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Liang Q, Muñoz-Amatriaín M, Shu S, Lo S, Wu X, Carlson JW, Davidson P, Goodstein DM, Phillips J, Janis NM, Lee EJ, Liang C, Morrell PL, Farmer AD, Xu P, Close TJ, Lonardi S. A view of the pan-genome of domesticated Cowpea (Vigna unguiculata [L.] Walp.). Plant Genome 2024; 17:e20319. [PMID: 36946261 DOI: 10.1002/tpg2.20319] [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] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/19/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
Cowpea, Vigna unguiculata L. Walp., is a diploid warm-season legume of critical importance as both food and fodder in sub-Saharan Africa. This species is also grown in Northern Africa, Europe, Latin America, North America, and East to Southeast Asia. To capture the genomic diversity of domesticates of this important legume, de novo genome assemblies were produced for representatives of six subpopulations of cultivated cowpea identified previously from genotyping of several hundred diverse accessions. In the most complete assembly (IT97K-499-35), 26,026 core and 4963 noncore genes were identified, with 35,436 pan genes when considering all seven accessions. GO terms associated with response to stress and defense response were highly enriched among the noncore genes, while core genes were enriched in terms related to transcription factor activity, and transport and metabolic processes. Over 5 million single nucleotide polymorphisms (SNPs) relative to each assembly and over 40 structural variants >1 Mb in size were identified by comparing genomes. Vu10 was the chromosome with the highest frequency of SNPs, and Vu04 had the most structural variants. Noncore genes harbor a larger proportion of potentially disruptive variants than core genes, including missense, stop gain, and frameshift mutations; this suggests that noncore genes substantially contribute to diversity within domesticated cowpea.
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Affiliation(s)
- Qihua Liang
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
- Departamento de Biología Molecular, Universidad de León, León, Spain
| | - Shengqiang Shu
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Sassoum Lo
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
- Department of Plant Sciences, University of California Davis, Davis, CA, USA
| | - Xinyi Wu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Joseph W Carlson
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Patrick Davidson
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David M Goodstein
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy Phillips
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nadia M Janis
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN, USA
| | - Elaine J Lee
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN, USA
| | - Chenxi Liang
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN, USA
| | - Peter L Morrell
- Department of Agronomy and Plant Genetics, University of Minnesota Twin Cities, Saint Paul, MN, USA
| | | | - Pei Xu
- Key Lab of Specialty Agri-Product Quality and Hazard Controlling Technology of Zhejiang Province, China Jiliang University, Hangzhou, China
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA, USA
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Tipton M, Baxter BA, Pfluger BA, Sayre-Chavez B, Muñoz-Amatriaín M, Broeckling CD, Shani I, Steiner-Asiedu M, Manary M, Ryan EP. Urine and Dried Blood Spots From Children and Pregnant Women Reveal Phytochemicals, Amino Acids, and Carnitine Metabolites as Cowpea Consumption Biomarkers. Mol Nutr Food Res 2024; 68:e2300222. [PMID: 38233141 DOI: 10.1002/mnfr.202300222] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 10/23/2023] [Indexed: 01/19/2024]
Abstract
SCOPE Legumes consumption has been proven to promote health across the lifespan; cowpeas have demonstrated efficacy in combating childhood malnutrition and growth faltering, with an estimated malnutrition prevalence of 35.6% of children in Ghana. This cowpea feeding study aimed to identify a suite of metabolic consumption biomarkers in children and adults. METHODS AND RESULTS Urine and dried blood spots (DBS) from 24 children (9-21 months) and 21 pregnant women (>18 years) in Northern Ghana are collected before and after dose-escalated consumption of four cowpea varieties for 15 days. Untargeted metabolomics identified significant increases in amino acids, phytochemicals, and lipids. The carnitine metabolism pathway is represented by 137 urine and 43 DBS metabolites, with significant changes to tiglylcarnitine and acetylcarnitine. Additional noteworthy candidate biomarkers are mansouramycin C, N-acetylalliin, proline betaine, N2, N5-diacetylornithine, S-methylcysteine, S-methylcysteine sulfoxide, and cis-urocanate. S-methylcysteine and S-methylcysteine sulfoxide are targeted and quantified in urine. CONCLUSION This feeding study for cowpea biomarkers supports the utility of a suite of key metabolites classified as amino acids, lipids, and phytochemicals for dietary legume and cowpea-specific food exposures of global health importance.
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Affiliation(s)
- Madison Tipton
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Bridget A Baxter
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Brigitte A Pfluger
- Nutrition and Health Sciences, Laney Graduate School, Emory University, Atlanta, Georgia, 30322, USA
| | - Brooke Sayre-Chavez
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, 80521, USA
| | - María Muñoz-Amatriaín
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, Colorado, 80521, USA
- Departamento de Biología Molecular - Área de Genética, Universidad de León, León, 24071, Spain
| | - Corey D Broeckling
- Analytical Resources Core: Bioanalysis and Omics Center, Colorado State University, Fort Collins, Colorado, 80523, USA
| | - Issah Shani
- Department of Nutrition and Food Science, College of Basic and Applied Science, University of Ghana, Legon, Accra, P.O. Box LG 134 Legon, Ghana
| | - Matilda Steiner-Asiedu
- Department of Nutrition and Food Science, College of Basic and Applied Science, University of Ghana, Legon, Accra, P.O. Box LG 134 Legon, Ghana
| | - Mark Manary
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, 63110, USA
| | - Elizabeth P Ryan
- Department of Environmental and Radiological Health Sciences, College of Veterinary Medicine and Biomedical Sciences, Colorado State University, Fort Collins, Colorado, 80523, USA
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Herniter IA, Lo R, Muñoz-Amatriaín M, Lo S, Guo YN, Huynh BL, Lucas M, Jia Z, Roberts PA, Lonardi S, Close TJ. Corrigendum: Seed coat pattern QTL and development in cowpea ( Vigna unguiculata [L.] Walp.). Front Plant Sci 2023; 14:1299051. [PMID: 38023847 PMCID: PMC10646776 DOI: 10.3389/fpls.2023.1299051] [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] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 09/25/2023] [Indexed: 12/01/2023]
Abstract
[This corrects the article DOI: 10.3389/fpls.2019.01346.].
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Affiliation(s)
- Ira A. Herniter
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States
| | - Ryan Lo
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States
| | - Sassoum Lo
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States
| | - Yi-Ning Guo
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States
| | - Bao-Lam Huynh
- Department of Nematology, University of California, Riverside, CA, United States
| | - Mitchell Lucas
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States
| | - Philip A. Roberts
- Department of Nematology, University of California, Riverside, CA, United States
| | - Stefano Lonardi
- Department of Computer Sciences and Engineering, University of California, Riverside, CA, United States
| | - Timothy J. Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States
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Sayre-Chavez B, Baxter B, Broeckling CD, Muñoz-Amatriaín M, Manary M, Ryan EP. Non-targeted metabolomics of cooked cowpea (Vigna unguiculata) and pigeon pea (Cajanus cajan) from Ghana using two distinct and complementary analytical platforms. Food Chemistry: Molecular Sciences 2022; 4:100087. [PMID: 35415674 PMCID: PMC8991828 DOI: 10.1016/j.fochms.2022.100087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/29/2022] [Accepted: 02/11/2022] [Indexed: 11/13/2022]
Abstract
Cowpea varieties represent diverse staple foods in Sub-Saharan Africa. Cowpea metabolite composition is different from pigeon pea and common bean. Cowpea metabolites included tonkinelin, pheophytin A, and linoleoyl ethanolamide. Pheophytin A was only detected in the cowpea variety Sangyi. Pipecolic acid identification was confirmed for all three legumes.
Legumes are global staple foods with multiple human health properties that merit detailed composition analysis in cooked forms. This study analyzed cowpea [Vigna unguiculata] (three varieties: Dagbantuya, Sangyi, and Tukara), pigeon pea [Cajanus cajan], and common bean [Phaseolus vulgaris] using two distinct ultra-performance liquid chromatography mass spectrometry (UPLC-MS) platforms and analytical workflows. Comparisons between cowpea and pigeon pea consumed in Ghana, and common bean (navy bean) from USA, revealed 75 metabolites that differentiated cowpeas. Metabolite fold-change comparisons resulted in 142 metabolites with significantly higher abundance in cowpea, and 154 higher in abundance from pigeon pea. 3-(all-trans-nonaprenyl)benzene-1,2-diol, N-tetracosanoylphytosphingosine, and sitoindoside II are novel identifications in cowpea, with notably higher abundance than other legumes tested. Cowpea variety specific markers were tonkinelin (Dagbantuya), pheophytin A (Sangyi), and linoleoyl ethanolamide (Tukara). This study identified novel cowpea and pigeon pea food metabolites that warrant continued investigation as bioactive food components following consumption in people.
