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Ro N, Haile M, Ko HC, Cho GT, Lee J, Kim B, Lee S, Kim SH. Genome-Wide Association Study of Phenolic Content and Antioxidant Properties in Eggplant Germplasm. Genes (Basel) 2023; 14:1315. [PMID: 37510220 PMCID: PMC10379237 DOI: 10.3390/genes14071315] [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: 05/27/2023] [Revised: 06/19/2023] [Accepted: 06/21/2023] [Indexed: 07/30/2023] Open
Abstract
The phenolic compounds in eggplant offer potential natural antioxidants for improved health. A large number of samples were examined in order to find eggplant germplasm with a high potential for health promotion. A genome-wide association study (GWAS) was conducted to identify single nucleotide polymorphisms (SNPs) associated with variations in total phenolic content (TPC) and antioxidant activity in eggplants, including ABTS (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)) scavenging activity and ferric reducing antioxidant power (FRAP). TPC values varied from 14.19 to 842.90 mg gallic acid equivalent (GAE)/100 g of dry weight of eggplant fruit powder. TPC showed a strong positive correlation with both FRAP and ABTS (r = 0.89 *** and 0.77 ***, respectively). The GWAS identified 20 SNPs that were significantly associated out of 29,183 SNPs. Out of the 20 significant SNPs, 11 showed associations with TPC, 4 with ABTS activity, and 5 with FRAP. Among the SNPs associated with TPC, one SNP was found on each of Chromosomes 3, 4, 7, and 12. In contrast, Chromosome 5 comprised two SNPs associated to TPC. Furthermore, the gene encoding IRX12 laccase-4 on Chromosome 10 was found to contain five SNPs associated with TPC. Four significantly linked SNPs on Chromosomes 1 (1 SNP), 4 (2 SNPs), and 10 (1 SNP) were found to be related to ABTS activity. The identified SNPs will be further examined as markers for selecting desirable eggplant varieties and exploring the links between candidate genes, phenolic content, and antioxidant activity. The findings of this study could assist in further study and the development of eggplants with improved health advantages through targeted breeding.
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Affiliation(s)
- Nayoung Ro
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Mesfin Haile
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Ho-Cheol Ko
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Gyu-Taek Cho
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Jungro Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Bichsaem Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Sookyeong Lee
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
| | - Seong-Hoon Kim
- National Agrobiodiversity Center, National Institute of Agricultural Sciences, Rural Development Administration, Jeonju 54874, Republic of Korea
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Calderón-González Á, Pérez-Vich B, Pouilly N, Boniface MC, Louarn J, Velasco L, Muños S. Association mapping for broomrape resistance in sunflower. FRONTIERS IN PLANT SCIENCE 2023; 13:1056231. [PMID: 36714707 PMCID: PMC9875907 DOI: 10.3389/fpls.2022.1056231] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
INTRODUCTION Sunflower breeding for resistance to the parasitic plant sunflower broomrape (Orobanche cumana Wallr.) requires the identification of novel resistance genes. In this research, we conducted a genome-wide association study (GWAS) to identify QTLs associated with broomrape resistance. METHODS The marker-trait associations were examined across a germplasm set composed of 104 sunflower accessions. They were genotyped with a 600k AXIOM® genome-wide array and evaluated for resistance to three populations of the parasite with varying levels of virulence (races EFR, FGV, and GTK) in two environments. RESULTS AND DISCUSSION The analysis of the genetic structure of the germplasm set revealed the presence of two main groups. The application of optimized treatments based on the general linear model (GLM) and the mixed linear model (MLM) allowed the detection of 14 SNP markers significantly associated with broomrape resistance. The highest number of marker-trait associations were identified on chromosome 3, clustered in two different genomic regions of this chromosome. Other associations were identified on chromosomes 5, 10, 13, and 16. Candidate genes for the main genomic regions associated with broomrape resistance were studied and discussed. Particularly, two significant SNPs on chromosome 3 associated with races EFR and FGV were found at two tightly linked SWEET sugar transporter genes. The results of this study have confirmed the role of some QTL on resistance to sunflower broomrape and have revealed new ones that may play an important role in the development of durable resistance to this parasitic weed in sunflower.
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Affiliation(s)
- Álvaro Calderón-González
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Córdoba, Spain
| | - Begoña Pérez-Vich
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Córdoba, Spain
| | - Nicolas Pouilly
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
| | - Marie-Claude Boniface
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
| | - Johann Louarn
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
| | - Leonardo Velasco
- Instituto de Agricultura Sostenible, Consejo Superior de Investigaciones Científicas (IAS-CSIC), Córdoba, Spain
| | - Stéphane Muños
- Laboratoire des Interactions Plantes Microbes-Environnement (LIPME), Université de Toulouse, CNRS, INRAE, Castanet-Tolosan, France
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Amiteye S. Basic concepts and methodologies of DNA marker systems in plant molecular breeding. Heliyon 2021; 7:e08093. [PMID: 34765757 PMCID: PMC8569399 DOI: 10.1016/j.heliyon.2021.e08093] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 08/25/2021] [Accepted: 09/27/2021] [Indexed: 12/27/2022] Open
Abstract
The concepts, methodologies and applications of some of the major molecular or DNA markers commonly used in plant science have been presented. The general principles of molecular marker techniques have been elucidated with detailed explanation of some notable basic concepts associated with marker applications: marker polymorphism, dominant or co-dominant mode of inheritance, agronomic trait-marker linkage, genetic mutations and variation. The molecular marker methods that have been extensively reviewed are RFLP, RAPD, SCAR, AFLP, SSR, CpSSR, ISSR, RAMP, SAMPL, SRAP, SSCP, CAPS, SNP, DArT, EST, and STS. In addition, the practicality of the retrotransposon-based marker methods, IRAP, REMAP, RBIP, and IPBS, have been discussed. Moreover, some salient characteristics of DNA markers have been compared and the various marker systems classified as PCR- or non-PCR-based, dominantly or co-dominantly inherited, locus specific or non-specific as well as at the levels of marker polymorphism and efficiency of marker reproducibility. Furthermore, the principles and methods of the following DNA markers have been highlighted: Penta-primer amplification refractory mutation system (PARMS), Conserved DNA-Derived Polymorphism (CDDP), P450-based analogue (PBA) markers, Tubulin-Based Polymorphism (TBP), Inter-SINE amplified polymorphism (ISAP), Sequence specific amplified polymorphism (S-SAP), Intron length polymorphisms (ILPs), Inter small RNA polymorphism (iSNAP), Direct amplification of length polymorphisms (DALP), Promoter anchored amplified polymorphism (PAAP), Target region amplification polymorphism (TRAP), Conserved region amplification polymorphism (CoRAP), Start Codon Targeted (SCoT) Polymorphism, and Directed Amplification of Minisatellite DNA (DAMD). Some molecular marker applications that have been recently employed to achieve various objectives in plant research have also been outlined. This review will serve as a useful reference resource for plant breeders and other scientists, as well as technicians and students who require basic know-how in the use of molecular or DNA marker technologies.
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Affiliation(s)
- Samuel Amiteye
- Department of Nuclear Agriculture and Radiation Processing (NARP), Graduate School of Nuclear and Allied Sciences (SNAS), College of Basic and Applied Sciences, University of Ghana, P. O. Box AE 1, Accra, Ghana
- Biotechnology Centre, Biotechnology and Nuclear Agriculture Research Institute (BNARI), Ghana Atomic Energy Commission (GAEC), P. O. Box AE 50, Accra, Ghana
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Nkhata W, Shimelis H, Melis R, Chirwa R, Mzengeza T, Mathew I, Shayanowako A. Genome-wide association analysis of bean fly resistance and agro-morphological traits in common bean. PLoS One 2021; 16:e0250729. [PMID: 33914796 PMCID: PMC8084209 DOI: 10.1371/journal.pone.0250729] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/12/2021] [Indexed: 11/19/2022] Open
Abstract
The bean fly (Ophiomyia spp) is a key insect pest causing significant crop damage and yield loss in common bean (Phaseolus vulgaris L., 2n = 2x = 22). Development and deployment of agronomic superior and bean fly resistant common bean varieties aredependent on genetic variation and the identification of genes and genomic regions controlling economic traits. This study's objective was to determine the population structure of a diverse panel of common bean genotypes and deduce associations between bean fly resistance and agronomic traits based on single nucleotide polymorphism (SNP) markers. Ninety-nine common bean genotypes were phenotyped in two seasons at two locations and genotyped with 16 565 SNP markers. The genotypes exhibited significant variation for bean fly damage severity (BDS), plant mortality rate (PMR), and pupa count (PC). Likewise, the genotypes showed significant variation for agro-morphological traits such as days to flowering (DTF), days to maturity (DTM), number of pods per plant (NPP), number of seeds per pod (NSP), and grain yield (GYD). The genotypes were delineated into two populations, which were based on the Andean and Mesoamerican gene pools. The genotypes exhibited a minimum membership coefficient of 0.60 to their respective populations. Eighty-three significant (P<0.01) markers were identified with an average linkage disequilibrium of 0.20 at 12Mb across the 11 chromosomes. Three markers were identified, each having pleiotropic effects on two traits: M100049197 (BDS and NPP), M3379537 (DTF and PC), and M13122571 (NPP and GYD). The identified markers are useful for marker-assisted selection in the breeding program to develop common bean genotypes with resistance to bean fly damage.
