bims-plasge 2019-01-06 papers

on Plastid genes

Issue of 2019‒01‒06
nine papers selected by
Vera S. Bogdanova
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences

A MYB transcription factor is a candidate to control pungency in Capsicum annuum.
Genetic dissection of domestication-related traits in soybean through genotyping-by-sequencing of two interspecific mapping populations.
Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica.
Transcriptome Comparison Reveals Distinct Selection Patterns in Domesticated and Wild Agave Species, the Important CAM Plants.
Marker-free transgenic rice plant overexpressing pea LecRLK imparts salinity tolerance by inhibiting sodium accumulation.
GmBRC1 is a Candidate Gene for Branching in Soybean (Glycine max (L.) Merrill).
Uncoupled Expression of Nuclear and Plastid Photosynthesis-associated Genes Contributes to Cell Death in a Lesion Mimic Mutant.
An APETALA1 ortholog affects plant architecture and seed yield component in oilseed rape (Brassica napus L.).
Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance.

Theor Appl Genet. 2019 Jan 03.

A MYB transcription factor is a candidate to control pungency in Capsicum annuum.

Koeun Han, Siyoung Jang, Joung-Ho Lee, Do-Gyeong Lee, Jin-Kyung Kwon, Byoung-Cheorl Kang.

KEY MESSAGE: Identification of a novel pungency-controlling gene Pun3, which acts as a master regulator of capsaicinoid biosynthetic genes in Capsicum annuum. Capsaicinoid is a unique compound that gives hot peppers (Capsicum spp.) their spicy taste. The Pun1 and Pun2 loci are known to control pungency in Capsicum species. Whereas Pun1 encodes an acyltransferase, the identity of Pun2 is currently unknown. Here, we used recombinant inbred lines and F2 plants derived from a cross between the non-pungent C. annuum accession 'YCM334' and the pungent C. annuum cultivar 'Tean' to identify a novel non-pungency locus. Inheritance studies showed that non-pungency in C. annuum 'YCM334' is controlled by a single recessive gene, which we named Pun3. Using a high-density SNP map derived from genotyping-by-sequencing, Pun3 was mapped to chromosome 7. By comparing physical information about the Pun3 region in the C. annuum 'Zunla-1' and C. chinense 'PI159236' reference genomes, we identified candidate genes in this target region. One cDNA sequence from 'PI159236' was homologous to an unannotated gene in 'Zunla-1.' This sequence was also homologous to CaMYB31, which is expressed only in 'Tean' and harbors one stop codon in the non-pungent accession 'YCM334.' RNA-Seq analysis showed that major structural genes in the capsaicinoid biosynthetic pathway were significantly downregulated in 'YCM334' compared to pungent pepper. Therefore, CaMYB31 is a candidate gene for Pun3, which may act as a master regulator of capsaicinoid biosynthetic genes in pepper.

DOI: https://doi.org/10.1007/s00122-018-03275-z
Theor Appl Genet. 2019 Jan 03.

Genetic dissection of domestication-related traits in soybean through genotyping-by-sequencing of two interspecific mapping populations.

Stephen A Swarm, Lianjun Sun, Xutong Wang, Weidong Wang, Patrick J Brown, Jianxin Ma, Randall L Nelson.

KEY MESSAGE: A total of 132 domestication-related QTLs, of which 41 were novel, were identified through genotyping-by-sequencing of two Glycine max × Glycine soja populations. Soybean [Glycine max (L.) Merr.] was domesticated in East Asia from the wild progenitor Glycine soja. The domestication process led to many distinct morphological changes that adapt it to cultivation. These include larger seeds, erect growth, larger stem diameter, reduced pod shattering, and altered growth habit. The objective of this study was to identify QTLs controlling key domestication-related traits (DRTs) using interspecific mapping populations. A total of 151 RILs from Williams 82 × PI 468916 and 510 RILs from Williams 82 × PI 479752 were utilized for QTL mapping. These lines were genotyped using a genotyping-by-sequencing protocol which resulted in approximately 5000 polymorphic SNP markers. The number of QTLs detected for each of the eleven DRTs ranged between 0-4 QTLs in the smaller Williams 82 × PI 468916 population and 3-16 QTLs in the larger Williams 82 × PI 479752 population. A total of 132 QTLs were detected, of which 51 are associated with selective sweeps previously related to soybean domestication. These QTLs were detected across all 20 chromosomes within 42 genomic regions. This study identifies 41 novel QTLs not detected in previous studies using smaller populations while also confirming the quantitative nature for several of the important DRTs in soybeans. These results would enable more effective use of the wild germplasm for soybean improvement.

