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Errbii M, Ernst UR, Lajmi A, Privman E, Gadau J, Schrader L. Evolutionary genomics of socially polymorphic populations of Pogonomyrmex californicus. BMC Biol 2024; 22:109. [PMID: 38735942 PMCID: PMC11089791 DOI: 10.1186/s12915-024-01907-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 04/30/2024] [Indexed: 05/14/2024] Open
Abstract
BACKGROUND Social insects vary considerably in their social organization both between and within species. In the California harvester ant, Pogonomyrmex californicus (Buckley 1867), colonies are commonly founded and headed by a single queen (haplometrosis, primary monogyny). However, in some populations in California (USA), unrelated queens cooperate not only during founding (pleometrosis) but also throughout the life of the colony (primary polygyny). The genetic architecture and evolutionary dynamics of this complex social niche polymorphism (haplometrosis vs pleometrosis) have remained unknown. RESULTS We provide a first analysis of its genomic basis and evolutionary history using population genomics comparing individuals from a haplometrotic population to those from a pleometrotic population. We discovered a recently evolved (< 200 k years), 8-Mb non-recombining region segregating with the observed social niche polymorphism. This region shares several characteristics with supergenes underlying social polymorphisms in other socially polymorphic ant species. However, we also find remarkable differences from previously described social supergenes. Particularly, four additional genomic regions not in linkage with the supergene show signatures of a selective sweep in the pleometrotic population. Within these regions, we find for example genes crucial for epigenetic regulation via histone modification (chameau) and DNA methylation (Dnmt1). CONCLUSIONS Altogether, our results suggest that social morph in this species is a polygenic trait involving a potential young supergene. Further studies targeting haplo- and pleometrotic individuals from a single population are however required to conclusively resolve whether these genetic differences underlie the alternative social phenotypes or have emerged through genetic drift.
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Affiliation(s)
- Mohammed Errbii
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany
| | - Ulrich R Ernst
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany
- Present Address: Apicultural State Institute, University of Hohenheim, Erna-Hruschka-Weg 6, Stuttgart, DE-70599, Germany
- Center for Biodiversity and Integrative Taxonomy (KomBioTa), University of Hohenheim, Stuttgart, DE-70599, Germany
| | - Aparna Lajmi
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Eyal Privman
- Department of Evolutionary and Environmental Biology, Institute of Evolution, University of Haifa, Haifa, Israel
| | - Jürgen Gadau
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany.
| | - Lukas Schrader
- Molecular Evolution and Sociobiology Group, Institute for Evolution and Biodiversity, University of Münster, Hüfferstr. 1, Münster, DE-48149, Germany.
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Lopez-Ortiz C, Reddy UK, Zhang C, Natarajan P, Nimmakayala P, Benedito VA, Fabian M, Stommel J. QTL and PACE analyses identify candidate genes for anthracnose resistance in tomato. FRONTIERS IN PLANT SCIENCE 2023; 14:1200999. [PMID: 37615029 PMCID: PMC10443646 DOI: 10.3389/fpls.2023.1200999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/17/2023] [Indexed: 08/25/2023]
Abstract
Anthracnose, caused by the fungal pathogen Colletotrichum spp., is one of the most significant tomato diseases in the United States and worldwide. No commercial cultivars with anthracnose resistance are available, limiting resistant breeding. Cultivars with genetic resistance would significantly reduce crop losses, reduce the use of fungicides, and lessen the risks associated with chemical application. A recombinant inbred line (RIL) mapping population (N=243) has been made from a cross between the susceptible US28 cultivar and the resistant but semiwild and small-fruited 95L368 to identify quantitative trait loci (QTLs) associated with anthracnose resistance. The RIL population was phenotyped for resistance by inoculating ripe field-harvested tomato fruits with Colletotrichum coccodes for two seasons. In this study, we identified twenty QTLs underlying resistance, with a range of phenotypic variance of 4.5 to 17.2% using a skeletal linkage map and a GWAS. In addition, a QTLseq analysis was performed using deep sequencing of extreme bulks that validated QTL positions identified using traditional mapping and resolved candidate genes underlying various QTLs. We further validated AP2-like ethylene-responsive transcription factor, N-alpha-acetyltransferase (NatA), cytochrome P450, amidase family protein, tetratricopeptide repeat, bHLH transcription factor, and disease resistance protein RGA2-like using PCR allelic competitive extension (PACE) genotyping. PACE assays developed in this study will enable high-throughput screening for use in anthracnose resistance breeding in tomato.
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Affiliation(s)
- Carlos Lopez-Ortiz
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, United States
| | - Umesh K. Reddy
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, United States
| | - Chong Zhang
- The Genetic Improvement for Fruits & Vegetables Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - Purushothaman Natarajan
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, United States
| | - Padma Nimmakayala
- Department of Biology, Gus R. Douglass Institute, West Virginia State University, Institute, WV, United States
| | | | - Matthew Fabian
- The Genetic Improvement for Fruits & Vegetables Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
| | - John Stommel
- The Genetic Improvement for Fruits & Vegetables Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, MD, United States
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Zhang Y, Wei W, Wang Z. Progressive Learning Hill Climbing Algorithm with Energy-Map-Based Initialization for Image Reconstruction. Biomimetics (Basel) 2023; 8:biomimetics8020174. [PMID: 37218760 DOI: 10.3390/biomimetics8020174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 04/14/2023] [Accepted: 04/19/2023] [Indexed: 05/24/2023] Open
Abstract
Image reconstruction is an interesting yet challenging optimization problem that has several potential applications. The task is to reconstruct an image using a fixed number of transparent polygons. Traditional gradient-based algorithms cannot be applied to the problem since the optimization objective has no explicit expression and cannot be represented by computational graphs. Metaheuristic search algorithms are powerful optimization techniques for solving complex optimization problems, especially in the context of incomplete information or limited computational capability. In this paper, we developed a novel metaheuristic search algorithm named progressive learning hill climbing (ProHC) for image reconstruction. Instead of placing all the polygons on a blank canvas at once, ProHC starts from one polygon and gradually adds new polygons to the canvas until reaching the number limit. Furthermore, an energy-map-based initialization operator was designed to facilitate the generation of new solutions. To assess the performance of the proposed algorithm, we constructed a benchmark problem set containing four different types of images. The experimental results demonstrated that ProHC was able to produce visually pleasing reconstructions of the benchmark images. Moreover, the time consumed by ProHC was much shorter than that of the existing approach.
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Affiliation(s)
- Yuhui Zhang
- School of Computer Science and Technology, Dongguan University of Technology, Dongguan 523808, China
| | - Wenhong Wei
- School of Computer Science and Technology, Dongguan University of Technology, Dongguan 523808, China
| | - Zijia Wang
- School of Computer Science and Cyber Engineering, Guangzhou University, Guangzhou 510006, China
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Nelson MN, Jabbari JS, Turakulov R, Pradhan A, Pazos-Navarro M, Stai JS, Cannon SB, Real D. The First Genetic Map for a Psoraleoid Legume ( Bituminaria bituminosa) Reveals Highly Conserved Synteny with Phaseoloid Legumes. PLANTS (BASEL, SWITZERLAND) 2020; 9:E973. [PMID: 32752081 PMCID: PMC7463921 DOI: 10.3390/plants9080973] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 07/27/2020] [Accepted: 07/29/2020] [Indexed: 11/17/2022]
Abstract
We present the first genetic map of tedera (Bituminaria bituminosa (L.) C.H. Stirton), a drought-tolerant forage legume from the Canary Islands with useful pharmaceutical properties. It is also the first genetic map for any species in the tribe Psoraleeae (Fabaceae). The map comprises 2042 genotyping-by-sequencing (GBS) markers distributed across 10 linkage groups, consistent with the haploid chromosome count for this species (n = 10). Sequence tags from the markers were used to find homologous matches in the genome sequences of the closely related species in the Phaseoleae tribe: soybean, common bean, and cowpea. No tedera linkage groups align in their entirety to chromosomes in any of these phaseoloid species, but there are long stretches of collinearity that could be used in tedera research for gene discovery purposes using the better-resourced phaseoloid species. Using Ks analysis of a tedera transcriptome against five legume genomes provides an estimated divergence time of 17.4 million years between tedera and soybean. Genomic information and resources developed here will be invaluable for breeding tedera varieties for forage and pharmaceutical purposes.
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Affiliation(s)
- Matthew N. Nelson
- CSIRO Agriculture & Food, Floreat, WA 6014, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA 6009, Australia
- Royal Botanic Gardens Kew, Millennium Seed Bank, Ardingly RH17 6TN, UK
| | - Jafar S. Jabbari
- Australian Genome Research Facility, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia; (J.S.J.); (R.T.)
| | - Rust Turakulov
- Australian Genome Research Facility, Victorian Comprehensive Cancer Centre, Melbourne, VIC 3000, Australia; (J.S.J.); (R.T.)
- Research School of Biology & Centre for Biodiversity Analysis, 134 Linnaeus Way, Acton, ACT 2601, Australia
| | - Aneeta Pradhan
- School of Biological Sciences, The University of Western Australia, Perth, WA 6009, Australia;
| | - Maria Pazos-Navarro
- School of Agriculture and Environment, The University of Western Australia, Perth, WA 6009, Australia;
| | - Jacob S. Stai
- Interdepartmental Genetics and Genomics Graduate Program, Iowa State University, Ames, IA 50010, USA;
| | - Steven B. Cannon
- USDA-ARS, Corn Insects and Crop Genetics Research Unit, Ames, IA 50011, USA;
| | - Daniel Real
- Department of Primary Industries and Regional Development, South Perth, WA 6151, Australia;
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Fatiukha A, Filler N, Lupo I, Lidzbarsky G, Klymiuk V, Korol AB, Pozniak C, Fahima T, Krugman T. Grain protein content and thousand kernel weight QTLs identified in a durum × wild emmer wheat mapping population tested in five environments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020. [PMID: 31562566 DOI: 10.1101/601773] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Genetic dissection of GPC and TKW in tetraploid durum × WEW RIL population, based on high-density SNP genetic map, revealed 12 GPC QTLs and 11 TKW QTLs, with favorable alleles for 11 and 5 QTLs, respectively, derived from WEW. Wild emmer wheat (Triticum turgidum ssp. dicoccoides, WEW) was shown to exhibit high grain protein content (GPC) and therefore possess a great potential for improvement of cultivated wheat nutritional value. Genetic dissection of thousand kernel weight (TKW) and grain protein content (GPC) was performed using a high-density genetic map constructed based on a recombinant inbred line (RIL) population derived from a cross between T. durum var. Svevo and WEW acc. Y12-3. Genotyping of 208 F6 RILs with a 15 K wheat single nucleotide polymorphism (SNP) array yielded 4166 polymorphic SNP markers, of which 1510 were designated as skeleton markers. A total map length of 2169 cM was obtained with an average distance of 1.5 cM between SNPs. A total of 12 GPC QTLs and 11 TKW QTLs were found under five different environments. No significant correlations were found between GPC and TKW across all environments. Four major GPC QTLs with favorable alleles from WEW were found on chromosomes 4BS, 5AS, 6BS and 7BL. The 6BS GPC QTL coincided with the physical position of the NAC transcription factor TtNAM-B1, underlying the cloned QTL, Gpc-B1. Comparisons of the physical intervals of the GPC QTLs described here with the results previously reported in other durum × WEW RIL population led to the discovery of seven novel GPC QTLs. Therefore, our research emphasizes the importance of GPC QTL dissection in diverse WEW accessions as a source of novel alleles for improvement of GPC in cultivated wheat.
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Affiliation(s)
- Andrii Fatiukha
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Naveh Filler
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Itamar Lupo
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Gabriel Lidzbarsky
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Abraham B Korol
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel.
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel.
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel.
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Fatiukha A, Filler N, Lupo I, Lidzbarsky G, Klymiuk V, Korol AB, Pozniak C, Fahima T, Krugman T. Grain protein content and thousand kernel weight QTLs identified in a durum × wild emmer wheat mapping population tested in five environments. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:119-131. [PMID: 31562566 DOI: 10.1007/s00122-019-03444-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Accepted: 09/18/2019] [Indexed: 05/14/2023]
Abstract
Genetic dissection of GPC and TKW in tetraploid durum × WEW RIL population, based on high-density SNP genetic map, revealed 12 GPC QTLs and 11 TKW QTLs, with favorable alleles for 11 and 5 QTLs, respectively, derived from WEW. Wild emmer wheat (Triticum turgidum ssp. dicoccoides, WEW) was shown to exhibit high grain protein content (GPC) and therefore possess a great potential for improvement of cultivated wheat nutritional value. Genetic dissection of thousand kernel weight (TKW) and grain protein content (GPC) was performed using a high-density genetic map constructed based on a recombinant inbred line (RIL) population derived from a cross between T. durum var. Svevo and WEW acc. Y12-3. Genotyping of 208 F6 RILs with a 15 K wheat single nucleotide polymorphism (SNP) array yielded 4166 polymorphic SNP markers, of which 1510 were designated as skeleton markers. A total map length of 2169 cM was obtained with an average distance of 1.5 cM between SNPs. A total of 12 GPC QTLs and 11 TKW QTLs were found under five different environments. No significant correlations were found between GPC and TKW across all environments. Four major GPC QTLs with favorable alleles from WEW were found on chromosomes 4BS, 5AS, 6BS and 7BL. The 6BS GPC QTL coincided with the physical position of the NAC transcription factor TtNAM-B1, underlying the cloned QTL, Gpc-B1. Comparisons of the physical intervals of the GPC QTLs described here with the results previously reported in other durum × WEW RIL population led to the discovery of seven novel GPC QTLs. Therefore, our research emphasizes the importance of GPC QTL dissection in diverse WEW accessions as a source of novel alleles for improvement of GPC in cultivated wheat.
