regulate lipid homeostasis, and promote plant adaptation to low temperatures. Furthermore, plants assume abnormal morphology, including chlorosis and growth retardation, with some even exhibiting severe necrosis under chilling stress. Here, we review the response of chloroplasts to low temperatures and focus on photosynthesis, redox regulation, lipid homeostasis, and chloroplast development to elucidate the processes involved in plant responses and adaptation to chilling stress.

Keywords:  ROS; chilling; chloroplast structure; chloroplasts; development; photosynthesis

DOI:  https://doi.org/10.3389/fpls.2018.01715
Plant Biotechnol J. 2018 Dec 13.

Discovery of genomic regions and candidate genes controlling shelling percentage using QTL-seq approach in cultivated peanut (Arachis hypogaea L.).

Huaiyong Luo, Manish K Pandey, Aamir W Khan, Jianbin Guo, Bei Wu, Yan Cai, Li Huang, Xiaojing Zhou, Yuning Chen, Weigang Chen, Nian Liu, Yong Lei, Boshou Liao, Rajeev K Varshney, Huifang Jiang.

  Cultivated peanut (Arachis hypogaea L.) is an important grain legume providing high-quality cooking oil, rich proteins and other nutrients. Shelling percentage (SP) is the 2nd most important agronomic trait after pod yield and this trait significantly affects the economic value of peanut in the market. Deployment of diagnostic markers through genomics-assisted breeding (GAB) can accelerate the process of developing improved varieties with enhanced SP. In this context, we deployed the QTL-seq approach to identify genomic regions and candidate genes controlling SP in a recombinant inbred line population (Yuanza 9102 × Xuzhou 68-4). Four libraries (two parents and two extreme bulks) were constructed and sequenced, generating 456.89-790.32 million reads and achieving 91.85%-93.18% genome coverage and 14.04-21.37 mean read depth. Comprehensive analysis of two sets of data (Yuanza 9102/two bulks and Xuzhou 68-4/two bulks) using the QTL-seq pipeline resulted in discovery of two overlapped genomic regions (2.75Mb on A09 and 1.1Mb on B02). Nine candidate genes affected by ten SNPs with nonsynonymous effects or in UTRs were identified in these regions for SP. Cost-effective KASP (Kompetitive Allele Specific PCR) markers were developed for one SNP from A09 and three SNPs from B02 chromosome. Genotyping of the mapping population with these newly developed KASP markers confirmed the major control and stable expressions of these genomic regions across five environments. The identified candidate genomic regions and genes for SP further provide opportunity for gene cloning and deployment of diagnostic markers in molecular breeding for achieving high SP in improved varieties. This article is protected by copyright. All rights reserved.

Keywords:  Peanut; QTL-seq; candidate genes; genomic regions; shelling percentage

DOI:  https://doi.org/10.1111/pbi.13050
BMC Plant Biol. 2018 Dec 12. 18(1): 345

Genome-wide association study discovered favorable single nucleotide polymorphisms and candidate genes associated with ramet number in ramie (Boehmeria nivea L.).

Kunmei Chen, Mingbao Luan, Heping Xiong, Ping Chen, Jikang Chen, Gang Gao, Kunyong Huang, Aiguo Zhu, Chunming Yu.

   BACKGROUND: Ramie (Boehmeria nivea L.) is one of the most important natural fiber crops and an important forage grass in south China. Ramet number, which is a quantitative trait controlled by multigenes, is one of the most important agronomic traits in plants because the ramet number per plant is a key component of grain yield and biomass. However, the genetic variation and genetic architecture of ramie ramet number are rarely known.
RESULTS: A genome-wide association study was performed using a panel of 112 core germplasms and 108,888 single nucleotide polymorphisms (SNPs) detected using specific-locus amplified fragment sequencing technology. Trait-SNP association analysis detected 44 significant SNPs that were associated with ramet number at P < 0.01. The favorable SNP Marker20170-64 emerged at least twice in the three detected stages and was validated to be associated with the ramie ramet number using genomic DNA polymerase chain reaction with an F1 hybrid progeny population. Comparative genome analysis predicted nine candidate genes for ramet number based on Marker20170-64. Real-time quantitative polymerase chain reaction analysis indicated that six of the genes were specific to upregulation in the ramie variety with high ramet number. These results suggest that these genes could be considered as ramet number-associated candidates in ramie.
CONCLUSIONS: The identified loci or genes may be promising targets for genetic engineering and selection for modulating the ramet number in ramie. Our work improves understanding of the genetics of ramet number in ramie core germplasms and provides tools for marker-assisted selection for improvement of agricultural traits.

