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Peñafiel Loaiza N, Chafe AH, Moraes R M, Oleas NH, Roncal J. Genotyping-by-sequencing informs conservation of Andean palms sources of non-timber forest products. Evol Appl 2024; 17:e13765. [PMID: 39091352 PMCID: PMC11291087 DOI: 10.1111/eva.13765] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/30/2024] [Accepted: 07/18/2024] [Indexed: 08/04/2024] Open
Abstract
Conservation and sustainable management of lineages providing non-timber forest products are imperative under the current global biodiversity loss. Most non-timber forest species, however, lack genomic studies that characterize their intraspecific variation and evolutionary history, which inform species' conservation practices. Contrary to many lineages in the Andean biodiversity hotspot that exhibit high diversification, the genus Parajubaea (Arecaceae) has only three species despite the genus' origin 22 million years ago. Two of the three palm species, P. torallyi and P. sunkha, are non-timber forest species endemic to the Andes of Bolivia and are listed as IUCN endangered. The third species, P. cocoides, is a vulnerable species with unknown wild populations. We investigated the evolutionary relationships of Parajubaea species and the genetic diversity and structure of wild Bolivian populations. Sequencing of five low-copy nuclear genes (3753 bp) challenged the hypothesis that P. cocoides is a cultigen that originated from the wild Bolivian species. We further obtained up to 15,134 de novo single-nucleotide polymorphism markers by genotyping-by-sequencing of 194 wild Parajubaea individuals. Our total DNA sequencing effort rejected the taxonomic separation of the two Bolivian species. As expected for narrow endemic species, we observed low genetic diversity, but no inbreeding signal. We found three genetic clusters shaped by geographic distance, which we use to propose three management units. Different percentages of missing genotypic data did not impact the genetic structure of populations. We use the management units to recommend in situ conservation by creating new protected areas, and ex situ conservation through seed collection.
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Affiliation(s)
- Nicolás Peñafiel Loaiza
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
- Present address:
Chone y BabahoyoLojaEcuador
| | - Abigail H. Chafe
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
| | - Mónica Moraes R
- Herbario Nacional de Bolivia, Instituto de EcologíaUniversidad Mayor de San AndrésLa PazBolivia
| | - Nora H. Oleas
- Centro de Investigación de la Biodiversidad y Cambio Climático – BioCamb e Ingeniería en Biodiversidad y Recursos Genéticos, Facultad de Ciencias de Medio AmbienteUniversidad IndoaméricaQuitoEcuador
| | - Julissa Roncal
- Department of BiologyMemorial University of NewfoundlandSt. John'sNewfoundland and LabradorCanada
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Lavaud C, Lesné A, Leprévost T, Pilet-Nayel ML. Fine mapping of Ae-Ps4.5, a major locus for resistance to pathotype III of Aphanomyces euteiches in pea. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:47. [PMID: 38334777 DOI: 10.1007/s00122-024-04548-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 01/10/2024] [Indexed: 02/10/2024]
Abstract
KEY MESSAGE QTL mapping and recombinant screening confirmed the major effect of QTL Ae-Ps4.5 on pea resistance to pathotype III of Aphanomyces euteiches and fine-mapped the QTL to a 3.06-Mb interval. Aphanomyces root rot, caused by Aphanomyces euteiches, is the most important disease of pea (Pisum sativum L.) worldwide. The development of pea-resistant varieties is a major challenge to control the disease. Previous linkage studies identified seven main resistance quantitative trait loci (QTL), including the QTL Ae-Ps4.5 associated with partial resistance in US nurseries infested by the pea pathotype III of A. euteiches. This study aimed to confirm the major effect of Ae-Ps4.5 on A. euteiches pathotype III, refine its interval, and identify candidate genes underlying the QTL. QTL mapping on an updated genetic map from the Puget × 90-2079 pea recombinant inbred line population identified Ae-Ps4.5 in a 0.8-cM confidence interval with a high effect (R2 = 89%) for resistance to the Ae109 reference strain of A. euteiches (pathotype III) under controlled conditions. However, the QTL mapping did not detect Ae-Ps4.5 for resistance to the RB84 reference strain of A. euteiches (pathotype I). Screening 224-pea BC5F2 plant progeny derived from three near-isogenic lines (NILs) carrying the 90-2079 allele at Ae-Ps4.5 in the Puget genetic background with 26 SNP markers identified 15 NILs showing recombination in the QTL interval. Phenotyping of the recombinant lines for resistance to the Ae109 strain of A. euteiches reduced the QTL to a physical interval of 3.06 Mb, containing 50 putative annotated genes on the Caméor pea genome V1a among which three candidate genes highlighted. This study provides closely linked SNP markers and putative candidate genes to accelerate pea breeding for resistant varieties to Aphanomyces root rot.
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Affiliation(s)
- Clément Lavaud
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Angélique Lesné
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
| | - Théo Leprévost
- IGEPP, INRAE, Institut Agro, Univ Rennes, 35653, Le Rheu, France
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Šišić A, Baćanović-Šišić J, Gamba FM, Finckh MR. Didymella pinodella: An Important Pea Root Rot Pathogen in France to Watch Out For? J Fungi (Basel) 2024; 10:44. [PMID: 38248955 PMCID: PMC10820343 DOI: 10.3390/jof10010044] [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: 11/27/2023] [Revised: 12/24/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024] Open
Abstract
Root rot pathogens restrict pea and wheat production globally. In the EU, pea and pea-based cereal mixtures are being promoted; however, root rot pathogen dynamics in such mixtures are poorly understood. Winter pea and wheat were grown either in pure stands or in mixtures in the field in western France, and the severity of root rot in pea, wheat, and their mixtures, as well as the key pathogens associated with these crops, were assessed. Disease severity was moderate in pea and low in wheat, with no effect of sowing pattern. Didymella pinodella, a previously unreported pathogen in the pea-root rot complex in France, emerged as the most dominant pathogen in pea. It also occurred in low frequencies in wheat. Subsequent greenhouse aggressiveness tests showed that ten of the commonly grown pea cultivars in France lack resistance to D. pinodella. Among the Fusarium spp. isolated, F. avenaceum was the most frequent, occurring at similar frequencies in pea and wheat. In conclusion, D. pinodella may be an important pea root rot pathogen in France and there is a lack of resistance in the tested pea cultivars. In addition, F. avenaceum is a shared pathogen of wheat and pea.
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Affiliation(s)
- Adnan Šišić
- Section of Ecological Plant Protection, University of Kassel, 37213 Witzenhausen, Germany;
| | - Jelena Baćanović-Šišić
- Section of Organic Plant Breeding and Agrobiodiversity, University of Kassel, 37213 Witzenhausen, Germany;
| | - Fernanda M. Gamba
- Plant Protection Department, Faculty of Agronomy, University of the Oriental Republic of Uruguay (UDELAR), Research Station Dr. M.A. Cassinoni, Ruta 3 K 363, Paysandú 60000, Uruguay;
| | - Maria R. Finckh
- Section of Ecological Plant Protection, University of Kassel, 37213 Witzenhausen, Germany;
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Leprévost T, Boutet G, Lesné A, Rivière JP, Vetel P, Glory I, Miteul H, Le Rat A, Dufour P, Regnault-Kraut C, Sugio A, Lavaud C, Pilet-Nayel ML. Advanced backcross QTL analysis and comparative mapping with RIL QTL studies and GWAS provide an overview of QTL and marker haplotype diversity for resistance to Aphanomyces root rot in pea ( Pisum sativum). FRONTIERS IN PLANT SCIENCE 2023; 14:1189289. [PMID: 37841625 PMCID: PMC10569610 DOI: 10.3389/fpls.2023.1189289] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Accepted: 07/25/2023] [Indexed: 10/17/2023]
Abstract
Aphanomyces euteiches is the most damaging soilborne pea pathogen in France. Breeding of pea resistant varieties combining a diversity of quantitative trait loci (QTL) is a promising strategy considering previous research achievements in dissecting polygenic resistance to A. euteiches. The objective of this study was to provide an overview of the diversity of QTL and marker haplotypes for resistance to A. euteiches, by integrating a novel QTL mapping study in advanced backcross (AB) populations with previous QTL analyses and genome-wide association study (GWAS) using common markers. QTL analysis was performed in two AB populations derived from the cross between the susceptible spring pea variety "Eden" and the two new sources of partial resistance "E11" and "LISA". The two AB populations were genotyped using 993 and 478 single nucleotide polymorphism (SNP) markers, respectively, and phenotyped for resistance to A. euteiches in controlled conditions and in infested fields at two locations. GWAS and QTL mapping previously reported in the pea-Aphanomyces collection and from four recombinant inbred line (RIL) populations, respectively, were updated using a total of 1,850 additional markers, including the markers used in the Eden x E11 and Eden x LISA populations analysis. A total of 29 resistance-associated SNPs and 171 resistance QTL were identified by GWAS and RIL or AB QTL analyses, respectively, which highlighted 10 consistent genetic regions confirming the previously reported QTL. No new consistent resistance QTL was detected from both Eden x E11 and Eden x LISA AB populations. However, a high diversity of resistance haplotypes was identified at 11 linkage disequilibrium (LD) blocks underlying consistent genetic regions, especially in 14 new sources of resistance from the pea-Aphanomyces collection. An accumulation of favorable haplotypes at these 11 blocks was confirmed in the most resistant pea lines of the collection. This study provides new SNP markers and rare haplotypes associated with the diversity of Aphanomyces root rot resistance QTL investigated, which will be useful for QTL pyramiding strategies to increase resistance levels in future pea varieties.
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Affiliation(s)
- Théo Leprévost
- IGEPP, INRAE, Institut Agro, University of Rennes, Le Rheu, France
| | - Gilles Boutet
- IGEPP, INRAE, Institut Agro, University of Rennes, Le Rheu, France
| | - Angélique Lesné
- IGEPP, INRAE, Institut Agro, University of Rennes, Le Rheu, France
| | | | - Pierrick Vetel
- IGEPP, INRAE, Institut Agro, University of Rennes, Le Rheu, France
| | - Isabelle Glory
- IGEPP, INRAE, Institut Agro, University of Rennes, Le Rheu, France
| | - Henri Miteul
- IGEPP, INRAE, Institut Agro, University of Rennes, Le Rheu, France
| | - Anaïs Le Rat
- IGEPP, INRAE, Institut Agro, University of Rennes, Le Rheu, France
| | | | | | - Akiko Sugio
- IGEPP, INRAE, Institut Agro, University of Rennes, Le Rheu, France
| | - Clément Lavaud
- IGEPP, INRAE, Institut Agro, University of Rennes, Le Rheu, France
- KWS MOMONT Recherche SARL, Allonnes, France
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Boutet G, Lavaud C, Lesné A, Miteul H, Pilet-Nayel ML, Andrivon D, Lejeune-Hénaut I, Baranger A. Five Regions of the Pea Genome Co-Control Partial Resistance to D. pinodes, Tolerance to Frost, and Some Architectural or Phenological Traits. Genes (Basel) 2023; 14:1399. [PMID: 37510304 PMCID: PMC10379203 DOI: 10.3390/genes14071399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 06/08/2023] [Accepted: 06/14/2023] [Indexed: 07/30/2023] Open
Abstract
Evidence for reciprocal links between plant responses to biotic or abiotic stresses and architectural and developmental traits has been raised using approaches based on epidemiology, physiology, or genetics. Winter pea has been selected for years for many agronomic traits contributing to yield, taking into account architectural or phenological traits such as height or flowering date. It remains nevertheless particularly susceptible to biotic and abiotic stresses, among which Didymella pinodes and frost are leading examples. The purpose of this study was to identify and resize QTL localizations that control partial resistance to D. pinodes, tolerance to frost, and architectural or phenological traits on pea dense genetic maps, considering how QTL colocalizations may impact future winter pea breeding. QTL analysis revealed five metaQTLs distributed over three linkage groups contributing to both D. pinodes disease severity and frost tolerance. At these loci, the haplotypes of alleles increasing both partial resistance to D. pinodes and frost tolerance also delayed the flowering date, increased the number of branches, and/or decreased the stipule length. These results question both the underlying mechanisms of the joint control of biotic stress resistance, abiotic stress tolerance, and plant architecture and phenology and the methods of marker-assisted selection optimizing stress control and productivity in winter pea breeding.
