bims-plasge 2018-11-25 papers

bims-plasge

Biomed News

on Plastid genes

Issue of 2018–11–25
eightteen papers selected by
Vera S. Bogdanova, ИЦиГ СО РАН

Reconstituting the genome of a young allopolyploid crop, Brassica napus, with its related species.
Natural variation of ZmHKT1 affects root morphology in maize at the seedling stage.
Construction of introgression lines of Oryza rufipogon and evaluation of important agronomic traits.
Dissecting the genetics underlying the relationship between protein content and grain yield in a large hybrid wheat population.
FLOURY ENDOSPERM11 encoding a plastid heat shock protein 70 is essential for amyloplast development in rice.
Large Scale Phenotyping Provides Insight into the Diversity of Vegetative and Reproductive Organs in a Wide Collection of Wild and Domesticated Peppers (Capsicum spp.).
Connecting genome structural variation with complex traits in crop plants.
Targeted deletion of rice retrotransposon Tos17 via CRISPR/Cas9.
Preferential Homologous Chromosome Pairing in a Tetraploid Intergeneric Somatic Hybrid (Citrus reticulata + Poncirus trifoliata) Revealed by Molecular Marker Inheritance.
The molecular evolution of C4 photosynthesis: opportunities for understanding and improving the world's most productive plants.
Legume Cytosolic and Plastid Acetyl-Coenzyme-A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications.
Single-molecule real-time (SMRT) sequencing reveals diverse allelic variations in carotenoid biosynthetic genes in pepper (Capsicum spp.).
Actin Bundles in The Pollen Tube.
Using Maize Chromosome Segment Substitution Line Populations for the Identification of Loci Associated with Multiple Disease Resistance.
A novel cysteine-rich peptide regulates cell expansion in the tobacco pistil and influences its final size.
Rice UCL8, a plantacyanin gene targeted by miR408, regulates fertility by controlling pollen tube germination and growth.
The molecular and evolutionary basis of reproductive isolation in plants.
TIC236 links the outer and inner membrane translocons of the chloroplast.

Plant Biotechnol J. 2018 Nov 22.

Reconstituting the genome of a young allopolyploid crop, Brassica napus, with its related species.

Dandan Hu, Wenshan Zhang, Yikai Zhang, Shihao Chang, Lunlin Chen, Yingying Chen, Yongdi Shi, Jinxiong Shen, Jinling Meng, Jun Zou.

  Brassica napus (An An Cn Cn ) is an important worldwide oilseed crop, but it is a young allotetraploid with a short evolutionary history and limited genetic diversity. To significantly broaden its genetic diversity and create a novel heterotic population for sustainable rapeseed breeding, this study reconstituted the genome of B. napus by replacing it with the subgenomes from 122 accessions of B. rapa (Ar Ar ) and 74 accessions of B. carinata (Bc Bc Cc Cc ) and developing a novel gene pool of B. napus through five rounds of extensive recurrent selection. When compared with traditional B. napus using SSR markers and high-throughput SNP/Indel markers through genotyping by sequencing, the newly developed gene pool and its homozygous progenies exhibited a large genetic distance, rich allelic diversity, new alleles, and exotic allelic introgression across all 19 AC chromosomes. In addition to the abundant genomic variation detected in the AC genome, we also detected considerable introgression from the eight chromosomes of the B genome. Extensive trait variation and some genetic improvements were present from the early recurrent selection to later generations. This novel gene pool produced equally rich phenotypic variation and should be valuable for rapeseed genetic improvement. By reconstituting the genome of B. napus by introducing subgenomic variation within and between the related species using intense selection and recombination, the whole genome could be substantially reorganized. These results serve as an example of the manipulation of the genome of a young allopolyploid and provide insights into its rapid genome evolution affected by interspecific and intraspecific crosses. This article is protected by copyright. All rights reserved.

Keywords:   Brassica ; genetic diversity; genome evolution; introgression; recurrent selection

DOI:  https://doi.org/10.1111/pbi.13041
Planta. 2018 Nov 20.

Natural variation of ZmHKT1 affects root morphology in maize at the seedling stage.

Pengcheng Li, Ting Pan, Houmiao Wang, Jie Wei, Minjun Chen, Xiaohong Hu, Yu Zhao, Xiaoyi Yang, Shuangyi Yin, Yang Xu, Huimin Fang, Jun Liu, Chenwu Xu, Zefeng Yang.