Keywords:  Genome-wide association study; Ramet number; Ramie; Significant SNPs; qPCR

DOI:  https://doi.org/10.1186/s12870-018-1573-1
Int J Mol Sci. 2018 Dec 12. pii: E4022. [Epub ahead of print]19(12):

Transcriptome and Hormone Comparison of Three Cytoplasmic Male Sterile Systems in Brassica napus.

Bingli Ding, Mengyu Hao, Desheng Mei, Qamar U Zaman, Shifei Sang, Hui Wang, Wenxiang Wang, Li Fu, Hongtao Cheng, Qiong Hu.

  The interaction between plant mitochondria and the nucleus markedly influences stress responses and morphological features, including growth and development. An important example of this interaction is cytoplasmic male sterility (CMS), which results in plants producing non-functional pollen. In current research work, we compared the phenotypic differences in floral buds of different Brassica napus CMS (Polima, Ogura, Nsa) lines with their corresponding maintainer lines. By comparing anther developmental stages between CMS and maintainer lines, we identified that in the Nsa CMS line abnormality occurred at the tetrad stage of pollen development. Phytohormone assays demonstrated that IAA content decreased in sterile lines as compared to maintainer lines, while the total hormone content was increased two-fold in the S₂ stage compared with the S₁ stage. ABA content was higher in the S₁ stage and exhibited a two-fold decreasing trend in S₂ stage. Sterile lines however, had increased ABA content at both stages compared with the corresponding maintainer lines. Through transcriptome sequencing, we compared differentially expressed unigenes in sterile and maintainer lines at both (S₁ and S₂) developmental stages. We also explored the co-expressed genes of the three sterile lines in the two stages and classified these genes by gene function. By analyzing transcriptome data and validating by RT-PCR, it was shown that some transcription factors (TFs) and hormone-related genes were weakly or not expressed in the sterile lines. This research work provides preliminary identification of the pollen abortion stage in Nsa CMS line. Our focus on genes specifically expressed in sterile lines may be useful to understand the regulation of CMS.

Keywords:  Brassica napus; cytoplasmic male sterility (CMS); differentially expressed genes; phytohormones; pollen development

DOI:  https://doi.org/10.3390/ijms19124022
Theor Appl Genet. 2018 Dec 07.

Divergence between bread wheat and Triticum militinae in the powdery mildew resistance QPm.tut-4A locus and its implications for cloning of the resistance gene.

Eva Janáková, Irena Jakobson, Hilma Peusha, Michael Abrouk, Monika Škopová, Hana Šimková, Jan Šafář, Jan Vrána, Jaroslav Doležel, Kadri Järve, Miroslav Valárik.

A segment of Triticum militinae chromosome 7G harbors a gene(s) conferring powdery mildew resistance which is effective at both the seedling and the adult plant stages when transferred into bread wheat (T. aestivum). The introgressed segment replaces a piece of wheat chromosome arm 4AL. An analysis of segregating materials generated to positionally clone the gene highlighted that in a plant heterozygous for the introgression segment, only limited recombination occurs between the introgressed region and bread wheat 4A. Nevertheless, 75 genetic markers were successfully placed within the region, thereby confining the gene to a 0.012 cM window along the 4AL arm. In a background lacking the Ph1 locus, the localized rate of recombination was raised 33-fold, enabling the reduction in the length of the region containing the resistance gene to a 480 kbp stretch harboring 12 predicted genes. The substituted segment in the reference sequence of bread wheat cv. Chinese Spring is longer (640 kbp) and harbors 16 genes. A comparison of the segments' sequences revealed a high degree of divergence with respect to both their gene content and nucleotide sequence. Of the 12 T. militinae genes, only four have a homolog in cv. Chinese Spring. Possible candidate genes for the resistance have been identified based on function predicted from their sequence.