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Affiliation(s)
- Wilson Nkhata
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Hussein Shimelis
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Rob Melis
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Rowland Chirwa
- Alliance of Biodiversity International and CIAT, Chitedze Agricultural Station, Lilongwe, Malawi
| | - Tenyson Mzengeza
- Department of Agricultural Research Service, Chitedze Agricultural Research Station, Lilongwe, Malawi
| | - Isack Mathew
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
| | - Admire Shayanowako
- African Centre for Crop Improvement, School of Agricultural, Earth and Environmental Sciences, University of KwaZulu-Natal, Scottsville, Pietermaritzburg, South Africa
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Filippi CV, Zubrzycki JE, Di Rienzo JA, Quiroz FJ, Puebla AF, Alvarez D, Maringolo CA, Escande AR, Hopp HE, Heinz RA, Paniego NB, Lia VV. Unveiling the genetic basis of Sclerotinia head rot resistance in sunflower. BMC PLANT BIOLOGY 2020; 20:322. [PMID: 32641108 PMCID: PMC7346337 DOI: 10.1186/s12870-020-02529-7] [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: 10/16/2019] [Accepted: 06/26/2020] [Indexed: 05/06/2023]
Abstract
BACKGROUND Sclerotinia sclerotiorum is a necrotrophic fungus that causes Sclerotinia head rot (SHR) in sunflower, with epidemics leading to severe yield losses. In this work, we present an association mapping (AM) approach to investigate the genetic basis of natural resistance to SHR in cultivated sunflower, the fourth most widely grown oilseed crop in the world. RESULTS Our association mapping population (AMP), which comprises 135 inbred breeding lines (ILs), was genotyped using 27 candidate genes, a panel of 9 Simple Sequence Repeat (SSR) markers previously associated with SHR resistance via bi-parental mapping, and a set of 384 SNPs located in genes with molecular functions related to stress responses. Moreover, given the complexity of the trait, we evaluated four disease descriptors (i.e, disease incidence, disease severity, area under the disease progress curve for disease incidence, and incubation period). As a result, this work constitutes the most exhaustive AM study of disease resistance in sunflower performed to date. Mixed linear models accounting for population structure and kinship relatedness were used for the statistical analysis of phenotype-genotype associations, allowing the identification of 13 markers associated with disease reduction. The number of favourable alleles was negatively correlated to disease incidence, disease severity and area under the disease progress curve for disease incidence, whereas it was positevily correlated to the incubation period. CONCLUSIONS Four of the markers identified here as associated with SHR resistance (HA1848, HaCOI_1, G33 and G34) validate previous research, while other four novel markers (SNP117, SNP136, SNP44, SNP128) were consistently associated with SHR resistance, emerging as promising candidates for marker-assisted breeding. From the germplasm point of view, the five ILs carrying the largest combination of resistance alleles provide a valuable resource for sunflower breeding programs worldwide.
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Affiliation(s)
- C V Filippi
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - J E Zubrzycki
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
- Present address: Biocódices, San Martín, Buenos Aires, Argentina
| | - J A Di Rienzo
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Ing Agr. Felix Aldo Marrone 746 (5000), Córdoba, Argentina
| | - F J Quiroz
- Estación Experimental Agropecuaria INTA Balcarce, Ruta 226 Km 73.5 (7620), Balcarce, Buenos Aires, Argentina
| | - A F Puebla
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
| | - D Alvarez
- Estación Experimental Agropecuaria INTA Manfredi, Ruta 9 Km 636 (5988), Manfredi, Córdoba, Argentina
| | - C A Maringolo
- Estación Experimental Agropecuaria INTA Balcarce, Ruta 226 Km 73.5 (7620), Balcarce, Buenos Aires, Argentina
| | - A R Escande
- Estación Experimental Agropecuaria INTA Balcarce, Ruta 226 Km 73.5 (7620), Balcarce, Buenos Aires, Argentina
| | - H E Hopp
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires, Intendente Güiraldes 2160, (1428), Ciudad Autónoma de Buenos Aires, Argentina
| | - R A Heinz
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires, Intendente Güiraldes 2160, (1428), Ciudad Autónoma de Buenos Aires, Argentina
| | - N B Paniego
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - V V Lia
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA); Instituto de Agrobiotecnología y Biología Molecular (IABIMO), INTA-CONICET Nicolas Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas y Técnicas-CONICET, Ciudad Autónoma de Buenos Aires, Argentina.
- Facultad de Ciencias Exactas y Naturales Universidad de Buenos Aires, Intendente Güiraldes 2160, (1428), Ciudad Autónoma de Buenos Aires, Argentina.
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Filippi CV, Merino GA, Montecchia JF, Aguirre NC, Rivarola M, Naamati G, Fass MI, Álvarez D, Di Rienzo J, Heinz RA, Contreras Moreira B, Lia VV, Paniego NB. Genetic Diversity, Population Structure and Linkage Disequilibrium Assessment among International Sunflower Breeding Collections. Genes (Basel) 2020; 11:E283. [PMID: 32155892 PMCID: PMC7140877 DOI: 10.3390/genes11030283] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/01/2020] [Accepted: 03/03/2020] [Indexed: 12/20/2022] Open
Abstract
Sunflower germplasm collections are valuable resources for broadening the genetic base of commercial hybrids and ameliorate the risk of climate events. Nowadays, the most studied worldwide sunflower pre-breeding collections belong to INTA (Argentina), INRA (France), and USDA-UBC (United States of America-Canada). In this work, we assess the amount and distribution of genetic diversity (GD) available within and between these collections to estimate the distribution pattern of global diversity. A mixed genotyping strategy was implemented, by combining proprietary genotyping-by-sequencing data with public whole-genome-sequencing data, to generate an integrative 11,834-common single nucleotide polymorphism matrix including the three breeding collections. In general, the GD estimates obtained were moderate. An analysis of molecular variance provided evidence of population structure between breeding collections. However, the optimal number of subpopulations, studied via discriminant analysis of principal components (K = 12), the bayesian STRUCTURE algorithm (K = 6) and distance-based methods (K = 9) remains unclear, since no single unifying characteristic is apparent for any of the inferred groups. Different overall patterns of linkage disequilibrium (LD) were observed across chromosomes, with Chr10, Chr17, Chr5, and Chr2 showing the highest LD. This work represents the largest and most comprehensive inter-breeding collection analysis of genomic diversity for cultivated sunflower conducted to date.
