Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice
Abstract We report here the genome-wide changes resulting from low N (N-W+), low water (N+W-)) and dual stresses (N-W-) in root and shoot tissues of two rice genotypes, namely, IR 64 (IR64) and Nagina 22 (N22), and their association with the QTLs for nitrogen use efficiency. For all the root paramet...
Main Authors: | , , , , , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
SpringerOpen
2021-06-01
|
Series: | Rice |
Subjects: | |
Online Access: | https://doi.org/10.1186/s12284-021-00487-8 |
id |
doaj-2cdd37477b044c8b8e73ee04d339f4ac |
---|---|
record_format |
Article |
spelling |
doaj-2cdd37477b044c8b8e73ee04d339f4ac2021-06-06T11:47:32ZengSpringerOpenRice1939-84251939-84332021-06-0114112810.1186/s12284-021-00487-8Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in RiceAmitha Mithra Sevanthi0Subodh Kumar Sinha1Sureshkumar V2Manju Rani3Manish Ranjan Saini4Sapna Kumari5Megha Kaushik6Chandra Prakash7Venkatesh K.8G. P. Singh9Trilochan Mohapatra10Pranab Kumar Mandal11ICAR-National Institute for Plant Biotechnology, Pusa CampusICAR-National Institute for Plant Biotechnology, Pusa CampusICAR-National Institute for Plant Biotechnology, Pusa CampusICAR-National Institute for Plant Biotechnology, Pusa CampusICAR-National Institute for Plant Biotechnology, Pusa CampusICAR-National Institute for Plant Biotechnology, Pusa CampusICAR-National Institute for Plant Biotechnology, Pusa CampusICAR-National Institute for Plant Biotechnology, Pusa CampusICAR-Indian Institute of Wheat and Barley ResearchICAR-Indian Institute of Wheat and Barley ResearchICAR-National Institute for Plant Biotechnology, Pusa CampusICAR-National Institute for Plant Biotechnology, Pusa CampusAbstract We report here the genome-wide changes resulting from low N (N-W+), low water (N+W-)) and dual stresses (N-W-) in root and shoot tissues of two rice genotypes, namely, IR 64 (IR64) and Nagina 22 (N22), and their association with the QTLs for nitrogen use efficiency. For all the root parameters, except for root length under N-W+, N22 performed better than IR64. Chlorophyll a, b and carotenoid content were higher in IR64 under N+W+ treatment and N-W+ and N+W- stresses; however, under dual stress, N22 had higher chlorophyll b content. While nitrite reductase, glutamate synthase (GS) and citrate synthase assays showed better specific activity in IR64, glutamate dehydrogenase showed better specific activity in N22 under dual stress (N-W-); the other N and C assimilating enzymes showed similar but low specific activities in both the genotypes. A total of 8926 differentially expressed genes (DEGs) were identified compared to optimal (N+W+) condition from across all treatments. While 1174, 698 and 903 DEGs in IR64 roots and 1197, 187 and 781 in N22 roots were identified, nearly double the number of DEGs were found in the shoot tissues; 3357, 1006 and 4005 in IR64 and 4004, 990 and 2143 in N22, under N-W+, N+W- and N-W- treatments, respectively. IR64 and N22 showed differential expression in 15 and 11 N-transporter genes respectively, under one or more stress treatments, out of which four showed differential expression also in N+W- condition. The negative regulators of N- stress, e.g., NIGT1, OsACTPK1 and OsBT were downregulated in IR64 while in N22, OsBT was not downregulated. Overall, N22 performed better under dual stress conditions owing to its better root architecture, chlorophyll and porphyrin synthesis and oxidative stress management. We identified 12 QTLs for seed and straw N content using 253 recombinant inbred lines derived from IR64 and N22 and a 5K SNP array. The QTL hotspot region on chromosome 6 comprised of 61 genes, of which, five were DEGs encoding for UDP-glucuronosyltransferase, serine threonine kinase, anthocyanidin 3-O-glucosyltransferase, and nitrate induced proteins. The DEGs, QTLs and candidate genes reported in this study can serve as a major resource for both rice improvement and functional biology.https://doi.org/10.1186/s12284-021-00487-8Nitrogen stressDrought stressRiceQTLs under nitrogen stressRNA-seqNitrogen use efficiency |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Amitha Mithra Sevanthi Subodh Kumar Sinha Sureshkumar V Manju Rani Manish Ranjan Saini Sapna Kumari Megha Kaushik Chandra Prakash Venkatesh K. G. P. Singh Trilochan Mohapatra Pranab Kumar Mandal |
spellingShingle |
Amitha Mithra Sevanthi Subodh Kumar Sinha Sureshkumar V Manju Rani Manish Ranjan Saini Sapna Kumari Megha Kaushik Chandra Prakash Venkatesh K. G. P. Singh Trilochan Mohapatra Pranab Kumar Mandal Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice Rice Nitrogen stress Drought stress Rice QTLs under nitrogen stress RNA-seq Nitrogen use efficiency |
author_facet |
Amitha Mithra Sevanthi Subodh Kumar Sinha Sureshkumar V Manju Rani Manish Ranjan Saini Sapna Kumari Megha Kaushik Chandra Prakash Venkatesh K. G. P. Singh Trilochan Mohapatra Pranab Kumar Mandal |
author_sort |
Amitha Mithra Sevanthi |
title |
Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice |
title_short |
Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice |
title_full |
Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice |
