Discovering useful genetic variation in the seed parent gene pool for sorghum improvement
Multi-parent populations contain valuable genetic material for dissecting complex, quantitative traits and provide a unique opportunity to capture multi-allelic variation compared to the biparental populations. A multi-parent advanced generation inter-cross (MAGIC) B-line (MBL) population composed o...
| Main Authors: | , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2023-09-01
|
| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fgene.2023.1221148/full |
| _version_ | 1797681899071602688 |
|---|---|
| author | Neeraj Kumar Neeraj Kumar J. Lucas Boatwright J. Lucas Boatwright Sirjan Sapkota Zachary W. Brenton Zachary W. Brenton Carolina Ballén-Taborda Carolina Ballén-Taborda Matthew T. Myers Matthew T. Myers William A. Cox William A. Cox Kathleen E. Jordan Kathleen E. Jordan Stephen Kresovich Stephen Kresovich Stephen Kresovich Richard E. Boyles Richard E. Boyles |
| author_facet | Neeraj Kumar Neeraj Kumar J. Lucas Boatwright J. Lucas Boatwright Sirjan Sapkota Zachary W. Brenton Zachary W. Brenton Carolina Ballén-Taborda Carolina Ballén-Taborda Matthew T. Myers Matthew T. Myers William A. Cox William A. Cox Kathleen E. Jordan Kathleen E. Jordan Stephen Kresovich Stephen Kresovich Stephen Kresovich Richard E. Boyles Richard E. Boyles |
| author_sort | Neeraj Kumar |
| collection | DOAJ |
| description | Multi-parent populations contain valuable genetic material for dissecting complex, quantitative traits and provide a unique opportunity to capture multi-allelic variation compared to the biparental populations. A multi-parent advanced generation inter-cross (MAGIC) B-line (MBL) population composed of 708 F6 recombinant inbred lines (RILs), was recently developed from four diverse founders. These selected founders strategically represented the four most prevalent botanical races (kafir, guinea, durra, and caudatum) to capture a significant source of genetic variation to study the quantitative traits in grain sorghum [Sorghum bicolor (L.) Moench]. MBL was phenotyped at two field locations for seven yield-influencing traits: panicle type (PT), days to anthesis (DTA), plant height (PH), grain yield (GY), 1000-grain weight (TGW), tiller number per meter (TN) and yield per panicle (YPP). High phenotypic variation was observed for all the quantitative traits, with broad-sense heritabilities ranging from 0.34 (TN) to 0.84 (PH). The entire population was genotyped using Diversity Arrays Technology (DArTseq), and 8,800 single nucleotide polymorphisms (SNPs) were generated. A set of polymorphic, quality-filtered markers (3,751 SNPs) and phenotypic data were used for genome-wide association studies (GWAS). We identified 52 marker-trait associations (MTAs) for the seven traits using BLUPs generated from replicated plots in two locations. We also identified desirable allelic combinations based on the plant height loci (Dw1, Dw2, and Dw3), which influences yield related traits. Additionally, two novel MTAs were identified each on Chr1 and Chr7 for yield traits independent of dwarfing genes. We further performed a multi-variate adaptive shrinkage analysis and 15 MTAs with pleiotropic effect were identified. The five best performing MBL progenies were selected carrying desirable allelic combinations. Since the MBL population was designed to capture significant diversity for maintainer line (B-line) accessions, these progenies can serve as valuable resources to develop superior sorghum hybrids after validation of their general combining abilities via crossing with elite pollinators. Further, newly identified desirable allelic combinations can be used to enrich the maintainer germplasm lines through marker-assisted backcross breeding. |
| first_indexed | 2024-03-11T23:51:42Z |
| format | Article |
| id | doaj.art-f6f872d0669e47339aed633505112428 |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-03-11T23:51:42Z |
| publishDate | 2023-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-f6f872d0669e47339aed6335051124282023-09-19T06:53:17ZengFrontiers Media S.A.Frontiers in Genetics1664-80212023-09-011410.3389/fgene.2023.12211481221148Discovering useful genetic variation in the seed parent gene pool for sorghum improvementNeeraj Kumar0Neeraj Kumar1J. Lucas Boatwright2J. Lucas Boatwright3Sirjan Sapkota4Zachary W. Brenton5Zachary W. Brenton6Carolina Ballén-Taborda7Carolina Ballén-Taborda8Matthew T. Myers9Matthew T. Myers10William A. Cox11William A. Cox12Kathleen E. Jordan13Kathleen E. Jordan14Stephen Kresovich15Stephen Kresovich16Stephen Kresovich17Richard E. Boyles18Richard E. Boyles19Advanced Plant Technology, Clemson University, Clemson, SC, United StatesDepartment of Plant and Environmental Sciences, Clemson University, Clemson, SC, United StatesAdvanced Plant Technology, Clemson University, Clemson, SC, United StatesDepartment of Plant and Environmental Sciences, Clemson University, Clemson, SC, United StatesAdvanced Plant Technology, Clemson University, Clemson, SC, United StatesAdvanced Plant Technology, Clemson University, Clemson, SC, United StatesCarolina Seed Systems, Darlington, SC, United StatesDepartment of Plant and Environmental Sciences, Clemson University, Clemson, SC, United StatesPee Dee Research and Education Center, Clemson University, Florence, SC, United StatesAdvanced Plant Technology, Clemson University, Clemson, SC, United StatesDepartment of Plant and Environmental Sciences, Clemson University, Clemson, SC, United StatesAdvanced Plant Technology, Clemson University, Clemson, SC, United StatesDepartment of Plant and Environmental Sciences, Clemson University, Clemson, SC, United StatesAdvanced Plant Technology, Clemson University, Clemson, SC, United StatesDepartment of Plant and Environmental Sciences, Clemson University, Clemson, SC, United StatesAdvanced Plant Technology, Clemson University, Clemson, SC, United StatesDepartment of Plant and