Insight into the Complex Genetic Relationship of Chinese Fir (<i>Cunninghamia lanceolata</i> (Lamb.) Hook.) Advanced Parent Trees Based on SSR and SNP Datasets
Accurate estimation of genetic relationships among breeding materials and their genetic diversity contributes to the optimal design of breeding programs. For Chinese fir (<i>Cunninghamia lanceolata</i> (Lamb.) Hook.), an important indigenous tree species in China, breeders have attempted...
| Main Authors: | , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-02-01
|
| Series: | Forests |
| Subjects: | |
| Online Access: | https://www.mdpi.com/1999-4907/14/2/347 |
| _version_ | 1797620985048858624 |
|---|---|
| author | Weishan Zeng Yan Su Rong Huang Dehuo Hu Shaowei Huang Huiquan Zheng |
| author_facet | Weishan Zeng Yan Su Rong Huang Dehuo Hu Shaowei Huang Huiquan Zheng |
| author_sort | Weishan Zeng |
| collection | DOAJ |
| description | Accurate estimation of genetic relationships among breeding materials and their genetic diversity contributes to the optimal design of breeding programs. For Chinese fir (<i>Cunninghamia lanceolata</i> (Lamb.) Hook.), an important indigenous tree species in China, breeders have attempted to employ different molecular markers to address the genetic architecture of their target population, but the power of an advanced parent tree population with a complex pedigree relationship is still rather limited. In this study, a partly known pedigree map combined with marker-derived (SSRs and SNPs) information was implemented for the first time in the assessment of the genetic relatedness of a complex advanced parent tree population (<i>n</i> = 50) in Chinese fir. The bivariate analysis showed that relatedness coefficients between individuals based on SSRs were significantly correlated with SNPs (<i>r</i> = 0.690, <i>p</i> < 0.01). Moreover, the heatmap generated by the SSR-based coefficient matrix was largely consistent with that derived from the SNP-based matrix. Additionally, STRUCTURE and ADMIXTURE analyses based on the two markers showed an analogical genetic clustering result. When compared to the recorded pedigree information, the genetic relationships estimated by the two molecular markers were broadly parallel with pedigree relatedness. These results indicated that SSRs and SNPs can be used as effective tools to clarify genetic relationships when complete pedigree records are not available in Chinese fir. Based on the two markers, the present study revealed a relatively wide genetic variation (SSRs: <i>PIC</i> = 0.573; SNPs: <i>PIC</i> = 0.231) in the selected parent trees. This investigation provides important input into the progress of Chinese fir advanced-generation breeding. |
| first_indexed | 2024-03-11T08:49:18Z |
| format | Article |
| id | doaj.art-d82cc6c955d84ff7a0d8e4489c90f42f |
| institution | Directory Open Access Journal |
| issn | 1999-4907 |
| language | English |
| last_indexed | 2024-03-11T08:49:18Z |
| publishDate | 2023-02-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Forests |
| spelling | doaj.art-d82cc6c955d84ff7a0d8e4489c90f42f2023-11-16T20:34:43ZengMDPI AGForests1999-49072023-02-0114234710.3390/f14020347Insight into the Complex Genetic Relationship of Chinese Fir (<i>Cunninghamia lanceolata</i> (Lamb.) Hook.) Advanced Parent Trees Based on SSR and SNP DatasetsWeishan Zeng0Yan Su1Rong Huang2Dehuo Hu3Shaowei Huang4Huiquan Zheng5College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, ChinaCollege of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, ChinaGuangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, ChinaGuangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, ChinaCollege of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, ChinaGuangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou 510520, ChinaAccurate estimation of genetic relationships among breeding materials and their genetic diversity contributes to the optimal design of breeding programs. For Chinese fir (<i>Cunninghamia lanceolata</i> (Lamb.) Hook.), an