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Novel Insights Into Genetic Responses for Waterlogging Stress in Two Local Wheat Cultivars in Yangtze River Basin

Wheat (Triticum aestivum L.), the most widely cultivated crop, is affected by waterlogging that limited the wheat production. Given the incompleteness of its genome annotation, PacBio SMRT plus Illumina short-read sequencing strategy provided an efficient approach to investigate the genetic regulati...

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Autores principales: Wei, Mingmei, Li, Xiu, Yang, Rui, Li, Liulong, Wang, Zhuangzhi, Wang, Xiaoyan, Sha, Aihua
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8201782/
https://www.ncbi.nlm.nih.gov/pubmed/34135945
http://dx.doi.org/10.3389/fgene.2021.681680
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author Wei, Mingmei
Li, Xiu
Yang, Rui
Li, Liulong
Wang, Zhuangzhi
Wang, Xiaoyan
Sha, Aihua
author_facet Wei, Mingmei
Li, Xiu
Yang, Rui
Li, Liulong
Wang, Zhuangzhi
Wang, Xiaoyan
Sha, Aihua
author_sort Wei, Mingmei
collection PubMed
description Wheat (Triticum aestivum L.), the most widely cultivated crop, is affected by waterlogging that limited the wheat production. Given the incompleteness of its genome annotation, PacBio SMRT plus Illumina short-read sequencing strategy provided an efficient approach to investigate the genetic regulation of waterlogging stress in wheat. A total of 947,505 full-length non-chimetric (FLNC) sequences were obtained with two wheat cultivars (XM55 and YM158) with PacBio sequencing. Of these, 5,309 long-non-coding RNAs, 1,574 fusion genes and 739 transcription factors were identified with the FLNC sequences. These full-length transcripts were derived from 49,368 genes, including 47.28% of the genes annotated in IWGSC RefSeq v1.0 and 40.86% genes encoded two or more isoforms, while 27.31% genes in the genome annotation of IWGSC RefSeq v1.0 were multiple-exon genes encoding two or more isoforms. Meanwhile, the individuals with waterlogging treatments (WL) and control group (CK) were selected for Illumina sequencing. Totally, 6,829 differentially expressed genes (DEGs) were detected from four pairwise comparisons. Notably, 942 DEGs were overlapped in the two comparisons (i.e., XM55-WL vs. YM158-WL and YM158-WL vs. YM158-CK). Undoubtedly, the genes involved in photosynthesis were downregulated after waterlogging treatment in two cultivars. Notably, the genes related to steroid biosynthesis, steroid hormone biosynthesis, and downstream plant hormone signal transduction were significantly upregulated after the waterlogging treatment, and the YM158 variety revealed different genetic regulation patterns compared with XM55. The findings provided valuable insights into unveiling regulation mechanisms of waterlogging stress in wheat at anthesis and contributed to molecular selective breeding of new wheat cultivars in future.
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spelling pubmed-82017822021-06-15 Novel Insights Into Genetic Responses for Waterlogging Stress in Two Local Wheat Cultivars in Yangtze River Basin Wei, Mingmei Li, Xiu Yang, Rui Li, Liulong Wang, Zhuangzhi Wang, Xiaoyan Sha, Aihua Front Genet Genetics Wheat (Triticum aestivum L.), the most widely cultivated crop, is affected by waterlogging that limited the wheat production. Given the incompleteness of its genome annotation, PacBio SMRT plus Illumina short-read sequencing strategy provided an efficient approach to investigate the genetic regulation of waterlogging stress in wheat. A total of 947,505 full-length non-chimetric (FLNC) sequences were obtained with two wheat cultivars (XM55 and YM158) with PacBio sequencing. Of these, 5,309 long-non-coding RNAs, 1,574 fusion genes and 739 transcription factors were identified with the FLNC sequences. These full-length transcripts were derived from 49,368 genes, including 47.28% of the genes annotated in IWGSC RefSeq v1.0 and 40.86% genes encoded two or more isoforms, while 27.31% genes in the genome annotation of IWGSC RefSeq v1.0 were multiple-exon genes encoding two or more isoforms. Meanwhile, the individuals with waterlogging treatments (WL) and control group (CK) were selected for Illumina sequencing. Totally, 6,829 differentially expressed genes (DEGs) were detected from four pairwise comparisons. Notably, 942 DEGs were overlapped in the two comparisons (i.e., XM55-WL vs. YM158-WL and YM158-WL vs. YM158-CK). Undoubtedly, the genes involved in photosynthesis were downregulated after waterlogging treatment in two cultivars. Notably, the genes related to steroid biosynthesis, steroid hormone biosynthesis, and downstream plant hormone signal transduction were significantly upregulated after the waterlogging treatment, and the YM158 variety revealed different genetic regulation patterns compared with XM55. The findings provided valuable insights into unveiling regulation mechanisms of waterlogging stress in wheat at anthesis and contributed to molecular selective breeding of new wheat cultivars in future. Frontiers Media S.A. 2021-05-31 /pmc/articles/PMC8201782/ /pubmed/34135945 http://dx.doi.org/10.3389/fgene.2021.681680 Text en Copyright © 2021 Wei, Li, Yang, Li, Wang, Wang and Sha. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Wei, Mingmei
Li, Xiu
Yang, Rui
Li, Liulong
Wang, Zhuangzhi
Wang, Xiaoyan
Sha, Aihua
Novel Insights Into Genetic Responses for Waterlogging Stress in Two Local Wheat Cultivars in Yangtze River Basin
title Novel Insights Into Genetic Responses for Waterlogging Stress in Two Local Wheat Cultivars in Yangtze River Basin
title_full Novel Insights Into Genetic Responses for Waterlogging Stress in Two Local Wheat Cultivars in Yangtze River Basin
title_fullStr Novel Insights Into Genetic Responses for Waterlogging Stress in Two Local Wheat Cultivars in Yangtze River Basin
title_full_unstemmed Novel Insights Into Genetic Responses for Waterlogging Stress in Two Local Wheat Cultivars in Yangtze River Basin
title_short Novel Insights Into Genetic Responses for Waterlogging Stress in Two Local Wheat Cultivars in Yangtze River Basin
title_sort novel insights into genetic responses for waterlogging stress in two local wheat cultivars in yangtze river basin
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8201782/
https://www.ncbi.nlm.nih.gov/pubmed/34135945
http://dx.doi.org/10.3389/fgene.2021.681680
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