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Affiliation(s)
- Gilles Boutet
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35653 Le Rheu, France
| | - Clément Lavaud
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35653 Le Rheu, France
| | - Angélique Lesné
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35653 Le Rheu, France
| | - Henri Miteul
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35653 Le Rheu, France
| | | | - Didier Andrivon
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35653 Le Rheu, France
| | - Isabelle Lejeune-Hénaut
- BioEcoAgro Joint Research Unit, INRAE, Université de Lille, Université de Liège, Université de Picardie Jules Verne, 80200 Estrées-Mons, France
| | - Alain Baranger
- IGEPP, INRAE, Institut Agro, Université de Rennes, 35653 Le Rheu, France
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Sudan J, Sharma S, Salgotra RK, Pandey RK, Neelam D, Singh R. Elucidating the process of SNPs identification in non-reference genome crops. J Biomol Struct Dyn 2023; 41:15682-15690. [PMID: 37021361 DOI: 10.1080/07391102.2023.2194002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 02/28/2023] [Indexed: 04/07/2023]
Abstract
Advances in the next generation sequencing technologies, genome reduction techniques and bioinformatics tools have given a big impetus to the identification of genome-wide single nucleotide polymorphisms (SNPs) in crops. NGS technologies can make available a large amount of sequence data in a short span of time. The huge data requires detailed bioinformatics analysis steps, including preprocessing, mapping, and identification of sequence variants. A plethora of available software meant for sequence analysis is used for different sequence analysis steps. However, SNPs identification is far more challenging for orphaned crops or non-reference genome crops. The current article reports different steps for in silico SNPs identification in a sequential manner and proposes some mapping approaches using CLC Genomics software that could provide an alternative method for SNPs identification in orphan crops having no reference genome. The three mapping approaches: Common reference map from progenitor genomes (CRMPG), step-wise use of progenitor genomes (SWPG) and de novo assembly of sequence read (DASR) were validated with the dd-RAD sequenced data of two genotypes from Brassica juncea.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jebi Sudan
- Department of Biotechnology, JECRC University, Jaipur, Rajasthan, India
| | - Susheel Sharma
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu (J&K), Jammu, India
| | - Romesh K Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu (J&K), Jammu, India
| | - Rajan Kumar Pandey
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
| | - Deepesh Neelam
- Department of Microbiology, JECRC University, Jaipur, Rajasthan, India
| | - Ravinder Singh
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu (J&K), Jammu, India
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Vidal A, Gauthier F, Rodrigez W, Guiglielmoni N, Leroux D, Chevrolier N, Jasson S, Tourrette E, Martin OC, Falque M. SeSAM: software for automatic construction of order-robust linkage maps. BMC Bioinformatics 2022; 23:499. [PMCID: PMC9675223 DOI: 10.1186/s12859-022-05045-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 11/08/2022] [Indexed: 11/21/2022] Open
Abstract
Background Genotyping and sequencing technologies produce increasingly large numbers of genetic markers with potentially high rates of missing or erroneous data. Therefore, the construction of linkage maps is more and more complex. Moreover, the size of segregating populations remains constrained by cost issues and is less and less commensurate with the numbers of SNPs available. Thus, guaranteeing a statistically robust marker order requires that maps include only a carefully selected subset of SNPs. Results In this context, the SeSAM software allows automatic genetic map construction using seriation and placement approaches, to produce (1) a high-robustness framework map which includes as many markers as possible while keeping the order robustness beyond a given statistical threshold, and (2) a high-density total map including the framework plus almost all polymorphic markers. During this process, care is taken to limit the impact of genotyping errors and of missing data on mapping quality. SeSAM can be used with a wide range of biparental populations including from outcrossing species for which phases are inferred on-the-fly by maximum-likelihood during map elongation. The package also includes functions to simulate data sets, convert data formats, detect putative genotyping errors, visualize data and map quality (including graphical genotypes), and merge several maps into a consensus. SeSAM is also suitable for interactive map construction, by providing lower-level functions for 2-point and multipoint EM analyses. The software is implemented in a R package including functions in C++. Conclusions SeSAM is a fully automatic linkage mapping software designed to (1) produce a framework map as robust as desired by optimizing the selection of a subset of markers, and (2) produce a high-density map including almost all polymorphic markers. The software can be used with a wide range of biparental mapping populations including cases from outcrossing. SeSAM is freely available under a GNU GPL v3 license and works on Linux, Windows, and macOS platforms. It can be downloaded together with its user-manual and quick-start tutorial from ForgeMIA (SeSAM project) at https://forgemia.inra.fr/gqe-acep/sesam/-/releases Supplementary Information The online version contains supplementary material available at 10.1186/s12859-022-05045-7.
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Affiliation(s)
- Adrien Vidal
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Franck Gauthier
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Willy Rodrigez
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Nadège Guiglielmoni
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Damien Leroux
- grid.507621.7INRAE, Unité de Mathématiques et Informatique Appliquées - Toulouse, Toulouse, France
| | - Nicolas Chevrolier
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Sylvain Jasson
- grid.507621.7INRAE, Unité de Mathématiques et Informatique Appliquées - Toulouse, Toulouse, France
| | - Elise Tourrette
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
| | - Olivier C. Martin
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France ,grid.503243.3Université Paris-Saclay, CNRS, INRAE, Université Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France ,Université Paris Cité, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91190 Gif-sur-Yvette, France
| | - Matthieu Falque
- grid.460789.40000 0004 4910 6535Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, 91190 Gif-sur-Yvette, France
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Salgotra RK, Stewart CN. Genetic Augmentation of Legume Crops Using Genomic Resources and Genotyping Platforms for Nutritional Food Security. PLANTS 2022; 11:plants11141866. [PMID: 35890499 PMCID: PMC9325189 DOI: 10.3390/plants11141866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 11/24/2022]
Abstract
Recent advances in next generation sequencing (NGS) technologies have led the surge of genomic resources for the improvement legume crops. Advances in high throughput genotyping (HTG) and high throughput phenotyping (HTP) enable legume breeders to improve legume crops more precisely and efficiently. Now, the legume breeder can reshuffle the natural gene combinations of their choice to enhance the genetic potential of crops. These genomic resources are efficiently deployed through molecular breeding approaches for genetic augmentation of important legume crops, such as chickpea, cowpea, pigeonpea, groundnut, common bean, lentil, pea, as well as other underutilized legume crops. In the future, advances in NGS, HTG, and HTP technologies will help in the identification and assembly of superior haplotypes to tailor the legume crop varieties through haplotype-based breeding. This review article focuses on the recent development of genomic resource databases and their deployment in legume molecular breeding programmes to secure global food security.
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Affiliation(s)
- Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu 190008, India
- Correspondence: (R.K.S.); (C.N.S.J.)
| | - Charles Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
- Correspondence: (R.K.S.); (C.N.S.J.)
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Alemu A, Brantestam AK, Chawade A. Unraveling the Genetic Basis of Key Agronomic Traits of Wrinkled Vining Pea ( Pisum sativum L.) for Sustainable Production. FRONTIERS IN PLANT SCIENCE 2022; 13:844450. [PMID: 35360298 PMCID: PMC8964273 DOI: 10.3389/fpls.2022.844450] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Estimating the allelic variation and exploring the genetic basis of quantitatively inherited complex traits are the two foremost breeding scenarios for sustainable crop production. The current study utilized 188 wrinkled vining pea genotypes comprising historical varieties and breeding lines to evaluate the existing genetic diversity and to detect molecular markers associated with traits relevant to vining pea production, such as wrinkled vining pea yield (YTM100), plant height (PH), earliness (ERL), adult plant resistance to downy mildew (DM), pod length (PDL), numbers of pods per plant (PDP), number of peas per pod (PPD), and percent of small wrinkled vining peas (PSP). Marker-trait associations (MTAs) were conducted using 6902 quality single nucleotide polymorphism (SNP) markers generated from the diversity arrays technology sequencing (DArTseq) and Genotyping-by-sequencing (GBS) sequencing methods. The best linear unbiased prediction (BLUP) values were estimated from the two-decades-long (1999-2020) unbalanced phenotypic data sets recorded from two private breeding programs, the Findus and the Birds eye, now owned by Nomad Foods. Analysis of variance revealed a highly significant variation between genotypes and genotype-by-environment interactions for the ten traits. The genetic diversity and population structure analyses estimated an intermediate level of genetic variation with two optimal sub-groups within the current panel. A total of 48 significant (P < 0.0001) MTAs were identified for eight different traits, including five for wrinkled vining pea yield on chr2LG1, chr4LG4, chr7LG7, and scaffolds (two), and six for adult plant resistance to downy mildew on chr1LG6, chr3LG5 (two), chr6LG2, and chr7LG7 (two). We reported several novel MTAs for different crucial traits with agronomic importance in wrinkled vining pea production for the first time, and these candidate markers could be easily validated and integrated into the active breeding programs for marker-assisted selection.
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Affiliation(s)
- Admas Alemu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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QTL Mapping of Resistance to Bacterial Wilt in Pepper Plants (Capsicum annuum) Using Genotyping-by-Sequencing (GBS). HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020115] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Bacterial wilt (BW) disease, which is caused by Ralstonia solanacearum, is one globally prevalent plant disease leading to significant losses of crop production and yield with the involvement of a diverse variety of monocot and dicot host plants. In particular, the BW of the soil-borne disease seriously influences solanaceous crops, including peppers (sweet and chili peppers), paprika, tomatoes, potatoes, and eggplants. Recent studies have explored genetic regions that are associated with BW resistance for pepper crops. However, owing to the complexity of BW resistance, the identification of the genomic regions controlling BW resistance is poorly understood and still remains to be unraveled in the pepper cultivars. In this study, we performed the quantitative trait loci (QTL) analysis to identify genomic loci and alleles, which play a critical role in the resistance to BW in pepper plants. The disease symptoms and resistance levels for BW were assessed by inoculation with R. solanacearum. Genotyping-by-sequencing (GBS) was utilized in 94 F2 segregating populations originated from a cross between a resistant line, KC352, and a susceptible line, 14F6002-14. A total of 628,437 single-nucleotide polymorphism (SNP) was obtained, and a pepper genetic linkage map was constructed with putative 1550 SNP markers via the filtering criteria. The linkage map exhibited 16 linkage groups (LG) with a total linkage distance of 828.449 cM. Notably, QTL analysis with CIM (composite interval mapping) method uncovered pBWR-1 QTL underlying on chromosome 01 and explained 20.13 to 25.16% by R2 (proportion of explained phenotyphic variance by the QTL) values. These results will be valuable for developing SNP markers associated with BW-resistant QTLs as well as for developing elite BW-resistant cultivars in pepper breeding programs.
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Díaz BG, Zucchi MI, Alves‐Pereira A, de Almeida CP, Moraes ACL, Vianna SA, Azevedo-Filho J, Colombo CA. Genome-wide SNP analysis to assess the genetic population structure and diversity of Acrocomia species. PLoS One 2021; 16:e0241025. [PMID: 34283830 PMCID: PMC8291712 DOI: 10.1371/journal.pone.0241025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 07/05/2021] [Indexed: 01/01/2023] Open
Abstract
Acrocomia (Arecaceae) is a genus widely distributed in tropical and subtropical America that has been achieving economic interest due to the great potential of oil production of some of its species. In particular A. aculeata, due to its vocation to supply oil with the same productive capacity as the oil palm (Elaeis guineenses) even in areas with water deficit. Although eight species are recognized in the genus, the taxonomic classification based on morphology and geographic distribution is still controversial. Knowledge about the genetic diversity and population structure of the species is limited, which has limited the understanding of the genetic relationships and the orientation of management, conservation, and genetic improvement activities of species of the genus. In the present study, we analyzed the genomic diversity and population structure of Acrocomia genus, including 172 samples from seven species, with a focus on A. aculeata with 117 samples covering a wide geographical area of occurrence of the species, using Single Nucleotide Polymorphism (SNP) markers originated from Genotyping By Sequencing (GBS).The genetic structure of the Acrocomia species were partially congruent with the current taxonomic classification based on morphological characters, recovering the separation of the species A. aculeata, A. totai, A. crispa and A. intumescens as distinct taxonomic groups. However, the species A. media was attributed to the cluster of A. aculeata while A. hassleri and A. glauscescens were grouped together with A. totai. The species that showed the highest and lowest genetic diversity were A. totai and A. media, respectively. When analyzed separately, the species A. aculeata showed a strong genetic structure, forming two genetic groups, the first represented mainly by genotypes from Brazil and the second by accessions from Central and North American countries. Greater genetic diversity was found in Brazil when compared to the other countries. Our results on the genetic diversity of the genus are unprecedented, as is also establishes new insights on the genomic relationships between Acrocomia species. It is also the first study to provide a more global view of the genomic diversity of A. aculeata. We also highlight the applicability of genomic data as a reference for future studies on genetic diversity, taxonomy, evolution and phylogeny of the Acrocomia genus, as well as to support strategies for the conservation, exploration and breeding of Acrocomia species and in particular A. aculeata.