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Sayre-Chavez B, Bettenhausen H, Windes S, Aron P, Cistué L, Fisk S, Helgerson L, Heuberger AL, Tynan S, Hayes P, Muñoz-Amatriaín M. Genetic basis of barley contributions to beer flavor. J Cereal Sci 2022. [DOI: 10.1016/j.jcs.2022.103430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Lo S, Parker T, Muñoz-Amatriaín M, Berny-Mier Y Teran JC, Jernstedt J, Close TJ, Gepts P. Genetic, anatomical, and environmental patterns related to pod shattering resistance in domesticated cowpea [Vigna unguiculata (L.) Walp]. J Exp Bot 2021; 72:6219-6229. [PMID: 34106233 DOI: 10.1093/jxb/erab259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 06/06/2021] [Indexed: 05/27/2023]
Abstract
Pod shattering, which causes the explosive release of seeds from the pod, is one of the main sources of yield losses in cowpea in arid and semi-arid areas. Reduction of shattering has therefore been a primary target for selection during domestication and improvement of cowpea, among other species. Using a mini-core diversity panel of 368 cowpea accessions, four regions with a statistically significant association with pod shattering were identified. Two genes (Vigun03g321100 and Vigun11g100600), involved in cell wall biosynthesis, were identified as strong candidates for pod shattering. Microscopic analysis was conducted on a subset of accessions representing the full spectrum of shattering phenotypes. This analysis indicated that the extent of wall fiber deposition was highly correlated with shattering. The results from this study also demonstrate that pod shattering in cowpea is exacerbated by arid environmental conditions. Finally, using a subset of West African landraces, patterns of historical selection for shattering resistance related to precipitation in the environment of origin were identified. Together, these results shed light on sources of resistance to pod shattering, which will, in turn, improve climate resilience of a major global nutritional staple.
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Affiliation(s)
- Sassoum Lo
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521,USA
- Department of Plant Sciences/MS1, University of California, Davis, CA 95616-8780,USA
| | - Travis Parker
- Department of Plant Sciences/MS1, University of California, Davis, CA 95616-8780,USA
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521,USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523,USA
| | | | - Judy Jernstedt
- Department of Plant Sciences/MS1, University of California, Davis, CA 95616-8780,USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521,USA
| | - Paul Gepts
- Department of Plant Sciences/MS1, University of California, Davis, CA 95616-8780,USA
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Paudel D, Dareus R, Rosenwald J, Muñoz-Amatriaín M, Rios EF. Genome-Wide Association Study Reveals Candidate Genes for Flowering Time in Cowpea ( Vigna unguiculata [L.] Walp.). Front Genet 2021; 12:667038. [PMID: 34220944 PMCID: PMC8242349 DOI: 10.3389/fgene.2021.667038] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 05/24/2021] [Indexed: 11/15/2022] Open
Abstract
Cowpea (Vigna unguiculata [L.] Walp., diploid, 2n = 22) is a major crop used as a protein source for human consumption as well as a quality feed for livestock. It is drought and heat tolerant and has been bred to develop varieties that are resilient to changing climates. Plant adaptation to new climates and their yield are strongly affected by flowering time. Therefore, understanding the genetic basis of flowering time is critical to advance cowpea breeding. The aim of this study was to perform genome-wide association studies (GWAS) to identify marker trait associations for flowering time in cowpea using single nucleotide polymorphism (SNP) markers. A total of 368 accessions from a cowpea mini-core collection were evaluated in Ft. Collins, CO in 2019 and 2020, and 292 accessions were evaluated in Citra, FL in 2018. These accessions were genotyped using the Cowpea iSelect Consortium Array that contained 51,128 SNPs. GWAS revealed seven reliable SNPs for flowering time that explained 8-12% of the phenotypic variance. Candidate genes including FT, GI, CRY2, LSH3, UGT87A2, LIF2, and HTA9 that are associated with flowering time were identified for the significant SNP markers. Further efforts to validate these loci will help to understand their role in flowering time in cowpea, and it could facilitate the transfer of some of this knowledge to other closely related legume species.
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Affiliation(s)
- Dev Paudel
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Rocheteau Dareus
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Julia Rosenwald
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - María Muñoz-Amatriaín
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
| | - Esteban F. Rios
- Agronomy Department, University of Florida, Gainesville, FL, United States
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do Vale Martins L, de Oliveira Bustamante F, da Silva Oliveira AR, da Costa AF, de Lima Feitoza L, Liang Q, Zhao H, Benko-Iseppon AM, Muñoz-Amatriaín M, Pedrosa-Harand A, Jiang J, Brasileiro-Vidal AC. BAC- and oligo-FISH mapping reveals chromosome evolution among Vigna angularis, V. unguiculata, and Phaseolus vulgaris. Chromosoma 2021; 130:133-147. [PMID: 33909141 DOI: 10.1007/s00412-021-00758-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 02/17/2021] [Accepted: 04/05/2021] [Indexed: 01/29/2023]
Abstract
Cytogenomic resources have accelerated synteny and chromosome evolution studies in plant species, including legumes. Here, we established the first cytogenetic map of V. angularis (Va, subgenus Ceratotropis) and compared this new map with those of V. unguiculata (Vu, subgenus Vigna) and P. vulgaris (Pv) by BAC-FISH and oligopainting approaches. We mapped 19 Vu BACs and 35S rDNA probes to the 11 chromosome pairs of Va, Vu, and Pv. Vigna angularis shared a high degree of macrosynteny with Vu and Pv, with five conserved syntenic chromosomes. Additionally, we developed two oligo probes (Pv2 and Pv3) used to paint Vigna orthologous chromosomes. We confirmed two reciprocal translocations (chromosomes 2 and 3 and 1 and 8) that have occurred after the Vigna and Phaseolus divergence (~9.7 Mya). Besides, two inversions (2 and 4) and one translocation (1 and 5) have occurred after Vigna and Ceratotropis subgenera separation (~3.6 Mya). We also observed distinct oligopainting patterns for chromosomes 2 and 3 of Vigna species. Both Vigna species shared similar major rearrangements compared to Pv: one translocation (2 and 3) and one inversion (chromosome 3). The sequence synteny identified additional inversions and/or intrachromosomal translocations involving pericentromeric regions of both orthologous chromosomes. We propose chromosomes 2 and 3 as hotspots for chromosomal rearrangements and de novo centromere formation within and between Vigna and Phaseolus. Our BAC- and oligo-FISH mapping contributed to physically trace the chromosome evolution of Vigna and Phaseolus and its application in further studies of both genera.
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Affiliation(s)
| | | | | | | | | | - Qihua Liang
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Hainan Zhao
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA
| | | | - María Muñoz-Amatriaín
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | | | - Jiming Jiang
- Department of Plant Biology, Michigan State University, East Lansing, MI, 48824, USA.,Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA
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Seo E, Kim K, Jun TH, Choi J, Kim SH, Muñoz-Amatriaín M, Sun H, Ha BK. Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers. Plants (Basel) 2020; 9:plants9091190. [PMID: 32932572 PMCID: PMC7569878 DOI: 10.3390/plants9091190] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 09/09/2020] [Accepted: 09/09/2020] [Indexed: 12/14/2022]
Abstract
Cowpea is one of the most essential legume crops providing inexpensive dietary protein and nutrients. The aim of this study was to understand the genetic diversity and population structure of global and Korean cowpea germplasms. A total of 384 cowpea accessions from 21 countries were genotyped with the Cowpea iSelect Consortium Array containing 51,128 single-nucleotide polymorphisms (SNPs). After SNP filtering, a genetic diversity study was carried out using 35,116 SNPs within 376 cowpea accessions, including 229 Korean accessions. Based on structure and principal component analysis, a total of 376 global accessions were divided into four major populations. Accessions in group 1 were from Asia and Europe, those in groups 2 and 4 were from Korea, and those in group 3 were from West Africa. In addition, 229 Korean accessions were divided into three major populations (Q1, Jeonra province; Q2, Gangwon province; Q3, a mixture of provinces). Additionally, the neighbor-joining tree indicated similar results. Further genetic diversity analysis within the global and Korean population groups indicated low heterozygosity, a low polymorphism information content, and a high inbreeding coefficient in the Korean cowpea accessions. The population structure analysis will provide useful knowledge to support the genetic potential of the cowpea breeding program, especially in Korea.
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Affiliation(s)
- Eunju Seo
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea;
| | - Kipoong Kim
- Department of Statistics, Pusan National University, Busan 46241, Korea;
| | - Tae-Hwan Jun
- Department of Plant Bioscience, Pusan National University, Busan 46241, Korea;
| | - Jinsil Choi
- Jeollanamdo Agricultural Research and Extension Services, Naju 58213, Korea;
| | - Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 54874, Korea;
| | - María Muñoz-Amatriaín
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USA;
| | - Hokeun Sun
- Department of Statistics, Pusan National University, Busan 46241, Korea;
- Correspondence: (H.S.); (B.-K.H.); Tel.: +92-51-510-2257 (H.S.); +82-62-530-2055 (B.-K.H.)
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Korea;
- Correspondence: (H.S.); (B.-K.H.); Tel.: +92-51-510-2257 (H.S.); +82-62-530-2055 (B.-K.H.)
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Lo S, Fatokun C, Boukar O, Gepts P, Close TJ, Muñoz-Amatriaín M. Identification of QTL for perenniality and floral scent in cowpea (Vigna unguiculata [L.] Walp.). PLoS One 2020; 15:e0229167. [PMID: 32343700 PMCID: PMC7188242 DOI: 10.1371/journal.pone.0229167] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 01/28/2020] [Indexed: 12/16/2022] Open
Abstract
Perennial habit and floral scent are major traits that distinguish domesticated cowpeas from their wild relatives. However, the genetic basis of these two important traits remains largely unknown in cowpea. Plant longevity, a perenniality-related trait, and floral scent, an outcrossing trait, were investigated using a RIL population derived from a cross between a domesticated and a wild cowpea. QTL analysis revealed three significant loci, one on chromosome 8 associated with plant longevity and two, on chromosomes 1 and 11, for floral scent. Genes within the QTL regions were identified. Genes encoding an F-box protein (Vigun08g215300) and two kinases (Vigun08g217000, Vigun08g217800), and involved in physiological processes including regulation of flowering time and plant longevity, were identified within the perenniality QTL region. A cluster of O-methyltransferase genes (Vigun11g096800, Vigun11g096900, Vigun11g097000, Vigun11g097600, and Vigun11g097800) was identified within the floral scent QTL region. These O-methyltransferase cowpea genes are orthologs of the Arabidopsis N-acetylserotonin O-methyltransferase (ASMT) gene, which is involved in the biosynthesis of melatonin. Melatonin is an indole derivative, which is an essential molecule for plant interactions with pollinators. These findings lay the foundation for further exploration of the genetic mechanisms of perenniality and floral scent in cowpea. Knowledge from this study can help in the development of new extended-growth cycle lines with increased yield or lines with increased outcrossing for population breeding.