   MAIN CONCLUSION: Eight variants in ZmHKT1 promoter were significantly associated with root diameter, four haplotypes based on these significant variants were found, and Hap2 has the largest root diameter. Roots play an important role in uptake of water, nutrients and plant anchorage. Identification of gene and corresponding SNPs associated with root traits would enable develop maize lines with better root traits that might help to improve capacity for absorbing nutrients and water acquisition. The genomic sequences of a salt tolerance gene ZmHKT1 was resequenced in 349 maize inbred lines, and the association between nucleotide polymorphisms and seedling root traits was detected. A total of 269 variants in ZmHKT1 were identified, including 226 single nucleotide polymorphisms and 43 insertions and deletions. The gene displayed high level of nucleotide diversity, especially in non-genic regions. A total of 19 variations in untranslated region of ZmHKT1 were found to be associated with six seedling traits. Eight variants in promoter region were significantly associated with average root diameter (ARD), four haplotypes were found based on these significant variants, and Hap2 has the largest ARD. Two SNPs in high-linkage disequilibrium (SNP-415 and SNP 2169) with pleiotropic effects were significantly associated with plant height, root surface area, root volume, and shoot dry weight. This result revealed that ZmHKT1 was an important contributor to the phenotypic variations of seedling root traits in maize, these significant variants could use to develop functional markers to improve root traits.

Keywords:  Gene-based association mapping; Maize; Nucleotide diversity; Root traits; ZmHKT1 gene

DOI:  https://doi.org/10.1007/s00425-018-3043-2
Theor Appl Genet. 2018 Nov 21.

Construction of introgression lines of Oryza rufipogon and evaluation of important agronomic traits.

Guannan Qin, Hung Manh Nguyen, Sinh Ngoc Luu, Yanwei Wang, Zhiguo Zhang.

Cultivated rice (Oryza sativa) originated from common wild rice (Oryza rufipogon) and inherited its advantages. However, during the rice domestication process, some valuable features of wild rice, such as tolerance to biotic and abiotic stress, were lost. To fully utilize wild rice germplasm resources, we constructed a set of introgression lines (ILs) using a common wild rice material from Lingshui, China. A set of high-resolution InDel molecular markers with an average interval of 2.39 Mb were designed to carry out marker-assisted selection and identification of segment characteristics. The ILs contained 77 lines including 1.286 introgressed fragments with an average length of 6.511 Mb, covering 93.59% of the donor parent's chromosomes. The agricultural traits of 77 lines were investigated. Many old quantitative trait loci (QTLs) involved in plant height, awn length, seed traits and other characteristics reappeared in our ILs, proving that our system was reliable. Further, many new QTLs were identified. A QTL related to drought tolerance located on chromosome 4 was thoroughly elaborated. This set of ILs provides a new resource for utilizing the excellent features of wild rice.

DOI: https://doi.org/10.1007/s00122-018-3241-0
Theor Appl Genet. 2018 Nov 19.

Dissecting the genetics underlying the relationship between protein content and grain yield in a large hybrid wheat population.

Patrick Thorwarth, Guozheng Liu, Erhard Ebmeyer, Johannes Schacht, Ralf Schachschneider, Ebrahim Kazman, Jochen Christoph Reif, Tobias Würschum, Carl Friedrich Horst Longin.

KEY MESSAGE: Additive and dominance effect QTL for grain yield and protein content display antagonistic pleiotropic effects, making genomic selection based on the index grain protein deviation a promising method to alleviate the negative correlation between these traits in wheat breeding. Grain yield and quality-related traits such as protein content and sedimentation volume are key traits in wheat breeding. In this study, we used a large population of 1604 hybrids and their 135 parental components to investigate the genetics and metabolomics underlying the negative relationship of grain yield and quality, and evaluated approaches for their joint improvement. We identified a total of nine trait-associated metabolites and show that prediction using genomic data alone resulted in the highest prediction ability for all traits. We dissected the genetic architecture of grain yield and quality-determining traits and show results of the first mapping of the derived trait grain protein deviation. Further, we provide a genetic analysis of the antagonistic relation of grain yield and protein content and dissect the mode of gene action (pleiotropy vs linkage) of identified QTL. Lastly, we demonstrate that the composition of the training set for genomic prediction is crucial when considering different quality classes in wheat breeding.