DOI: https://doi.org/10.1007/s00122-018-3272-6
Plant J. 2019 Jan 03.

Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica.

Julie Ferreira de Carvalho, Jérémy Lucas, Gwenaëlle Deniot, Cyril Falentin, Olivier Filangi, Marie Gilet, Fabrice Legeai, Maryse Lode, Jérôme Morice, Gwenn Trotoux, Jean-Marc Aury, Valérie Barbe, Jean Keller, Rod Snowdon, Zhesi He, France Denoeud, Patrick Wincker, Ian Bancroft, Anne-Marie Chèvre, Mathieu Rousseau-Gueutin.

  Several plastid macromolecular protein complexes are encoded by both nuclear and plastid genes. Therefore, cytonuclear interactions are held in place to prevent genomic conflicts that may lead to incompatibilities. Allopolyploidy resulting from hybridization and genome doubling of two divergent species, can disrupt these fine-tuned interactions, as newly formed allopolyploid species confront biparental nuclear chromosomes with uniparentally inherited plastid genome. To avoid any deleterious effects of unequal genome inheritance, preferential transcription of the plastid donor over the other one has been hypothesized to occur in allopolyploids. We used Brassica as a model to study the effects of paleopolyploidy in diploid parental species, as well as the effects of recent and ancient allopolyploidy in Brassica napus on genes implicated in plastid protein complexes. We first identified redundant nuclear copies involved in those complexes. Compared to cytosolic protein complexes and to genome-wide retention rates, genes involved in plastid protein complexes show a higher retention of genes in duplicated and triplicated copies. Those redundant copies are functional and undergoing strong purifying selection. We then compared transcription patterns and sequences of those redundant gene copies between resynthesized allopolyploids and their diploid parents. The neo-polyploids showed no biased subgenome expression or maternal homogenization via gene conversion despite presence of some non-synonymous substitutions between plastid genomes of parental progenitors. Instead, subgenome dominance was observed regardless of the maternal progenitor. Our results provide new insights on the evolution of plastid protein complexes which could be tested and generalized in other allopolyploid species. This article is protected by copyright. All rights reserved.

Keywords:   Brassica napus ; Brassica oleracea ; Brassica rapa ; allopolyploidy; chloroplast; duplicated genes; genome inheritance; intergenomic conflicts; interspecific hybridization

DOI:  https://doi.org/10.1111/tpj.14228
Int J Genomics. 2018 ;2018 5716518

Transcriptome Comparison Reveals Distinct Selection Patterns in Domesticated and Wild Agave Species, the Important CAM Plants.

Xing Huang, Bo Wang, Jingen Xi, Yajie Zhang, Chunping He, Jinlong Zheng, Jianming Gao, Helong Chen, Shiqing Zhang, Weihuai Wu, Yanqiong Liang, Kexian Yi.

Agave species are an important family of crassulacean acid metabolism (CAM) plants with remarkable tolerance to heat and drought stresses (Agave deserti) in arid regions and multiple agricultural applications, such as spirit (Agave tequilana) and fiber (Agave sisalana) production. The agave genomes are commonly too large to sequence, which has significantly restricted our understanding to the molecular basis of stress tolerance and economic traits in agaves. In this study, we collected three transcriptome databases for comparison to reveal the phylogenic relationships and evolution patterns of the three agave species. The results indicated the close but distinctly domesticated relations between A. tequilana and A. sisalana. Natural abiotic and biotic selections are very important factors that have contributed to distinct economic traits in agave domestication together with artificial selection. Besides, a series of candidate unigenes regulating fructan, fiber, and stress response-related traits were identified in A. tequilana, A. sisalana, and A. deserti, respectively. This study represents the first transcriptome comparison within domesticated and wild agaves, which would serve as a guidance for further studies on agave evolution, environmental adaptation, and improvement of economically important traits.

DOI: https://doi.org/10.1155/2018/5716518
Plant Mol Biol. 2019 Jan 02.

Marker-free transgenic rice plant overexpressing pea LecRLK imparts salinity tolerance by inhibiting sodium accumulation.

Nishat Passricha, Shabnam K Saifi, Pushpa Kharb, Narendra Tuteja.

