Identification of candidate genes related to soluble sugar contents in soybean seeds using multiple genetic analyses
Soluble sugar content in seeds is an important quality trait of soybean. In this study, 57 quantitative trait loci (QTLs) related to soluble sugar contents in soybean seeds were collected from databases and published papers. After meta-overview-collinearity integrated analysis to refine QTL interval...
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| Format: | Article |
| Language: | English |
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Elsevier
2022-07-01
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| Series: | Journal of Integrative Agriculture |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311921636535 |
| _version_ | 1818536031763300352 |
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| author | Wen-jing PAN Xue HAN Shi-yu HUANG Jing-yao YU Ying ZHAO Ke-xin QU Ze-xin ZHANG Zhen-gong YIN Hui-dong QI Guo-long YU Yong ZHANG Da-wei XIN Rong-sheng ZHU Chun-yan LIU Xiao-xia WU Hong-wei JIANG Zhen-bang HU Yu-hu ZUO Qing-shan CHEN Zhao-ming QI |
| author_facet | Wen-jing PAN Xue HAN Shi-yu HUANG Jing-yao YU Ying ZHAO Ke-xin QU Ze-xin ZHANG Zhen-gong YIN Hui-dong QI Guo-long YU Yong ZHANG Da-wei XIN Rong-sheng ZHU Chun-yan LIU Xiao-xia WU Hong-wei JIANG Zhen-bang HU Yu-hu ZUO Qing-shan CHEN Zhao-ming QI |
| author_sort | Wen-jing PAN |
| collection | DOAJ |
| description | Soluble sugar content in seeds is an important quality trait of soybean. In this study, 57 quantitative trait loci (QTLs) related to soluble sugar contents in soybean seeds were collected from databases and published papers. After meta-overview-collinearity integrated analysis to refine QTL intervals, eight consensus QTLs were identified. To further verify the consensus QTLs, a population of chromosome segment substitution lines (CSSLs) was analyzed. Two lines containing fragments covering the regions of consensus QTLs and the recurrent parent were selected: one line showed high soluble sugar contents associated with a consensus QTL fragment, and the other line showed low soluble sugar contents. Transcriptome sequencing was conducted for these two lines at the early, middle, and late stages of seed development, which identified 158, 109 and 329 differentially expressed genes, respectively. Based on the analyses of re-sequencing data of the CSSLs and the consensus QTL region, three candidate genes (Glyma.19G146800, Glyma.19G122500, and Glyma.19G128500) were identified in the genetic fragments introduced from wild soybean. Sequence comparisons between the two CSSL parents SN14 and ZYD00006 revealed a single nucleotide polymorphism (SNP) mutation in the coding sequence of Glyma.19G122500, causing a non-synonymous mutation in the amino acid sequence that affected the predicted protein structure. A Kompetitive allele-specific PCR (KASP) marker was developed based on this SNP and used to evaluate the CSSLs. These results lay the foundation for further research to identify genes related to soluble sugar contents in soybean seeds and for future soybean breeding. |
| first_indexed | 2024-12-11T18:32:45Z |
| format | Article |
| id | doaj.art-ab3b0fb710f149789cd350169adeef3f |
| institution | Directory Open Access Journal |
| issn | 2095-3119 |
| language | English |
| last_indexed | 2024-12-11T18:32:45Z |
| publishDate | 2022-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj.art-ab3b0fb710f149789cd350169adeef3f2022-12-22T00:54:52ZengElsevierJournal of Integrative Agriculture2095-31192022-07-0121718861902Identification of candidate genes related to soluble sugar contents in soybean seeds using multiple genetic analysesWen-jing PAN0Xue HAN1Shi-yu HUANG2Jing-yao YU3Ying ZHAO4Ke-xin QU5Ze-xin ZHANG6Zhen-gong YIN7Hui-dong QI8Guo-long YU9Yong ZHANG10Da-wei XIN11Rong-sheng ZHU12Chun-yan LIU13Xiao-xia WU14Hong-wei JIANG15Zhen-bang HU16Yu-hu ZUO17Qing-shan CHEN18Zhao-ming QI19College of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.ChinaHeilongjiang Bayi Agricultural University, Daqing 163000, P.R.ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.ChinaKeshan Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar 161300, P.R.ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.ChinaCollege of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.ChinaHeilongjiang Bayi Agricultural University, Daqing 163000, P.R.China; Correspondence ZUO Yu-huCollege of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.China; Correspondence CHEN Qing-shan, Tel: +86-451-55191945College of Agriculture, Northeast Agricultural University, Harbin 150030, P.R.China; Correspondence QI Zhao-ming, Tel: +86-451-55191945Soluble sugar content in seeds is an important quality trait of soybean. In this study, 57 quantitative trait loci (QTLs) related to soluble sugar contents in soybean seeds were collected from databases and published papers. After meta-overview-collinearity integrated analysis to refine QTL intervals, eight consensus QTLs were identified. To further verify the consensus QTLs, a population of chromosome segment substitution lines (CSSLs) was analyzed. Two lines containing fragments covering the regions of consensus QTLs and the recurrent parent were selected: one line showed high soluble sugar contents associated with a consensus QTL fragment, and the other line showed low soluble sugar contents. Transcriptome sequencing was conducted for these two lines at the early, middle, and late stages of seed development, which identified 158, 109 and 329 differentially expressed genes, respectively. Based on the analyses of re-sequencing data of the CSSLs and the consensus QTL region, three candidate genes (Glyma.19G146800, Glyma.19G122500, and Glyma.19G128500) were identified in the genetic fragments introduced from wild soybean. Sequence comparisons between the two CSSL parents SN14 and ZYD00006 revealed a single nucleotide polymorphism (SNP) mutation in the coding sequence of Glyma.19G122500, causing a non-synonymous mutation in the amino acid sequence that affected the predicted protein structure. A Kompetitive allele-specific PCR (KASP) marker was developed based on this SNP and used to evaluate the CSSLs. These results lay the foundation for further research to identify genes related to soluble sugar contents in soybean seeds and for future soybean breeding.http://www.sciencedirect.com/science/article/pii/S2095311921636535soybean soluble sugar contentsconsensus QTLmeta-overview-collinearity integrated analysispopulation validationRNA-seq and candidate gene mining |
| spellingShingle | Wen-jing PAN Xue HAN Shi-yu HUANG Jing-yao YU Ying ZHAO Ke-xin QU Ze-xin ZHANG Zhen-gong YIN Hui-dong QI Guo-long YU Yong ZHANG Da-wei XIN Rong-sheng ZHU Chun-yan LIU Xiao-xia WU Hong-wei JIANG Zhen-bang HU Yu-hu ZUO Qing-shan CHEN Zhao-ming QI Identification of candidate genes related to soluble sugar contents in soybean seeds using multiple genetic analyses Journal of Integrative Agriculture soybean soluble sugar contents consensus QTL meta-overview-collinearity integrated analysis population validation RNA-seq and candidate gene mining |
| title | Identification of candidate genes related to soluble sugar contents in soybean seeds using multiple genetic analyses |
| title_full | Identification of candidate genes related to soluble sugar contents in soybean seeds using multiple genetic analyses |
| title_fullStr | Identification of candidate genes related to soluble sugar contents in soybean seeds using multiple genetic analyses |
| title_full_unstemmed | Identification of candidate genes related to soluble sugar contents in soybean seeds using multiple genetic analyses |
| title_short | Identification of candidate genes related to soluble sugar contents in soybean seeds using multiple genetic analyses |
| title_sort | identification of candidate genes related to soluble sugar contents in soybean seeds using multiple genetic analyses |
| topic | soybean soluble sugar contents consensus QTL meta-overview-collinearity integrated analysis population validation RNA-seq and candidate gene mining |
| url | http://www.sciencedirect.com/science/article/pii/S2095311921636535 |
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