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Affiliation(s)
| | - Maria Imaculada Zucchi
- Biology Institute, University of Campinas UNICAMP, Campinas-SP, Brazil
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico-IAC, Campinas-SP, Brazil
| | | | - Caléo Panhoca de Almeida
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico-IAC, Campinas-SP, Brazil
| | | | - Suelen Alves Vianna
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico-IAC, Campinas-SP, Brazil
| | - Joaquim Azevedo-Filho
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico-IAC, Campinas-SP, Brazil
| | - Carlos Augusto Colombo
- Centro de Pesquisa de Recursos Genéticos Vegetais, Instituto Agronômico-IAC, Campinas-SP, Brazil
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12
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Kumar P, Choudhary M, Jat BS, Kumar B, Singh V, Kumar V, Singla D, Rakshit S. Skim sequencing: an advanced NGS technology for crop improvement. J Genet 2021. [DOI: 10.1007/s12041-021-01285-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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13
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Pandey AK, Rubiales D, Wang Y, Fang P, Sun T, Liu N, Xu P. Omics resources and omics-enabled approaches for achieving high productivity and improved quality in pea (Pisum sativum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2021; 134:755-776. [PMID: 33433637 DOI: 10.1007/s00122-020-03751-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Accepted: 12/10/2020] [Indexed: 05/09/2023]
Abstract
Pea (Pisum sativum L.), a cool-season legume crop grown in more than 85 countries, is the second most important grain legume and one of the major green vegetables in the world. While pea was historically studied as the genetic model leading to the discovery of the laws of genetics, pea research has lagged behind that of other major legumes in the genomics era, due to its large and complex genome. The evolving climate change and growing population have posed grand challenges to the objective of feeding the world, making it essential to invest research efforts to develop multi-omics resources and advanced breeding tools to support fast and continuous development of improved pea varieties. Recently, the pea researchers have achieved key milestones in omics and molecular breeding. The present review provides an overview of the recent important progress including the development of genetic resource databases, high-throughput genotyping assays, reference genome, genes/QTLs responsible for important traits, transcriptomic, proteomic, and phenomic atlases of various tissues under different conditions. These multi-faceted resources have enabled the successful implementation of various markers for monitoring early-generation populations as in marker-assisted backcrossing breeding programs. The emerging new breeding approaches such as CRISPR, speed breeding, and genomic selection are starting to change the paradigm of pea breeding. Collectively, the rich omics resources and omics-enable breeding approaches will enhance genetic gain in pea breeding and accelerate the release of novel pea varieties to meet the elevating demands on productivity and quality.
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Affiliation(s)
- Arun K Pandey
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, 14004, Córdoba, Spain
| | - Yonggang Wang
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Pingping Fang
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Ting Sun
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China
| | - Na Liu
- Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | - Pei Xu
- College of Life Sciences, China Jiliang University, Hangzhou, 310018, China.
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14
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Borges dos Santos L, Paulo Gomes Viana J, José Biasotto Francischini F, Victoria Fogliata S, L. Joyce A, Pereira de Souza A, Gabriela Murúa M, J. Clough S, Imaculada Zucchi M. A first draft genome of the Sugarcane borer, Diatraea saccharalis. F1000Res 2020. [DOI: 10.12688/f1000research.26614.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Background: The sugarcane borer (Diatraea saccharalis), a widely distributed moth throughout the Americas, is a pest that affects economically important crops such as sugarcane, sorghum, wheat, maize and rice. Given its significant impact on yield reduction, whole-genome information of the species is needed. Here, we report the first draft assembly of the D. saccharalis genome. Methods: The genomic sequences were obtained using the Illumina HiSeq 2500 whole-genome sequencing of a single adult male specimen. We assembled the short-reads using the SPAdes software and predicted protein-coding genes using MAKER. Genome assembly completeness was assessed through BUSCO and the repetitive content by RepeatMasker. Results: The 453 Mb assembled sequences contain 1,445 BUSCO gene orthologs and 1,161 predicted gene models identified based on homology evidence to the domestic silk moth, Bombyx mori. The repeat content composes 41.18% of the genomic sequences which is in the range of other lepidopteran species. Conclusions: Functional annotation reveals that predicted gene models are involved in important cellular mechanisms such as metabolic pathways and protein synthesis. Thus, the data generated in this study expands our knowledge on the genomic characteristics of this devastating pest and provides essential resources for future genetic studies of the species.
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15
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Yao Z, You FM, N'Diaye A, Knox RE, McCartney C, Hiebert CW, Pozniak C, Xu W. Evaluation of variant calling tools for large plant genome re-sequencing. BMC Bioinformatics 2020; 21:360. [PMID: 32807073 PMCID: PMC7430858 DOI: 10.1186/s12859-020-03704-1] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 07/28/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Discovering single nucleotide polymorphisms (SNPs) from agriculture crop genome sequences has been a widely used strategy for developing genetic markers for several applications including marker-assisted breeding, population diversity studies for eco-geographical adaption, genotyping crop germplasm collections, and others. Accurately detecting SNPs from large polyploid crop genomes such as wheat is crucial and challenging. A few variant calling methods have been previously developed but they show a low concordance between their variant calls. A gold standard of variant sets generated from one human individual sample was established for variant calling tool evaluations, however hitherto no gold standard of crop variant set is available for wheat use. The intent of this study was to evaluate seven SNP variant calling tools (FreeBayes, GATK, Platypus, Samtools/mpileup, SNVer, VarScan, VarDict) with the two most popular mapping tools (BWA-mem and Bowtie2) on wheat whole exome capture (WEC) re-sequencing data from allohexaploid wheat. RESULTS We found the BWA-mem mapping tool had both a higher mapping rate and a higher accuracy rate than Bowtie2. With the same mapping quality (MQ) cutoff, BWA-mem detected more variant bases in mapping reads than Bowtie2. The reads preprocessed with quality trimming or duplicate removal did not significantly affect the final mapping performance in terms of mapped reads. Based on the concordance and receiver operating characteristic (ROC), the Samtools/mpileup variant calling tool with BWA-mem mapping of raw sequence reads outperformed other tests followed by FreeBayes and GATK in terms of specificity and sensitivity. VarDict and VarScan were the poorest performing variant calling tools with the wheat WEC sequence data. CONCLUSION The BWA-mem and Samtools/mpileup pipeline, with no need to preprocess the raw read data before mapping onto the reference genome, was ascertained the optimum for SNP calling for the complex wheat genome re-sequencing. These results also provide useful guidelines for reliable variant identification from deep sequencing of other large polyploid crop genomes.
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Affiliation(s)
- Zhen Yao
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, Manitoba, R6M 1Y5, Canada
| | - Frank M You
- Ottawa Research and Development Centre, Agriculture and Agri-Food Canada, 960 Carling Avenue, Ottawa, Ontario, K1A 0C6, Canada
| | - Amidou N'Diaye
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5A8, Canada
| | - Ron E Knox
- Swift Current Research and Development Centre, Agriculture and Agri-Food Canada, Box 1030, Swift Current, Saskatchewan, S9H 3X2, Canada
| | - Curt McCartney
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, Manitoba, R6M 1Y5, Canada
| | - Colin W Hiebert
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, Manitoba, R6M 1Y5, Canada
| | - Curtis Pozniak
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5A8, Canada
| | - Wayne Xu
- Morden Research and Development Centre, Agriculture and Agri-Food Canada, 101 Route 100, Morden, Manitoba, R6M 1Y5, Canada.
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16
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Barilli E, Carrillo-Perdomo E, Cobos MJ, Kilian A, Carling J, Rubiales D. Identification of potential candidate genes controlling pea aphid tolerance in a Pisum fulvum high-density integrated DArTseq SNP-based genetic map. PEST MANAGEMENT SCIENCE 2020; 76:1731-1742. [PMID: 31758624 DOI: 10.1002/ps.5696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 11/08/2019] [Accepted: 11/20/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Pea (Pisum sativum) is one of the most important temperate grain legumes in the world, and its production is severely constrained by the pea aphid (Acyrthosiphon pisum). Wild relatives, such as P. fulvum, are valuable sources of allelic diversity to improve the genetic resistance of cultivated pea species against A. pisum attack. To unravel the genetic control underlying resistance to the pea aphid attack, a quantitative trait loci (QTL) analysis was performed using the previously developed high density integrated genetic linkage map originated from an intraspecific recombinant inbred line (RIL) population (P. fulvum: IFPI3260 × IFPI3251). RESULTS We accurately evaluated specific resistance responses to pea aphid that allowed the identification, for the first time, of genomic regions that control plant damage and aphid reproduction. Eight QTLs associated with tolerance to pea aphid were identified in LGs I, II, III, IV and V, which individually explained from 17.0% to 51.2% of the phenotypic variation depending on the trait scored, and as a whole from 17.0% to 88.6%. The high density integrated genetic linkage map also allowed the identification of potential candidate genes co-located with the QTLs identified. CONCLUSIONS Our work shows how the survival of P. fulvum after the pea aphid attack depends on the triggering of a multi-component protection strategy that implies a quantitative tolerance. The genomic regions associated with the tolerance responses of P. fulvum during A. pisum infestation have provided six potential candidate genes that could be useful in marker-assisted selection (MAS) and genomic assisted breeding (GAB) after functional validation in the future. © 2019 Society of Chemical Industry.
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Affiliation(s)
| | - Estefanía Carrillo-Perdomo
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
- Current address: Agroécologie, AgroSup Dijon, INRAE, Univ. Bourgogne, Univ. Bourgogne Franche-Comté, F-21000 Dijon, France
| | | | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Canberra, Australia
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, University of Canberra, Canberra, Australia
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
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Sanderson LA, Caron CT, Tan R, Shen Y, Liu R, Bett KE. KnowPulse: A Web-Resource Focused on Diversity Data for Pulse Crop Improvement. FRONTIERS IN PLANT SCIENCE 2019; 10:965. [PMID: 31428111 PMCID: PMC6690010 DOI: 10.3389/fpls.2019.00965] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 07/10/2019] [Indexed: 05/25/2023]
Abstract
KnowPulse (https://knowpulse.usask.ca) is a breeder-focused web portal for pulse breeders and geneticists. With a focus on diversity data, KnowPulse provides information on genetic markers, sequence variants, phenotypic traits and germplasm for chickpea, common bean, field pea, faba bean, and lentil. Genotypic data is accessible through the genotype matrix tool, displayed as a marker-by-germplasm table of genotype calls specific to germplasm chosen by the researcher. It is also summarized on genetic marker and sequence variant pages. Phenotypic data is visualized in trait distribution plots: violin plots for quantitative data and histograms for qualitative data. These plots are accessible through trait, germplasm, and experiment pages, as well as through a single page search tool. KnowPulse is built using the open-source Tripal toolkit and utilizes open-source tools including, but not limited to, species-specific JBrowse instances, a BLAST interface, and whole-genome CViTjs visualizations. KnowPulse is constantly evolving with data and tools added as they become available. Full integration of genetic maps and quantitative trait loci is imminent, and development of tools exploring structural variation is being explored.
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Affiliation(s)
| | | | | | | | | | - Kirstin E. Bett
- Department of Plant Sciences, University of Saskatchewan, Saskatoon, SK, Canada
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18
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Zwane AA, Schnabel RD, Hoff J, Choudhury A, Makgahlela ML, Maiwashe A, Van Marle-Koster E, Taylor JF. Genome-Wide SNP Discovery in Indigenous Cattle Breeds of South Africa. Front Genet 2019; 10:273. [PMID: 30988672 PMCID: PMC6452414 DOI: 10.3389/fgene.2019.00273] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 03/12/2019] [Indexed: 01/30/2023] Open
Abstract
Single nucleotide polymorphism arrays have created new possibilities for performing genome-wide studies to detect genomic regions harboring sequence variants that affect complex traits. However, the majority of validated SNPs for which allele frequencies have been estimated are limited primarily to European breeds. The objective of this study was to perform SNP discovery in three South African indigenous breeds (Afrikaner, Drakensberger, and Nguni) using whole genome sequencing. DNA was extracted from blood and hair samples, quantified and prepared at 50 ng/μl concentration for sequencing at the Agricultural Research Council Biotechnology Platform using an Illumina HiSeq 2500. The fastq files were used to call the variants using the Genome Analysis Tool Kit. A total of 1,678,360 were identified as novel using Run 6 of 1000 Bull Genomes Project. Annotation of the identified variants classified them into functional categories. Within the coding regions, about 30% of the SNPs were non-synonymous substitutions that encode for alternate amino acids. The study of distribution of SNP across the genome identified regions showing notable differences in the densities of SNPs among the breeds and highlighted many regions of functional significance. Gene ontology terms identified genes such as MLANA, SYT10, and CDC42EP5 that have been associated with coat color in mouse, and ADAMS3, DNAJC3, and PAG5 genes have been associated with fertility in cattle. Further analysis of the variants detected 688 candidate selective sweeps (ZHp Z-scores ≤ -4) across all three breeds, of which 223 regions were assigned as being putative selective sweeps (ZHp scores ≤-5). We also identified 96 regions with extremely low ZHp Z-scores (≤-6) in Afrikaner and Nguni. Genes such as KIT and MITF that have been associated with skin pigmentation in cattle and CACNA1C, which has been associated with biopolar disorder in human, were identified in these regions. This study provides the first analysis of sequence data to discover SNPs in indigenous South African cattle breeds. The information will play an important role in our efforts to understand the genetic history of our cattle and in designing appropriate breed improvement programmes.