title_fullStr |
Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice |
title_full_unstemmed |
Integration of Dual Stress Transcriptomes and Major QTLs from a Pair of Genotypes Contrasting for Drought and Chronic Nitrogen Starvation Identifies Key Stress Responsive Genes in Rice |
title_sort |
integration of dual stress transcriptomes and major qtls from a pair of genotypes contrasting for drought and chronic nitrogen starvation identifies key stress responsive genes in rice |
publisher |
SpringerOpen |
series |
Rice |
issn |
1939-8425 1939-8433 |
publishDate |
2021-06-01 |
description |
Abstract We report here the genome-wide changes resulting from low N (N-W+), low water (N+W-)) and dual stresses (N-W-) in root and shoot tissues of two rice genotypes, namely, IR 64 (IR64) and Nagina 22 (N22), and their association with the QTLs for nitrogen use efficiency. For all the root parameters, except for root length under N-W+, N22 performed better than IR64. Chlorophyll a, b and carotenoid content were higher in IR64 under N+W+ treatment and N-W+ and N+W- stresses; however, under dual stress, N22 had higher chlorophyll b content. While nitrite reductase, glutamate synthase (GS) and citrate synthase assays showed better specific activity in IR64, glutamate dehydrogenase showed better specific activity in N22 under dual stress (N-W-); the other N and C assimilating enzymes showed similar but low specific activities in both the genotypes. A total of 8926 differentially expressed genes (DEGs) were identified compared to optimal (N+W+) condition from across all treatments. While 1174, 698 and 903 DEGs in IR64 roots and 1197, 187 and 781 in N22 roots were identified, nearly double the number of DEGs were found in the shoot tissues; 3357, 1006 and 4005 in IR64 and 4004, 990 and 2143 in N22, under N-W+, N+W- and N-W- treatments, respectively. IR64 and N22 showed differential expression in 15 and 11 N-transporter genes respectively, under one or more stress treatments, out of which four showed differential expression also in N+W- condition. The negative regulators of N- stress, e.g., NIGT1, OsACTPK1 and OsBT were downregulated in IR64 while in N22, OsBT was not downregulated. Overall, N22 performed better under dual stress conditions owing to its better root architecture, chlorophyll and porphyrin synthesis and oxidative stress management. We identified 12 QTLs for seed and straw N content using 253 recombinant inbred lines derived from IR64 and N22 and a 5K SNP array. The QTL hotspot region on chromosome 6 comprised of 61 genes, of which, five were DEGs encoding for UDP-glucuronosyltransferase, serine threonine kinase, anthocyanidin 3-O-glucosyltransferase, and nitrate induced proteins. The DEGs, QTLs and candidate genes reported in this study can serve as a major resource for both rice improvement and functional biology. |
topic |
Nitrogen stress Drought stress Rice QTLs under nitrogen stress RNA-seq Nitrogen use efficiency |
url |
https://doi.org/10.1186/s12284-021-00487-8 |
work_keys_str_mv |
AT amithamithrasevanthi integrationofdualstresstranscriptomesandmajorqtlsfromapairofgenotypescontrastingfordroughtandchronicnitrogenstarvationidentifieskeystressresponsivegenesinrice AT subodhkumarsinha integrationofdualstresstranscriptomesandmajorqtlsfromapairofgenotypescontrastingfordroughtandchronicnitrogenstarvationidentifieskeystressresponsivegenesinrice AT sureshkumarv integrationofdualstresstranscriptomesandmajorqtlsfromapairofgenotypescontrastingfordroughtandchronicnitrogenstarvationidentifieskeystressresponsivegenesinrice AT manjurani integrationofdualstresstranscriptomesandmajorqtlsfromapairofgenotypescontrastingfordroughtandchronicnitrogenstarvationidentifieskeystressresponsivegenesinrice AT manishranjansaini integrationofdualstresstranscriptomesandmajorqtlsfromapairofgenotypescontrastingfordroughtandchronicnitrogenstarvationidentifieskeystressresponsivegenesinrice AT sapnakumari integrationofdualstresstranscriptomesandmajorqtlsfromapairofgenotypescontrastingfordroughtandchronicnitrogenstarvationidentifieskeystressresponsivegenesinrice AT meghakaushik integrationofdualstresstranscriptomesandmajorqtlsfromapairofgenotypescontrastingfordroughtandchronicnitrogenstarvationidentifieskeystressresponsivegenesinrice AT chandraprakash integrationofdualstresstranscriptomesandmajorqtlsfromapairofgenotypescontrastingfordroughtandchronicnitrogenstarvationidentifieskeystressresponsivegenesinrice AT venkateshk integrationofdualstresstranscriptomesandmajorqtlsfromapairofgenotypescontrastingfordroughtandchronicnitrogenstarvationidentifieskeystressresponsivegenesinrice AT gpsingh integrationofdualstresstranscriptomesandmajorqtlsfromapairofgenotypescontrastingfordroughtandchronicnitrogenstarvationidentifieskeystressresponsivegenesinrice AT trilochanmohapatra integrationofdualstresstranscriptomesandmajorqtlsfromapairofgenotypescontrastingfordroughtandchronicnitrogenstarvationidentifieskeystressresponsivegenesinrice AT pranabkumarmandal integrationofdualstresstranscriptomesandmajorqtlsfromapairofgenotypescontrastingfordroughtandchronicnitrogenstarvationidentifieskeystressresponsivegenesinrice |
_version_ |
1721393564745728000 |