88 results on '"Robert M. Larkin"'
Search Results
2. Launching Horticulture Advances: horticultural plants for a better life
- Author
-
Ji-Hong Liu, Robert M. Larkin, and Xiuxin Deng
- Subjects
Plant culture ,SB1-1110 - Published
- 2023
- Full Text
- View/download PDF
3. Heme oxygenase-independent bilin biosynthesis revealed by a hmox1 suppressor screening in Chlamydomonas reinhardtii
- Author
-
Weiqing Zhang, Rui Deng, Weida Shi, Zheng Li, Robert M. Larkin, Qiuling Fan, and Deqiang Duanmu
- Subjects
heme oxygenase ,heme ,bilin ,suppressor screening ,insertional mutagenesis ,Microbiology ,QR1-502 - Abstract
Bilins are open-chain tetrapyrroles synthesized in phototrophs by successive enzymic reactions catalyzed by heme oxygenases (HMOXs/HOs) and ferredoxin-dependent biliverdin reductases (FDBRs) that typically serve as chromophore cofactors for phytochromes and phycobiliproteins. Chlamydomonas reinhardtii lacks both phycobiliproteins and phytochromes. Nonetheless, the activity and stability of photosystem I (PSI) and the catalytic subunit of magnesium chelatase (MgCh) named CHLH1 are significantly reduced and phototropic growth is significantly attenuated in a hmox1 mutant that is deficient in bilin biosynthesis. Consistent with these findings, previous studies on hmox1 uncovered an essential role for bilins in chloroplast retrograde signaling, maintenance of a functional photosynthetic apparatus, and the direct regulation of chlorophyll biosynthesis. In this study, we generated and screened a collection of insertional mutants in a hmox1 genetic background for suppressor mutants with phototropic growth restored to rates observed in wild-type 4A+ C. reinhardtii cells. Here, we characterized a suppressor of hmox1 named ho1su1 with phototrophic growth rates and levels of CHLH1 and PSI proteins similar to 4A+. Tetrad analysis indicated that a plasmid insertion co-segregated with the suppressor phenotype of ho1su1. Results from TAIL-PCR and plasmid rescue experiments demonstrated that the plasmid insertion was located in exon 1 of the HMOX1 locus. Heterologous expression of the bilin-binding reporter Nostoc punctiforme NpF2164g5 in the chloroplast of ho1su1 indicated that bilin accumulated in the chloroplast of ho1su1 despite the absence of the HMOX1 protein. Collectively, our study reveals the presence of an alternative bilin biosynthetic pathway independent of HMOX1 in the chloroplasts of Chlamydomonas cells.
- Published
- 2022
- Full Text
- View/download PDF
4. Predicting and clustering plant CLE genes with a new method developed specifically for short amino acid sequences
- Author
-
Zhe Zhang, Lei Liu, Melis Kucukoglu, Dongdong Tian, Robert M. Larkin, Xueping Shi, and Bo Zheng
- Subjects
Peptide hormone ,CLE ,Machine learning ,Euclidean distance ,Gene prediction ,Gene clustering ,Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
Abstract Background The CLV3/ESR-RELATED (CLE) gene family encodes small secreted peptides (SSPs) and plays vital roles in plant growth and development by promoting cell-to-cell communication. The prediction and classification of CLE genes is challenging because of their low sequence similarity. Results We developed a machine learning-aided method for predicting CLE genes by using a CLE motif-specific residual score matrix and a novel clustering method based on the Euclidean distance of 12 amino acid residues from the CLE motif in a site-weight dependent manner. In total, 2156 CLE candidates—including 627 novel candidates—were predicted from 69 plant species. The results from our CLE motif-based clustering are consistent with previous reports using the entire pre-propeptide. Characterization of CLE candidates provided systematic statistics on protein lengths, signal peptides, relative motif positions, amino acid compositions of different parts of the CLE precursor proteins, and decisive factors of CLE prediction. The approach taken here provides information on the evolution of the CLE gene family and provides evidence that the CLE and IDA/IDL genes share a common ancestor. Conclusions Our new approach is applicable to SSPs or other proteins with short conserved domains and hence, provides a useful tool for gene prediction, classification and evolutionary analysis.
- Published
- 2020
- Full Text
- View/download PDF
5. Influence of Switchgrass TDIF-like Genes on Arabidopsis Vascular Development
- Author
-
Dongdong Tian, Jingwen Tang, Liwen Luo, Zhe Zhang, Kebing Du, Robert M. Larkin, Xueping Shi, and Bo Zheng
- Subjects
switchgrass ,CLE ,TDIF ,vascular development ,biomass ,Plant culture ,SB1-1110 - Abstract
As a member of the CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (CLE) family, the dodecapeptide tracheary element differentiation inhibitory factor (TDIF) has a major impact on vascular development in plants. However, the influence of polymorphisms in the TDIF peptide motif on activity remains poorly understood. The model plant, Arabidopsis provides a fast and effective tool for assaying the activity of TDIF homologs. Five TDIF homologs from a group of 93 CLE genes in switchgrass (Panicum virgatum), a perennial biomass crop, named PvTDIF-like (PvTDIFL) genes were studied. The expression levels of PvTDIFL1, PvTDIFL3MR3, and PvTDIFL3MR2 were relatively high and all of them were expressed at the highest levels in the rachis of switchgrass. The precursor proteins for PvTDIFL1, PvTDIFL3MR3, and PvTDIFL3MR2 contained one, three, and two TDIFL motifs, respectively. Treatments with exogenous PvTDIFL peptides increased the number of stele cells in the hypocotyls of Arabidopsis seedlings, with the exception of PvTDIFL_4p. Heterologous expression of PvTDIFL1 in Arabidopsis strongly inhibited plant growth, increased cell division in the vascular tissue of the hypocotyl, and disrupted the cellular organization of the hypocotyl. Although heterologous expression of PvTDIFL3MR3 and PvTDIFL3MR2 also affected plant growth and vascular development, PvTDIFL activity was not enhanced by the multiple TDIFL motifs encoded by PvTDIFL3MR3 and PvTDIFL3MR2. These data indicate that in general, PvTDIFLs are functionally similar to Arabidopsis TDIF but that the processing and activities of the PvTDIFL peptides are more complex.
- Published
- 2021
- Full Text
- View/download PDF
6. RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis
- Author
-
Lei Zhang, Wenqing Su, Rong Tao, Weiyi Zhang, Jiongjiong Chen, Peiyao Wu, Chenghuan Yan, Yue Jia, Robert M. Larkin, Dean Lavelle, Maria-Jose Truco, Sebastian Reyes Chin-Wo, Richard W. Michelmore, and Hanhui Kuang
- Subjects
Science - Abstract
Horticultural lettuce varieties vary considerably in phenotype. Here, via RNA-seq of 240 different lettuce accessions, the authors identify loci and expression patterns associated with flavonoid and anthocyanin content and show that cultivated lettuce likely arose via a single domestication event.
- Published
- 2017
- Full Text
- View/download PDF
7. Correction to: Predicting and clustering plant CLE genes with a new method developed specifically for short amino acid sequences
- Author
-
Zhe Zhang, Lei Liu, Melis Kucukoglu, Dongdong Tian, Robert M. Larkin, Xueping Shi, and Bo Zheng
- Subjects
Biotechnology ,TP248.13-248.65 ,Genetics ,QH426-470 - Abstract
An amendment to this paper has been published and can be accessed via the original article.
- Published
- 2020
- Full Text
- View/download PDF
8. Optimization of Nitrogen, Phosphorus, and Potassium Fertilization Rates for Overseeded Perennial Ryegrass Turf on Dormant Bermudagrass in a Transitional Climate
- Author
-
Muhammad Ihtisham, Shah Fahad, Tao Luo, Robert M. Larkin, Shaohua Yin, and Longqing Chen
- Subjects
turfgrass ,overseeding ,fertilizer optimization ,central composite rotatable design ,integrated turf performance ,modeling ,Plant culture ,SB1-1110 - Abstract
Bermudagrass [Cynodon dactylon (L.) Pers.] turf loss due to severe cold in transitional climates is a major concern. To overcome this problem, warm-season grass is often overseeded with a cool-season turfgrass. In this study, modeling and efficient nutrient management were used to evaluate this problem. A three-factor and five-level central composite rotatable design (CCRD) with a simulation of a regression model was used to optimize fertilization rates. The study investigated the combined effects of fertilization with nitrogen (N), phosphorus (P), and potassium (K) on both the morphological and physiological attributes and on the integrated turf performance (ITP) of overseeded perennial ryegrass (Lolium perenne). Fertilization with N and P significantly increased turf height, density, color, fresh and dry weights, while N, P, and K significantly affected turf cover, quality and winter-kill. The Spring transition was delayed by fertilization with N and P, and accelerated by fertilization with K. Photosynthesis (Pn), transpiration (Tr), and stomatal conductance (Gs) were considerably enhanced by fertilization with N, P, and K. Protein levels and total chlorophyll levels were substantially increased by fertilization with N and P and with N, P, and K, respectively, during a 2-year period. During two separate experiments conducted during 2 consecutive years, the optimal combinations of N, P, and K were N: 30, P: 24, K: 9, and N: 30, P: 27, K: 6 g m−2. The major conclusion of this study is that a balanced nutrient application utilizing N, P, and K is key to enhancing the winter performance of perennial ryegrass.
- Published
- 2018
- Full Text
- View/download PDF
9. Tetrapyrrole Signaling in Plants
- Author
-
Robert M. Larkin
- Subjects
Chlorophyll ,Heme ,chloroplast ,plastid ,tetrapyrrole ,plastid signaling ,Plant culture ,SB1-1110 - Abstract
Tetrapyrroles make critical contributions to a number of important processes in diverse organisms. In plants, tetrapyrroles are essential for light signaling, the detoxification of reactive oxygen species, the assimilation of nitrate and sulfate, respiration, photosynthesis, and programed cell death. Thus, it is not surprising that tetrapyrrole metabolism is strictly regulated and that tetrapyrrole metabolism affects signaling mechanisms that regulate gene expression. In plants and algae, tetrapyrroles are synthesized in plastids and were some of the first plastid signals demonstrated to regulate nuclear gene expression. In plants, the mechanism of tetrapyrrole-dependent plastid-to-nucleus signaling remains poorly understood. Additionally, some of experiments that tested ideas for possible signaling mechanisms appeared to produce conflicting data. In some instances, these conflicts are potentially explained by different experimental conditions. Although the biological function of tetrapyrrole signaling is poorly understood, there is compelling evidence that this signaling is significant. Specifically, this signaling appears to affect the accumulation of starch and may promote abiotic stress tolerance. Tetrapyrrole-dependent plastid-to-nucleus signaling interacts with a distinct plastid-to-nucleus signaling mechanism that depends on GENOMES UNCUOPLED1 (GUN1). GUN1 contributes to a variety of processes, such as chloroplast biogenesis, the circadian rhythm, abiotic stress tolerance, and development. Thus, the contribution of tetrapyrrole signaling to plant function is potentially broader than we currently appreciate. In this review, I discuss these aspects of tetrapyrrole signaling.