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Affiliation(s)
- Sassoum Lo
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, United States of America
- * E-mail: (MMA); (SL)
| | | | - Ousmane Boukar
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Paul Gepts
- Department of Plant Sciences, University of California Davis, Davis, CA, United States of America
| | - Timothy J. Close
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, United States of America
| | - María Muñoz-Amatriaín
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States of America
- * E-mail: (MMA); (SL)
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Muñoz-Amatriaín M, Hernandez J, Herb D, Baenziger PS, Bochard AM, Capettini F, Casas A, Cuesta-Marcos A, Einfeldt C, Fisk S, Genty A, Helgerson L, Herz M, Hu G, Igartua E, Karsai I, Nakamura T, Sato K, Smith K, Stockinger E, Thomas W, Hayes P. Perspectives on Low Temperature Tolerance and Vernalization Sensitivity in Barley: Prospects for Facultative Growth Habit. Front Plant Sci 2020; 11:585927. [PMID: 33469459 PMCID: PMC7814503 DOI: 10.3389/fpls.2020.585927] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Accepted: 10/01/2020] [Indexed: 05/13/2023]
Abstract
One option to achieving greater resiliency for barley production in the face of climate change is to explore the potential of winter and facultative growth habits: for both types, low temperature tolerance (LTT) and vernalization sensitivity are key traits. Sensitivity to short-day photoperiod is a desirable attribute for facultative types. In order to broaden our understanding of the genetics of these phenotypes, we mapped quantitative trait loci (QTLs) and identified candidate genes using a genome-wide association studies (GWAS) panel composed of 882 barley accessions that was genotyped with the Illumina 9K single-nucleotide polymorphism (SNP) chip. Fifteen loci including 5 known and 10 novel QTL/genes were identified for LTT-assessed as winter survival in 10 field tests and mapped using a GWAS meta-analysis. FR-H1, FR-H2, and FR-H3 were major drivers of LTT, and candidate genes were identified for FR-H3. The principal determinants of vernalization sensitivity were VRN-H1, VRN-H2, and PPD-H1. VRN-H2 deletions conferred insensitive or intermediate sensitivity to vernalization. A subset of accessions with maximum LTT were identified as a resource for allele mining and further characterization. Facultative types comprised a small portion of the GWAS panel but may be useful for developing germplasm with this growth habit.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, United States
- *Correspondence: María Muñoz-Amatriaín,
| | - Javier Hernandez
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
- Javier Hernandez,
| | - Dustin Herb
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - P. Stephen Baenziger
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, United States
| | | | - Flavio Capettini
- Field Crop Development Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada
| | - Ana Casas
- Consejo Superior de Investigaciones Científicas (CSIC), Aula Dei Experimental Station, Zaragoza, Spain
| | | | | | - Scott Fisk
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - Amelie Genty
- Secobra Recherches, Centre de Bois Henry, Maule, France
| | - Laura Helgerson
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
| | - Markus Herz
- Bavarian State Research Center for Agriculture, Institute for Crop Science, Freising, Germany
| | - Gongshe Hu
- United States Department of Agriculture-Agricultural Research Service (USDA-ARS), Aberdeen, ID, United States
| | - Ernesto Igartua
- Consejo Superior de Investigaciones Científicas (CSIC), Aula Dei Experimental Station, Zaragoza, Spain
| | - Ildiko Karsai
- Department of Molecular Breeding, Center for Agricultural Research, Martonvásár, Hungary
| | - Toshiki Nakamura
- Division of Field Crops and Horticulture Research Tohoku Agricultural Research Center National Agriculture and Food Research Organization (NARO), Morioka, Japan
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, Kurashiki, Japan
| | - Kevin Smith
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, United States
| | - Eric Stockinger
- Department of Horticulture and Crop Science, The Ohio State University/Ohio Agricultural Research and Development Center (OARDC), Wooster, OH, United States
| | - William Thomas
- The James Hutton Institute (JHI), Invergowrie, United Kingdom
| | - Patrick Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, United States
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12
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Lo S, Muñoz-Amatriaín M, Hokin SA, Cisse N, Roberts PA, Farmer AD, Xu S, Close TJ. A genome-wide association and meta-analysis reveal regions associated with seed size in cowpea [Vigna unguiculata (L.) Walp]. Theor Appl Genet 2019; 132:3079-3087. [PMID: 31367839 PMCID: PMC6791911 DOI: 10.1007/s00122-019-03407-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/24/2019] [Indexed: 05/19/2023]
Abstract
This paper combined GWAS, meta-analysis and sequence homology comparison with common bean to identify regions associated with seed size variation in domesticated cowpea. Seed size is an important trait for yield and commercial value in dry-grain cowpea. Seed size varies widely among different cowpea accessions, and the genetic basis of such variation is not yet well understood. To better decipher the genetic basis of seed size, a genome-wide association study (GWAS) and meta-analysis were conducted on a panel of 368 cowpea diverse accessions from 51 countries. Four traits, including seed weight, length, width and density were evaluated across three locations. Using 51,128 single nucleotide polymorphisms covering the cowpea genome, 17 loci were identified for these traits. One locus was common to weight, width and length, suggesting pleiotropy. By integrating synteny-based analysis with common bean, six candidate genes (Vigun05g036000, Vigun05g039600, Vigun05g204200, Vigun08g217000, Vigun11g187000, and Vigun11g191300) which are implicated in multiple functional categories related to seed size such as endosperm development, embryo development, and cell elongation were identified. These results suggest that a combination of GWAS meta-analysis with synteny comparison in a related plant is an efficient approach to identify candidate gene (s) for complex traits in cowpea. The identified loci and candidate genes provide useful information for improving cowpea varieties and for molecular investigation of seed size.
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Affiliation(s)
- Sassoum Lo
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA.
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, 80523, USA
| | - Samuel A Hokin
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Ndiaga Cisse
- Centre d'Etude Régional pour l'Amélioration de l'Adaptation à la Sècheresse, ISRA/CERAAS, Thies, Senegal
| | - Philip A Roberts
- Department of Nematology, University of California, Riverside, CA, 92521, USA
| | - Andrew D Farmer
- National Center for Genome Resources, Santa Fe, NM, 87505, USA
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
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13
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Herniter IA, Lo R, Muñoz-Amatriaín M, Lo S, Guo YN, Huynh BL, Lucas M, Jia Z, Roberts PA, Lonardi S, Close TJ. Seed Coat Pattern QTL and Development in Cowpea (Vigna unguiculata [L.] Walp.). Front Plant Sci 2019; 10:1346. [PMID: 31708953 PMCID: PMC6824211 DOI: 10.3389/fpls.2019.01346] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 09/27/2019] [Indexed: 05/23/2023]
Abstract
The appearance of the seed is an important aspect of consumer preference for cowpea (Vigna unguiculata [L.] Walp.). Seed coat pattern in cowpea has been a subject of study for over a century. This study makes use of newly available resources, including mapping populations, a reference genome and additional genome assemblies, and a high-density single nucleotide polymorphism genotyping platform, to map various seed coat pattern traits to three loci, concurrent with the Color Factor (C), Watson (W), and Holstein (H) factors identified previously. Several gene models encoding proteins involved in regulating the later stages of the flavonoid biosynthesis pathway have been identified as candidate genes, including a basic helix-loop-helix gene (Vigun07g110700) for the C locus, a WD-repeat gene (Vigun09g139900) for the W locus and an E3 ubiquitin ligase gene (Vigun10g163900) for the H locus. A model of seed coat development, consisting of six distinct stages, is described to explain some of the observed pattern phenotypes.
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Affiliation(s)
- Ira A. Herniter
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States
| | - Ryan Lo
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States
| | - Sassoum Lo
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States
| | - Yi-Ning Guo
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States
| | - Bao-Lam Huynh
- Department of Nematology, University of California, Riverside, CA, United States
| | - Mitchell Lucas
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States
| | - Zhenyu Jia
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States
| | - Philip A. Roberts
- Department of Nematology, University of California, Riverside, CA, United States
| | - Stefano Lonardi
- Department of Computer Sciences and Engineering, University of California, Riverside, CA, United States
| | - Timothy J. Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA, United States
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14
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Lo S, Muñoz-Amatriaín M, Boukar O, Herniter I, Cisse N, Guo YN, Roberts PA, Xu S, Fatokun C, Close TJ. Identification of QTL controlling domestication-related traits in cowpea (Vigna unguiculata L. Walp). Sci Rep 2018; 8:6261. [PMID: 29674702 PMCID: PMC5908840 DOI: 10.1038/s41598-018-24349-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 03/29/2018] [Indexed: 11/08/2022] Open
Abstract
Cowpea (Vigna unguiculata L. Walp) is a warm-season legume with a genetically diverse gene-pool composed of wild and cultivated forms. Cowpea domestication involved considerable phenotypic changes from the wild progenitor, including reduction of pod shattering, increased organ size, and changes in flowering time. Little is known about the genetic basis underlying these changes. In this study, 215 recombinant inbred lines derived from a cross between a cultivated and a wild cowpea accession were used to evaluate nine domestication-related traits (pod shattering, peduncle length, flower color, days to flowering, 100-seed weight, pod length, leaf length, leaf width and seed number per pod). A high-density genetic map containing 17,739 single nucleotide polymorphisms was constructed and used to identify 16 quantitative trait loci (QTL) for these nine traits. Based on annotations of the cowpea reference genome, genes within these regions are reported. Four regions with clusters of QTL were identified, including one on chromosome 8 related to increased organ size. This study provides new knowledge of the genomic regions controlling domestication-related traits in cowpea as well as candidate genes underlying those QTL. This information can help to exploit wild relatives in cowpea breeding programs.
