Loci and Natural Alleles for Low-Nitrogen-Induced Growth Response Revealed by the Genome-Wide Association Study Analysis in Rice (Oryza sativa L.)

Nitrogen is essential for plant growth and yield, and it is, therefore, crucial to increase the nitrogen-use efficiency (NUE) of crop plants in fields. In this study, we measured four major low-nitrogen-induced growth response (LNGR) agronomic traits (i.e., plant height, tiller number, chlorophyll c...

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Autores principales:	Yang Lv, Jie Ma, Yueying Wang, Quan Wang, Xueli Lu, Haitao Hu, Qian Qian, Longbiao Guo, Lianguang Shang
Formato:	article
Lenguaje:	EN
Publicado:	Frontiers Media S.A. 2021
Materias:	rice GWAS low-nitrogen-induced growth response haplotype analysis gene mining Plant culture SB1-1110
Acceso en línea:	https://doaj.org/article/dbc3e3f146014115b84e451a86fc6aa7
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spelling	oai:doaj.org-article:dbc3e3f146014115b84e451a86fc6aa72021-11-05T12:11:26ZLoci and Natural Alleles for Low-Nitrogen-Induced Growth Response Revealed by the Genome-Wide Association Study Analysis in Rice (Oryza sativa L.)1664-462X10.3389/fpls.2021.770736https://doaj.org/article/dbc3e3f146014115b84e451a86fc6aa72021-11-01T00:00:00Zhttps://www.frontiersin.org/articles/10.3389/fpls.2021.770736/fullhttps://doaj.org/toc/1664-462XNitrogen is essential for plant growth and yield, and it is, therefore, crucial to increase the nitrogen-use efficiency (NUE) of crop plants in fields. In this study, we measured four major low-nitrogen-induced growth response (LNGR) agronomic traits (i.e., plant height, tiller number, chlorophyll content, and leaf length) of the 225-rice-variety natural population from the Rice 3K Sequencing Project across normal nitrogen (NN) and low nitrogen (LN) environments. The LNGR phenotypic difference between NN and LN levels was used for gene analysis using a genome-wide association study (GWAS) combined with 111,205 single-nucleotide polymorphisms (SNPs) from the available sequenced data from the 3K project. We obtained a total of 56 significantly associated SNPs and 4 candidate genes for 4 LNGR traits. Some loci were located in the candidate regions, such as MYB61, OsOAT, and MOC2. To further study the role of candidate genes, we conducted haplotype analyses to identify the elite germplasms. Moreover, several other plausible candidate genes encoding LN-related or NUE proteins were worthy of mining. Our study provides novel insight into the genetic control of LNGR and further reveals some related novel haplotypes and potential genes with phenotypic variation in rice.Yang LvYang LvJie MaYueying WangQuan WangXueli LuHaitao HuQian QianLongbiao GuoLianguang ShangFrontiers Media S.A.articlericeGWASlow-nitrogen-induced growth responsehaplotype analysisgene miningPlant cultureSB1-1110ENFrontiers in Plant Science, Vol 12 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	rice GWAS low-nitrogen-induced growth response haplotype analysis gene mining Plant culture SB1-1110
spellingShingle	rice GWAS low-nitrogen-induced growth response haplotype analysis gene mining Plant culture SB1-1110 Yang Lv Yang Lv Jie Ma Yueying Wang Quan Wang Xueli Lu Haitao Hu Qian Qian Longbiao Guo Lianguang Shang Loci and Natural Alleles for Low-Nitrogen-Induced Growth Response Revealed by the Genome-Wide Association Study Analysis in Rice (Oryza sativa L.)
description	Nitrogen is essential for plant growth and yield, and it is, therefore, crucial to increase the nitrogen-use efficiency (NUE) of crop plants in fields. In this study, we measured four major low-nitrogen-induced growth response (LNGR) agronomic traits (i.e., plant height, tiller number, chlorophyll content, and leaf length) of the 225-rice-variety natural population from the Rice 3K Sequencing Project across normal nitrogen (NN) and low nitrogen (LN) environments. The LNGR phenotypic difference between NN and LN levels was used for gene analysis using a genome-wide association study (GWAS) combined with 111,205 single-nucleotide polymorphisms (SNPs) from the available sequenced data from the 3K project. We obtained a total of 56 significantly associated SNPs and 4 candidate genes for 4 LNGR traits. Some loci were located in the candidate regions, such as MYB61, OsOAT, and MOC2. To further study the role of candidate genes, we conducted haplotype analyses to identify the elite germplasms. Moreover, several other plausible candidate genes encoding LN-related or NUE proteins were worthy of mining. Our study provides novel insight into the genetic control of LNGR and further reveals some related novel haplotypes and potential genes with phenotypic variation in rice.
format	article
author	Yang Lv Yang Lv Jie Ma Yueying Wang Quan Wang Xueli Lu Haitao Hu Qian Qian Longbiao Guo Lianguang Shang
author_facet	Yang Lv Yang Lv Jie Ma Yueying Wang Quan Wang Xueli Lu Haitao Hu Qian Qian Longbiao Guo Lianguang Shang
author_sort	Yang Lv
title	Loci and Natural Alleles for Low-Nitrogen-Induced Growth Response Revealed by the Genome-Wide Association Study Analysis in Rice (Oryza sativa L.)
title_short	Loci and Natural Alleles for Low-Nitrogen-Induced Growth Response Revealed by the Genome-Wide Association Study Analysis in Rice (Oryza sativa L.)
title_full	Loci and Natural Alleles for Low-Nitrogen-Induced Growth Response Revealed by the Genome-Wide Association Study Analysis in Rice (Oryza sativa L.)
title_fullStr	Loci and Natural Alleles for Low-Nitrogen-Induced Growth Response Revealed by the Genome-Wide Association Study Analysis in Rice (Oryza sativa L.)
title_full_unstemmed	Loci and Natural Alleles for Low-Nitrogen-Induced Growth Response Revealed by the Genome-Wide Association Study Analysis in Rice (Oryza sativa L.)
title_sort	loci and natural alleles for low-nitrogen-induced growth response revealed by the genome-wide association study analysis in rice (oryza sativa l.)
publisher	Frontiers Media S.A.
publishDate	2021
url	https://doaj.org/article/dbc3e3f146014115b84e451a86fc6aa7
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Loci and Natural Alleles for Low-Nitrogen-Induced Growth Response Revealed by the Genome-Wide Association Study Analysis in Rice (Oryza sativa L.)

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