Combination of GWAS and FST-based approaches identified loci associated with economic traits in sugarcane
Sugarcane is a globally important plant for both sugar and biofuel production. Although conventional breeding has played an important role in increasing the productivity of sugarcane, it takes a long time to achieve breeding goals such as high yield and resistant to diseases. Molecular breeding, inc...
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| Veröffentlicht in: | Molecular genetics and genomics : MGG 2023-09, Vol.298 (5), p.1107-1120 |
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| creator | Wang, Le Yeo, Shadame Lee, May Endah, S. Alhuda, N. A. Yue, G. H. |
| description | Sugarcane is a globally important plant for both sugar and biofuel production. Although conventional breeding has played an important role in increasing the productivity of sugarcane, it takes a long time to achieve breeding goals such as high yield and resistant to diseases. Molecular breeding, including marker-assisted breeding and genomic selection, can accelerate genetic improvement by selecting elites at the seedling stage with DNA markers. However, only a few DNA markers associated with important traits were identified in sugarcane. The purpose of this study was to identify DNA markers associated with sugar content, stalk diameter, and sugarcane top borer resistance. The sugarcane samples with trait records were genotyped using the restriction site-associated DNA sequencing (RADseq) technology. Using
F
ST
analysis and genome-wide association study (GWAS), a total of 9, 23 and 9 DNA variants (single nucleotide polymorphisms (SNPs)/insertions and deletions (indels)) were associated with sugar content, stalk diameter, and sugarcane top borer resistance, respectively. The identified genetic variants were on different chromosomes, suggesting that these traits are complex and determined by multiple genetic factors. These DNA markers identified by both approaches have the potential to be used in selecting elite clones at the seeding stage in our sugarcane breeding program to accelerate genetic improvement. Certainly, it is essential to verify the reliability of the identified DNA markers associated with traits before they are used in molecular breeding in other populations. |
| doi_str_mv | 10.1007/s00438-023-02040-2 |
| format | Article |
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F
ST
analysis and genome-wide association study (GWAS), a total of 9, 23 and 9 DNA variants (single nucleotide polymorphisms (SNPs)/insertions and deletions (indels)) were associated with sugar content, stalk diameter, and sugarcane top borer resistance, respectively. The identified genetic variants were on different chromosomes, suggesting that these traits are complex and determined by multiple genetic factors. These DNA markers identified by both approaches have the potential to be used in selecting elite clones at the seeding stage in our sugarcane breeding program to accelerate genetic improvement. Certainly, it is essential to verify the reliability of the identified DNA markers associated with traits before they are used in molecular breeding in other populations.</description><identifier>ISSN: 1617-4615</identifier><identifier>EISSN: 1617-4623</identifier><identifier>DOI: 10.1007/s00438-023-02040-2</identifier><language>eng</language><publisher>Berlin/Heidelberg: Springer Berlin Heidelberg</publisher><subject>Animal Genetics and Genomics ; Biochemistry ; Biofuels ; Biomedical and Life Sciences ; Borers ; Chromosomes ; DNA sequencing ; Genetic diversity ; Genetic factors ; Genome-wide association studies ; Human Genetics ; Life Sciences ; Microbial Genetics and Genomics ; Original Article ; Plant breeding ; Plant Genetics and Genomics ; Single-nucleotide polymorphism ; Sugar ; Sugarcane</subject><ispartof>Molecular genetics and genomics : MGG, 2023-09, Vol.298 (5), p.1107-1120</ispartof><rights>The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature 2023. Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.</rights><lds50>peer_reviewed</lds50><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c352t-4f2622496a0f616b754a81214ba0f10c1cb516eb3a0552351f6a7d76efdf21e13</citedby><cites>FETCH-LOGICAL-c352t-4f2622496a0f616b754a81214ba0f10c1cb516eb3a0552351f6a7d76efdf21e13</cites><orcidid>0000-0002-3537-2248</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://link.springer.com/content/pdf/10.1007/s00438-023-02040-2$$EPDF$$P50$$Gspringer$$H</linktopdf><linktohtml>$$Uhttps://link.springer.com/10.1007/s00438-023-02040-2$$EHTML$$P50$$Gspringer$$H</linktohtml><link.rule.ids>314,780,784,27924,27925,41488,42557,51319</link.rule.ids></links><search><creatorcontrib>Wang, Le</creatorcontrib><creatorcontrib>Yeo, Shadame</creatorcontrib><creatorcontrib>Lee, May</creatorcontrib><creatorcontrib>Endah, S.