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Affiliation(s)
- Avhashoni A. Zwane
- Department of Animal Breeding and Genetics, Agricultural Research Council-Animal Production, Irene, South Africa
- Department of Animal and Wildlife Sciences, University of Pretoria, Pretoria, South Africa
| | - Robert D. Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
- Informatics Institute, University of Missouri, Columbia, MO, United States
| | - Jesse Hoff
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
| | - Ananyo Choudhury
- Sydney Brenner Institute of Molecular Bioscience, University of the Witwatersrand, Johannesburg, South Africa
| | - Mahlako Linah Makgahlela
- Department of Animal Breeding and Genetics, Agricultural Research Council-Animal Production, Irene, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - Azwihangwisi Maiwashe
- Department of Animal Breeding and Genetics, Agricultural Research Council-Animal Production, Irene, South Africa
- Department of Animal, Wildlife and Grassland Sciences, University of the Free State, Bloemfontein, South Africa
| | - Este Van Marle-Koster
- Department of Animal and Wildlife Sciences, University of Pretoria, Pretoria, South Africa
| | - Jeremy F. Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States
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Coyne CJ, Porter LD, Boutet G, Ma Y, McGee RJ, Lesné A, Baranger A, Pilet-Nayel ML. Confirmation of Fusarium root rot resistance QTL Fsp-Ps 2.1 of pea under controlled conditions. BMC PLANT BIOLOGY 2019; 19:98. [PMID: 30866817 PMCID: PMC6417171 DOI: 10.1186/s12870-019-1699-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 02/28/2019] [Indexed: 05/07/2023]
Abstract
BACKGROUND Dry pea production has increased substantially in North America over the last few decades. With this expansion, significant yield losses have been attributed to an escalation in Fusarium root rots in pea fields. Among the most significant rot rotting pathogenic fungal species, Fusarium solani fsp. pisi (Fsp) is one of the main causal agents of root rot of pea. High levels of partial resistance to Fsp has been identified in plant genetic resources. Genetic resistance offers one of the best solutions to control this root rotting fungus. A recombinant inbred population segregating for high levels of partial resistance, previously single nucleotide polymorphism (SNP) genotyped using genotyping-by-sequencing, was phenotyped for disease reaction in replicated and repeated greenhouse trials. Composite interval mapping was deployed to identify resistance-associated quantitative trait loci (QTL). RESULTS Three QTL were identified using three disease reaction criteria: root disease severity, ratios of diseased vs. healthy shoot heights and dry plant weights under controlled conditions using pure cultures of Fusarium solani fsp. pisi. One QTL Fsp-Ps 2.1 explains 44.4-53.4% of the variance with a narrow confidence interval of 1.2 cM. The second and third QTL Fsp-Ps3.2 and Fsp-Ps3.3 are closely linked and explain only 3.6-4.6% of the variance. All of the alleles are contributed by the resistant parent PI 180693. CONCLUSION With the confirmation of Fsp-Ps 2.1 now in two RIL populations, SNPs associated with this region make a good target for marker-assisted selection in pea breeding programs to obtain high levels of partial resistance to Fusarium root rot caused by Fusarium solani fsp. pisi.
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Affiliation(s)
- Clarice J. Coyne
- USDA-ARS Plant Germplasm Introduction & Testing Research, Washington State University, Pullman, WA 99164 USA
| | - Lyndon D. Porter
- USDA-ARS Grain Legume Genetics & Physiology Research, 24106 N. Bunn Road, Prosser, WA 99350 USA
| | - Gilles Boutet
- Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université Rennes 1, 35650 Le Rheu, France
| | - Yu Ma
- Department of Horticulture, Washington State University, Pullman, WA 99164 USA
| | - Rebecca J. McGee
- USDA-ARS, Grain Legume Genetics & Physiology Research, Pullman, WA 99164 USA
| | - Angélique Lesné
- Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université Rennes 1, 35650 Le Rheu, France
| | - Alain Baranger
- Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université Rennes 1, 35650 Le Rheu, France
| | - Marie-Laure Pilet-Nayel
- Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université Rennes 1, 35650 Le Rheu, France
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20
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Paudel L, Clevenger J, McGregor C. Chromosomal Locations and Interactions of Four Loci Associated With Seed Coat Color in Watermelon. FRONTIERS IN PLANT SCIENCE 2019; 10:788. [PMID: 31293604 PMCID: PMC6603093 DOI: 10.3389/fpls.2019.00788] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 05/29/2019] [Indexed: 05/13/2023]
Abstract
Different species of edible seed watermelons (Citrullus spp.) are cultivated in Asia and Africa for their colorful nutritious seeds. Consumer preference varies for watermelon seed coat color. Therefore, it is an important consideration for watermelon breeders. In 1940s, a genetic model of four genes, R, T, W and D, was proposed to elucidate the inheritance of seed coat color in watermelon. In this study, we developed three segregating F2 populations: Sugar Baby (dotted black seed, RRTTWW) × plant introduction (PI) 482379 (green seed, rrTTWW), Charleston Gray (dotted black seed, RRTTWW) × PI 189225 (red seed, rrttWW), and Charleston Gray (dotted black seed, RRTTWWdd) × UGA147 (clump seed, RRTTwwDD) to re-examine the four-gene model and to map the four genes. In the dotted black × green population, the dotted black seed coat color (R_) is dominant to green seed coat color (rr). In the dotted black × red population, the dominant dotted black seed coat color and the recessive red seed coat color segregate for the R and T genes, where the R gene is dominantly epistatic to the T gene. However, the inheritance of the T locus did not fit the four-gene model, thus we named it T1 . In the dotted black × clump population, the clump seed coat color and the dotted black seed coat color segregate for W and D, where D is recessively epistatic to W. The R, T1 , W, and D loci were mapped on chromosomes 3, 5, 6, and 8, respectively, using QTL-seq and genotyping-by-sequencing (GBS). Kompetitive Allele Specific PCR (KASP™) assays and SNP markers linked to the four loci were developed to facilitate maker-assisted selection (MAS) for watermelon seed coat color.
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Affiliation(s)
- Lucky Paudel
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Josh Clevenger
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Cecilia McGregor
- Institute for Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Department of Horticulture, University of Georgia, Athens, GA, United States
- *Correspondence: Cecilia McGregor,
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Malmberg MM, Barbulescu DM, Drayton MC, Shinozuka M, Thakur P, Ogaji YO, Spangenberg GC, Daetwyler HD, Cogan NOI. Evaluation and Recommendations for Routine Genotyping Using Skim Whole Genome Re-sequencing in Canola. FRONTIERS IN PLANT SCIENCE 2018; 9:1809. [PMID: 30581450 PMCID: PMC6292936 DOI: 10.3389/fpls.2018.01809] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 11/21/2018] [Indexed: 05/25/2023]
Abstract
Whole genome sequencing offers genome wide, unbiased markers, and inexpensive library preparation. With the cost of sequencing decreasing rapidly, many plant genomes of modest size are amenable to skim whole genome resequencing (skim WGR). The use of skim WGR in diverse sample sets without the use of imputation was evaluated in silico in 149 canola samples representative of global diversity. Fastq files with an average of 10x coverage of the reference genome were used to generate skim samples representing 0.25x, 0.5x, 1x, 2x, 3x, 4x, and 5x sequencing coverage. Applying a pre-defined list of SNPs versus de novo SNP discovery was evaluated. As skim WGR is expected to result in some degree of insufficient allele sampling, all skim coverage levels were filtered at a range of minimum read depths from a relaxed minimum read depth of 2 to a stringent read depth of 5, resulting in 28 list-based SNP sets. As a broad recommendation, genotyping pre-defined SNPs between 1x and 2x coverage with relatively stringent depth filtering is appropriate for a diverse sample set of canola due to a balance between marker number, sufficient accuracy, and sequencing cost, but depends on the intended application. This was experimentally examined in two sample sets with different genetic backgrounds: 1x coverage of 1,590 individuals from 84 Australian spring type four-parent crosses aimed at maximizing diversity as well as one commercial F1 hybrid, and 2x coverage of 379 doubled haploids (DHs) derived from a subset of the four-parent crosses. To determine optimal coverage in a simpler genetic background, the DH sample sequence coverage was further down sampled in silico. The flexible and cost-effective nature of the protocol makes it highly applicable across a range of species and purposes.
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Affiliation(s)
- M. Michelle Malmberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | | | - Michelle C. Drayton
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Maiko Shinozuka
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Preeti Thakur
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - Yvonne O. Ogaji
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
| | - German C. Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Hans D. Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Noel O. I. Cogan
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
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22
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Agarwal G, Clevenger J, Pandey MK, Wang H, Shasidhar Y, Chu Y, Fountain JC, Choudhary D, Culbreath AK, Liu X, Huang G, Wang X, Deshmukh R, Holbrook CC, Bertioli DJ, Ozias‐Akins P, Jackson SA, Varshney RK, Guo B. High-density genetic map using whole-genome resequencing for fine mapping and candidate gene discovery for disease resistance in peanut. PLANT BIOTECHNOLOGY JOURNAL 2018; 16:1954-1967. [PMID: 29637729 PMCID: PMC6181220 DOI: 10.1111/pbi.12930] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/28/2018] [Accepted: 03/25/2018] [Indexed: 05/04/2023]
Abstract
Whole-genome resequencing (WGRS) of mapping populations has facilitated development of high-density genetic maps essential for fine mapping and candidate gene discovery for traits of interest in crop species. Leaf spots, including early leaf spot (ELS) and late leaf spot (LLS), and Tomato spotted wilt virus (TSWV) are devastating diseases in peanut causing significant yield loss. We generated WGRS data on a recombinant inbred line population, developed a SNP-based high-density genetic map, and conducted fine mapping, candidate gene discovery and marker validation for ELS, LLS and TSWV. The first sequence-based high-density map was constructed with 8869 SNPs assigned to 20 linkage groups, representing 20 chromosomes, for the 'T' population (Tifrunner × GT-C20) with a map length of 3120 cM and an average distance of 1.45 cM. The quantitative trait locus (QTL) analysis using high-density genetic map and multiple season phenotyping data identified 35 main-effect QTLs with phenotypic variation explained (PVE) from 6.32% to 47.63%. Among major-effect QTLs mapped, there were two QTLs for ELS on B05 with 47.42% PVE and B03 with 47.38% PVE, two QTLs for LLS on A05 with 47.63% and B03 with 34.03% PVE and one QTL for TSWV on B09 with 40.71% PVE. The epistasis and environment interaction analyses identified significant environmental effects on these traits. The identified QTL regions had disease resistance genes including R-genes and transcription factors. KASP markers were developed for major QTLs and validated in the population and are ready for further deployment in genomics-assisted breeding in peanut.
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Affiliation(s)
- Gaurav Agarwal
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Josh Clevenger
- Center for Applied Genetic TechnologiesMars Wrigley ConfectioneryAthensGAUSA
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - Manish K. Pandey
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Hui Wang
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | - Yaduru Shasidhar
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Ye Chu
- Department of Horticulture and Institute of Plant Breeding & GenomicsUniversity of GeorgiaTiftonGAUSA
| | - Jake C. Fountain
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | - Divya Choudhary
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
- Department of Plant PathologyUniversity of GeorgiaTiftonGAUSA
| | | | | | | | - Xingjun Wang
- Shandong Academy of Agricultural SciencesBiotechnology Research CenterJinanChina
| | | | | | - David J. Bertioli
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - Peggy Ozias‐Akins
- Department of Horticulture and Institute of Plant Breeding & GenomicsUniversity of GeorgiaTiftonGAUSA
| | - Scott A. Jackson
- Center for Applied Genetic TechnologiesUniversity of GeorgiaAthensGAUSA
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems BiologyInternational Crops Research Institute for the Semi‐Arid Tropics (ICRISAT)HyderabadIndia
| | - Baozhu Guo
- Crop Protection and Management Research UnitUSDA‐ARSTiftonGAUSA
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23
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D'Agostino N, Taranto F, Camposeo S, Mangini G, Fanelli V, Gadaleta S, Miazzi MM, Pavan S, di Rienzo V, Sabetta W, Lombardo L, Zelasco S, Perri E, Lotti C, Ciani E, Montemurro C. GBS-derived SNP catalogue unveiled wide genetic variability and geographical relationships of Italian olive cultivars. Sci Rep 2018; 8:15877. [PMID: 30367101 PMCID: PMC6203791 DOI: 10.1038/s41598-018-34207-y] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 10/12/2018] [Indexed: 11/08/2022] Open
Abstract
Information on the distribution of genetic variation is essential to preserve olive germplasm from erosion and to recover alleles lost through selective breeding. In addition, knowledge on population structure and genotype-phenotype associations is crucial to support modern olive breeding programs that must respond to new environmental conditions imposed by climate change and novel biotic/abiotic stressors. To further our understanding of genetic variation in the olive, we performed genotype-by-sequencing on a panel of 94 Italian olive cultivars. A reference-based and a reference-independent SNP calling pipeline generated 22,088 and 8,088 high-quality SNPs, respectively. Both datasets were used to model population structure via parametric and non parametric clustering. Although the two pipelines yielded a 3-fold difference in the number of SNPs, both described wide genetic variability among our study panel and allowed individuals to be grouped based on fruit weight and the geographical area of cultivation. Multidimensional scaling analysis on identity-by-state allele-sharing values as well as inference of population mixtures from genome-wide allele frequency data corroborated the clustering pattern we observed. These findings allowed us to formulate hypotheses about geographical relationships of Italian olive cultivars and to confirm known and uncover novel cases of synonymy.