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Affiliation(s)
- Sassoum Lo
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA.
| | - Ousmane Boukar
- International Institute of Tropical Agriculture, Ibadan, Nigeria
| | - Ira Herniter
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
| | - Ndiaga Cisse
- Centre d'Etude Régional pour l'Amélioration de l'Adaptation à la Sècheresse, ISRA/CERAAS, Thies, Senegal
| | - Yi-Ning Guo
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
| | - Philip A Roberts
- Department of Nematology, University of California Riverside, Riverside, CA, USA
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
| | | | - Timothy J Close
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, USA
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15
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Huynh BL, Ehlers JD, Huang BE, Muñoz-Amatriaín M, Lonardi S, Santos JRP, Ndeve A, Batieno BJ, Boukar O, Cisse N, Drabo I, Fatokun C, Kusi F, Agyare RY, Guo YN, Herniter I, Lo S, Wanamaker SI, Xu S, Close TJ, Roberts PA. A multi-parent advanced generation inter-cross (MAGIC) population for genetic analysis and improvement of cowpea (Vigna unguiculata L. Walp.). Plant J 2018; 93:1129-1142. [PMID: 29356213 DOI: 10.1111/tpj.13827] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 11/30/2017] [Accepted: 01/03/2018] [Indexed: 05/20/2023]
Abstract
Multi-parent advanced generation inter-cross (MAGIC) populations are an emerging type of resource for dissecting the genetic structure of traits and improving breeding populations. We developed a MAGIC population for cowpea (Vigna unguiculata L. Walp.) from eight founder parents. These founders were genetically diverse and carried many abiotic and biotic stress resistance, seed quality and agronomic traits relevant to cowpea improvement in the United States and sub-Saharan Africa, where cowpea is vitally important in the human diet and local economies. The eight parents were inter-crossed using structured matings to ensure that the population would have balanced representation from each parent, followed by single-seed descent, resulting in 305 F8 recombinant inbred lines each carrying a mosaic of genome blocks contributed by all founders. This was confirmed by single nucleotide polymorphism genotyping with the Illumina Cowpea Consortium Array. These lines were on average 99.74% homozygous but also diverse in agronomic traits across environments. Quantitative trait loci (QTLs) were identified for several parental traits. Loci with major effects on photoperiod sensitivity and seed size were also verified by biparental genetic mapping. The recombination events were concentrated in telomeric regions. Due to its broad genetic base, this cowpea MAGIC population promises breakthroughs in genetic gain, QTL and gene discovery, enhancement of breeding populations and, for some lines, direct releases as new varieties.
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Affiliation(s)
- Bao-Lam Huynh
- Department of Nematology, University of California, 900 University Avenue, Riverside, CA, 92521, USA
| | - Jeffrey D Ehlers
- Department of Botany and Plant Sciences, University of California, 900 University Avenue, Riverside, CA, 92521, USA
| | - Bevan Emma Huang
- Discovery Sciences, Janssen R&D, 329 Oyster Point Blvd, South San Francisco, CA, 94080, USA
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, 900 University Avenue, Riverside, CA, 92521, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, 900 University Avenue, Riverside, CA, 92521, USA
| | - Jansen R P Santos
- Department of Nematology, University of California, 900 University Avenue, Riverside, CA, 92521, USA
| | - Arsenio Ndeve
- Department of Nematology, University of California, 900 University Avenue, Riverside, CA, 92521, USA
| | - Benoit J Batieno
- Institut de l'Environnement et de Recherches Agricoles, BP 476 Ouagadougou 01, Burkina Faso
| | - Ousmane Boukar
- International Institute of Tropical Agriculture, PMB 5320, Oyo Road, Ibadan, Nigeria
| | - Ndiaga Cisse
- Institut Sénégalais de Recherches Agricoles, BP 3320, Thiès, Sénégal
| | - Issa Drabo
- Institut de l'Environnement et de Recherches Agricoles, 01 BP 10 Koudougou 01, Burkina Faso
| | - Christian Fatokun
- International Institute of Tropical Agriculture, Entrance Rd, Ibadan, Nigeria
| | - Francis Kusi
- Savanna Agricultural Research Institute, P. O. Box TL 52, Tamale, Ghana
| | - Richard Y Agyare
- Savanna Agricultural Research Institute, P. O. Box TL 52, Tamale, Ghana
| | - Yi-Ning Guo
- Department of Botany and Plant Sciences, University of California, 900 University Avenue, Riverside, CA, 92521, USA
| | - Ira Herniter
- Department of Botany and Plant Sciences, University of California, 900 University Avenue, Riverside, CA, 92521, USA
| | - Sassoum Lo
- Department of Botany and Plant Sciences, University of California, 900 University Avenue, Riverside, CA, 92521, USA
| | - Steve I Wanamaker
- Department of Botany and Plant Sciences, University of California, 900 University Avenue, Riverside, CA, 92521, USA
| | - Shizhong Xu
- Department of Botany and Plant Sciences, University of California, 900 University Avenue, Riverside, CA, 92521, USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, 900 University Avenue, Riverside, CA, 92521, USA
| | - Philip A Roberts
- Department of Nematology, University of California, 900 University Avenue, Riverside, CA, 92521, USA
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16
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Carvalho M, Muñoz-Amatriaín M, Castro I, Lino-Neto T, Matos M, Egea-Cortines M, Rosa E, Close T, Carnide V. Genetic diversity and structure of Iberian Peninsula cowpeas compared to world-wide cowpea accessions using high density SNP markers. BMC Genomics 2017; 18:891. [PMID: 29162034 PMCID: PMC5697113 DOI: 10.1186/s12864-017-4295-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 11/13/2017] [Indexed: 11/23/2022] Open
Abstract
Background Cowpea (Vigna unguiculata L. Walp) is an important legume crop due to its high protein content, adaptation to heat and drought and capacity to fix nitrogen. Europe has a deficit of cowpea production. Knowledge of genetic diversity among cowpea landraces is important for the preservation of local varieties and is the basis to obtain improved varieties. The aims of this study were to explore diversity and the genetic structure of a set of Iberian Peninsula cowpea accessions in comparison to a worldwide collection and to infer possible dispersion routes of cultivated cowpea. Results The Illumina Cowpea iSelect Consortium Array containing 51,128 SNPs was used to genotype 96 cowpea accessions including 43 landraces and cultivars from the Iberian Peninsula, and 53 landraces collected worldwide. Four subpopulations were identified. Most Iberian Peninsula accessions clustered together with those from other southern European and northern African countries. Only one accession belonged to another subpopulation, while two accessions were ‘admixed’. A lower genetic diversity level was found in the Iberian Peninsula accessions compared to worldwide cowpeas. Conclusions The genetic analyses performed in this study brought some insights into worldwide genetic diversity and structure and possible dispersion routes of cultivated cowpea. Also, it provided an in-depth analysis of genetic diversity in Iberian Peninsula cowpeas that will help guide crossing strategies in breeding programs. Electronic supplementary material The online version of this article (10.1186/s12864-017-4295-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Márcia Carvalho
- Centre for Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521-0124, USA
| | - Isaura Castro
- Centre for Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal. .,Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal.
| | - Teresa Lino-Neto
- Biosystems & Integrative Sciences Institute (BioISI), Plant Functional Biology Center (CBFP), University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal
| | - Manuela Matos
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal.,Biosystems & Integrative Sciences Institute (BioISI), Sciences Faculty, University of Lisbon, Campo Grande, 1749-016, Lisbon, Portugal
| | - Marcos Egea-Cortines
- Instituto de Biotecnología Vegetal, Universidad Politécnica de Cartagena, 30202, Cartagena, Spain
| | - Eduardo Rosa
- Centre for Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
| | - Timothy Close
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521-0124, USA
| | - Valdemar Carnide
- Centre for Research and Technology of Agro-Environmental and Biological Sciences (CITAB), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal.,Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801, Vila Real, Portugal
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17
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Beier S, Himmelbach A, Colmsee C, Zhang XQ, Barrero RA, Zhang Q, Li L, Bayer M, Bolser D, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Sampath D, Heavens D, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Houben A, Doležel J, Ayling S, Lonardi S, Langridge P, Muehlbauer GJ, Kersey P, Clark MD, Caccamo M, Schulman AH, Platzer M, Close TJ, Hansson M, Zhang G, Braumann I, Li C, Waugh R, Scholz U, Stein N, Mascher M. Construction of a map-based reference genome sequence for barley, Hordeum vulgare L. Sci Data 2017; 4:170044. [PMID: 28448065 PMCID: PMC5407242 DOI: 10.1038/sdata.2017.44] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 02/09/2017] [Indexed: 12/30/2022] Open
Abstract
Barley (Hordeum vulgare L.) is a cereal grass mainly used as animal fodder and raw material for the malting industry. The map-based reference genome sequence of barley cv. ‘Morex’ was constructed by the International Barley Genome Sequencing Consortium (IBSC) using hierarchical shotgun sequencing. Here, we report the experimental and computational procedures to (i) sequence and assemble more than 80,000 bacterial artificial chromosome (BAC) clones along the minimum tiling path of a genome-wide physical map, (ii) find and validate overlaps between adjacent BACs, (iii) construct 4,265 non-redundant sequence scaffolds representing clusters of overlapping BACs, and (iv) order and orient these BAC clusters along the seven barley chromosomes using positional information provided by dense genetic maps, an optical map and chromosome conformation capture sequencing (Hi-C). Integrative access to these sequence and mapping resources is provided by the barley genome explorer (BARLEX).