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Affiliation(s)
- Carla V. Filippi
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
- Programa Académico para la Investigación e Innovación en Biotecnología, Universidad Nacional de Moreno–UNM, Moreno 1744, Argentina
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Gabriela A. Merino
- Instituto de Investigación y Desarrollo en Bioingeniería y Bioinformática–IBB, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional de Entre Ríos, Oro Verde 3100, Argentina
- Instituto de Investigación en Señales, Sistemas e Inteligencia Computacional-sinc(i), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Universidad Nacional del Litoral, Santa Fe 3000, Argentina
| | - Juan F. Montecchia
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Natalia C. Aguirre
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Máximo Rivarola
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Guy Naamati
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Mónica I. Fass
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Daniel Álvarez
- Estación Experimental Agropecuaria INTA Manfredi, Manfredi 5988, Argentina
| | - Julio Di Rienzo
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Ruth A. Heinz
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Bruno Contreras Moreira
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Verónica V. Lia
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
| | - Norma B. Paniego
- Instituto de Agrobiotecnología y Biología Molecular–IABiMo–INTA-CONICET, Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas, Instituto Nacional de Tecnología Agropecuaria, Hurlingham 1686, Argentina
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Li GH, Chen HC, Liu JL, Luo WL, Xie DS, Luo SB, Wu TQ, Akram W, Zhong YJ. A high-density genetic map developed by specific-locus amplified fragment (SLAF) sequencing and identification of a locus controlling anthocyanin pigmentation in stalk of Zicaitai (Brassica rapa L. ssp. chinensis var. purpurea). BMC Genomics 2019; 20:343. [PMID: 31064320 PMCID: PMC6503552 DOI: 10.1186/s12864-019-5693-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 04/15/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Caixin and Zicaitai (Brassica rapa) belong to Southern and Central China respectively. Zicaitai contains high amount of anthocyanin in leaf and stalk resulting to the purple color. Stalk is the major edible part and stalk color is an economically important trait for the two vegetables. The aim of this study is to construct a high density genetic map using the specific length amplified fragment sequencing (SLAF-seq) technique to explore genetic basis for anthocyanin pigmentation traits via quantitative trait loci (QTL) mapping. RESULTS We constructed a high generation linkage map with a mapping panel of F2 populations derived from 150 individuals of parental lines "Xianghongtai 01" and "Yinong 50D" with purple and green stalk respectively. The map was constructed containing 4253 loci, representing 10,940 single nucleotide polymorphism (SNP) markers spanning 1030.04 centiMorgans (cM) over 10 linkage groups (LGs), with an average distance between markers of 0.27 cM. Quantitative trait loci (QTL) analysis revealed that a major locus on chromosome 7 and 4 minor QTLs explaining 2.69-61.21% of phenotypic variation (PVE) were strongly responsible for variation in stalk color trait. Bioinformatics analysis of the major locus identified 62 protein-coding genes. Among the major locus, there were no biosynthetic genes related to anthocyanin. However, there were several transcription factors like helix-loop-helix (bHLH) bHLH, MYB in the locus. Seven predicted candidate genes were selected for the transcription level analysis. Only bHLH49 transcription factor, was significantly higher expressed in both stalks and young leaves of Xianghongtai01 than Yinong50D. An insertion and deletion (InDel) marker developed from deletion/insertion in the promoter region of bHLH49 showed significant correlation with the stalk color trait in the F2 population. CONCLUSION Using the constructed high-qualified linkage map, this study successfully identified QTLs for stalk color trait. The identified valuable markers and candidate genes for anthocyanin accumulation in stalk will provide useful information for molecular regulation of anthocyanin biosynthesis. Overall our findings will lay a foundation for functional gene cloning, marker-assisted selection (MAS) and molecular breeding of important economic traits in B. rapa.
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Affiliation(s)
- Gui-Hua Li
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Han-Cai Chen
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China
| | - Jia-Li Liu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Wen-Long Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Da-Sen Xie
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Shao-Bo Luo
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Ting-Quan Wu
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Waheed Akram
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China.,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China
| | - Yu-Juan Zhong
- Vegetable Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, 510640, People's Republic of China. .,Guangdong Key Laboratory for New Technology Research of Vegetables, Guangzhou, 510640, People's Republic of China.
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8
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Zubrzycki JE, Maringolo CA, Filippi CV, Quiróz FJ, Nishinakamasu V, Puebla AF, Di Rienzo JA, Escande A, Lia VV, Heinz RA, Hopp HE, Cervigni GDL, Paniego NB. Main and epistatic QTL analyses for Sclerotinia Head Rot resistance in sunflower. PLoS One 2017; 12:e0189859. [PMID: 29261806 PMCID: PMC5738076 DOI: 10.1371/journal.pone.0189859] [Citation(s) in RCA: 9] [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: 04/01/2017] [Accepted: 12/04/2017] [Indexed: 02/04/2023] Open
Abstract
Sclerotinia Head Rot (SHR), a disease caused by Sclerotinia sclerotiorum, is one of the most limiting factors in sunflower production. In this study, we identified genomic loci associated with resistance to SHR to support the development of assisted breeding strategies. We genotyped 114 Recombinant Inbred Lines (RILs) along with their parental lines (PAC2 -partially resistant-and RHA266 -susceptible-) by using a 384 single nucleotide polymorphism (SNP) Illumina Oligo Pool Assay to saturate a sunflower genetic map. Subsequently, we tested these lines for SHR resistance using assisted inoculations with S. sclerotiorum ascospores. We also conducted a randomized complete-block assays with three replicates to visually score disease incidence (DI), disease severity (DS), disease intensity (DInt) and incubation period (IP) through four field trials (2010-2014). We finally assessed main effect quantitative trait loci (M-QTLs) and epistatic QTLs (E-QTLs) by composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM), respectively. As a result of this study, the improved map incorporates 61 new SNPs over candidate genes. We detected a broad range of narrow sense heritability (h2) values (1.86-59.9%) as well as 36 M-QTLs and 13 E-QTLs along 14 linkage groups (LGs). On LG1, LG10, and LG15, we repeatedly detected QTLs across field trials; which emphasizes their putative effectiveness against SHR. In all selected variables, most of the identified QTLs showed high determination coefficients, associated with moderate to high heritability values. Using markers shared with previous Sclerotinia resistance studies, we compared the QTL locations in LG1, LG2, LG8, LG10, LG11, LG15 and LG16. This study constitutes the largest report of QTLs for SHR resistance in sunflower. Further studies focusing on the regions in LG1, LG10, and LG15 harboring the detected QTLs are necessary to identify causal alleles and contribute to unraveling the complex genetic basis governing the resistance.
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Affiliation(s)
- Jeremías Enrique Zubrzycki
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
| | - Carla Andrea Maringolo
- Laboratorio de Patología Vegetal, Unidad Integrada Universidad Nacional de Mar del Plata, Estación Experimental Agropecuaria INTA Balcarce, Balcarce, Buenos Aires, Argentina
| | - Carla Valeria Filippi
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
| | - Facundo José Quiróz
- Laboratorio de Patología Vegetal, Unidad Integrada Universidad Nacional de Mar del Plata, Estación Experimental Agropecuaria INTA Balcarce, Balcarce, Buenos Aires, Argentina
| | - Verónica Nishinakamasu
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
| | - Andrea Fabiana Puebla
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
| | - Julio A. Di Rienzo
- Cátedra de Estadística y Biometría, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba, Argentina
| | - Alberto Escande
- Laboratorio de Patología Vegetal, Unidad Integrada Universidad Nacional de Mar del Plata, Estación Experimental Agropecuaria INTA Balcarce, Balcarce, Buenos Aires, Argentina
| | - Verónica Viviana Lia
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Ruth Amalia Heinz
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Horacio Esteban Hopp
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
| | - Gerardo D. L. Cervigni
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
- Centro de Estudios Fotosintéticos y Bioquímicos, Rosario, Santa Fe, Argentina
| | - Norma Beatriz Paniego
- Instituto de Biotecnología, Centro de Investigaciones en Ciencias Agronómicas y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, Hurlingham, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de Buenos Aires, Argentina
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9
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Saini N, Singh N, Kumar A, Vihan N, Yadav S, Vasudev S, Yadava D. Development and validation of functional CAPS markers for the FAE genes in Brassica juncea and their use in marker-assisted selection. BREEDING SCIENCE 2016; 66:831-837. [PMID: 28163599 PMCID: PMC5282766 DOI: 10.1270/jsbbs.16132] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/14/2016] [Indexed: 05/25/2023]
Abstract
Low erucic acid is a major breeding target to improve the edible oil quality in Brassica juncea. The single nucleotide polymorphism (SNP) in fatty acid elongase 1 (FAE1.1 and FAE1.2) gene was exploited to expedite the breeding program. The paralogs of FAE1 gene were sequenced from low erucic acid genotype Pusa Mustard 30 and SNPs were identified through homologous alignment with sequence downloaded from NCBI GenBank. Two SNPs in FAE1.1 at position 591 and 1265 and one in FAE1.2 at 237 were found polymorphic among low and high erucic acid genotypes. These SNPs either create or change the recognition site of restriction enzymes. Transition of a single nucleotide at position 591 and 1265 in FAE1.1, and at position 237 in FAE1.2, leads to a change in the recognition site of Hpy99I, BglII and MnlI restriction enzymes, respectively. Two CAPS markers for FAE1.1 and one for FAE1.2 were developed to differentiate low and high erucic acid genotypes. The efficiency of these CAPS markers was found 100 per cent when validated in Brassica juncea, and B. nigra genotypes and used in back-cross breeding. These CAPS markers will facilitate in marker-assisted selection for improvement of oil quality in Brassica juncea.