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Affiliation(s)
- Nunzio D'Agostino
- CREA Research Centre for Vegetable and Ornamental Crops, Pontecagnano Faiano, Italy.
| | - Francesca Taranto
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy.
| | - Salvatore Camposeo
- Department of Agricultural and Environmental sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Giacomo Mangini
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Valentina Fanelli
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy
| | - Susanna Gadaleta
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy
| | - Monica Marilena Miazzi
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Stefano Pavan
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Valentina di Rienzo
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy
| | - Wilma Sabetta
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy
| | - Luca Lombardo
- Center for Agriculture, Food ad Environment (C3A), University of Trento, San Michele all'Adige, Italy
| | - Samanta Zelasco
- CREA Research Centre for Olive, Citrus and Tree Fruit, Rende, Italy
| | - Enzo Perri
- CREA Research Centre for Olive, Citrus and Tree Fruit, Rende, Italy
| | - Concetta Lotti
- Department of the Sciences of Agriculture, Food and Environment, University of Foggia, Foggia, Italy
| | - Elena Ciani
- Department of Biosciences, Biotechnologies and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Cinzia Montemurro
- SINAGRI S.r.l. - Spin Off of the University of Bari "Aldo Moro", Bari, Italy
- Department of Soil, Plant and Food Sciences, University of Bari "Aldo Moro", Bari, Italy
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24
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Conson ARO, Taniguti CH, Amadeu RR, Andreotti IAA, de Souza LM, dos Santos LHB, Rosa JRBF, Mantello CC, da Silva CC, José Scaloppi Junior E, Ribeiro RV, Le Guen V, Garcia AAF, Gonçalves PDS, de Souza AP. High-Resolution Genetic Map and QTL Analysis of Growth-Related Traits of Hevea brasiliensis Cultivated Under Suboptimal Temperature and Humidity Conditions. FRONTIERS IN PLANT SCIENCE 2018; 9:1255. [PMID: 30197655 PMCID: PMC6117502 DOI: 10.3389/fpls.2018.01255] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 08/08/2018] [Indexed: 06/02/2023]
Abstract
Rubber tree (Hevea brasiliensis) cultivation is the main source of natural rubber worldwide and has been extended to areas with suboptimal climates and lengthy drought periods; this transition affects growth and latex production. High-density genetic maps with reliable markers support precise mapping of quantitative trait loci (QTL), which can help reveal the complex genome of the species, provide tools to enhance molecular breeding, and shorten the breeding cycle. In this study, QTL mapping of the stem diameter, tree height, and number of whorls was performed for a full-sibling population derived from a GT1 and RRIM701 cross. A total of 225 simple sequence repeats (SSRs) and 186 single-nucleotide polymorphism (SNP) markers were used to construct a base map with 18 linkage groups and to anchor 671 SNPs from genotyping by sequencing (GBS) to produce a very dense linkage map with small intervals between loci. The final map was composed of 1,079 markers, spanned 3,779.7 cM with an average marker density of 3.5 cM, and showed collinearity between markers from previous studies. Significant variation in phenotypic characteristics was found over a 59-month evaluation period with a total of 38 QTLs being identified through a composite interval mapping method. Linkage group 4 showed the greatest number of QTLs (7), with phenotypic explained values varying from 7.67 to 14.07%. Additionally, we estimated segregation patterns, dominance, and additive effects for each QTL. A total of 53 significant effects for stem diameter were observed, and these effects were mostly related to additivity in the GT1 clone. Associating accurate genome assemblies and genetic maps represents a promising strategy for identifying the genetic basis of phenotypic traits in rubber trees. Then, further research can benefit from the QTLs identified herein, providing a better understanding of the key determinant genes associated with growth of Hevea brasiliensis under limiting water conditions.
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Affiliation(s)
- André R. O. Conson
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | - Cristiane H. Taniguti
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Rodrigo R. Amadeu
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Livia M. de Souza
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | | | - João R. B. F. Rosa
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
- FTS Sementes S.A., Research and Development Center, Ponta Grossa, Brazil
| | - Camila C. Mantello
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- National Institute of Agricultural Botany (NIAB), Cambridge, United Kingdom
| | - Carla C. da Silva
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
| | | | - Rafael V. Ribeiro
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
| | - Vincent Le Guen
- French Agricultural Research Centre for International Development (CIRAD), UMR AGAP, Montpellier, France
| | - Antonio A. F. Garcia
- Department of Genetics, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Anete P. de Souza
- Molecular Biology and Genetic Engineering Center, University of Campinas, Campinas, Brazil
- Department of Plant Biology, Institute of Biology, University of Campinas, Campinas, Brazil
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25
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Gali KK, Liu Y, Sindhu A, Diapari M, Shunmugam ASK, Arganosa G, Daba K, Caron C, Lachagari RVB, Tar’an B, Warkentin TD. Construction of high-density linkage maps for mapping quantitative trait loci for multiple traits in field pea (Pisum sativum L.). BMC PLANT BIOLOGY 2018; 18:172. [PMID: 30115030 PMCID: PMC6097431 DOI: 10.1186/s12870-018-1368-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 07/20/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND The objective of this research was to map quantitative trait loci (QTLs) of multiple traits of breeding importance in pea (Pisum sativum L.). Three recombinant inbred line (RIL) populations, PR-02 (Orb x CDC Striker), PR-07 (Carerra x CDC Striker) and PR-15 (1-2347-144 x CDC Meadow) were phenotyped for agronomic and seed quality traits under field conditions over multiple environments in Saskatchewan, Canada. The mapping populations were genotyped using genotyping-by-sequencing (GBS) method for simultaneous single nucleotide polymorphism (SNP) discovery and construction of high-density linkage maps. RESULTS After filtering for read depth, segregation distortion, and missing values, 2234, 3389 and 3541 single nucleotide polymorphism (SNP) markers identified by GBS in PR-02, PR-07 and PR-15, respectively, were used for construction of genetic linkage maps. Genetic linkage groups were assigned by anchoring to SNP markers previously positioned on these linkage maps. PR-02, PR-07 and PR-15 genetic maps represented 527, 675 and 609 non-redundant loci, and cover map distances of 951.9, 1008.8 and 914.2 cM, respectively. Based on phenotyping of the three mapping populations in multiple environments, 375 QTLs were identified for important traits including days to flowering, days to maturity, lodging resistance, Mycosphaerella blight resistance, seed weight, grain yield, acid and neutral detergent fiber concentration, seed starch concentration, seed shape, seed dimpling, and concentration of seed iron, selenium and zinc. Of all the QTLs identified, the most significant in terms of explained percentage of maximum phenotypic variance (PVmax) and occurrence in multiple environments were the QTLs for days to flowering (PVmax = 47.9%), plant height (PVmax = 65.1%), lodging resistance (PVmax = 35.3%), grain yield (PVmax = 54.2%), seed iron concentration (PVmax = 27.4%), and seed zinc concentration (PVmax = 43.2%). CONCLUSION We have identified highly significant and reproducible QTLs for several agronomic and seed quality traits of breeding importance in pea. The QTLs identified will be the basis for fine mapping candidate genes, while some of the markers linked to the highly significant QTLs are useful for immediate breeding applications.
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Affiliation(s)
- Krishna K. Gali
- Crop Development Centre, Department of Plant Sciences, 51 Campus Drive, University of Saskatchewan, Saskatoon, SK Canada
| | - Yong Liu
- Crop Development Centre, Department of Plant Sciences, 51 Campus Drive, University of Saskatchewan, Saskatoon, SK Canada
| | - Anoop Sindhu
- CHS, Inc, 220 Clement Ave., Grandin, ND 58038 USA
| | - Marwan Diapari
- Agriculture and Agri-Food Canada, London Research and Development centre, 1391 Sandford Street, London, ON N5V 4T3 Canada
| | - Arun S. K. Shunmugam
- National Research Council Canada, 110 Gymnasium Place, Saskatoon, SK S7N 0W9 Canada
| | - Gene Arganosa
- Crop Development Centre, Department of Plant Sciences, 51 Campus Drive, University of Saskatchewan, Saskatoon, SK Canada
| | - Ketema Daba
- Crop Development Centre, Department of Plant Sciences, 51 Campus Drive, University of Saskatchewan, Saskatoon, SK Canada
| | - Carolyn Caron
- Crop Development Centre, Department of Plant Sciences, 51 Campus Drive, University of Saskatchewan, Saskatoon, SK Canada
| | - Reddy V. B. Lachagari
- AgriGenome Labs Pvt Ltd., BTIC, MN iHub, Genome Valley, Shamirpet, Hyderabad, 500 078 India
| | - Bunyamin Tar’an
- Crop Development Centre, Department of Plant Sciences, 51 Campus Drive, University of Saskatchewan, Saskatoon, SK Canada
| | - Thomas D. Warkentin
- Crop Development Centre, Department of Plant Sciences, 51 Campus Drive, University of Saskatchewan, Saskatoon, SK Canada
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26
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Mogga M, Sibiya J, Shimelis H, Lamo J, Yao N. Diversity analysis and genome-wide association studies of grain shape and eating quality traits in rice (Oryza sativa L.) using DArT markers. PLoS One 2018; 13:e0198012. [PMID: 29856872 PMCID: PMC5983461 DOI: 10.1371/journal.pone.0198012] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 05/11/2018] [Indexed: 11/18/2022] Open
Abstract
Microarray-based markers such as Diversity Arrays Technology (DArT) have become the genetic markers of choice for construction of high-density maps, quantitative trait loci (QTL) mapping and genetic diversity analysis based on their efficiency and low cost. More recently, the DArT technology was further developed in combination with high-throughput next-generation sequencing (NGS) technologies to generate the DArTseq platform representing a new sequencing tool of complexity-reduced representations. In this study, we used DArTseq markers to investigate genetic diversity and genome-wide association studies (GWAS) of grain quality traits in rice (Oryza sativa L.). The study was performed using 59 rice genotypes with 525 SNPs derived from DArTseq platform. Population structure analysis revealed only two distinct genetic clusters where genotypes were grouped based on environmental adaptation and pedigree information. Analysis of molecular variance indicated a low degree of differentiation among populations suggesting the need for broadening the genetic base of the current germplasm collection. GWAS revealed 22 significant associations between DArTseq-derived SNP markers and rice grain quality traits in the test genotypes. In general, 2 of the 22 significant associations were in chromosomal regions where the QTLs associated with the given traits had previously been reported, the other 20 significant SNP marker loci were indicative of the likelihood discovery of novel alleles associated with rice grain quality traits. DArTseq-derived SNP markers that include SNP12_100006178, SNP13_3052560 and SNP14_3057360 individually co-localised with two functional gene groups that were associated with QTLs for grain width and grain length to width ratio on chromosome 3, indicating trait dependency or pleiotropic-effect loci. This study demonstrated that DArTseq markers were useful genomic resources for genome-wide association studies of rice grain quality traits to accelerate varietal development and release.
