Evolutionary Insights into the Nature of Plant Domestication

Current Biology, Journal Year: 2019, Volume and Issue: 29(14), P. R705 - R714

Published: July 1, 2019

Domestication is a co-evolutionary process that occurs when wild plants are brought into cultivation by humans, leading to origin of new species and/or differentiated populations critical for human survival. Darwin used domesticated as early models evolution, highlighting their variation and the key role selection in differentiation. Over last two decades, growing synthesis plant genetics, genomics, archaeobotany has led challenges old orthodoxies advent fresh perspectives on how crop domestication diversification proceed. I discuss four insights — general protracted process, unconscious (natural) plays prominent role, interspecific hybridization may be an important mechanism range expansion, similar genes across multiple underlies parallel/convergent phenotypic evolution between taxa. Insights evolutionary can help us developing varieties (and possibly even species) deal with current future environmental sustainable manner.

Language: Английский

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Modification of the PthA4 effector binding elements in Type I CsLOB1 promoter using Cas9/sgRNA to produce transgenic Duncan grapefruit alleviating XccΔpthA4:dCsLOB1.3 infection

Plant Biotechnology Journal, Journal Year: 2015, Volume and Issue: 14(5), P. 1291 - 1301

Published: Nov. 2, 2015

Citrus canker caused by Xanthomonas citri subspecies (Xcc) is a severe disease for most commercial citrus cultivars and responsible significant economic losses worldwide. Generating canker-resistant varieties will provide an efficient sustainable solution to control canker. Here, we report our progress in generating grapefruit modifying the PthA4 effector binding elements (EBEs) CsLOB1 Promoter (EBEPthA4 -CsLOBP) of (Citrus sinensis Lateral Organ Boundaries) gene. susceptibility gene induced pathogenicity factor PthA4, which binds EBEPthA4 -CsLOBP induce expression. There are two alleles, Type I II, Duncan grapefruit. binary vector was designed disrupt EBEs (TI CsLOBP) via epicotyl transformation Four transgenic plants with targeted modification -T1 CsLOBP were successfully created. As promoter, mutation rate 15.63% (#D13), 14.29% (#D17), 54.54% (#D18) 81.25% (#D22). In presence wild-type Xcc, developed symptoms similarly as wild type. An artificially dTALE dCsLOB1.3, specifically recognizes CsLOBP, but not mutated or II infect transformants. Consequently, #D18 had weakened #D22 no visible XccΔpthA4:dCsLOB1.3. Our data suggest that activation single allele sufficient disease, promoters both alleles probably required generate plants. This work lays groundwork Cas9/sgRNA future.

Language: Английский

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Huanglongbing impairs the rhizosphere-to-rhizoplane enrichment process of the citrus root-associated microbiome

Microbiome, Journal Year: 2017, Volume and Issue: 5(1)

Published: Aug. 10, 2017

Roots are the primary site for plant-microbe interactions. Among three root-associated layers (i.e., rhizosphere, rhizoplane, and endorhiza), rhizoplane is a key component serving critical gating role that controls microbial entry into plant roots. The communities colonizing believed to be gradually enriched from bulk soil inoculum. However, it unknown how this enrichment process, particularly rhizosphere step, affected by biotic stresses, such as disease. In study, we address question using citrus microbiome model. We identified rhizosphere-to-rhizoplane-enriched taxonomic functional properties of determined they were Huanglongbing (HLB), severe systemic disease caused Candidatus Liberibacter asiaticus, metagenomic metatranscriptomic approaches. Multiple rhizoplane-enriched genera identified, with Bradyrhizobium Burkholderia being most dominant. Plant-derived carbon sources an important driving force process. attributes, motility, chemotaxis, secretion systems, lipopolysaccharide (LPS) synthesis, demonstrated more active microbe-plant interactions on than rhizosphere. observed HLB impaired rhizosphere-to-rhizoplane process in ways: (1) decreasing relative abundance genera; (2) reducing and/or expression activity attributes involved interactions; (3) recruiting features autotrophic life cycle adaptation, fixation nitrogen nitrification microbiome. Finally, our data showed inoculation strains isolated healthy could trigger genes induced resistance inoculated plants. causes decreased properties, collectively resulting host-microbiome Manipulation microbiome, instance, inoculating roots beneficial strains, has potential promote health. Our results provide novel insights understanding contributions community hosts.

Language: Английский

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GREENC: a Wiki-based database of plant lncRNAs

Nucleic Acids Research, Journal Year: 2015, Volume and Issue: 44(D1), P. D1161 - D1166

Published: Nov. 17, 2015

Long non-coding RNAs (lncRNAs) are functional non-translated molecules greater than 200 nt. Their roles diverse and they usually involved in transcriptional regulation. LncRNAs still remain largely uninvestigated plants with few exceptions. Experimentally validated plant lncRNAs have been shown to regulate important agronomic traits such as phosphate starvation response, flowering time interaction symbiotic organisms, making them of great interest biology breeding. There is a lack most sequenced species, those where annotated, different methods used, so the less useful comparisons within between species. We developed pipeline annotate applied it 37 species six algae, resulting annotation more 120 000 lncRNAs. To facilitate study for research community, information gathered organised Green Non-Coding Database (GreeNC, http://greenc.sciencedesigners.com/).

