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A first look at the ability to use genomic prediction for improving the ratooning ability of sugarcane
The sugarcane ratooning ability (RA) is the most important target trait for breeders seeking to enhance the profitability of sugarcane production by reducing the planting cost. Understanding the genetics governing the RA could help breeders by identifying molecular markers that could be used for gen...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10433174/ https://www.ncbi.nlm.nih.gov/pubmed/37600177 http://dx.doi.org/10.3389/fpls.2023.1205999 |
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author | Islam, Md. Sariful Corak, Keo McCord, Per Hulse-Kemp, Amanda M. Lipka, Alexander E. |
author_facet | Islam, Md. Sariful Corak, Keo McCord, Per Hulse-Kemp, Amanda M. Lipka, Alexander E. |
author_sort | Islam, Md. Sariful |
collection | PubMed |
description | The sugarcane ratooning ability (RA) is the most important target trait for breeders seeking to enhance the profitability of sugarcane production by reducing the planting cost. Understanding the genetics governing the RA could help breeders by identifying molecular markers that could be used for genomics-assisted breeding (GAB). A replicated field trial was conducted for three crop cycles (plant cane, first ratoon, and second ratoon) using 432 sugarcane clones and used for conducting genome-wide association and genomic prediction of five sugar and yield component traits of the RA. The RA traits for economic index (EI), stalk population (SP), stalk weight (SW), tonns of cane per hectare (TCH), and tonns of sucrose per hectare (TSH) were estimated from the yield and sugar data. A total of six putative quantitative trait loci and eight nonredundant single-nucleotide polymorphism (SNP) markers were associated with all five tested RA traits and appear to be unique. Seven putative candidate genes were colocated with significant SNPs associated with the five RA traits. The genomic prediction accuracies for those tested traits were moderate and ranged from 0.21 to 0.36. However, the models fitting fixed effects for the most significant associated markers for each respective trait did not give any advantages over the standard models without fixed effects. As a result of this study, more robust markers could be used in the future for clone selection in sugarcane, potentially helping resolve the genetic control of the RA in sugarcane. |
format | Online Article Text |
id | pubmed-10433174 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-104331742023-08-18 A first look at the ability to use genomic prediction for improving the ratooning ability of sugarcane Islam, Md. Sariful Corak, Keo McCord, Per Hulse-Kemp, Amanda M. Lipka, Alexander E. Front Plant Sci Plant Science The sugarcane ratooning ability (RA) is the most important target trait for breeders seeking to enhance the profitability of sugarcane production by reducing the planting cost. Understanding the genetics governing the RA could help breeders by identifying molecular markers that could be used for genomics-assisted breeding (GAB). A replicated field trial was conducted for three crop cycles (plant cane, first ratoon, and second ratoon) using 432 sugarcane clones and used for conducting genome-wide association and genomic prediction of five sugar and yield component traits of the RA. The RA traits for economic index (EI), stalk population (SP), stalk weight (SW), tonns of cane per hectare (TCH), and tonns of sucrose per hectare (TSH) were estimated from the yield and sugar data. A total of six putative quantitative trait loci and eight nonredundant single-nucleotide polymorphism (SNP) markers were associated with all five tested RA traits and appear to be unique. Seven putative candidate genes were colocated with significant SNPs associated with the five RA traits. The genomic prediction accuracies for those tested traits were moderate and ranged from 0.21 to 0.36. However, the models fitting fixed effects for the most significant associated markers for each respective trait did not give any advantages over the standard models without fixed effects. As a result of this study, more robust markers could be used in the future for clone selection in sugarcane, potentially helping resolve the genetic control of the RA in sugarcane. Frontiers Media S.A. 2023-08-02 /pmc/articles/PMC10433174/ /pubmed/37600177 http://dx.doi.org/10.3389/fpls.2023.1205999 Text en Copyright © 2023 Islam, Corak, McCord, Hulse-Kemp and Lipka https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Plant Science Islam, Md. Sariful Corak, Keo McCord, Per Hulse-Kemp, Amanda M. Lipka, Alexander E. A first look at the ability to use genomic prediction for improving the ratooning ability of sugarcane |
title | A first look at the ability to use genomic prediction for improving the ratooning ability of sugarcane |
title_full | A first look at the ability to use genomic prediction for improving the ratooning ability of sugarcane |
title_fullStr | A first look at the ability to use genomic prediction for improving the ratooning ability of sugarcane |
title_full_unstemmed | A first look at the ability to use genomic prediction for improving the ratooning ability of sugarcane |
title_short | A first look at the ability to use genomic prediction for improving the ratooning ability of sugarcane |
title_sort | first look at the ability to use genomic prediction for improving the ratooning ability of sugarcane |
topic | Plant Science |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10433174/ https://www.ncbi.nlm.nih.gov/pubmed/37600177 http://dx.doi.org/10.3389/fpls.2023.1205999 |
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