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Affiliation(s)
- Andrii Fatiukha
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Naveh Filler
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Itamar Lupo
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Gabriel Lidzbarsky
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Valentyna Klymiuk
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Abraham B Korol
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
| | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, S7N 5A8, Canada
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel.
- Department of Evolutionary and Environmental Biology, University of Haifa, Mt. Carmel, 31905, Haifa, Israel.
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Mt. Carmel, 31905, Haifa, Israel.
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Dresvyannikova AE, Watanabe N, Muterko AF, Krasnikov AA, Goncharov NP, Dobrovolskaya OB. Characterization of a dominant mutation for the liguleless trait: Aegilops tauschii liguleless (Lg t). BMC PLANT BIOLOGY 2019; 19:55. [PMID: 30813900 PMCID: PMC6393956 DOI: 10.1186/s12870-019-1635-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
BACKGROUND Leaves of Poaceae have a unique morphological feature: they consist of a proximal sheath and a distal blade separated by a ligular region. The sheath provides structural support and protects young developing leaves, whereas the main function of the blade is photosynthesis. The auricles allow the blade to tilt back for optimal photosynthesis and determine the angle of a leaf, whereas the ligule protects the stem from the entry of water, microorganisms, and pests. Liguleless variants have an upright leaf blade that wraps around the culm. Research on liguleless mutants of maize and other cereals has led to identification of genes that are involved in leaf patterning and differentiation. RESULTS We characterized an induced liguleless mutant (LM) of Aegilops tauschii Coss., a donor of genome D of bread wheat Triticum aestivum L.. The liguleless phenotype of LM is under dominant monogenic control (Lgt). To determine precise position of Lgt on the Ae. tauschii genetic map, highly saturated genetic maps were constructed containing 887 single-nucleotide polymorphism (SNP) markers derived via diversity arrays technology (DArT)seq. The Lgt gene was mapped to chromosome 5DS. Taking into account coordinates of the SNP markers, flanking Lgt, on the pseudomolecule 5D, a chromosomal region that contains this gene was determined, and a list of candidate genes was identified. Morphological features of the LM phenotype suggest that Lgt participates in the control of leaf development, mainly, in leaf proximal-distal patterning, and its dominant mutation causes abnormal ligular region but does not affect reproductive development. CONCLUSIONS Here we report characterization of a liguleless Ae. tauschii mutant, whose phenotype is under control of a dominant mutation of Lgt. The dominant mode of inheritance of the liguleless trait in a Triticeae species is reported for the first time. The position of the Lgt locus on chromosome 5DS allowed us to identify a list of candidate genes. This list does not contain Ae. tauschii orthologs of any well-characterized cereal genes whose mutations cause liguleless phenotypes. Thus, the characterized Lgt mutant represents a new model for further investigation of plant leaf patterning and differentiation.
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Affiliation(s)
- Alina E. Dresvyannikova
- Institute of Cytology and Genetics, SB RAS, Lavrenvieva ave. 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, Pirogova, 2, Novosibirsk, 630090 Russia
| | | | - Alexander F. Muterko
- Institute of Cytology and Genetics, SB RAS, Lavrenvieva ave. 10, Novosibirsk, 630090 Russia
| | - Alexander A. Krasnikov
- Central Siberian Botanical Garden SB RAS, Zolotodolinskaya Str., 101, Novosibirsk, 630090 Russia
| | - Nikolay P. Goncharov
- Institute of Cytology and Genetics, SB RAS, Lavrenvieva ave. 10, Novosibirsk, 630090 Russia
| | - Oxana B. Dobrovolskaya
- Institute of Cytology and Genetics, SB RAS, Lavrenvieva ave. 10, Novosibirsk, 630090 Russia
- Novosibirsk State University, Pirogova, 2, Novosibirsk, 630090 Russia
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Singh J, Kalberer SR, Belamkar V, Assefa T, Nelson MN, Farmer AD, Blackmon WJ, Cannon SB. A transcriptome-SNP-derived linkage map of Apios americana (potato bean) provides insights about genome re-organization and synteny conservation in the phaseoloid legumes. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2018; 131:333-351. [PMID: 29071392 PMCID: PMC5787225 DOI: 10.1007/s00122-017-3004-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2017] [Accepted: 10/10/2017] [Indexed: 06/07/2023]
Abstract
KEY MESSAGE We report a linkage map for Apios americana and describe synteny with selected warm-season legumes. A translocation event in common bean and soybean is confirmed against Apios and Vigna species. Apios (Apios americana; "apios"), a tuberous perennial legume in the Phaseoleae tribe, was widely used as a food by Native Americans. Work in the last 40 years has led to several improved breeding lines. Aspects of the pollination biology (complex floral structure and tripping mechanism) have made controlled crosses difficult, and the previous reports indicated that the plant is likely primarily an outcrosser. We used a pseudo-testcross strategy to construct a genetic map specific to the maternal parent. The map was built using single-nucleotide polymorphism markers identified by comparing the expressed sequences of individuals in the mapping population against a de novo maternal reference transcriptome assembly. The apios map consists of 11 linkage groups and 1121 recombinationally distinct loci, covering ~ 938.6 cM. By sequencing the transcriptomes of all potential pollen parents, we were able to identify the probable pollen donors and to discover new aspects of the pollination biology in apios. No selfing was observed, but multiple pollen parents were seen within individual pods. Comparisons with genome sequences in other species in the Phaseoleae showed extended synteny for most apios linkage groups. This synteny supports the robustness of the map, and also sheds light on the history of the Phaseoleae, as apios is relatively early diverging in this tribe. We detected a translocation event that separates apios and two Vigna species from Phaseolus vulgaris and Glycine max. This apios mapping work provides a general protocol for sequencing-based construction of high-density linkage maps in outcrossing species with heterogeneous pollen parents.
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Affiliation(s)
- Jugpreet Singh
- ORISE Fellow, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011 USA
| | - Scott R. Kalberer
- Crop Genome Informatics Laboratory, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011 USA
| | - Vikas Belamkar
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583 USA
| | - Teshale Assefa
- ORISE Fellow, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011 USA
| | - Matthew N. Nelson
- Royal Botanic Gardens, Kew, Wakehurst Place, Ardingly, West Sussex RH17 6TN UK
| | | | | | - Steven B. Cannon
- Crop Genome Informatics Laboratory, Corn Insects and Crop Genetics Research Unit, USDA-ARS, Ames, IA 50011 USA
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Monroe JG, Allen ZA, Tanger P, Mullen JL, Lovell JT, Moyers BT, Whitley D, McKay JK. TSPmap, a tool making use of traveling salesperson problem solvers in the efficient and accurate construction of high-density genetic linkage maps. BioData Min 2017; 10:38. [PMID: 29270228 PMCID: PMC5735504 DOI: 10.1186/s13040-017-0158-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 12/04/2017] [Indexed: 11/10/2022] Open
Abstract
Background Recent advances in nucleic acid sequencing technologies have led to a dramatic increase in the number of markers available to generate genetic linkage maps. This increased marker density can be used to improve genome assemblies as well as add much needed resolution for loci controlling variation in ecologically and agriculturally important traits. However, traditional genetic map construction methods from these large marker datasets can be computationally prohibitive and highly error prone. Results We present TSPmap, a method which implements both approximate and exact Traveling Salesperson Problem solvers to generate linkage maps. We demonstrate that for datasets with large numbers of genomic markers (e.g. 10,000) and in multiple population types generated from inbred parents, TSPmap can rapidly produce high quality linkage maps with low sensitivity to missing and erroneous genotyping data compared to two other benchmark methods, JoinMap and MSTmap. TSPmap is open source and freely available as an R package. Conclusions With the advancement of low cost sequencing technologies, the number of markers used in the generation of genetic maps is expected to continue to rise. TSPmap will be a useful tool to handle such large datasets into the future, quickly producing high quality maps using a large number of genomic markers. Electronic supplementary material The online version of this article (10.1186/s13040-017-0158-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- J Grey Monroe
- Department of Bioagricultural Sciences & Pest Management, Colorado State University, 1177 Campus Delivery, Fort Collins, CO 80523 USA
| | - Zachariah A Allen
- Department of Computer Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Paul Tanger
- Department of Bioagricultural Sciences & Pest Management, Colorado State University, 1177 Campus Delivery, Fort Collins, CO 80523 USA
| | - Jack L Mullen
- Department of Bioagricultural Sciences & Pest Management, Colorado State University, 1177 Campus Delivery, Fort Collins, CO 80523 USA
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806 USA
| | - Brook T Moyers
- Department of Bioagricultural Sciences & Pest Management, Colorado State University, 1177 Campus Delivery, Fort Collins, CO 80523 USA
| | - Darrell Whitley
- Department of Computer Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - John K McKay
- Department of Bioagricultural Sciences & Pest Management, Colorado State University, 1177 Campus Delivery, Fort Collins, CO 80523 USA
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N’Diaye A, Haile JK, Fowler DB, Ammar K, Pozniak CJ. Effect of Co-segregating Markers on High-Density Genetic Maps and Prediction of Map Expansion Using Machine Learning Algorithms. FRONTIERS IN PLANT SCIENCE 2017; 8:1434. [PMID: 28878789 PMCID: PMC5572363 DOI: 10.3389/fpls.2017.01434] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/03/2017] [Indexed: 05/28/2023]
Abstract
Advances in sequencing and genotyping methods have enable cost-effective production of high throughput single nucleotide polymorphism (SNP) markers, making them the choice for linkage mapping. As a result, many laboratories have developed high-throughput SNP assays and built high-density genetic maps. However, the number of markers may, by orders of magnitude, exceed the resolution of recombination for a given population size so that only a minority of markers can accurately be ordered. Another issue attached to the so-called 'large p, small n' problem is that high-density genetic maps inevitably result in many markers clustering at the same position (co-segregating markers). While there are a number of related papers, none have addressed the impact of co-segregating markers on genetic maps. In the present study, we investigated the effects of co-segregating markers on high-density genetic map length and marker order using empirical data from two populations of wheat, Mohawk × Cocorit (durum wheat) and Norstar × Cappelle Desprez (bread wheat). The maps of both populations consisted of 85% co-segregating markers. Our study clearly showed that excess of co-segregating markers can lead to map expansion, but has little effect on markers order. To estimate the inflation factor (IF), we generated a total of 24,473 linkage maps (8,203 maps for Mohawk × Cocorit and 16,270 maps for Norstar × Cappelle Desprez). Using seven machine learning algorithms, we were able to predict with an accuracy of 0.7 the map expansion due to the proportion of co-segregating markers. For example in Mohawk × Cocorit, with 10 and 80% co-segregating markers the length of the map inflated by 4.5 and 16.6%, respectively. Similarly, the map of Norstar × Cappelle Desprez expanded by 3.8 and 11.7% with 10 and 80% co-segregating markers. With the increasing number of markers on SNP-chips, the proportion of co-segregating markers in high-density maps will continue to increase making map expansion unavoidable. Therefore, we suggest developers improve linkage mapping algorithms for efficient analysis of high-throughput data. This study outlines a practical strategy to estimate the IF due to the proportion of co-segregating markers and outlines a method to scale the length of the map accordingly.
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Affiliation(s)
- Amidou N’Diaye
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, SaskatoonSK, Canada
| | - Jemanesh K. Haile
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, SaskatoonSK, Canada
| | - D. Brian Fowler
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, SaskatoonSK, Canada
| | - Karim Ammar
- International Maize and Wheat Improvement Center (CIMMYT)Texcoco, Mexico
| | - Curtis J. Pozniak
- Department of Plant Sciences, Crop Development Centre, University of Saskatchewan, SaskatoonSK, Canada
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11
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Yang L, Zhang X, Zhang X, Wang J, Luo M, Yang M, Wang H, Xiang L, Zeng F, Yu D, Fu D, Rosewarne GM. Identification and evaluation of resistance to powdery mildew and yellow rust in a wheat mapping population. PLoS One 2017; 12:e0177905. [PMID: 28542459 PMCID: PMC5441593 DOI: 10.1371/journal.pone.0177905] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/04/2017] [Indexed: 11/19/2022] Open
Abstract
Deployment of cultivars with genetic resistance is an effective approach to control the diseases of powdery mildew (PM) and yellow rust (YR). Chinese wheat cultivar XK0106 exhibits high levels of resistance to both diseases, while cultivar E07901 has partial, adult plant resistance (APR). The aim of this study was to map resistance loci derived from the two cultivars and analyze their effects against PM and YR in a range of environments. A doubled haploid population (388 lines) was used to develop a framework map consisting of 117 SSR markers, while a much higher density map using the 90K Illumina iSelect SNP array was produced with a subset of 80 randomly selected lines. Seedling resistance was characterized against a range of PM and YR isolates, while field scores in multiple environments were used to characterize APR. Composite interval mapping (CIM) of seedling PM scores identified two QTLs (QPm.haas-6A and QPm.haas-2A), the former being located at the Pm21 locus. These QTLs were also significant in field scores, as were Qpm.haas-3A and QPm.haas-5A. QYr.haas-1B-1 and QYr.haas-2A were identified in field scores of YR and were located at the Yr24/26 and Yr17 chromosomal regions respectively. A second 1B QTL, QYr.haas-1B-2 was also identified. QPm.haas-2A and QYr.haas-1B-2 are likely to be new QTLs that have not been previously identified. Effects of the QTLs were further investigated in multiple environments through the testing of selected lines predicted to contain various QTL combinations. Significant additive interactions between the PM QTLs highlighted the ability to pyramid these loci to provide higher level of resistance. Interactions between the YR QTLs gave insights into the pathogen populations in the different locations as well as showing genetic interactions between these loci.