DOI: https://doi.org/10.1007/s00122-018-3236-x
Plant Sci. 2018 Dec;pii: S0168-9452(18)30789-1. [Epub ahead of print]277 89-99

FLOURY ENDOSPERM11 encoding a plastid heat shock protein 70 is essential for amyloplast development in rice.

Xiaopin Zhu, Xuan Teng, Yunlong Wang, Yuanyuan Hao, Ruonan Jing, Yongfei Wang, Yi Liu, Jianping Zhu, Mingming Wu, Mingsheng Zhong, Xiaoli Chen, Yuanyan Zhang, Wenwei Zhang, Chunming Wang, Yihua Wang, Jianmin Wan.

  Mutations of stromal Hsp70 cause chloroplast developmental abnormalities and knockout mutants of stromal Hsp70 usually exhibit protein import deficiencies. However, their effects have not been studied in amyloplast development. Here, we identified an amyloplast abnormal development mutant, floury endosperm11 (flo11) that exhibited an opaque phenotype in the inner core and the periphery of grains. Semi-thin section revealed defective amyloplast development in the flo11 endosperm. Map-based cloning and subsequent complementation test demonstrated that FLO11 encoded a plastid-localized heat shock protein 70 (OsHsp70cp-2). OsHsp70cp-2 was abundantly expressed in developing endosperm, whereas its paralogous gene OsHsp70cp-1 was mainly expressed in photosynthetic tissues. Ectopic expression of OsHsp70cp-1 under the control of OsHsp70cp-2 promoter rescued the mutant phenotype of flo11. Moreover, simultaneous knockdown of both OsHsp70cp genes resulted in white stripe leaves and opaque endosperm. BiFC and Co-IP assays revealed that OsHsp70cp-2 was associated with Tic complex. Taken together, OsHsp70cp-2 may regulate protein import into amyloplasts, which is essential for amyloplast development in rice.

Keywords:  Amyloplast development; Floury endosperm; Heat shock protein 70; Oryza sativa; Tic complex

DOI:  https://doi.org/10.1016/j.plantsci.2018.09.020
Plants (Basel). 2018 Nov 19. pii: E103. [Epub ahead of print]7(4):

Large Scale Phenotyping Provides Insight into the Diversity of Vegetative and Reproductive Organs in a Wide Collection of Wild and Domesticated Peppers (Capsicum spp.).

Pasquale Tripodi, Barbara Greco.

  In the past years, the diversity of Capsicum has been mainly investigated through genetics and genomics approaches, fewer efforts have been made in the field of plant phenomics. Assessment of crop traits with high-throughput methodologies could enhance the knowledge of the plant phenome, giving at the same time a key contribution to the understanding of the function of many genes. In this study, a wide germplasm collection of 307 accessions retrieved from 48 world regions, and belonging to nine Capsicum species was characterized for 54 plant, leaf, flower and fruit traits. Conventional descriptors and semi-automated tools based on image analysis and colour coordinate detection were used. Significant differences were found among accessions, between species and between sweet and spicy cultivated types, revealing a large diversity. The results highlighted how the domestication process and the continued selection have increased the variability of fruit shape and colour. Hierarchical clustering based on conventional and fruit morphological descriptors reflected the separation of species on the basis of their phylogenetic relationships. These observations suggested that the flow between distinct gene pools could have contributed to determine the similarity of the species on the basis of morphological plant and fruit parameters. The approach used represents the first high-throughput phenotyping effort in Capsicum spp. aimed at broadening the knowledge of the diversity of domesticated and wild peppers. The data could help to select best the candidates for breeding and provide new insight into the understanding of the genetic base of the fruit shape of pepper.

Keywords:  Capsicum; Tomato Analyzer; germplasm diversity; high-throughput phenotyping; plant descriptors; wild species

DOI:  https://doi.org/10.3390/plants7040103
Theor Appl Genet. 2018 Nov 17.

Connecting genome structural variation with complex traits in crop plants.

Iulian Gabur, Harmeet Singh Chawla, Rod J Snowdon, Isobel A P Parkin.