  KEY MESSAGE: PsLecRLK overexpression in rice provides tolerance against salinity stress and cause upregulation of SOS1 pathway genes, which are responsible for extrusion of excess Na+ ion under stress condition. Soil salinity is one of the most devastating factors threatening cultivable land. Rice is a major staple crop and immensely affected by soil salinity. The small genome size of rice relative to wheat and barley, together with its salt sensitivity, makes it an ideal candidate for studies on salt stress response caused by a particular gene. Under stress conditions crosstalk between organelles and cell to cell response is imperative. LecRLK is an important family, which plays a key role under stress conditions and regulates the physiology of the plant. Here we have functionally validated the PsLecRLK gene in rice for salinity stress tolerance and hypothesized the model for its working. Salt stress sensitive rice variety IR64 was used for developing marker-free transgenic with modified binary vector pCAMBIA1300 overexpressing PsLecRLK gene. Comparison of transgenic and wild-type (WT) plants showed better physiological and biochemical results in transgenic lines with a low level of ROS, MDA and ion accumulation and a higher level of proline, relative water content, root/shoot ration, enzymatic activities of ROS scavengers and upregulation of stress-responsive genes. Based on the relative expression of stress-responsive genes and ionic content, the working model highlights the role of PsLecRLK in the extrusion of Na+ ion from the cell. This extrusion of Na+ ion is facilitated by higher expression of SOS1 (Na+/K+ channel) in transgenic plants as compared to WT plants. Altered expression of stress-responsive genes and change in biochemical and physiological properties of the cell suggests an extensive reprogramming of the stress-responsive metabolic pathways by PsLecRLK under stress condition, which could be responsible for the salt tolerance capability.

Keywords:  Abiotic; LecRLK; Rice; SOS; Salinity

DOI:  https://doi.org/10.1007/s11103-018-0816-8
Int J Mol Sci. 2019 Jan 01. pii: E135. [Epub ahead of print]20(1):

GmBRC1 is a Candidate Gene for Branching in Soybean (Glycine max (L.) Merrill).

Sangrea Shim, Jungmin Ha, Moon Young Kim, Man Soo Choi, Sung-Taeg Kang, Soon-Chun Jeong, Jung-Kyung Moon, Suk-Ha Lee.

  Branch number is one of the main factors affecting the yield of soybean (Glycine max (L.)). In this study, we conducted a genome-wide association study combined with linkage analysis for the identification of a candidate gene controlling soybean branching. Five quantitative trait nucleotides (QTNs) were associated with branch numbers in a soybean core collection. Among these QTNs, a linkage disequilibrium (LD) block qtnBR6-1 spanning 20 genes was found to overlap a previously identified major quantitative trait locus qBR6-1. To validate and narrow down qtnBR6-1, we developed a set of near-isogenic lines (NILs) harboring high-branching (HB) and low-branching (LB) alleles of qBR6-1, with 99.96% isogenicity and different branch numbers. A cluster of single nucleotide polymorphisms (SNPs) segregating between NIL-HB and NIL-LB was located within the qtnBR6-1 LD block. Among the five genes showing differential expression between NIL-HB and NIL-LB, BRANCHED1 (BRC1; Glyma.06G210600) was down-regulated in the shoot apex of NIL-HB, and one missense mutation and two SNPs upstream of BRC1 were associated with branch numbers in 59 additional soybean accessions. BRC1 encodes TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTORS 1 and 2 transcription factor and functions as a regulatory repressor of branching. On the basis of these results, we propose BRC1 as a candidate gene for branching in soybean.

Keywords:  BRANCHED1 (BRC1); TCP transcription factor; branching; genome-wide association study (GWAS); near-isogenic line (NIL); soybean

DOI:  https://doi.org/10.3390/ijms20010135
Plant Cell. 2019 Jan 03. pii: tpc.00813.2018. [Epub ahead of print]

Uncoupled Expression of Nuclear and Plastid Photosynthesis-associated Genes Contributes to Cell Death in a Lesion Mimic Mutant.

Ruiqing Lv, Zihao Li, Mengping Li, Vivek Dogra, Shanshan Lv, Renyi Liu, Keun Pyo Lee, Chanhong Kim.

Chloroplast-to-nucleus retrograde signaling is essential for the coupled expression of photosynthesis-associated nuclear genes (PhANGs) and plastid genes (PhAPGs) to ensure the functional status of chloroplasts in plants. Although various signaling components involved in the process have been identified in Arabidopsis thaliana, the biological relevance of such coordination remains an enigma. Here, we show that the uncoupled expression of PhANGs and PhAPGs contributes to the cell death in the lesion simulating disease 1 (lsd1) mutant of Arabidopsis. A day length-dependent increase of salicylic acid (SA) appears to rapidly upregulate a gene encoding SIGMA FACTOR BINDING PROTEIN 1 (SIB1), a transcriptional coregulator, in lsd1 prior to the onset of cell death. The dual targeting of SIB1 to the nucleus and the chloroplasts leads to a simultaneous upregulation of PhANGs and downregulation of PhAPGs. Consequently, this disrupts the stoichiometry of photosynthetic proteins, especially in photosystem II, resulting in the generation of the highly reactive species singlet oxygen (1O2) in chloroplasts. Accordingly, inactivation of the nuclear-encoded chloroplast protein EXECUTER1, a putative 1O2 sensor, significantly attenuates the lsd1-conferred cell death. Together, these results provide a pathway from the SA- to the 1O2-signaling pathway, which are intertwined via the uncoupled expression of PhANGs and PhAPGs, contributing to the lesion-mimicking cell death in lsd1.

