Integrating Dense Genotyping with High‐Throughput Phenotyping Empowers the Genetic Dissection of Berry Quality and Resilience Traits in Grapevine
Abstract Investigating the genetic architecture of important agronomic traits in grapevine, like berry quality and resilience to abiotic stress, has been hampered by bottlenecks in genotyping and phenotyping. To address these limitations, this study aimed to develop innovative tools to unravel the c...
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| Format: | Article |
| Language: | English |
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Wiley
2025-08-01
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| Series: | Advanced Science |
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| Online Access: | https://doi.org/10.1002/advs.202412587 |
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| author | Yuyu Zhang Yongjian Wang Michael Henke Pablo Carbonell‐Bejerano Zemin Wang Pierre‐François Bert Yi Wang Huayang Li Junhua Kong Peige Fan Zhanwu Dai Zhenchang Liang |
| author_facet | Yuyu Zhang Yongjian Wang Michael Henke Pablo Carbonell‐Bejerano Zemin Wang Pierre‐François Bert Yi Wang Huayang Li Junhua Kong Peige Fan Zhanwu Dai Zhenchang Liang |
| author_sort | Yuyu Zhang |
| collection | DOAJ |
| description | Abstract Investigating the genetic architecture of important agronomic traits in grapevine, like berry quality and resilience to abiotic stress, has been hampered by bottlenecks in genotyping and phenotyping. To address these limitations, this study aimed to develop innovative tools to unravel the complex polygenic genomic architecture of these traits. Specifically, a high‐density 200K single nucleotide polymorphism array is developed and validated its effectiveness by genotyping 471 accessions from three F1 breeding populations. A high‐throughput grape phenotyping tool is developed to accurately capture berry color, shape, and size. By integrating data from the two platforms, associated loci are identified over three growing seasons. Association mapping and haplotype analysis identified novel loci and candidate genes for berry shape (bHLH017), soluble sugars (ACT), and organic acids (ALMT1 and FUSC2), as well as vine cold tolerance (NAC08), and fine‐mapped the flower sex determination locus. Furthermore, the functional role of NAC08 is validated, demonstrating that it activates the expression of a raffinose synthase gene, thereby increasing raffinose levels and conferring cold tolerance. Together, these augmented tools, the integrated data, and novel loci establish a better foundation for trait aggregation that will enhance breeding efficiency and boost the development of high‐quality grape varieties. |
| format | Article |
| id | doaj-art-16f41fb8b73e41309ef4491bdf2b03f0 |
| institution | Kabale University |
| issn | 2198-3844 |
| language | English |
| publishDate | 2025-08-01 |
| publisher | Wiley |
| record_format | Article |
| series | Advanced Science |
| spelling | doaj-art-16f41fb8b73e41309ef4491bdf2b03f02025-08-20T04:01:15ZengWileyAdvanced Science2198-38442025-08-011229n/an/a10.1002/advs.202412587Integrating Dense Genotyping with High‐Throughput Phenotyping Empowers the Genetic Dissection of Berry Quality and Resilience Traits in GrapevineYuyu Zhang0Yongjian Wang1Michael Henke2Pablo Carbonell‐Bejerano3Zemin Wang4Pierre‐François Bert5Yi Wang6Huayang Li7Junhua Kong8Peige Fan9Zhanwu Dai10Zhenchang Liang11State Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology Institute of Botany Chinese Academy of Sciences Beijing 100093 ChinaState Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology Institute of Botany Chinese Academy of Sciences Beijing 100093 ChinaState Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology Institute of Botany Chinese Academy of Sciences Beijing 100093 ChinaInstituto de Ciencias de la Vid y del Vino (ICVV) Consejo Superior de Investigaciones Científicas‐Universidad de La Rioja‐Gobierno de La Rioja Logrono 26007 SpainState Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology Institute of Botany Chinese Academy of Sciences Beijing 100093 ChinaEGFV, Bordeaux Sciences Agro INRAE, ISVV, Univ. Bordeaux Villenave d'Ornon 33882 FranceState Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology Institute of Botany Chinese Academy of Sciences Beijing 100093 ChinaState Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology Institute of Botany Chinese Academy of Sciences Beijing 100093 ChinaState Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology Institute of Botany Chinese Academy of Sciences Beijing 100093 ChinaState Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology Institute of Botany Chinese Academy of Sciences Beijing 100093 ChinaState Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology Institute of Botany Chinese Academy of Sciences Beijing 100093 ChinaState Key Laboratory of Plant Diversity and Specialty Crops and Beijing Key Laboratory of Grape Science and Enology Institute of Botany Chinese Academy of Sciences Beijing 100093 ChinaAbstract Investigating the genetic architecture of important agronomic traits in grapevine, like berry quality and resilience to abiotic stress, has been hampered by bottlenecks in genotyping and phenotyping. To address these limitations, this study aimed to develop innovative tools to unravel the complex polygenic genomic architecture of these traits. Specifically, a high‐density 200K single nucleotide polymorphism array is developed and validated its effectiveness by genotyping 471 accessions from three F1 breeding populations. A high‐throughput grape phenotyping tool is developed to accurately capture berry color, shape, and size. By integrating data from the two platforms, associated loci are identified over three growing seasons. Association mapping and haplotype analysis identified novel loci and candidate genes for berry shape (bHLH017), soluble sugars (ACT), and organic acids (ALMT1 and FUSC2), as well as vine cold tolerance (NAC08), and fine‐mapped the flower sex determination locus. Furthermore, the functional role of NAC08 is validated, demonstrating that it activates the expression of a raffinose synthase gene, thereby increasing raffinose levels and conferring cold tolerance. Together, these augmented tools, the integrated data, and novel loci establish a better foundation for trait aggregation that will enhance breeding efficiency and boost the development of high‐quality grape varieties.https://doi.org/10.1002/advs.202412587200K axiom SNP arrayassociation mappingfine mappinghaplotype analysishigh‐throughput phenotypingNAC08 |
| spellingShingle | Yuyu Zhang Yongjian Wang Michael Henke Pablo Carbonell‐Bejerano Zemin Wang Pierre‐François Bert Yi Wang Huayang Li Junhua Kong Peige Fan Zhanwu Dai Zhenchang Liang Integrating Dense Genotyping with High‐Throughput Phenotyping Empowers the Genetic Dissection of Berry Quality and Resilience Traits in Grapevine Advanced Science 200K axiom SNP array association mapping fine mapping haplotype analysis high‐throughput phenotyping NAC08 |
| title | Integrating Dense Genotyping with High‐Throughput Phenotyping Empowers the Genetic Dissection of Berry Quality and Resilience Traits in Grapevine |
| title_full | Integrating Dense Genotyping with High‐Throughput Phenotyping Empowers the Genetic Dissection of Berry Quality and Resilience Traits in Grapevine |
| title_fullStr | Integrating Dense Genotyping with High‐Throughput Phenotyping Empowers the Genetic Dissection of Berry Quality and Resilience Traits in Grapevine |
| title_full_unstemmed | Integrating Dense Genotyping with High‐Throughput Phenotyping Empowers the Genetic Dissection of Berry Quality and Resilience Traits in Grapevine |
| title_short | Integrating Dense Genotyping with High‐Throughput Phenotyping Empowers the Genetic Dissection of Berry Quality and Resilience Traits in Grapevine |
| title_sort | integrating dense genotyping with high throughput phenotyping empowers the genetic dissection of berry quality and resilience traits in grapevine |
| topic | 200K axiom SNP array association mapping fine mapping haplotype analysis high‐throughput phenotyping NAC08 |
| url | https://doi.org/10.1002/advs.202412587 |
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