</creatorcontrib><creatorcontrib>Alhuda, N. A.</creatorcontrib><creatorcontrib>Yue, G. H.</creatorcontrib><title>Combination of GWAS and FST-based approaches identified loci associated with economic traits in sugarcane</title><title>Molecular genetics and genomics : MGG</title><addtitle>Mol Genet Genomics</addtitle><description>Sugarcane is a globally important plant for both sugar and biofuel production. Although conventional breeding has played an important role in increasing the productivity of sugarcane, it takes a long time to achieve breeding goals such as high yield and resistant to diseases. Molecular breeding, including marker-assisted breeding and genomic selection, can accelerate genetic improvement by selecting elites at the seedling stage with DNA markers. However, only a few DNA markers associated with important traits were identified in sugarcane. The purpose of this study was to identify DNA markers associated with sugar content, stalk diameter, and sugarcane top borer resistance. The sugarcane samples with trait records were genotyped using the restriction site-associated DNA sequencing (RADseq) technology. Using
F
ST
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A.</au><au>Yue, G. H.</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Combination of GWAS and FST-based approaches identified loci associated with economic traits in sugarcane</atitle><jtitle>Molecular genetics and genomics : MGG</jtitle><stitle>Mol Genet Genomics</stitle><date>2023-09-01</date><risdate>2023</risdate><volume>298</volume><issue>5</issue><spage>1107</spage><epage>1120</epage><pages>1107-1120</pages><issn>1617-4615</issn><eissn>1617-4623</eissn><abstract>Sugarcane is a globally important plant for both sugar and biofuel production. Although conventional breeding has played an important role in increasing the productivity of sugarcane, it takes a long time to achieve breeding goals such as high yield and resistant to diseases. Molecular breeding, including marker-assisted breeding and genomic selection, can accelerate genetic improvement by selecting elites at the seedling stage with DNA markers. However, only a few DNA markers associated with important traits were identified in sugarcane. The purpose of this study was to identify DNA markers associated with sugar content, stalk diameter, and sugarcane top borer resistance. The sugarcane samples with trait records were genotyped using the restriction site-associated DNA sequencing (RADseq) technology. Using
F
ST
analysis and genome-wide association study (GWAS), a total of 9, 23 and 9 DNA variants (single nucleotide polymorphisms (SNPs)/insertions and deletions (indels)) were associated with sugar content, stalk diameter, and sugarcane top borer resistance, respectively. The identified genetic variants were on different chromosomes, suggesting that these traits are complex and determined by multiple genetic factors. These DNA markers identified by both approaches have the potential to be used in selecting elite clones at the seeding stage in our sugarcane breeding program to accelerate genetic improvement. Certainly, it is essential to verify the reliability of the identified DNA markers associated with traits before they are used in molecular breeding in other populations.</abstract><cop>Berlin/Heidelberg</cop><pub>Springer Berlin Heidelberg</pub><doi>10.1007/s00438-023-02040-2</doi><tpages>14</tpages><orcidid>https://orcid.org/0000-0002-3537-2248</orcidid></addata></record> |
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| subjects | Animal Genetics and Genomics Biochemistry Biofuels Biomedical and Life Sciences Borers Chromosomes DNA sequencing Genetic diversity Genetic factors Genome-wide association studies Human Genetics Life Sciences Microbial Genetics and Genomics Original Article Plant breeding Plant Genetics and Genomics Single-nucleotide polymorphism Sugar Sugarcane |
| title | Combination of GWAS and FST-based approaches identified loci associated with economic traits in sugarcane |
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