DOI: https://doi.org/10.1007/s00122-018-3259-3
Front Plant Sci. 2018 ;9 1529

Genetic Contribution of Emmer Wheat (Triticum dicoccon Schrank) to Heat Tolerance of Bread Wheat.

Smi Ullah, Helen Bramley, Hans Daetwyler, Sang He, Tariq Mahmood, Rebecca Thistlethwaite, Richard Trethowan.

  Rising global temperatures cause substantial yield losses in many wheat growing environments. Emmer wheat (Triticum dicoccon Schrank), one of the first wheat species domesticated, carries significant variation for tolerance to abiotic stresses. This study identified new genetic variability for high-temperature tolerance in hexaploid progeny derived from crosses with emmer wheat. Eight hexaploid and 11 tetraploid parents were recombined in 43 backcross combinations using the hexaploid as the recurrent parent. A total of 537 emmer-based hexaploid lines were developed by producing approximately 10 doubled haploids on hexaploid like BC1F1 progeny and subsequent selection for hexaploid morphology. These materials and 17 commercial cultivars and hexaploid recurrent parents were evaluated under two times of sowing in the field, in 2014-2016. The materials were genotyped using a 90K SNP platform and these data were used to estimate the contribution of emmer wheat to the progeny. Significant phenotypic and genetic variation for key agronomical traits including grain yield, TKW and screenings was observed. Many of the emmer derived lines showed improved performance under heat stress (delayed sowing) compared with parents and commercial cultivars. Emmer derived lines were the highest yielding material in both sowing dates. The emmer wheat parent contributed between 1 and 44% of the genome of the derived lines. Emmer derived lines with superior kernel weight and yield generally had a greater genetic contribution from the emmer parent compared to those with lower trait values. The study showed that new genetic variation for key traits such as yield, kernel weight and screenings can be introduced to hexaploid wheat from emmer wheat. These genetic resources should be explored more systematically to stabilize grain yield and quality in a changing climate.

Keywords:  agronomic traits; emmer wheat; genetic diversity; genotyping; heat tolerance; hexaploid wheat

DOI:  https://doi.org/10.3389/fpls.2018.01529
Nat Plants. 2018 Dec 10.

Sensitive detection of pre-integration intermediates of long terminal repeat retrotransposons in crop plants.

Jungnam Cho, Matthias Benoit, Marco Catoni, Hajk-Georg Drost, Anna Brestovitsky, Matthijs Oosterbeek, Jerzy Paszkowski.

Retrotransposons have played an important role in the evolution of host genomes1,2. Their impact is mainly deduced from the composition of DNA sequences that have been fixed over evolutionary time2. Such studies provide important 'snapshots' reflecting the historical activities of transposons but do not predict current transposition potential. We previously reported sequence-independent retrotransposon trapping (SIRT) as a method that, by identification of extrachromosomal linear DNA (eclDNA), revealed the presence of active long terminal repeat (LTR) retrotransposons in Arabidopsis3. However, SIRT cannot be applied to large and transposon-rich genomes, as found in crop plants. We have developed an alternative approach named ALE-seq (amplification of LTR of eclDNAs followed by sequencing) for such situations. ALE-seq reveals sequences of 5' LTRs of eclDNAs after two-step amplification: in vitro transcription and subsequent reverse transcription. Using ALE-seq in rice, we detected eclDNAs for a novel Copia family LTR retrotransposon, Go-on, which is activated by heat stress. Sequencing of rice accessions revealed that Go-on has preferentially accumulated in Oryza sativa ssp. indica rice grown at higher temperatures. Furthermore, ALE-seq applied to tomato fruits identified a developmentally regulated Gypsy family of retrotransposons. A bioinformatic pipeline adapted for ALE-seq data analyses is used for the direct and reference-free annotation of new, active retroelements. This pipeline allows assessment of LTR retrotransposon activities in organisms for which genomic sequences and/or reference genomes are either unavailable or of low quality.