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Affiliation(s)
- Lijun Yang
- College of Life Sciences, Wuhan University, Wuhan, China
- Institute for Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences (HAAS), Key laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture, Wuhan, China
| | - Xuejiang Zhang
- Institute for Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences (HAAS), Key laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture, Wuhan, China
| | - Xu Zhang
- Institute of Biotechnology, Jiangsu Academy of Agricultural Sciences (JAAS), Nanjing, China
| | - Jirui Wang
- Triticeae Research Institute, Sichuan Agricultural University, Wenjiang, Chengdu, Sichuan, China
| | - Mingcheng Luo
- Department of Plant Sciences, University of California Davis, Davis, CA, United States of America
| | - Mujun Yang
- Food Crops Research Institute, Yunnan Academy of Agricultural Sciences (YAAS), Kunming, China
| | - Hua Wang
- Institute for Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences (HAAS), Key laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture, Wuhan, China
| | - Libo Xiang
- Institute for Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences (HAAS), Key laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture, Wuhan, China
| | - Fansong Zeng
- Institute for Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences (HAAS), Key laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture, Wuhan, China
| | - Dazhao Yu
- Institute for Plant Protection and Soil Science, Hubei Academy of Agricultural Sciences (HAAS), Key laboratory of Integrated Pest Management on Crop in Central China, Ministry of Agriculture, Wuhan, China
| | - Daolin Fu
- State Key Laboratory of Crop Biology, Shandong, Key Laboratory of Crop Biology, Shandong Agricultural University, Tai’an, China
| | - Garry M. Rosewarne
- International Maize and Wheat Improvement Centre (CIMMYT) c/o Crop Research Institute, Sichuan Academy of Agricultural Science, Jinjiang, Chengdu, China
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12
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Building Ultra-High-Density Linkage Maps Based on Efficient Filtering of Trustable Markers. Genetics 2017; 206:1285-1295. [PMID: 28512186 DOI: 10.1534/genetics.116.197491] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 05/09/2017] [Indexed: 12/18/2022] Open
Abstract
The study is focused on addressing the problem of building genetic maps in the presence of ∼103-104 of markers per chromosome. We consider a spectrum of situations with intrachromosomal heterogeneity of recombination rate, different level of genotyping errors, and missing data. In the ideal scenario of the absence of errors and missing data, the majority of markers should appear as groups of cosegregating markers ("twins") representing no challenge for map construction. The central aspect of the proposed approach is to take into account the structure of the marker space, where each twin group (TG) and singleton markers are represented as points of this space. The confounding effect of genotyping errors and missing data leads to reduction of TG size, but upon a low level of these effects surviving TGs can still be used as a source of reliable skeletal markers. Increase in the level of confounding effects results in a considerable decrease in the number or even disappearance of usable TGs and, correspondingly, of skeletal markers. Here, we show that the paucity of informative markers can be compensated by detecting kernels of markers in the marker space using a clustering procedure, and demonstrate the utility of this approach for high-density genetic map construction on simulated and experimentally obtained genotyping datasets.
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13
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Emebiri LC, Tan MK, El-Bouhssini M, Wildman O, Jighly A, Tadesse W, Ogbonnaya FC. QTL mapping identifies a major locus for resistance in wheat to Sunn pest (Eurygaster integriceps) feeding at the vegetative growth stage. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:309-318. [PMID: 27744491 DOI: 10.1007/s00122-016-2812-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 10/08/2016] [Indexed: 06/06/2023]
Abstract
This research provides the first report of a major locus controlling wheat resistance to Sunn pest. It developed and validated SNP markers that will be useful for marker-assisted selection. Sunn pest (Eurygaster integriceps Puton) is the most destructive insect pest of bread wheat and durum wheat in West and Central Asia and East Europe. Breeding for resistance at the vegetative stage of growth is vital in reducing the damage caused by overwintered adult populations that feed on shoot and leaves of seedlings, and in reducing the next generation of pest populations (nymphs and adults), which can cause damage to grain quality by feeding on spikes. In the present study, two doubled haploid (DH) populations involving resistant landraces from Afghanistan were genotyped with the 90k SNP iSelect assay and candidate gene-based KASP markers. The DH lines and parents were phenotyped for resistance to Sunn pest feeding, using artificial infestation cages at Terbol station, in Lebanon, over three years. Quantitative trait locus (QTL) analysis identified a single major locus on chromosome 4BS in the two populations, with the resistance allele derived from the landrace accessions, IG139431 and IG139883. The QTL explained a maximum of 42 % of the phenotypic variation in the Cham6 × IG139431 and 56 % in the Cham6 × IG139883 populations. SNP markers closest to the QTL showed high similarity to rice genes that putatively encode proteins for defense response to herbivory and wounding. The markers were validated in a large, unrelated population of parental wheat genotypes. All wheat lines carrying the 'C-G' haplotype at the identified SNPs were resistant, suggesting that selection based on a haplotype of favourable alleles would be effective in predicting resistance status of unknown genotypes.
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Affiliation(s)
- L C Emebiri
- Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, NSW, 2650, Australia.
| | - M-K Tan
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW, Menangle, NSW, 2568, Australia
| | - M El-Bouhssini
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Instituts, P. O. Box 6299, Rabat, Morocco
| | - O Wildman
- NSW Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Woodbridge Rd, Menangle NSW, Menangle, NSW, 2568, Australia
| | - A Jighly
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Instituts, P. O. Box 6299, Rabat, Morocco
| | - W Tadesse
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Instituts, P. O. Box 6299, Rabat, Morocco
| | - F C Ogbonnaya
- The International Center for Agricultural Research in the Dry Areas (ICARDA), Rabat Instituts, P. O. Box 6299, Rabat, Morocco
- Grains Research and Development Corporation, P. O. Box 5367, Kingston, ACT, 2604, Australia
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14
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Wang H, van Eeuwijk FA, Jansen J. The potential of probabilistic graphical models in linkage map construction. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2017; 130:433-444. [PMID: 27921120 PMCID: PMC5263214 DOI: 10.1007/s00122-016-2824-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/03/2016] [Indexed: 06/06/2023]
Abstract
Probabilistic graphical models show great potential for robust and reliable construction of linkage maps. We show how to use probabilistic graphical models to construct high-quality linkage maps in the face of data perturbations caused by genotyping errors and reciprocal translocations. It has been shown that linkage map construction can be hampered by the presence of genotyping errors and chromosomal rearrangements such as inversions and translocations. Here, we report a novel method for linkage map construction using probabilistic graphical models. The method is proven, both theoretically and practically, to be effective in filtering out markers that contain genotyping errors. In particular, it carries out marker filtering and ordering simultaneously, and is therefore superior to the standard post hoc filtering using nearest-neighbour stress. Furthermore, we demonstrate empirically that the proposed method offers a promising solution to linkage map construction in the case of a reciprocal translocation.
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Affiliation(s)
- Huange Wang
- Biometris, Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands.
| | - Fred A van Eeuwijk
- Biometris, Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
| | - Johannes Jansen
- Biometris, Wageningen University and Research Centre, P.O. Box 16, 6700 AA, Wageningen, The Netherlands
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15
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Balcárková B, Frenkel Z, Škopová M, Abrouk M, Kumar A, Chao S, Kianian SF, Akhunov E, Korol AB, Doležel J, Valárik M. A High Resolution Radiation Hybrid Map of Wheat Chromosome 4A. FRONTIERS IN PLANT SCIENCE 2017; 7:2063. [PMID: 28119729 PMCID: PMC5222868 DOI: 10.3389/fpls.2016.02063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Accepted: 12/26/2016] [Indexed: 05/18/2023]
Abstract
Bread wheat has a large and complex allohexaploid genome with low recombination level at chromosome centromeric and peri-centromeric regions. This significantly hampers ordering of markers, contigs of physical maps and sequence scaffolds and impedes obtaining of high-quality reference genome sequence. Here we report on the construction of high-density and high-resolution radiation hybrid (RH) map of chromosome 4A supported by high-density chromosome deletion map. A total of 119 endosperm-based RH lines of two RH panels and 15 chromosome deletion bin lines were genotyped with 90K iSelect single nucleotide polymorphism (SNP) array. A total of 2316 and 2695 markers were successfully mapped to the 4A RH and deletion maps, respectively. The chromosome deletion map was ordered in 19 bins and allowed precise identification of centromeric region and verification of the RH panel reliability. The 4A-specific RH map comprises 1080 mapping bins and spans 6550.9 cR with a resolution of 0.13 Mb/cR. Significantly higher mapping resolution in the centromeric region was observed as compared to recombination maps. Relatively even distribution of deletion frequency along the chromosome in the RH panel was observed and putative functional centromere was delimited within a region characterized by two SNP markers.
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Affiliation(s)
- Barbora Balcárková
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Zeev Frenkel
- Institute of Evolution, University of HaifaHaifa, Israel
| | - Monika Škopová
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Michael Abrouk
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Ajay Kumar
- Department of Plant Sciences, North Dakota State University, FargoND, USA
| | - Shiaoman Chao
- Biosciences Research Laboratory, United States Department of Agriculture-Agricultural Research Service, FargoND, USA
| | - Shahryar F. Kianian
- Cereal Disease Laboratory, United States Department of Agriculture-Agricultural Research Service, University of Minnesota, St. PaulMN, USA
| | - Eduard Akhunov
- Department of Plant Pathology, Kansas State University, ManhattanKS, USA
| | | | - Jaroslav Doležel
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
| | - Miroslav Valárik
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural ResearchOlomouc, Czechia
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16
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Bheema Lingeswara Reddy IN, Chandrasekhar K, Zewdu Y, Dinoor A, Keller B, Ben-David R. Identification and genetic mapping of PmAF7DS a powdery mildew resistance gene in bread wheat (Triticum aestivum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2016; 129:1127-1137. [PMID: 26934890 DOI: 10.1007/s00122-016-2688-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Accepted: 01/30/2016] [Indexed: 06/05/2023]
Abstract
Gene PmAF7DS confers resistance to wheat powdery mildew (isolate Bgt#211 ); it was mapped to a 14.6-cM interval ( Xgwm350 a- Xbarc184 ) on chromosome 7DS. The flanking markers could be applied in MAS breeding. Wheat powdery mildew (Pm) is caused by the biotrophic pathogen Blumeria graminis tritici (DC.) (Bgt). An ongoing threat of breakdown of race-specific resistance to Pm requires a continuous effort to discover new alleles in the wheat gene pool. Developing new cultivars with improved disease resistance is an economically and environmentally safe approach to reduce yield losses. To identify and characterize genes for resistance against Pm in bread wheat we used the (Arina × Forno) RILs population. Initially, the two parental lines were screened with a collection of 61 isolates of Bgt from Israel. Three Pm isolates Bgt#210 , Bgt#211 and Bgt#213 showed differential reactions in the parents: Arina was resistant (IT = 0), whereas Forno was moderately susceptible (IT = -3). Isolate Bgt#211 was then used to inoculate the RIL population. The segregation pattern of plant reactions among the RILs indicates that a single dominant gene controls the conferred resistance. A genetic map of the region containing this gene was assembled with DNA markers and assigned to the 7D physical bin map. The gene, temporarily designated PmAF7DS, was located in the distal region of chromosome arm 7DS. The RILs were also inoculated with Bgt#210 and Bgt#213. The plant reactions to these isolates showed high identity with the reaction to Bgt#211, indicating the involvement of the same gene or closely linked, but distinct single genes. The genomic location of PmAF7DS, in light of other Pm genes on 7DS is discussed.
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Affiliation(s)
- I N Bheema Lingeswara Reddy
- Department of Vegetables and Field Crops, Institute of Plant Sciences, Agricultural Research Organization (ARO)-Volcani Center, 5025000, Bet Dagan, Israel
| | - K Chandrasekhar
- Department of Vegetables and Field Crops, Institute of Plant Sciences, Agricultural Research Organization (ARO)-Volcani Center, 5025000, Bet Dagan, Israel
| | - Y Zewdu
- Department of Vegetables and Field Crops, Institute of Plant Sciences, Agricultural Research Organization (ARO)-Volcani Center, 5025000, Bet Dagan, Israel
| | - A Dinoor
- Department of Plant Pathology and Microbiology, Robert H. Smith Faculty of Agriculture, Food and Environment, Hebrew University of Jerusalem, 7610001, Rehovot, Israel
| | - B Keller
- Institute of Plant Biology, University of Zurich, Zollikerstrasse 107, 8008, Zurich, Switzerland
| | - R Ben-David
- Department of Vegetables and Field Crops, Institute of Plant Sciences, Agricultural Research Organization (ARO)-Volcani Center, 5025000, Bet Dagan, Israel.