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Affiliation(s)
- Maurice Mogga
- Ministry of Agriculture and Food Security, Juba, South Sudan
| | - Julia Sibiya
- African Centre for Crop Improvement, School of Agricultural Sciences and Agribusiness, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Hussein Shimelis
- African Centre for Crop Improvement, School of Agricultural Sciences and Agribusiness, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Jimmy Lamo
- Cereals Program, National Crops Resources Research Institute (NaCRRI), Kampala, Uganda
| | - Nasser Yao
- Biosciences eastern and central Africa-International Livestock Research Institute (BecA-ILRI) Hub, Nairobi, Kenya
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27
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Desgroux A, Baudais VN, Aubert V, Le Roy G, de Larambergue H, Miteul H, Aubert G, Boutet G, Duc G, Baranger A, Burstin J, Manzanares-Dauleux M, Pilet-Nayel ML, Bourion V. Comparative Genome-Wide-Association Mapping Identifies Common Loci Controlling Root System Architecture and Resistance to Aphanomyces euteiches in Pea. FRONTIERS IN PLANT SCIENCE 2018; 8:2195. [PMID: 29354146 PMCID: PMC5761208 DOI: 10.3389/fpls.2017.02195] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 12/13/2017] [Indexed: 05/04/2023]
Abstract
Combining plant genetic resistance with architectural traits that are unfavorable to disease development is a promising strategy for reducing epidemics. However, few studies have identified root system architecture (RSA) traits with the potential to limit root disease development. Pea is a major cultivated legume worldwide and has a wide level of natural genetic variability for plant architecture. The root pathogen Aphanomyces euteiches is a major limiting factor of pea crop yield. This study aimed to increase the knowledge on the diversity of loci and candidate genes controlling RSA traits in pea and identify RSA genetic loci associated with resistance to A. euteiches which could be combined with resistance QTL in breeding. A comparative genome wide association (GWA) study of plant architecture and resistance to A. euteiches was conducted at the young plant stage in a collection of 266 pea lines contrasted for both traits. The collection was genotyped using 14,157 SNP markers from recent pea genomic resources. It was phenotyped for ten root, shoot and overall plant architecture traits, as well as three disease resistance traits in controlled conditions, using image analysis. We identified a total of 75 short-size genomic intervals significantly associated with plant architecture and overlapping with 46 previously detected QTL. The major consistent intervals included plant shoot architecture or flowering genes (PsLE, PsTFL1) with putative pleiotropic effects on root architecture. A total of 11 genomic intervals were significantly associated with resistance to A. euteiches confirming several consistent previously identified major QTL. One significant SNP, mapped to the major QTL Ae-Ps7.6, was associated with both resistance and RSA traits. At this marker, the resistance-enhancing allele was associated with an increased total root projected area, in accordance with the correlation observed between resistance and larger root systems in the collection. Seven additional intervals associated with plant architecture overlapped with GWA intervals previously identified for resistance to A. euteiches. This study provides innovative results about genetic interdependency of root disease resistance and RSA inheritance. It identifies pea lines, QTL, closely-linked markers and candidate genes for marker-assisted-selection of RSA loci to reduce Aphanomyces root rot severity in future pea varieties.
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Affiliation(s)
- Aurore Desgroux
- Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université Rennes 1, Le Rheu, France
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
- PISOM, UMT INRA/Terre Inovia, Le Rheu, France
| | - Valentin N. Baudais
- Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université Rennes 1, Le Rheu, France
| | - Véronique Aubert
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Gwenola Le Roy
- Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université Rennes 1, Le Rheu, France
- PISOM, UMT INRA/Terre Inovia, Le Rheu, France
| | - Henri de Larambergue
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Henri Miteul
- Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université Rennes 1, Le Rheu, France
- PISOM, UMT INRA/Terre Inovia, Le Rheu, France
| | - Grégoire Aubert
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Gilles Boutet
- Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université Rennes 1, Le Rheu, France
- PISOM, UMT INRA/Terre Inovia, Le Rheu, France
| | - Gérard Duc
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Alain Baranger
- Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université Rennes 1, Le Rheu, France
- PISOM, UMT INRA/Terre Inovia, Le Rheu, France
| | - Judith Burstin
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
| | - Maria Manzanares-Dauleux
- Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université Rennes 1, Le Rheu, France
| | - Marie-Laure Pilet-Nayel
- Institut de Génétique, Environnement et Protection des Plantes, INRA, Agrocampus Ouest, Université Rennes 1, Le Rheu, France
- PISOM, UMT INRA/Terre Inovia, Le Rheu, France
| | - Virginie Bourion
- Agroécologie, INRA, AgroSup Dijon, Université Bourgogne Franche-Comté, Dijon, France
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28
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Barilli E, Cobos MJ, Carrillo E, Kilian A, Carling J, Rubiales D. A High-Density Integrated DArTseq SNP-Based Genetic Map of Pisum fulvum and Identification of QTLs Controlling Rust Resistance. FRONTIERS IN PLANT SCIENCE 2018; 9:167. [PMID: 29497430 PMCID: PMC5818415 DOI: 10.3389/fpls.2018.00167] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 01/30/2018] [Indexed: 05/05/2023]
Abstract
Pisum fulvum, a wild relative of pea is an important source of allelic diversity to improve the genetic resistance of cultivated species against fungal diseases of economic importance like the pea rust caused by Uromyces pisi. To unravel the genetic control underlying resistance to this fungal disease, a recombinant inbred line (RIL) population was generated from a cross between two P. fulvum accessions, IFPI3260 and IFPI3251, and genotyped using Diversity Arrays Technology. A total of 9,569 high-quality DArT-Seq and 8,514 SNPs markers were generated. Finally, a total of 12,058 markers were assembled into seven linkage groups, equivalent to the number of haploid chromosomes of P. fulvum and P. sativum. The newly constructed integrated genetic linkage map of P. fulvum covered an accumulated distance of 1,877.45 cM, an average density of 1.19 markers cM-1 and an average distance between adjacent markers of 1.85 cM. The composite interval mapping revealed three QTLs distributed over two linkage groups that were associated with the percentage of rust disease severity (DS%). QTLs UpDSII and UpDSIV were located in the LGs II and IV respectively and were consistently identified both in adult plants over 3 years at the field (Córdoba, Spain) and in seedling plants under controlled conditions. Whenever they were detected, their contribution to the total phenotypic variance varied between 19.8 and 29.2. A third QTL (UpDSIV.2) was also located in the LGIVand was environmentally specific as was only detected for DS % in seedlings under controlled conditions. It accounted more than 14% of the phenotypic variation studied. Taking together the data obtained in the study, it could be concluded that the expression of resistance to fungal diseases in P. fulvum originates from the resistant parent IFPI3260.
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Affiliation(s)
| | - María J Cobos
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
| | | | - Andrzej Kilian
- Diversity Arrays Technology Pty Ltd, University of Canberra, Canberra, ACT, Australia
| | - Jason Carling
- Diversity Arrays Technology Pty Ltd, University of Canberra, Canberra, ACT, Australia
| | - Diego Rubiales
- Institute for Sustainable Agriculture, CSIC, Córdoba, Spain
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Jiao K, Li X, Guo W, Su S, Luo D. High-Throughput RNA-Seq Data Analysis of the Single Nucleotide Polymorphisms (SNPs) and Zygomorphic Flower Development in Pea (Pisum sativum L.). Int J Mol Sci 2017; 18:E2710. [PMID: 29261120 PMCID: PMC5751311 DOI: 10.3390/ijms18122710] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/10/2017] [Accepted: 12/12/2017] [Indexed: 11/17/2022] Open
Abstract
Pea (Pisum sativum L.) is a model plant that has been used in classical genetics and organ development studies. However, its large and complex genome has hindered research investigations in pea. Here, we generated transcriptomes from different tissues or organs of three pea accessions using next-generation sequencing to assess single nucleotide polymorphisms (SNPs), and further investigated petal differentially expressed genes to elucidate the mechanisms regulating floral zygomorphy. Eighteen samples were sequenced, which yielded a total of 617 million clean reads, and de novo assembly resulted in 87,137 unigenes. A total of 9044 high-quality SNPs were obtained among the three accessions, and a consensus map was constructed. We further discovered several dorsoventral asymmetrically expressed genes that were confirmed by qRT-PCR among different petals, including previously reported three CYC-like proliferating cell factor (TCP) genes. One MADS-box gene was highly expressed in dorsal petals, and several MYB factors were predominantly expressed among dorsal, lateral, and/or ventral petals, together with a ventrally expressed TCP gene. In sum, our comprehensive database complements the existing resources for comparative genetic mapping and facilitates future investigations in legume zygomorphic flower development.
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Affiliation(s)
- Keyuan Jiao
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Xin Li
- College of Life Sciences, Laboratory Center of Life Sciences, Nanjing Agricultural University, Nanjing 210014, China.
| | - Wuxiu Guo
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Shihao Su
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
| | - Da Luo
- Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China.
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Kulaeva OA, Zhernakov AI, Afonin AM, Boikov SS, Sulima AS, Tikhonovich IA, Zhukov VA. Pea Marker Database (PMD) - A new online database combining known pea (Pisum sativum L.) gene-based markers. PLoS One 2017; 12:e0186713. [PMID: 29073280 PMCID: PMC5658071 DOI: 10.1371/journal.pone.0186713] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Accepted: 08/17/2017] [Indexed: 11/19/2022] Open
Abstract
Pea (Pisum sativum L.) is the oldest model object of plant genetics and one of the most agriculturally important legumes in the world. Since the pea genome has not been sequenced yet, identification of genes responsible for mutant phenotypes or desirable agricultural traits is usually performed via genetic mapping followed by candidate gene search. Such mapping is best carried out using gene-based molecular markers, as it opens the possibility for exploiting genome synteny between pea and its close relative Medicago truncatula Gaertn., possessing sequenced and annotated genome. In the last 5 years, a large number of pea gene-based molecular markers have been designed and mapped owing to the rapid evolution of "next-generation sequencing" technologies. However, the access to the complete set of markers designed worldwide is limited because the data are not uniformed and therefore hard to use. The Pea Marker Database was designed to combine the information about pea markers in a form of user-friendly and practical online tool. Version 1 (PMD1) comprises information about 2484 genic markers, including their locations in linkage groups, the sequences of corresponding pea transcripts and the names of related genes in M. truncatula. Version 2 (PMD2) is an updated version comprising 15944 pea markers in the same format with several advanced features. To test the performance of the PMD, fine mapping of pea symbiotic genes Sym13 and Sym27 in linkage groups VII and V, respectively, was carried out. The results of mapping allowed us to propose the Sen1 gene (a homologue of SEN1 gene of Lotus japonicus (Regel) K. Larsen) as the best candidate gene for Sym13, and to narrow the list of possible candidate genes for Sym27 to ten, thus proving PMD to be useful for pea gene mapping and cloning. All information contained in PMD1 and PMD2 is available at www.peamarker.arriam.ru.
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Affiliation(s)
- Olga A. Kulaeva
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse, Saint-Petersburg, Russia
| | - Aleksandr I. Zhernakov
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse, Saint-Petersburg, Russia
| | - Alexey M. Afonin
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse, Saint-Petersburg, Russia
| | - Sergei S. Boikov
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse, Saint-Petersburg, Russia
| | - Anton S. Sulima
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse, Saint-Petersburg, Russia
| | - Igor A. Tikhonovich
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse, Saint-Petersburg, Russia
- Saint-Petersburg State University, Universitetskaya embankment, Saint-Petersburg, Russia
| | - Vladimir A. Zhukov
- All-Russia Research Institute for Agricultural Microbiology, Podbelsky chausse, Saint-Petersburg, Russia
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NGS-Based Genotyping, High-Throughput Phenotyping and Genome-Wide Association Studies Laid the Foundations for Next-Generation Breeding in Horticultural Crops. DIVERSITY-BASEL 2017. [DOI: 10.3390/d9030038] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Demographic trends and changes to climate require a more efficient use of plant genetic resources in breeding programs. Indeed, the release of high-yielding varieties has resulted in crop genetic erosion and loss of diversity. This has produced an increased susceptibility to severe stresses and a reduction of several food quality parameters. Next generation sequencing (NGS) technologies are being increasingly used to explore “gene space” and to provide high-resolution profiling of nucleotide variation within germplasm collections. On the other hand, advances in high-throughput phenotyping are bridging the genotype-to-phenotype gap in crop selection. The combination of allelic and phenotypic data points via genome-wide association studies is facilitating the discovery of genetic loci that are associated with key agronomic traits. In this review, we provide a brief overview on the latest NGS-based and phenotyping technologies and on their role to unlocking the genetic potential of vegetable crops; then, we discuss the paradigm shift that is underway in horticultural crop breeding.