DOI: https://doi.org/10.1105/tpc.18.00813
BMC Plant Biol. 2018 Dec 29. 18(1): 380

An APETALA1 ortholog affects plant architecture and seed yield component in oilseed rape (Brassica napus L.).

Smit Shah, Nirosha L Karunarathna, Christian Jung, Nazgol Emrani.

  BACKGROUND: Increasing the productivity of rapeseed as one of the widely cultivated oil crops in the world is of upmost importance. As flowering time and plant architecture play a key role in the regulation of rapeseed yield, understanding the genetic mechanism underlying these traits can boost the rapeseed breeding. Meristem identity genes are known to have pleiotropic effects on plant architecture and seed yield in various crops. To understand the function of one of the meristem identity genes, APETALA1 (AP1) in rapeseed, we performed phenotypic analysis of TILLING mutants under greenhouse conditions. Three stop codon mutant families carrying a mutation in Bna.AP1.A02 paralog were analyzed for different plant architecture and seed yield-related traits.RESULTS: It was evident that stop codon mutation in the K domain of Bna.AP1.A02 paralog caused significant changes in flower morphology as well as plant architecture related traits like plant height, branch height, and branch number. Furthermore, yield-related traits like seed yield per plant and number of seeds per plants were also significantly altered in the same mutant family. Apart from phenotypic changes, stop codon mutation in K domain of Bna.AP1.A02 paralog also altered the expression of putative downstream target genes like Bna.TFL1 and Bna.FUL in shoot apical meristem (SAM) of rapeseed. Mutant plants carrying stop codon mutations in the COOH domain of Bna.AP1.A02 paralog did not have a significant effect on plant architecture, yield-related traits or the expression of the downstream targets.
CONCLUSIONS: We found that Bna.AP1.A02 paralog has pleiotropic effect on plant architecture and yield-related traits in rapeseed. The allele we found in the current study with a beneficial effect on seed yield can be incorporated into rapeseed breeding pool to develop new varieties.

Keywords:  Branch height; EMS-induced mutations; Meristem identity genes; Plant height; Seed yield; TILLING

DOI:  https://doi.org/10.1186/s12870-018-1606-9
Nat Plants. 2018 Dec 31.

Sunflower pan-genome analysis shows that hybridization altered gene content and disease resistance.

Sariel Hübner, Natalia Bercovich, Marco Todesco, Jennifer R Mandel, Jens Odenheimer, Emanuel Ziegler, Joon S Lee, Gregory J Baute, Gregory L Owens, Christopher J Grassa, Daniel P Ebert, Katherine L Ostevik, Brook T Moyers, Sarah Yakimowski, Rishi R Masalia, Lexuan Gao, Irina Ćalić, John E Bowers, Nolan C Kane, Dirk Z H Swanevelder, Timo Kubach, Stephane Muños, Nicolas B Langlade, John M Burke, Loren H Rieseberg.

Domesticated plants and animals often display dramatic responses to selection, but the origins of the genetic diversity underlying these responses remain poorly understood. Despite domestication and improvement bottlenecks, the cultivated sunflower remains highly variable genetically, possibly due to hybridization with wild relatives. To characterize genetic diversity in the sunflower and to quantify contributions from wild relatives, we sequenced 287 cultivated lines, 17 Native American landraces and 189 wild accessions representing 11 compatible wild species. Cultivar sequences failing to map to the sunflower reference were assembled de novo for each genotype to determine the gene repertoire, or 'pan-genome', of the cultivated sunflower. Assembled genes were then compared to the wild species to estimate origins. Results indicate that the cultivated sunflower pan-genome comprises 61,205 genes, of which 27% vary across genotypes. Approximately 10% of the cultivated sunflower pan-genome is derived through introgression from wild sunflower species, and 1.5% of genes originated solely through introgression. Gene ontology functional analyses further indicate that genes associated with biotic resistance are over-represented among introgressed regions, an observation consistent with breeding records. Analyses of allelic variation associated with downy mildew resistance provide an example in which such introgressions have contributed to resistance to a globally challenging disease.

DOI: https://doi.org/10.1038/s41477-018-0329-0