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Combination of Genomics, Transcriptomics Identifies Candidate Loci Related to Cold Tolerance in Dongxiang Wild Rice

Rice, a cold-sensitive crop, is a staple food for more than 50% of the world’s population. Low temperature severely compromises the growth of rice and challenges China’s food safety. Dongxiang wild rice (DXWR) is the most northerly common wild rice in China and has strong cold tolerance, but the gen...

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Autores principales: Wang, Dianwen, Xiao, Yulong, Chen, Hongping, Huang, Cheng, Chen, Ping, Chen, Dazhou, Deng, Wei, Wang, Jilin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9506393/
https://www.ncbi.nlm.nih.gov/pubmed/36145730
http://dx.doi.org/10.3390/plants11182329
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author Wang, Dianwen
Xiao, Yulong
Chen, Hongping
Huang, Cheng
Chen, Ping
Chen, Dazhou
Deng, Wei
Wang, Jilin
author_facet Wang, Dianwen
Xiao, Yulong
Chen, Hongping
Huang, Cheng
Chen, Ping
Chen, Dazhou
Deng, Wei
Wang, Jilin
author_sort Wang, Dianwen
collection PubMed
description Rice, a cold-sensitive crop, is a staple food for more than 50% of the world’s population. Low temperature severely compromises the growth of rice and challenges China’s food safety. Dongxiang wild rice (DXWR) is the most northerly common wild rice in China and has strong cold tolerance, but the genetic basis of its cold tolerance is still unclear. Here, we report quantitative trait loci (QTLs) analysis for seedling cold tolerance (SCT) using a high-density single nucleotide polymorphism linkage map in the backcross recombinant inbred lines that were derived from a cross of DXWR, and an indica cultivar, GZX49. A total of 10 putative QTLs were identified for SCT under 4 °C cold treatment, each explaining 2.0–6.8% of the phenotypic variation in this population. Furthermore, transcriptome sequencing of DXWR seedlings before and after cold treatment was performed, and 898 and 3413 differentially expressed genes (DEGs) relative to 0 h in cold-tolerant for 4 h and 12 h were identified, respectively. Gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) analysis were performed on these DEGs. Using transcriptome data and genetic linkage analysis, combined with qRT-PCR, sequence comparison, and bioinformatics, LOC_Os08g04840 was putatively identified as a candidate gene for the major effect locus qSCT8. These findings provided insights into the genetic basis of SCT for the improvement of cold stress potential in rice breeding programs.
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spelling pubmed-95063932022-09-24 Combination of Genomics, Transcriptomics Identifies Candidate Loci Related to Cold Tolerance in Dongxiang Wild Rice Wang, Dianwen Xiao, Yulong Chen, Hongping Huang, Cheng Chen, Ping Chen, Dazhou Deng, Wei Wang, Jilin Plants (Basel) Article Rice, a cold-sensitive crop, is a staple food for more than 50% of the world’s population. Low temperature severely compromises the growth of rice and challenges China’s food safety. Dongxiang wild rice (DXWR) is the most northerly common wild rice in China and has strong cold tolerance, but the genetic basis of its cold tolerance is still unclear. Here, we report quantitative trait loci (QTLs) analysis for seedling cold tolerance (SCT) using a high-density single nucleotide polymorphism linkage map in the backcross recombinant inbred lines that were derived from a cross of DXWR, and an indica cultivar, GZX49. A total of 10 putative QTLs were identified for SCT under 4 °C cold treatment, each explaining 2.0–6.8% of the phenotypic variation in this population. Furthermore, transcriptome sequencing of DXWR seedlings before and after cold treatment was performed, and 898 and 3413 differentially expressed genes (DEGs) relative to 0 h in cold-tolerant for 4 h and 12 h were identified, respectively. Gene ontology and Kyoto encyclopedia of genes and genomes (KEGG) analysis were performed on these DEGs. Using transcriptome data and genetic linkage analysis, combined with qRT-PCR, sequence comparison, and bioinformatics, LOC_Os08g04840 was putatively identified as a candidate gene for the major effect locus qSCT8. These findings provided insights into the genetic basis of SCT for the improvement of cold stress potential in rice breeding programs. MDPI 2022-09-06 /pmc/articles/PMC9506393/ /pubmed/36145730 http://dx.doi.org/10.3390/plants11182329 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
Wang, Dianwen
Xiao, Yulong
Chen, Hongping
Huang, Cheng
Chen, Ping
Chen, Dazhou
Deng, Wei
Wang, Jilin
Combination of Genomics, Transcriptomics Identifies Candidate Loci Related to Cold Tolerance in Dongxiang Wild Rice
title Combination of Genomics, Transcriptomics Identifies Candidate Loci Related to Cold Tolerance in Dongxiang Wild Rice
title_full Combination of Genomics, Transcriptomics Identifies Candidate Loci Related to Cold Tolerance in Dongxiang Wild Rice
title_fullStr Combination of Genomics, Transcriptomics Identifies Candidate Loci Related to Cold Tolerance in Dongxiang Wild Rice
title_full_unstemmed Combination of Genomics, Transcriptomics Identifies Candidate Loci Related to Cold Tolerance in Dongxiang Wild Rice
title_short Combination of Genomics, Transcriptomics Identifies Candidate Loci Related to Cold Tolerance in Dongxiang Wild Rice
title_sort combination of genomics, transcriptomics identifies candidate loci related to cold tolerance in dongxiang wild rice
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9506393/
https://www.ncbi.nlm.nih.gov/pubmed/36145730
http://dx.doi.org/10.3390/plants11182329
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