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17
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Nimmakayala P, Tomason YR, Abburi VL, Alvarado A, Saminathan T, Vajja VG, Salazar G, Panicker GK, Levi A, Wechter WP, McCreight JD, Korol AB, Ronin Y, Garcia-Mas J, Reddy UK. Genome-Wide Differentiation of Various Melon Horticultural Groups for Use in GWAS for Fruit Firmness and Construction of a High Resolution Genetic Map. FRONTIERS IN PLANT SCIENCE 2016; 7:1437. [PMID: 27713759 PMCID: PMC5031849 DOI: 10.3389/fpls.2016.01437] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Accepted: 09/08/2016] [Indexed: 05/06/2023]
Abstract
Melon (Cucumis melo L.) is a phenotypically diverse eudicot diploid (2n = 2x = 24) has climacteric and non-climacteric morphotypes and show wide variation for fruit firmness, an important trait for transportation and shelf life. We generated 13,789 SNP markers using genotyping-by-sequencing (GBS) and anchored them to chromosomes to understand genome-wide fixation indices (Fst) between various melon morphotypes and genomewide linkage disequilibrium (LD) decay. The FST between accessions of cantalupensis and inodorus was 0.23. The FST between cantalupensis and various agrestis accessions was in a range of 0.19-0.53 and between inodorus and agrestis accessions was in a range of 0.21-0.59 indicating sporadic to wide ranging introgression. The EM (Expectation Maximization) algorithm was used for estimation of 1436 haplotypes. Average genome-wide LD decay for the melon genome was noted to be 9.27 Kb. In the current research, we focused on the genome-wide divergence underlying diverse melon horticultural groups. A high-resolution genetic map with 7153 loci was constructed. Genome-wide segregation distortion and recombination rate across various chromosomes were characterized. Melon has climacteric and non-climacteric morphotypes and wide variation for fruit firmness, a very important trait for transportation and shelf life. Various levels of QTLs were identified with high to moderate stringency and linked to fruit firmness using both genome-wide association study (GWAS) and biparental mapping. Gene annotation revealed some of the SNPs are located in β-D-xylosidase, glyoxysomal malate synthase, chloroplastic anthranilate phosphoribosyltransferase, and histidine kinase, the genes that were previously characterized for fruit ripening and softening in other crops.
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Affiliation(s)
- Padma Nimmakayala
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
| | - Yan R. Tomason
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
- Department of Selection and Seed Production, Dnepropetrovsk State Agrarian and Economic UniversityDnepropetrovsk, Ukraine
| | - Venkata L. Abburi
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
| | - Alejandra Alvarado
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
| | - Thangasamy Saminathan
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
| | - Venkata G. Vajja
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
| | - Germania Salazar
- Department of Agriculture, Alcorn State UniversityLorman, MS, USA
| | | | - Amnon Levi
- U.S. Vegetable Laboratory, United States Department of Agriculture, Agricultural Research ServiceCharleston, SC, USA
| | - William P. Wechter
- U.S. Vegetable Laboratory, United States Department of Agriculture, Agricultural Research ServiceCharleston, SC, USA
| | | | - Abraham B. Korol
- Department of Evolutionary and Environmental Biology, Haifa UniversityHaifa, Israel
| | - Yefim Ronin
- Department of Evolutionary and Environmental Biology, Haifa UniversityHaifa, Israel
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics, Consejo Superior de Investigaciones Científicas-Institute for Food and Agricultural Research and Technology-Universitat Autònoma de Barcelona-Universitat de BarcelonaBarcelona, Spain
| | - Umesh K. Reddy
- Gus R. Douglass Institute and Department of Biology, West Virginia State UniversityInstitute, WV, USA
- *Correspondence: Umesh K. Reddy
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18
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Golan G, Oksenberg A, Peleg Z. Genetic evidence for differential selection of grain and embryo weight during wheat evolution under domestication. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5703-11. [PMID: 26019253 PMCID: PMC4566971 DOI: 10.1093/jxb/erv249] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Wheat is one of the Neolithic founder crops domesticated ~10 500 years ago. Following the domestication episode, its evolution under domestication has resulted in various genetic modifications. Grain weight, embryo weight, and the interaction between those factors were examined among domesticated durum wheat and its direct progenitor, wild emmer wheat. Experimental data show that grain weight has increased over the course of wheat evolution without any parallel change in embryo weight, resulting in a significantly reduced (30%) embryo weight/grain weight ratio in domesticated wheat. The genetic factors associated with these modifications were further investigated using a population of recombinant inbred substitution lines that segregated for chromosome 2A. A cluster of loci affecting grain weight and shape was identified on the long arm of chromosome 2AL. Interestingly, a novel locus controlling embryo weight was mapped on chromosome 2AS, on which the wild emmer allele promotes heavier embryos and greater seedling vigour. To the best of our knowledge, this is the first report of a QTL for embryo weight in wheat. The results suggest a differential selection of grain and embryo weight during the evolution of domesticated wheat. It is argued that conscious selection by early farmers favouring larger grains and smaller embryos appears to have resulted in a significant change in endosperm weight/embryo weight ratio in the domesticated wheat. Exposing the genetic factors associated with endosperm and embryo size improves our understanding of the evolutionary dynamics of wheat under domestication and is likely to be useful for future wheat-breeding efforts.
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Affiliation(s)
- Guy Golan
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Adi Oksenberg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Zvi Peleg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
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19
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Abstract
Multiparental populations are of considerable interest in high-density genetic mapping due to their increased levels of polymorphism and recombination relative to biparental populations. However, errors in map construction can have significant impact on QTL discovery in later stages of analysis, and few methods have been developed to quantify the uncertainty attached to the reported order of markers or intermarker distances. Current methods are computationally intensive or limited to assessing uncertainty only for order or distance, but not both simultaneously. We derive the asymptotic joint distribution of maximum composite likelihood estimators for intermarker distances. This approach allows us to construct hypothesis tests and confidence intervals for simultaneously assessing marker-order instability and distance uncertainty. We investigate the effects of marker density, population size, and founder distribution patterns on map confidence in multiparental populations through simulations. Using these data, we provide guidelines on sample sizes necessary to map markers at sub-centimorgan densities with high certainty. We apply these approaches to data from a bread wheat Multiparent Advanced Generation Inter-Cross (MAGIC) population genotyped using the Illumina 9K SNP chip to assess regions of uncertainty and validate them against the recently released pseudomolecule for the wheat chromosome 3B.
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20
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Fast and accurate construction of ultra-dense consensus genetic maps using evolution strategy optimization. PLoS One 2015; 10:e0122485. [PMID: 25867943 PMCID: PMC4395089 DOI: 10.1371/journal.pone.0122485] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Accepted: 02/22/2015] [Indexed: 11/19/2022] Open
Abstract
Our aim was to develop a fast and accurate algorithm for constructing consensus genetic maps for chip-based SNP genotyping data with a high proportion of shared markers between mapping populations. Chip-based genotyping of SNP markers allows producing high-density genetic maps with a relatively standardized set of marker loci for different mapping populations. The availability of a standard high-throughput mapping platform simplifies consensus analysis by ignoring unique markers at the stage of consensus mapping thereby reducing mathematical complicity of the problem and in turn analyzing bigger size mapping data using global optimization criteria instead of local ones. Our three-phase analytical scheme includes automatic selection of ~100-300 of the most informative (resolvable by recombination) markers per linkage group, building a stable skeletal marker order for each data set and its verification using jackknife re-sampling, and consensus mapping analysis based on global optimization criterion. A novel Evolution Strategy optimization algorithm with a global optimization criterion presented in this paper is able to generate high quality, ultra-dense consensus maps, with many thousands of markers per genome. This algorithm utilizes "potentially good orders" in the initial solution and in the new mutation procedures that generate trial solutions, enabling to obtain a consensus order in reasonable time. The developed algorithm, tested on a wide range of simulated data and real world data (Arabidopsis), outperformed two tested state-of-the-art algorithms by mapping accuracy and computation time.
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Kamphuis LG, Hane JK, Nelson MN, Gao L, Atkins CA, Singh KB. Transcriptome sequencing of different narrow-leafed lupin tissue types provides a comprehensive uni-gene assembly and extensive gene-based molecular markers. PLANT BIOTECHNOLOGY JOURNAL 2015; 13:14-25. [PMID: 25060816 PMCID: PMC4309465 DOI: 10.1111/pbi.12229] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 05/27/2014] [Accepted: 06/12/2014] [Indexed: 05/18/2023]
Abstract
Narrow-leafed lupin (NLL; Lupinus angustifolius L.) is an important grain legume crop that is valuable for sustainable farming and is becoming recognized as a human health food. NLL breeding is directed at improving grain production, disease resistance, drought tolerance and health benefits. However, genetic and genomic studies have been hindered by a lack of extensive genomic resources for the species. Here, the generation, de novo assembly and annotation of transcriptome datasets derived from five different NLL tissue types of the reference accession cv. Tanjil are described. The Tanjil transcriptome was compared to transcriptomes of an early domesticated cv. Unicrop, a wild accession P27255, as well as accession 83A:476, together being the founding parents of two recombinant inbred line (RIL) populations. In silico predictions for transcriptome-derived gene-based length and SNP polymorphic markers were conducted and corroborated using a survey assembly sequence for NLL cv. Tanjil. This yielded extensive indel and SNP polymorphic markers for the two RIL populations. A total of 335 transcriptome-derived markers and 66 BAC-end sequence-derived markers were evaluated, and 275 polymorphic markers were selected to genotype the reference NLL 83A:476 × P27255 RIL population. This significantly improved the completeness, marker density and quality of the reference NLL genetic map.
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Affiliation(s)
- Lars G Kamphuis
- CSIRO Plant IndustryWembley, WA, Australia
- The UWA Institute of Agriculture, University of Western AustraliaCrawley, WA, Australia
| | | | - Matthew N Nelson
- The UWA Institute of Agriculture, University of Western AustraliaCrawley, WA, Australia
- The School of Plant Biology, University of Western AustraliaCrawley, WA, Australia
| | | | - Craig A Atkins
- The School of Plant Biology, University of Western AustraliaCrawley, WA, Australia
| | - Karam B Singh
- CSIRO Plant IndustryWembley, WA, Australia
- The UWA Institute of Agriculture, University of Western AustraliaCrawley, WA, Australia
- *Correspondence (Tel +61 8 9333 6320; fax +61 8 9383 9673; email )
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Yaniv E, Raats D, Ronin Y, Korol AB, Grama A, Bariana H, Dubcovsky J, Schulman AH. Evaluation of marker-assisted selection for the stripe rust resistance gene Yr15, introgressed from wild emmer wheat. MOLECULAR BREEDING : NEW STRATEGIES IN PLANT IMPROVEMENT 2015; 35:43. [PMID: 27818611 PMCID: PMC5091809 DOI: 10.1007/s11032-015-0238-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Stripe rust disease is caused by the fungus Puccinia striiformis f. sp. tritici and severely threatens wheat worldwide, repeatedly breaking resistance conferred by resistance genes and evolving more aggressive strains. Wild emmer wheat, Triticum dicoccoides, is an important source for novel stripe rust resistance (Yr) genes. Yr15, a major gene located on chromosome 1BS of T. dicoccoides, was previously reported to confer resistance to a broad spectrum of stripe rust isolates, at both seedling and adult plant stages. Introgressions of Yr15 into cultivated T. aestivum bread wheat and T. durum pasta wheat that began in the 1980s are widely used. In the present study, we aimed to validate SSR markers from the Yr15 region as efficient tools for marker-assisted selection (MAS) for introgression of Yr15 into wheat and to compare the outcome of gene introgression by MAS and by conventional phenotypic selection. Our findings establish the validity of MAS for introgression of Yr15 into wheat. We show that the size of the introgressed segment, defined by flanking markers, varies for both phenotypic selection and MAS. The genetic distance of the MAS marker from Yr15 and the number of backcross steps were the main factors affecting the length of the introgressed donor segments. Markers Xbarc8 and Xgwm493, which are the nearest flanking markers studied, were consistent and polymorphic in all 34 introgressions reported here and are therefore the most recommended markers for the introgression of Yr15 into wheat cultivars. Introgression directed by markers, rather than by phenotype, will facilitate simultaneous selection for multiple stripe rust resistant genes and will help to avoid escapees during the selection process.