- Published
- 2016
- Full Text
- View/download PDF
10. CProtMEDIAS: clustering of amino acid sequences encoded by gene families by MErging and DIgitizing Aligned Sequences.
- Author
-
Zhe Zhang, Miaomiao Zhu, Qi Xie, Robert M. Larkin, Xueping Shi, and Bo Zheng
- Published
- 2022
- Full Text
- View/download PDF
11. Neofunctionalization of an OMT cluster dominates polymethoxyflavone biosynthesis associated with the domestication of citrus.
- Author
-
Zhaoxin Peng, Lizhi Song, Minghua Chen, Zeyang Liu, Ziyu Yuan, Huan Wen, Haipeng Zhang, Yue Huang, Zhaowen Peng, Hongbin Yang, Gu Li, Huixian Zhang, Zhehui Hu, Wenyun Li, Xia Wang, Robert M. Larkin, Xiuxin Deng, Qiang Xu, Jiajing Chen, and Juan Xu
- Subjects
CITRUS ,CITRUS fruits ,ESSENTIAL amino acids ,AMINO acid residues ,BIOSYNTHESIS - Abstract
Polymethoxyflavones (PMFs) are a class of abundant specialized metabolites with remarkable anticancer properties in citrus. Multiple methoxy groups in PMFs are derived from methylation modification catalyzed by a series of hydroxylases and O-methyltransferases (OMTs). However, the specific OMTs that catalyze the systematic O-methylation of hydroxyflavones remain largely unknown. Here, we report that PMFs are highly accumulated in wild mandarins and mandarin-derived accessions, while undetectable in early-diverging citrus species and related species. Our results demonstrated that three homologous genes, CreOMT3, CreOMT4, and CreOMT5, are crucial for PMF biosynthesis in citrus, and their encoded methyltransferases exhibit multisite O-methylation activities for hydroxyflavones, producing seven PMFs in vitro and in vivo. Comparative genomic and syntenic analyses indicated that the tandem CreOMT3, CreOMT4, and CreOMT5 may be duplicated from CreOMT6 and contributes to the genetic basis of PMF biosynthesis in the mandarin group through neofunctionalization. We also demonstrated that N17 in CreOMT4 is an essential amino acid residue for C3-, C5-, C6-, and C3'-O-methylation activity and provided a rationale for the functional deficiency of OMT6 to produce PMFs in early-diverging citrus and some domesticated citrus species. A 1,041-bp deletion in the CreOMT4 promoter, which is found in most modern cultivated mandarins, has reduced the PMF content relative to that in wild and early-admixture mandarins. This study provides a framework for reconstructing PMF biosynthetic pathways, which may facilitate the breeding of citrus fruits with enhanced health benefits. [ABSTRACT FROM AUTHOR]
- Published
- 2024
- Full Text
- View/download PDF
12. SlBBX20 attenuates JA signalling and regulates resistance to Botrytis cinerea by inhibiting SlMED25 in tomato
- Author
-
Dan Luo, Wenhui Sun, Jun Cai, Guoyu Hu, Danqiu Zhang, Xiaoyan Zhang, Robert M. Larkin, Junhong Zhang, Changxian Yang, Zhibiao Ye, and Taotao Wang
- Subjects
Plant Science ,Agronomy and Crop Science ,Biotechnology - Abstract
Jasmonic acid (JA) plays an important role in regulating plant growth and defense responses. Here, we show that a transcription factor that belongs to the B-box (BBX) family named SlBBX20 regulates resistance to Botrytis cinerea in tomato by modulating JA signaling. The response to JA was significantly suppressed when SlBBX20 was overexpressed in tomato. In contrast, the JA response was enhanced in SlBBX20 knockout lines. RNA sequencing analysis provided more evidence that SlBBX20 modulates the expression of genes that are involved in JA signaling. We found that SlBBX20 interacts with SlMED25, a subunit of the Mediator transcriptional co-activator complex, and prevents the accumulation of the SlMED25 protein and transcription of JA-responsive genes. JA contributes to the defense response against necrotrophic pathogens. Knocking out SlBBX20 or overexpressing SlMED25 enhanced tomato resistance to B. cinerea. The resistance was impaired when SlBBX20 was overexpressed in plants that also overexpressed SlMED25. These data show that SlBBX20 attenuates JA signaling by regulating SlMED25. Interestingly, in addition to developing enhanced resistance to B. cinerea, SlBBX20-KO plants also produced higher fruit yields. SlBBX20 is a potential target gene for efforts that aim to develop elite crop varieties using gene editing technologies.
- Published
- 2023
13. A novel regulatory complex mediated by Lanata ( Ln ) controls multicellular trichome formation in tomato
- Author
-
Qingmin Xie, Cheng Xiong, Qihong Yang, Fangyan Zheng, Robert M. Larkin, Junhong Zhang, Taotao Wang, Yuyang Zhang, Bo Ouyang, Yongen Lu, Jie Ye, Zhibiao Ye, and Changxian Yang
- Subjects
Solanum lycopersicum ,Gene Expression Regulation, Plant ,Physiology ,Trichomes ,Plant Science ,Plant Proteins ,Plant Epidermis - Abstract
Trichomes that originate from plant aerial epidermis act as mechanical and chemical barriers against herbivores. Although several regulators have recently been identified, the regulatory pathway underlying multicellular trichome formation remains largely unknown in tomato. Here, we report a novel HD-ZIP IV transcription factor, Lanata (Ln), a missense mutation which caused the hairy phenotype. Biochemical analyses demonstrate that Ln separately interacts with two trichome regulators, Woolly (Wo) and Hair (H). Genetic and molecular evidence demonstrates that Ln directly regulates the expression of H. The interaction between Ln and Wo can increase trichome density by enhancing the expression of SlCycB2 and SlCycB3, which we previously showed are involved in tomato trichome formation. Furthermore, SlCycB2 represses the transactivation of the SlCycB3 gene by Ln and vice versa. Our findings provide new insights into the novel regulatory network controlling multicellular trichome formation in tomato.
- Published
- 2022
14. The transcription factors DcHB30 and DcWRKY75 antagonistically regulate ethylene-induced petal senescence in carnation (Dianthus caryophyllus)
- Author
-
Han Xu, Siqi Wang, Robert M Larkin, and Fan Zhang
- Subjects
Physiology ,Plant Science - Abstract
Although numerous transcription factors with antagonistic activities have been shown to contribute to growth and development, whether and how they regulate senescence in plants is largely unknown. In this study, we investigated the role of antagonistic transcription factors in petal senescence in carnation (Dianthus caryophyllus), one of the most common types of ethylene-sensitive cut flowers produced worldwide. We identified DcHB30 that encodes a ZF-HD transcription factor that is down-regulated in ethylene-treated petal transcriptomes. We found that silencing DcHB30 accelerated ethylene-induced petal senescence and that DcHB30 physically interacts with DcWRKY75, a positive regulator of ethylene-induced petal senescence. Phenotypic characterization and molecular evidence indicated that DcHB30 and DcWRKY75 competitively regulate the expression of their co-targeted genes DcACS1, DcACO1, DcSAG12, and DcSAG29 by reciprocally inhibiting the DNA-binding activity of each other on the gene promoters. This transcriptional regulation mechanism demonstrates that these transcription factors serve as positive and negative regulators in ethylene-induced petal senescence in carnation. Thus, our study provides insights into how antagonizing transcription factors regulate plant senescence.
- Published
- 2022
15. Systems and breakdown of self-incompatibility
- Author
-
Muhammad Husnain Ahmad, Muhammad Junaid Rao, Jianbing Hu, Qiang Xu, Chenchen Liu, Zonghong Cao, Robert M. Larkin, Xiuxin Deng, Maurice Bosch, and Lijun Chai
- Subjects
Plant Science - Published
- 2022
16. Pan-mitogenomics reveals the genetic basis of cytonuclear conflicts in citrus hybridization, domestication, and diversification
- Author
-
Nan Wang, Chaochao Li, Lihua Kuang, Xiaomeng Wu, Kaidong Xie, Andan Zhu, Qiang Xu, Robert M. Larkin, Yongfeng Zhou, Xiuxin Deng, and Wenwu Guo
- Subjects
Domestication ,Citrus ,Plant Breeding ,Multidisciplinary ,Genome, Chloroplast ,Genome-Wide Association Study - Abstract
Although interactions between the cytoplasmic and nuclear genomes occurred during diversification of many plants, the evolutionary conflicts due to cytonuclear interactions are poorly understood in crop breeding. Here, we constructed a pan-mitogenome and identified chimeric open reading frames (ORFs) generated by extensive structural variations (SVs). Meanwhile, short reads from 184 accessions of citrus species were combined to construct three variation maps for the nuclear, mitochondrial, and chloroplast genomes. The population genomic data showed discordant topologies between the cytoplasmic and nuclear genomes because of differences in mutation rates and levels of heteroplasmy from paternal leakage. An analysis of species-specific SVs indicated that mitochondrial heteroplasmy was common and that chloroplast heteroplasmy was undetectable. Interestingly, we found a prominent divergence in the mitogenomes and the highest genetic load in the, which may provide the basis for cytoplasmic male sterility (CMS) and thus influence the reshuffling of the cytoplasmic and nuclear genomes during hybridization. Using cytoplasmic replacement experiments, we identified a type of species-specific CMS in mandarin related to two chimeric mitochondrial genes. Our analyses indicate that cytoplasmic genomes from mandarin have rarely been maintained in hybrids and that paternal leakage produced very low levels of mitochondrial heteroplasmy in mandarin. A genome-wide association study (GWAS) provided evidence for three nuclear genes that encode pentatricopeptide repeat (PPR) proteins contributing to the cytonuclear interactions in theCitrusgenus. Our study demonstrates the occurrence of evolutionary conflicts between cytoplasmic and nuclear genomes in citrus and has important implications for genetics and breeding.