KEY MESSAGE: Structural genome variation is a major determinant of useful trait diversity. We describe how genome analysis methods are enabling discovery of trait-associated structural variants and their potential impact on breeding. As our understanding of complex crop genomes continues to grow, there is growing evidence that structural genome variation plays a major role in determining traits important for breeding and agriculture. Identifying the extent and impact of structural variants in crop genomes is becoming increasingly feasible with ongoing advances in the sophistication of genome sequencing technologies, particularly as it becomes easier to generate accurate long sequence reads on a genome-wide scale. In this article, we discuss the origins of structural genome variation in crops from ancient and recent genome duplication and polyploidization events and review high-throughput methods to assay such variants in crop populations in order to find associations with phenotypic traits. There is increasing evidence from such studies that gene presence-absence and copy number variation resulting from segmental chromosome exchanges may be at the heart of adaptive variation of crops to counter abiotic and biotic stress factors. We present examples from major crops that demonstrate the potential of pangenomic diversity as a key resource for future plant breeding for resilience and sustainability.

DOI: https://doi.org/10.1007/s00122-018-3233-0
Plant Cell Rep. 2018 Nov 21.

Targeted deletion of rice retrotransposon Tos17 via CRISPR/Cas9.

Hiroaki Saika, Akiko Mori, Masaki Endo, Seiichi Toki.

   KEY MESSAGE: A successful example of transposon deletion via CRISPR/Cas9-mediated genome editing suggests a novel alternative approach to plant breeding. Transposition of transposable elements (TEs) can affect adjacent genes, leading to changes in genetic traits. Expression levels and patterns, splicing and epigenetic status, and function of genes located in, or near, the inserted/excised locus can be affected. Artificial modification of loci adjacent to TEs, or TEs themselves, by genome editing could mimic the translocation of TEs that occurs in nature, suggesting that it might be possible to produce novel plants by modification of TEs via genome editing. To our knowledge, there are no reports thus far of modification of TEs by genome editing in plants. In this study, we performed targeted deletion of the Tos17 retrotransposon, which is flanked at both ends by long terminal repeat (LTR) sequences, via genome editing in rice. We succeeded in targeted mutagenesis of the LTR, and targeted deletion between LTRs, in calli transformed with CRISPR/Cas9 vectors for the Tos17 LTR. Moreover, we also successfully obtained regenerated plants derived from transformed calli and plants homozygous for lacking Tos17 in the next generation. Taken together, our results demonstrate successful deletion of the Tos17 retrotransposon from the rice genome by targeted mutagenesis using CRISPR/Cas9. We believe that this strategy could be applied to other TEs in many plant species, providing a rapid breeding technology as an alternative means to re-activate expression of agronomically important genes that have been inactivated by TE insertion, especially in plants such as fruit trees, in which it is difficult to maintain parental agronomical traits by cross-breeding due to high heterozygosity.

Keywords:  CRISPR/Cas9; Genome editing; Long terminal repeat; Rice; Targeted deletion; Transposable elements

DOI:  https://doi.org/10.1007/s00299-018-2357-7
Front Plant Sci. 2018 ;9 1557

Preferential Homologous Chromosome Pairing in a Tetraploid Intergeneric Somatic Hybrid (Citrus reticulata + Poncirus trifoliata) Revealed by Molecular Marker Inheritance.

Mourad Kamiri, Marc Stift, Gilles Costantino, Dominique Dambier, Tariq Kabbage, Patrick Ollitrault, Yann Froelicher.

  The creation of intergeneric somatic hybrids between Citrus and Poncirus is an efficient approach for citrus rootstock breeding, offering the possibility of combining beneficial traits from both genera into novel rootstock lineages. These somatic hybrids are also used as parents for further tetraploid sexual breeding. In order to optimize these latter breeding schemes, it is essential to develop knowledge on the mode of inheritance in the intergeneric tetraploid hybrids. We assessed the meiotic behavior of an intergeneric tetraploid somatic hybrid resulting from symmetric protoplast fusion of diploid Citrus reticulata and diploid Poncirus trifoliata. The analysis was based on the segregation patterns of 16 SSR markers and 9 newly developed centromeric/pericentromeric SNP markers, representing all nine linkage groups of the Citrus genetic map. We found strong but incomplete preferential pairing between homologues of the same ancestral genome. The proportion of gametes that can be explained by random meiotic chromosome associations (τ) varied significantly between chromosomes, from 0.09 ± 0.02 to 0.47 ± 0.09, respectively, in chromosome 2 and 1. This intermediate inheritance between strict disomy and tetrasomy, with global preferential disomic tendency, resulted in a high level of intergeneric heterozygosity of the diploid gametes. Although limited, intergeneric recombinations occurred, whose observed rates, ranging from 0.09 to 0.29, respectively, in chromosome 2 and 1, were significantly correlated with τ. Such inheritance is of particular interest for rootstock breeding because a large part of the multi-trait value selected at the teraploid parent level is transmitted to the progeny, while the potential for some intergeneric recombination offers opportunities for generating plants with novel allelic combinations that can be targeted by selection.