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Dwivedi SL, Scheben A, Edwards D, Spillane C, Ortiz R. Assessing and Exploiting Functional Diversity in Germplasm Pools to Enhance Abiotic Stress Adaptation and Yield in Cereals and Food Legumes. FRONTIERS IN PLANT SCIENCE 2017; 8:1461. [PMID: 28900432 PMCID: PMC5581882 DOI: 10.3389/fpls.2017.01461] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/07/2017] [Indexed: 05/03/2023]
Abstract
There is a need to accelerate crop improvement by introducing alleles conferring host plant resistance, abiotic stress adaptation, and high yield potential. Elite cultivars, landraces and wild relatives harbor useful genetic variation that needs to be more easily utilized in plant breeding. We review genome-wide approaches for assessing and identifying alleles associated with desirable agronomic traits in diverse germplasm pools of cereals and legumes. Major quantitative trait loci and single nucleotide polymorphisms (SNPs) associated with desirable agronomic traits have been deployed to enhance crop productivity and resilience. These include alleles associated with variation conferring enhanced photoperiod and flowering traits. Genetic variants in the florigen pathway can provide both environmental flexibility and improved yields. SNPs associated with length of growing season and tolerance to abiotic stresses (precipitation, high temperature) are valuable resources for accelerating breeding for drought-prone environments. Both genomic selection and genome editing can also harness allelic diversity and increase productivity by improving multiple traits, including phenology, plant architecture, yield potential and adaptation to abiotic stresses. Discovering rare alleles and useful haplotypes also provides opportunities to enhance abiotic stress adaptation, while epigenetic variation has potential to enhance abiotic stress adaptation and productivity in crops. By reviewing current knowledge on specific traits and their genetic basis, we highlight recent developments in the understanding of crop functional diversity and identify potential candidate genes for future use. The storage and integration of genetic, genomic and phenotypic information will play an important role in ensuring broad and rapid application of novel genetic discoveries by the plant breeding community. Exploiting alleles for yield-related traits would allow improvement of selection efficiency and overall genetic gain of multigenic traits. An integrated approach involving multiple stakeholders specializing in management and utilization of genetic resources, crop breeding, molecular biology and genomics, agronomy, stress tolerance, and reproductive/seed biology will help to address the global challenge of ensuring food security in the face of growing resource demands and climate change induced stresses.
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Affiliation(s)
| | - Armin Scheben
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, PerthWA, Australia
| | - David Edwards
- School of Biological Sciences, Institute of Agriculture, University of Western Australia, PerthWA, Australia
| | - Charles Spillane
- Plant and AgriBiosciences Research Centre, Ryan Institute, National University of Ireland GalwayGalway, Ireland
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural SciencesAlnarp, Sweden
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Molecular, Genetic and Agronomic Approaches to Utilizing Pulses as Cover Crops and Green Manure into Cropping Systems. Int J Mol Sci 2017; 18:ijms18061202. [PMID: 28587254 PMCID: PMC5486025 DOI: 10.3390/ijms18061202] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/28/2017] [Accepted: 05/30/2017] [Indexed: 11/17/2022] Open
Abstract
Cover crops constitute one of the most promising agronomic practices towards a more sustainable agriculture. Their beneficial effects on main crops, soil and environment are many and various, while risks and disadvantages may also appear. Several legumes show a high potential but further research is required in order to suggest the optimal legume cover crops for each case in terms of their productivity and ability to suppress weeds. The additional cost associated with cover crops should also be addressed and in this context the use of grain legumes such as cowpea, faba bean and pea could be of high interest. Some of the aspects of these grain legumes as far as their use as cover crops, their genetic diversity and their breeding using conventional and molecular approaches are discussed in the present review. The specific species seem to have a high potential for use as cover crops, especially if their noticeable genetic diversity is exploited and their breeding focuses on several desirable traits.
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Nunes JDRDS, Liu S, Pértille F, Perazza CA, Villela PMS, de Almeida-Val VMF, Hilsdorf AWS, Liu Z, Coutinho LL. Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing. Sci Rep 2017; 7:46112. [PMID: 28387238 PMCID: PMC5384230 DOI: 10.1038/srep46112] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Accepted: 03/06/2017] [Indexed: 11/11/2022] Open
Abstract
Colossoma macropomum, or tambaqui, is the largest native Characiform species found in the Amazon and Orinoco river basins, yet few resources for genetic studies and the genetic improvement of tambaqui exist. In this study, we identified a large number of single-nucleotide polymorphisms (SNPs) for tambaqui and constructed a high-resolution genetic linkage map from a full-sib family of 124 individuals and their parents using the genotyping by sequencing method. In all, 68,584 SNPs were initially identified using minimum minor allele frequency (MAF) of 5%. Filtering parameters were used to select high-quality markers for linkage analysis. We selected 7,734 SNPs for linkage mapping, resulting in 27 linkage groups with a minimum logarithm of odds (LOD) of 8 and maximum recombination fraction of 0.35. The final genetic map contains 7,192 successfully mapped markers that span a total of 2,811 cM, with an average marker interval of 0.39 cM. Comparative genomic analysis between tambaqui and zebrafish revealed variable levels of genomic conservation across the 27 linkage groups which allowed for functional SNP annotations. The large-scale SNP discovery obtained here, allowed us to build a high-density linkage map in tambaqui, which will be useful to enhance genetic studies that can be applied in breeding programs.
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Affiliation(s)
- José de Ribamar da Silva Nunes
- Animal Science department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil.,The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, United States of America.,Nature and Culture Institute, Federal University of Amazon (UFAM), Benjamin Constant, Amazonas, Brazil
| | - Shikai Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, United States of America
| | - Fábio Pértille
- Animal Science department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Caio Augusto Perazza
- Unit of Biotechnology, University of Mogi das Cruzes, P.O. Box 411, 08701-970, Mogi das Cruzes, SP, Brazil
| | - Priscilla Marqui Schmidt Villela
- Animal Science department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
| | - Vera Maria Fonseca de Almeida-Val
- Brazilian National Institute for Research of the Amazon, Laboratory of Ecophysiology and Molecular Evolution, Manaus, Amazonas, Brazil.,University Nilton Lins, Aquaculture Graduate Program, Manaus, Amazonas, Brazil
| | | | - Zhanjiang Liu
- The Fish Molecular Genetics and Biotechnology Laboratory, Aquatic Genomics Unit, School of Fisheries, Aquaculture and Aquatic Sciences and Program of Cell and Molecular Biosciences, Auburn University, Auburn, AL, 36849, United States of America
| | - Luiz Lehmann Coutinho
- Animal Science department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, São Paulo, Brazil
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Ma Y, Coyne CJ, Grusak MA, Mazourek M, Cheng P, Main D, McGee RJ. Genome-wide SNP identification, linkage map construction and QTL mapping for seed mineral concentrations and contents in pea (Pisum sativum L.). BMC PLANT BIOLOGY 2017; 17:43. [PMID: 28193168 PMCID: PMC5307697 DOI: 10.1186/s12870-016-0956-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 12/20/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND Marker-assisted breeding is now routinely used in major crops to facilitate more efficient cultivar improvement. This has been significantly enabled by the use of next-generation sequencing technology to identify loci and markers associated with traits of interest. While rich in a range of nutritional components, such as protein, mineral nutrients, carbohydrates and several vitamins, pea (Pisum sativum L.), one of the oldest domesticated crops in the world, remains behind many other crops in the availability of genomic and genetic resources. To further improve mineral nutrient levels in pea seeds requires the development of genome-wide tools. The objectives of this research were to develop these tools by: identifying genome-wide single nucleotide polymorphisms (SNPs) using genotyping by sequencing (GBS); constructing a high-density linkage map and comparative maps with other legumes, and identifying quantitative trait loci (QTL) for levels of boron, calcium, iron, potassium, magnesium, manganese, molybdenum, phosphorous, sulfur, and zinc in the seed, as well as for seed weight. RESULTS In this study, 1609 high quality SNPs were found to be polymorphic between 'Kiflica' and 'Aragorn', two parents of an F6-derived recombinant inbred line (RIL) population. Mapping 1683 markers including 75 previously published markers and 1608 SNPs developed from the present study generated a linkage map of size 1310.1 cM. Comparative mapping with other legumes demonstrated that the highest level of synteny was observed between pea and the genome of Medicago truncatula. QTL analysis of the RIL population across two locations revealed at least one QTL for each of the mineral nutrient traits. In total, 46 seed mineral concentration QTLs, 37 seed mineral content QTLs, and 6 seed weight QTLs were discovered. The QTLs explained from 2.4% to 43.3% of the phenotypic variance. CONCLUSION The genome-wide SNPs and the genetic linkage map developed in this study permitted QTL identification for pea seed mineral nutrients that will serve as important resources to enable marker-assisted selection (MAS) for nutritional quality traits in pea breeding programs.
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Affiliation(s)
- Yu Ma
- Department of Horticulture, Washington State University, Pullman, WA USA
| | - Clarice J Coyne
- USDA-ARS Plant Germplasm Introduction and Testing, Pullman, WA USA
| | | | - Michael Mazourek
- Department of Plant Breeding and Genetics, Cornell University, Ithaca, NY USA
| | - Peng Cheng
- Department of Plant Sciences, University of Missouri, Columbia, MO USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, WA USA
| | - Rebecca J McGee
- USDA-ARS Grain Legume Genetics and Physiology Research, Pullman, WA USA
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Muñoz N, Liu A, Kan L, Li MW, Lam HM. Potential Uses of Wild Germplasms of Grain Legumes for Crop Improvement. Int J Mol Sci 2017; 18:E328. [PMID: 28165413 PMCID: PMC5343864 DOI: 10.3390/ijms18020328] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 01/26/2017] [Accepted: 01/26/2017] [Indexed: 01/14/2023] Open
Abstract
Challenged by population increase, climatic change, and soil deterioration, crop improvement is always a priority in securing food supplies. Although the production of grain legumes is in general lower than that of cereals, the nutritional value of grain legumes make them important components of food security. Nevertheless, limited by severe genetic bottlenecks during domestication and human selection, grain legumes, like other crops, have suffered from a loss of genetic diversity which is essential for providing genetic materials for crop improvement programs. Illustrated by whole-genome-sequencing, wild relatives of crops adapted to various environments were shown to maintain high genetic diversity. In this review, we focused on nine important grain legumes (soybean, peanut, pea, chickpea, common bean, lentil, cowpea, lupin, and pigeonpea) to discuss the potential uses of their wild relatives as genetic resources for crop breeding and improvement, and summarized the various genetic/genomic approaches adopted for these purposes.
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Affiliation(s)
- Nacira Muñoz
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
- Centro de Investigaciones Agropecuarias-INTA, Instituto de Fisiología y Recursos Genéticos Vegetales, Córdoba X5000, Argentina.
- Cátedra de Fisiología Vegetal, Facultad de Ciencias Exactas Físicas y Naturales, Universidad Nacional de Córdoba, Córdoba X5000, Argentina.
| | - Ailin Liu
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Leo Kan
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Man-Wah Li
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Hon-Ming Lam
- Centre for Soybean Research of the Partner State Key Laboratory of Agrobiotechnology and School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China.
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Holdsworth WL, Gazave E, Cheng P, Myers JR, Gore MA, Coyne CJ, McGee RJ, Mazourek M. A community resource for exploring and utilizing genetic diversity in the USDA pea single plant plus collection. HORTICULTURE RESEARCH 2017; 4:17017. [PMID: 28503311 PMCID: PMC5405346 DOI: 10.1038/hortres.2017.17] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 04/07/2017] [Accepted: 04/09/2017] [Indexed: 05/04/2023]
Abstract
Globally, pea (Pisum sativum L.) is an important temperate legume crop for food, feed and fodder, and many breeding programs develop cultivars adapted to these end-uses. In order to assist pea development efforts, we assembled the USDA Pea Single Plant Plus Collection (PSPPC), which contains 431 P. sativum accessions with morphological, geographic and taxonomic diversity. The collection was characterized genetically in order to maximize its value for trait mapping and genomics-assisted breeding. To that end, we used genotyping-by-sequencing-a cost-effective method for de novo single-nucleotide polymorphism (SNP) marker discovery-to generate 66 591 high-quality SNPs. These data facilitated the identification of accessions divergent from mainstream breeding germplasm that could serve as sources of novel, favorable alleles. In particular, a group of accessions from Central Asia appear nearly as diverse as a sister species, P. fulvum, and subspecies, P. sativum subsp. elatius. PSPPC genotypes can be paired with new and existing phenotype data for trait mapping; as proof-of-concept, we localized Mendel's A gene controlling flower color to its known position. We also used SNP data to define a smaller core collection of 108 accessions with similar levels of genetic diversity as the entire PSPPC, resulting in a smaller germplasm set for research screening and evaluation under limited resources. Taken together, the results presented in this study along with the release of a publicly available SNP data set comprise a valuable resource for supporting worldwide pea genetic improvement efforts.
