The influence of genetic structure on phenotypic diversity in the Australian mango (Mangifera indica) gene pool
Abstract Genomic selection is a promising breeding technique for tree crops to accelerate the development of new cultivars. However, factors such as genetic structure can create spurious associations between genotype and phenotype due to the shared history between populations with different trait va...
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2022-11-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-022-24800-7 |
| _version_ | 1811190482404900864 |
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| author | Melanie J. Wilkinson Risa Yamashita Maddie E. James Ian S. E. Bally Natalie L. Dillon Asjad Ali Craig M. Hardner Daniel Ortiz-Barrientos |
| author_facet | Melanie J. Wilkinson Risa Yamashita Maddie E. James Ian S. E. Bally Natalie L. Dillon Asjad Ali Craig M. Hardner Daniel Ortiz-Barrientos |
| author_sort | Melanie J. Wilkinson |
| collection | DOAJ |
| description | Abstract Genomic selection is a promising breeding technique for tree crops to accelerate the development of new cultivars. However, factors such as genetic structure can create spurious associations between genotype and phenotype due to the shared history between populations with different trait values. Genetic structure can therefore reduce the accuracy of the genotype to phenotype map, a fundamental requirement of genomic selection models. Here, we employed 272 single nucleotide polymorphisms from 208 Mangifera indica accessions to explore whether the genetic structure of the Australian mango gene pool explained variation in trunk circumference, fruit blush colour and intensity. Multiple population genetic analyses indicate the presence of four genetic clusters and show that the most genetically differentiated cluster contains accessions imported from Southeast Asia (mainly those from Thailand). We find that genetic structure was strongly associated with three traits: trunk circumference, fruit blush colour and intensity in M. indica. This suggests that the history of these accessions could drive spurious associations between loci and key mango phenotypes in the Australian mango gene pool. Incorporating such genetic structure in associations between genotype and phenotype can improve the accuracy of genomic selection, which can assist the future development of new cultivars. |
| first_indexed | 2024-04-11T14:51:52Z |
| format | Article |
| id | doaj.art-8e0342c4f24248678557a5f7bb3ebc49 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-04-11T14:51:52Z |
| publishDate | 2022-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-8e0342c4f24248678557a5f7bb3ebc492022-12-22T04:17:26ZengNature PortfolioScientific Reports2045-23222022-11-0112111310.1038/s41598-022-24800-7The influence of genetic structure on phenotypic diversity in the Australian mango (Mangifera indica) gene poolMelanie J. Wilkinson0Risa Yamashita1Maddie E. James2Ian S. E. Bally3Natalie L. Dillon4Asjad Ali5Craig M. Hardner6Daniel Ortiz-Barrientos7School of Biological Sciences, The University of QueenslandQueensland Alliance for Agriculture and Food Innovation, The University of QueenslandSchool of Biological Sciences, The University of QueenslandQueensland Department of Agriculture and FisheriesQueensland Department of Agriculture and FisheriesQueensland Department of Agriculture and FisheriesQueensland Alliance for Agriculture and Food Innovation, The University of QueenslandSchool of Biological Sciences, The University of QueenslandAbstract Genomic selection is a promising breeding technique for tree crops to accelerate the development of new cultivars. However, factors such as genetic structure can create spurious associations between genotype and phenotype due to the shared history between populations with different trait values. Genetic structure can therefore reduce the accuracy of the genotype to phenotype map, a fundamental requirement of genomic selection models. Here, we employed 272 single nucleotide polymorphisms from 208 Mangifera indica accessions to explore whether the genetic structure of the Australian mango gene pool explained variation in trunk circumference, fruit blush colour and intensity. Multiple population genetic analyses indicate the presence of four genetic clusters and show that the most genetically differentiated cluster contains accessions imported from Southeast Asia (mainly those from Thailand). We find that genetic structure was strongly associated with three traits: trunk circumference, fruit blush colour and intensity in M. indica. This suggests that the history of these accessions could drive spurious associations between loci and key mango phenotypes in the Australian mango gene pool. Incorporating such genetic structure in associations between genotype and phenotype can improve the accuracy of genomic selection, which can assist the future development of new cultivars.https://doi.org/10.1038/s41598-022-24800-7 |
| spellingShingle | Melanie J. Wilkinson Risa Yamashita Maddie E. James Ian S. E. Bally Natalie L. Dillon Asjad Ali Craig M. Hardner Daniel Ortiz-Barrientos The influence of genetic structure on phenotypic diversity in the Australian mango (Mangifera indica) gene pool Scientific Reports |
| title | The influence of genetic structure on phenotypic diversity in the Australian mango (Mangifera indica) gene pool |
| title_full | The influence of genetic structure on phenotypic diversity in the Australian mango (Mangifera indica) gene pool |
| title_fullStr | The influence of genetic structure on phenotypic diversity in the Australian mango (Mangifera indica) gene pool |
| title_full_unstemmed | The influence of genetic structure on phenotypic diversity in the Australian mango (Mangifera indica) gene pool |
| title_short | The influence of genetic structure on phenotypic diversity in the Australian mango (Mangifera indica) gene pool |
| title_sort | influence of genetic structure on phenotypic diversity in the australian mango mangifera indica gene pool |
| url | https://doi.org/10.1038/s41598-022-24800-7 |
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