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Affiliation(s)
- Navinder Saini
- Division of Genetics, ICAR-Indian Agricultural Research Institute,
New Delhi,
India
| | - Naveen Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute,
New Delhi,
India
| | - Anil Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute,
New Delhi,
India
| | - Nitika Vihan
- Division of Genetics, ICAR-Indian Agricultural Research Institute,
New Delhi,
India
| | - Sangita Yadav
- Division of Seed Science and Technology, ICAR-IARI,
New Delhi,
India
| | - Sujata Vasudev
- Division of Genetics, ICAR-Indian Agricultural Research Institute,
New Delhi,
India
| | - D.K. Yadava
- Division of Genetics, ICAR-Indian Agricultural Research Institute,
New Delhi,
India
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10
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Jiang B, Liu W, Xie D, Peng Q, He X, Lin Y, Liang Z. High-density genetic map construction and gene mapping of pericarp color in wax gourd using specific-locus amplified fragment (SLAF) sequencing. BMC Genomics 2015; 16:1035. [PMID: 26647294 PMCID: PMC4673774 DOI: 10.1186/s12864-015-2220-y] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 11/16/2015] [Indexed: 11/10/2022] Open
Abstract
Background High-density map is a valuable tool for genetic and genomic analysis. Although wax gourd is a widely distributed vegetable of Cucurbitaceae and has important medicinal and health value, no genetic map has been constructed because of the lack of efficient markers. Specific-locus amplified fragment sequencing (SLAF-seq) is a newly developed high-throughput strategy for large-scale single nucleotide polymorphism (SNP) discovery and genotyping. Results In our present study, we constructed a high-density genetic map by using SLAF-seq and identified a locus controlling pericarp color in wax gourd. An F2 population of 140 individuals and their two parents were subjected to SLAF-seq. A total of 143.38 M pair-end reads were generated. The average sequencing depth was 26.51 in the maternal line (B214), 27.01 in the parental line (B227), and 5.11 in each F2 individual. When filtering low-depth SLAF tags, a total of 142,653 high-quality SLAFs were detected, and 22,151 of them were polymorphic, with a polymorphism rate of 15.42 %. And finally, 4,607 of the polymorphic markers were selected for genetic map construction, and 12 linkage groups (LGs) were generated. The map spanned 2,172.86 cM with an average distance between adjacent markers for 0.49 cM. The inheritance of pericarp color was also studied, which showed that the pericarp color was controlled by one single gene. And based on the newly constructed high-density map, a single locus locating on chromosome 5 was identified for controlling the pericarp color of wax gourd. Conclusions This is the first report of high-density genetic map construction and gene mapping in wax gourd, which will be served as an invaluable tool for gene mapping, marker assisted breeding, map-based gene cloning, comparative mapping and draft genome assembling of wax gourd. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-2220-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Biao Jiang
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.,Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China
| | - Wenrui Liu
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.,Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China
| | - Dasen Xie
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China. .,Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China.
| | - Qingwu Peng
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China
| | - Xiaoming He
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China.,Guangdong Provincial Key Lab for New Technology Research on Vegetables, Guangzhou, 510640, China
| | - Yu'e Lin
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China
| | - Zhaojun Liang
- Vegetable Research Institute, Guangdong Academy of Agriculture Science, Guangzhou, 510640, China
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11
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Cho YI, Ahn YK, Tripathi S, Kim JH, Lee HE, Kim DS. Comparative analysis of disease-linked single nucleotide polymorphic markers from Brassica rapa for their applicability to Brassica oleracea. PLoS One 2015; 10:e0120163. [PMID: 25790283 PMCID: PMC4366180 DOI: 10.1371/journal.pone.0120163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2014] [Accepted: 01/12/2015] [Indexed: 11/18/2022] Open
Abstract
Numerous studies using single nucleotide polymorphisms (SNPs) have been conducted in humans, and other animals, and in major crops, including rice, soybean, and Chinese cabbage. However, the number of SNP studies in cabbage is limited. In this present study, we evaluated whether 7,645 SNPs previously identified as molecular markers linked to disease resistance in the Brassica rapa genome could be applied to B. oleracea. In a BLAST analysis using the SNP sequences of B. rapa and B. oleracea genomic sequence data registered in the NCBI database, 256 genes for which SNPs had been identified in B. rapa were found in B. oleracea. These genes were classified into three functional groups: molecular function (64 genes), biological process (96 genes), and cellular component (96 genes). A total of 693 SNP markers, including 145 SNP markers [BRH—developed from the B. rapa genome for high-resolution melt (HRM) analysis], 425 SNP markers (BRP—based on the B. rapa genome that could be applied to B. oleracea), and 123 new SNP markers (BRS—derived from BRP and designed for HRM analysis), were investigated for their ability to amplify sequences from cabbage genomic DNA. In total, 425 of the SNP markers (BRP-based on B. rapa genome), selected from 7,645 SNPs, were successfully applied to B. oleracea. Using PCR, 108 of 145 BRH (74.5%), 415 of 425 BRP (97.6%), and 118 of 123 BRS (95.9%) showed amplification, suggesting that it is possible to apply SNP markers developed based on the B. rapa genome to B. oleracea. These results provide valuable information that can be utilized in cabbage genetics and breeding programs using molecular markers derived from other Brassica species.
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Affiliation(s)
- Young-Il Cho
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
| | - Yul-Kyun Ahn
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
- * E-mail:
| | - Swati Tripathi
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
| | - Jeong-Ho Kim
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
| | - Hye-Eun Lee
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
| | - Do-Sun Kim
- Vegetable Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Suwon, Republic of Korea
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12
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Filippi CV, Aguirre N, Rivas JG, Zubrzycki J, Puebla A, Cordes D, Moreno MV, Fusari CM, Alvarez D, Heinz RA, Hopp HE, Paniego NB, Lia VV. Population structure and genetic diversity characterization of a sunflower association mapping population using SSR and SNP markers. BMC PLANT BIOLOGY 2015; 15:52. [PMID: 25848813 PMCID: PMC4351844 DOI: 10.1186/s12870-014-0360-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 11/27/2014] [Indexed: 05/20/2023]
Abstract
BACKGROUND Argentina has a long tradition of sunflower breeding, and its germplasm is a valuable genetic resource worldwide. However, knowledge of the genetic constitution and variability levels of the Argentinean germplasm is still scarce, rendering the global map of cultivated sunflower diversity incomplete. In this study, 42 microsatellite loci and 384 single nucleotide polymorphisms (SNPs) were used to characterize the first association mapping population used for quantitative trait loci mapping in sunflower, along with a selection of allied open-pollinated and composite populations from the germplasm bank of the National Institute of Agricultural Technology of Argentina. The ability of different kinds of markers to assess genetic diversity and population structure was also evaluated. RESULTS The analysis of polymorphism in the set of sunflower accessions studied here showed that both the microsatellites and SNP markers were informative for germplasm characterization, although to different extents. In general, the estimates of genetic variability were moderate. The average genetic diversity, as quantified by the expected heterozygosity, was 0.52 for SSR loci and 0.29 for SNPs. Within SSR markers, those derived from non-coding regions were able to capture higher levels of diversity than EST-SSR. A significant correlation was found between SSR and SNP- based genetic distances among accessions. Bayesian and multivariate methods were used to infer population structure. Evidence for the existence of three different genetic groups was found consistently across data sets (i.e., SSR, SNP and SSR + SNP), with the maintainer/restorer status being the most prevalent characteristic associated with group delimitation. CONCLUSION The present study constitutes the first report comparing the performance of SSR and SNP markers for population genetics analysis in cultivated sunflower. We show that the SSR and SNP panels examined here, either used separately or in conjunction, allowed consistent estimations of genetic diversity and population structure in sunflower breeding materials. The generated knowledge about the levels of diversity and population structure of sunflower germplasm is an important contribution to this crop breeding and conservation.