Keywords:  Citrus; SNP markers; SSR markers; disomic; intermediate inheritance; somatic hybrid; tetraploid; tetrasomic

DOI:  https://doi.org/10.3389/fpls.2018.01557
J Exp Bot. 2018 Nov 21.

The molecular evolution of C4 photosynthesis: opportunities for understanding and improving the world's most productive plants.

M Niklaus, S Kelly.

C4 photosynthesis is a convergent evolutionary trait that enhances photosynthetic efficiency in a variety of environmental conditions. It has evolved repeatedly following a fall in atmospheric CO2 concentration such that there is up to 30 million years difference in the amount of time that natural selection has had to improve C4 function between the oldest and youngest C4 lineages. This large difference in time, coupled with the phylogenetic distance between lineages, has resulted in a large disparity in anatomy, physiology, and biochemistry between extant C4 species. This review summarises the myriad of molecular sequence changes that have been linked to the evolution of C4 photosynthesis. These range from single nucleotide changes to duplication of entire genes, and provide a roadmap for how natural selection has adapted enzymes and pathways for enhanced C4 function. Finally, this review discusses how this molecular diversity can provide opportunities for understanding and improving photosynthesis for multiple important C4 food, feed, and bioenergy crops.

DOI: https://doi.org/10.1093/jxb/ery416
Genes (Basel). 2018 Nov 21. pii: E563. [Epub ahead of print]9(11):

Legume Cytosolic and Plastid Acetyl-Coenzyme-A Carboxylase Genes Differ by Evolutionary Patterns and Selection Pressure Schemes Acting before and after Whole-Genome Duplications.

Anna Szczepaniak, Michał Książkiewicz, Jan Podkowiński, Katarzyna B Czyż, Marek Figlerowicz, Barbara Naganowska.

  Acetyl-coenzyme A carboxylase (ACCase, E.C.6.4.1.2) catalyzes acetyl-coenzyme A carboxylation to malonyl coenzyme A. Plants possess two distinct ACCases differing by cellular compartment and function. Plastid ACCase contributes to de novo fatty acid synthesis, whereas cytosolic enzyme to the synthesis of very long chain fatty acids, phytoalexins, flavonoids, and anthocyanins. The narrow leafed lupin (Lupinus angustifolius L.) represents legumes, a plant family which evolved by whole-genome duplications (WGDs). The study aimed on the contribution of these WGDs to the multiplication of ACCase genes and their further evolutionary patterns. The molecular approach involved bacterial artificial chromosome (BAC) library screening, fluorescent in situ hybridization, linkage mapping, and BAC sequencing. In silico analysis encompassed sequence annotation, comparative mapping, selection pressure calculation, phylogenetic inference, and gene expression profiling. Among sequenced legumes, the highest number of ACCase genes was identified in lupin and soybean. The most abundant plastid ACCase subunit genes were accB. ACCase genes in legumes evolved by WGDs, evidenced by shared synteny and Bayesian phylogenetic inference. Transcriptional activity of almost all copies was confirmed. Gene duplicates were conserved by strong purifying selection, however, positive selection occurred in Arachis (accB2) and Lupinus (accC) lineages, putatively predating the WGD event(s). Early duplicated accA and accB genes underwent transcriptional sub-functionalization.

Keywords:  acetyl-coenzyme A carboxylase; duplication; evolution; fatty acid synthesis; legumes; synteny

DOI:  https://doi.org/10.3390/genes9110563
Plant Biotechnol J. 2018 Nov 22.

Single-molecule real-time (SMRT) sequencing reveals diverse allelic variations in carotenoid biosynthetic genes in pepper (Capsicum spp.).