- Published
- 2023
17. Recent progress on mechanisms that allocate cellular space to plastids
- Author
-
Robert M. Larkin
- Subjects
Multidisciplinary - Published
- 2022
18. Somatic variations led to the selection of acidic and acidless orange cultivars
- Author
-
Peng Chen, Bin Zeng, Xiuxin Deng, Xiaolin Jiang, Shuizhi Yang, Robert M. Larkin, Fa He, Ray Ming, Dong Jiang, Jiaxian He, ZiAng Liu, Huiwen Yu, Ling-Jun Ke, Zhihao Lu, Lun Wang, Yue Huang, Edward S. Buckler, Qiang Xu, and Zongzhou Xie
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetics ,Mutation ,Somatic cell ,food and beverages ,Chromosome ,Plant Science ,Biology ,medicine.disease_cause ,01 natural sciences ,Genome ,03 medical and health sciences ,030104 developmental biology ,Apomixis ,Genetic variation ,medicine ,Ploidy ,010606 plant biology & botany ,Reference genome - Abstract
Somatic variations are a major source of genetic diversification in asexual plants, and underpin clonal evolution and the breeding of asexual crops. Sweet orange is a model species for studying somatic variation because it reproduces asexually through apomixis and is propagated asexually through grafting. To dissect the genomic basis of somatic variation, we de novo assembled a reference genome of sweet orange with an average of three gaps per chromosome and a N50 contig of 24.2 Mb, as well as six diploid genomes of somatic mutants of sweet oranges. We then sequenced 114 somatic mutants with an average genome coverage of 41×. Categorization of the somatic variations yielded insights into the single-nucleotide somatic mutations, structural variations and transposable element (TE) transpositions. We detected 877 TE insertions, and found TE insertions in the transporter or its regulatory genes associated with variation in fruit acidity. Comparative genomic analysis of sweet oranges from three diversity centres supported a dispersal from South China to the Mediterranean region and to the Americas. This study provides a global view on the somatic variations, the diversification and dispersal history of sweet orange and a set of candidate genes that will be useful for improving fruit taste and flavour.
- Published
- 2021
19. Producing fluorescent plants to lure and trap insect pests
- Author
-
Qinglin Peng, Jing Zhao, Siya Xiang, Jiajia Li, Chaochao He, Xingting Huang, ManZhu Bao, Jihua Wang, Genfa Zhu, Robert M. Larkin, Hong Luo, and Guogui Ning
- Subjects
Insecta ,Animals ,Plant Science ,Agronomy and Crop Science ,Insect Control ,Biotechnology - Published
- 2022
20. LsNRL4 enhances photosynthesis and decreases leaf angles in lettuce
- Author
-
Guanghui An, Yetong Qi, Weiyi Zhang, Hairong Gao, Jinlong Qian, Robert M. Larkin, Jiongjiong Chen, and Hanhui Kuang
- Subjects
Plant Leaves ,Plant Breeding ,Chloroplasts ,Plant Science ,Lettuce ,Photosynthesis ,Agronomy and Crop Science ,Biotechnology - Abstract
Lettuce (Lactuca sativa) is one of the most important vegetables worldwide and an ideal plant for producing protein drugs. Both well-functioning chloroplasts that perform robust photosynthesis and small leaf angles that enable dense planting are essential for high yields. In this study, we used an F
- Published
- 2022
21. A conservative pathway for coordination of cell wall biosynthesis and cell cycle progression in plants
- Author
-
Wang Xiuqing, Jiewei Shi, Hong Luo, Robert M. Larkin, Delin Zhang, Guogui Ning, Nachaisin Anupol, Xu Yan, Yuxiao Shen, Qin Zhou, Manzhu Bao, and Qunxia Zhang
- Subjects
0106 biological sciences ,0301 basic medicine ,Cell ,Arabidopsis ,Plant Science ,Biology ,Genes, Plant ,Rosa ,01 natural sciences ,Cell wall ,03 medical and health sciences ,Downregulation and upregulation ,Cell Wall ,Gene Expression Regulation, Plant ,Genetics ,medicine ,Arabidopsis thaliana ,Gene ,Phylogeny ,Plant Proteins ,Arabidopsis Proteins ,Cell growth ,Cell Cycle ,Cell Biology ,Cell cycle ,biology.organism_classification ,Cell biology ,Plant Leaves ,030104 developmental biology ,medicine.anatomical_structure ,Transcriptome ,Transcription Factors ,010606 plant biology & botany - Abstract
The mechanism that coordinates cell growth and cell cycle progression remains poorly understood; in particular, whether the cell cycle and cell wall biosynthesis are coordinated remains unclear. Recently, cell wall biosynthesis and cell cycle progression were reported to respond to wounding. Nonetheless, no genes are reported to synchronize the biosynthesis of the cell wall and the cell cycle. Here, we report that wounding induces the expression of genes associated with cell wall biosynthesis and the cell cycle, and that two genes, AtMYB46 in Arabidopsis thaliana and RrMYB18 in Rosa rugosa, are induced by wounding. We found that AtMYB46 and RrMYB18 promote the biosynthesis of the cell wall by upregulating the expression of cell wall-associated genes, and that both of them also upregulate the expression of a battery of genes associated with cell cycle progression. Ultimately, this response leads to the development of curled leaves of reduced size. We also found that the coordination of cell wall biosynthesis and cell cycle progression by AtMYB46 and RrMYB18 is evolutionarily conservative in multiple species. In accordance with wounding promoting cell regeneration by regulating the cell cycle, these findings also provide novel insight into the coordination between cell growth and cell cycle progression and a method for producing miniature plants.
- Published
- 2021
22. NF‐Y plays essential roles in flavonoid biosynthesis by modulating histone modifications in tomato
- Author
-
Chunli Zhang, Jiafa Wang, Changxing Li, Fangyan Zheng, Zhibiao Ye, Xin Wang, Dedi Zhang, Guo Ai, Junhong Zhang, Long Cui, Robert M. Larkin, and Guobin Li
- Subjects
0106 biological sciences ,0301 basic medicine ,Chalcone synthase ,Physiology ,Flavonoid ,Locus (genetics) ,Plant Science ,01 natural sciences ,03 medical and health sciences ,Solanum lycopersicum ,Gene ,Transcription factor ,Flavonoids ,chemistry.chemical_classification ,biology ,food and beverages ,Ripening ,Cell biology ,Histone Code ,030104 developmental biology ,Flavonoid biosynthesis ,Histone ,CCAAT-Binding Factor ,chemistry ,Fruit ,biology.protein ,Transcription Factors ,010606 plant biology & botany - Abstract
NF-Y transcription factors are reported to play diverse roles in a wide range of biological processes in plants. However, only a few active NF-Y complexes are known in plants and the precise functions of NF-Y complexes in flavonoid biosynthesis have not been determined. Using various molecular, genetic and biochemical approaches, we found that NF-YB8a, NF-YB8b and NF-YB8c - a NF-YB subgroup - can interact with a specific subgroup of NF-YC and then recruit either of two distinct NF-YAs to form NF-Y complexes that bind the CCAAT element in the CHS1 promoter. Furthermore, suppressing the expression of particular NF-YB genes increased the levels of H3K27me3 at the CHS1 locus and significantly suppressed the expression of CHS1 during tomato fruit ripening, which led to the development of pink-coloured fruit with colourless peels. Altogether, by demonstrating that NF-Y transcription factors play essential roles in flavonoid biosynthesis and by providing significant molecular insight into the regulatory mechanisms that drive the development of pink-coloured tomato fruit, we provide a major advance to our fundamental knowledge and information that has considerable practical value for horticulture.
- Published
- 2020
23. Evolution of self-compatibility by a mutant Sm-RNase in citrus
- Author
-
Mei Liang, Zonghong Cao, Andan Zhu, Yuanlong Liu, Mengqin Tao, Huayan Yang, Qiang Xu, Shaohua Wang, Junjie Liu, Yongping Li, Chuanwu Chen, Zongzhou Xie, Chongling Deng, Junli Ye, Wenwu Guo, Rui Xia, Robert M. Larkin, Xiuxin Deng, Maurice Bosch, Vernonica E. Franklin-Tong, and Lijun Chai
- Subjects
0106 biological sciences ,0301 basic medicine ,Genetics ,RNase P ,Mutant ,Haplotype ,food and beverages ,Plant Science ,Biology ,01 natural sciences ,Single nucleotide mutation ,03 medical and health sciences ,030104 developmental biology ,Gene ,Inbreeding ,Loss function ,010606 plant biology & botany ,Hybrid - Abstract
Self-incompatibility (SI) is an important mechanism that prevents self-fertilization and inbreeding in flowering plants. The most widespread SI system utilizes S ribonucleases (S-RNases) and S-locus F-boxes (SLFs) as S determinants. In citrus, SI is ancestral, and Citrus maxima (pummelo) is self-incompatible, while Citrus reticulata (mandarin) and its hybrids are self-compatible (SC). Here, we identify nine highly polymorphic pistil-specific, developmentally expressed S-RNases from pummelo that segregate with S haplotypes in a gametophytic manner and cluster with authentic S-RNases. We provide evidence that these S-RNases function as the female S determinants in citrus. Moreover, we show that each S-RNase is linked to approximately nine SLFs. In an analysis of 117 citrus SLF and SFL-like (SLFL) genes, we reveal that they cluster into 12 types and that the S-RNases and intra-haplotypic SLF and SLFL genes co-evolved. Our data support the notion that citrus have a S locus comprising a S-RNase and several SLFs that fit the non-self-recognition model. We identify a predominant single nucleotide mutation, Sm-RNase, in SC citrus, which provides a 'natural' loss of function. We show that SI-SC transitions due to the Sm-RNase initially arose in mandarin, spreading to its hybrids and became fixed. Identification of an evolutionarily distant new genus utilizing the S-RNase-based SI system, >100 million years separated from the nearest S-RNase family, is a milestone for evolutionary comparative studies.
- Published
- 2020
24. Loss-of-function of SAWTOOTH 1 affects leaf dorsiventrality genes to promote leafy heads in lettuce
- Author
-
Guanghui An, Changchun Yu, Chenghuan Yan, Menglu Wang, Weiyi Zhang, Yue Jia, Chunmei Shi, Robert M Larkin, Jiongjiong Chen, Dean Lavelle, Richard W Michelmore, and Hanhui Kuang
- Subjects
Plant Leaves ,Arabidopsis Proteins ,Gene Expression Regulation, Plant ,Arabidopsis ,Cell Biology ,Plant Science ,Lettuce ,Transcription Factors - Abstract
The mechanisms underlying leafy heads in vegetables are poorly understood. Here, we cloned a quantitative trait locus (QTL) controlling leafy heads in lettuce (Lactuca sativa). The QTL encodes a transcription factor, SAWTOOTH 1 (LsSAW1), which has a BEL1-like homeodomain and is a homolog of Arabidopsis thaliana. A 1-bp deletion in Lssaw1 contributes to the development of leafy heads. Laser-capture microdissection and RNA-sequencing showed that LsSAW1 regulates leaf dorsiventrality and loss-of-function of Lssaw1 downregulates the expression of many adaxial genes but upregulates abaxial genes. LsSAW1 binds to the promoter region of the adaxial gene ASYMMETRIC LEAVES 1 (LsAS1) to upregulate its expression. Overexpression of LsAS1 compromised the effects of Lssaw1 on heading. LsSAW1 also binds to the promoter region of the abaxial gene YABBY 1 (LsYAB1), but downregulates its expression. Overexpression of LsYAB1 led to bending leaves in LsSAW1 genotypes. LsSAW1 directly interacts with KNOTTED 1 (LsKN1), which is necessary for leafy heads in lettuce. RNA-seq data showed that LsSAW1 and LsKN1 exert antagonistic effects on the expression of thousands of genes. LsSAW1 compromises the ability of LsKN1 to repress LsAS1. Our results suggest that downregulation or loss-of-function of adaxial genes and upregulation of abaxial genes allow for the development of leafy heads.
