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http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/86260
Title: | Investigating the Genetic Architecture of Stomatal Density in Wheat using a Convolutional Neural Network and GWAS |
Authors: | Julien Hennequart 朱立安 |
Advisor: | 董致韡(Chih-Wei Tung) 董致韡(Chih-Wei Tung | chihweitung@ntu.edu.tw | ), |
Keyword: | 氣孔密度,氣孔區,全基因組關聯研究,深度學習,小麥, stomatal density,stomatal area,genome-wide association study,deep learning,wheat, |
Publication Year : | 2022 |
Degree: | 碩士 |
Abstract: | none Bread wheat (Triticum aestivum) is one of the most important crops in the world and is grown in a wide range of environments. Wheat yields are mainly limited by the lack of precipitations in certain parts of the world. Stomatal density (SD) and stomatal area (SA) are important traits for gas exchanges between the plant and the atmosphere, and thus, for water-use efficiency. Therefore, understanding the genetic architecture of SD and SA is essential for the breeding of drought tolerant wheat. However, the ability to discover genetic loci controlling stomatal traits has been hindered by the low throughput manual phenotyping methods employed for measuring SD and SA. We used a deep learning method to automatically measure SD and SA on 133 bread wheat accessions. The automatic measurements of SD were compared with SD measured manually. The deep learning model was able to accurately detect stomata with a precision, recall and F1-score of 0.990, 0.982 and 0.986 respectively. A genome-wide association study (GWAS) identified 58 quantitative trait loci associated with SA as well as automatically and manually measured SD. QTL were consistently detected between manual and automatic phenotyping. Thus, the two methods can be used in conjunction in order to validate the detected loci. Our results demonstrate that deep learning can be used to investigate the diversity and genetic control of SD on large populations accurately. |
URI: | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/86260 |
DOI: | 10.6342/NTU202202886 |
Fulltext Rights: | 同意授權(全球公開) |
metadata.dc.date.embargo-lift: | 2024-08-29 |
Appears in Collections: | 農藝學系 |
Files in This Item:
File | Size | Format | |
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U0001-2708202220323300.pdf Until 2024-08-29 | 3.8 MB | Adobe PDF |
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