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Affiliation(s)
- Carla V Filippi
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA Ciudad Autónoma de Buenos Aires, Argentina
| | - Natalia Aguirre
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
| | - Juan G Rivas
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
| | - Jeremias Zubrzycki
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA Ciudad Autónoma de Buenos Aires, Argentina
| | - Andrea Puebla
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
| | - Diego Cordes
- />Estación Experimental Agropecuaria Manfredi, Ruta Nac. nro. 9 km 636 (5988), Manfredi, Córdoba (INTA) Argentina
| | - Maria V Moreno
- />Estación Experimental Agropecuaria Manfredi, Ruta Nac. nro. 9 km 636 (5988), Manfredi, Córdoba (INTA) Argentina
| | - Corina M Fusari
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Currently at System Regulation Group, Metabolic Networks Department, Max Planck Institute of Molecular Plant Physiology, Am Mühlemberg 1, D-14476 Potsdam-Golm, Germany
| | - Daniel Alvarez
- />Estación Experimental Agropecuaria Manfredi, Ruta Nac. nro. 9 km 636 (5988), Manfredi, Córdoba (INTA) Argentina
| | - Ruth A Heinz
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA Ciudad Autónoma de Buenos Aires, Argentina
- />Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria (1428), Buenos Aires, Argentina
| | - Horacio E Hopp
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria (1428), Buenos Aires, Argentina
| | - Norma B Paniego
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA Ciudad Autónoma de Buenos Aires, Argentina
| | - Veronica V Lia
- />Instituto de Biotecnología, Centro de Investigaciones en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), Nicolás Repetto y Los Reseros s/n (1686), Hurlingham, Buenos Aires Argentina
- />Consejo Nacional de Investigaciones Científicas y Técnicas–CONICET, Saavedra 15, C1083ACA Ciudad Autónoma de Buenos Aires, Argentina
- />Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Pabellón 2, Ciudad Universitaria (1428), Buenos Aires, Argentina
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13
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Talukder ZI, Gong L, Hulke BS, Pegadaraju V, Song Q, Schultz Q, Qi L. A high-density SNP Map of sunflower derived from RAD-sequencing facilitating fine-mapping of the rust resistance gene R12. PLoS One 2014; 9:e98628. [PMID: 25014030 PMCID: PMC4094432 DOI: 10.1371/journal.pone.0098628] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 05/06/2014] [Indexed: 11/19/2022] Open
Abstract
A high-resolution genetic map of sunflower was constructed by integrating SNP data from three F2 mapping populations (HA 89/RHA 464, B-line/RHA 464, and CR 29/RHA 468). The consensus map spanned a total length of 1443.84 cM, and consisted of 5,019 SNP markers derived from RAD tag sequencing and 118 publicly available SSR markers distributed in 17 linkage groups, corresponding to the haploid chromosome number of sunflower. The maximum interval between markers in the consensus map is 12.37 cM and the average distance is 0.28 cM between adjacent markers. Despite a few short-distance inversions in marker order, the consensus map showed high levels of collinearity among individual maps with an average Spearman's rank correlation coefficient of 0.972 across the genome. The order of the SSR markers on the consensus map was also in agreement with the order of the individual map and with previously published sunflower maps. Three individual and one consensus maps revealed the uneven distribution of markers across the genome. Additionally, we performed fine mapping and marker validation of the rust resistance gene R12, providing closely linked SNP markers for marker-assisted selection of this gene in sunflower breeding programs. This high resolution consensus map will serve as a valuable tool to the sunflower community for studying marker-trait association of important agronomic traits, marker assisted breeding, map-based gene cloning, and comparative mapping.
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Affiliation(s)
- Zahirul I. Talukder
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, United States of America
| | - Li Gong
- Department of Plant Pathology, North Dakota State University, Fargo, North Dakota, United States of America
| | - Brent S. Hulke
- Northern Crop Science Laboratory, USDA- Agricultural Research Service, Fargo, North Dakota, United States of America
| | | | - Qijian Song
- Soybean Genomics and Improvement Lab, USDA- Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Quentin Schultz
- BioDiagnostics Inc., River Falls, Wisconsin, United States of America
| | - Lili Qi
- Northern Crop Science Laboratory, USDA- Agricultural Research Service, Fargo, North Dakota, United States of America
- * E-mail:
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14
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Xu X, Xu R, Zhu B, Yu T, Qu W, Lu L, Xu Q, Qi X, Chen X. A high-density genetic map of cucumber derived from Specific Length Amplified Fragment sequencing (SLAF-seq). FRONTIERS IN PLANT SCIENCE 2014; 5:768. [PMID: 25610449 PMCID: PMC4285734 DOI: 10.3389/fpls.2014.00768] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Accepted: 12/12/2014] [Indexed: 05/18/2023]
Abstract
High-density genetic map provides an essential framework for accurate and efficient genome assembly and QTL fine mapping. Construction of high-density genetic maps appears more feasible since the advent of next-generation sequencing (NGS), which eases SNP discovery and high-throughput genotyping of large population. In this research, a high-density genetic map of cucumber (Cucumis sativus L.) was successfully constructed across an F2 population by a recently developed Specific Length Amplified Fragment sequencing (SLAF-seq) method. In total, 18.69 GB of data containing 93,460,000 paired-end reads were obtained after preprocessing. The average sequencing depth was 44.92 in the D8 (female parent), 42.16 in the Jin5-508 (male parent), and 5.01 in each progeny. 79,092 high-quality SLAFs were detected, of which 6784 SLAFs were polymorphic, and 1892 of the polymorphic markers met the requirements for constructing genetic map. The genetic map spanned 845.87 cm with an average genetic distance of 0.45 cm. It is a reliable linkage map for fine mapping and molecular breeding of cucumber for its high marker density and well-ordered markers.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xuehao Chen
- *Correspondence: Xuehao Chen, Department of Horticulture, School of Horticulture and Plant Protection, Yangzhou University, 48 Wenhui East Road, Yangzhou 225009, China e-mail:
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15
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Talukder ZI, Hulke BS, Qi L, Scheffler BE, Pegadaraju V, McPhee K, Gulya TJ. Candidate gene association mapping of Sclerotinia stalk rot resistance in sunflower (Helianthus annuus L.) uncovers the importance of COI1 homologs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:193-209. [PMID: 24193356 DOI: 10.1007/s00122-013-2210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 10/03/2013] [Indexed: 05/20/2023]
Abstract
Functional markers for Sclerotinia basal stalk rot resistance in sunflower were obtained using gene-level information from the model species Arabidopsis thaliana. Sclerotinia stalk rot, caused by Sclerotinia sclerotiorum, is one of the most destructive diseases of sunflower (Helianthus annuus L.) worldwide. Markers for genes controlling resistance to S. sclerotiorum will enable efficient marker-assisted selection (MAS). We sequenced eight candidate genes homologous to Arabidopsis thaliana defense genes known to be associated with Sclerotinia disease resistance in a sunflower association mapping population evaluated for Sclerotinia stalk rot resistance. The total candidate gene sequence regions covered a concatenated length of 3,791 bp per individual. A total of 187 polymorphic sites were detected for all candidate gene sequences, 149 of which were single nucleotide polymorphisms (SNPs) and 38 were insertions/deletions. Eight SNPs in the coding regions led to changes in amino acid codons. Linkage disequilibrium decay throughout the candidate gene regions declined on average to an r (2) = 0.2 for genetic intervals of 120 bp, but extended up to 350 bp with r (2) = 0.1. A general linear model with modification to account for population structure was found the best fitting model for this population and was used for association mapping. Both HaCOI1-1 and HaCOI1-2 were found to be strongly associated with Sclerotinia stalk rot resistance and explained 7.4 % of phenotypic variation in this population. These SNP markers associated with Sclerotinia stalk rot resistance can potentially be applied to the selection of favorable genotypes, which will significantly improve the efficiency of MAS during the development of stalk rot resistant cultivars.
