Genome-wide association study and genomic prediction for resistance to brown planthopper in rice
The brown planthopper (BPH) is the most destructive insect pest that threatens rice production globally. Developing rice varieties incorporating BPH-resistant genes has proven to be an effective control measure against BPH. In this study, we assessed the resistance of a core collection consisting of...
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| Format: | Article |
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Frontiers Media S.A.
2024-03-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1373081/full |
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| author | Cong Zhou Cong Zhou Weihua Jiang Jianping Guo Lili Zhu Lijiang Liu Shengyi Liu Rongzhi Chen Bo Du Jin Huang |
| author_facet | Cong Zhou Cong Zhou Weihua Jiang Jianping Guo Lili Zhu Lijiang Liu Shengyi Liu Rongzhi Chen Bo Du Jin Huang |
| author_sort | Cong Zhou |
| collection | DOAJ |
| description | The brown planthopper (BPH) is the most destructive insect pest that threatens rice production globally. Developing rice varieties incorporating BPH-resistant genes has proven to be an effective control measure against BPH. In this study, we assessed the resistance of a core collection consisting of 502 rice germplasms by evaluating resistance scores, weight gain rates and honeydew excretions. A total of 117 rice varieties (23.31%) exhibited resistance to BPH. Genome-wide association studies (GWAS) were performed on both the entire panel of 502 rice varieties and its subspecies, and 6 loci were significantly associated with resistance scores (P value < 1.0e-8). Within these loci, we identified eight candidate genes encoding receptor-like protein kinase (RLK), nucleotide-binding and leucine-rich repeat (NB-LRR), or LRR proteins. Two loci had not been detected in previous study and were entirely novel. Furthermore, we evaluated the predictive ability of genomic selection for resistance to BPH. The results revealed that the highest prediction accuracy for BPH resistance reached 0.633. As expected, the prediction accuracy increased progressively with an increasing number of SNPs, and a total of 6.7K SNPs displayed comparable accuracy to 268K SNPs. Among various statistical models tested, the random forest model exhibited superior predictive accuracy. Moreover, increasing the size of training population improved prediction accuracy; however, there was no significant difference in prediction accuracy between a training population size of 737 and 1179. Additionally, when there existed close genetic relatedness between the training and validation populations, higher prediction accuracies were observed compared to scenarios when they were genetically distant. These findings provide valuable resistance candidate genes and germplasm resources and are crucial for the application of genomic selection for breeding durable BPH-resistant rice varieties. |
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| language | English |
| last_indexed | 2024-04-24T21:43:30Z |
| publishDate | 2024-03-01 |
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| spelling | doaj.art-4d788046011f4fb48dca7c6dc615dc6b2024-03-21T05:04:00ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2024-03-011510.3389/fpls.2024.13730811373081Genome-wide association study and genomic prediction for resistance to brown planthopper in riceCong Zhou0Cong Zhou1Weihua Jiang2Jianping Guo3Lili Zhu4Lijiang Liu5Shengyi Liu6Rongzhi Chen7Bo Du8Jin Huang9Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan, ChinaState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, ChinaState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, ChinaState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, ChinaState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, ChinaOil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan, ChinaOil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan, ChinaState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, ChinaState Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, ChinaCash Crops Research Institute, Hubei Academy of Agricultural Sciences, Wuhan, ChinaThe brown planthopper (BPH) is the most destructive insect pest that threatens rice production globally. Developing rice varieties incorporating BPH-resistant genes has proven to be an effective control measure against BPH. In this study, we assessed the resistance of a core collection consisting of 502 rice germplasms by evaluating resistance scores, weight gain rates and honeydew excretions. A total of 117 rice varieties (23.31%) exhibited resistance to BPH. Genome-wide association studies (GWAS) were performed on both the entire panel of 502 rice varieties and its subspecies, and 6 loci were significantly associated with resistance scores (P value < 1.0e-8). Within these loci, we identified eight candidate genes encoding receptor-like protein kinase (RLK), nucleotide-binding and leucine-rich repeat (NB-LRR), or LRR proteins. Two loci had not been detected in previous study and were entirely novel. Furthermore, we evaluated the predictive ability of genomic selection for resistance to BPH. The results revealed that the highest prediction accuracy for BPH resistance reached 0.633. As expected, the prediction accuracy increased progressively with an increasing number of SNPs, and a total of 6.7K SNPs displayed comparable accuracy to 268K SNPs. Among various statistical models tested, the random forest model exhibited superior predictive accuracy. Moreover, increasing the size of training population improved prediction accuracy; however, there was no significant difference in prediction accuracy between a training population size of 737 and 1179. Additionally, when there existed close genetic relatedness between the training and validation populations, higher prediction accuracies were observed compared to scenarios when they were genetically distant. These findings provide valuable resistance candidate genes and germplasm resources and are crucial for the application of genomic selection for breeding durable BPH-resistant rice varieties.https://www.frontiersin.org/articles/10.3389/fpls.2024.1373081/fullricebrown planthopperGWAScandidate genesgenomic prediction |
| spellingShingle | Cong Zhou Cong Zhou Weihua Jiang Jianping Guo Lili Zhu Lijiang Liu Shengyi Liu Rongzhi Chen Bo Du Jin Huang Genome-wide association study and genomic prediction for resistance to brown planthopper in rice Frontiers in Plant Science rice brown planthopper GWAS candidate genes genomic prediction |
| title | Genome-wide association study and genomic prediction for resistance to brown planthopper in rice |
| title_full | Genome-wide association study and genomic prediction for resistance to brown planthopper in rice |
| title_fullStr | Genome-wide association study and genomic prediction for resistance to brown planthopper in rice |
| title_full_unstemmed | Genome-wide association study and genomic prediction for resistance to brown planthopper in rice |
| title_short | Genome-wide association study and genomic prediction for resistance to brown planthopper in rice |
| title_sort | genome wide association study and genomic prediction for resistance to brown planthopper in rice |
| topic | rice brown planthopper GWAS candidate genes genomic prediction |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1373081/full |
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