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Tandem duplicate expression patterns are conserved between maize haplotypes of the α‐zein gene family

Tandem duplication gives rise to copy number variation and subsequent functional novelty among genes as well as diversity between individuals in a species. Functional novelty can result from either divergence in coding sequence or divergence in patterns of gene transcriptional regulation. Here, we i...

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Detalles Bibliográficos
Autores principales: Hurst, Preston, Schnable, James C., Holding, David R.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: John Wiley and Sons Inc. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8438537/
https://www.ncbi.nlm.nih.gov/pubmed/34541444
http://dx.doi.org/10.1002/pld3.346
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author Hurst, Preston
Schnable, James C.
Holding, David R.
author_facet Hurst, Preston
Schnable, James C.
Holding, David R.
author_sort Hurst, Preston
collection PubMed
description Tandem duplication gives rise to copy number variation and subsequent functional novelty among genes as well as diversity between individuals in a species. Functional novelty can result from either divergence in coding sequence or divergence in patterns of gene transcriptional regulation. Here, we investigate conservation and divergence of both gene sequence and gene regulation between the copies of the α‐zein gene family in maize inbreds B73 and W22. We used RNA‐seq data generated from developing, self‐pollinated kernels at three developmental stages timed to coincide with early and peak zein expression. The reference genome annotations for B73 and W22 were modified to ensure accurate inclusion of their respective α‐zein gene models to accurately assess copy‐specific expression. Expression analysis indicated that although the total expression of α‐zeins is higher in W22, the pattern of expression in both lines is conserved. Additional analysis of publicly available RNA‐seq data from a diverse population of maize inbreds also demonstrates variation in absolute expression, but conservation of expression patterns across a wide range of maize genotypes and α‐zein haplotypes.
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spelling pubmed-84385372021-09-17 Tandem duplicate expression patterns are conserved between maize haplotypes of the α‐zein gene family Hurst, Preston Schnable, James C. Holding, David R. Plant Direct Original Research Tandem duplication gives rise to copy number variation and subsequent functional novelty among genes as well as diversity between individuals in a species. Functional novelty can result from either divergence in coding sequence or divergence in patterns of gene transcriptional regulation. Here, we investigate conservation and divergence of both gene sequence and gene regulation between the copies of the α‐zein gene family in maize inbreds B73 and W22. We used RNA‐seq data generated from developing, self‐pollinated kernels at three developmental stages timed to coincide with early and peak zein expression. The reference genome annotations for B73 and W22 were modified to ensure accurate inclusion of their respective α‐zein gene models to accurately assess copy‐specific expression. Expression analysis indicated that although the total expression of α‐zeins is higher in W22, the pattern of expression in both lines is conserved. Additional analysis of publicly available RNA‐seq data from a diverse population of maize inbreds also demonstrates variation in absolute expression, but conservation of expression patterns across a wide range of maize genotypes and α‐zein haplotypes. John Wiley and Sons Inc. 2021-09-14 /pmc/articles/PMC8438537/ /pubmed/34541444 http://dx.doi.org/10.1002/pld3.346 Text en © 2021 The Authors. Plant Direct published by American Society of Plant Biologists and the Society for Experimental Biology and John Wiley & Sons Ltd. https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ (https://creativecommons.org/licenses/by-nc-nd/4.0/) License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.
spellingShingle Original Research
Hurst, Preston
Schnable, James C.
Holding, David R.
Tandem duplicate expression patterns are conserved between maize haplotypes of the α‐zein gene family
title Tandem duplicate expression patterns are conserved between maize haplotypes of the α‐zein gene family
title_full Tandem duplicate expression patterns are conserved between maize haplotypes of the α‐zein gene family
title_fullStr Tandem duplicate expression patterns are conserved between maize haplotypes of the α‐zein gene family
title_full_unstemmed Tandem duplicate expression patterns are conserved between maize haplotypes of the α‐zein gene family
title_short Tandem duplicate expression patterns are conserved between maize haplotypes of the α‐zein gene family
title_sort tandem duplicate expression patterns are conserved between maize haplotypes of the α‐zein gene family
topic Original Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8438537/
https://www.ncbi.nlm.nih.gov/pubmed/34541444
http://dx.doi.org/10.1002/pld3.346
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