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Affiliation(s)
- Elitsur Yaniv
- Plant Genomics and Disease Resistance Laboratory, Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Dina Raats
- Plant Genomics and Disease Resistance Laboratory, Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Yefim Ronin
- Plant Genomics and Disease Resistance Laboratory, Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Abraham B Korol
- Plant Genomics and Disease Resistance Laboratory, Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Haifa, Israel
| | - Adriana Grama
- Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel
| | - Harbans Bariana
- Department of Plant and Food Sciences, University of Sydney, Sydney, Australia
| | - Jorge Dubcovsky
- Department of Plant Sciences, University of California, Davis, CA, USA
| | - Alan H Schulman
- LUKE/BI Plant Genomics Lab, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, P.O. Box 65, Helsinki, Finland
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High-resolution genetic map for understanding the effect of genome-wide recombination rate on nucleotide diversity in watermelon. G3-GENES GENOMES GENETICS 2014; 4:2219-30. [PMID: 25227227 PMCID: PMC4232547 DOI: 10.1534/g3.114.012815] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
We used genotyping by sequencing to identify a set of 10,480 single nucleotide polymorphism (SNP) markers for constructing a high-resolution genetic map of 1096 cM for watermelon. We assessed the genome-wide variation in recombination rate (GWRR) across the map and found an association between GWRR and genome-wide nucleotide diversity. Collinearity between the map and the genome-wide reference sequence for watermelon was studied to identify inconsistency and chromosome rearrangements. We assessed genome-wide nucleotide diversity, linkage disequilibrium (LD), and selective sweep for wild, semi-wild, and domesticated accessions of Citrullus lanatus var. lanatus to track signals of domestication. Principal component analysis combined with chromosome-wide phylogenetic study based on 1563 SNPs obtained after LD pruning with minor allele frequency of 0.05 resolved the differences between semi-wild and wild accessions as well as relationships among worldwide sweet watermelon. Population structure analysis revealed predominant ancestries for wild, semi-wild, and domesticated watermelons as well as admixture of various ancestries that were important for domestication. Sliding window analysis of Tajima’s D across various chromosomes was used to resolve selective sweep. LD decay was estimated for various chromosomes. We identified a strong selective sweep on chromosome 3 consisting of important genes that might have had a role in sweet watermelon domestication.
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Emebiri LC. QTL dissection of the loss of green colour during post-anthesis grain maturation in two-rowed barley. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1873-1884. [PMID: 23604470 DOI: 10.1007/s00122-013-2102-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2012] [Accepted: 04/10/2013] [Indexed: 06/02/2023]
Abstract
Ability to genetically manipulate the loss of green colour during grain maturation has potentials for increasing productivity, disease resistance, and drought and heat tolerance in crop plants. Two doubled haploid, two-rowed barley populations (Vlamingh × Buloke and VB9524 × ND11231*12) were monitored over 2 years for loss of green colour during grain filling using a portable active sensor. The aims were to determine the genomic regions that control trait heritability by quantitative trait locus (QTL) analysis, and to examine patterns of QTL-environment interactions under different conditions of water stress. In the Vlamingh × Buloke cross, broad-sense heritability estimate for loss of green colour (measured as the difference in sensor readings taken at anthesis and maturity, ∆SRI) was 0.68, and 0.78 for the VB9524 × ND11231*12 population. In the VB9524 × ND11231*12 population, rapid loss of green colour was positively associated with grain yield and percent plump grains, but in the Vlamingh × Buloke population, a slower loss of green colour (low ∆SRI) was associated with increased grain plumpness. With the aid of a dense array of single nucleotide polymorphisms (SNPs) and EST-derived SSR markers, a total of nine QTLs were detected across the two populations. Of these, a single major locus on the short arm of barley chromosome 5H was consistently linked with trait variation across the populations and multiple environments. The QTL was independent of flowering time and explained between 5.4 and 15.4 % of the variation observed in both populations, depending on the environment, and although a QTL × E interaction was detected, it was largely due to a change in the magnitude of the effect, rather than a change in direction. The results suggest that loss of green colour during grain maturation may be under the control of a simple genetic architecture, but a careful study of target populations and environments would be required for breeding purposes.
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Affiliation(s)
- Livinus C Emebiri
- EH Graham Centre for Agricultural Innovation (Industry and Investment NSW and Charles Sturt University), Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia.
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Singh RK, Singh SP, Tiwari DK, Srivastava S, Singh SB, Sharma ML, Singh R, Mohapatra T, Singh NK. Genetic mapping and QTL analysis for sugar yield-related traits in sugarcane. EUPHYTICA 2013. [PMID: 0 DOI: 10.1007/s10681-012-0841-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
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Shatalina M, Wicker T, Buchmann JP, Oberhaensli S, Simková H, Doležel J, Keller B. Genotype-specific SNP map based on whole chromosome 3B sequence information from wheat cultivars Arina and Forno. PLANT BIOTECHNOLOGY JOURNAL 2013; 11:23-32. [PMID: 23046423 DOI: 10.1111/pbi.12003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 08/27/2012] [Accepted: 08/30/2012] [Indexed: 05/10/2023]
Abstract
Agronomically important traits are frequently controlled by rare, genotype-specific alleles. Such genes can only be mapped in a population derived from the donor genotype. This requires the development of a specific genetic map, which is difficult in wheat because of the low level of polymorphism among elite cultivars. The absence of sufficient polymorphism, the complexity of the hexaploid wheat genome as well as the lack of complete sequence information make the construction of genetic maps with a high density of reproducible and polymorphic markers challenging. We developed a genotype-specific genetic map of chromosome 3B from winter wheat cultivars Arina and Forno. Chromosome 3B was isolated from the two cultivars and then sequenced to 10-fold coverage. This resulted in a single-nucleotide polymorphisms (SNP) database of the complete chromosome. Based on proposed synteny with the Brachypodium model genome and gene annotation, sequences close to coding regions were used for the development of 70 SNP-based markers. They were mapped on a Arina × Forno Recombinant Inbred Lines population and found to be spread over the complete chromosome 3B. While overall synteny was well maintained, numerous exceptions and inversions of syntenic gene order were identified. Additionally, we found that the majority of recombination events occurred in distal parts of chromosome 3B, particularly in hot-spot regions. Compared with the earlier map based on SSR and RFLP markers, the number of markers increased fourfold. The approach presented here allows fast development of genotype-specific polymorphic markers that can be used for mapping and marker-assisted selection.
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Development of an ultra-dense genetic map of the sunflower genome based on single-feature polymorphisms. PLoS One 2012; 7:e51360. [PMID: 23284684 PMCID: PMC3526535 DOI: 10.1371/journal.pone.0051360] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 11/06/2012] [Indexed: 11/19/2022] Open
Abstract
The development of ultra-dense genetic maps has the potential to facilitate detailed comparative genomic analyses and whole genome sequence assemblies. Here we describe the use of a custom Affymetrix GeneChip containing nearly 2.4 million features (25 bp sequences) targeting 86,023 unigenes from sunflower (Helianthus annuus L.) and related species to test for single-feature polymorphisms (SFPs) in a recombinant inbred line (RIL) mapping population derived from a cross between confectionery and oilseed sunflower lines (RHA280×RHA801). We then employed an existing genetic map derived from this same population to rigorously filter out low quality data and place 67,486 features corresponding to 22,481 unigenes on the sunflower genetic map. The resulting map contains a substantial fraction of all sunflower genes and will thus facilitate a number of downstream applications, including genome assembly and the identification of candidate genes underlying QTL or traits of interest.
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Two-phase analysis in consensus genetic mapping. G3-GENES GENOMES GENETICS 2012; 2:537-49. [PMID: 22670224 PMCID: PMC3362937 DOI: 10.1534/g3.112.002428] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2012] [Accepted: 03/01/2012] [Indexed: 01/25/2023]
Abstract
Numerous mapping projects conducted on different species have generated an abundance of mapping data. Consequently, many multilocus maps have been constructed using diverse mapping populations and marker sets for the same organism. The quality of maps varies broadly among populations, marker sets, and software used, necessitating efforts to integrate the mapping information and generate consensus maps. The problem of consensus genetic mapping (MCGM) is by far more challenging compared with genetic mapping based on a single dataset, which by itself is also cumbersome. The additional complications introduced by consensus analysis include inter-population differences in recombination rate and exchange distribution along chromosomes; variations in dominance of the employed markers; and use of different subsets of markers in different labs. Hence, it is necessary to handle arbitrary patterns of shared sets of markers and different level of mapping data quality. In this article, we introduce a two-phase approach for solving MCGM. In phase 1, for each dataset, multilocus ordering is performed combined with iterative jackknife resampling to evaluate the stability of marker orders. In this phase, the ordering problem is reduced to the well-known traveling salesperson problem (TSP). Namely, for each dataset, we look for order that gives minimum sum of recombination distances between adjacent markers. In phase 2, the optimal consensus order of shared markers is selected from the set of allowed orders and gives the minimal sum of total lengths of nonconflicting maps of the chromosome. This criterion may be used in different modifications to take into account the variation in quality of the original data (population size, marker quality, etc.). In the foregoing formulation, consensus mapping is considered as a specific version of TSP that can be referred to as “synchronized TSP.” The conflicts detected after phase 1 are resolved using either a heuristic algorithm over the entire chromosome or an exact/heuristic algorithm applied subsequently to the revealed small non-overlapping regions with conflicts separated by non-conflicting regions. The proposed approach was tested on a wide range of simulated data and real datasets from maize.
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Xie W, Ben-David R, Zeng B, Distelfeld A, Röder MS, Dinoor A, Fahima T. Identification and characterization of a novel powdery mildew resistance gene PmG3M derived from wild emmer wheat, Triticum dicoccoides. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2012; 124:911-22. [PMID: 22159825 DOI: 10.1007/s00122-011-1756-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2011] [Accepted: 11/05/2011] [Indexed: 05/18/2023]
Abstract
Powdery mildew, caused by Blumeria graminis f. sp. tritici (Bgt) is one of the most important wheat diseases worldwide. Wild emmer wheat, Triticum turgidum ssp. dicoccoides, the tetraploid ancestor (AABB) of domesticated bread and durum wheat, harbors many important alleles for resistance to various diseases, including powdery mildew. In the current study, two tetraploid wheat mapping populations, derived from a cross between durum wheat (cv. Langdon) and wild emmer wheat (accession G-305-3M), were used to identify and map a novel powdery mildew resistance gene. Wild emmer accession G-305-3M was resistant to all 47 Bgt isolates tested, from Israel and Switzerland. Segregation ratios of F(2) progenies and F(6) recombinant inbred line (RIL) mapping populations, in their reactions to inoculation with Bgt, revealed a Mendelian pattern (3:1 and 1:1, respectively), indicating the role of a single dominant gene derived from T. dicoccoides accession G-305-3M. This gene, temporarily designated PmG3M, was mapped on chromosome 6BL and physically assigned to chromosome deletion bin 6BL-0.70-1.00. The F(2) mapping population was used to construct a genetic map of the PmG3M gene region consisted of six simple sequence repeats (SSR), 11 resistance gene analog (RGA), and two target region amplification polymorphism (TRAP) markers. A second map, constructed based on the F(6) RIL population, using a set of skeleton SSR markers, confirmed the order of loci and distances obtained for the F(2) population. The discovery and mapping of this novel powdery mildew resistance gene emphasize the importance of the wild emmer wheat gene pool as a source for crop improvement.
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Affiliation(s)
- Weilong Xie
- Department of Evolutionary and Environmental Biology, Institute of Evolution, Faculty of Natural Sciences, University of Haifa, Mt. Carmel, Haifa, Israel
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Distelfeld A, Pearce SP, Avni R, Scherer B, Uauy C, Piston F, Slade A, Zhao R, Dubcovsky J. Divergent functions of orthologous NAC transcription factors in wheat and rice. PLANT MOLECULAR BIOLOGY 2012; 78:515-24. [PMID: 22278768 PMCID: PMC4773031 DOI: 10.1007/s11103-012-9881-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2011] [Accepted: 01/10/2012] [Indexed: 05/18/2023]
Abstract
The wheat GPC-B1 gene located on chromosome 6B is an early regulator of senescence and affects remobilization of protein and minerals to the grain. GPC-B1 is a NAC transcription factor and has a paralogous copy on chromosome 2B in wheat, GPC-B2. The closest rice homolog to both wheat GPC genes is Os07g37920 which is located on rice chromosome 7 and is colinear with GPC-B2. Since rice is a diploid species with a sequenced genome, we initiated the study of Os07g37920 to develop a simpler model to study senescence and mineral remobilization in cereals. We developed eleven independent RNA interference transgenic rice lines (Os07g37920-RNAi) and 10 over-expressing transgenic lines (Os07g37920-OE), but none of them showed differences in senescence. Transgenic Os07g37920-RNAi rice plants had reduced proportions of viable pollen grains and were male-sterile, but were able to produce seeds by cross pollination. Analysis of the flower morphology of the transgenic rice plants showed that anthers failed to dehisce. Transgenic Os07g37920-OE lines showed no sterility or anther dehiscence problems. Os07g37920 transcript levels were higher in stamens compared to leaves and significantly reduced in the transgenic Os07g37920-RNAi plants. Wheat GPC genes showed the opposite transcription profile (higher transcript levels in leaves than in flowers) and plants carrying knock-out mutations of all GPC-1 and GPC-2 genes exhibited delayed senescence but normal anther dehiscence and fertility. These results indicate a functional divergence of the homologous wheat and rice NAC genes and suggest the need for separate studies of the function and targets of these transcription factors in wheat and rice.