Hyo-Bong Jeong, Min-Young Kang, Ayoung Jung, Koeun Han, Joung-Ho Lee, Jinkwan Jo, Hea-Young Lee, Jong-Wook An, Suna Kim, Byoung-Cheorl Kang.

  The diverse colors of mature pepper (Capsicum spp.) fruit result from the accumulation of different carotenoids. The carotenoid biosynthetic pathway has been well elucidated in Solanaceous plants, and analysis of candidate genes involved in this process has revealed variations in carotenoid biosynthetic genes in Capsicum spp. However, the allelic variations revealed by previous studies could not fully explain the variation in fruit color in Capsicum spp. due to technical difficulties in detecting allelic variation in multiple candidate genes in numerous samples. In this study, we uncovered allelic variations in six carotenoid biosynthetic genes, including phytoene synthase (PSY1, PSY2), lycopene β-cyclase (Lcyb), β-carotene hydroxylase (CrtZ-2), zeaxanthin epoxidase (ZEP), and capsanthin-capsorubin synthase (CCS) genes, in 94 pepper accessions by single-molecule real-time (SMRT) sequencing. To investigate the relationship between allelic variations in the candidate genes and differences in fruit color, we performed ultra-performance liquid chromatography (UPLC) analysis using 43 accessions representing each allelic variation. Different combinations of dysfunctional mutations in PSY1 and CCS could explain variation in the compositions and levels of carotenoids in the accessions examined in this study. Our results demonstrate that SMRT sequencing technology can be used to rapidly identify allelic variation of target genes in various germplasms. The newly identified allelic variants will be useful for pepper breeding and for further analysis of carotenoid biosynthesis pathways. This article is protected by copyright. All rights reserved.

Keywords:   Capsicum ; SMRT sequencing; capsanthin-capsorubin synthase; carotenoid; phytoene synthase

DOI:  https://doi.org/10.1111/pbi.13039
Int J Mol Sci. 2018 Nov 22. pii: E3710. [Epub ahead of print]19(12):

Actin Bundles in The Pollen Tube.

Shujuan Zhang, Chunbo Wang, Min Xie, Jinyu Liu, Zhe Kong, Hui Su.

  The angiosperm pollen tube delivers two sperm cells into the embryo sac through a unique growth strategy, named tip growth, to accomplish fertilization. A great deal of experiments have demonstrated that actin bundles play a pivotal role in pollen tube tip growth. There are two distinct actin bundle populations in pollen tubes: the long, rather thick actin bundles in the shank and the short, highly dynamic bundles near the apex. With the development of imaging techniques over the last decade, great breakthroughs have been made in understanding the function of actin bundles in pollen tubes, especially short subapical actin bundles. Here, we tried to draw an overall picture of the architecture, functions and underlying regulation mechanism of actin bundles in plant pollen tubes.

Keywords:  Arabidopsis; actin bundles; actin-binding proteins; pollen tube

DOI:  https://doi.org/10.3390/ijms19123710
G3 (Bethesda). 2018 Nov 20. pii: g3.200866.2018. [Epub ahead of print]

Using Maize Chromosome Segment Substitution Line Populations for the Identification of Loci Associated with Multiple Disease Resistance.

Luis O Lopez-Zuniga, Petra Wolters, Scott Davis, Teclemariam Weldekidan, Judith M Kolkman, Rebecca Nelson, K S Hooda, Elizabeth Rucker, Wade Thomason, Randall Wisser, Peter Balint-Kurti.

