Genomic and transcriptomic-based analysis of agronomic traits in sugar beet (Beta vulgaris L.) pure line IMA1
Sugar beet (Beta vulgaris L.) is an important sugar-producing and energy crop worldwide. The sugar beet pure line IMA1 independently bred by Chinese scientists is a standard diploid parent material that is widely used in hybrid-breeding programs. In this study, a high-quality, chromosome-level genom...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-10-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1028885/full |
| _version_ | 1798019547469447168 |
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| author | Xiaodong Li Wenjin He Jingping Fang Yahui Liang Yahui Liang Huizhong Zhang Huizhong Zhang Duo Chen Xingrong Wu Xingrong Wu Ziqiang Zhang Ziqiang Zhang Liang Wang Liang Wang Pingan Han Pingan Han Bizhou Zhang Bizhou Zhang Ting Xue Wenzhe Zheng Wenzhe Zheng Jiangfeng He Jiangfeng He Chen Bai Chen Bai |
| author_facet | Xiaodong Li Wenjin He Jingping Fang Yahui Liang Yahui Liang Huizhong Zhang Huizhong Zhang Duo Chen Xingrong Wu Xingrong Wu Ziqiang Zhang Ziqiang Zhang Liang Wang Liang Wang Pingan Han Pingan Han Bizhou Zhang Bizhou Zhang Ting Xue Wenzhe Zheng Wenzhe Zheng Jiangfeng He Jiangfeng He Chen Bai Chen Bai |
| author_sort | Xiaodong Li |
| collection | DOAJ |
| description | Sugar beet (Beta vulgaris L.) is an important sugar-producing and energy crop worldwide. The sugar beet pure line IMA1 independently bred by Chinese scientists is a standard diploid parent material that is widely used in hybrid-breeding programs. In this study, a high-quality, chromosome-level genome assembly for IMA1was conducted, and 99.1% of genome sequences were assigned to nine chromosomes. A total of 35,003 protein-coding genes were annotated, with 91.56% functionally annotated by public databases. Compared with previously released sugar beet assemblies, the new genome was larger with at least 1.6 times larger N50 size, thereby substantially improving the completeness and continuity of the sugar beet genome. A Genome-Wide Association Studies analysis identified 10 disease-resistance genes associated with three important beet diseases and five genes associated with sugar yield per hectare, which could be key targets to improve sugar productivity. Nine highly expressed genes associated with pollen fertility of sugar beet were also identified. The results of this study provide valuable information to identify and dissect functional genes affecting sugar beet agronomic traits, which can increase sugar beet production and help screen for excellent sugar beet breeding materials. In addition, information is provided that can precisely incorporate biotechnology tools into breeding efforts. |
| first_indexed | 2024-04-11T16:41:19Z |
| format | Article |
| id | doaj.art-2edc91ef79154198b6aca27624a2ae63 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-11T16:41:19Z |
| publishDate | 2022-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-2edc91ef79154198b6aca27624a2ae632022-12-22T04:13:39ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-10-011310.3389/fpls.2022.10288851028885Genomic and transcriptomic-based analysis of agronomic traits in sugar beet (Beta vulgaris L.) pure line IMA1Xiaodong Li0Wenjin He1Jingping Fang2Yahui Liang3Yahui Liang4Huizhong Zhang5Huizhong Zhang6Duo Chen7Xingrong Wu8Xingrong Wu9Ziqiang Zhang10Ziqiang Zhang11Liang Wang12Liang Wang13Pingan Han14Pingan Han15Bizhou Zhang16Bizhou Zhang17Ting Xue18Wenzhe Zheng19Wenzhe Zheng20Jiangfeng He21Jiangfeng He22Chen Bai23Chen Bai24Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaLife Science College of Fujian Normal University, Fuzhou, ChinaLife Science College of Fujian Normal University, Fuzhou, ChinaInner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaInner Mongolia Key Laboratory of Sugarbeet Genetics & Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaInner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaInner Mongolia Key Laboratory of Sugarbeet Genetics & Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaLife Science College of Fujian Normal University, Fuzhou, ChinaInner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaInner Mongolia Key Laboratory of Sugarbeet Genetics & Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaInner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaInner Mongolia Key Laboratory of Sugarbeet