Regional differences in the abiotic environment contribute to genomic divergence within a wild tomato species

Gibson, Matthew J. S.; Moyle, Leonie C.

doi:10.1111/mec.15477

Cited by 36 publications

(35 citation statements)

References 83 publications

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“…Interestingly, although The Ka/Ks ratio of most duplicated gene pairs were <1 in wild tomato, there were still a considerable number of duplicated genes Ka/Ks > 1, and some of them were from tandem repeats, implying that they were subject to environmental positive selection and still in a rapid evolutionary stage. We speculate that the more complex survival environment has forced wild tomatoes to retain the viability of some adaptive genes (Pailles et al, 2017;Gibson and Moyle, 2020) The evolution of genes in the same family often reflects certain key events in the process of species differentiation and maps the source of conservation and differential functions of its family members. Multispecies orthologous genes showed the complete evolutionary trajectory of the SRO family in tomato.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Evolutionary Analysis of the SRO Gene Family in Tomato

Wang

et al. 2021

Front. Genet.

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SRO (SIMILAR TO RCD ONE) is a family of plant-specific small molecule proteins that play an important role in plant growth and development and environmental responses. However, SROs still lack systematic characterization in tomato. Based on bioinformatics methods, SRO family genes were identified and characterized from cultivated tomatoes and several wild tomatoes. qRT-PCR was used to study the expression of SRO gene in cultivated tomatoes. Phylogenetic and evolutionary analyses showed that SRO genes in angiosperms share a common ancestor and that the number of SRO family members changed as plants diverged and evolved. Cultivated tomato had six SRO members, five of which still shared some degree of identity with the ancestral SRO genes. Genetic structure and physicochemical properties showed that tomato SRO genes were highly conserved with chromosomal distribution. They could be divided into three groups based on exon-intron structure, and cultivated tomato contained only two of these subclades. A number of hormonal, light and abiotic stress-responsive cis-regulatory elements were identified from the promoter of the tomato SRO gene, and they also interacted with a variety of stress-responsive proteins and microRNAs. RNA-seq analysis showed that SRO genes were widely expressed in different tissues and developmental stages of tomato, with significant tissue-specific features. Expression analysis also showed that SRO genes respond significantly to high temperature and salt stress and mediate the tomato hormone regulatory network. These results provide a theoretical basis for further investigation of the functional expression of tomato SRO genes and provide potential genetic resources for tomato resistance breeding.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Evolutionary Analysis of the SRO Gene Family in Tomato

Wang

et al. 2021

Front. Genet.

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“…First, although we included a large number of environmental variables in our study, many other unmeasured ecological forces may also play a role. Second, other evolutionary forces that maintain local genetic diversity, such as balancing selection, may weaken the signal of locusenvironment associations [46]. Third, the multivariate environmental association approach models only linear associations, so nonlinear statistical relationships will not be captured.…”

Section: Evidence For Local Adaptationmentioning

confidence: 99%

Population transcriptomic sequencing reveals allopatric divergence and local adaptation in Pseudotaxus chienii (Taxaceae)

Liu

Wang

et al. 2021

BMC Genomics

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Background Elucidating the effects of geography and selection on genetic variation is critical for understanding the relative importance of adaptation in driving differentiation and identifying the environmental factors underlying its occurrence. Adaptive genetic variation is common in tree species, especially widely distributed long-lived species. Pseudotaxus chienii can occupy diverse habitats with environmental heterogeneity and thus provides an ideal material for investigating the process of population adaptive evolution. Here, we characterize genetic and expression variation patterns and investigate adaptive genetic variation in P. chienii populations. Results We generated population transcriptome data and identified 13,545 single nucleotide polymorphisms (SNPs) in 5037 unigenes across 108 individuals from 10 populations. We observed lower nucleotide diversity (π = 0.000701) among the 10 populations than observed in other gymnosperms. Significant negative correlations between expression diversity and nucleotide diversity in eight populations suggest that when the species adapts to the surrounding environment, gene expression and nucleotide diversity have a reciprocal relationship. Genetic structure analyses indicated that each distribution region contains a distinct genetic group, with high genetic differentiation among them due to geographical isolation and local adaptation. We used FST outlier, redundancy analysis, and latent factor mixed model methods to detect molecular signatures of local adaptation. We identified 244 associations between 164 outlier SNPs and 17 environmental variables. The mean temperature of the coldest quarter, soil Fe and Cu contents, precipitation of the driest month, and altitude were identified as the most important determinants of adaptive genetic variation. Most candidate unigenes with outlier signatures were related to abiotic and biotic stress responses, and the monoterpenoid biosynthesis and ubiquitin-mediated proteolysis KEGG pathways were significantly enriched in certain populations and deserve further attention in other long-lived trees. Conclusions Despite the strong population structure in P. chienii, genomic data revealed signatures of divergent selection associated with environmental variables. Our research provides SNPs, candidate unigenes, and biological pathways related to environmental variables to facilitate elucidation of the genetic variation in P. chienii in relation to environmental adaptation. Our study provides a promising tool for population genomic analyses and insights into the molecular basis of local adaptation.

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“…Drought tolerance pathways [27] and QTL are widely studied in common bean [28]. Various candidate genes have been identified [29], most with moderate effects as expected for a complex adaptive trait [26].…”

Section: Introductionmentioning

confidence: 99%

Allelic Diversity at Abiotic Stress Responsive Genes in Relationship to Ecological Drought Indices for Cultivated Tepary Bean, Phaseolus acutifolius A. Gray, and Its Wild Relatives

Buitrago-Bitar

Cortés

López-Hernández

et al. 2021

Genes

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Some of the major impacts of climate change are expected in regions where drought stress is already an issue. Grain legumes are generally drought susceptible. However, tepary bean and its wild relatives within Phaseolus acutifolius or P. parvifolius are from arid areas between Mexico and the United States. Therefore, we hypothesize that these bean accessions have diversity signals indicative of adaptation to drought at key candidate genes such as: Asr2, Dreb2B, and ERECTA. By sequencing alleles of these genes and comparing to estimates of drought tolerance indices from climate data for the collection site of geo-referenced, tepary bean accessions, we determined the genotype x environmental association (GEA) of each gene. Diversity analysis found that cultivated and wild P. acutifolius were intermingled with var. tenuifolius and P. parvifolius, signifying that allele diversity was ample in the wild and cultivated clade over a broad sense (sensu lato) evaluation. Genes Dreb2B and ERECTA harbored signatures of directional selection, represented by six SNPs correlated with the environmental drought indices. This suggests that wild tepary bean is a reservoir of novel alleles at genes for drought tolerance, as expected for a species that originated in arid environments. Our study corroborated that candidate gene approach was effective for marker validation across a broad genetic base of wild tepary accessions.

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Regional differences in the abiotic environment contribute to genomic divergence within a wild tomato species

Abstract: This is the author manuscript accepted for publication and has undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as

Cited by 36 publications

References 83 publications

Genome-Wide Identification and Evolutionary Analysis of the SRO Gene Family in Tomato

Genome-Wide Identification and Evolutionary Analysis of the SRO Gene Family in Tomato

Population transcriptomic sequencing reveals allopatric divergence and local adaptation in Pseudotaxus chienii (Taxaceae)

Allelic Diversity at Abiotic Stress Responsive Genes in Relationship to Ecological Drought Indices for Cultivated Tepary Bean, Phaseolus acutifolius A. Gray, and Its Wild Relatives

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