important indigenous tree species in China, breeders have attempted to employ different molecular markers to address the genetic architecture of their target population, but the power of an advanced parent tree population with a complex pedigree relationship is still rather limited. In this study, a partly known pedigree map combined with marker-derived (SSRs and SNPs) information was implemented for the first time in the assessment of the genetic relatedness of a complex advanced parent tree population (<i>n</i> = 50) in Chinese fir. The bivariate analysis showed that relatedness coefficients between individuals based on SSRs were significantly correlated with SNPs (<i>r</i> = 0.690, <i>p</i> < 0.01). Moreover, the heatmap generated by the SSR-based coefficient matrix was largely consistent with that derived from the SNP-based matrix. Additionally, STRUCTURE and ADMIXTURE analyses based on the two markers showed an analogical genetic clustering result. When compared to the recorded pedigree information, the genetic relationships estimated by the two molecular markers were broadly parallel with pedigree relatedness. These results indicated that SSRs and SNPs can be used as effective tools to clarify genetic relationships when complete pedigree records are not available in Chinese fir. Based on the two markers, the present study revealed a relatively wide genetic variation (SSRs: <i>PIC</i> = 0.573; SNPs: <i>PIC</i> = 0.231) in the selected parent trees. This investigation provides important input into the progress of Chinese fir advanced-generation breeding.https://www.mdpi.com/1999-4907/14/2/347Chinese firpedigreeSSRSNPgenetic relationship |
| spellingShingle | Weishan Zeng Yan Su Rong Huang Dehuo Hu Shaowei Huang Huiquan Zheng Insight into the Complex Genetic Relationship of Chinese Fir (<i>Cunninghamia lanceolata</i> (Lamb.) Hook.) Advanced Parent Trees Based on SSR and SNP Datasets Forests Chinese fir pedigree SSR SNP genetic relationship |
| title | Insight into the Complex Genetic Relationship of Chinese Fir (<i>Cunninghamia lanceolata</i> (Lamb.) Hook.) Advanced Parent Trees Based on SSR and SNP Datasets |
| title_full | Insight into the Complex Genetic Relationship of Chinese Fir (<i>Cunninghamia lanceolata</i> (Lamb.) Hook.) Advanced Parent Trees Based on SSR and SNP Datasets |
| title_fullStr | Insight into the Complex Genetic Relationship of Chinese Fir (<i>Cunninghamia lanceolata</i> (Lamb.) Hook.) Advanced Parent Trees Based on SSR and SNP Datasets |
| title_full_unstemmed | Insight into the Complex Genetic Relationship of Chinese Fir (<i>Cunninghamia lanceolata</i> (Lamb.) Hook.) Advanced Parent Trees Based on SSR and SNP Datasets |
| title_short | Insight into the Complex Genetic Relationship of Chinese Fir (<i>Cunninghamia lanceolata</i> (Lamb.) Hook.) Advanced Parent Trees Based on SSR and SNP Datasets |
| title_sort | insight into the complex genetic relationship of chinese fir i cunninghamia lanceolata i lamb hook advanced parent trees based on ssr and snp datasets |
| topic | Chinese fir pedigree SSR SNP genetic relationship |
| url | https://www.mdpi.com/1999-4907/14/2/347 |
| work_keys_str_mv | AT weishanzeng insightintothecomplexgeneticrelationshipofchinesefiricunninghamialanceolatailambhookadvancedparenttreesbasedonssrandsnpdatasets AT yansu insightintothecomplexgeneticrelationshipofchinesefiricunninghamialanceolatailambhookadvancedparenttreesbasedonssrandsnpdatasets AT ronghuang insightintothecomplexgeneticrelationshipofchinesefiricunninghamialanceolatailambhookadvancedparenttreesbasedonssrandsnpdatasets AT dehuohu insightintothecomplexgeneticrelationshipofchinesefiricunninghamialanceolatailambhookadvancedparenttreesbasedonssrandsnpdatasets AT shaoweihuang insightintothecomplexgeneticrelationshipofchinesefiricunninghamialanceolatailambhookadvancedparenttreesbasedonssrandsnpdatasets AT huiquanzheng insightintothecomplexgeneticrelationshipofchinesefiricunninghamialanceolatailambhookadvancedparenttreesbasedonssrandsnpdatasets |