  Southern Leaf Blight (SLB), Northern Leaf Blight (NLB), and Gray Leaf Spot (GLS) caused by Cochliobolus heterostrophus, Setosphaeria turcica, and Cercospora zeae-maydis respectively, are among the most important diseases of corn worldwide. Previously, moderately high and significantly positive genetic correlations between resistance levels to each of these diseases were identified in a panel of 253 diverse maize inbred lines. The goal of this study was to identify loci underlying disease resistance in some of the most multiple disease resistant (MDR) lines by the creation of chromosome segment substitution line (CSSL) populations in multiple disease susceptible (MDS) backgrounds. Four MDR lines (NC304, NC344, Ki3, NC262) were used as donor parents and two MDS lines (Oh7B, H100) were used as recurrent parents to produce eight BC3F4:5 CSSL populations comprising 1,611 lines in total. Each population was genotyped and assessed for each disease in replicated trials in two environments. Moderate to high heritabilities on an entry mean basis were observed (0.32 to 0.83). Several lines in each population were significantly more resistant than the MDS parental lines for each disease. Multiple quantitative trait loci (QTL) for disease resistance were detected for each disease in most of the populations. Seventeen QTLs were associated with variation in resistance to more than one disease (SLB/NLB: 2; SLB/GLS: 7; NLB/GLS: 2 and 6 to all three diseases). For most populations and most disease combinations, significant correlations were observed between disease scores and also between marker effects for each disease. The number of lines that were resistant to more than one disease was significantly higher than would be expected by chance. Using the results from individual QTL analyses, a composite statistic based on Mahalanobis distance (Md) was used to identify joint marker associations with multiple diseases. Across all populations and diseases, 246 markers had significant Md values. However further analysis revealed that most of these associations were due to strong QTL effects on a single disease. Together, these findings reinforce our previous conclusions that loci associated with resistance to different diseases are clustered in the genome more often than would be expected by chance. Nevertheless true MDR loci which have significant effects on more than one disease are still much rarer than loci with single disease effects.

Keywords:  Maize disease resistance; Multiple disease resistance; QTL

DOI:  https://doi.org/10.1534/g3.118.200866
Plant Sci. 2018 Dec;pii: S0168-9452(18)30819-7. [Epub ahead of print]277 55-67

A novel cysteine-rich peptide regulates cell expansion in the tobacco pistil and influences its final size.

Michael S Brito, Henrique C DePaoli, Viviani Cossalter, Nilton C Avanci, Pedro B Ferreira, Mariana S Azevedo, Edward J Strini, Andréa C Quiapim, Gustavo H Goldman, Lázaro E P Peres, Maria Helena S Goldman.

  Plant morphogenesis is dependent on cell proliferation and cell expansion, which are responsible for establishing final organ size and shape during development. Several genes have been described as encoding components of the plant cell development machinery, among which are the plant peptides. Here we describe a novel cysteine-rich plant peptide (68 amino acids), encoded by a small open reading frame gene (sORF). It is specifically expressed in the reproductive organs of Nicotiana tabacum and is developmentally regulated. N- and C-terminal translational fusions with GFP in protoplasts have demonstrated that the peptide is not secreted. Knockdown transgenic plants produced by RNAi exhibited enlarged pistils due to cell expansion and the gene was named Small Peptide Inhibitor of Cell Expansion (SPICE). Estimation of nuclear DNA content using flow cytometry has shown that cell expansion in pistils was not correlated with endoreduplication. Decreased SPICE expression also affected anther growth and pollen formation, resulting in male sterility in at least one transgenic plant. Our results revealed that SPICE is a novel reproductive organ specific gene that controls cell expansion, probably as a component of a signal transduction pathway.

Keywords:  Cell expansion; Cysteine-rich peptide; Pistil development; Plant organ growth

DOI:  https://doi.org/10.1016/j.plantsci.2018.09.002
Rice (N Y). 2018 Nov 19. 11(1): 60

Rice UCL8, a plantacyanin gene targeted by miR408, regulates fertility by controlling pollen tube germination and growth.

Fan Zhang, Yu-Chan Zhang, Jin-Ping Zhang, Yang Yu, Yan-Fei Zhou, Yan-Zhao Feng, Yu-Wei Yang, Meng-Qi Lei, Huang He, Jian-Pin Lian, Yue-Qin Chen.

BACKGROUND: Pollen tube formation and growth are crucial steps that lead to seed production. Despite the importance of pollen tube growth, the molecular mechanisms implicated in its spatial and temporal control are not fully known. In this study, we found an uclacyanin gene, OsUCL8, that regulates pollen intine deposition and pollen tube growth.
FINDINGS: The overexpression of OsUCL8 led to a striking irregularity in pollen tube growth and pollination and thus affected the seed setting rate in rice; many pollen tubes appeared to lose the ability to grow directly into the style. Conversely, plants with OsUCL8 knocked out and plants overexpressing miR408, a negative regulator of OsUCL8, had vigorous pollens with a higher germination rate. We further demonstrated that OsUCL8 mainly affects pollen intine formation. The addition of Vitamin B1 (VB1) significantly contributed to the germination of OXUCL8 pollen grains, suggesting that OsUCL8 could be associated with VB1 production. Using a yeast two-hybrid system, we revealed that OsUCL8 interacts with the protein OsPKIWI, a homolog of the Arabidopsis FNRL protein. We thus hypothesized that OsUCL8 might regulate the production of VB components by interacting with OsPKIWI. This study revealed a novel molecular mechanism of pollen tube growth regulation.
CONCLUSIONS: The rice plantacyanin family member OsUCL8 plays an important role in pollen tube formation and growth and, in turn, regulates fertility and the seed setting rate.

