A multi-trait GWAS-based genetic association network controlling soybean architecture and seed traits
Ideal plant architecture is essential for enhancing crop yields. Ideal soybean (Glycine max) architecture encompasses an appropriate plant height, increased node number, moderate seed weight, and compact architecture with smaller branch angles for growth under high-density planting. However, the fun...
| Main Authors: | , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2024-01-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2023.1302359/full |
| _version_ | 1797362424683167744 |
|---|---|
| author | Mengrou Niu Mengrou Niu Mengrou Niu Mengrou Niu Kewei Tian Kewei Tian Kewei Tian Kewei Tian Qiang Chen Chunyan Yang Mengchen Zhang Shiyong Sun Shiyong Sun Shiyong Sun Xuelu Wang Xuelu Wang Xuelu Wang |
| author_facet | Mengrou Niu Mengrou Niu Mengrou Niu Mengrou Niu Kewei Tian Kewei Tian Kewei Tian Kewei Tian Qiang Chen Chunyan Yang Mengchen Zhang Shiyong Sun Shiyong Sun Shiyong Sun Xuelu Wang Xuelu Wang Xuelu Wang |
| author_sort | Mengrou Niu |
| collection | DOAJ |
| description | Ideal plant architecture is essential for enhancing crop yields. Ideal soybean (Glycine max) architecture encompasses an appropriate plant height, increased node number, moderate seed weight, and compact architecture with smaller branch angles for growth under high-density planting. However, the functional genes regulating plant architecture are far not fully understood in soybean. In this study, we investigated the genetic basis of 12 agronomic traits in a panel of 496 soybean accessions with a wide geographical distribution in China. Analysis of phenotypic changes in 148 historical elite soybean varieties indicated that seed-related traits have mainly been improved over the past 60 years, with targeting plant architecture traits having the potential to further improve yields in future soybean breeding programs. In a genome-wide association study (GWAS) of 12 traits, we detected 169 significantly associated loci, of which 61 overlapped with previously reported loci and 108 new loci. By integrating the GWAS loci for different traits, we constructed a genetic association network and identified 90 loci that were associated with a single trait and 79 loci with pleiotropic effects. Of these 79 loci, 7 hub-nodes were strongly linked to at least three related agronomic traits. qHub_5, containing the previously characterized Determinate 1 (Dt1) locus, was associated not only with plant height and node number (as determined previously), but also with internode length and pod range. Furthermore, we identified qHub_7, which controls three branch angle-related traits; the candidate genes in this locus may be beneficial for breeding soybean with compact architecture. These findings provide insights into the genetic relationships among 12 important agronomic traits in soybean. In addition, these studies uncover valuable loci for further functional gene studies and will facilitate molecular design breeding of soybean architecture. |
| first_indexed | 2024-03-08T16:06:49Z |
| format | Article |
| id | doaj.art-d90e4a741be94d369aa42412bbb798e8 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-03-08T16:06:49Z |
| publishDate | 2024-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-d90e4a741be94d369aa42412bbb798e82024-01-08T05:27:09ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2024-01-011410.3389/fpls.2023.13023591302359A multi-trait GWAS-based genetic association network controlling soybean architecture and seed traitsMengrou Niu0Mengrou Niu1Mengrou Niu2Mengrou Niu3Kewei Tian4Kewei Tian5Kewei Tian6Kewei Tian7Qiang Chen8Chunyan Yang9Mengchen Zhang10Shiyong Sun11Shiyong Sun12Shiyong Sun13Xuelu Wang14Xuelu Wang15Xuelu Wang16Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, ChinaSanya Institute of Henan University, Henan University, Sanya, Hainan, ChinaState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Zhengzhou, ChinaThe Academy for Advanced Interdisciplinary Studies, Henan University, Zhengzhou, ChinaCenter of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, ChinaSanya Institute of Henan University, Henan University, Sanya, Hainan, ChinaState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Zhengzhou, ChinaThe Academy for Advanced Interdisciplinary Studies, Henan University, Zhengzhou, ChinaInstitute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang, Hebei, ChinaInstitute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang, Hebei, ChinaInstitute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang, Hebei, ChinaSanya Institute of Henan University, Henan University, Sanya, Hainan, ChinaState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Zhengzhou, ChinaThe Academy for Advanced Interdisciplinary Studies, Henan University, Zhengzhou, ChinaSanya Institute of Henan University, Henan University, Sanya, Hainan, ChinaState Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Zhengzhou, ChinaThe Academy for Advanced Interdisciplinary Studies, Henan University, Zhengzhou, ChinaIdeal plant architecture is essential for enhancing crop yields. Ideal soybean (Glycine max) architecture encompasses an appropriate plant height, increased node number, moderate seed weight, and compact architecture with smaller branch angles for growth under high-density planting. However, the functional genes regulating plant architecture are far not fully understood in soybean. In