DOI: https://doi.org/10.1038/s41477-018-0320-9
Sci Adv. 2018 Dec;4(12): eaat6797

Convergent evolution of a metabolic switch between aphid and caterpillar resistance in cereals.

B Li, C Förster, C A M Robert, T Züst, L Hu, R A R Machado, J-D Berset, V Handrick, T Knauer, G Hensel, W Chen, J Kumlehn, P Yang, B Keller, J Gershenzon, G Jander, T G Köllner, M Erb.

Tailoring defense responses to different attackers is important for plant performance. Plants can use secondary metabolites with dual functions in resistance and defense signaling to mount herbivore-specific responses. To date, the specificity and evolution of this mechanism are unclear. Here, we studied the functional architecture, specificity, and genetic basis of defense regulation by benzoxazinoids in cereals. We document that DIMBOA-Glc induces callose as an aphid resistance factor in wheat. O-methylation of DIMBOA-Glc to HDMBOA-Glc increases plant resistance to caterpillars but reduces callose inducibility and resistance to aphids. DIMBOA-Glc induces callose in wheat and maize, but not in Arabidopsis, while the glucosinolate 4MO-I3M does the opposite. We identify a wheat O-methyltransferase (TaBX10) that is induced by caterpillar feeding and converts DIMBOA-Glc to HDMBOA-Glc in vitro. While the core pathway of benzoxazinoid biosynthesis is conserved between wheat and maize, the wheat genome does not contain close homologs of the maize DIMBOA-Glc O-methyltransferase genes, and TaBx10 is only distantly related. Thus, the functional architecture of herbivore-specific defense regulation is similar in maize and wheat, but the regulating biosynthetic genes likely evolved separately. This study shows how two different cereal species independently achieved herbivore-specific defense activation by regulating secondary metabolite production.

DOI: https://doi.org/10.1126/sciadv.aat6797
Theor Appl Genet. 2018 Dec 07.

Mapping resistance to Phytophthora root rot identifies independent loci from cultivated (Cicer arietinum L.) and wild (Cicer echinospermum P.H. Davis) chickpea.

Amritha Amalraj, Julian Taylor, Sean Bithell, Yongle Li, Kevin Moore, Kristy Hobson, Tim Sutton.

KEY MESSAGE: Major QTL for Phytophthora root rot resistance have been identified in three mapping populations with independent sources of resistance contributed by C. echinospermum and C. arietinum. Phytophthora root rot (PRR) caused by the oomycete Phytophthora medicaginis is a major soil-borne disease of chickpea in Australia. With no economic in-crop control of PRR, a genetic approach to improve resistance is the most practical management option. Moderate field resistance has been incorporated in the cultivated C. arietinum variety, Yorker, and a higher level of resistance has been identified in a derivative of wild chickpea (C. echinospermum, interspecific breeding line 04067-81-2-1-1). These genotypes and two other released varieties were used to develop one intra-specific and two interspecific F6-derived recombinant inbred line mapping populations for genetic analysis of resistance. The Yorker × Genesis114 (YG), Rupali × 04067-81-2-1-1 (RB) and Yorker × 04067-81-2-1-1 (YB) populations were genotyped using genotyping-by-sequencing and phenotyped for PRR under three field environments with a mixture of 10 P. medicaginis isolates. Whole-genome QTL analysis identified major QTL QRBprrsi01, QYBprrsi01, QRBprrsi03 and QYBprrsi02 for PRR resistance on chromosomes 3 and 6, in RB and YB populations, respectively, with the resistance source derived from the wild Cicer species. QTL QYGprrsi02 and QYGprrsi03 were also identified on chromosomes 5 and 6 in YG population from C. arietinum. Aligning QTL regions to the corresponding chickpea reference genome suggested that the resistance source from C. arietinum and C. echinospermum may be different. The findings from this study provide tools for marker-assisted selection in chickpea breeding and information to assist the development of populations suitable for fine-mapping of resistance loci to determine the molecular basis for PRR resistance in chickpea.