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Affiliation(s)
- Sebastian Beier
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Christian Colmsee
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Xiao-Qi Zhang
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Roberto A Barrero
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Qisen Zhang
- Australian Export Grains Innovation Centre, South Perth, Western Australia 6151, Australia
| | - Lin Li
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, Minnesota 55108, USA
| | - Micha Bayer
- The James Hutton Institute, Dundee DD2 5DA, UK
| | - Daniel Bolser
- European Molecular Biology Laboratory-The European Bioinformatics Institute, Hinxton CB10 1SD, UK
| | - Stefan Taudien
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Marco Groth
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Marius Felder
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Alex Hastie
- BioNano Genomics Inc., San Diego, California 92121, USA
| | - Hana Šimková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic
| | - Helena Staňková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic
| | - Jan Vrána
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic
| | - Saki Chan
- BioNano Genomics Inc., San Diego, California 92121, USA
| | - María Muñoz-Amatriaín
- Department of Botany &Plant Sciences, University of California, Riverside, Riverside, California 92521, USA
| | - Rachid Ounit
- Department of Computer Science and Engineering, University of California, Riverside, Riverside, California 92521, USA
| | - Steve Wanamaker
- Department of Botany &Plant Sciences, University of California, Riverside, Riverside, California 92521, USA
| | - Thomas Schmutzer
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Lala Aliyeva-Schnorr
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Stefano Grasso
- Department of Agricultural and Environmental Sciences, University of Udine, 33100 Udine, Italy
| | - Jaakko Tanskanen
- Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | | | | | - Sujie Cao
- BGI-Shenzhen, Shenzhen 518083, China
| | - Brett Chapman
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Fei Dai
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Yong Han
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hua Li
- BGI-Shenzhen, Shenzhen 518083, China
| | - Xuan Li
- BGI-Shenzhen, Shenzhen 518083, China
| | | | - John K McCooke
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Cong Tan
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | | | - Shuya Yin
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Gaofeng Zhou
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Jesse A Poland
- Kansas State University, Wheat Genetics Resource Center, Department of Plant Pathology and Department of Agronomy, Manhattan, Kansas 66506, USA
| | - Matthew I Bellgard
- Centre for Comparative Genomics, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Andreas Houben
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, 78371 Olomouc, Czech Republic
| | | | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, Riverside, California 92521, USA
| | - Peter Langridge
- School of Agriculture, University of Adelaide, Urrbrae, South Australia 5064, Australia
| | - Gary J Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St Paul, Minnesota 55108, USA.,Department of Plant and Microbial Biology, University of Minnesota, St Paul, Minnesota 55108, USA
| | - Paul Kersey
- European Molecular Biology Laboratory-The European Bioinformatics Institute, Hinxton CB10 1SD, UK
| | - Matthew D Clark
- Earlham Institute, Norwich NR4 7UH, UK.,School of Environmental Sciences, University of East Anglia, Norwich NR4 7UH, UK
| | - Mario Caccamo
- Earlham Institute, Norwich NR4 7UH, UK.,National Institute of Agricultural Botany, Cambridge CB3 0LE, UK
| | - Alan H Schulman
- Green Technology, Natural Resources Institute (Luke), Viikki Plant Science Centre, and Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland
| | - Matthias Platzer
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), 07745 Jena, Germany
| | - Timothy J Close
- Department of Botany &Plant Sciences, University of California, Riverside, Riverside, California 92521, USA
| | - Mats Hansson
- Department of Biology, Lund University, 22362 Lund, Sweden
| | - Guoping Zhang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Ilka Braumann
- Carlsberg Research Laboratory, 1799 Copenhagen, Denmark
| | - Chengdao Li
- School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia 6150, Australia.,Department of Agriculture and Food, Government of Western Australia, South Perth, Western Australia 6150, Australia.,Hubei Collaborative Innovation Centre for Grain Industry, Yangtze University, Jingzhou, Hubei 434025, China
| | - Robbie Waugh
- The James Hutton Institute, Dundee DD2 5DA, UK.,School of Life Sciences, University of Dundee, Dundee DD2 5DA, UK
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.,School of Plant Biology, University of Western Australia, Crawley 6009, Australia
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466 Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, 04103 Leipzig, Germany
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18
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Mascher M, Gundlach H, Himmelbach A, Beier S, Twardziok SO, Wicker T, Radchuk V, Dockter C, Hedley PE, Russell J, Bayer M, Ramsay L, Liu H, Haberer G, Zhang XQ, Zhang Q, Barrero RA, Li L, Taudien S, Groth M, Felder M, Hastie A, Šimková H, Staňková H, Vrána J, Chan S, Muñoz-Amatriaín M, Ounit R, Wanamaker S, Bolser D, Colmsee C, Schmutzer T, Aliyeva-Schnorr L, Grasso S, Tanskanen J, Chailyan A, Sampath D, Heavens D, Clissold L, Cao S, Chapman B, Dai F, Han Y, Li H, Li X, Lin C, McCooke JK, Tan C, Wang P, Wang S, Yin S, Zhou G, Poland JA, Bellgard MI, Borisjuk L, Houben A, Doležel J, Ayling S, Lonardi S, Kersey P, Langridge P, Muehlbauer GJ, Clark MD, Caccamo M, Schulman AH, Mayer KFX, Platzer M, Close TJ, Scholz U, Hansson M, Zhang G, Braumann I, Spannagl M, Li C, Waugh R, Stein N. A chromosome conformation capture ordered sequence of the barley genome. Nature 2017; 544:427-433. [DOI: 10.1038/nature22043] [Citation(s) in RCA: 966] [Impact Index Per Article: 138.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 03/03/2017] [Indexed: 02/06/2023]
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19
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Muñoz-Amatriaín M, Mirebrahim H, Xu P, Wanamaker SI, Luo M, Alhakami H, Alpert M, Atokple I, Batieno BJ, Boukar O, Bozdag S, Cisse N, Drabo I, Ehlers JD, Farmer A, Fatokun C, Gu YQ, Guo YN, Huynh BL, Jackson SA, Kusi F, Lawley CT, Lucas MR, Ma Y, Timko MP, Wu J, You F, Barkley NA, Roberts PA, Lonardi S, Close TJ. Genome resources for climate-resilient cowpea, an essential crop for food security. Plant J 2017; 89:1042-1054. [PMID: 27775877 DOI: 10.1111/tpj.13404] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Revised: 10/16/2016] [Accepted: 10/18/2016] [Indexed: 05/20/2023]
Abstract
Cowpea (Vigna unguiculata L. Walp.) is a legume crop that is resilient to hot and drought-prone climates, and a primary source of protein in sub-Saharan Africa and other parts of the developing world. However, genome resources for cowpea have lagged behind most other major crops. Here we describe foundational genome resources and their application to the analysis of germplasm currently in use in West African breeding programs. Resources developed from the African cultivar IT97K-499-35 include a whole-genome shotgun (WGS) assembly, a bacterial artificial chromosome (BAC) physical map, and assembled sequences from 4355 BACs. These resources and WGS sequences of an additional 36 diverse cowpea accessions supported the development of a genotyping assay for 51 128 SNPs, which was then applied to five bi-parental RIL populations to produce a consensus genetic map containing 37 372 SNPs. This genetic map enabled the anchoring of 100 Mb of WGS and 420 Mb of BAC sequences, an exploration of genetic diversity along each linkage group, and clarification of macrosynteny between cowpea and common bean. The SNP assay enabled a diversity analysis of materials from West African breeding programs. Two major subpopulations exist within those materials, one of which has significant parentage from South and East Africa and more diversity. There are genomic regions of high differentiation between subpopulations, one of which coincides with a cluster of nodulin genes. The new resources and knowledge help to define goals and accelerate the breeding of improved varieties to address food security issues related to limited-input small-holder farming and climate stress.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Hamid Mirebrahim
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Pei Xu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences (ZAAS), Hangzhou, 310021, China
| | - Steve I Wanamaker
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - MingCheng Luo
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Hind Alhakami
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Matthew Alpert
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Ibrahim Atokple
- Council for Scientific and Industrial Research, Savanna Agricultural Research Institute, Tamale, Ghana
| | - Benoit J Batieno
- Institut de l'Environnement et de Recherches Agricoles, Saria, Burkina Faso
| | - Ousmane Boukar
- International Institute of Tropical Agriculture, Kano, Nigeria
| | - Serdar Bozdag
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
- Department of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, USA
| | - Ndiaga Cisse
- Institut Sénégalais de Recherches Agricoles, Thiès, Senegal
| | - Issa Drabo
- Institut de l'Environnement et de Recherches Agricoles, Saria, Burkina Faso
| | - Jeffrey D Ehlers
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
- The Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Andrew Farmer
- National Center for Genome Resources, Santa Fe, NM, USA
| | | | - Yong Q Gu
- USDA-ARS Western Regional Research Center, Albany, CA, USA
| | - Yi-Ning Guo
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Bao-Lam Huynh
- Department of Nematology, University of California, Riverside, CA, USA
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, Athens, GA, USA
| | - Francis Kusi
- Council for Scientific and Industrial Research, Savanna Agricultural Research Institute, Tamale, Ghana
| | | | - Mitchell R Lucas
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
| | - Yaqin Ma
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Jiajie Wu
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Frank You
- Department of Plant Sciences, University of California, Davis, CA, USA
- Agriculture and Agri-Food Canada, Morden, MB, Canada
| | - Noelle A Barkley
- USDA-ARS Plant Genetic Resources Conservation Unit, Griffin, GA, USA
| | - Philip A Roberts
- Department of Nematology, University of California, Riverside, CA, USA
| | - Stefano Lonardi
- Department of Computer Science and Engineering, University of California, Riverside, CA, USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA, USA
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20
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Li K, Hegarty J, Zhang C, Wan A, Wu J, Guedira GB, Chen X, Muñoz-Amatriaín M, Fu D, Dubcovsky J. Fine mapping of barley locus Rps6 conferring resistance to wheat stripe rust. Theor Appl Genet 2016; 129:845-859. [PMID: 26875072 PMCID: PMC4799263 DOI: 10.1007/s00122-015-2663-1] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 12/22/2015] [Indexed: 05/22/2023]
Abstract
KEY MESSAGE Barley resistance to wheat stripe rust has remained effective for a long time and, therefore, the genes underlying this resistance can be a valuable tool to engineer durable resistance in wheat. Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is a major disease of wheat that is causing large economic losses in many wheat-growing regions of the world. Deployment of Pst resistance genes has been an effective strategy for controlling this pathogen, but many of these genes have been defeated by new Pst races. In contrast, genes providing resistance to this wheat pathogen in other grass species (nonhost resistance) have been more durable. Barley varieties (Hordeum vulgare ssp. vulgare) are predominately immune to wheat Pst, but we identified three accessions of wild barley (Hordeum vulgare ssp. spontaneum) that are susceptible to Pst. Using these accessions, we mapped a barley locus conferring resistance to Pst on the distal region of chromosome arm 7HL and designated it as Rps6. The detection of the same locus in the cultivated barley 'Tamalpais' and in the Chinese barley 'Y12' by an allelism test suggests that Rps6 may be a frequent component of barley intermediate host resistance to Pst. Using a high-density mapping population (>10,000 gametes) we precisely mapped Rps6 within a 0.14 cM region (~500 kb contig) that is colinear to regions in Brachypodium (<94 kb) and rice (<9 kb). Since no strong candidate gene was identified in these colinear regions, a dedicated positional cloning effort in barley will be required to identify Rps6. The identification of this and other barley genes conferring resistance to Pst can contribute to our understanding of the mechanisms for durable resistance against this devastating wheat pathogen.