- Published
- 2022
25. Single cell-type transcriptome profiling reveals genes that promote nitrogen fixation in the infected and uninfected cells of legume nodules
- Author
-
Longlong Wang, Yu Zhou, Runhui Li, Jianjun Liang, Tao Tian, Jie Ji, Runzhou Chen, Yumiao Zhou, Qiuling Fan, Guogui Ning, Robert M. Larkin, Manuel Becana, Deqiang Duanmu, National Natural Science Foundation of China, China Postdoctoral Science Foundation, Fundamental Research Funds for the Central Universities (China), Ministerio de Ciencia e Innovación (España), Becana Ausejo, Manuel [0000-0002-1083-0804], and Becana Ausejo, Manuel
- Subjects
leghaemoglobin ,symbiotic nitrogen fixation ,Nitrogen ,Gene Expression Profiling ,haem ,Fabaceae ,Plant Science ,single-celltranscriptomics ,Nitrogen Fixation ,Root Nodules, Plant ,Symbiosis ,Agronomy and Crop Science ,legume nodules ,Rhizobium ,Biotechnology - Abstract
2 Pags.- 1 Fig. © 2022 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd. This is an open access article under the terms of the Creative Commons Attribution License, which permits use,distribution and reproduction in any medium, provided the original work is properly cited., Excessive application of nitrogen fertilizers has inevitably resultedin environmental problems. The symbiotic nitrogen fixation (SNF) that occurs in the root nodules of leguminous plants provides asustainable source of reduced nitrogen in agricultural ecosystems. More than 200 genes have been reported to regulate SNF, including rhizobial infection, nodule organogenesis and senescence (Royet al., 2020). Mature nodules consist mainly of twocell types: infected cells (IC) that contain nitrogen-fixing bac-teroids and uninfected cells (UC) that mediate active metabolismand nutrient transport. Although it is well known that SNFrequires functional specialization, the specific genes responsiblefor transcriptional regulation and carbon/nitrogen metabolismand transport in IC and UC remain largely unexplored.Single-cell transcriptomics has emerged as a powerful tech-nique for investigating spatiotemporal patterns of gene expression., This work was supported by the National Natural Science Foundation of China (31870220, 32000192), the China Post-doctoral Science Foundation (2020M680103), Fundamental Research Funds for the Central Universities 2662020SKPY007 and MCIN/AEI/10.13039/501100011033 (grant PID2020-113985GB-I00)
- Published
- 2022
26. Variation in the fruit development gene POINTED TIP regulates protuberance of tomato fruit tip
- Author
-
Jianwen Song, Lele Shang, Changxing Li, Wenqian Wang, Xin Wang, Chunli Zhang, Guo Ai, Jie Ye, Changxian Yang, Hanxia Li, Zonglie Hong, Robert M. Larkin, Zhibiao Ye, and Junhong Zhang
- Subjects
Multidisciplinary ,Indoleacetic Acids ,Solanum lycopersicum ,Gene Expression Regulation, Plant ,Fruit ,General Physics and Astronomy ,Histidine ,General Chemistry ,Arginine ,General Biochemistry, Genetics and Molecular Biology ,Genome-Wide Association Study ,Plant Proteins ,Transcription Factors - Abstract
The domestication of tomato has led to striking variations in fruit morphology. Here, we show a genome-wide association study (GWAS) to understand the development of the fruit tip and describe aPOINTED TIP(PT) gene that encodes a C2H2-type zinc finger transcription factor. A single nucleotide polymorphism is found to change a histidine (H) to an arginine (R) in the C2H2 domain of PT and the two alleles are referred to asPTHandPTR. Knocking outPTHleads to development of pointed tip fruit.PTHfunctions to suppress pointed tip formation by downregulating the transcription ofFRUTFULL 2(FUL2), which alters the auxin transport. Our evolutionary analysis and previous studies by others suggest that thePTRallele likely hitch-hiked along with other selected loci during the domestication process. This study uncovers variation inPTand molecular mechanism underlying fruit tip development in tomato.
- Published
- 2021
27. Downregulated expression of S2-RNase attenuates self-incompatibility in 'Guiyou No. 1' pummelo
- Author
-
Chuanwu Chen, Junli Ye, Muhammad Husnain Ahmad, Hao Wen, Xiangling Chen, Chenchen Liu, Chongling Deng, Wei Zhuangmin, Kang Peng, Qiang Xu, Peng Chen, Lijun Chai, Hu Jianbing, Robert M. Larkin, Binghao Liu, and Xiuxin Deng
- Subjects
Genetics ,Mutation ,Candidate gene ,Mutant ,Haplotype ,Plant Science ,Horticulture ,Biology ,medicine.disease_cause ,Biochemistry ,Gene expression ,Transcriptional regulation ,medicine ,Pollen tube ,Gene ,Biotechnology - Abstract
Self-incompatibility (SI) substantially restricts the yield and quality of citrus. Therefore, breeding and analyzing self-compatible germplasm is of great theoretical and practical significance for citrus. Here, we focus on the mechanism of a self-compatibility mutation in ‘Guiyou No. 1’ pummelo (Citrus maxima), which is a spontaneous mutant of ‘Shatian’ pummelo (Citrus maxima, self-incompatibility). The rate of fruit set and the growth of pollen tubes in the pistil confirmed that a spontaneous mutation in the pistil is responsible for the self-compatibility of ‘Guiyou No. 1’. Segregation ratios of the S genotype in F1 progeny, expression analysis, and western blotting validated that the reduced levels of S2-RNase mRNA contribute to the loss of SI in ‘Guiyou No. 1’. Furthermore, we report a phased assembly of the ‘Guiyou No. 1’ pummelo genome and obtained two complete and well-annotated S haplotypes. Coupled with an analysis of SV variations, methylation levels, and gene expression, we identified a candidate gene (CgHB40), that may influence the regulation of the S2-RNase promoter. Our data provide evidence that a mutation that affects the pistil led to the loss of SI in ‘Guiyou No. 1’ by influencing a poorly understood mechanism that affects transcriptional regulation. This work significantly advances our understanding of the genetic basis of the SI system in citrus and provides information on the regulation of S-RNase genes.
- Published
- 2021
28. REDUCED CHLOROPLAST COVERAGE genes from Arabidopsis thaliana help to establish the size of the chloroplast compartment
- Author
-
Robert M. Larkin, Giovanni Stefano, Michael E. Ruckle, Andrea K. Stavoe, Christopher A. Sinkler, Federica Brandizzi, Carolyn M. Malmstrom, and Katherine W. Osteryoung
- Published
- 2016
- Full Text
- View/download PDF
29. Two TOBAMOVIRUS MULTIPLICATION 2A homologs in tobacco control asymptomatic response to tobacco mosaic virus
- Author
-
Kunpeng Li, Qun Hu, Zefan Chen, Lei Zhang, Hui Zhang, Huang Changjun, Hanhui Kuang, Yong Liu, Robert M. Larkin, Cheng Yuan, and Jiongjiong Chen
- Subjects
Genetics ,Regular Issue ,biology ,Physiology ,Host (biology) ,viruses ,Nicotiana tabacum ,fungi ,Arabidopsis ,food and beverages ,Tobamovirus ,Plant Science ,biology.organism_classification ,Virus Replication ,Tobacco Mosaic Virus ,Tobacco ,Tobacco mosaic virus ,Tomato mosaic virus ,Gene ,Nicotiana ,Plant Diseases ,Plant Proteins - Abstract
The most common response of a host to pathogens is arguably the asymptomatic response. However, the genetic and molecular mechanisms responsible for asymptomatic responses to pathogens are poorly understood. Here we report on the genetic cloning of two genes controlling the asymptomatic response to tobacco mosaic virus (TMV) in cultivated tobacco (Nicotiana tabacum). These two genes are homologous to tobamovirus multiplication 2A (TOM2A) from Arabidopsis, which was shown to be critical for the accumulation of TMV. Expression analysis indicates that the TOM2A genes might play fundamental roles in plant development or in responses to stresses. Consistent with this hypothesis, a null allele of the TOM2A ortholog in tomato (Solanum lycopersicum) led to the development of bent branches and a high tolerance to both TMV and tomato mosaic virus (ToMV). However, the TOM2A ortholog in Nicotiana glauca did not account for the asymptomatic response to TMV in N. glauca. We showed that TOM2A family is plant-specific and originated from Chlorophyte, and the biological functions of TOM2A orthologs to promote TMV accumulation are highly conserved in the plant kingdom—in both TMV host and nonhost species. In addition, we showed that the interaction between tobacco TOM1 and TOM2A orthologs in plant species is conserved, suggesting a conserved nature of TOM1–TOM2A module in promoting TMV multiplication in plants. The tradeoff between host development, the resistance of hosts to pathogens, and their influence on gene evolution are discussed. Our results shed light on mechanisms that contribute to asymptomatic responses to viruses in plants and provide approaches for developing TMV/ToMV-resistant crops.
- Published
- 2021
30. Influence of Switchgrass
- Author
-
Dongdong, Tian, Jingwen, Tang, Liwen, Luo, Zhe, Zhang, Kebing, Du, Robert M, Larkin, Xueping, Shi, and Bo, Zheng
- Subjects
biomass ,fungi ,CLE ,food and beverages ,switchgrass ,Plant Science ,vascular development ,Original Research ,TDIF - Abstract
As a member of the CLAVATA3 (CLV3)/EMBRYO SURROUNDING REGION (CLE) family, the dodecapeptide tracheary element differentiation inhibitory factor (TDIF) has a major impact on vascular development in plants. However, the influence of polymorphisms in the TDIF peptide motif on activity remains poorly understood. The model plant, Arabidopsis provides a fast and effective tool for assaying the activity of TDIF homologs. Five TDIF homologs from a group of 93 CLE genes in switchgrass (Panicum virgatum), a perennial biomass crop, named PvTDIF-like (PvTDIFL) genes were studied. The expression levels of PvTDIFL1, PvTDIFL3MR3, and PvTDIFL3MR2 were relatively high and all of them were expressed at the highest levels in the rachis of switchgrass. The precursor proteins for PvTDIFL1, PvTDIFL3MR3, and PvTDIFL3MR2 contained one, three, and two TDIFL motifs, respectively. Treatments with exogenous PvTDIFL peptides increased the number of stele cells in the hypocotyls of Arabidopsis seedlings, with the exception of PvTDIFL_4p. Heterologous expression of PvTDIFL1 in Arabidopsis strongly inhibited plant growth, increased cell division in the vascular tissue of the hypocotyl, and disrupted the cellular organization of the hypocotyl. Although heterologous expression of PvTDIFL3MR3 and PvTDIFL3MR2 also affected plant growth and vascular development, PvTDIFL activity was not enhanced by the multiple TDIFL motifs encoded by PvTDIFL3MR3 and PvTDIFL3MR2. These data indicate that in general, PvTDIFLs are functionally similar to Arabidopsis TDIF but that the processing and activities of the PvTDIFL peptides are more complex.
