Cargando…

Genomic Characteristics of Elite Maize Inbred Line 18-599 and Its Transcriptional Response to Drought and Low-Temperature Stresses

Elite inbred line 18-599 was developed via triple test cross from introduced hybrid P78599 and used as parents of dozens of maize hybrids adapting to the diverse ecological conditions of the maize ecological region in Southwest China. In this study, its genomic DNA was resequenced and aligned with t...

Descripción completa

Detalles Bibliográficos
Autores principales: Cao, Yang, Qu, Jingtao, Yu, Haoqiang, Yang, Qingqing, Li, Wanchen, Fu, Fengling
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9739999/
https://www.ncbi.nlm.nih.gov/pubmed/36501283
http://dx.doi.org/10.3390/plants11233242
_version_ 1784847949202718720
author Cao, Yang
Qu, Jingtao
Yu, Haoqiang
Yang, Qingqing
Li, Wanchen
Fu, Fengling
author_facet Cao, Yang
Qu, Jingtao
Yu, Haoqiang
Yang, Qingqing
Li, Wanchen
Fu, Fengling
author_sort Cao, Yang
collection PubMed
description Elite inbred line 18-599 was developed via triple test cross from introduced hybrid P78599 and used as parents of dozens of maize hybrids adapting to the diverse ecological conditions of the maize ecological region in Southwest China. In this study, its genomic DNA was resequenced and aligned with the B73 genome sequence to identify single nucleotide polymorphism (SNP), and insertion (In) and deletion (Del) loci. These loci were aligned with those between B73 and 1020 inbred lines in the HapMap database to identify specific variation loci of 18-599. The results showed that there were 930,439 specific SNPs and 358,750 InDels between 18-599 and the 1020 lines. In total, 21,961 of them showed significant impacts on the functions of 12,297 genes, such as frameshift, change of splicing site, stop gain, change of start site, and stop loss. Phylogenetic analysis showed that 18-599 was closely related to inbred lines ZEAxujRAUDIAAPE and 2005-4, but far from some inbred lines directly isolated from P78599. This result indicated that 18-599 not only pyramided the elite genes of P78599, but also acquired genetic divergence during the repetitive backcrosses of triple test cross to confer its elite agronomic characteristics. Subsequently, the RNA of 18-599 was sequenced. The aligned 9713 and 37,528 of the 165,098 unigenes were screened and aligned with annotated transcripts of the B73 genome differentially expressed under drought and low-temperature stress, respectively, and their functions were involved in the responses to these stresses. The quantitative PCR results of fourteen random genes verified the RNA sequencing results. These findings suggest that the transcriptional responses of many resistance-related genes were an important mechanism for 18-599 to adapt to diverse ecological conditions.
format Online
Article
Text
id pubmed-9739999
institution National Center for Biotechnology Information
language English
publishDate 2022
publisher MDPI
record_format MEDLINE/PubMed
spelling pubmed-97399992022-12-11 Genomic Characteristics of Elite Maize Inbred Line 18-599 and Its Transcriptional Response to Drought and Low-Temperature Stresses Cao, Yang Qu, Jingtao Yu, Haoqiang Yang, Qingqing Li, Wanchen Fu, Fengling Plants (Basel) Article Elite inbred line 18-599 was developed via triple test cross from introduced hybrid P78599 and used as parents of dozens of maize hybrids adapting to the diverse ecological conditions of the maize ecological region in Southwest China. In this study, its genomic DNA was resequenced and aligned with the B73 genome sequence to identify single nucleotide polymorphism (SNP), and insertion (In) and deletion (Del) loci. These loci were aligned with those between B73 and 1020 inbred lines in the HapMap database to identify specific variation loci of 18-599. The results showed that there were 930,439 specific SNPs and 358,750 InDels between 18-599 and the 1020 lines. In total, 21,961 of them showed significant impacts on the functions of 12,297 genes, such as frameshift, change of splicing site, stop gain, change of start site, and stop loss. Phylogenetic analysis showed that 18-599 was closely related to inbred lines ZEAxujRAUDIAAPE and 2005-4, but far from some inbred lines directly isolated from P78599. This result indicated that 18-599 not only pyramided the elite genes of P78599, but also acquired genetic divergence during the repetitive backcrosses of triple test cross to confer its elite agronomic characteristics. Subsequently, the RNA of 18-599 was sequenced. The aligned 9713 and 37,528 of the 165,098 unigenes were screened and aligned with annotated transcripts of the B73 genome differentially expressed under drought and low-temperature stress, respectively, and their functions were involved in the responses to these stresses. The quantitative PCR results of fourteen random genes verified the RNA sequencing results. These findings suggest that the transcriptional responses of many resistance-related genes were an important mechanism for 18-599 to adapt to diverse ecological conditions. MDPI 2022-11-25 /pmc/articles/PMC9739999/ /pubmed/36501283 http://dx.doi.org/10.3390/plants11233242 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Cao, Yang
Qu, Jingtao
Yu, Haoqiang
Yang, Qingqing
Li, Wanchen
Fu, Fengling
Genomic Characteristics of Elite Maize Inbred Line 18-599 and Its Transcriptional Response to Drought and Low-Temperature Stresses
title Genomic Characteristics of Elite Maize Inbred Line 18-599 and Its Transcriptional Response to Drought and Low-Temperature Stresses
title_full Genomic Characteristics of Elite Maize Inbred Line 18-599 and Its Transcriptional Response to Drought and Low-Temperature Stresses
title_fullStr Genomic Characteristics of Elite Maize Inbred Line 18-599 and Its Transcriptional Response to Drought and Low-Temperature Stresses
title_full_unstemmed Genomic Characteristics of Elite Maize Inbred Line 18-599 and Its Transcriptional Response to Drought and Low-Temperature Stresses
title_short Genomic Characteristics of Elite Maize Inbred Line 18-599 and Its Transcriptional Response to Drought and Low-Temperature Stresses
title_sort genomic characteristics of elite maize inbred line 18-599 and its transcriptional response to drought and low-temperature stresses
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9739999/
https://www.ncbi.nlm.nih.gov/pubmed/36501283
http://dx.doi.org/10.3390/plants11233242
work_keys_str_mv AT caoyang genomiccharacteristicsofelitemaizeinbredline18599anditstranscriptionalresponsetodroughtandlowtemperaturestresses
AT qujingtao genomiccharacteristicsofelitemaizeinbredline18599anditstranscriptionalresponsetodroughtandlowtemperaturestresses
AT yuhaoqiang genomiccharacteristicsofelitemaizeinbredline18599anditstranscriptionalresponsetodroughtandlowtemperaturestresses
AT yangqingqing genomiccharacteristicsofelitemaizeinbredline18599anditstranscriptionalresponsetodroughtandlowtemperaturestresses
AT liwanchen genomiccharacteristicsofelitemaizeinbredline18599anditstranscriptionalresponsetodroughtandlowtemperaturestresses
AT fufengling genomiccharacteristicsofelitemaizeinbredline18599anditstranscriptionalresponsetodroughtandlowtemperaturestresses