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Affiliation(s)
- Zahirul I Talukder
- Department of Plant Sciences, North Dakota State University, 166 Loftsgard Hall, Fargo, ND, 58108-6050, USA
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16
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Talukder ZI, Hulke BS, Qi L, Scheffler BE, Pegadaraju V, McPhee K, Gulya TJ. Candidate gene association mapping of Sclerotinia stalk rot resistance in sunflower (Helianthus annuus L.) uncovers the importance of COI1 homologs. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2014; 127:193-209. [PMID: 24193356 DOI: 10.1007/s00122-013-2210-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Accepted: 10/03/2013] [Indexed: 05/02/2023]
Abstract
Functional markers for Sclerotinia basal stalk rot resistance in sunflower were obtained using gene-level information from the model species Arabidopsis thaliana. Sclerotinia stalk rot, caused by Sclerotinia sclerotiorum, is one of the most destructive diseases of sunflower (Helianthus annuus L.) worldwide. Markers for genes controlling resistance to S. sclerotiorum will enable efficient marker-assisted selection (MAS). We sequenced eight candidate genes homologous to Arabidopsis thaliana defense genes known to be associated with Sclerotinia disease resistance in a sunflower association mapping population evaluated for Sclerotinia stalk rot resistance. The total candidate gene sequence regions covered a concatenated length of 3,791 bp per individual. A total of 187 polymorphic sites were detected for all candidate gene sequences, 149 of which were single nucleotide polymorphisms (SNPs) and 38 were insertions/deletions. Eight SNPs in the coding regions led to changes in amino acid codons. Linkage disequilibrium decay throughout the candidate gene regions declined on average to an r (2) = 0.2 for genetic intervals of 120 bp, but extended up to 350 bp with r (2) = 0.1. A general linear model with modification to account for population structure was found the best fitting model for this population and was used for association mapping. Both HaCOI1-1 and HaCOI1-2 were found to be strongly associated with Sclerotinia stalk rot resistance and explained 7.4 % of phenotypic variation in this population. These SNP markers associated with Sclerotinia stalk rot resistance can potentially be applied to the selection of favorable genotypes, which will significantly improve the efficiency of MAS during the development of stalk rot resistant cultivars.
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Affiliation(s)
- Zahirul I Talukder
- Department of Plant Sciences, North Dakota State University, 166 Loftsgard Hall, Fargo, ND, 58108-6050, USA
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17
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Livaja M, Wang Y, Wieckhorst S, Haseneyer G, Seidel M, Hahn V, Knapp SJ, Taudien S, Schön CC, Bauer E. BSTA: a targeted approach combines bulked segregant analysis with next- generation sequencing and de novo transcriptome assembly for SNP discovery in sunflower. BMC Genomics 2013; 14:628. [PMID: 24330545 PMCID: PMC3848877 DOI: 10.1186/1471-2164-14-628] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Accepted: 09/16/2013] [Indexed: 01/31/2023] Open
Abstract
Background Sunflower belongs to the largest plant family on earth, the genomically poorly explored Compositae. Downy mildew Plasmopara halstedii (Farlow) Berlese & de Toni is one of the major diseases of cultivated sunflower (Helianthus annuus L.). In the search for new sources of downy mildew resistance, the locus PlARG on linkage group 1 (LG1) originating from H. argophyllus is promising since it confers resistance against all known races of the pathogen. However, the mapping resolution in the PlARG region is hampered by significantly suppressed recombination and by limited availability of polymorphic markers. Here we examined a strategy developed for the enrichment of molecular markers linked to this specific genomic region. We combined bulked segregant analysis (BSA) with next-generation sequencing (NGS) and de novo assembly of the sunflower transcriptome for single nucleotide polymorphism (SNP) discovery in a sequence resource combining reads originating from two sunflower species, H. annuus and H. argophyllus. Results A computational pipeline developed for SNP calling and pattern detection identified 219 candidate genes. For a proof of concept, 42 resistance gene-like sequences were subjected to experimental SNP validation. Using a high-resolution mapping population, 12 SNP markers were mapped to LG1. We successfully verified candidate sequences either co-segregating with or closely flanking PlARG. Conclusions This study is the first successful example to improve bulked segregant analysis with de novo transcriptome assembly using next generation sequencing. The BSTA pipeline we developed provides a useful guide for similar studies in other non-model organisms. Our results demonstrate this method is an efficient way to enrich molecular markers and to identify candidate genes in a specific mapping interval.
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Cadic E, Coque M, Vear F, Grezes-Besset B, Pauquet J, Piquemal J, Lippi Y, Blanchard P, Romestant M, Pouilly N, Rengel D, Gouzy J, Langlade N, Mangin B, Vincourt P. Combined linkage and association mapping of flowering time in Sunflower (Helianthus annuus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2013; 126:1337-56. [PMID: 23435733 DOI: 10.1007/s00122-013-2056-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2012] [Accepted: 01/20/2013] [Indexed: 05/20/2023]
Abstract
Association mapping and linkage mapping were used to identify quantitative trait loci (QTL) and/or causative mutations involved in the control of flowering time in cultivated sunflower Helianthus annuus. A panel of 384 inbred lines was phenotyped through testcrosses with two tester inbred lines across 15 location × year combinations. A recombinant inbred line (RIL) population comprising 273 lines was phenotyped both per se and through testcrosses with one or two testers in 16 location × year combinations. In the association mapping approach, kinship estimation using 5,923 single nucleotide polymorphisms was found to be the best covariate to correct for effects of panel structure. Linkage disequilibrium decay ranged from 0.08 to 0.26 cM for a threshold of 0.20, after correcting for structure effects, depending on the linkage group (LG) and the ancestry of inbred lines. A possible hitchhiking effect is hypothesized for LG10 and LG08. A total of 11 regions across 10 LGs were found to be associated with flowering time, and QTLs were mapped on 11 LGs in the RIL population. Whereas eight regions were demonstrated to be common between the two approaches, the linkage disequilibrium approach did not detect a documented QTL that was confirmed using the linkage mapping approach.
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Affiliation(s)
- Elena Cadic
- Laboratoire des Interactions Plantes-Microorganismes (LIPM), INRA, UMR441, 31326 Castanet-Tolosan, France.
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19
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Reif JC, Zhao Y, Würschum T, Gowda M, Hahn V. Genomic prediction of sunflower hybrid performance. PLANT BREEDING 2013; 132:107-114. [PMID: 0 DOI: 10.1111/pbr.12007] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Affiliation(s)
- Jochen C. Reif
- State Plant Breeding Institute; University of Hohenheim; 70599; Stuttgart; Germany
| | - Yusheng Zhao
- State Plant Breeding Institute; University of Hohenheim; 70599; Stuttgart; Germany
| | - Tobias Würschum
- State Plant Breeding Institute; University of Hohenheim; 70599; Stuttgart; Germany
| | - Manje Gowda
- State Plant Breeding Institute; University of Hohenheim; 70599; Stuttgart; Germany
| | - Volker Hahn
- State Plant Breeding Institute; University of Hohenheim; 70599; Stuttgart; Germany
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20
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Monteiro F, Romeiras MM, Batista D, Duarte MC. Biodiversity Assessment of Sugar Beet Species and Its Wild Relatives: Linking Ecological Data with New Genetic Approaches. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ajps.2013.48a003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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21
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Fusari CM, Di Rienzo JA, Troglia C, Nishinakamasu V, Moreno MV, Maringolo C, Quiroz F, Álvarez D, Escande A, Hopp E, Heinz R, Lia VV, Paniego NB. Association mapping in sunflower for Sclerotinia Head Rot resistance. BMC PLANT BIOLOGY 2012; 12:93. [PMID: 22708963 PMCID: PMC3778846 DOI: 10.1186/1471-2229-12-93] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Accepted: 05/21/2012] [Indexed: 05/04/2023]
Abstract
BACKGROUND Sclerotinia Head Rot (SHR) is one of the most damaging diseases of sunflower in Europe, Argentina, and USA, causing average yield reductions of 10 to 20 %, but leading to total production loss under favorable environmental conditions for the pathogen. Association Mapping (AM) is a promising choice for Quantitative Trait Locus (QTL) mapping, as it detects relationships between phenotypic variation and gene polymorphisms in existing germplasm without development of mapping populations. This article reports the identification of QTL for resistance to SHR based on candidate gene AM. RESULTS A collection of 94 sunflower inbred lines were tested for SHR under field conditions using assisted inoculation with the fungal pathogen Sclerotinia sclerotiorum. Given that no biological mechanisms or biochemical pathways have been clearly identified for SHR, 43 candidate genes were selected based on previous transcript profiling studies in sunflower and Brassica napus infected with S. sclerotiorum. Associations among SHR incidence and haplotype polymorphisms in 16 candidate genes were tested using Mixed Linear Models (MLM) that account for population structure and kinship relationships. This approach allowed detection of a significant association between the candidate gene HaRIC_B and SHR incidence (P < 0.01), accounting for a SHR incidence reduction of about 20 %. CONCLUSIONS These results suggest that AM will be useful in dissecting other complex traits in sunflower, thus providing a valuable tool to assist in crop breeding.