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Affiliation(s)
- Kun Li
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Joshua Hegarty
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Chaozhong Zhang
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Anmin Wan
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
| | - Jiajie Wu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China
| | - Gina Brown Guedira
- USDA-ARS, Plant Science Research Unit, Department of Crop Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Xianming Chen
- Department of Plant Pathology, Washington State University, Pullman, WA, 99164, USA
- USDA-ARS, Wheat Genetics, Quality, Physiology, and Disease Research Unit, Pullman, WA, 99164, USA
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Daolin Fu
- State Key Laboratory of Crop Biology, Shandong Key Laboratory of Crop Biology, Shandong Agricultural University, Tai'an, 271018, Shandong, China.
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, 20815, USA.
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21
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Cuesta-Marcos A, Muñoz-Amatriaín M, Filichkin T, Karsai I, Trevaskis B, Yasuda S, Hayes P, Sato K. The Relationships between Development and Low Temperature Tolerance in Barley Near Isogenic Lines Differing for Flowering Behavior. Plant Cell Physiol 2015; 56:2312-24. [PMID: 26443377 DOI: 10.1093/pcp/pcv147] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Accepted: 09/28/2015] [Indexed: 05/25/2023]
Abstract
Flowering time, vernalization requirement, photoperiod sensitivity and low temperature tolerance are key traits in the Triticeae. We characterized a set of isogenic genetic stocks-representing single and pairwise substitutions of spring alleles at the VRN-H1, VRN-H2 and VRN-H3 loci in a winter barley background-at the structural, functional and phenotypic levels. High density mapping with reference to the barley genome sequence confirmed that in all cases target VRN alleles were present in the near isogenic lines (NILs) and allowed estimates of introgression size (at the genetic and physical levels) and gene content. Expression data corroborated the structural and phenotypic results. The latter confirmed that substitution of a spring allele at any of the VRN loci is sufficient to eliminate vernalization requirement. There was no significant change in low temperature tolerance with substitution of a spring allele at VRN-H2, but there were significant losses in cold tolerance with substitutions at VRN-H1 and VRN-H3. Reductions in cold tolerance are ascribed to an accelerated transition from the vegetative to reproductive state. The set of NILs will be a rich resource for understanding the genetics of vernalization, low temperature tolerance and other traits encoded/regulated by genes within the introgressed intervals.
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Affiliation(s)
- Alfonso Cuesta-Marcos
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA These authors contributed equally to this work
| | - María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA These authors contributed equally to this work
| | - Tanya Filichkin
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA
| | - Ildikó Karsai
- MTA ATK, Martonvásár, Brunszvik u. 2. H-2462, Hungary
| | - Ben Trevaskis
- CSIRO, Agriculture Flagship, Canberra, 2601, Australia
| | - Shozo Yasuda
- Institute of Plant Science and Resources, Okayama University, 2-20-1, Chuo, Kurashiki, Okayama, 710-0046, Japan
| | - Patrick Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331, USA
| | - Kazuhiro Sato
- Institute of Plant Science and Resources, Okayama University, 2-20-1, Chuo, Kurashiki, Okayama, 710-0046, Japan
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22
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Muñoz-Amatriaín M, Lonardi S, Luo M, Madishetty K, Svensson JT, Moscou MJ, Wanamaker S, Jiang T, Kleinhofs A, Muehlbauer GJ, Wise RP, Stein N, Ma Y, Rodriguez E, Kudrna D, Bhat PR, Chao S, Condamine P, Heinen S, Resnik J, Wing R, Witt HN, Alpert M, Beccuti M, Bozdag S, Cordero F, Mirebrahim H, Ounit R, Wu Y, You F, Zheng J, Simková H, Dolezel J, Grimwood J, Schmutz J, Duma D, Altschmied L, Blake T, Bregitzer P, Cooper L, Dilbirligi M, Falk A, Feiz L, Graner A, Gustafson P, Hayes PM, Lemaux P, Mammadov J, Close TJ. Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome. Plant J 2015; 84:216-27. [PMID: 26252423 PMCID: PMC5014227 DOI: 10.1111/tpj.12959] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 07/15/2015] [Accepted: 07/24/2015] [Indexed: 05/18/2023]
Abstract
Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome (BACs) in the physical map were sequenced, fine structure was limited. To gain access to the gene-containing portion of the barley genome at high resolution, we identified and sequenced 15 622 BACs representing the minimal tiling path of 72 052 physical-mapped gene-bearing BACs. This generated ~1.7 Gb of genomic sequence containing an estimated 2/3 of all Morex barley genes. Exploration of these sequenced BACs revealed that although distal ends of chromosomes contain most of the gene-enriched BACs and are characterized by high recombination rates, there are also gene-dense regions with suppressed recombination. We made use of published map-anchored sequence data from Aegilops tauschii to develop a synteny viewer between barley and the ancestor of the wheat D-genome. Except for some notable inversions, there is a high level of collinearity between the two species. The software HarvEST:Barley provides facile access to BAC sequences and their annotations, along with the barley-Ae. tauschii synteny viewer. These BAC sequences constitute a resource to improve the efficiency of marker development, map-based cloning, and comparative genomics in barley and related crops. Additional knowledge about regions of the barley genome that are gene-dense but low recombination is particularly relevant.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Stefano Lonardi
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - MingCheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Kavitha Madishetty
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Jan T Svensson
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Nordic Genetic Resource Center, SE-23053, Alnarp, Sweden
| | - Matthew J Moscou
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- The Sainsbury Laboratory, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Steve Wanamaker
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Tao Jiang
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Andris Kleinhofs
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
| | - Gary J Muehlbauer
- Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Roger P Wise
- Corn Insects and Crop Genetics Research, USDA-Agricultural Research Service & Department of Plant Pathology and Microbiology, Iowa State University, Ames, IA, 50011-1020, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Yaqin Ma
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Molefarming Laboratory USA, Davis, CA, 95616, USA
| | - Edmundo Rodriguez
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Departamento de Ciencias Basicas, Universidad Autonoma Agraria Antonio Narro, Narro 1923, Saltillo, Coah, 25315, México
| | - Dave Kudrna
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Prasanna R Bhat
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Monsanto Research Center, Bangalore, 560092, India
| | - Shiaoman Chao
- USDA-ARS Biosciences Research Lab, Fargo, ND, 58105, USA
| | - Pascal Condamine
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
| | - Shane Heinen
- Department of Plant Biology, Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN, 55108, USA
| | - Josh Resnik
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
- Ronald Reagan UCLA Medical Center, Los Angeles, CA, 90095, USA
| | - Rod Wing
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, 85721, USA
| | - Heather N Witt
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
- Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Matthew Alpert
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Turtle Rock Studios, Lake Forest, CA, 92630, USA
| | - Marco Beccuti
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Department of Computer Science, University of Turin, Corso Svizzera 185, 10149, Turin, Italy
| | - Serdar Bozdag
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Deptartment of Mathematics, Statistics and Computer Science, Marquette University, Milwaukee, WI, 53233, USA
| | - Francesca Cordero
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Department of Computer Science, University of Turin, Corso Svizzera 185, 10149, Turin, Italy
| | - Hamid Mirebrahim
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Rachid Ounit
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
| | - Yonghui Wu
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Google Inc., Mountain View, CA, 94043, USA
| | - Frank You
- USDA-ARS, Albany, CA, 94710, USA
- Agriculture and Agri-Food Canada, Morden, MB, R6M 1Y5, Canada
| | - Jie Zheng
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- School of Computer Engineering, Nanyang Technological University, Nanyang Avenue, Singapore, 639798, Singapore
| | - Hana Simková
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic
| | - Jaroslav Dolezel
- Centre of the Region Hana for Biotechnological and Agricultural Research, Institute of Experimental Botany, Sokolovskį 6, CZ-77200, Olomouc, Czech Republic
| | - Jane Grimwood
- Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Hudson Alpha Genome Sequencing Center, DOE Joint Genome Institute, Huntsville, AL, 35806, USA
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Denisa Duma
- Department of Computer Science, University of California, Riverside, CA, 92521, USA
- Baylor College of Medicine, Jan and Dan Duncan Neurological Research Institute, Houston, TX, 77030, USA
| | - Lothar Altschmied
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | - Tom Blake
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
| | | | - Laurel Cooper
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, 97331, USA
| | - Muharrem Dilbirligi
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164, USA
- International Cooperation Department, The Scientific and Technological Research Council of Turkey, Tunus cad. No: 80, 06100, Kavaklidere, Ankara, Turkey
| | - Anders Falk
- Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - Leila Feiz
- Department of Plant Sciences & Plant Pathology, Montana State University, Bozeman, MT, 59717-3150, USA
