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Tilhou N, Kissing Kucek L, Carr B, Douglas J, Englert J, Ali S, Raasch J, Bhamidimarri S, Mirsky S, Monteros MJ, Hayes R, Riday H. Pooled DNA sequencing in hairy vetch ( Vicia villosa Roth) reveals QTL for seed dormancy but not pod dehiscence. Front Plant Sci 2024; 15:1384596. [PMID: 38638346 PMCID: PMC11024373 DOI: 10.3389/fpls.2024.1384596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/21/2024] [Indexed: 04/20/2024]
Abstract
Introduction Hairy vetch (Vicia villosa Roth) is a promising legume cover crop, but its use is limited by high rates of pod dehiscence and seed dormancy. Methods We 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 discussion Genomic 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.
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Affiliation(s)
- Neal Tilhou
- United States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | - Lisa Kissing Kucek
- United States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | - Brandon Carr
- United States Department of Agriculture-Natural Resources Conservation Service (USDA-NRCS), James E. “Bud” Smith Plant Materials Center, Knox City, TX, United States
| | - Joel Douglas
- United States Department of Agriculture-Natural Resources Conservation Service (USDA-NRCS), Central National Technology Support Center, Fort Worth, TX, United States
| | - John Englert
- United States Department of Agriculture-Natural Resources Conservation Service (USDA-NRCS), National Plant Materials Program, Washington, DC, United States
| | - Shahjahan Ali
- United States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | - John Raasch
- United States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | | | - Steven Mirsky
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Beltsville, MD, United States
| | - Maria J. Monteros
- Bayer Crop Science, North America (NA) Breeding, Chesterfield, MO, United States
| | - Ryan Hayes
- Forage Seed and Cereal Research Unit, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Corvallis, OR, United States
| | - Heathcliffe Riday
- United States (US) Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
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Fuller T, Bickhart DM, Koch LM, Kucek LK, Ali S, Mangelson H, Monteros MJ, Hernandez T, Smith TPL, Riday H, Sullivan ML. A reference assembly for the legume cover crop hairy vetch ( Vicia villosa). GigaByte 2023; 2023:gigabyte98. [PMID: 38023065 PMCID: PMC10659084 DOI: 10.46471/gigabyte.98] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 11/03/2023] [Indexed: 12/01/2023] Open
Abstract
Vicia villosa is an incompletely domesticated annual legume of the Fabaceae family native to Europe and Western Asia. V. villosa is widely used as a cover crop and forage due to its ability to withstand harsh winters. Here, we generated a reference-quality genome assembly (Vvill1.0) from low error-rate long-sequence reads to improve the genetic-based trait selection of this species. Our Vvill1.0 assembly includes seven scaffolds corresponding to the seven estimated linkage groups and comprising approximately 68% of the total genome size of 2.03 Gbp. This assembly is expected to be a useful resource for genetically improving this emerging cover crop species and provide useful insights into legume genomics and plant genome evolution.
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Affiliation(s)
- Tyson Fuller
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | - Derek M. Bickhart
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | - Lisa M. Koch
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | - Lisa Kissing Kucek
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | - Shahjahan Ali
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | | | - Maria J. Monteros
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Timothy Hernandez
- Noble Research Institute, 2510 Sam Noble Parkway, Ardmore, OK 73401, USA
| | - Timothy P. L. Smith
- US Meat Animal Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), PO Box 166 (State Spur 18D), Clay Center, NE 68933, USA
| | - Heathcliffe Riday
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
| | - Michael L. Sullivan
- US Dairy Forage Research Center, United States Department of Agriculture Agricultural Research Service (USDA-ARS), 1925 Linden Drive, Madison, WI 53706, USA
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Tilhou N, Kucek LK, Carr B, Marion A, Douglas J, Englert J, Ali S, Raasch J, Bhamidimarri S, Mirsky SB, Monteros MJ, Krogman S, Hayes R, Azevedo M, Riday H. Genome-wide association mapping in hairy vetch ( Vicia villosa) discovers a large effect locus controlling seed dormancy. Front Plant Sci 2023; 14:1282187. [PMID: 37941659 PMCID: PMC10628312 DOI: 10.3389/fpls.2023.1282187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/06/2023] [Indexed: 11/10/2023]
Abstract
Hairy vetch (Vicia villosa Roth), a winter-hardy annual legume, is a promising cover crop. To fully leverage its potential, seed production and field performance of V. villosa must be improved to facilitate producer adoption. Two classic domestication traits, seed dormancy (hard seed) and dehiscence (pod shatter), are selection targets in an ongoing breeding program. This study reports a genome-wide association study of 1,019 V. villosa individuals evaluated at two sites (Knox City, Texas and Corvallis, Oregon) for the proportion of dormant seed, visual pod dehiscence scores, and two dehiscence surrogate measures (force to dehiscence and pod spiraling score). Trait performance varied between sites, but reliability (related to heritability) across sites was strong (dormant seed proportion: 0.68; dehiscence score: 0.61; spiraling score: 0.42; force to dehiscence: 0.41). A major locus controlling seed dormancy was found (q-value: 1.29 × 10-5; chromosome 1: position: 63611165), which can be used by breeding programs to rapidly reduce dormancy in breeding populations. No significant dehiscence score QTL was found, primarily due to the high dehiscence rates in Corvallis, Oregon. Since Oregon is a potentially major V. villosa seed production region, further dehiscence resistance screening is necessary.
