Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat
Abstract Germplasm collections are rich sources of genetic variation to improve crops for many valuable traits. Nested association mapping (NAM) populations can overcome the limitations of genome‐wide association studies (GWAS) in germplasm collections by reducing the effect of population structure....
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Wiley
2020-11-01
|
| Series: | The Plant Genome |
| Online Access: | https://doi.org/10.1002/tpg2.20051 |
| _version_ | 1818204860235907072 |
|---|---|
| author | Ahmad H. Sallam Fazal Manan Prabin Bajgain Matthew Martin Tamas Szinyei Emily Conley Gina Brown‐Guedira Gary J. Muehlbauer James A. Anderson Brian J. Steffenson |
| author_facet | Ahmad H. Sallam Fazal Manan Prabin Bajgain Matthew Martin Tamas Szinyei Emily Conley Gina Brown‐Guedira Gary J. Muehlbauer James A. Anderson Brian J. Steffenson |
| author_sort | Ahmad H. Sallam |
| collection | DOAJ |
| description | Abstract Germplasm collections are rich sources of genetic variation to improve crops for many valuable traits. Nested association mapping (NAM) populations can overcome the limitations of genome‐wide association studies (GWAS) in germplasm collections by reducing the effect of population structure. We exploited the genetic diversity of the USDA‐ARS wheat (Triticum aestivum L.) core collection by developing the Spring Wheat Multiparent Introgression Population (SWMIP). To develop this population, twenty‐five core parents were crossed and backcrossed to the Minnesota spring wheat cultivar RB07. The NAM population and 26 founder parents were genotyped using genotyping‐by‐sequencing and phenotyped for heading date, height, test weight, and grain protein content. After quality control, 20,312 markers with physical map positions were generated for 2,038 recombinant inbred lines (RILs). The number of RILs in each family varied between 58 and 96. Three GWAS models were utilized for quantitative trait loci (QTL) detection and accounted for known family stratification, genetic kinship, and both covariates. GWAS was performed on the whole population and also by bootstrap sampling of an equal number of RILs from each family. Greater power of QTL detection was achieved by treating families equally through bootstrapping. In total 16, 15, 12, and 13 marker‐trait associations (MTAs) were identified for heading date, height, test weight, and grain protein content, respectively. Some of these MTAs were coincident with major genes known to control the traits, but others were novel and contributed by the wheat core parents. The SWMIP will be a valuable source of genetic variation for spring wheat breeding. |
| first_indexed | 2024-12-12T03:47:57Z |
| format | Article |
| id | doaj.art-80c8eed0d264443e901cb4dbeb2abd9b |
| institution | Directory Open Access Journal |
| issn | 1940-3372 |
| language | English |
| last_indexed | 2024-12-12T03:47:57Z |
| publishDate | 2020-11-01 |
| publisher | Wiley |
| record_format | Article |
| series | The Plant Genome |
| spelling | doaj.art-80c8eed0d264443e901cb4dbeb2abd9b2022-12-22T00:39:28ZengWileyThe Plant Genome1940-33722020-11-01133n/an/a10.1002/tpg2.20051Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheatAhmad H. Sallam0Fazal Manan1Prabin Bajgain2Matthew Martin3Tamas Szinyei4Emily Conley5Gina Brown‐Guedira6Gary J. Muehlbauer7James A. Anderson8Brian J. Steffenson9Department of Plant Pathology University of Minnesota St. Paul MN 55108 USADepartment of Plant Pathology University of Minnesota St. Paul MN 55108 USADepartment of Agronomy and Plant Genetics University of Minnesota St. Paul MN 55108 USADepartment of Plant Pathology University of Minnesota St. Paul MN 55108 USADepartment of Plant Pathology University of Minnesota St. Paul MN 55108 USADepartment of Agronomy and Plant Genetics University of Minnesota St. Paul MN 55108 USAPlant Science Research USDA‐ARS Raleigh NC 27695 USADepartment of Agronomy and Plant Genetics University of Minnesota St. Paul MN 55108 USADepartment of Agronomy and Plant Genetics University of Minnesota St. Paul MN 55108 USADepartment of Plant Pathology University of Minnesota St. Paul MN 55108 USAAbstract Germplasm collections are rich sources of genetic variation to improve crops for many valuable traits. Nested association mapping (NAM) populations can overcome the limitations of genome‐wide association studies (GWAS) in germplasm collections by reducing the effect of population structure. We exploited the genetic diversity of the USDA‐ARS wheat (Triticum aestivum L.) core collection by developing the Spring Wheat Multiparent Introgression Population (SWMIP). To develop this population, twenty‐five core parents were crossed and backcrossed to the Minnesota spring wheat cultivar RB07. The NAM population and 26 founder parents were genotyped using genotyping‐by‐sequencing and phenotyped for heading date, height, test weight, and grain protein content. After quality control, 20,312 markers with physical map positions were generated for 2,038 recombinant inbred lines (RILs). The number of RILs in each family varied between 58 and 96. Three GWAS models were utilized for quantitative trait loci (QTL) detection and accounted for known family stratification, genetic kinship, and both covariates. GWAS was performed on the whole population and also by bootstrap sampling of an equal number of RILs from each family. Greater power of QTL detection was achieved by treating families equally through bootstrapping. In total 16, 15, 12, and 13 marker‐trait associations (MTAs) were identified for heading date, height, test weight, and grain protein content, respectively. Some of these MTAs were coincident with major genes known to control the traits, but others were novel and contributed by the wheat core parents. The SWMIP will be a valuable source of genetic variation for spring wheat breeding.https://doi.org/10.1002/tpg2.20051 |
| spellingShingle | Ahmad H. Sallam Fazal Manan Prabin Bajgain Matthew Martin Tamas Szinyei Emily Conley Gina Brown‐Guedira Gary J. Muehlbauer James A. Anderson Brian J. Steffenson Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat The Plant Genome |
| title | Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat |
| title_full | Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat |
| title_fullStr | Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat |
| title_full_unstemmed | Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat |
| title_short | Genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat |
| title_sort | genetic architecture of agronomic and quality traits in a nested association mapping population of spring wheat |
| url | https://doi.org/10.1002/tpg2.20051 |
| work_keys_str_mv | AT ahmadhsallam geneticarchitectureofagronomicandqualitytraitsinanestedassociationmappingpopulationofspringwheat AT fazalmanan geneticarchitectureofagronomicandqualitytraitsinanestedassociationmappingpopulationofspringwheat AT prabinbajgain geneticarchitectureofagronomicandqualitytraitsinanestedassociationmappingpopulationofspringwheat AT matthewmartin geneticarchitectureofagronomicandqualitytraitsinanestedassociationmappingpopulationofspringwheat AT tamasszinyei geneticarchitectureofagronomicandqualitytraitsinanestedassociationmappingpopulationofspringwheat AT emilyconley geneticarchitectureofagronomicandqualitytraitsinanestedassociationmappingpopulationofspringwheat AT ginabrownguedira geneticarchitectureofagronomicandqualitytraitsinanestedassociationmappingpopulationofspringwheat AT garyjmuehlbauer geneticarchitectureofagronomicandqualitytraitsinanestedassociationmappingpopulationofspringwheat AT jamesaanderson geneticarchitectureofagronomicandqualitytraitsinanestedassociationmappingpopulationofspringwheat AT brianjsteffenson geneticarchitectureofagronomicandqualitytraitsinanestedassociationmappingpopulationofspringwheat |