DOI: https://doi.org/10.1007/s00122-018-3256-6
J Exp Bot. 2018 Dec 07.

The mitochondrial pentatricopeptide repeat protein EMP12 is involved in the splicing of three nad2 introns and seed development in maize.

Feng Sun, Zhihui Xiu, Ruicheng Jiang, Yiwei Liu, Xiaoyan Zhang, Yan-Zhuo Yang, Xiaojie Li, Xin Zhang, Yong Wang, Bao-Cai Tan.

Plant mitochondrial genes contain cis- and trans- group II introns that must be spliced before translation. The mechanism by which these introns are spliced is not well understood. Several families of proteins have been implicated in the intron splicing, of which the pentatricopeptide repeat (PPR) proteins are proposed to confer the substrate binding specificity. However, very few PPRs are characterized. Here, we report the function of a P-type PPR protein EMP12 and its role in seed development. EMP12 is targeted to mitochondria. Loss-of-function mutation in Emp12 severely arrests embryo and endosperm development, causing embryo lethality. The trans-splicing of mitochondrial nad2 intron 2, and cis-splicing of nad2 intron 4 are abolished, whereas the cis-splicing of nad2 intron 1 is reduced in emp12 mutants. As a result, the complex I assembly is disrupted, and its activity strongly reduced in the mutants. The expression of the alternative oxidase (AOX) and several components of other mitochondrial complexes is increased, possibly in response to the defective complex I. These results suggest that Emp12 is required for the trans-splicing of nad2 intron 2, cis-splicing of nad2 introns 1 and 4, and is important to the complex I biogenesis, and the embryogenesis and endosperm development in maize.

DOI: https://doi.org/10.1093/jxb/ery432
Front Plant Sci. 2018 ;9 1719

Identification of New Sources of Resistance to Wheat Stem Rust in Aegilops spp. in the Tertiary Genepool of Wheat.

Pablo D Olivera, Matthew N Rouse, Yue Jin.

  Recent stem rust epidemics in eastern Africa and elsewhere demonstrated that wheat stem rust is a re-emerging disease posing a threat to wheat production worldwide. The cultivated wheat gene pool has a narrow genetic base for resistance to virulent races, such as races in the Ug99 race group. Wild relatives of wheat are a tractable source of stem rust resistance genes. Aegilops species in the tertiary genepool have not been exploited to any great extent as a source of stem rust resistance. We evaluated 1,422 accessions of Aegilops spp. for resistance to three highly virulent races (TTKSK, TRTTF, and TTTTF) of Puccinia graminis f. sp. tritici. Species studied include Ae. biuncialis, Ae. caudata, Ae. comosa, Ae. cylindrica, Ae. geniculata, Ae. neglecta, Ae. peregrina, Ae. triuncialis, and Ae. umbellulata that do not share common genomes with cultivated wheat. High frequencies of resistance were observed as 977 (68.8%), 927 (65.2%), and 850 (59.8%) accessions exhibited low infection types to races TTKSK, TTTTF, and TRTTF, respectively. Contingency table analyses showed strong association for resistance to different races in several Aegilops spp., indicating that for a given species, the resistance genes effective against multiple races. Inheritance studies in selected accessions showed that resistance to race TTKSK is simply inherited.

Keywords:  Ug99; disease resistance; genetic resources; tertiary genepool; wild wheats

DOI:  https://doi.org/10.3389/fpls.2018.01719