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Affiliation(s)
- Neal Tilhou
- US Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | - Lisa Kissing Kucek
- US Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | - Brandon Carr
- James E. “Bud” Smith Plant Materials Center, United States Department of Agriculture-Natural Resources Conservation Service (USDA-NRCS), Knox City, TX, United States
| | - Annie Marion
- Corvallis Plant Materials Center, USDA-NRCS, Corvallis, OR, United States
| | - Joel Douglas
- Central National Technology Support Center, USDA-NRCS, Fort Worth, TX, United States
| | - John Englert
- National Plant Materials Program, USDA-NRCS, Washington, DC, United States
| | - Shahjahan Ali
- US Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | - John Raasch
- US Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
| | | | - Steven Brian Mirsky
- Sustainable Agricultural Systems Laboratory, United States Department of Agriculture-Natural Resources Conservation Service (USDA-ARS), Beltsville, MD, United States
| | | | - Sarah Krogman
- School of Medicine in Kansas, University of Kansas Medical Center, Wichita, KS, United States
| | - Ryan Hayes
- Forage Seed and Cereal Research Unit, USDA-ARS, Corvaillis, OR, United States
| | - Mark Azevedo
- Forage Seed and Cereal Research Unit, USDA-ARS, Corvaillis, OR, United States
| | - Heathcliffe Riday
- US Dairy Forage Research Center, United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Madison, WI, United States
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Ali S, Kucek LK, Riday H, Krom N, Krogman S, Cooper K, Jacobs L, Mehta P, Trammell M, Bhamidimarri S, Butler T, Saha MC, Monteros MJ. Transcript profiling of hairy vetch (Vicia villosa Roth) identified interesting genes for seed dormancy. Plant Genome 2023; 16:e20330. [PMID: 37125613 DOI: 10.1002/tpg2.20330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 02/27/2023] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Hairy vetch, a diploid annual legume species, has a robust growth habit, high biomass yield, and winter hardy characteristics. Seed hardness is a major constraint for growing hairy vetch commercially. Hard seeded cultivars are valuable as forages, whereas soft seeded and shatter resistant cultivars have advantages for their use as a cover crop. Transcript analysis of hairy vetch was performed to understand the genetic mechanisms associated with important hairy vetch traits. RNA was extracted from leaves, flowers, immature pods, seed coats, and cotyledons of contrasting soft and hard seeded "AU Merit" plants. A range of 31.22-79.18 Gb RNA sequence data per tissue sample were generated with estimated coverage of 1040-2639×. RNA sequence assembly and mapping of the contigs against the Medicago truncatula (V4.0) genome identified 76,422 gene transcripts. A total of 24,254 transcripts were constitutively expressed in hairy vetch tissues. Key genes, such as KNOX4 (a class II KNOTTED-like homeobox KNOXII gene), qHs1 (endo-1,4-β-glucanase), GmHs1-1 (calcineurin-like metallophosphoesterase), chitinase, shatterproof 1 and 2 (SHP1, SHP2), shatter resistant 1-5 (SHAT1-5)(NAC transcription factor), PDH1 (prephenate dehydrogenase 1), and pectin methylesterases with a potential role in seed hardness and pod shattering, were further explored based on genes involved in seed hardness from other species to query the hairy vetch transcriptome data. Identification of interesting candidate genes in hairy vetch can facilitate the development of improved cultivars with desirable seed characteristics for use as a forage and as a cover crop.