- Published
- 2021
31. Characterization of four polymorphic genes controlling red leaf colour in lettuce that have undergone disruptive selection since domestication
- Author
-
Qun Hu, Richard W Michelmore, Wenqing Su, Zhen Yue, Jiongjiong Chen, Robert M. Larkin, Changchun Yu, Rong Tao, Weiyi Zhang, Liu Wenye, Lei Zhang, Yu Zhang, Guanghui An, He Shuping, Dean Lavelle, and Hanhui Kuang
- Subjects
0106 biological sciences ,0301 basic medicine ,Technology ,Plant Science ,medicine.disease_cause ,Medical and Health Sciences ,01 natural sciences ,anthocyanin ,Anthocyanins ,Domestication ,chemistry.chemical_compound ,Gene Expression Regulation, Plant ,disruptive selection ,Arabidopsis ,Gene duplication ,Research Articles ,Plant Proteins ,Genetics ,Mutation ,Pigmentation ,food and beverages ,QTL‐seq ,Plants ,Lettuce ,Biological Sciences ,Plants, Genetically Modified ,leaf colour ,Research Article ,Biotechnology ,Sequence analysis ,Genetically Modified ,Biology ,03 medical and health sciences ,Genetic ,bulked segregant analysis ,medicine ,Selection, Genetic ,Selection ,Gene ,Transcription factor ,fungi ,Promoter ,Plant ,biology.organism_classification ,Plant Leaves ,030104 developmental biology ,Gene Expression Regulation ,chemistry ,QTL-seq ,Anthocyanin ,Generic health relevance ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
Summary Anthocyanins protect plants from biotic and abiotic stressors and provide great health benefits to consumers. In this study, we cloned four genes (Red Lettuce Leaves 1 to 4: RLL1 to RLL4) that contribute to colour variations in lettuce. The RLL1 gene encodes a bHLH transcription factor, and a 5‐bp deletion in some cultivars abolishes its function to activate the anthocyanin biosynthesis pathway. The RLL2 gene encodes an R2R3‐MYB transcription factor, which was derived from a duplication followed by mutations in its promoter region. The RLL3 gene encodes an R2‐MYB transcription factor, which down‐regulates anthocyanin biosynthesis through competing with RLL2 for interaction with RLL1; a mis‐sense mutation compromises the capacity of RLL3 to bind RLL1. The RLL4 gene encodes a WD‐40 transcription factor, homologous to the RUP genes suppressing the UV‐B signal transduction pathway in Arabidopsis; a mis‐sense mutation in rll4 attenuates its suppressing function, leading to a high concentration of anthocyanins. Sequence analysis of the RLL1‐RLL4 genes from wild and cultivated lettuce showed that their function‐changing mutations occurred after domestication. The mutations in rll1 disrupt anthocyanin biosynthesis, while the mutations in RLL2, rll3 and rll4 activate anthocyanin biosynthesis, showing disruptive selection for leaf colour during domestication of lettuce. The characterization of multiple polymorphic genes in this study provides the necessary molecular resources for the rational breeding of lettuce cultivars with distinct levels of red pigments and green cultivars with high levels of health‐promoting flavonoids.
- Published
- 2019
32. Overexpression of particular MADS‐box transcription factors in heat‐stressed plants induces chloroplast biogenesis in petals
- Author
-
Deqiang Duanmu, Yuxiao Shen, Rongcheng Lin, Manzhu Bao, Robert M. Larkin, Xiao Yang, Bo Zheng, Qi Pan, Zhen Wang, Guangying Ma, and Guogui Ning
- Subjects
0106 biological sciences ,0301 basic medicine ,Chloroplasts ,Physiology ,Arabidopsis ,MADS Domain Proteins ,Flowers ,Plant Science ,Biology ,Photosynthesis ,01 natural sciences ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Tobacco ,Plastid ,Transcription factor ,MADS-box ,Plant Proteins ,Organelle Biogenesis ,Arabidopsis Proteins ,Gene Expression Profiling ,food and beverages ,Plants, Genetically Modified ,biology.organism_classification ,Cell biology ,Petunia ,Plant Leaves ,Chloroplast ,030104 developmental biology ,Petal ,Heat-Shock Response ,Biogenesis ,Transcription Factors ,010606 plant biology & botany - Abstract
Chloroplasts convert solar energy into biologically useful forms of energy by performing photosynthesis. Although light and particular genes are known to promote chloroplast development, little is known about the mechanisms that regulate the tissue-specificity and cell-specificity of chloroplast biogenesis. Thus, the mechanisms that determine whether non-photosynthetic plastids rather than chloroplasts develop in petals remain largely unexplored. Although heat stress is known to inhibit photosynthesis, we do not know whether heat stress affects chloroplast biogenesis. Here, we report that heat stress up-regulates the expression of chlorophyll biosynthesis-related genes and promotes chloroplasts biogenesis in petals overexpressing SOC1 (suppressor of overexpression of CO) and novel SOC1-like genes. We also found that these specific MADS-box transcription factors are present in most photosynthetic eukaryotes and that the expression of more than one homolog is observed in chloroplast-containing tissues. These findings not only provide novel insights into the tissue specificity of chloroplast biogenesis and a method for producing green petals but also are consistent with heat stress influencing chloroplast biogenesis in higher plants.
- Published
- 2018
33. Downregulated expression of S
- Author
-
Jianbing, Hu, Qiang, Xu, Chenchen, Liu, Binghao, Liu, Chongling, Deng, Chuanwu, Chen, Zhuangmin, Wei, Muhammad Husnain, Ahmad, Kang, Peng, Hao, Wen, Xiangling, Chen, Peng, Chen, Robert M, Larkin, Junli, Ye, Xiuxin, Deng, and Lijun, Chai
- Subjects
Self incompatability ,food and beverages ,Article ,Gene regulation - Abstract
Self-incompatibility (SI) substantially restricts the yield and quality of citrus. Therefore, breeding and analyzing self-compatible germplasm is of great theoretical and practical significance for citrus. Here, we focus on the mechanism of a self-compatibility mutation in ‘Guiyou No. 1’ pummelo (Citrus maxima), which is a spontaneous mutant of ‘Shatian’ pummelo (Citrus maxima, self-incompatibility). The rate of fruit set and the growth of pollen tubes in the pistil confirmed that a spontaneous mutation in the pistil is responsible for the self-compatibility of ‘Guiyou No. 1’. Segregation ratios of the S genotype in F1 progeny, expression analysis, and western blotting validated that the reduced levels of S2-RNase mRNA contribute to the loss of SI in ‘Guiyou No. 1’. Furthermore, we report a phased assembly of the ‘Guiyou No. 1’ pummelo genome and obtained two complete and well-annotated S haplotypes. Coupled with an analysis of SV variations, methylation levels, and gene expression, we identified a candidate gene (CgHB40), that may influence the regulation of the S2-RNase promoter. Our data provide evidence that a mutation that affects the pistil led to the loss of SI in ‘Guiyou No. 1’ by influencing a poorly understood mechanism that affects transcriptional regulation. This work significantly advances our understanding of the genetic basis of the SI system in citrus and provides information on the regulation of S-RNase genes.
- Published
- 2021
34. L2, a chloroplast metalloproteinase, regulates fruit ripening by participating in ethylene autocatalysis under the control of ethylene response factors
- Author
-
Jing Wei, Junhong Zhang, Robert M. Larkin, Wenzhao Zhu, Guobin Li, Dedi Zhang, Chunli Zhang, Jiafa Wang, Changbao Li, Guo Ai, and Cai Liangyu
- Subjects
Ethylene ,Chloroplasts ,Physiology ,Chemistry ,Mutant ,Wild type ,food and beverages ,Ripening ,Plant Science ,Ethylenes ,Cell biology ,White (mutation) ,chemistry.chemical_compound ,Transcription (biology) ,Gene Expression Regulation, Plant ,Fruit ,Metalloproteases ,Climacteric ,Gene ,Plant Proteins - Abstract
Although autocatalytic ethylene biosynthesis plays an important role in the ripening of climacteric fruits, our knowledge of the network that promotes it remains limited. We identified white fruit (wf), a tomato mutant that produces immature fruit that are white and that ripen slowly. We found that an inversion on chromosome 10 disrupts the LUTESCENT2 (L2) gene, and that white fruit is allelic to lutescent2. Using CRISPR/Cas9 technology we knocked out L2 in wild type tomato and found that the l2-cr mutants produced phenotypes that were very similar to white fruit (lutescent2). In the l2-cr fruit, chloroplast development was impaired and the accumulation of carotenoids and lycopene occurred more slowly than in wild type. During fruit ripening in l2-cr mutants, the peak of ethylene release was delayed, less ethylene was produced, and the expression of ACO genes was significantly suppressed. We also found that exogenous ethylene induces the expression of L2 and that ERF.B3, an ethylene response factor, binds to the promoter of the L2 gene and activates its transcription. Thus, the expression of L2 is regulated by exogenous ethylene. Taken together, our results indicate that ethylene may affect the expression of L2 gene and that L2 participates in autocatalytic ethylene biosynthesis during tomato fruit ripening.