this study, we investigated the genetic basis of 12 agronomic traits in a panel of 496 soybean accessions with a wide geographical distribution in China. Analysis of phenotypic changes in 148 historical elite soybean varieties indicated that seed-related traits have mainly been improved over the past 60 years, with targeting plant architecture traits having the potential to further improve yields in future soybean breeding programs. In a genome-wide association study (GWAS) of 12 traits, we detected 169 significantly associated loci, of which 61 overlapped with previously reported loci and 108 new loci. By integrating the GWAS loci for different traits, we constructed a genetic association network and identified 90 loci that were associated with a single trait and 79 loci with pleiotropic effects. Of these 79 loci, 7 hub-nodes were strongly linked to at least three related agronomic traits. qHub_5, containing the previously characterized Determinate 1 (Dt1) locus, was associated not only with plant height and node number (as determined previously), but also with internode length and pod range. Furthermore, we identified qHub_7, which controls three branch angle-related traits; the candidate genes in this locus may be beneficial for breeding soybean with compact architecture. These findings provide insights into the genetic relationships among 12 important agronomic traits in soybean. In addition, these studies uncover valuable loci for further functional gene studies and will facilitate molecular design breeding of soybean architecture.https://www.frontiersin.org/articles/10.3389/fpls.2023.1302359/fullsoybeanagronomic traitsarchitectureGWASbranch angle |
| spellingShingle | Mengrou Niu Mengrou Niu Mengrou Niu Mengrou Niu Kewei Tian Kewei Tian Kewei Tian Kewei Tian Qiang Chen Chunyan Yang Mengchen Zhang Shiyong Sun Shiyong Sun Shiyong Sun Xuelu Wang Xuelu Wang Xuelu Wang A multi-trait GWAS-based genetic association network controlling soybean architecture and seed traits Frontiers in Plant Science soybean agronomic traits architecture GWAS branch angle |
| title | A multi-trait GWAS-based genetic association network controlling soybean architecture and seed traits |
| title_full | A multi-trait GWAS-based genetic association network controlling soybean architecture and seed traits |
| title_fullStr | A multi-trait GWAS-based genetic association network controlling soybean architecture and seed traits |
| title_full_unstemmed | A multi-trait GWAS-based genetic association network controlling soybean architecture and seed traits |
| title_short | A multi-trait GWAS-based genetic association network controlling soybean architecture and seed traits |
| title_sort | multi trait gwas based genetic association network controlling soybean architecture and seed traits |
| topic | soybean agronomic traits architecture GWAS branch angle |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2023.1302359/full |
| work_keys_str_mv | AT mengrouniu amultitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT mengrouniu amultitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT mengrouniu amultitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT mengrouniu amultitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT keweitian amultitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT keweitian amultitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT keweitian amultitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT keweitian amultitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT qiangchen amultitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT chunyanyang amultitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT mengchenzhang amultitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT shiyongsun amultitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT shiyongsun amultitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT shiyongsun amultitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT xueluwang amultitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT xueluwang amultitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT xueluwang amultitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT mengrouniu multitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT mengrouniu multitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT mengrouniu multitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT mengrouniu multitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT keweitian multitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT keweitian multitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT keweitian multitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT keweitian multitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT qiangchen multitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT chunyanyang multitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT mengchenzhang multitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT shiyongsun multitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT shiyongsun multitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT shiyongsun multitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT xueluwang multitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT xueluwang multitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits AT xueluwang multitraitgwasbasedgeneticassociationnetworkcontrollingsoybeanarchitectureandseedtraits |