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Affiliation(s)
- Corina M Fusari
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), 1686, Hurlingham, Buenos Aires, Argentina
| | - Julio A Di Rienzo
- Cátedra de Estadística y Biometría, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, 5000, Córdoba, Argentina
| | - Carolina Troglia
- Estación Experimental Agropecuaria Balcarce, INTA, 7620, Balcarce, Buenos Aires, Argentina
| | - Verónica Nishinakamasu
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), 1686, Hurlingham, Buenos Aires, Argentina
| | - María Valeria Moreno
- Estación Experimental Agropecuaria Manfredi, INTA, 5988, Manfredi, Córdoba, Argentina
| | - Carla Maringolo
- Estación Experimental Agropecuaria Balcarce, INTA, 7620, Balcarce, Buenos Aires, Argentina
| | - Facundo Quiroz
- Estación Experimental Agropecuaria Balcarce, INTA, 7620, Balcarce, Buenos Aires, Argentina
| | - Daniel Álvarez
- Estación Experimental Agropecuaria Manfredi, INTA, 5988, Manfredi, Córdoba, Argentina
| | - Alberto Escande
- Estación Experimental Agropecuaria Balcarce, INTA, 7620, Balcarce, Buenos Aires, Argentina
| | - Esteban Hopp
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), 1686, Hurlingham, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ruth Heinz
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), 1686, Hurlingham, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Verónica V Lia
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), 1686, Hurlingham, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Norma B Paniego
- Instituto de Biotecnología, Centro Investigación en Ciencias Veterinarias y Agronómicas (CICVyA), Instituto Nacional de Tecnología Agropecuaria (INTA), 1686, Hurlingham, Buenos Aires, Argentina
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Xia Y, Ning Z, Bai G, Li R, Yan G, Siddique KHM, Baum M, Guo P. Allelic variations of a light harvesting chlorophyll a/b-binding protein gene (Lhcb1) associated with agronomic traits in barley. PLoS One 2012; 7:e37573. [PMID: 22662173 PMCID: PMC3360778 DOI: 10.1371/journal.pone.0037573] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2012] [Accepted: 04/21/2012] [Indexed: 11/19/2022] Open
Abstract
Light-harvesting chlorophyll a/b-binding protein (LHCP) is one of the most abundant chloroplast proteins in plants. Its main function is to collect and transfer light energy to photosynthetic reaction centers. However, the roles of different LHCPs in light-harvesting antenna systems remain obscure. Exploration of nucleotide variation in the genes encoding LHCP can facilitate a better understanding of the functions of LHCP. In this study, nucleotide variations in Lhcb1, a LHCP gene in barley, were investigated across 292 barley accessions collected from 35 different countries using EcoTILLING technology, a variation of the Targeting Induced Local Lesions In Genomes (TILLING). A total of 23 nucleotide variations were detected including three insert/deletions (indels) and 20 single nucleotide polymorphisms (SNPs). Among them, 17 SNPs were in the coding region with nine missense changes. Two SNPs with missense changes are predicted to be deleterious to protein function. Seventeen SNP formed 31 distinguishable haplotypes in the barley collection. The levels of nucleotide diversity in the Lhcb1 locus differed markedly with geographic origins and species of accessions. The accessions from Middle East Asia exhibited the highest nucleotide and haplotype diversity. H. spontaneum showed greater nucleotide diversity than H. vulgare. Five SNPs in Lhcb1 were significantly associated with at least one of the six agronomic traits evaluated, namely plant height, spike length, number of grains per spike, thousand grain weight, flag leaf area and leaf color, and these SNPs may be used as potential markers for improvement of these barley traits.
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Affiliation(s)
- Yanshi Xia
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
- College of Light Industry and Food Science, South China University of Technology, Guangzhou, China
| | - Zhengxiang Ning
- College of Light Industry and Food Science, South China University of Technology, Guangzhou, China
| | - Guihua Bai
- Hard Winter Wheat Genetics Research Unit, United States Department of Agriculture - Agricultural Research Service, Manhattan, Kansas, United States of America
| | - Ronghua Li
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
| | - Guijun Yan
- The Institute of Agriculture, The University of Western Australia, Crawley, Perth, Australia
| | - Kadambot H. M. Siddique
- The Institute of Agriculture, The University of Western Australia, Crawley, Perth, Australia
| | - Michael Baum
- International Center for Agricultural Research in the Dry Areas, Aleppo, Syria
| | - Peiguo Guo
- International Crop Research Center for Stress Resistance, College of Life Sciences, Guangzhou University, Guangzhou, China
- * E-mail:
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Bachlava E, Taylor CA, Tang S, Bowers JE, Mandel JR, Burke JM, Knapp SJ. SNP discovery and development of a high-density genotyping array for sunflower. PLoS One 2012; 7:e29814. [PMID: 22238659 PMCID: PMC3251610 DOI: 10.1371/journal.pone.0029814] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2011] [Accepted: 12/06/2011] [Indexed: 11/23/2022] Open
Abstract
Recent advances in next-generation DNA sequencing technologies have made possible the development of high-throughput SNP genotyping platforms that allow for the simultaneous interrogation of thousands of single-nucleotide polymorphisms (SNPs). Such resources have the potential to facilitate the rapid development of high-density genetic maps, and to enable genome-wide association studies as well as molecular breeding approaches in a variety of taxa. Herein, we describe the development of a SNP genotyping resource for use in sunflower (Helianthus annuus L.). This work involved the development of a reference transcriptome assembly for sunflower, the discovery of thousands of high quality SNPs based on the generation and analysis of ca. 6 Gb of transcriptome re-sequencing data derived from multiple genotypes, the selection of 10,640 SNPs for inclusion in the genotyping array, and the use of the resulting array to screen a diverse panel of sunflower accessions as well as related wild species. The results of this work revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, greater than 95% of successful SNP assays revealed polymorphism, and more than 90% of these assays could be successfully transferred to related wild species. Analysis of the polymorphism data revealed patterns of genetic differentiation that were largely congruent with the evolutionary history of sunflower, though the large number of markers allowed for finer resolution than has previously been possible.
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Affiliation(s)
- Eleni Bachlava
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, United States of America
| | - Christopher A. Taylor
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, United States of America
| | - Shunxue Tang
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, United States of America
| | - John E. Bowers
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, United States of America
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - Jennifer R. Mandel
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
| | - John M. Burke
- Department of Plant Biology, University of Georgia, Athens, Georgia, United States of America
- * E-mail:
| | - Steven J. Knapp
- Center for Applied Genetic Technologies, University of Georgia, Athens, Georgia, United States of America
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Fritsche S, Wang X, Li J, Stich B, Kopisch-Obuch FJ, Endrigkeit J, Leckband G, Dreyer F, Friedt W, Meng J, Jung C. A candidate gene-based association study of tocopherol content and composition in rapeseed (Brassica napus). FRONTIERS IN PLANT SCIENCE 2012; 3:129. [PMID: 22740840 PMCID: PMC3382996 DOI: 10.3389/fpls.2012.00129] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2012] [Accepted: 05/30/2012] [Indexed: 05/06/2023]
Abstract
Rapeseed (Brassica napus L.) is the most important oil crop of temperate climates. Rapeseed oil contains tocopherols, also known as vitamin E, which is an indispensable nutrient for humans and animals due to its antioxidant and radical scavenging abilities. Moreover, tocopherols are also important for the oxidative stability of vegetable oils. Therefore, seed oil with increased tocopherol content or altered tocopherol composition is a target for breeding. We investigated the role of nucleotide variations within candidate genes from the tocopherol biosynthesis pathway. Field trials were carried out with 229 accessions from a worldwide B. napus collection which was divided into two panels of 96 and 133 accessions. Seed tocopherol content and composition were measured by HPLC. High heritabilities were found for both traits, ranging from 0.62 to 0.94. We identified polymorphisms by sequencing selected regions of the tocopherol genes from the 96 accession panel. Subsequently, we determined the population structure (Q) and relative kinship (K) as detected by genotyping with genome-wide distributed SSR markers. Association studies were performed using two models, the structure-based GLM + Q and the PK-mixed model. Between 26 and 12 polymorphisms within two genes (BnaX.VTE3.a, BnaA.PDS1.c) were significantly associated with tocopherol traits. The SNPs explained up to 16.93% of the genetic variance for tocopherol composition and up to 10.48% for total tocopherol content. Based on the sequence information we designed CAPS markers for genotyping the 133 accessions from the second panel. Significant associations with various tocopherol traits confirmed the results from the first experiment. We demonstrate that the polymorphisms within the tocopherol genes clearly impact tocopherol content and composition in B. napus seeds. We suggest that these nucleotide variations may be used as selectable markers for breeding rapeseed with enhanced tocopherol quality.