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Affiliation(s)
- Shahjahan Ali
- USDA-ARS, US Dairy Forage Research Center, Madison, Wisconsin, USA
| | | | | | - Nick Krom
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Sarah Krogman
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | | | - Lynne Jacobs
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Perdeep Mehta
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Michael Trammell
- Oklahoma State University Cooperative Extension, Shawnee, Oklahoma, USA
| | | | - Twain Butler
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
| | - Malay C Saha
- Noble Research Institute, LLC, Ardmore, Oklahoma, USA
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Sandro P, Kucek LK, Sorrells ME, Dawson JC, Gutierrez L. Developing high-quality value-added cereals for organic systems in the US Upper Midwest: hard red winter wheat (Triticum aestivum L.) breeding. Theor Appl Genet 2022; 135:4005-4027. [PMID: 35633380 PMCID: PMC9142347 DOI: 10.1007/s00122-022-04112-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 04/19/2022] [Indexed: 06/15/2023]
Abstract
There is an increased demand for food-grade grains grown sustainably. Hard red winter wheat has comparative advantages for organic farm rotations due to fall soil cover, weed competition, and grain yields. However, limitations of currently available cultivars such as poor disease resistance, winter hardiness, and baking quality, challenges its adoption and use. Our goal was to develop a participatory hard red winter wheat breeding program for the US Upper Midwest involving farmers, millers, and bakers. Specifically, our goals include (1) an evaluation of genotype-by-environment interaction (GEI) and genotypic stability for both agronomic and quality traits, and (2) the development of on-farm trials as well as baking and sensory evaluations of genotypes to include farmers, millers, and bakers' perspectives in the breeding process. Selection in early generations for diseases and protein content was followed by multi-environment evaluations for agronomic, disease, and quality traits in three locations during five years, on-farm evaluations, baking trials, and sensory evaluations. GEI was substantial for most traits, but no repeatable environmental conditions were significant contributors to GEI making selection for stability a critical trait. Breeding lines had similar performance in on-station and on-farm trials compared to commercial checks, but some breeding lines were more stable than the checks for agronomic, quality traits, and baking performance. These results suggest that stable lines can be developed using a participatory breeding approach under organic management. Crop improvement explicitly targeting sustainable agriculture practices for selection with farm to table participatory perspectives are critical to achieve long-term sustainable crop production. KEY MESSAGE: We describe a hard red winter wheat breeding program focused on developing genotypes adapted to organic systems in the US Upper Midwest for high-end artisan baking quality using participatory approaches.
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Affiliation(s)
- Pablo Sandro
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | | | - Mark E Sorrells
- Plant Breeding, and Genetics Section, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Julie C Dawson
- Department of Horticulture, University of Wisconsin-Madison, Madison, WI, 53706, USA.
| | - Lucia Gutierrez
- Department of Agronomy, University of Wisconsin-Madison, Madison, WI, 53706, USA.
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Kissing Kucek L, Riday H, Rufener BP, Burke AN, Eagen SS, Ehlke N, Krogman S, Mirsky SB, Reberg-Horton C, Ryan MR, Wayman S, Wiering NP. Pod Dehiscence in Hairy Vetch ( Vicia villosa Roth). Front Plant Sci 2020; 11:82. [PMID: 32194580 PMCID: PMC7063115 DOI: 10.3389/fpls.2020.00082] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 01/21/2020] [Indexed: 05/03/2023]
Abstract
Hairy vetch, Vicia villosa (Roth), is a cover crop that does not exhibit a typical domestication syndrome. Pod dehiscence reduces seed yield and creates weed problems for subsequent crops. Breeding efforts aim to reduce pod dehiscence in hairy vetch. To characterize pod dehiscence in the species, we quantified visual dehiscence and force required to cause dehiscence among 606 genotypes grown among seven environments of the United States. To identify potential secondary selection traits, we correlated pod dehiscence with various morphological pod characteristics and field measurements. Genotypes of hairy vetch exhibited wide variation in pod dehiscence, from completely indehiscent to completely dehiscent ratings. Mean force to dehiscence also varied widely, from 0.279 to 8.97 N among genotypes. No morphological traits were consistently correlated with pod dehiscence among environments where plants were grown. Results indicated that visual ratings of dehiscence would efficiently screen against genotypes with high pod dehiscence early in the breeding process. Force to dehiscence may be necessary to identify the indehiscent genotypes during advanced stages of selection.