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Affiliation(s)
- Assaf Distelfeld
- Dept. of Plant Sciences, University of California, Davis, CA, 95616, USA
- Faculty of Life Sciences, Dept. of Molecular Biology and Ecology of Plants, Tel Aviv University, Israel
| | - Stephen P. Pearce
- Dept. of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Raz Avni
- Faculty of Life Sciences, Dept. of Molecular Biology and Ecology of Plants, Tel Aviv University, Israel
| | - Beatrice Scherer
- Dept. of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Cristobal Uauy
- Dept. of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Fernando Piston
- Dept. of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Ann Slade
- Arcadia Biosciences Inc., Davis, CA, 95616, USA
| | - Rongrong Zhao
- Dept. of Plant Sciences, University of California, Davis, CA, 95616, USA
- College of Resources and Environmental Science, China Agricultural University, Beijing, 100193, P. R. China
| | - Jorge Dubcovsky
- Dept. of Plant Sciences, University of California, Davis, CA, 95616, USA
- Howard Hughes Medical Institute and Gordon & Betty Moore Foundation
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Raman H, Raman R, Nelson MN, Aslam MN, Rajasekaran R, Wratten N, Cowling WA, Kilian A, Sharpe AG, Schondelmaier J. Diversity array technology markers: genetic diversity analyses and linkage map construction in rapeseed (Brassica napus L.). DNA Res 2011; 19:51-65. [PMID: 22193366 PMCID: PMC3276259 DOI: 10.1093/dnares/dsr041] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
We developed Diversity Array Technology (DArT) markers for application in genetic studies of Brassica napus and other Brassica species with A or C genomes. Genomic representation from 107 diverse genotypes of B. napus L. var. oleifera (rapeseed, AACC genomes) and B. rapa (AA genome) was used to develop a DArT array comprising 11 520 clones generated using PstI/BanII and PstI/BstN1 complexity reduction methods. In total, 1547 polymorphic DArT markers of high technical quality were identified and used to assess molecular diversity among 89 accessions of B. napus, B. rapa, B. juncea, and B. carinata collected from different parts of the world. Hierarchical cluster and principal component analyses based on genetic distance matrices identified distinct populations clustering mainly according to their origin/pedigrees. DArT markers were also mapped in a new doubled haploid population comprising 131 lines from a cross between spring rapeseed lines ‘Lynx-037DH’ and ‘Monty-028DH’. Linkage groups were assigned on the basis of previously mapped simple sequence repeat (SSRs), intron polymorphism (IP), and gene-based markers. The map consisted of 437 DArT, 135 SSR, 6 IP, and 6 gene-based markers and spanned 2288 cM. Our results demonstrate that DArT markers are suitable for genetic diversity analysis and linkage map construction in rapeseed.
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Affiliation(s)
- Harsh Raman
- EH Graham Centre for Agricultural Innovation, Wagga Wagga Agricultural Institute, Wagga Wagga, NSW 2650, Australia.
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Oliver RE, Jellen EN, Ladizinsky G, Korol AB, Kilian A, Beard JL, Dumlupinar Z, Wisniewski-Morehead NH, Svedin E, Coon M, Redman RR, Maughan PJ, Obert DE, Jackson EW. New Diversity Arrays Technology (DArT) markers for tetraploid oat (Avena magna Murphy et Terrell) provide the first complete oat linkage map and markers linked to domestication genes from hexaploid A. sativa L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:1159-71. [PMID: 21805339 DOI: 10.1007/s00122-011-1656-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2011] [Accepted: 07/09/2011] [Indexed: 05/22/2023]
Abstract
Nutritional benefits of cultivated oat (Avena sativa L., 2n = 6x = 42, AACCDD) are well recognized; however, seed protein levels are modest and resources for genetic improvement are scarce. The wild tetraploid, A. magna Murphy et Terrell (syn A. maroccana Gdgr., 2n = 4x = 28, CCDD), which contains approximately 31% seed protein, was hybridized with cultivated oat to produce a domesticated A. magna. Wild and cultivated accessions were crossed to generate a recombinant inbred line (RIL) population. Although these materials could be used to develop domesticated, high-protein oat, mapping and quantitative trait loci introgression is hindered by a near absence of genetic markers. Objectives of this study were to develop high-throughput, A. magna-specific markers; generate a genetic linkage map based on the A. magna RIL population; and map genes controlling oat domestication. A Diversity Arrays Technology (DArT) array derived from 10 A. magna genotypes was used to generate 2,688 genome-specific probes. These, with 12,672 additional oat clones, produced 2,349 polymorphic markers, including 498 (21.2%) from A. magna arrays and 1,851 (78.8%) from other Avena libraries. Linkage analysis included 974 DArT markers, 26 microsatellites, 13 SNPs, and 4 phenotypic markers, and resulted in a 14-linkage-group map. Marker-to-marker correlation coefficient analysis allowed classification of shared markers as unique or redundant, and putative linkage-group-to-genome anchoring. Results of this study provide for the first time a collection of high-throughput tetraploid oat markers and a comprehensive map of the genome, providing insights to the genome ancestry of oat and affording a resource for study of oat domestication, gene transfer, and comparative genomics.
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Affiliation(s)
- R E Oliver
- USDA-ARS Small Grains and Potato Germplasm Research Unit, Aberdeen, ID, USA
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Wu J, Jenkins JN, McCarty JC, Lou XY. Comparisons of four approximation algorithms for large-scale linkage map construction. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:649-655. [PMID: 21611760 PMCID: PMC3172867 DOI: 10.1007/s00122-011-1614-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2010] [Accepted: 05/09/2011] [Indexed: 05/30/2023]
Abstract
Efficient construction of large-scale linkage maps is highly desired in current gene mapping projects. To evaluate the performance of available approaches in the literature, four published methods, the insertion (IN), seriation (SER), neighbor mapping (NM), and unidirectional growth (UG) were compared on the basis of simulated F(2) data with various population sizes, interferences, missing genotype rates, and mis-genotyping rates. Simulation results showed that the IN method outperformed, or at least was comparable to, the other three methods. These algorithms were also applied to a real data set and results showed that the linkage order obtained by the IN algorithm was superior to the other methods. Thus, this study suggests that the IN method should be used when constructing large-scale linkage maps.
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Affiliation(s)
- Jixiang Wu
- Department of Plant Sciences, Mississippi State University, Mississippi State, MS 39762, USA.
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Wu J, Lou XY, Gonda M. Stochastic deletion-insertion algorithm to construct dense linkage maps. STATISTICS AND ITS INTERFACE 2011; 4:381-388. [PMID: 21927641 PMCID: PMC3173768 DOI: 10.4310/sii.2011.v4.n3.a12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In this study, we proposed a stochastic deletion-insertion (SDI) algorithm for constructing large-scale linkage maps. This SDI algorithm was compared with three published approximation approaches, the seriation (SER), neighbor mapping (NM), and unidirectional growth (UG) approaches, on the basis of simulated F(2) data with different population sizes, missing genotype rates, and numbers of markers. Simulation results showed that the SDI method had a similar or higher percentage of correct linkage orders than the other three methods. This SDI algorithm was also applied to a real dataset and compared with the other three methods. The total linkage map distance (cM) obtained by the SDI method (148.08 cM) was smaller than the distance obtained by SER (225.52 cM) and two published distances (150.11 cM and 150.38 cM). Since this SDI algorithm is stochastic, a more accurate linkage order can be quickly obtained by repeating this algorithm. Thus, this SDI method, which combines the advantages of accuracy and speed, is an important addition to the current linkage mapping toolkit for constructing improved linkage maps.
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Affiliation(s)
- Jixiang Wu
- Plant Science Department, South Dakota State University, Box 2140C,Brookings, SD 57007,
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Frenkel Z, Paux E, Mester D, Feuillet C, Korol A. LTC: a novel algorithm to improve the efficiency of contig assembly for physical mapping in complex genomes. BMC Bioinformatics 2010; 11:584. [PMID: 21118513 PMCID: PMC3098104 DOI: 10.1186/1471-2105-11-584] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2010] [Accepted: 11/30/2010] [Indexed: 11/25/2022] Open
Abstract
Background Physical maps are the substrate of genome sequencing and map-based cloning and their construction relies on the accurate assembly of BAC clones into large contigs that are then anchored to genetic maps with molecular markers. High Information Content Fingerprinting has become the method of choice for large and repetitive genomes such as those of maize, barley, and wheat. However, the high level of repeated DNA present in these genomes requires the application of very stringent criteria to ensure a reliable assembly with the FingerPrinted Contig (FPC) software, which often results in short contig lengths (of 3-5 clones before merging) as well as an unreliable assembly in some difficult regions. Difficulties can originate from a non-linear topological structure of clone overlaps, low power of clone ordering algorithms, and the absence of tools to identify sources of gaps in Minimal Tiling Paths (MTPs). Results To address these problems, we propose a novel approach that: (i) reduces the rate of false connections and Q-clones by using a new cutoff calculation method; (ii) obtains reliable clusters robust to the exclusion of single clone or clone overlap; (iii) explores the topological contig structure by considering contigs as networks of clones connected by significant overlaps; (iv) performs iterative clone clustering combined with ordering and order verification using re-sampling methods; and (v) uses global optimization methods for clone ordering and Band Map construction. The elements of this new analytical framework called Linear Topological Contig (LTC) were applied on datasets used previously for the construction of the physical map of wheat chromosome 3B with FPC. The performance of LTC vs. FPC was compared also on the simulated BAC libraries based on the known genome sequences for chromosome 1 of rice and chromosome 1 of maize. Conclusions The results show that compared to other methods, LTC enables the construction of highly reliable and longer contigs (5-12 clones before merging), the detection of "weak" connections in contigs and their "repair", and the elongation of contigs obtained by other assembly methods.
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Affiliation(s)
- Zeev Frenkel
- University of Haifa, Institute of Evolution, Haifa 31905, Israel.
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Ben-David R, Xie W, Peleg Z, Saranga Y, Dinoor A, Fahima T. Identification and mapping of PmG16, a powdery mildew resistance gene derived from wild emmer wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 121:499-510. [PMID: 20407741 DOI: 10.1007/s00122-010-1326-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2009] [Accepted: 03/12/2010] [Indexed: 05/04/2023]
Abstract
The gene-pool of wild emmer wheat, Triticum turgidum ssp. dicoccoides, harbors a rich allelic repertoire for disease resistance. In the current study, we made use of tetraploid wheat mapping populations derived from a cross between durum wheat (cv. Langdon) and wild emmer (accession G18-16) to identify and map a new powdery mildew resistance gene derived from wild emmer wheat. Initially, the two parental lines were screened with a collection of 42 isolates of Blumeria graminis f. sp. tritici (Bgt) from Israel and 5 isolates from Switzerland. While G18-16 was resistant to 34 isolates, Langdon was resistant only to 5 isolates and susceptible to 42 isolates. Isolate Bgt#15 was selected to differentiate between the disease reactions of the two genotypes. Segregation ratio of F(2-3) and recombinant inbreed line (F(7)) populations to inoculation with isolate Bgt#15 indicated the role of a single dominant gene in conferring resistance to Bgt#15. This gene, temporarily designated PmG16, was located on the distal region of chromosome arm 7AL. Genetic map of PmG16 region was assembled with 32 simple sequence repeat (SSR), sequence tag site (STS), Diversity array technology (DArT) and cleaved amplified polymorphic sequence (CAPS) markers and assigned to the 7AL physical bin map (7AL-16). Using four DNA markers we established colinearity between the genomic region spanning the PmG16 locus within the distal region of chromosome arm 7AL and the genomic regions on rice chromosome 6 and Brachypodium Bd1. A comparative analysis was carried out between PmG16 and other known Pm genes located on chromosome arm 7AL. The identified PmG16 may facilitate the use of wild alleles for improvement of powdery mildew resistance in elite wheat cultivars via marker-assisted selection.
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Affiliation(s)
- Roi Ben-David
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Mt. Carmel, 31905, Haifa, Israel
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Emebiri LC. An EST-SSR Marker Tightly Linked to the Barley Male Sterility Gene (msg6) Located on Chromosome 6H. J Hered 2010; 101:769-74. [DOI: 10.1093/jhered/esq083] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
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Jordan DR, Mace ES, Henzell RG, Klein PE, Klein RR. Molecular mapping and candidate gene identification of the Rf2 gene for pollen fertility restoration in sorghum [Sorghum bicolor (L.) Moench]. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2010; 120:1279-1287. [PMID: 20091293 DOI: 10.1007/s00122-009-1255-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2009] [Accepted: 12/15/2009] [Indexed: 05/28/2023]
Abstract
The A1 cytoplasmic-nuclear male sterility system in sorghum is used almost exclusively for the production of commercial hybrid seed and thus, the dominant genes that restore male fertility in F(1) hybrids are of critical importance to commercial seed production. The genetics of fertility restoration in sorghum can appear complex, being controlled by at least two major genes with additional modifiers and additional gene-environment interaction. To elucidate the molecular processes controlling fertility restoration and to develop a marker screening system for this important trait, two sorghum recombinant inbred line populations were created by crossing a restorer and a non-restoring inbred line, with fertility phenotypes evaluated in hybrid combination with three unique cytoplasmic male sterile lines. In both populations, a single major gene segregated for restoration which was localized to chromosome SBI-02 at approximately 0.5 cM from microsatellite marker, Xtxp304. In the two populations we observed that approximately 85 and 87% of the phenotypic variation in seed set was associated with the major Rf gene on SBI-02. Some evidence for modifier genes was also observed since a continuum of partial restored fertility was exhibited by lines in both RIL populations. With the prior report (Klein et al. in Theor Appl Genet 111:994-1012, 2005) of the cloning of the major fertility restoration gene Rf1 in sorghum, the major fertility restorer locus identified in this study was designated Rf2. A fine-mapping population was used to resolve the Rf2 locus to a 236,219-bp region of chromosome SBI-02, which spanned ~31 predicted open reading frames including a pentatricopeptide repeat (PPR) gene family member. The PPR gene displayed high homology with rice Rf1. Progress towards the development of a marker-assisted screen for fertility restoration is discussed.