- Boyce Thompson Institute for Plant Research, Cornell University, 533 Tower Road, Ithaca, NY, 14853-1801, USA
| | - Andreas Graner
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466, Gatersleben, Germany
| | | | - Patrick M Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR, 97331, USA
| | - Peggy Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Jafar Mammadov
- Department of Crop & Soil Environmental Sciences, Virginia Tech, Blacksburg, VA, 24061, USA
- Dow AgroSciences LLC, Indianapolis, IN, 46268-1054, USA
| | - Timothy J Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA, 92521, USA
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23
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Muñoz-Amatriaín M, Cuesta-Marcos A, Endelman JB, Comadran J, Bonman JM, Bockelman HE, Chao S, Russell J, Waugh R, Hayes PM, Muehlbauer GJ. The USDA barley core collection: genetic diversity, population structure, and potential for genome-wide association studies. PLoS One 2014; 9:e94688. [PMID: 24732668 PMCID: PMC3986206 DOI: 10.1371/journal.pone.0094688] [Citation(s) in RCA: 154] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 03/18/2014] [Indexed: 11/18/2022] Open
Abstract
New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and phenotypic diversity, but characterization of these resources is required to increase their utility for breeding programs. We used a barley SNP iSelect platform with 7,842 SNPs to genotype 2,417 barley accessions sampled from the USDA National Small Grains Collection of 33,176 accessions. Most of the accessions in this core collection are categorized as landraces or cultivars/breeding lines and were obtained from more than 100 countries. Both STRUCTURE and principal component analysis identified five major subpopulations within the core collection, mainly differentiated by geographical origin and spike row number (an inflorescence architecture trait). Different patterns of linkage disequilibrium (LD) were found across the barley genome and many regions of high LD contained traits involved in domestication and breeding selection. The genotype data were used to define 'mini-core' sets of accessions capturing the majority of the allelic diversity present in the core collection. These 'mini-core' sets can be used for evaluating traits that are difficult or expensive to score. Genome-wide association studies (GWAS) of 'hull cover', 'spike row number', and 'heading date' demonstrate the utility of the core collection for locating genetic factors determining important phenotypes. The GWAS results were referenced to a new barley consensus map containing 5,665 SNPs. Our results demonstrate that GWAS and high-density SNP genotyping are effective tools for plant breeders interested in accessing genetic diversity in large germplasm collections.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
| | - Alfonso Cuesta-Marcos
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
| | - Jeffrey B. Endelman
- Department of Horticulture, University of Wisconsin, Madison, Wisconsin, United States of America
| | - Jordi Comadran
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - John M. Bonman
- USDA-ARS, Small Grains and Potato Germplasm Research Unit, Aberdeen, Idaho, United States of America
| | - Harold E. Bockelman
- USDA-ARS, Small Grains and Potato Germplasm Research Unit, Aberdeen, Idaho, United States of America
| | - Shiaoman Chao
- USDA-ARS, Biosciences Research Lab, Fargo, North Dakota, United States of America
| | - Joanne Russell
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Robbie Waugh
- The James Hutton Institute, Invergowrie, Dundee, United Kingdom
| | - Patrick M. Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, Oregon, United States of America
| | - Gary J. Muehlbauer
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, United States of America
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, United States of America
- * E-mail:
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24
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Abstract
Genetic variation is crucial for successful barley improvement. Genomic technologies are improving dramatically and are providing access to the genetic diversity within this important crop species. Diverse collections of barley germplasm are being assembled and mined via genome-wide association studies and the identified variation can be linked to the barley sequence assembly. Introgression of favorable alleles via marker-assisted selection is now faster and more efficient due to the availability of single nucleotide polymorphism platforms. High-throughput genotyping is also making genomic selection an essential tool in modern barley breeding. Contemporary plant breeders now benefit from publicly available user-friendly databases providing genotypic and phenotypic information on large numbers of barley accessions. These resources facilitate access to allelic variation. In this review we explore how the most recent genomics and molecular breeding advances are changing breeding practices. The Coordinated Agricultural Projects (CAPs), Barley CAP and Triticeae CAP coupled with international collaborations, are discussed in detail as examples of a collaborative approach to exploit diverse germplasm resources for barley improvement.
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Mascher M, Muehlbauer GJ, Rokhsar DS, Chapman J, Schmutz J, Barry K, Muñoz-Amatriaín M, Close TJ, Wise RP, Schulman AH, Himmelbach A, Mayer KFX, Scholz U, Poland JA, Stein N, Waugh R. Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ). Plant J 2013; 76:718-27. [PMID: 23998490 PMCID: PMC4298792 DOI: 10.1111/tpj.12319] [Citation(s) in RCA: 129] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 08/07/2013] [Accepted: 08/29/2013] [Indexed: 05/18/2023]
Abstract
Next-generation whole-genome shotgun assemblies of complex genomes are highly useful, but fail to link nearby sequence contigs with each other or provide a linear order of contigs along individual chromosomes. Here, we introduce a strategy based on sequencing progeny of a segregating population that allows de novo production of a genetically anchored linear assembly of the gene space of an organism. We demonstrate the power of the approach by reconstructing the chromosomal organization of the gene space of barley, a large, complex and highly repetitive 5.1 Gb genome. We evaluate the robustness of the new assembly by comparison to a recently released physical and genetic framework of the barley genome, and to various genetically ordered sequence-based genotypic datasets. The method is independent of the need for any prior sequence resources, and will enable rapid and cost-efficient establishment of powerful genomic information for many species.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)D–06466 Seeland OT, Gatersleben, Germany
- For correspondence (e-mails ; )
| | - Gary J Muehlbauer
- University of Minnesota, Department of Agronomy and Plant GeneticsSt Paul, MN, 55108, USA
- University of Minnesota, Department of Plant BiologySt Paul, MN 55108, USA
- For correspondence (e-mails ; )
| | - Daniel S Rokhsar
- Department of Energy Joint Genome Institute2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- Department of Molecular and Cell Biology, University of CaliforniaBerkeley, CA, 94720, USA
| | - Jarrod Chapman
- Department of Energy Joint Genome Institute2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute of BiotechnologyHuntsville, AL, 35806, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - María Muñoz-Amatriaín
- University of Minnesota, Department of Agronomy and Plant GeneticsSt Paul, MN, 55108, USA
| | - Timothy J Close
- Department of Botany & Plant Sciences, University of CaliforniaRiverside, CA, 92521, USA
| | - Roger P Wise
- US Department of Agriculture/Agricultural Research Service, Department of Plant Pathology & Microbiology, Iowa State UniversityAmes, IA, 50011–1020, USA
| | - Alan H Schulman
- Institute of Biotechnology, University of Helsinki/MTT Agrifood ResearchPO Box 65, 00014, Helsinki, Finland
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)D–06466 Seeland OT, Gatersleben, Germany
| | - Klaus FX Mayer
- Munich Information Center for Protein Sequences/Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum MünchenD–85764, Neuherberg, Germany
| | - Uwe Scholz
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)D–06466 Seeland OT, Gatersleben, Germany
| | - Jesse A Poland
- US Department of Agriculture/Agricultural Research Service, Hard Winter Wheat Genetics Research Unit and Department of Agronomy, Kansas State UniversityManhattan, KS, 65506, USA
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)D–06466 Seeland OT, Gatersleben, Germany
| | - Robbie Waugh
- Division of Plant Sciences, University of Dundee at the James Hutton InstituteInvergowrie, Dundee, DD2 5DA, UK
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Walker CK, Ford R, Muñoz-Amatriaín M, Panozzo JF. The detection of QTLs in barley associated with endosperm hardness, grain density, grain size and malting quality using rapid phenotyping tools. Theor Appl Genet 2013; 126:2533-51. [PMID: 23884598 DOI: 10.1007/s00122-013-2153-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 07/01/2013] [Indexed: 05/18/2023]
Abstract
Using a barley mapping population, 'Vlamingh' × 'Buloke' (V × B), whole grain analyses were undertaken for physical seed traits and malting quality. Grain density and size were predicted by digital image analysis (DIA), while malt extract and protein content were predicted using near infrared (NIR) analysis. Validation of DIA and NIR algorithms confirmed that data for QTL analysis was highly correlated (R (2) > 0.82), with high RPD values (the ratio of the standard error of prediction to the standard deviation, 2.31-9.06). Endosperm hardness was measured on this mapping population using the single kernel characterisation system. Grain density and endosperm hardness were significantly inter-correlated in all three environments (r > 0.22, P < 0.001); however, other grain components were found to interact with the traits. QTL for these traits were also found on different genomic regions, for example, grain density QTLs were found on chromosomes 2H and 6H, whereas endosperm hardness QTLs were found on 1H, 5H, and 7H. In this study, the majority of the genomic regions associated with grain texture were also coincident with QTLs for grain size, yield, flowering date and/or plant development genes. This study highlights the complexity of genomic regions associated with the variation of endosperm hardness and grain density, and their relationships with grain size traits, agronomic-related traits, and plant development loci.
