Pooled DNA sequencing in hairy vetch (Vicia villosa Roth) reveals QTL for seed dormancy but not pod dehiscence
IntroductionHairy vetch (Vicia villosa Roth) is a promising legume cover crop, but its use is limited by high rates of pod dehiscence and seed dormancy.MethodsWe used phenotypically contrasting pooled DNA samples (n=24 with 29-74 individuals per sample) from an ongoing cover crop breeding program ac...
| Main Authors: | , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2024-04-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2024.1384596/full |
| _version_ | 1797224220921430016 |
|---|---|
| author | Neal Tilhou Lisa Kissing Kucek Brandon Carr Joel Douglas John Englert Shahjahan Ali John Raasch Suresh Bhamidimarri Steven Mirsky Maria J. Monteros Ryan Hayes Heathcliffe Riday |
| author_facet | Neal Tilhou Lisa Kissing Kucek Brandon Carr Joel Douglas John Englert Shahjahan Ali John Raasch Suresh Bhamidimarri Steven Mirsky Maria J. Monteros Ryan Hayes Heathcliffe Riday |
| author_sort | Neal Tilhou |
| collection | DOAJ |
| description | IntroductionHairy vetch (Vicia villosa Roth) is a promising legume cover crop, but its use is limited by high rates of pod dehiscence and seed dormancy.MethodsWe used phenotypically contrasting pooled DNA samples (n=24 with 29-74 individuals per sample) from an ongoing cover crop breeding program across four environments (site-year combinations: Maryland 2020, Maryland 2022, Wisconsin 2021, Wisconsin 2022) to find genetic associations and genomic prediction accuracies for pod dehiscence and seed dormancy. We also combined pooled DNA sample genetic association results with the results of a prior genome-wide association study.Results and discussionGenomic prediction resulted in positive predictive abilities for both traits between environments and with an independent dataset (0.34-0.50), but reduced predictive ability for DNA pools with divergent seed dormancy in the Maryland environments (0.07-0.15). The pooled DNA samples found six significant (false discovery rate q-value<0.01) quantitative trait loci (QTL) for seed dormancy and four significant QTL for pod dehiscence. Unfortunately, the minor alleles of the pod dehiscence QTL increased the rate of pod dehiscence and are not useful for marker-assisted selection. When combined with a prior association study, sixteen seed dormancy QTL and zero pod dehiscence QTL were significant. Combining the association studies did not increase the detection of useful QTL. |
| first_indexed | 2024-04-24T13:49:40Z |
| format | Article |
| id | doaj.art-bc840bba98cf456b9563f2f39bf8276d |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-24T13:49:40Z |
| publishDate | 2024-04-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-bc840bba98cf456b9563f2f39bf8276d2024-04-04T05:05:14ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2024-04-011510.3389/fpls.2024.13845961384596Pooled DNA sequencing in hairy vetch (Vicia villosa Roth) reveals QTL for seed dormancy but not pod dehiscenceNeal Tilhou0Lisa Kissing Kucek1Brandon Carr2Joel Douglas3John Englert4Shahjahan Ali5John Raasch6Suresh Bhamidimarri7Steven Mirsky8Maria J. Monteros9Ryan Hayes10Heathcliffe Riday11United States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United StatesUnited States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United StatesUnited States Department of Agriculture-Natural Resources Conservation Service (USDA-NRCS), James E. “Bud” Smith Plant Materials Center, Knox City, TX, United StatesUnited States Department of Agriculture-Natural Resources Conservation Service (USDA-NRCS), Central National Technology Support Center, Fort Worth, TX, United StatesUnited States Department of Agriculture-Natural Resources Conservation Service (USDA-NRCS), National Plant Materials Program, Washington, DC, United StatesUnited States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United StatesUnited States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United StatesCorteva Agriscience, Connell, WA, United StatesSustainable Agricultural Systems Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD, United StatesBayer Crop Science, North America (NA) Breeding, Chesterfield, MO, United StatesForage Seed and Cereal Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Corvallis, OR, United StatesUnited