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Affiliation(s)
- D R Jordan
- Queensland Primary Industries and Fisheries, Hermitage Research Station, MS508, Warwick, QLD, 4370, Australia.
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Nelson MN, Moolhuijzen PM, Boersma JG, Chudy M, Lesniewska K, Bellgard M, Oliver RP, Swiecicki W, Wolko B, Cowling WA, Ellwood SR. Aligning a new reference genetic map of Lupinus angustifolius with the genome sequence of the model legume, Lotus japonicus. DNA Res 2010; 17:73-83. [PMID: 20133394 PMCID: PMC2853381 DOI: 10.1093/dnares/dsq001] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We have developed a dense reference genetic map of Lupinus angustifolius (2n = 40) based on a set of 106 publicly available recombinant inbred lines derived from a cross between domesticated and wild parental lines. The map comprised 1090 loci in 20 linkage groups and three small clusters, drawing together data from several previous mapping publications plus almost 200 new markers, of which 63 were gene-based markers. A total of 171 mainly gene-based, sequence-tagged site loci served as bridging points for comparing the Lu. angustifolius genome with the genome sequence of the model legume, Lotus japonicus via BLASTn homology searching. Comparative analysis indicated that the genomes of Lu. angustifolius and Lo. japonicus are highly diverged structurally but with significant regions of conserved synteny including the region of the Lu. angustifolius genome containing the pod-shatter resistance gene, lentus. We discuss the potential of synteny analysis for identifying candidate genes for domestication traits in Lu. angustifolius and in improving our understanding of Fabaceae genome evolution.
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Affiliation(s)
- Matthew N Nelson
- School of Plant Biology and International Centre for Plant Breeding Education and Research, The University of Western Australia, 35 Stirling Highway, Crawley, WA 6009, Australia.
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Beukeboom LW, Niehuis O, Pannebakker BA, Koevoets T, Gibson JD, Shuker DM, van de Zande L, Gadau J. A comparison of recombination frequencies in intraspecific versus interspecific mapping populations of Nasonia. Heredity (Edinb) 2010; 104:302-9. [PMID: 20087389 DOI: 10.1038/hdy.2009.185] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
We present the first intraspecific linkage map for Nasonia vitripennis based on molecular markers. The map consists of 36 new microsatellite markers, extracted from the Nasonia genome sequence, and spans 515 cM. The five inferred linkage groups correspond to the five chromosomes of Nasonia. Comparison of recombination frequencies of the marker intervals spread over the whole genome (N=33 marker intervals) between the intraspecific N. vitripennis map and an interspecific N. vitripennis x N. giraulti map revealed a slightly higher (1.8%) recombination frequency in the intraspecific cross. We further considered an N. vitripennis x N. longicornis map with 29 microsatellite markers spanning 430 cM. Recombination frequencies in the two interspecific crosses differed neither between reciprocal crosses nor between mapping populations of embryos and adults. No major chromosomal rearrangements were found for the analyzed genomic segments. The observed differential F(2) hybrid male mortality has no significant effect on the genome-wide recombination frequency in Nasonia. We conclude that interspecific crosses between the different Nasonia species, a hallmark of Nasonia genetics, are generally suitable for mapping quantitative and qualitative trait loci for species differences.
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Affiliation(s)
- L W Beukeboom
- Evolutionary Genetics, Centre for Ecological and Evolutionary Studies, University of Groningen, Haren, The Netherlands.
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Niehuis O, Gibson JD, Rosenberg MS, Pannebakker BA, Koevoets T, Judson AK, Desjardins CA, Kennedy K, Duggan D, Beukeboom LW, van de Zande L, Shuker DM, Werren JH, Gadau J. Recombination and its impact on the genome of the haplodiploid parasitoid wasp Nasonia. PLoS One 2010; 5:e8597. [PMID: 20087411 PMCID: PMC2799529 DOI: 10.1371/journal.pone.0008597] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2009] [Accepted: 06/14/2009] [Indexed: 12/17/2022] Open
Abstract
Homologous meiotic recombination occurs in most sexually reproducing organisms, yet its evolutionary advantages are elusive. Previous research explored recombination in the honeybee, a eusocial hymenopteran with an exceptionally high genome-wide recombination rate. A comparable study in a non-social member of the Hymenoptera that would disentangle the impact of sociality from Hymenoptera-specific features such as haplodiploidy on the evolution of the high genome-wide recombination rate in social Hymenoptera is missing. Utilizing single-nucleotide polymorphisms (SNPs) between two Nasonia parasitoid wasp genomes, we developed a SNP genotyping microarray to infer a high-density linkage map for Nasonia. The map comprises 1,255 markers with an average distance of 0.3 cM. The mapped markers enabled us to arrange 265 scaffolds of the Nasonia genome assembly 1.0 on the linkage map, representing 63.6% of the assembled N. vitripennis genome. We estimated a genome-wide recombination rate of 1.4-1.5 cM/Mb for Nasonia, which is less than one tenth of the rate reported for the honeybee. The local recombination rate in Nasonia is positively correlated with the distance to the center of the linkage groups, GC content, and the proportion of simple repeats. In contrast to the honeybee genome, gene density in the parasitoid wasp genome is positively associated with the recombination rate; regions of low recombination are characterized by fewer genes with larger introns and by a greater distance between genes. Finally, we found that genes in regions of the genome with a low recombination frequency tend to have a higher ratio of non-synonymous to synonymous substitutions, likely due to the accumulation of slightly deleterious non-synonymous substitutions. These findings are consistent with the hypothesis that recombination reduces interference between linked sites and thereby facilitates adaptive evolution and the purging of deleterious mutations. Our results imply that the genomes of haplodiploid and of diploid higher eukaryotes do not differ systematically in their recombination rates and associated parameters.
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Affiliation(s)
- Oliver Niehuis
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA.
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42
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Emebiri LC. EST-SSR markers derived from an elite barley cultivar (Hordeum vulgare L. 'Morex'): polymorphism and genetic marker potential. Genome 2009; 52:665-76. [PMID: 19767897 DOI: 10.1139/g09-040] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microsatellites or simple sequence repeats have become the markers of choice for marker-assisted selection because of their low template DNA requirement, high reproducibility, and high level of polymorphism. This study investigated a new set of barley (Hordeum vulgare L.) EST-derived SSR markers designed to target gene sequences expressed during grain development, as they are more likely to be important in determining grain quality. The EST sequences (HVSMEh and HVSMEi) were derived from cDNA libraries of the elite six-rowed cultivar Morex, made from spikes harvested at 5 to 45 days after pollination. Approximately half of the 110 SSR markers derived from the ESTs were polymorphic in a panel of 8 diverse barley genotypes, with PIC values between 0.19 and 0.79. Twenty of the new markers were mapped to chromosomal locations using 2 doubled haploid populations. To demonstrate marker potential, quantitative trait locus (QTL) analyses were carried out with phenotypic data on wort beta-glucan content and beta-glucanase activity, two traits with a long history of genetic studies. Most of the EST-SSR markers mapped to within 10 cM of the cellulose synthase (HvCesA) and cellulose synthase-like (HvCslF) genes, which provides highly informative functional markers for tracking these genes in breeding programs. It was also observed that on any given chromosome, the QTL for beta-glucan content and beta-glucanase activity were rarely coincident but tended to occur in adjacent intervals along chromosomal regions, which agreed with their independent genetic basis; the adjacent localization may be important for coordination of cell wall degradation during germination and malting.
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Affiliation(s)
- Livinus C Emebiri
- Biosciences Research Division, Department of Primary Industries, Grains Innovation Park, Private Bag 260, Horsham, VIC 3401, Australia
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Liu S, Yeh CT, Ji T, Ying K, Wu H, Tang HM, Fu Y, Nettleton D, Schnable PS. Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome. PLoS Genet 2009; 5:e1000733. [PMID: 19936291 PMCID: PMC2774946 DOI: 10.1371/journal.pgen.1000733] [Citation(s) in RCA: 151] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2009] [Accepted: 10/19/2009] [Indexed: 11/19/2022] Open
Abstract
The Mu transposon system of maize is highly active, with each of the ∼50–100 copies transposing on average once each generation. The approximately one dozen distinct Mu transposons contain highly similar ∼215 bp terminal inverted repeats (TIRs) and generate 9-bp target site duplications (TSDs) upon insertion. Using a novel genome walking strategy that uses these conserved TIRs as primer binding sites, Mu insertion sites were amplified from Mu stocks and sequenced via 454 technology. 94% of ∼965,000 reads carried Mu TIRs, demonstrating the specificity of this strategy. Among these TIRs, 21 novel Mu TIRs were discovered, revealing additional complexity of the Mu transposon system. The distribution of >40,000 non-redundant Mu insertion sites was strikingly non-uniform, such that rates increased in proportion to distance from the centromere. An identified putative Mu transposase binding consensus site does not explain this non-uniformity. An integrated genetic map containing more than 10,000 genetic markers was constructed and aligned to the sequence of the maize reference genome. Recombination rates (cM/Mb) are also strikingly non-uniform, with rates increasing in proportion to distance from the centromere. Mu insertion site frequencies are strongly correlated with recombination rates. Gene density does not fully explain the chromosomal distribution of Mu insertion and recombination sites, because pronounced preferences for the distal portion of chromosome are still observed even after accounting for gene density. The similarity of the distributions of Mu insertions and meiotic recombination sites suggests that common features, such as chromatin structure, are involved in site selection for both Mu insertion and meiotic recombination. The finding that Mu insertions and meiotic recombination sites both concentrate in genomic regions marked with epigenetic marks of open chromatin provides support for the hypothesis that open chromatin enhances rates of both Mu insertion and meiotic recombination. Genomic insertion sites of Mu transposons were amplified and sequenced via next generation technology, revealing more than 40,000 non-redundant Mu insertion sites that are non-uniformly distributed across the maize genome and within genes. Along chromosomes, frequencies of Mu transposon insertions are strongly correlated with recombination rates. Although both Mu and recombination occur preferentially in genes, gene density does not fully explain these patterns. Instead, the finding that Mu insertions and meiotic recombination sites both concentrate in genomic regions marked with epigenetic marks of open chromatin provides support for the hypothesis that open chromatin enhances rates of both Mu insertion and meiotic recombination.
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Affiliation(s)
- Sanzhen Liu
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, Iowa, United States of America
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Cheng-Ting Yeh
- Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
| | - Tieming Ji
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, United States of America
- Department of Statistics, Iowa State University, Ames, Iowa, United States of America
| | - Kai Ying
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, Iowa, United States of America
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, United States of America
| | - Haiyan Wu
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, United States of America
| | - Ho Man Tang
- Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
| | - Yan Fu
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
- Center for Carbon Capturing Crops, Iowa State University, Ames, Iowa, United States of America
| | - Dan Nettleton
- Department of Statistics, Iowa State University, Ames, Iowa, United States of America
| | - Patrick S. Schnable
- Interdepartmental Genetics Graduate Program, Iowa State University, Ames, Iowa, United States of America
- Department of Genetics, Development, and Cell Biology, Iowa State University, Ames, Iowa, United States of America
- Center for Plant Genomics, Iowa State University, Ames, Iowa, United States of America
- Department of Agronomy, Iowa State University, Ames, Iowa, United States of America
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, United States of America
- Center for Carbon Capturing Crops, Iowa State University, Ames, Iowa, United States of America
- * E-mail:
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High-throughput genetic mapping of mutants via quantitative single nucleotide polymorphism typing. Genetics 2009; 184:19-26. [PMID: 19884313 DOI: 10.1534/genetics.109.107557] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Advances in next-generation sequencing technology have facilitated the discovery of single nucleotide polymorphisms (SNPs). Sequenom-based SNP-typing assays were developed for 1359 maize SNPs identified via comparative next-generation transcriptomic sequencing. Approximately 75% of these SNPs were successfully converted into genetic markers that can be scored reliably and used to generate a SNP-based genetic map by genotyping recombinant inbred lines from the intermated B73 x Mo17 population. The quantitative nature of Sequenom-based SNP assays led to the development of a time- and cost-efficient strategy to genetically map mutants via quantitative bulked segregant analysis. This strategy was used to rapidly map the loci associated with several dozen recessive mutants. Because a mutant can be mapped using as few as eight multiplexed sets of SNP assays on a bulk of as few as 20 mutant F(2) individuals, this strategy is expected to be widely adopted for mapping in many species.