Language: Английский

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Progress, challenges and the future of crop genomes

Current Opinion in Plant Biology, Journal Year: 2015, Volume and Issue: 24, P. 71 - 81

Published: Feb. 19, 2015

Language: Английский

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Key determinants of citrus fruit quality: Metabolites and main changes during maturation

Scientia Horticulturae, Journal Year: 2018, Volume and Issue: 233, P. 238 - 248

Published: Feb. 3, 2018

Language: Английский

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Meta‐analysis of chromosome‐scale crossover rate variation in eukaryotes and its significance to evolutionary genomics

Molecular Ecology, Journal Year: 2018, Volume and Issue: 27(11), P. 2477 - 2497

Published: April 20, 2018

Abstract Understanding the distribution of crossovers along chromosomes is crucial to evolutionary genomics because crossover rate determines how strongly a genome region influenced by natural selection on linked sites. Nevertheless, generalities in chromosome‐scale have not been investigated formally. We fill this gap synthesizing joint information genetic and physical maps across 62 animal, plant fungal species. Our quantitative analysis reveals strong taxonomically widespread reduction centre relative their peripheries. demonstrate that pattern poorly explained position centromere, but find magnitude chromosome centres increases with length. That is, long often display dramatically low centre, whereas short exhibit relatively homogeneous rate. This observation compatible model which initiated from tips, an idea preliminary support mechanistic investigations meiotic recombination. Consequently, we show organisms achieve higher genome‐wide evolving smaller chromosomes. Summarizing theory providing empirical examples, finally highlight systematic heterogeneity generates predictable broad‐scale trends diversity population differentiation modifying impact among regions within genome. conclude emphasizing should urgently be incorporated into analytical tools genomics, interpretation resulting patterns.

Language: Английский

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Genome of Wild Mandarin and Domestication History of Mandarin

Molecular Plant, Journal Year: 2018, Volume and Issue: 11(8), P. 1024 - 1037

Published: June 6, 2018

Language: Английский

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Phylogenetic origin of limes and lemons revealed by cytoplasmic and nuclear markers

Annals of Botany, Journal Year: 2016, Volume and Issue: 117(4), P. 565 - 583

Published: March 4, 2016

The origin of limes and lemons has been a source conflicting taxonomic opinions. Biochemical studies, numerical taxonomy recent molecular studies suggested that cultivated Citrus species result from interspecific hybridization between four basic taxa (C. reticulata,C. maxima,C. medica C. micrantha). However, the most remains controversial or unknown. aim this study was to perform extended analyses diversity, genetic structure lemons.The based on 133 accessions. It combined maternal phylogeny mitochondrial chloroplastic markers, nuclear analysis evaluation ploidy level use 123 including 73 diagnostic single nucleotide polymorphism (SNP) indel markers.The lime lemon horticultural group appears be highly polymorphic, with diploid, triploid tetraploid varieties, many independent reticulation events which defined sub-groups. Maternal involves cytoplasmic types out six encountered in genus. All accessions were heterozygous, admixture two, three even ancestral genomes. Molecular varieties same sub-group very low.Citrus contributed all direct male parent for main sub-groups combination micrantha close papeda (for aurata, excelsa, macrophylla aurantifolia--'Mexican' Tanaka's taxa), reticulata(for limonia, karna jambhiri taxa, popular citrus rootstocks such as 'Rangpur' lime, 'Volkamer' 'Rough' lemons), aurantium limetta limon--yellow types--varieties taxa) maxima × reticulate hybrid limettioides--'Palestine sweet' types--and meyeri). Among limes, latifolia ('Tahiti' 'Persian' types) fertilization haploid ovule limon by diploid gamete aurantifolia, while aurantifolia ('Tanepao' 'Madagascar' lemon) probably an backcross (a fertilized medica). As vegetatively propagated (apomixis, practices) intra-sub-group phenotypic diversity results asexual variations.

Language: Английский

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Characterization and Metabolic Diversity of Flavonoids in Citrus Species

Scientific Reports, Journal Year: 2017, Volume and Issue: 7(1)

Published: Aug. 30, 2017

Flavonoids are widely distributed in plants and play important roles many biological processes. Citrus fruits rich dietary sources of flavonoids. However, there have been very few reports about the comprehensive metabolic profile natural diversity flavonoids different tissues various cultivars. In this study, based on 7416 signals detected with non-targeted metabolomics approach, Principal Component Analysis revealed flavedo has largest differences from other metabolite levels; as 198 flavonoid were then 62 germplasms 5 species mainly cultivated worldwide, while 117 identified, including 39 polymethoxylated (PMFs), 7 flavones, 10 C-O-glycosylflavonoids, 44 O-glycosylflavonoids, C-glycosylflavonoids newly annotated O-glycosylpolymethoxylated Tissue-specific accumulations observed: O-glycosylated abundant all fruit tissues, PMFs accumulated preferentially flavedo. Among species, mandarins had highest levels flavonoids, followed by sweet oranges. Based profiles, could be clearly grouped into five distinct clusters via hierarchical clustering analysis, which perfectly matched their oranges closely being further away three species.

Language: Английский

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