Genetics & Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaInner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaInner Mongolia Key Laboratory of Sugarbeet Genetics & Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaInner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaInner Mongolia Key Laboratory of Sugarbeet Genetics & Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaInner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaInner Mongolia Key Laboratory of Sugarbeet Genetics & Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaLife Science College of Fujian Normal University, Fuzhou, ChinaInner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaInner Mongolia Key Laboratory of Sugarbeet Genetics & Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaInner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaInner Mongolia Key Laboratory of Sugarbeet Genetics & Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaInner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaInner Mongolia Key Laboratory of Sugarbeet Genetics & Germplasm Enhancement, Inner Mongolia Academy of Agricultural and Animal Husbandry Sciences, Hohhot, ChinaSugar beet (Beta vulgaris L.) is an important sugar-producing and energy crop worldwide. The sugar beet pure line IMA1 independently bred by Chinese scientists is a standard diploid parent material that is widely used in hybrid-breeding programs. In this study, a high-quality, chromosome-level genome assembly for IMA1was conducted, and 99.1% of genome sequences were assigned to nine chromosomes. A total of 35,003 protein-coding genes were annotated, with 91.56% functionally annotated by public databases. Compared with previously released sugar beet assemblies, the new genome was larger with at least 1.6 times larger N50 size, thereby substantially improving the completeness and continuity of the sugar beet genome. A Genome-Wide Association Studies analysis identified 10 disease-resistance genes associated with three important beet diseases and five genes associated with sugar yield per hectare, which could be key targets to improve sugar productivity. Nine highly expressed genes associated with pollen fertility of sugar beet were also identified. The results of this study provide valuable information to identify and dissect functional genes affecting sugar beet agronomic traits, which can increase sugar beet production and help screen for excellent sugar beet breeding materials. In addition, information is provided that can precisely incorporate biotechnology tools into breeding efforts.https://www.frontiersin.org/articles/10.3389/fpls.2022.1028885/fullBeta vulgariswhole-gene sequencingwhole genome duplications (WGD)gene familygenome wide association study (GWAS)male sterility |
| spellingShingle | Xiaodong Li Wenjin He Jingping Fang Yahui Liang Yahui Liang Huizhong Zhang Huizhong Zhang Duo Chen Xingrong Wu Xingrong Wu Ziqiang Zhang Ziqiang Zhang Liang Wang Liang Wang Pingan Han Pingan Han Bizhou Zhang Bizhou Zhang Ting Xue Wenzhe Zheng Wenzhe Zheng Jiangfeng He Jiangfeng He Chen Bai Chen Bai Genomic and transcriptomic-based analysis of agronomic traits in sugar beet (Beta vulgaris L.) pure line IMA1 Frontiers in Plant Science Beta vulgaris whole-gene sequencing whole genome duplications (WGD) gene family genome wide association study (GWAS) male sterility |
| title | Genomic and transcriptomic-based analysis of agronomic traits in sugar beet (Beta vulgaris L.) pure line IMA1 |
| title_full | Genomic and transcriptomic-based analysis of agronomic traits in sugar beet (Beta vulgaris L.) pure line IMA1 |
| title_fullStr | Genomic and transcriptomic-based analysis of agronomic traits in sugar beet (Beta vulgaris L.) pure line IMA1 |
| title_full_unstemmed | Genomic and transcriptomic-based analysis of agronomic traits in sugar beet (Beta vulgaris L.) pure line IMA1 |
| title_short | Genomic and transcriptomic-based analysis of agronomic traits in sugar beet (Beta vulgaris L.) pure line IMA1 |
| title_sort | genomic and transcriptomic based analysis of agronomic traits in sugar beet beta vulgaris l pure line ima1 |
| topic | Beta vulgaris whole-gene sequencing whole genome duplications (WGD) gene family genome wide association study (GWAS) male sterility |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1028885/full |
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