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Abstract
When building genetic maps, it is necessary to choose from several marker ordering algorithms and criteria, and the choice is not always simple. In this study, we evaluate the efficiency of algorithms try (TRY), seriation (SER), rapid chain delineation (RCD), recombination counting and ordering (RECORD) and unidirectional growth (UG), as well as the criteria PARF (product of adjacent recombination fractions), SARF (sum of adjacent recombination fractions), SALOD (sum of adjacent LOD scores) and LHMC (likelihood through hidden Markov chains), used with the RIPPLE algorithm for error verification, in the construction of genetic linkage maps. A linkage map of a hypothetical diploid and monoecious plant species was simulated containing one linkage group and 21 markers with fixed distance of 3 cM between them. In all, 700 F(2) populations were randomly simulated with 100 and 400 individuals with different combinations of dominant and co-dominant markers, as well as 10 and 20% of missing data. The simulations showed that, in the presence of co-dominant markers only, any combination of algorithm and criteria may be used, even for a reduced population size. In the case of a smaller proportion of dominant markers, any of the algorithms and criteria (except SALOD) investigated may be used. In the presence of high proportions of dominant markers and smaller samples (around 100), the probability of repulsion linkage increases between them and, in this case, use of the algorithms TRY and SER associated to RIPPLE with criterion LHMC would provide better results.
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Mace ES, Rami JF, Bouchet S, Klein PE, Klein RR, Kilian A, Wenzl P, Xia L, Halloran K, Jordan DR. A consensus genetic map of sorghum that integrates multiple component maps and high-throughput Diversity Array Technology (DArT) markers. BMC PLANT BIOLOGY 2009; 9:13. [PMID: 19171067 PMCID: PMC2671505 DOI: 10.1186/1471-2229-9-13] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2008] [Accepted: 01/26/2009] [Indexed: 05/19/2023]
Abstract
BACKGROUND Sorghum genome mapping based on DNA markers began in the early 1990s and numerous genetic linkage maps of sorghum have been published in the last decade, based initially on RFLP markers with more recent maps including AFLPs and SSRs and very recently, Diversity Array Technology (DArT) markers. It is essential to integrate the rapidly growing body of genetic linkage data produced through DArT with the multiple genetic linkage maps for sorghum generated through other marker technologies. Here, we report on the colinearity of six independent sorghum component maps and on the integration of these component maps into a single reference resource that contains commonly utilized SSRs, AFLPs, and high-throughput DArT markers. RESULTS The six component maps were constructed using the MultiPoint software. The lengths of the resulting maps varied between 910 and 1528 cM. The order of the 498 markers that segregated in more than one population was highly consistent between the six individual mapping data sets. The framework consensus map was constructed using a "Neighbours" approach and contained 251 integrated bridge markers on the 10 sorghum chromosomes spanning 1355.4 cM with an average density of one marker every 5.4 cM, and were used for the projection of the remaining markers. In total, the sorghum consensus map consisted of a total of 1997 markers mapped to 2029 unique loci (1190 DArT loci and 839 other loci) spanning 1603.5 cM and with an average marker density of 1 marker/0.79 cM. In addition, 35 multicopy markers were identified. On average, each chromosome on the consensus map contained 203 markers of which 58.6% were DArT markers. Non-random patterns of DNA marker distribution were observed, with some clear marker-dense regions and some marker-rare regions. CONCLUSION The final consensus map has allowed us to map a larger number of markers than possible in any individual map, to obtain a more complete coverage of the sorghum genome and to fill a number of gaps on individual maps. In addition to overall general consistency of marker order across individual component maps, good agreement in overall distances between common marker pairs across the component maps used in this study was determined, using a difference ratio calculation. The obtained consensus map can be used as a reference resource for genetic studies in different genetic backgrounds, in addition to providing a framework for transferring genetic information between different marker technologies and for integrating DArT markers with other genomic resources. DArT markers represent an affordable, high throughput marker system with great utility in molecular breeding programs, especially in crops such as sorghum where SNP arrays are not publicly available.
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Affiliation(s)
- Emma S Mace
- The Department of Primary Industries & Fisheries, Queensland (DPI&F), Hermitage Research Station, Warwick, QLD 4370, Australia
| | - Jean-Francois Rami
- CIRAD UMR DAP, TA A-96/03, Av Agropolis, 34398 Montpellier CEDEX 5, France
| | - Sophie Bouchet
- CIRAD UMR DAP, TA A-96/03, Av Agropolis, 34398 Montpellier CEDEX 5, France
| | - Patricia E Klein
- Department of Horticulture and Institute for Plant Genomics and Biotechnology, Texas A&M University, College Station, TX 77843-2123, USA
| | - Robert R Klein
- USDA-ARS, Southern Plains Agricultural Research Center, College Station, TX 77845, USA
| | - Andrzej Kilian
- Diversity Arrays Technology P/L, PO Box 7141, Yarralumla ACT 2600, Australia
| | - Peter Wenzl
- Diversity Arrays Technology P/L, PO Box 7141, Yarralumla ACT 2600, Australia
| | - Ling Xia
- Diversity Arrays Technology P/L, PO Box 7141, Yarralumla ACT 2600, Australia
| | - Kirsten Halloran
- The Department of Primary Industries & Fisheries, Queensland (DPI&F), Hermitage Research Station, Warwick, QLD 4370, Australia
| | - David R Jordan
- The Department of Primary Industries & Fisheries, Queensland (DPI&F), Hermitage Research Station, Warwick, QLD 4370, Australia
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Genetics of phenotypic plasticity: QTL analysis in barley, Hordeum vulgare. Heredity (Edinb) 2008; 102:163-73. [PMID: 18941472 DOI: 10.1038/hdy.2008.76] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Phenotypic plasticity is the variation in phenotypic traits produced by a genotype in different environments. In contrast, environmental canalization is defined as the insensitivity of a genotype's phenotype to variation in environments. Despite the extensive literature on the evolutionary significance and potential genetic mechanisms driving plasticity and canalization, few studies tried to unravel the genetic basis of this phenomenon. Using both simulations and real data from barley (Hordeum vulgare), we used QTL mapping to obtain insights into the genetics of phenotypic plasticity. We explored two ways of quantifying phenotypic plasticity, namely the phenotypic variance across environments and the Finlay-Wilkinson's regression slope. Each relates to a different concept of stability. Through QTL detection with real and simulated data, we show that each measure of plasticity detects specific types of plasticity QTL. Most of the plasticity QTLs were detected in the data set with the lowest number of environments. All plasticity QTL co-located with loci showing QTL x E interaction and there were no QTL that only affected plasticity. The number of environments that are considered and their homogeneity is a key to interpret the genetic control of phenotypic plasticity. Regulatory pathways of plasticity may vary from one set of environments to another due to unique features of each environment. Therefore, with an increasing number of environments, it may become impossible to detect a single 'consistent' regulatory pathway for all environments.
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Parh DK, Jordan DR, Aitken EAB, Mace ES, Jun-ai P, McIntyre CL, Godwin ID. QTL analysis of ergot resistance in sorghum. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:369-82. [PMID: 18481043 DOI: 10.1007/s00122-008-0781-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2007] [Accepted: 04/23/2008] [Indexed: 05/05/2023]
Abstract
Sorghum ergot, caused predominantly by Claviceps africana Frederickson, Mantle, de Milliano, is a significant threat to the sorghum industry worldwide. The objectives of this study were firstly, to identify molecular markers linked to ergot resistance and to two pollen traits, pollen quantity (PQ) and pollen viability (PV), and secondly, to assess the relationship between the two pollen traits and ergot resistance in sorghum. A genetic linkage map of sorghum RIL population R931945-2-2 x IS 8525 (resistance source) was constructed using 303 markers including 36 SSR, 117 AFLP , 148 DArT and two morphological trait loci. Composite interval mapping identified nine, five, and four QTL linked to molecular markers for percentage ergot infection (PCERGOT), PQ and PV, respectively, at a LOD >2.0. Co-location/linkage of QTL were identified on four chromosomes while other QTL for the three traits mapped independently, indicating that both pollen and non pollen-based mechanisms of ergot resistance were operating in this sorghum population. Of the nine QTL identified for PCERGOT, five were identified using the overall data set while four were specific to the group data sets defined by temperature and humidity. QTL identified on SBI-02 and SBI-06 were further validated in additional populations. This is the first report of QTL associated with ergot resistance in sorghum. The markers reported herein could be used for marker-assisted selection for this important disease of sorghum.
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Affiliation(s)
- D K Parh
- School of Land and Food Sciences, University of Queensland, Brisbane, QLD 4072, Australia.
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Peleg Z, Saranga Y, Suprunova T, Ronin Y, Röder MS, Kilian A, Korol AB, Fahima T. High-density genetic map of durum wheat x wild emmer wheat based on SSR and DArT markers. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 117:103-15. [PMID: 18437346 DOI: 10.1007/s00122-008-0756-9] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Accepted: 03/26/2008] [Indexed: 05/18/2023]
Abstract
A genetic linkage map of tetraploid wheat was constructed based on a cross between durum wheat [Triticum turgidum ssp. durum (Desf.) MacKey] cultivar Langdon and wild emmer wheat [T. turgidum ssp. dicoccoides (Körn.) Thell.] accession G18-16. One hundred and fifty-two single-seed descent derived F(6) recombinant inbred lines (RILs) were analyzed with a total of 690 loci, including 197 microsatellite and 493 DArT markers. Linkage analysis defined 14 linkage groups. Most markers were mapped to the B-genome (60%), with an average of 57 markers per chromosome and the remaining 40% mapped to the A-genome, with an average of 39 markers per chromosome. To construct a stabilized (skeleton) map, markers interfering with map stability were removed. The skeleton map consisted of 307 markers with a total length of 2,317 cM and average distance of 7.5 cM between adjacent markers. The length of individual chromosomes ranged between 112 cM for chromosome 4B to 217 cM for chromosome 3B. A fraction (30.1%) of the markers deviated significantly from the expected Mendelian ratios; clusters of loci showing distorted segregation were found on chromosomes 1A, 1BL, 2BS, 3B, and 4B. DArT markers showed high proportion of clustering, which may be indicative of gene-rich regions. Three hundred and fifty-two new DArT markers were mapped for the first time on the current map. This map provides a useful groundwork for further genetic analyses of important quantitative traits, positional cloning, and marker-assisted selection, as well as for genome comparative genomics and genome organization studies in wheat and other cereals.
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Affiliation(s)
- Zvi Peleg
- Department of Evolutionary and Environmental Biology, The Institute of Evolution, Faculty of Science and Science Education, University of Haifa, Mt. Carmel, 31905 Haifa, Israel
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Ogbonnaya FC, Imtiaz M, Ye G, Hearnden PR, Hernandez E, Eastwood RF, van Ginkel M, Shorter SC, Winchester JM. Genetic and QTL analyses of seed dormancy and preharvest sprouting resistance in the wheat germplasm CN10955. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2008; 116:891-902. [PMID: 18368385 DOI: 10.1007/s00122-008-0712-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2007] [Accepted: 01/08/2008] [Indexed: 05/06/2023]
Abstract
The inheritance and genetic linkage analysis for seed dormancy and preharvest sprouting (PHS) resistance were carried out in an F8 recombinant inbred lines (RILs) derived from the cross between "CN19055" (white-grained, PHS-resistant) with locally adapted Australian cultivar "Annuello" (white-grained, PHS-susceptible). Seed dormancy was assessed as germination index (GI7) while assessment for preharvest sprouting resistance was based on whole head assay (sprouting index, SI) and visibly sprouted seeds (VI). Segregation analysis of the F2, F3 data from the glasshouse and the RIL population in 2004 and 2005 field data sets indicated that seed dormancy and PHS resistance in CN19055 is controlled by at least two genes. Heritabilities for GI7 and VI were high and moderate for SI. The most accurate method for assessing PHS resistance was achieved using VI and GI7 while SI exhibited large genotype by environment interaction. Two quantitative trait loci (QTLs) QPhs.dpivic.4A.1 and QPhs.dpivic.4A.2 were identified. On pooled data across four environments, the major QTL, QPhs.dpivic.4A.2, explained 45% of phenotypic variation for GI7, 43% for VI and 20% for SI, respectively. On the other hand, QPhs.dpivic.4A.1 which accounted for 31% of the phenotypic variation in GI7 in 2004 Horsham field trial, was not stable across environments. Physical mapping of two SSR markers, Xgwm937 and Xgwm894 linked to the major QTL for PHS resistance, using Chinese Spring deletions lines for chromosome 4AS and 4AL revealed that the markers were located in the deletion bins 4AL-12 and 4AL-13. The newly identified SSR markers (Xgwm937/Xgwm894) showed strong association with seed dormancy and PHS resistance in a range of wheat lines reputed to possess PHS resistance. The results suggest that Xgwm937/Xgwm894 could be used in marker-assisted selection (MAS) for incorporating preharvest sprouting resistance into elite wheat cultivars susceptible to PHS.
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Affiliation(s)
- F C Ogbonnaya
- Department of Primary Industries, Primary Industries Research Victoria, VIC 3401, Australia.
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