Dataset Information

The Genetic Regulation of Alternative Splicing in Populus deltoides.

ABSTRACT: Alternative splicing (AS) is a mechanism of regulation of the proteome via enabling the production of multiple mRNAs from a single gene. To date, the dynamics of AS and its effects on the protein sequences of individuals in a large and genetically unrelated population of trees have not been investigated. Here we describe the diversity of AS events within a previously genotyped population of 268 individuals of Populus deltoides and their putative downstream functional effects. Using a robust bioinformatics pipeline, the AS events and resulting transcript isoforms were discovered and quantified for each individual in the population. Analysis of the AS revealed that, as expected, most AS isoforms are conserved. However, we also identified a substantial collection of new, unannotated splice junctions and transcript isoforms. Heritability estimates for the expression of transcript isoforms showed that approximately half of the isoforms are heritable. The genetic regulators of these AS isoforms and splice junction usage were then identified using a genome-wide association analysis. The expression of AS isoforms was predominately cis regulated while splice junction usage was generally regulated in trans. Additionally, we identified 696 genes encoding alternatively spliced isoforms that changed putative protein domains relative to the longest protein coding isoform of the gene, and 859 genes exhibiting this same phenomenon relative to the most highly expressed isoform. Finally, we found that 748 genes gained or lost micro-RNA binding sites relative to the longest protein coding isoform of a given gene, while 940 gained or lost micro-RNA binding sites relative to the most highly expressed isoform. These results indicate that a significant fraction of AS events are genetically regulated and that this isoform usage can result in protein domain architecture changes.

SUBMITTER: Noble JD

PROVIDER: S-EPMC7291814 | biostudies-literature | 2020

REPOSITORIES: biostudies-literature

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The Genetic Regulation of Alternative Splicing in <i>Populus deltoides</i>.

Noble Jerald D JD Balmant Kelly M KM Dervinis Christopher C de Los Campos Gustavo G Resende Márcio F R MFR Kirst Matias M Barbazuk William Brad WB

Frontiers in plant science 20200605

Alternative splicing (AS) is a mechanism of regulation of the proteome via enabling the production of multiple mRNAs from a single gene. To date, the dynamics of AS and its effects on the protein sequences of individuals in a large and genetically unrelated population of trees have not been investigated. Here we describe the diversity of AS events within a previously genotyped population of 268 individuals of <i>Populus deltoides</i> and their putative downstream functional effects. Using a robu ...[more]

PMID: 32582229

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Project description:BACKGROUND:Black cottonwood (Populus deltoides) is one of the keystone forest tree species, and has become the main breeding parents in poplar hybrid breeding. However, the genetic diversity and population structure of the introduced resources are not fully understood. RESULTS:In the present study, five loci containing null alleles were excluded and 15 pairs of SSR (simple sequence repeat) primers were used to analyze the genetic diversity and population structure of 384 individuals from six provenances (Missouri, Iowa, Washington, Louisiana, and Tennessee (USA), and Quebec in Canada) of P. deltoides. Ultimately, 108 alleles (Na) were detected; the expected heterozygosity (He) per locus ranged from 0.070 to 0.905, and the average polymorphic information content (PIC) was 0.535. The provenance 'Was' had a relatively low genetic diversity, while 'Que', 'Lou', and 'Ten' provenances had high genetic diversity, with Shannon's information index (I) above 1.0. The mean coefficient of genetic differentiation (Fst) and gene flow (Nm) were 0.129 and 1.931, respectively. Analysis of molecular variance (AMOVA) showed that 84.88% of the genetic variation originated from individuals. Based on principal coordinate analysis (PCoA) and STRUCTURE cluster analysis, individuals distributed in the Mississippi River Basin were roughly classified as one group, while those distributed in the St. Lawrence River Basin and Columbia River Basin were classified as another group. The cluster analysis based on the population level showed that provenance 'Iow' had a small gene flow and high degree of genetic differentiation compared with the other provenances, and was classified into one group. There was a significant relationship between genetic distance and geographical distance. CONCLUSIONS:P. deltoides resources have high genetic diversity and there is a moderate level of genetic differentiation among provenances. Geographical isolation and natural conditions may be the main factors causing genetic differences among individuals. Individuals reflecting population genetic information can be selected to build a core germplasm bank. Meanwhile, the results could provide theoretical support for the scientific management and efficient utilization of P. deltoides genetic resources, and promote the development of molecular marker-assisted breeding of poplar.

Project description:BackgroundPoplar trees provide a large amount of wood material, but many parts of the world are arid or semi-arid areas because of insufficient annual precipitation, which seriously affects the growth of poplar trees. Populus simonii 'Tongliao1' shows strong tolerance to stress environments, and Populus deltoides 'Danhong' shows a stronger growth rate in a suitable environment. To identify drought tolerance-related QTLs and genes, an F1 population derived from the cross between the 'Danhong' and 'Tongliao 1' Populus was assessed under drought stress.ResultsWe measured drought-related traits such as the relative height growth, relative diameter growth, leaf senescence number, specific leaf area, and leaf relative water content in the population under control and drought environments. The results showed that drought stress reduced the plant height relative growth, ground diameter relative growth, specific leaf area and leaf relative water content and increased the number of leaf drops. A total of 208 QTLs were identified by QTL mapping analysis, and they consisted of 92, 63 and 53 QTLs under control, drought stress treatment and drought index conditions, respectively. A molecular identification marker for drought tolerance, np2841, which was associated with a QTL (qDLRWC-LG10-1) for relative leaf water content, was initially developed. We mined 187 candidate genes for QTL regions of five traits under a drought environment. The reference genome annotation for Populus trichocarpa and a homologous gene analysis of Arabidopsis thaliana identified two candidate genes, Potri.003G171300 and Potri.012G123900, with significant functions in response to drought stress. We identified five key regulatory genes (Potri.006G273500, Potri.007G111500, Potri.007G111600, Potri.007G111700, and Potri.007G111800) related to drought tolerance through the poplar coexpression network.ConclusionIn this study, our results indicate that the QTLs can effectively enhance the drought tolerance of poplar. It is a step closer towards unravelling the genetic basis of poplar drought tolerance-related traits, and to providing validated candidate genes and molecular markers for future genetic improvement.

Dataset Information

The Genetic Regulation of Alternative Splicing in Populus deltoides.

Publications

The Genetic Regulation of Alternative Splicing in <i>Populus deltoides</i>.

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