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Affiliation(s)
- Cassandra K Walker
- Department of Environment and Primary Industries, Horsham, VIC, 3400, Australia,
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Muñoz-Amatriaín M, Eichten SR, Wicker T, Richmond TA, Mascher M, Steuernagel B, Scholz U, Ariyadasa R, Spannagl M, Nussbaumer T, Mayer KFX, Taudien S, Platzer M, Jeddeloh JA, Springer NM, Muehlbauer GJ, Stein N. Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome. Genome Biol 2013; 14:R58. [PMID: 23758725 PMCID: PMC3706897 DOI: 10.1186/gb-2013-14-6-r58] [Citation(s) in RCA: 93] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Accepted: 06/12/2013] [Indexed: 12/20/2022] Open
Abstract
Background There is growing evidence for the prevalence of copy number variation (CNV) and its role in phenotypic variation in many eukaryotic species. Here we use array comparative genomic hybridization to explore the extent of this type of structural variation in domesticated barley cultivars and wild barleys. Results A collection of 14 barley genotypes including eight cultivars and six wild barleys were used for comparative genomic hybridization. CNV affects 14.9% of all the sequences that were assessed. Higher levels of CNV diversity are present in the wild accessions relative to cultivated barley. CNVs are enriched near the ends of all chromosomes except 4H, which exhibits the lowest frequency of CNVs. CNV affects 9.5% of the coding sequences represented on the array and the genes affected by CNV are enriched for sequences annotated as disease-resistance proteins and protein kinases. Sequence-based comparisons of CNV between cultivars Barke and Morex provided evidence that DNA repair mechanisms of double-strand breaks via single-stranded annealing and synthesis-dependent strand annealing play an important role in the origin of CNV in barley. Conclusions We present the first catalog of CNVs in a diploid Triticeae species, which opens the door for future genome diversity research in a tribe that comprises the economically important cereal species wheat, barley, and rye. Our findings constitute a valuable resource for the identification of CNV affecting genes of agronomic importance. We also identify potential mechanisms that can generate variation in copy number in plant genomes.
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Sato K, Close TJ, Bhat P, Muñoz-Amatriaín M, Muehlbauer GJ. Single Nucleotide Polymorphism Mapping and Alignment of Recombinant Chromosome Substitution Lines in Barley. ACTA ACUST UNITED AC 2011; 52:728-37. [DOI: 10.1093/pcp/pcr024] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Muñoz-Amatriaín M, Xiong Y, Schmitt MR, Bilgic H, Budde AD, Chao S, Smith KP, Muehlbauer GJ. Transcriptome analysis of a barley breeding program examines gene expression diversity and reveals target genes for malting quality improvement. BMC Genomics 2010; 11:653. [PMID: 21092286 PMCID: PMC3091773 DOI: 10.1186/1471-2164-11-653] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2010] [Accepted: 11/23/2010] [Indexed: 11/10/2022] Open
Abstract
Background Advanced cycle breeding utilizes crosses among elite lines and is a successful method to develop new inbreds. However, it results in a reduction in genetic diversity within the breeding population. The development of malting barley varieties requires the adherence to a narrow malting quality profile and thus the use of advanced cycle breeding strategies. Although attention has been focused on diversity in gene expression and its association with genetic diversity, there are no studies performed in a single breeding program examining the implications that consecutive cycles of breeding have on gene expression variation and identifying the variability still available for future improvement. Results Fifteen lines representing the historically important six-rowed malting barley breeding program of the University of Minnesota were genotyped with 1,524 SNPs, phenotypically examined for six malting quality traits, and analyzed for transcript accumulation during germination using the Barley1 GeneChip array. Significant correlation was detected between genetic and transcript-level variation. We observed a reduction in both genetic and gene expression diversity through the breeding process, although the expression of many genes have not been fixed. A high number of quality-related genes whose expression was fixed during the breeding process was identified, indicating that much of the diversity reduction was associated with the improvement of the complex phenotype "malting quality", the main goal of the University of Minnesota breeding program. We also identified 49 differentially expressed genes between the most recent lines of the program that were correlated with one or more of the six primary malting quality traits. These genes constitute potential targets for the improvement of malting quality within the breeding program. Conclusions The present study shows the repercussion of advanced cycle breeding on gene expression diversity within an important barley breeding program. A reduction in gene expression diversity was detected, although there is diversity still present after forty years of breeding that can exploited for future crop improvement. In addition, the identification of candidate genes for enhancing malting quality may be used to optimize the selection of targets for further improvements in this economically important phenotype.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, 55108, USA
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Muñoz-Amatriaín M, Cistué L, Xiong Y, Bilgic H, Budde AD, Schmitt MR, Smith KP, Hayes PM, Muehlbauer GJ. Structural and functional characterization of a winter malting barley. Theor Appl Genet 2010; 120:971-84. [PMID: 19960335 DOI: 10.1007/s00122-009-1225-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/16/2009] [Accepted: 11/18/2009] [Indexed: 05/18/2023]
Abstract
The development of winter malting barley (Hordeum vulgare L.) varieties is emerging as a worldwide priority due to the numerous advantages of these varieties over spring types. However, the complexity of both malting quality and winter hardiness phenotypes makes simultaneous improvement a challenge. To obtain an understanding of the relationship between loci controlling winter hardiness and malt quality and to assess the potential for breeding winter malting barley varieties, we structurally and functionally characterized the six-row accession "88Ab536", a cold-tolerant line with superior malting quality characteristics that derives from the cross of NE76129/Morex//Morex. We used 4,596 SNPs to construct the haplotype structure of 88Ab536 on which malting quality and winter hardiness loci reported in the literature were aligned. The genomic regions determining malting quality and winter hardiness traits have been defined in this founder germplasm, which will assist breeders in targeting regions for marker-assisted selection. The Barley1 GeneChip array was used to functionally characterize 88Ab536 during malting. Its gene expression profile was similar to that of the archetypical malting variety Morex, which is consistent with their similar malting quality characteristics. The characterization of 88Ab536 has increased our understanding of the genetic relationships of malting quality and winter hardiness, and will provide a genetic foundation for further development of more cold-tolerant varieties that have malt quality characteristics that meet or exceed current benchmarks.
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Affiliation(s)
- María Muñoz-Amatriaín
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA.
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Muñoz-Amatriaín M, Svensson JT, Castillo AM, Close TJ, Vallés MP. Microspore embryogenesis: assignment of genes to embryo formation and green vs. albino plant production. Funct Integr Genomics 2009; 9:311-23. [PMID: 19229567 PMCID: PMC2700865 DOI: 10.1007/s10142-009-0113-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2008] [Revised: 01/16/2009] [Accepted: 01/24/2009] [Indexed: 11/30/2022]
Abstract
Plant microspores can be reprogrammed from their normal pollen development to an embryogenic route in a process termed microspore embryogenesis or androgenesis. Stress treatment has a critical role in this process, inducing the dedifferentiation of microspores and conditioning the following androgenic response. In this study, we have used three barley doubled haploid lines with similar genetic background but different androgenic response. The Barley1 GeneChip was used for transcriptome comparison of these lines after mannitol stress treatment, allowing the identification of 213 differentially expressed genes. Most of these genes belong to the functional categories "cell rescue, defense, and virulence"; "metabolism"; "transcription"; and "transport". These genes were grouped into clusters according to their expression profiles among lines. A principal component analysis allowed us to associate specific gene expression clusters to phenotypic variables. Genes associated with the ability of microspores to divide and form embryos were mainly involved in changes in the structure and function of membranes, efficient use of available energy sources, and cell fate. Genes related to stress response, transcription and translation regulation, and degradation of pollen-specific proteins were associated with green plant production, while expression of genes related to plastid development was associated with albino plant regeneration.
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Affiliation(s)
- M. Muñoz-Amatriaín
- Departamento de Genética y Producción Vegetal, Estación Experimental Aula Dei, Consejo Superior de Investigaciones Científicas, Apdo 13034, 50080 Zaragoza, Spain
| | - J. T. Svensson
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
| | - A. M. Castillo
- Departamento de Genética y Producción Vegetal, Estación Experimental Aula Dei, Consejo Superior de Investigaciones Científicas, Apdo 13034, 50080 Zaragoza, Spain
| | - T. J. Close
- Department of Botany and Plant Sciences, University of California, Riverside, CA 92521 USA
| | - M. P. Vallés
- Departamento de Genética y Producción Vegetal, Estación Experimental Aula Dei, Consejo Superior de Investigaciones Científicas, Apdo 13034, 50080 Zaragoza, Spain
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