- Published
- 2021
35. Regulation of carotenoid and chlorophyll pools in hesperidia, anatomically unique fruits found only in Citrus
- Author
-
Yunliu Zeng, Estela Pérez-Román, Xiongjie Zheng, Junli Ye, Manuel Talon, Robert M. Larkin, Xuehan Mei, Zongzhou Xie, Hongyan Chen, Cecilia Zumajo-Cardona, Qiang Xu, Eleanore T. Wurtzel, Kaijie Zhu, Xiuxin Deng, Yue Huang, and Lixin Cao
- Subjects
Chlorophyll ,0106 biological sciences ,0301 basic medicine ,Citrus ,Regular Issue ,Perennial plant ,Plant domestication ,Physiology ,STAY-GREEN protein ,Plant Science ,Orange (colour) ,Biology ,01 natural sciences ,Hesperidium ,Crop ,03 medical and health sciences ,chemistry.chemical_compound ,E21 Agro-industry ,Botany ,Genetics ,Multi-omics strategy ,Carotenoid ,Gene ,chemistry.chemical_classification ,Fruit quality ,food and beverages ,Chlorophylls ,F60 Plant physiology and biochemistry ,Carotenoids ,030104 developmental biology ,chemistry ,Fruit ,Citrus crops improvement ,Citrus varieties ,Citrus × sinensis ,010606 plant biology & botany ,F30 Plant genetics and breeding ,Citrus sinensis - Abstract
Domesticated citrus varieties are woody perennials and interspecific hybrid crops of global economic and nutritional importance. The citrus fruit “hesperidium” is a unique morphological innovation not found in any other plant lineage. Efforts to improve the nutritional quality of the fruit are predicated on understanding the underlying regulatory mechanisms responsible for fruit development, including temporal control of chlorophyll degradation and carotenoid biosynthesis. Here, we investigated the molecular basis of the navel orange (Citrus sinensis) brown flavedo mutation, which conditions flavedo that is brown instead of orange. To overcome the limitations of using traditional genetic approaches in citrus and other woody perennials, we developed a strategy to elucidate the underlying genetic lesion. We used a multi-omics approach to collect data from several genetic sources and plant chimeras to successfully decipher this mutation. The multi-omics strategy applied here will be valuable in driving future gene discovery efforts in citrus as well as in other woody perennial plants. The comparison of transcriptomic and genomic data from multiple genotypes and plant sectors revealed an underlying lesion in the gene encoding STAY-GREEN (SGR) protein, which simultaneously regulates carotenoid biosynthesis and chlorophyll degradation. However, unlike SGR of other plant species, we found that the carotenoid and chlorophyll regulatory activities could be uncoupled in the case of certain SGR alleles in citrus and thus we propose a model for the molecular mechanism underlying the brown flavedo phenotype. The economic and nutritional value of citrus makes these findings of wide interest. The strategy implemented, and the results obtained, constitute an advance for agro-industry by driving opportunities for citrus crop improvement.
- Published
- 2021
36. Upregulation of a
- Author
-
Changchun, Yu, Chenghuan, Yan, Yuling, Liu, Yali, Liu, Yue, Jia, Dean, Lavelle, Guanghui, An, Weiyi, Zhang, Lei, Zhang, Rongkui, Han, Robert M, Larkin, Jiongjiong, Chen, Richard W, Michelmore, and Hanhui, Kuang
- Subjects
Base Sequence ,Transcription, Genetic ,Quantitative Trait Loci ,food and beverages ,Lettuce ,Biological Sciences ,Genes, Plant ,Up-Regulation ,Plant Leaves ,Mutagenesis, Insertional ,Gene Expression Regulation, Plant ,Gene Duplication ,Sequence Homology, Nucleic Acid ,DNA Transposable Elements ,Promoter Regions, Genetic ,Phylogeny ,Plant Proteins ,Protein Binding - Abstract
Leafy head is a unique type of plant architecture found in some vegetable crops, with leaves bending inward to form a compact head. The genetic and molecular mechanisms underlying leafy head in vegetables remain poorly understood. We genetically fine-mapped and cloned a major quantitative trait locus controlling heading in lettuce. The candidate gene (LsKN1) is a homolog of knotted 1 (KN1) from Zea mays. Complementation and CRISPR/Cas9 knockout experiments confirmed the role of LsKN1 in heading. In heading lettuce, there is a CACTA-like transposon inserted into the first exon of LsKN1 (LsKN1▽). The transposon sequences act as a promoter rather than an enhancer and drive high expression of LsKN1▽. The enhanced expression of LsKN1▽ is necessary but not sufficient for heading in lettuce. Data from ChIP-sequencing, electrophoretic mobility shift assays, and dual luciferase assays indicate that the LsKN1▽ protein binds the promoter of LsAS1 and down-regulates its expression to alter leaf dorsoventrality. This study provides insight into plant leaf development and will be useful for studies on heading in other vegetable crops.
- Published
- 2020
37. Genomic basis of high-altitude adaptation in Tibetan Prunus fruit trees
- Author
-
Zhao Fan, Gesang Pingcuo, Robert M. Larkin, Xiuxin Deng, Qiang Xu, Zeng Xiuli, Yanjun Zan, Yue Huang, Shengjun Liu, Junwei Liu, Hao Zuo, Xia Wang, Ting-Shuang Yi, Hong Ying, Weikang Zheng, Zhang Shanshan, and Li Yuanrong
- Subjects
Germplasm ,Evolutionary Biology ,Altitude ,Retrotransposon ,Locus (genetics) ,Biology ,Tibet ,Genome ,General Biochemistry, Genetics and Molecular Biology ,Trees ,Prunus ,Fruit ,Botany ,Adaptation ,General Agricultural and Biological Sciences ,Gene - Abstract
Summary The Great Himalayan Mountains and their foothills are believed to be the place of origin and development of many plant species. The genetic basis of adaptation to high plateaus is a fascinating topic that is poorly understood at the population level. We comprehensively collected and sequenced 377 accessions of Prunus germplasm along altitude gradients ranging from 2,067 to 4,492 m in the Himalayas. We de novo assembled three high-quality genomes of Tibetan Prunus species. A comparative analysis of Prunus genomes indicated a remarkable expansion of the SINE retrotransposons occurred in the genomes of Tibetan species. We observed genetic differentiation between Tibetan peaches from high and low altitudes and that genes associated with light stress signaling, especially UV stress signaling, were enriched in the differentiated regions. By profiling the metabolomes of Tibetan peach fruit, we determined 379 metabolites had significant genetic correlations with altitudes and that in particular phenylpropanoids were positively correlated with altitudes. We identified 62 Tibetan peach-specific SINEs that colocalized with metabolites differentially accumualted in Tibetan relative to cultivated peach. We demonstrated that two SINEs were inserted in a locus controlling the accumulation of 3-O-feruloyl quinic acid. SINE1 was specific to Tibetan peach. SINE2 was predominant in high altitudes and associated with the accumulation of 3-O-feruloyl quinic acid. These genomic and metabolic data for Prunus populations native to the Himalayan region indicate that the expansion of SINE retrotransposons helped Tibetan Prunus species adapt to the harsh environment of the Himalayan plateau by promoting the accumulation of beneficial metabolites.
- Published
- 2020
38. Upregulation of a KN1 homolog by transposon insertion promotes leafy head development in lettuce
- Author
-
Lei Zhang, Rongkui Han, Dean Lavelle, Richard W Michelmore, Chenghuan Yan, Guanghui An, Weiyi Zhang, Robert M. Larkin, Yali Liu, Yuling Liu, Jiongjiong Chen, Yue Jia, Hanhui Kuang, and Changchun Yu
- Subjects
Transposable element ,Candidate gene ,transposon ,Quantitative Trait Loci ,Sequence Homology ,Biology ,Promoter Regions ,Exon ,Genetic ,Insertional ,Gene Duplication ,Genetics ,CRISPR ,Luciferase ,Enhancer ,Leafy ,Phylogeny ,Plant Proteins ,Multidisciplinary ,Base Sequence ,Nucleic Acid ,food and beverages ,Plant ,Lettuce ,Up-Regulation ,Complementation ,Plant Leaves ,Gene Expression Regulation ,Genes ,Mutagenesis ,DNA Transposable Elements ,leafy head ,Transcription ,leaf development ,Protein Binding ,dorsoventrality - Abstract
Leafy head is a unique type of plant architecture found in some vegetable crops, with leaves bending inward to form a compact head. The genetic and molecular mechanisms underlying leafy head in vegetables remain poorly understood. We genetically fine-mapped and cloned a major quantitative trait locus controlling heading in lettuce. The candidate gene (LsKN1) is a homolog of knotted 1 (KN1) from Zea mays Complementation and CRISPR/Cas9 knockout experiments confirmed the role of LsKN1 in heading. In heading lettuce, there is a CACTA-like transposon inserted into the first exon of LsKN1 (LsKN1▽). The transposon sequences act as a promoter rather than an enhancer and drive high expression of LsKN1▽. The enhanced expression of LsKN1▽ is necessary but not sufficient for heading in lettuce. Data from ChIP-sequencing, electrophoretic mobility shift assays, and dual luciferase assays indicate that the LsKN1▽ protein binds the promoter of LsAS1 and down-regulates its expression to alter leaf dorsoventrality. This study provides insight into plant leaf development and will be useful for studies on heading in other vegetable crops.
- Published
- 2020
39. Somatic variations led to the selection of acidic and acidless orange cultivars
- Author
-
Lun, Wang, Yue, Huang, ZiAng, Liu, Jiaxian, He, Xiaolin, Jiang, Fa, He, Zhihao, Lu, Shuizhi, Yang, Peng, Chen, Huiwen, Yu, Bin, Zeng, Lingjun, Ke, Zongzhou, Xie, Robert M, Larkin, Dong, Jiang, Ray, Ming, Edward S, Buckler, Xiuxin, Deng, and Qiang, Xu
- Subjects
China ,Plant Breeding ,Genotype ,Gene Expression Regulation, Plant ,Fruit ,Mutation ,Genetic Variation ,Genes, Plant ,Acids ,Genome, Plant ,Citrus sinensis - Abstract
Somatic variations are a major source of genetic diversification in asexual plants, and underpin clonal evolution and the breeding of asexual crops. Sweet orange is a model species for studying somatic variation because it reproduces asexually through apomixis and is propagated asexually through grafting. To dissect the genomic basis of somatic variation, we de novo assembled a reference genome of sweet orange with an average of three gaps per chromosome and a N50 contig of 24.2 Mb, as well as six diploid genomes of somatic mutants of sweet oranges. We then sequenced 114 somatic mutants with an average genome coverage of 41×. Categorization of the somatic variations yielded insights into the single-nucleotide somatic mutations, structural variations and transposable element (TE) transpositions. We detected 877 TE insertions, and found TE insertions in the transporter or its regulatory genes associated with variation in fruit acidity. Comparative genomic analysis of sweet oranges from three diversity centres supported a dispersal from South China to the Mediterranean region and to the Americas. This study provides a global view on the somatic variations, the diversification and dispersal history of sweet orange and a set of candidate genes that will be useful for improving fruit taste and flavour.