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Affiliation(s)
| | - Heathcliffe Riday
- Dairy Forage Research Center, USDA-ARS, Madison, WI, United States
- *Correspondence: Heathcliffe Riday,
| | - Bryce P. Rufener
- Dairy Forage Research Center, USDA-ARS, Madison, WI, United States
| | - Allen N. Burke
- Sustainable Agricultural Systems Laboratory, Beltsville Agricultural Research Center, USDA-ARS, Beltsville, MD, United States
| | - Sarah Seehaver Eagen
- Crop and Soil Science, North Carolina State University, Raleigh, NC, United States
| | - Nancy Ehlke
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - Sarah Krogman
- Noble Research Institute, Ardmore, OK, United States
| | - Steven B. Mirsky
- Sustainable Agricultural Systems Laboratory, Beltsville Agricultural Research Center, USDA-ARS, Beltsville, MD, United States
| | - Chris Reberg-Horton
- Crop and Soil Science, North Carolina State University, Raleigh, NC, United States
| | - Matthew R. Ryan
- School of Integrated Plant Science, Cornell University, Ithaca, NY, United States
| | - Sandra Wayman
- School of Integrated Plant Science, Cornell University, Ithaca, NY, United States
| | - Nick P. Wiering
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
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Kissing Kucek L, Dyck E, Russell J, Clark L, Hamelman J, Burns-Leader S, Senders S, Jones J, Benscher D, Davis M, Roth G, Zwinger S, Sorrells ME, Dawson J. Evaluation of wheat and emmer varieties for artisanal baking, pasta making, and sensory quality. J Cereal Sci 2017. [DOI: 10.1016/j.jcs.2016.12.010] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Kucek LK, Veenstra LD, Amnuaycheewa P, Sorrells ME. A Grounded Guide to Gluten: How Modern Genotypes and Processing Impact Wheat Sensitivity. Compr Rev Food Sci Food Saf 2015; 14:285-302. [PMID: 33401796 DOI: 10.1111/1541-4337.12129] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/04/2015] [Indexed: 12/30/2022]
Abstract
The role of wheat, and particularly of gluten protein, in our diet has recently been scrutinized. This article provides a summary of the main pathologies related to wheat in the human body, including celiac disease, wheat allergy, nonceliac wheat sensitivity, fructose malabsorption, and irritable bowel syndrome. Differences in reactivity are discussed for ancient, heritage, and modern wheats. Due to large variability among species and genotypes, it might be feasible to select wheat varieties with lower amounts and fewer types of reactive prolamins and fructans. Einkorn is promising for producing fewer immunotoxic effects in a number of celiac research studies. Additionally, the impact of wheat processing methods on wheat sensitivity is reviewed. Research indicates that germination and fermentation technologies can effectively alter certain immunoreactive components. For individuals with wheat sensitivity, less-reactive wheat products can slow down disease development and improve quality of life. While research has not proven causation in the increase in wheat sensitivity over the last decades, modern wheat processing may have increased exposure to immunoreactive compounds. More research is necessary to understand the influence of modern wheat cultivars on epidemiological change.
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Affiliation(s)
- Lisa Kissing Kucek
- School of Integrated Plant Science, Plant Breeding and Genetics Section, 240 Emerson Hall, Cornell Univ., Ithaca, NY, 14853, U.S.A
| | - Lynn D Veenstra
- School of Integrated Plant Science, Plant Breeding and Genetics Section, 240 Emerson Hall, Cornell Univ., Ithaca, NY, 14853, U.S.A
| | - Plaimein Amnuaycheewa
- Dept. of Agro-Industrial, Food, and Environmental Technology, Faculty of Applied Science, King Mongkut's Univ. of Technology North Bangkok, Bangkok, 10800, Thailand
| | - Mark E Sorrells
- School of Integrated Plant Science, Plant Breeding and Genetics Section, 240 Emerson Hall, Cornell Univ., Ithaca, NY, 14853, U.S.A
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