DOI: https://doi.org/10.1186/s12284-018-0253-y
J Genet Genomics. 2018 Nov 05. pii: S1673-8527(18)30191-7. [Epub ahead of print]

The molecular and evolutionary basis of reproductive isolation in plants.

Yidan Ouyang, Qifa Zhang.

  Reproductive isolation is defined as processes that prevent individuals of different populations from mating, survival or producing fertile offspring. Reproductive isolation is critical for driving speciation and maintaining species identity, which has been a fundamental concern in evolutionary biology. In plants, reproductive isolation can be divided into prezygotic and postzygotic reproductive barriers, according to its occurrence at different developmental stages. Postzygotic reproductive isolation caused by reduced fitness in hybrids is frequently observed in plants, which hinders gene flow between divergent populations and has substantial effects on genetic differentiation and speciation, and thus is a major obstacle for utilization of heterosis in hybrid crops. During the past decade, China has made tremendous progress in molecular and evolutionary basis of prezygotic and postzygotic reproductive barriers in plants. Present understandings in reproductive isolation especially with new data in the last several years well support three evolutionary genetic models, which represent a general mechanism underlying genomic differentiation and speciation. The updated understanding will offer new approaches for the development of wide-compatibility or neutral varieties, which facilitate breeding of hybrid rice as well as other hybrid crops.

Keywords:  Hybrid lethality; Hybrid necrosis/weakness; Hybrid sterility; Parallel divergence model; Parallel-sequential divergence model; Reproductive isolation; Sequential divergence model; Wide-compatibility

DOI:  https://doi.org/10.1016/j.jgg.2018.10.004
Nature. 2018 Nov 21.

TIC236 links the outer and inner membrane translocons of the chloroplast.

Yih-Lin Chen, Lih-Jen Chen, Chiung-Chih Chu, Po-Kai Huang, Jie-Ru Wen, Hsou-Min Li.

The two-membrane envelope is a defining feature of chloroplasts. Chloroplasts evolved from a Gram-negative cyanobacterial endosymbiont. During evolution, genes of the endosymbiont have been transferred to the host nuclear genome. Most chloroplast proteins are synthesized in the cytosol as higher-molecular-mass preproteins with an N-terminal transit peptide. Preproteins are transported into chloroplasts by the TOC and TIC (translocons at the outer- and inner-envelope membranes of chloroplasts, respectively) machineries1,2, but how TOC and TIC are assembled together is unknown. Here we report the identification of the TIC component TIC236; TIC236 is an integral inner-membrane protein that projects a 230-kDa domain into the intermembrane space, which binds directly to the outer-membrane channel TOC75. The knockout mutation of TIC236 is embryonically lethal. In TIC236-knockdown mutants, a smaller amount of the inner-membrane channel TIC20 was associated with TOC75; the amount of TOC-TIC supercomplexes was also reduced. This resulted in a reduced import rate into the stroma, though outer-membrane protein insertion was unaffected. The size and the essential nature of TIC236 indicate that-unlike in mitochondria, in which the outer- and inner-membrane translocons exist as separate complexes and a supercomplex is only transiently assembled during preprotein translocation3,4-a long and stable protein bridge in the intermembrane space is required for protein translocation into chloroplasts. Furthermore, TIC236 and TOC75 are homologues of bacterial inner-membrane TamB5 and outer-membrane BamA, respectively. Our evolutionary analyses show that, similar to TOC75, TIC236 is preserved only in plants and has co-evolved with TOC75 throughout the plant lineage. This suggests that the backbone of the chloroplast protein-import machinery evolved from the bacterial TamB-BamA protein-secretion system.

DOI: https://doi.org/10.1038/s41586-018-0713-y