- Published
- 2020
40. Revisiting the Plant CLE Gene Family with a New Method for Predicting and Clustering Short Amino Acid Sequences
- Author
-
Zhe Zhang, Lei Liu, Melis Kucukoglu, Dongdong Tian, Robert M. Larkin, Xueping Shi, and Bo Zheng
- Subjects
fungi - Abstract
Background: The CLV3 / ESR-RELATED ( CLE ) gene family encodes small secreted peptides (SSPs) and plays vital roles in plant growth and development through cell-to-cell communication. The prediction and classification of CLE genes is challenging because of their low sequence similarity. Results: We developed a machine learning-aided method for predicting CLE genes by using a CLE motif-specific residual score matrix and a novel clustering method based on the Euclidean distance of the 12 amino acid residues from CLE motifs in a site-weight dependent manner. In total, 2156 CLE candidates—including 627 novel candidates—were predicted from 69 plant species. The results from our CLE motif-based clustering are consistent with previous reports using the entire pre-propeptide. Characterization of CLE candidates provided systematic statistics on protein lengths, signal peptides, relative motif positions, amino acid compositions of different parts of the CLE precursor proteins, and decisive factors of CLE prediction. The approach taken here provides information on the evolution of the CLE gene family and provides evidence that the CLE and IDA/IDL genes share a common ancestor. Conclusions: Our new approach is applicable to SSPs or other proteins with short conserved domains and hence, provides a useful tool for gene prediction, classification and evolutionary analysis.
- Published
- 2020
41. Predicting and clustering plant CLE genes with a new method developed specifically for short amino acid sequences
- Author
-
Xueping Shi, Robert M. Larkin, Melis Kucukoglu, Zhe Zhang, Lei Liu, Dongdong Tian, and Bo Zheng
- Subjects
0106 biological sciences ,Signal peptide ,lcsh:QH426-470 ,Evolution ,Gene prediction ,lcsh:Biotechnology ,Computational biology ,Biology ,Protein Sorting Signals ,Proteomics ,01 natural sciences ,03 medical and health sciences ,Gene Expression Regulation, Plant ,lcsh:TP248.13-248.65 ,Machine learning ,Genetics ,Gene family ,Cluster Analysis ,Amino Acid Sequence ,Cluster analysis ,Gene ,Gene clustering ,030304 developmental biology ,chemistry.chemical_classification ,0303 health sciences ,Methodology Article ,fungi ,Correction ,Plants ,Peptide hormone ,Amino acid ,lcsh:Genetics ,ComputingMethodologies_PATTERNRECOGNITION ,chemistry ,CLE ,DNA microarray ,Euclidean distance ,Peptides ,010606 plant biology & botany ,Biotechnology - Abstract
Background The CLV3/ESR-RELATED (CLE) gene family encodes small secreted peptides (SSPs) and plays vital roles in plant growth and development by promoting cell-to-cell communication. The prediction and classification of CLE genes is challenging because of their low sequence similarity. Results We developed a machine learning-aided method for predicting CLE genes by using a CLE motif-specific residual score matrix and a novel clustering method based on the Euclidean distance of 12 amino acid residues from the CLE motif in a site-weight dependent manner. In total, 2156 CLE candidates—including 627 novel candidates—were predicted from 69 plant species. The results from our CLE motif-based clustering are consistent with previous reports using the entire pre-propeptide. Characterization of CLE candidates provided systematic statistics on protein lengths, signal peptides, relative motif positions, amino acid compositions of different parts of the CLE precursor proteins, and decisive factors of CLE prediction. The approach taken here provides information on the evolution of the CLE gene family and provides evidence that the CLE and IDA/IDL genes share a common ancestor. Conclusions Our new approach is applicable to SSPs or other proteins with short conserved domains and hence, provides a useful tool for gene prediction, classification and evolutionary analysis.
- Published
- 2020
42. The genomes uncoupled Mutants Are More Sensitive to Norflurazon Than Wild Type
- Author
-
Zefan Chen, Lijuan Song, and Robert M. Larkin
- Subjects
0106 biological sciences ,0301 basic medicine ,Regulation of gene expression ,Genetics ,Chlorophyll metabolism ,Mutation ,Physiology ,Chemistry ,fungi ,Mutant ,Wild type ,food and beverages ,Plant Science ,medicine.disease_cause ,01 natural sciences ,Phenotype ,Genome ,03 medical and health sciences ,030104 developmental biology ,medicine ,Signal transduction ,010606 plant biology & botany - Abstract
The increased sensitivity of the genomes uncoupled mutants to norflurazon indicates that they are probably deficient in plastid-to-nucleus signaling and are unequivocally not resistant to norflurazon.
- Published
- 2018
43. Genome of Wild Mandarin and Domestication History of Mandarin
- Author
-
Xiaolin Jiang, Jiaxian He, Hongyan Zhang, Fa He, Huiwen Yu, Lun Wang, Guangyan Zhong, Changfu Zhou, Robert M. Larkin, Yue Huang, Xiaoming Yang, Qiang Xu, Chongling Deng, Yiwen Fang, Zongzhou Xie, Xiuxin Deng, Shuizhi Yang, Wen Shaohua, Rangwei Xu, Jiwu Zeng, Chuanwu Chen, and Xiang Yan
- Subjects
0301 basic medicine ,Citrus ,South china ,Genotype ,Population size ,Genetic Variation ,Introgression ,Plant Science ,Interspecific competition ,Biology ,Mandarin Chinese ,Genome ,Citric Acid ,language.human_language ,Domestication ,03 medical and health sciences ,030104 developmental biology ,Effective population size ,Botany ,language ,Molecular Biology ,Genome, Plant ,Phylogeny - Abstract
Mandarin (Citrus reticulata) is one of the most important citrus crops worldwide. Its domestication is believed to have occurred in South China, which has been one of the centers of mandarin cultivation for four millennia. We collected natural wild populations of mandarin around the Nanling region and cultivated landraces in the vicinity. We found that the citric acid level was dramatically reduced in cultivated mandarins. To understand genetic basis of mandarin domestication, we de novo assembled a draft genome of wild mandarin and analyzed a set of 104 citrus genomes. We found that the Mangshan mandarin is a primitive type and that two independent domestication events have occurred, resulting in two groups of cultivated mandarins (MD1 and MD2) in the North and South Nanling Mountains, respectively. Two bottlenecks and two expansions of effective population size were identified for the MD1 group of cultivated mandarins. However, in the MD2 group there was a long and continuous decrease in the population size. MD1 and MD2 mandarins showed different patterns of interspecific introgression from cultivated pummelo species. We identified a region of high divergence in an aconitate hydratase (ACO) gene involved in the regulation of citrate content, which was possibly under selection during the domestication of mandarin. This study provides concrete genetic evidence for the geographical origin of extant wild mandarin populations and sheds light on the domestication and evolutionary history of mandarin.
- Published
- 2018
44. RNA editing implicated in chloroplast-to-nucleus communication
- Author
-
Robert M. Larkin
- Subjects
0106 biological sciences ,0301 basic medicine ,Mitochondrial DNA ,Nuclear gene ,Arabidopsis ,Biology ,01 natural sciences ,Genome ,Mitochondrial Proteins ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Commentaries ,Plastids ,Plastid ,Gene ,Multidisciplinary ,Arabidopsis Proteins ,food and beverages ,RNA ,Cell biology ,DNA-Binding Proteins ,Chloroplast ,030104 developmental biology ,RNA editing ,RNA Editing ,010606 plant biology & botany - Abstract
Photosynthesis and respiration provide the chemical energy that sustains life on Earth. In eukaryotes, this essential metabolism is performed by chloroplasts and mitochondria. Although both of these organelles have small genomes that are remnants of their endosymbiotic origins, most of the proteins in these organelles are encoded by nuclear genes. One consequence of this distribution of genetic material is that many of the multisubunit protein complexes that are central to energy metabolism are composed of proteins encoded by nuclear genes and either chloroplast genes (photosynthesis) or mitochondrial genes (respiration). Thus, the coordination of nuclear and chloroplast (or mitochondrial) activities requires the anterograde flow of information from the nucleus and retrograde signaling back to the nucleus. Although we know that retrograde signals from chloroplasts (i.e., chloroplast signals) influence numerous chloroplastic and extrachloroplastic processes, we still have major gaps in our knowledge of this type of signaling (1, 2). RNA editing refers to processes that change the identities of nucleotides and processes that add or delete nucleotides from RNAs. RNA editing has been reported in viruses and diverse eukaryotes. In flowering plants, RNA editing converts cytidines to uridines in the RNAs transcribed from the chloroplast and mitochondrial genomes (3). In PNAS, Zhao et al. (4) make a strong case that RNA editing in chloroplasts contributes to a type of chloroplast-to-nucleus signaling defined by the genomes uncoupled ( gun ) mutants in Arabidopsis . The gun mutant screen was the first forward genetic screen developed that specifically interrogates chloroplast-to-nucleus signaling. The mutant alleles from this screen uncouple the expression of photosynthesis-associated nuclear genes (PhANGs) from chloroplast function. Chloroplasts develop from nonphotosynthetic proplastids during the development of photosynthetic organs such as cotyledons and leaves. Light is a major positive regulator of PhANG expression. When light-grown plants are treated with inhibitors or harbor mutant alleles that … [↵][1]1Email: larkin{at}mail.hzau.edu.cn. [1]: #xref-corresp-1-1
- Published
- 2019
45. Correction to: Predicting and clustering plant CLE genes with a new method developed specifically for short amino acid sequences
- Author
-
Lei Liu, Melis Kucukoglu, Robert M. Larkin, Dongdong Tian, Bo Zheng, Zhe Zhang, and Xueping Shi
- Subjects
chemistry.chemical_classification ,lcsh:QH426-470 ,lcsh:Biotechnology ,Computational biology ,Biology ,Proteomics ,Amino acid ,lcsh:Genetics ,chemistry ,lcsh:TP248.13-248.65 ,Genetics ,DNA microarray ,Cluster analysis ,Gene ,Biotechnology - Abstract
An amendment to this paper has been published and can be accessed via the original article.