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Affiliation(s)
- William L. Holdsworth
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Elodie Gazave
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Peng Cheng
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
| | - James R. Myers
- Department of Horticulture, Oregon State University, Corvallis, OR 97331, USA
| | - Michael A. Gore
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
| | - Clarice J. Coyne
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA 99164, USA
- US Department of Agriculture, Agricultural Research Service, Western Regional Plant Introduction Station, Pullman, WA 99164, USA
| | - Rebecca J. McGee
- US Department of Agriculture, Agricultural Research Service, Grain Legume Genetics and Physiology Research Unit, Pullman, WA 99164, USA
| | - Michael Mazourek
- Plant Breeding and Genetics Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA
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Yin M, Liu X, Xu B, Huang J, Zheng Q, Yang Z, Feng Z, Han ZG, Hu W. Genetic variation between Schistosoma japonicum lineages from lake and mountainous regions in China revealed by resequencing whole genomes. Acta Trop 2016; 161:79-85. [PMID: 27207135 DOI: 10.1016/j.actatropica.2016.05.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Revised: 04/25/2016] [Accepted: 05/16/2016] [Indexed: 02/08/2023]
Abstract
Schistosoma infection is a major cause of morbidity and mortality worldwide. Schistosomiasis japonica is endemic in mainland China along the Yangtze River, typically distributed in two geographical categories of lake and mountainous regions. Study on schistosome genetic diversity is of interest in respect of understanding parasite biology and transmission, and formulating control strategy. Certain genetic variations may be associated with adaptations to different ecological habitats. The aim of this study is to gain insight into Schistosoma japonicum genetic variation, evolutionary origin and associated causes of different geographic lineages through examining homozygous Single Nucleotide Polymorphisms (SNPs) based on resequenced genome data. We collected S. japonicum samples from four sites, three in the lake regions (LR) of mid-east (Guichi and Tonglin in Anhui province, Laogang in Hunan province) and one in mountainous region (MR) (Xichang in Sichuan province) of south-west of China, resequenced their genomes using Next Generation Sequencing (NGS) technology, and made use of the available database of S. japonicum draft genomic sequence as a reference in genome mapping. A total of 14,575 SNPs from 2059 genes were identified in the four lineages. Phylogenetic analysis confirmed significant genetic variation exhibited between the different geographical lineages, and further revealed that the MR Xichang lineage is phylogenetically closer to LR Guich lineage than to other two LR lineages, and the MR lineage might be evolved from LR lineages. More than two thirds of detected SNPs were nonsynonymous; functional annotation of the SNP-containing genes showed that they are involved mainly in biological processes such as signaling and response to stimuli. Notably, unique nonsynonymous SNP variations were detected in 66 genes of MR lineage, inferring possible genetic adaption to mountainous ecological condition.
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Desgroux A, L'Anthoëne V, Roux-Duparque M, Rivière JP, Aubert G, Tayeh N, Moussart A, Mangin P, Vetel P, Piriou C, McGee RJ, Coyne CJ, Burstin J, Baranger A, Manzanares-Dauleux M, Bourion V, Pilet-Nayel ML. Genome-wide association mapping of partial resistance to Aphanomyces euteiches in pea. BMC Genomics 2016; 17:124. [PMID: 26897486 PMCID: PMC4761183 DOI: 10.1186/s12864-016-2429-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2015] [Accepted: 02/02/2016] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Genome-wide association (GWA) mapping has recently emerged as a valuable approach for refining the genetic basis of polygenic resistance to plant diseases, which are increasingly used in integrated strategies for durable crop protection. Aphanomyces euteiches is a soil-borne pathogen of pea and other legumes worldwide, which causes yield-damaging root rot. Linkage mapping studies reported quantitative trait loci (QTL) controlling resistance to A. euteiches in pea. However the confidence intervals (CIs) of these QTL remained large and were often linked to undesirable alleles, which limited their application in breeding. The aim of this study was to use a GWA approach to validate and refine CIs of the previously reported Aphanomyces resistance QTL, as well as identify new resistance loci. METHODS A pea-Aphanomyces collection of 175 pea lines, enriched in germplasm derived from previously studied resistant sources, was evaluated for resistance to A. euteiches in field infested nurseries in nine environments and with two strains in climatic chambers. The collection was genotyped using 13,204 SNPs from the recently developed GenoPea Infinium® BeadChip. RESULTS GWA analysis detected a total of 52 QTL of small size-intervals associated with resistance to A. euteiches, using the recently developed Multi-Locus Mixed Model. The analysis validated six of the seven previously reported main Aphanomyces resistance QTL and detected novel resistance loci. It also provided marker haplotypes at 14 consistent QTL regions associated with increased resistance and highlighted accumulation of favourable haplotypes in the most resistant lines. Previous linkages between resistance alleles and undesired late-flowering alleles for dry pea breeding were mostly confirmed, but the linkage between loci controlling resistance and coloured flowers was broken due to the high resolution of the analysis. A high proportion of the putative candidate genes underlying resistance loci encoded stress-related proteins and others suggested that the QTL are involved in diverse functions. CONCLUSION This study provides valuable markers, marker haplotypes and germplasm lines to increase levels of partial resistance to A. euteiches in pea breeding.
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Affiliation(s)
- Aurore Desgroux
- INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- INRA, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon Cedex, France.
| | - Virginie L'Anthoëne
- INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- Present Address: Nestlé R&D Center Tours, 101 Avenue Gustave Eiffel, 37097, Tours Cedex 2, France.
| | - Martine Roux-Duparque
- GSP, Domaine Brunehaut, 80200, Estrées-Mons Cedex, France.
- Present Address: Chambre d'Agriculture de l'Aisne, 1 rue René Blondelle, 02007, Laon Cedex, France.
| | - Jean-Philippe Rivière
- INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
| | - Grégoire Aubert
- INRA, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon Cedex, France.
| | - Nadim Tayeh
- INRA, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon Cedex, France.
| | - Anne Moussart
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- Terres Inovia, 11 rue de Monceau, CS 60003, 75378, Paris Cedex, France.
| | - Pierre Mangin
- INRA, Domaine Expérimental d'Epoisses, UE0115, 21110, Bretenières Cedex, France.
| | - Pierrick Vetel
- INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
| | - Christophe Piriou
- INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
| | - Rebecca J McGee
- USDA, ARS, Grain Legume Genetics and Physiology Research Unit, Pullman, WA, 99164-6434, USA.
| | - Clarice J Coyne
- USDA, ARS, Western Regional Plant Introduction Station, Washington State University, Pullman, WA, 99164-6402, USA.
| | - Judith Burstin
- INRA, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon Cedex, France.
| | - Alain Baranger
- INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
| | - Maria Manzanares-Dauleux
- INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- AgroCampus Ouest, UMR IGEPP 1349 IGEPP, 65 rue de Saint Brieuc, 35042, Rennes Cedex, France.
| | - Virginie Bourion
- INRA, UMR 1347 Agroécologie, 17 rue de Sully, 21065, Dijon Cedex, France.
| | - Marie-Laure Pilet-Nayel
- INRA, UMR IGEPP 1349, Institut de Génétique et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
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40
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Hulse-Kemp AM, Ashrafi H, Plieske J, Lemm J, Stoffel K, Hill T, Luerssen H, Pethiyagoda CL, Lawley CT, Ganal MW, Van Deynze A. A HapMap leads to a Capsicum annuum SNP infinium array: a new tool for pepper breeding. HORTICULTURE RESEARCH 2016; 3:16036. [PMID: 27602231 PMCID: PMC4962762 DOI: 10.1038/hortres.2016.36] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 07/06/2016] [Accepted: 07/08/2016] [Indexed: 05/18/2023]
Abstract
The Capsicum genus (Pepper) is a part of the Solanacae family. It has been important in many cultures worldwide for its key nutritional components and uses as spices, medicines, ornamentals and vegetables. Worldwide population growth is associated with demand for more nutritionally valuable vegetables while contending with decreasing resources and available land. These conditions require increased efficiency in pepper breeding to deal with these imminent challenges. Through resequencing of inbred lines we have completed a valuable haplotype map (HapMap) for the pepper genome based on single-nucleotide polymorphisms (SNP). The identified SNPs were annotated and classified based on their gene annotation in the pepper draft genome sequence and phenotype of the sequenced inbred lines. A selection of one marker per gene model was utilized to create the PepperSNP16K array, which simultaneously genotyped 16 405 SNPs, of which 90.7% were found to be informative. A set of 84 inbred and hybrid lines and a mapping population of 90 interspecific F2 individuals were utilized to validate the array. Diversity analysis of the inbred lines shows a distinct separation of bell versus chile/hot pepper types and separates them into five distinct germplasm groups. The interspecific population created between Tabasco (C. frutescens chile type) and P4 (C. annuum blocky type) produced a linkage map with 5546 markers separated into 1361 bins on twelve 12 linkage groups representing 1392.3 cM. This publically available genotyping platform can be used to rapidly assess a large number of markers in a reproducible high-throughput manner for pepper. As a standardized tool for genetic analyses, the PepperSNP16K can be used worldwide to share findings and analyze QTLs for important traits leading to continued improvement of pepper for consumers. Data and information on the array are available through the Solanaceae Genomics Network.
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Affiliation(s)
- Amanda M Hulse-Kemp
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
| | - Hamid Ashrafi
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
| | - Joerg Plieske
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, Gatersleben, Germany
| | - Jana Lemm
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, Gatersleben, Germany
| | - Kevin Stoffel
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
| | - Theresa Hill
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
| | - Hartmut Luerssen
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, Gatersleben, Germany
| | | | - Cindy T Lawley
- Illumina Incorporated, 5200 Illumina Way, San Diego, CA 92122, USA
| | - Martin W Ganal
- TraitGenetics GmbH, Am Schwabeplan 1b, Stadt Seeland OT, Gatersleben, Germany
| | - Allen Van Deynze
- Department of Plant Sciences, University of California-Davis, Davis, California 95616, USA
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41
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Lavaud C, Lesné A, Piriou C, Le Roy G, Boutet G, Moussart A, Poncet C, Delourme R, Baranger A, Pilet-Nayel ML. Validation of QTL for resistance to Aphanomyces euteiches in different pea genetic backgrounds using near-isogenic lines. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2015; 128:2273-88. [PMID: 26215183 DOI: 10.1007/s00122-015-2583-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 07/10/2015] [Indexed: 05/07/2023]
Abstract
KEY MESSAGE Marker-assisted backcrossing was used to generate pea NILs carrying individual or combined resistance alleles at main Aphanomyces resistance QTL. The effects of several QTL were successfully validated depending on genetic backgrounds. Quantitative trait loci (QTL) validation is an important and often overlooked step before subsequent research in QTL cloning or marker-assisted breeding for disease resistance in plants. Validation of QTL controlling partial resistance to Aphanomyces root rot, one of the most damaging diseases of pea worldwide, is of major interest for the future development of resistant varieties. The aim of this study was to validate, in different genetic backgrounds, the effects of various resistance alleles at seven main resistance QTL recently identified. Five backcross-assisted selection programs were developed. In each, resistance alleles at one to three of the seven main Aphanomyces resistance QTL were transferred into three genetic backgrounds, including two agronomically important spring (Eden) and winter (Isard) pea cultivars. The subsequent near-isogenic lines (NILs) were evaluated for resistance to two reference strains of the main A. euteiches pathotypes under controlled conditions. The NILs carrying resistance alleles at the major-effect QTL Ae-Ps4.5 and Ae-Ps7.6, either individually or in combination with resistance alleles at other QTL, showed significantly reduced disease severity compared to NILs without resistance alleles. Resistance alleles at some minor-effect QTL, especially Ae-Ps2.2 and Ae-Ps5.1, were also validated for their individual or combined effects on resistance. QTL × genetic background interactions were observed, mainly for QTL Ae-Ps7.6, the effect of which increased in the winter cultivar Isard. The pea NILs are a novel and valuable resource for further understanding the mechanisms underlying QTL and their integration in breeding programs.
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Affiliation(s)
- C Lavaud
- INRA, UMR IGEPP 1349, Institut de Génétique, Environnement et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France
| | - A Lesné
- INRA, UMR IGEPP 1349, Institut de Génétique, Environnement et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France
- Terres Univia, 11 rue de Monceau, CS 60003, 75378, Paris Cedex 08, France
| | - C Piriou
- INRA, UMR IGEPP 1349, Institut de Génétique, Environnement et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France
| | - G Le Roy
- INRA, UMR IGEPP 1349, Institut de Génétique, Environnement et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France
| | - G Boutet
- INRA, UMR IGEPP 1349, Institut de Génétique, Environnement et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France
| | - A Moussart
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France
- Terres Inovia, 11 rue de Monceau, CS 60003, 75378, Paris Cedex 08, France
| | - C Poncet
- INRA, UMR GDEC 1095, Génétique, Diversité, Ecophysiologie des Céréales, 5 chemin de Beaulieu, 63039, Clermont-Ferrand Cedex 2, France
| | - R Delourme
- INRA, UMR IGEPP 1349, Institut de Génétique, Environnement et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France
| | - A Baranger
- INRA, UMR IGEPP 1349, Institut de Génétique, Environnement et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France
| | - M-L Pilet-Nayel
- INRA, UMR IGEPP 1349, Institut de Génétique, Environnement et Protection des Plantes, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
- PISOM, UMT INRA/Terres Inovia, UMR IGEPP 1349, Domaine de la Motte au Vicomte, BP 35327, 35653, Le Rheu Cedex, France.
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