Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants

Abstract Phytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than o...

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Autores principales:	Hangxia Jin, Xiaomin Yu, Qinghua Yang, Xujun Fu, Fengjie Yuan
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2021
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/3b81067d26bd4cbfbcd21d1623decbfe
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spelling	oai:doaj.org-article:3b81067d26bd4cbfbcd21d1623decbfe2021-12-02T17:32:59ZTranscriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants10.1038/s41598-021-88055-42045-2322https://doaj.org/article/3b81067d26bd4cbfbcd21d1623decbfe2021-04-01T00:00:00Zhttps://doi.org/10.1038/s41598-021-88055-4https://doaj.org/toc/2045-2322Abstract Phytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than one mutated gene (lpa) have lower PA contents than mutants with a single lpa mutant gene. However, little is known about the link between PA pathway intermediates and downstream regulatory activities following the mutation of these genes in soybean. Consequently, we performed a comparative transcriptome analysis using an advanced generation recombinant inbred line with low PA levels [2mlpa (mips1/ipk1)] and a sibling line with homozygous non-mutant alleles and normal PA contents [2MWT (MIPS1/IPK1)]. An RNA sequencing analysis of five seed developmental stages revealed 7945 differentially expressed genes (DEGs) between the 2mlpa and 2MWT seeds. Moreover, 3316 DEGs were associated with 128 metabolic and signal transduction pathways and 4980 DEGs were annotated with 345 Gene Ontology terms related to biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were among the DEGs in 2mlpa. Of these genes, 36 contributed to PA metabolism, including 22 genes possibly mediating the low-PA phenotype of 2mlpa. The expression of most of the genes associated with photosynthesis (81 of 117) was down-regulated in 2mlpa at the late seed developmental stage. In contrast, the expression of three genes involved in sucrose metabolism was up-regulated at the late seed developmental stage, which might explain the high sucrose content of 2mlpa soybeans. Furthermore, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this study, we detected a low PA content as well as changes to multiple metabolites in the 2mlpa mutant. These results may help elucidate the regulation of metabolic events in 2mlpa. Many genes involved in PA metabolism may contribute to the substantial decrease in the PA content and the moderate accumulation of InsP3–InsP5 in the 2mlpa mutant. The other regulated genes related to photosynthesis, starch and sucrose metabolism, and defense mechanisms may provide additional insights into the nutritional and agronomic performance of 2mlpa seeds.Hangxia JinXiaomin YuQinghua YangXujun FuFengjie YuanNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 11, Iss 1, Pp 1-14 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Hangxia Jin Xiaomin Yu Qinghua Yang Xujun Fu Fengjie Yuan Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants
description	Abstract Phytic acid (PA) is a major antinutrient that cannot be digested by monogastric animals, but it can decrease the bioavailability of micronutrients (e.g., Zn and Fe). Lowering the PA content of crop seeds will lead to enhanced nutritional traits. Low-PA mutant crop lines carrying more than one mutated gene (lpa) have lower PA contents than mutants with a single lpa mutant gene. However, little is known about the link between PA pathway intermediates and downstream regulatory activities following the mutation of these genes in soybean. Consequently, we performed a comparative transcriptome analysis using an advanced generation recombinant inbred line with low PA levels [2mlpa (mips1/ipk1)] and a sibling line with homozygous non-mutant alleles and normal PA contents [2MWT (MIPS1/IPK1)]. An RNA sequencing analysis of five seed developmental stages revealed 7945 differentially expressed genes (DEGs) between the 2mlpa and 2MWT seeds. Moreover, 3316 DEGs were associated with 128 metabolic and signal transduction pathways and 4980 DEGs were annotated with 345 Gene Ontology terms related to biological processes. Genes associated with PA metabolism, photosynthesis, starch and sucrose metabolism, and defense mechanisms were among the DEGs in 2mlpa. Of these genes, 36 contributed to PA metabolism, including 22 genes possibly mediating the low-PA phenotype of 2mlpa. The expression of most of the genes associated with photosynthesis (81 of 117) was down-regulated in 2mlpa at the late seed developmental stage. In contrast, the expression of three genes involved in sucrose metabolism was up-regulated at the late seed developmental stage, which might explain the high sucrose content of 2mlpa soybeans. Furthermore, 604 genes related to defense mechanisms were differentially expressed between 2mlpa and 2MWT. In this study, we detected a low PA content as well as changes to multiple metabolites in the 2mlpa mutant. These results may help elucidate the regulation of metabolic events in 2mlpa. Many genes involved in PA metabolism may contribute to the substantial decrease in the PA content and the moderate accumulation of InsP3–InsP5 in the 2mlpa mutant. The other regulated genes related to photosynthesis, starch and sucrose metabolism, and defense mechanisms may provide additional insights into the nutritional and agronomic performance of 2mlpa seeds.
format	article
author	Hangxia Jin Xiaomin Yu Qinghua Yang Xujun Fu Fengjie Yuan
author_facet	Hangxia Jin Xiaomin Yu Qinghua Yang Xujun Fu Fengjie Yuan
author_sort	Hangxia Jin
title	Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants
title_short	Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants
title_full	Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants
title_fullStr	Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants
title_full_unstemmed	Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants
title_sort	transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants
publisher	Nature Portfolio
publishDate	2021
url	https://doaj.org/article/3b81067d26bd4cbfbcd21d1623decbfe
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Transcriptome analysis identifies differentially expressed genes in the progenies of a cross between two low phytic acid soybean mutants

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