- Published
- 2020
46. An R2R3‐MYB transcription factor represses the transformation of α‐ and β‐branch carotenoids by negatively regulating expression of CrBCH2 and CrNCED5 in flavedo of Citrus reticulate
- Author
-
Mingfei Zhang, Wen-Wu Guo, Qiang Xu, Chaoyang Liu, Rangwei Xu, Robert M. Larkin, Li Zheng, Xue Xiao, Wei Yang, Feng Zhu, Xiuxin Deng, Yang Wang, Hongbin Yang, Yunjiang Cheng, Jianguo Xu, Tao Luo, Yunliu Zeng, and Juan Xu
- Subjects
0106 biological sciences ,0301 basic medicine ,Citrus ,DNA, Plant ,Genotype ,Physiology ,Mutant ,Nicotiana benthamiana ,Plant Science ,Biology ,01 natural sciences ,03 medical and health sciences ,Gene Expression Regulation, Plant ,Consensus Sequence ,Tobacco ,Gene expression ,Transcriptional regulation ,MYB ,Amino Acid Sequence ,Promoter Regions, Genetic ,Carotenoid ,Transcription factor ,Plant Proteins ,chemistry.chemical_classification ,Base Sequence ,fungi ,food and beverages ,Plants, Genetically Modified ,biology.organism_classification ,Carotenoids ,Plant Leaves ,Transformation (genetics) ,Phenotype ,030104 developmental biology ,chemistry ,Biochemistry ,Mutation ,Metabolome ,Transcriptome ,Sequence Alignment ,Protein Binding ,Subcellular Fractions ,Transcription Factors ,010606 plant biology & botany - Abstract
Although the functions of carotenogenic genes are well documented, little is known about the mechanisms that regulate their expression, especially those genes involved in α - and β-branch carotenoid metabolism. In this study, an R2R3-MYB transcriptional factor (CrMYB68) that directly regulates the transformation of α- and β-branch carotenoids was identified using Green Ougan (MT), a stay-green mutant of Citrus reticulata cv Suavissima. A comprehensive analysis of developing and harvested fruits indicated that reduced expression of β-carotene hydroxylases 2 (CrBCH2) and 9-cis-epoxycarotenoid dioxygenase 5 (CrNCED5) was responsible for the delay in the transformation of α- and β-carotene and the biosynthesis of ABA. Additionally, the expression of these genes was negatively correlated with the expression of CrMYB68 in MT. Further, electrophoretic mobility shift assays (EMSAs) and dual luciferase assays indicated that CrMYB68 can directly and negatively regulate CrBCH2 and CrNCED5. Moreover, transient overexpression experiments using leaves of Nicotiana benthamiana indicated that CrMYB68 can also negatively regulate NbBCH2 and NbNCED5. To overcome the difficulty of transgenic validation, we quantified the concentrations of carotenoids and ABA, and gene expression in a revertant of MT. The results of these experiments provide more evidence that CrMYB68 is an important regulator of carotenoid metabolism.
- Published
- 2017
47. Genomic analyses of primitive, wild and cultivated citrus provide insights into asexual reproduction
- Author
-
Shilin Tian, Xia Wang, Yijun Ruan, Hong Lan, Yan Liu, Yue Huang, Meilian Tan, Xiaoming Yang, Bin-Guang Ma, Robert M. Larkin, Qiang Xu, Lun Wang, Xiuxin Deng, Siqi Zhang, Ling-Ling Chen, Xiaolin Jiang, Zongzhou Xie, Junfeng Cheng, Jidi Xu, Li Cao, Yuantao Xu, Nan Wang, Guizhi Wu, Huiwen Yu, and Chunli Chen
- Subjects
0106 biological sciences ,0301 basic medicine ,Transposable element ,Citrus ,Candidate gene ,Population ,Polyembryony ,Asexual reproduction ,Biology ,Polymorphism, Single Nucleotide ,01 natural sciences ,Genome ,Chromosomes, Plant ,03 medical and health sciences ,Species Specificity ,Gene Expression Regulation, Plant ,Apomixis ,Reproduction, Asexual ,Genetics ,Cluster Analysis ,education ,Gene ,Phylogeny ,education.field_of_study ,Reverse Transcriptase Polymerase Chain Reaction ,Gene Expression Profiling ,Chromosome Mapping ,Genetic Variation ,food and beverages ,Genomics ,Sequence Analysis, DNA ,Gene Ontology ,030104 developmental biology ,Genome, Plant ,010606 plant biology & botany - Abstract
Qiang Xu and colleagues sequence four citrus species de novo, along with 100 accessions, including primitive, wild and cultivated citrus. Their genomic analyses associate the CitRWP gene with polyembryony and suggest that regions harboring energy- and reproduction-associated genes are probably under selection in cultivated citrus. The emergence of apomixis—the transition from sexual to asexual reproduction—is a prominent feature of modern citrus. Here we de novo sequenced and comprehensively studied the genomes of four representative citrus species. Additionally, we sequenced 100 accessions of primitive, wild and cultivated citrus. Comparative population analysis suggested that genomic regions harboring energy- and reproduction-associated genes are probably under selection in cultivated citrus. We also narrowed the genetic locus responsible for citrus polyembryony, a form of apomixis, to an 80-kb region containing 11 candidate genes. One of these, CitRWP, is expressed at higher levels in ovules of polyembryonic cultivars. We found a miniature inverted-repeat transposable element insertion in the promoter region of CitRWP that cosegregated with polyembryony. This study provides new insights into citrus apomixis and constitutes a promising resource for the mining of agriculturally important genes.
- Published
- 2017
48. A NAC transcription factor and its interaction protein hinder abscisic acid biosynthesis by synergistically repressing NCED5 in Citrus reticulata
- Author
-
Robert M. Larkin, Yunjiang Cheng, Xiuxin Deng, Mingfei Zhang, Tao Luo, Pengwei Wang, Chaoyang Liu, Junli Ye, Juan Xu, Wei Yang, Rangwei Xu, Li Zheng, Alisdair R. Fernie, Yang Wang, Hongbin Yang, Xue Xiao, Jianguo Xu, Yunliu Zeng, Feng Zhu, and Weiwei Wen
- Subjects
Citrus ,Physiology ,Mutant ,NAC transcription factor ,Plant Science ,postharvest ,synergistic transcriptional regulation ,Transcriptome ,chemistry.chemical_compound ,Bimolecular fluorescence complementation ,Biosynthesis ,Gene Expression Regulation, Plant ,Luciferase ,Abscisic acid ,Transcription factor ,Plant Proteins ,Chemistry ,AcademicSubjects/SCI01210 ,fruit ripening, MYB transcription factor ,fungi ,food and beverages ,Ripening ,Research Papers ,Cell biology ,ABA ,Fruit ,Citrus reticulata ,Abscisic Acid ,Transcription Factors ,Photosynthesis and Metabolism - Abstract
A novel NAC transcription factor, CrNAC036, can interact with CrMYB68 to synergistically regulate the ripening process of citrus fruit by down-regulating the expression of 9-cis-epoxycarotenoid dioxygenase 5., Although abscisic acid (ABA) is a vital regulator of fruit ripening and several transcription factors have been reported to regulate ABA biosynthesis, reports of the effect of ABA on citrus ripening and the regulation of its biosynthesis by a multiple-transcription-factor complex are scarce. In the present study, a systematic metabolic, cytological, and transcriptome analysis of an ABA-deficient mutant (MT) of Citrus reticulata cv. Suavissima confirmed the positive effect of ABA on the citrus ripening process. The analysis of transcriptome profiles indicated that CrNAC036 played an important role in the ABA deficiency of the mutant, most likely due to an effect on the expression of 9-cis-epoxycarotenoid dioxygenase 5 (CrNCED5). Electrophoretic mobility shift assays and dual luciferase assays demonstrated that CrNAC036 can directly bind and negatively regulate CrNCED5 expression. Furthermore, yeast two-hybrid, bimolecular fluorescence complementation, and dual luciferase assays demonstrated that CrNAC036 interacted with CrMYB68, also down-regulating the expression of CrNCED5. Taken together, our results suggest that CrNAC036 and CrMYB68 synergistically inhibit ABA biosynthesis in citrus fruit by regulating the expression of CrNCED5.
- Published
- 2019
49. Genome editing with the CRISPR-Cas system: an art, ethics and global regulatory perspective
- Author
-
Fang Ding, Hakim Manghwar, Amjad Hussain, Debin Zhang, Kabin Xie, Ping Qing, Shengsong Xie, Robert M. Larkin, Shuhong Zhao, and Shuangxia Jin
- Subjects
0106 biological sciences ,0301 basic medicine ,Plant Science ,Review ,Biology ,01 natural sciences ,Genome ,03 medical and health sciences ,Genome editing ,regulations ,CRISPR ,Animals ,Humans ,genome editing ,Clustered Regularly Interspaced Short Palindromic Repeats ,Biomedicine ,Gene Editing ,Transcription activator-like effector nuclease ,Ethical issues ,Scope (project management) ,CRISPR‐Cas system ,business.industry ,Agriculture ,Plants ,Data science ,ethics ,030104 developmental biology ,Human genome ,CRISPR-Cas Systems ,business ,Agronomy and Crop Science ,risks ,010606 plant biology & botany ,Biotechnology - Abstract
Summary Over the last three decades, the development of new genome editing techniques, such as ODM, TALENs, ZFNs and the CRISPR‐Cas system, has led to significant progress in the field of plant and animal breeding. The CRISPR‐Cas system is the most versatile genome editing tool discovered in the history of molecular biology because it can be used to alter diverse genomes (e.g. genomes from both plants and animals) including human genomes with unprecedented ease, accuracy and high efficiency. The recent development and scope of CRISPR‐Cas system have raised new regulatory challenges around the world due to moral, ethical, safety and technical concerns associated with its applications in pre‐clinical and clinical research, biomedicine and agriculture. Here, we review the art, applications and potential risks of CRISPR‐Cas system in genome editing. We also highlight the patent and ethical issues of this technology along with regulatory frameworks established by various nations to regulate CRISPR‐Cas‐modified organisms/products.
- Published
- 2019
50. Evolution of self-compatibility by a mutant S
- Author
-
Mei, Liang, Zonghong, Cao, Andan, Zhu, Yuanlong, Liu, Mengqin, Tao, Huayan, Yang, Qiang, Xu, Shaohua, Wang, Junjie, Liu, Yongping, Li, Chuanwu, Chen, Zongzhou, Xie, Chongling, Deng, Junli, Ye, Wenwu, Guo, Rui, Xia, Robert M, Larkin, Xiuxin, Deng, Maurice, Bosch, Vernonica E, Franklin-Tong, and Lijun, Chai
- Subjects
Citrus ,Ribonucleases ,Reproduction ,Mutation ,Biological Evolution ,Plant Proteins - Abstract
Self-incompatibility (SI) is an important mechanism that prevents self-fertilization and inbreeding in flowering plants. The most widespread SI system utilizes S ribonucleases (S-RNases) and S-locus F-boxes (SLFs) as S determinants. In citrus, SI is ancestral, and Citrus maxima (pummelo) is self-incompatible, while Citrus reticulata (mandarin) and its hybrids are self-compatible (SC). Here, we identify nine highly polymorphic pistil-specific, developmentally expressed S-RNases from pummelo that segregate with S haplotypes in a gametophytic manner and cluster with authentic S-RNases. We provide evidence that these S-RNases function as the female S determinants in citrus. Moreover, we show that each S-RNase is linked to approximately nine SLFs. In an analysis of 117 citrus SLF and SFL-like (SLFL) genes, we reveal that they cluster into 12 types and that the S-RNases and intra-haplotypic SLF and SLFL genes co-evolved. Our data support the notion that citrus have a S locus comprising a S-RNase and several SLFs that fit the non-self-recognition model. We identify a predominant single nucleotide mutation, S
- Published
- 2019
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.