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Affiliation(s)
- Steffi Fritsche
- Faculty of Agricultural and Nutritional Sciences, Plant Breeding Institute, Christian-Albrechts-UniversityKiel, Germany
| | - Xingxing Wang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
| | - Jinquan Li
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Benjamin Stich
- Quantitative Crop Genetics, Max Planck Institute for Plant Breeding ResearchCologne, Germany
| | - Friedrich J. Kopisch-Obuch
- Faculty of Agricultural and Nutritional Sciences, Plant Breeding Institute, Christian-Albrechts-UniversityKiel, Germany
| | - Jessica Endrigkeit
- Faculty of Agricultural and Nutritional Sciences, Plant Breeding Institute, Christian-Albrechts-UniversityKiel, Germany
| | - Gunhild Leckband
- Norddeutsche Pflanzenzucht Hans-Georg Lembke KGHohenlieth, Germany
| | - Felix Dreyer
- Norddeutsche Pflanzenzucht Hans-Georg Lembke KGHohenlieth, Germany
| | - Wolfgang Friedt
- Faculty of Agricultural Sciences, Nutritional Sciences and Environmental Management, Institute of Agronomy and Plant Breeding I, Justus-Liebig-UniversityGiessen, Germany
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityWuhan, China
| | - Christian Jung
- Faculty of Agricultural and Nutritional Sciences, Plant Breeding Institute, Christian-Albrechts-UniversityKiel, Germany
- *Correspondence: Christian Jung, Plant Breeding Institute, Christian-Albrechts-University, Olshausenstrasse 40, 24118 Kiel, Germany. e-mail:
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Mandel JR, Dechaine JM, Marek LF, Burke JM. Genetic diversity and population structure in cultivated sunflower and a comparison to its wild progenitor, Helianthus annuus L. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2011; 123:693-704. [PMID: 21638000 DOI: 10.1007/s00122-011-1619-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2010] [Accepted: 05/14/2011] [Indexed: 05/20/2023]
Abstract
Crop germplasm collections are valuable resources for ongoing plant breeding efforts. To fully utilize such collections, however, researchers need detailed information about the amount and distribution of genetic diversity present within collections. Here, we report the results of a population genetic analysis of the primary gene pool of sunflower (Helianthus annuus L.) based on a broad sampling of 433 cultivated accessions from North America and Europe, as well as a range-wide collection of 24 wild sunflower populations. Gene diversity across the cultivars was 0.47, as compared with 0.70 in the wilds, indicating that cultivated sunflower harbors roughly two-thirds of the total genetic diversity present in wild sunflower. Population structure analyses revealed that wild sunflower can be subdivided into four genetically distinct population clusters throughout its North American range, whereas the cultivated sunflower gene pool could be split into two main clusters separating restorer lines from the balance of the gene pool. Use of a maximum likelihood method to estimate the contribution of the wild gene pool to the cultivated sunflower germplasm revealed that the bulk of the cultivar diversity is derived from two wild sunflower population genetic clusters that are primarily composed of individuals from the east-central United States, the same general region in which sunflower domestication is believed to have occurred. We also identified a nested subset of accessions that capture as much of the allelic diversity present within the sampled cultivated sunflower germplasm collection as possible. At the high end, a core set of 288 captured nearly 90% of the alleles present in the full set of 433, whereas a core set of just 12 accessions was sufficient to capture nearly 50% of the total allelic diversity present within this sample of cultivated sunflower.
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Affiliation(s)
- J R Mandel
- Miller Plant Sciences, University of Georgia, Athens, GA 30602, USA
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Abstract
Determining the identity and distribution of molecular changes leading to the evolution of modern crop species provides major insights into the timing and nature of historical forces involved in rapid phenotypic evolution. In this study, we employed an integrated candidate gene strategy to identify loci involved in the evolution of flowering time during early domestication and modern improvement of the sunflower (Helianthus annuus). Sunflower homologs of many genes with known functions in flowering time were isolated and cataloged. Then, colocalization with previously mapped quantitative trait loci (QTLs), expression, or protein sequence differences between wild and domesticated sunflower, and molecular evolutionary signatures of selective sweeps were applied as step-wise criteria for narrowing down an original pool of 30 candidates. This process led to the discovery that five paralogs in the flowering locus T/terminal flower 1 gene family experienced selective sweeps during the evolution of cultivated sunflower and may be the causal loci underlying flowering time QTLs. Our findings suggest that gene duplication fosters evolutionary innovation and that natural variation in both coding and regulatory sequences of these paralogs responded to a complex history of artificial selection on flowering time during the evolution of cultivated sunflower.
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Blackman BK, Strasburg JL, Raduski AR, Michaels SD, Rieseberg LH. The role of recently derived FT paralogs in sunflower domestication. Curr Biol 2010; 20:629-35. [PMID: 20303265 DOI: 10.1016/j.cub.2010.01.059] [Citation(s) in RCA: 161] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2009] [Revised: 01/26/2010] [Accepted: 01/27/2010] [Indexed: 11/17/2022]
Abstract
Gene duplication provides an important source of genetic raw material for phenotypic diversification, but few studies have detailed the mechanisms through which duplications produce evolutionary novelty within species. Here, we investigate how a set of recently duplicated homologs of the floral inducer FLOWERING LOCUS T (FT) has contributed to sunflower domestication. We find that changes in expression of these duplicates are associated with differences in flowering behavior between wild and domesticated sunflower. In addition, we present genetic and functional evidence demonstrating that a frameshift mutation in one paralog, Helianthus annuus FT 1 (HaFT1), underlies a major QTL for flowering time and experienced a selective sweep during early domestication. Notably, this dominant-negative allele delays flowering through interference with action of another paralog, HaFT4. Together, these data reveal that changes affecting the expression, sequence, and gene interactions of HaFT paralogs have played key roles during sunflower domestication. Our findings also illustrate the important role that evolving interactions between new gene family members may play in fostering phenotypic change.
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Westermeier P, Wenzel G, Mohler V. Development and evaluation of single-nucleotide polymorphism markers in allotetraploid rapeseed (Brassica napus L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2009; 119:1301-11. [PMID: 19756476 DOI: 10.1007/s00122-009-1135-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Accepted: 08/12/2009] [Indexed: 05/08/2023]
Abstract
Single-nucleotide polymorphisms (SNPs) and insertion-deletions (INDELs) are currently the important classes of genetic markers for major crop species. In this study, methods for developing SNP markers in rapeseed (Brassica napus L.) and their in silico mapping and use for genotyping are demonstrated. For the development of SNP and INDEL markers, 181 fragments from 121 different gene sequences spanning 86 kb were examined. A combination of different selection methods (genome-specific amplification, hetero-duplex analysis and sequence analysis) allowed the detection of 18 singular fragments that showed a total of 87 SNPs and 6 INDELs between 6 different rapeseed varieties. The average frequency of sequence polymorphism was estimated to be one SNP every 247 bp and one INDEL every 3,583 bp. Most SNPs and INDELs were found in non-coding regions. Polymorphism information content values for SNP markers ranged between 0.02 and 0.50 in a set of 86 varieties. Using comparative genetics data for B. napus and Arabidopsis thaliana, an allocation of SNP markers to linkage groups in rapeseed was achieved: a unique location was determined for seven gene sequences; two and three possible locations were found for six and four sequences, respectively. The results demonstrate the usefulness of existing genomic resources for SNP discovery in rapeseed.
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Affiliation(s)
- Peter Westermeier
- Plant Breeding, Department of Plant Sciences, Center of Life and Food Sciences Weihenstephan, Technische Universität München, Am Hochanger 4, 85350 Freising, Germany.
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Labate JA, Robertson LD, Baldo AM. Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.). Heredity (Edinb) 2009; 103:257-67. [DOI: 10.1038/hdy.2009.58] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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