States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United StatesIntroductionHairy vetch (Vicia villosa Roth) is a promising legume cover crop, but its use is limited by high rates of pod dehiscence and seed dormancy.MethodsWe used phenotypically contrasting pooled DNA samples (n=24 with 29-74 individuals per sample) from an ongoing cover crop breeding program across four environments (site-year combinations: Maryland 2020, Maryland 2022, Wisconsin 2021, Wisconsin 2022) to find genetic associations and genomic prediction accuracies for pod dehiscence and seed dormancy. We also combined pooled DNA sample genetic association results with the results of a prior genome-wide association study.Results and discussionGenomic prediction resulted in positive predictive abilities for both traits between environments and with an independent dataset (0.34-0.50), but reduced predictive ability for DNA pools with divergent seed dormancy in the Maryland environments (0.07-0.15). The pooled DNA samples found six significant (false discovery rate q-value<0.01) quantitative trait loci (QTL) for seed dormancy and four significant QTL for pod dehiscence. Unfortunately, the minor alleles of the pod dehiscence QTL increased the rate of pod dehiscence and are not useful for marker-assisted selection. When combined with a prior association study, sixteen seed dormancy QTL and zero pod dehiscence QTL were significant. Combining the association studies did not increase the detection of useful QTL.https://www.frontiersin.org/articles/10.3389/fpls.2024.1384596/fullgenomic predictionbulk sequencingcover cropdomestication traitsgenome wide association analyses |
| spellingShingle | Neal Tilhou Lisa Kissing Kucek Brandon Carr Joel Douglas John Englert Shahjahan Ali John Raasch Suresh Bhamidimarri Steven Mirsky Maria J. Monteros Ryan Hayes Heathcliffe Riday Pooled DNA sequencing in hairy vetch (Vicia villosa Roth) reveals QTL for seed dormancy but not pod dehiscence Frontiers in Plant Science genomic prediction bulk sequencing cover crop domestication traits genome wide association analyses |
| title | Pooled DNA sequencing in hairy vetch (Vicia villosa Roth) reveals QTL for seed dormancy but not pod dehiscence |
| title_full | Pooled DNA sequencing in hairy vetch (Vicia villosa Roth) reveals QTL for seed dormancy but not pod dehiscence |
| title_fullStr | Pooled DNA sequencing in hairy vetch (Vicia villosa Roth) reveals QTL for seed dormancy but not pod dehiscence |
| title_full_unstemmed | Pooled DNA sequencing in hairy vetch (Vicia villosa Roth) reveals QTL for seed dormancy but not pod dehiscence |
| title_short | Pooled DNA sequencing in hairy vetch (Vicia villosa Roth) reveals QTL for seed dormancy but not pod dehiscence |
| title_sort | pooled dna sequencing in hairy vetch vicia villosa roth reveals qtl for seed dormancy but not pod dehiscence |
| topic | genomic prediction bulk sequencing cover crop domestication traits genome wide association analyses |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2024.1384596/full |
| work_keys_str_mv | AT nealtilhou pooleddnasequencinginhairyvetchviciavillosarothrevealsqtlforseeddormancybutnotpoddehiscence AT lisakissingkucek pooleddnasequencinginhairyvetchviciavillosarothrevealsqtlforseeddormancybutnotpoddehiscence AT brandoncarr pooleddnasequencinginhairyvetchviciavillosarothrevealsqtlforseeddormancybutnotpoddehiscence AT joeldouglas pooleddnasequencinginhairyvetchviciavillosarothrevealsqtlforseeddormancybutnotpoddehiscence AT johnenglert pooleddnasequencinginhairyvetchviciavillosarothrevealsqtlforseeddormancybutnotpoddehiscence AT shahjahanali pooleddnasequencinginhairyvetchviciavillosarothrevealsqtlforseeddormancybutnotpoddehiscence AT johnraasch pooleddnasequencinginhairyvetchviciavillosarothrevealsqtlforseeddormancybutnotpoddehiscence AT sureshbhamidimarri pooleddnasequencinginhairyvetchviciavillosarothrevealsqtlforseeddormancybutnotpoddehiscence AT stevenmirsky pooleddnasequencinginhairyvetchviciavillosarothrevealsqtlforseeddormancybutnotpoddehiscence AT mariajmonteros pooleddnasequencinginhairyvetchviciavillosarothrevealsqtlforseeddormancybutnotpoddehiscence AT ryanhayes pooleddnasequencinginhairyvetchviciavillosarothrevealsqtlforseeddormancybutnotpoddehiscence AT heathclifferiday pooleddnasequencinginhairyvetchviciavillosarothrevealsqtlforseeddormancybutnotpoddehiscence |