Environmental Sciences, Clemson University, Clemson, SC, United StatesFeed the Future Innovation Lab for Crop Improvement, Cornell University, Ithaca, NY, United StatesDepartment of Plant and Environmental Sciences, Clemson University, Clemson, SC, United StatesPee Dee Research and Education Center, Clemson University, Florence, SC, United StatesMulti-parent populations contain valuable genetic material for dissecting complex, quantitative traits and provide a unique opportunity to capture multi-allelic variation compared to the biparental populations. A multi-parent advanced generation inter-cross (MAGIC) B-line (MBL) population composed of 708 F6 recombinant inbred lines (RILs), was recently developed from four diverse founders. These selected founders strategically represented the four most prevalent botanical races (kafir, guinea, durra, and caudatum) to capture a significant source of genetic variation to study the quantitative traits in grain sorghum [Sorghum bicolor (L.) Moench]. MBL was phenotyped at two field locations for seven yield-influencing traits: panicle type (PT), days to anthesis (DTA), plant height (PH), grain yield (GY), 1000-grain weight (TGW), tiller number per meter (TN) and yield per panicle (YPP). High phenotypic variation was observed for all the quantitative traits, with broad-sense heritabilities ranging from 0.34 (TN) to 0.84 (PH). The entire population was genotyped using Diversity Arrays Technology (DArTseq), and 8,800 single nucleotide polymorphisms (SNPs) were generated. A set of polymorphic, quality-filtered markers (3,751 SNPs) and phenotypic data were used for genome-wide association studies (GWAS). We identified 52 marker-trait associations (MTAs) for the seven traits using BLUPs generated from replicated plots in two locations. We also identified desirable allelic combinations based on the plant height loci (Dw1, Dw2, and Dw3), which influences yield related traits. Additionally, two novel MTAs were identified each on Chr1 and Chr7 for yield traits independent of dwarfing genes. We further performed a multi-variate adaptive shrinkage analysis and 15 MTAs with pleiotropic effect were identified. The five best performing MBL progenies were selected carrying desirable allelic combinations. Since the MBL population was designed to capture significant diversity for maintainer line (B-line) accessions, these progenies can serve as valuable resources to develop superior sorghum hybrids after validation of their general combining abilities via crossing with elite pollinators. Further, newly identified desirable allelic combinations can be used to enrich the maintainer germplasm lines through marker-assisted backcross breeding.https://www.frontiersin.org/articles/10.3389/fgene.2023.1221148/fullDArT markersgenome-wide association studies (GWAS)multi-parent advanced generation inter-cross (MAGIC)grain sorghumyield components |
| spellingShingle | Neeraj Kumar Neeraj Kumar J. Lucas Boatwright J. Lucas Boatwright Sirjan Sapkota Zachary W. Brenton Zachary W. Brenton Carolina Ballén-Taborda Carolina Ballén-Taborda Matthew T. Myers Matthew T. Myers William A. Cox William A. Cox Kathleen E. Jordan Kathleen E. Jordan Stephen Kresovich Stephen Kresovich Stephen Kresovich Richard E. Boyles Richard E. Boyles Discovering useful genetic variation in the seed parent gene pool for sorghum improvement Frontiers in Genetics DArT markers genome-wide association studies (GWAS) multi-parent advanced generation inter-cross (MAGIC) grain sorghum yield components |
| title | Discovering useful genetic variation in the seed parent gene pool for sorghum improvement |
| title_full | Discovering useful genetic variation in the seed parent gene pool for sorghum improvement |
| title_fullStr | Discovering useful genetic variation in the seed parent gene pool for sorghum improvement |
| title_full_unstemmed | Discovering useful genetic variation in the seed parent gene pool for sorghum improvement |
| title_short | Discovering useful genetic variation in the seed parent gene pool for sorghum improvement |
| title_sort | discovering useful genetic variation in the seed parent gene pool for sorghum improvement |
| topic | DArT markers genome-wide association studies (GWAS) multi-parent advanced generation inter-cross (MAGIC) grain sorghum yield components |
| url | https://www.frontiersin.org/articles/10.3389/fgene.2023.1221148/full |
| work_keys_str_mv | AT neerajkumar discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT neerajkumar discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT jlucasboatwright discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT jlucasboatwright discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT sirjansapkota discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT zacharywbrenton discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT zacharywbrenton discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT carolinaballentaborda discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT carolinaballentaborda discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT matthewtmyers discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT matthewtmyers discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT williamacox discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT williamacox discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT kathleenejordan discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT kathleenejordan discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT stephenkresovich discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT stephenkresovich discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT stephenkresovich discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT richardeboyles discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement AT richardeboyles discoveringusefulgeneticvariationintheseedparentgenepoolforsorghumimprovement |