Single-nucleotide polymorphisms(SNPs) in a sucrose synthase gene are associated with wood properties in Catalpa fargesii bur
Abstract Background Association study is a powerful means for identifying molecular markers, such as single-nucleotide polymorphisms (SNPs) associated with important traits in forest trees. Catalpa fargesii Bur is a valuable commercial tree in China and identifying SNPs that associate with wood prop...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2018-11-01
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| Series: | BMC Genetics |
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| Online Access: | http://link.springer.com/article/10.1186/s12863-018-0686-8 |
| _version_ | 1818013460720517120 |
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| author | Nan Lu Fang Mei Zhi Wang Nan Wang Yao Xiao Lisheng Kong Guanzheng Qu Wenjun Ma Junhui Wang |
| author_facet | Nan Lu Fang Mei Zhi Wang Nan Wang Yao Xiao Lisheng Kong Guanzheng Qu Wenjun Ma Junhui Wang |
| author_sort | Nan Lu |
| collection | DOAJ |
| description | Abstract Background Association study is a powerful means for identifying molecular markers, such as single-nucleotide polymorphisms (SNPs) associated with important traits in forest trees. Catalpa fargesii Bur is a valuable commercial tree in China and identifying SNPs that associate with wood property would make a foundation of the marker-assisted breeding in the future. However, related work has not been reported yet. Results We cloned a 2887 bp long sucrose synthase (SUS) gene from the genome of C. fargesii, which is a key enzyme in sucrose metabolism and also associated to wood formation in trees, coding 806 amino acids that expressed mainly in young branches, xylem, and leaves according to real-time quantitative PCR. Then we identified allelic variations of CfSUS associated with nine wood quality associated traits in Catalpa fargesii Bur. Totally, 135 SNPs were identified through cloning and sequencing the CfSUS locus from a mapping population (including 93 unrelated individuals) and 47 of which were genotyped as common SNPs (minor allele frequency > 5%) in the association population that comprised of 125 unrelated individuals collected from main distribution area. Nucleotide diversity and linkage disequilibrium (LD) analysis showed CfSUS has a relative low SNP diversity (π T = 0.0034) and low LD (r2 dropped below 0.1 within 1600 bp). Using the association analysis, we found 11 common SNPs and 14 haplotypes were significantly associated with the traits (false discovery rate, Q<0.1), explaining 3.21–12.41% of the phenotypic variance. These results provide molecular markers above associated with wood basic density, pore rate, and six other traits of wood, which have potential applications in breeding of Catalpa fargesii Bur. Conclusion We first cloned a SUS gene in C. fargesii, then identified several SNPs and haplotypes that associated with wood properties within this gene, suggesting CfSUS participates in the wood formation of C. fargesii. Moreover, molecular markers we identified in this study may be applied into marker-assisted breeding of C. fargesii in the future. |
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| language | English |
| last_indexed | 2024-04-14T06:33:24Z |
| publishDate | 2018-11-01 |
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| series | BMC Genetics |
| spelling | doaj.art-3ef8bfac1de34d28a3ccab811bc48a602022-12-22T02:07:33ZengBMCBMC Genetics1471-21562018-11-0119111510.1186/s12863-018-0686-8Single-nucleotide polymorphisms(SNPs) in a sucrose synthase gene are associated with wood properties in Catalpa fargesii burNan Lu0Fang Mei1Zhi Wang2Nan Wang3Yao Xiao4Lisheng Kong5Guanzheng Qu6Wenjun Ma7Junhui Wang8State Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryState Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryState Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryState Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryState Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryDepartment of Biology, Centre for Forest Biology, University of VictoriaState Key Laboratory of Tree Genetics and Breeding, Northeast Forestry UniversityState Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryState Key Laboratory of Forest Genetics and Tree Breeding, Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of ForestryAbstract Background Association study is a powerful means for identifying molecular markers, such as single-nucleotide polymorphisms (SNPs) associated with important traits in forest trees. Catalpa fargesii Bur is a valuable commercial tree in China and identifying SNPs that associate with wood property would make a foundation of the marker-assisted breeding in the future. However, related work has not been reported yet. Results We cloned a 2887 bp long sucrose synthase (SUS) gene from the genome of C. fargesii, which is a key enzyme in sucrose metabolism and also associated to wood formation in trees, coding 806 amino acids that expressed mainly in young branches, xylem, and leaves according to real-time quantitative PCR. Then we identified allelic variations of CfSUS associated with nine wood quality associated traits in Catalpa fargesii Bur. Totally, 135 SNPs were identified through cloning and sequencing the CfSUS locus from a mapping population (including 93 unrelated individuals) and 47 of which were genotyped as common SNPs (minor allele frequency > 5%) in the association population that comprised of 125 unrelated individuals collected from main distribution area. Nucleotide diversity and linkage disequilibrium (LD) analysis showed CfSUS has a relative low SNP diversity (π T = 0.0034) and low LD (r2 dropped below 0.1 within 1600 bp). Using the association analysis, we found 11 common SNPs and 14 haplotypes were significantly associated with the traits (false discovery rate, Q<0.1), explaining 3.21–12.41% of the phenotypic variance. These results provide molecular markers above associated with wood basic density, pore rate, and six other traits of wood, which have potential applications in breeding of Catalpa fargesii Bur. Conclusion We first cloned a SUS gene in C. fargesii, then identified several SNPs and haplotypes that associated with wood properties within this gene, suggesting CfSUS participates in the wood formation of C. fargesii. Moreover, molecular markers we identified in this study may be applied into marker-assisted breeding of C. fargesii in the future.http://link.springer.com/article/10.1186/s12863-018-0686-8Association studySingle-nucleotide polymorphismLinkage disequilibriumSucrose synthaseWood propertiesCatalpa fargesii bur |
| spellingShingle | Nan Lu Fang Mei Zhi Wang Nan Wang Yao Xiao Lisheng Kong Guanzheng Qu Wenjun Ma Junhui Wang Single-nucleotide polymorphisms(SNPs) in a sucrose synthase gene are associated with wood properties in Catalpa fargesii bur BMC Genetics Association study Single-nucleotide polymorphism Linkage disequilibrium Sucrose synthase Wood properties Catalpa fargesii bur |
| title | Single-nucleotide polymorphisms(SNPs) in a sucrose synthase gene are associated with wood properties in Catalpa fargesii bur |
| title_full | Single-nucleotide polymorphisms(SNPs) in a sucrose synthase gene are associated with wood properties in Catalpa fargesii bur |
| title_fullStr | Single-nucleotide polymorphisms(SNPs) in a sucrose synthase gene are associated with wood properties in Catalpa fargesii bur |
| title_full_unstemmed | Single-nucleotide polymorphisms(SNPs) in a sucrose synthase gene are associated with wood properties in Catalpa fargesii bur |
| title_short | Single-nucleotide polymorphisms(SNPs) in a sucrose synthase gene are associated with wood properties in Catalpa fargesii bur |
| title_sort | single nucleotide polymorphisms snps in a sucrose synthase gene are associated with wood properties in catalpa fargesii bur |
| topic | Association study Single-nucleotide polymorphism Linkage disequilibrium Sucrose synthase Wood properties Catalpa fargesii bur |
| url | http://link.springer.com/article/10.1186/s12863-018-0686-8 |
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