Dissecting the genetic basis of fruiting efficiency for genetic enhancement of harvest index, grain number, and yield in wheat
Abstract Background Grain number (GN) is one of the key yield contributing factors in modern wheat (Triticum aestivum) varieties. Fruiting efficiency (FE) is a key trait for increasing GN by making more spike assimilates available to reproductive structures. Thousand grain weight (TGW) is also an im...
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2025-01-01
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| Online Access: | https://doi.org/10.1186/s12870-025-06072-1 |
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| author | Dipendra Shahi Jia Guo Md Ali Babar Sumit Pradhan Muhsin AVCI Jordan McBreen Zhao Liu Guihua Bai Paul St. Amand Amy Bernardo Matthew Reynolds Gemma Molero Sivakumar Sukumaran John Foulkes Jahangir Khan |
| author_facet | Dipendra Shahi Jia Guo Md Ali Babar Sumit Pradhan Muhsin AVCI Jordan McBreen Zhao Liu Guihua Bai Paul St. Amand Amy Bernardo Matthew Reynolds Gemma Molero Sivakumar Sukumaran John Foulkes Jahangir Khan |
| author_sort | Dipendra Shahi |
| collection | DOAJ |
| description | Abstract Background Grain number (GN) is one of the key yield contributing factors in modern wheat (Triticum aestivum) varieties. Fruiting efficiency (FE) is a key trait for increasing GN by making more spike assimilates available to reproductive structures. Thousand grain weight (TGW) is also an important component of grain yield. To understand the genetic architecture of FE and TGW, we performed a genome-wide association study (GWAS) in a panel of 236 US soft facultative wheats that were phenotyped in three experiments at two locations in Florida and genotyped with 20,706 single nucleotide polymorphisms (SNPs) generated from genotyping-by-sequencing (GBS). Results FE showed significant positive associations with GN, grain yield (GY), and harvest index (HI). Likewise, TGW mostly had a positive correlation with GY and HI, but a negative correlation with GN. Eighteen marker-trait associations (MTAs) for FE and TGW were identified on 11 chromosomes, with nine MTAs within genes. Several MTAs associated with other traits were found within genes with different biological and metabolic functions including nuclear pore complex protein, F-box protein, oligopeptide transporter, and glycoside vacuolar protein. Two KASP markers showed significant mean differences for FE and TGW traits in a validation population. Conclusions KASP marker development and validation demonstrated the utility of these markers for improving FE and TGW in breeding programs. The results suggest that optimizing intra-spike partitioning and utilizing marker-assisted selection (MAS) can enhance GY and HI. |
| format | Article |
| id | doaj-art-0016739847b0431b874ad4ab4dff10ef |
| institution | Kabale University |
| issn | 1471-2229 |
| language | English |
| publishDate | 2025-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Plant Biology |
| spelling | doaj-art-0016739847b0431b874ad4ab4dff10ef2025-01-26T12:23:16ZengBMCBMC Plant Biology1471-22292025-01-0125111510.1186/s12870-025-06072-1Dissecting the genetic basis of fruiting efficiency for genetic enhancement of harvest index, grain number, and yield in wheatDipendra Shahi0Jia Guo1Md Ali Babar2Sumit Pradhan3Muhsin AVCI4Jordan McBreen5Zhao Liu6Guihua Bai7Paul St. Amand8Amy Bernardo9Matthew Reynolds10Gemma Molero11Sivakumar Sukumaran12John Foulkes13Jahangir Khan14School of Plant, Environmental and Soil Sciences, Louisiana State Agricultural Center, Louisiana State UniversityInari AgricultureDepartment of Agronomy, University of FloridaDepartment of Agronomy, University of FloridaDepartment of Agronomy, University of FloridaDepartment of Agronomy, University of FloridaDepartment of Agronomy, Kansas State UniversityUSDA-ARS Hard Winter Wheat Genetics Research UnitUSDA-ARS Hard Winter Wheat Genetics Research UnitUSDA-ARS Hard Winter Wheat Genetics Research UnitInternational Maize and Wheat Improvement Center (CIMMYT)International Maize and Wheat Improvement Center (CIMMYT)International Maize and Wheat Improvement Center (CIMMYT)Division of Plant and Crop Sciences, School of Biosciences, University of NottinghamPARC-Balochistan Agricultural Research and Development CenterAbstract Background Grain number (GN) is one of the key yield contributing factors in modern wheat (Triticum aestivum) varieties. Fruiting efficiency (FE) is a key trait for increasing GN by making more spike assimilates available to reproductive structures. Thousand grain weight (TGW) is also an important component of grain yield. To understand the genetic architecture of FE and TGW, we performed a genome-wide association study (GWAS) in a panel of 236 US soft facultative wheats that were phenotyped in three experiments at two locations in Florida and genotyped with 20,706 single nucleotide polymorphisms (SNPs) generated from genotyping-by-sequencing (GBS). Results FE showed significant positive associations with GN, grain yield (GY), and harvest index (HI). Likewise, TGW mostly had a positive correlation with GY and HI, but a negative correlation with GN. Eighteen marker-trait associations (MTAs) for FE and TGW were identified on 11 chromosomes, with nine MTAs within genes. Several MTAs associated with other traits were found within genes with different biological and metabolic functions including nuclear pore complex protein, F-box protein, oligopeptide transporter, and glycoside vacuolar protein. Two KASP markers showed significant mean differences for FE and TGW traits in a validation population. Conclusions KASP marker development and validation demonstrated the utility of these markers for improving FE and TGW in breeding programs. The results suggest that optimizing intra-spike partitioning and utilizing marker-assisted selection (MAS) can enhance GY and HI.https://doi.org/10.1186/s12870-025-06072-1Fruiting efficiencyHarvest indexKASP markerGWASMarker-trait association |
| spellingShingle | Dipendra Shahi Jia Guo Md Ali Babar Sumit Pradhan Muhsin AVCI Jordan McBreen Zhao Liu Guihua Bai Paul St. Amand Amy Bernardo Matthew Reynolds Gemma Molero Sivakumar Sukumaran John Foulkes Jahangir Khan Dissecting the genetic basis of fruiting efficiency for genetic enhancement of harvest index, grain number, and yield in wheat BMC Plant Biology Fruiting efficiency Harvest index KASP marker GWAS Marker-trait association |
| title | Dissecting the genetic basis of fruiting efficiency for genetic enhancement of harvest index, grain number, and yield in wheat |
| title_full | Dissecting the genetic basis of fruiting efficiency for genetic enhancement of harvest index, grain number, and yield in wheat |
| title_fullStr | Dissecting the genetic basis of fruiting efficiency for genetic enhancement of harvest index, grain number, and yield in wheat |
| title_full_unstemmed | Dissecting the genetic basis of fruiting efficiency for genetic enhancement of harvest index, grain number, and yield in wheat |
| title_short | Dissecting the genetic basis of fruiting efficiency for genetic enhancement of harvest index, grain number, and yield in wheat |
| title_sort | dissecting the genetic basis of fruiting efficiency for genetic enhancement of harvest index grain number and yield in wheat |
| topic | Fruiting efficiency Harvest index KASP marker GWAS Marker-trait association |
| url | https://doi.org/10.1186/s12870-025-06072-1 |
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