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Costa EN, Gomes ES, Reis LC, Foresti AC, Scalon SDPQ, Fernandes MG. Assessing common bean genotypes for resistance to Diabrotica speciosa (Coleoptera: Chrysomelidae). BULLETIN OF ENTOMOLOGICAL RESEARCH 2023; 113:546-554. [PMID: 37334552 DOI: 10.1017/s0007485323000226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Diabrotica speciosa (Germar) (Coleoptera: Chrysomelidae) is a major pest of common bean (Phaseolus vulgaris L.; Fabales: Fabaceae), and adults can defoliate plants during the whole crop cycle. This study was conducted to evaluate the resistance to D. speciosa in 16 common bean genotypes (14 landraces and 2 cultivars), through three different experiments. In the laboratory, choice and no-choice feeding tests were performed to evaluate the percentage of leaf consumption. In the greenhouse, plant height, numbers of leaves, percentage of injured leaves, percentage of injury per leaf, weight of seeds, and D. speciosa survival were evaluated. Furthermore, trichome density, levels of peroxidase (POD), superoxide dismutase (SOD), and protein content in common bean leaves were assessed. In the laboratory, the genotypes Chumbinho Branco, Dobalde, Manteigado, IPR Tuiuiú, and 90D Mouro were the least consumed by D. speciosa. In the greenhouse, the genotypes Dobalde, Manteigado, and IPR Tuiuiú expressed tolerance to the pest, which was associated with a higher plant height and/or unchanged POD and SOD levels and protein content following insect feeding, and no reduction in seed production. The landrace 90D Mouro exhibited antixenosis and tolerance to D. speciosa, observed as a lower leaf injury, higher trichome density, lower protein contents, higher SOD level and no reduction in seed weight. Overall, we have shown that antixenosis and tolerance can help overcome damages resulting from D. speciosa feeding, with emphasis on four common bean genotypes that may be useful in plant breeding programs aimed at controlling D. speciosa in common bean crops.
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Affiliation(s)
- Eduardo Neves Costa
- Universidade Federal da Grande Dourados, Faculdade de Ciências Agrárias, Programa de Pós-graduação em Agronomia, Rodovia Dourados/Itahum, Km 12, 79.804-970, Dourados, MS, Brazil
- Universidade Federal da Grande Dourados, Faculdade de Ciências Biológicas e Ambientais, Programa de Pós-Graduação em Entomologia e Conservação da Biodiversidade, Rodovia Dourados/Itahum, Km 12, 79.804-970, Dourados, MS, Brazil
| | - Elias Soares Gomes
- Universidade Federal da Grande Dourados, Faculdade de Ciências Biológicas e Ambientais, Programa de Pós-Graduação em Entomologia e Conservação da Biodiversidade, Rodovia Dourados/Itahum, Km 12, 79.804-970, Dourados, MS, Brazil
| | - Lucas Coutinho Reis
- Universidade Federal da Grande Dourados, Faculdade de Ciências Agrárias, Programa de Pós-graduação em Agronomia, Rodovia Dourados/Itahum, Km 12, 79.804-970, Dourados, MS, Brazil
| | - Andressa Caroline Foresti
- Universidade Federal da Grande Dourados, Faculdade de Ciências Agrárias, Programa de Pós-graduação em Agronomia, Rodovia Dourados/Itahum, Km 12, 79.804-970, Dourados, MS, Brazil
| | - Silvana de Paula Quintão Scalon
- Universidade Federal da Grande Dourados, Faculdade de Ciências Agrárias, Programa de Pós-graduação em Agronomia, Rodovia Dourados/Itahum, Km 12, 79.804-970, Dourados, MS, Brazil
| | - Marcos Gino Fernandes
- Universidade Federal da Grande Dourados, Faculdade de Ciências Agrárias, Programa de Pós-graduação em Agronomia, Rodovia Dourados/Itahum, Km 12, 79.804-970, Dourados, MS, Brazil
- Universidade Federal da Grande Dourados, Faculdade de Ciências Biológicas e Ambientais, Programa de Pós-Graduação em Entomologia e Conservação da Biodiversidade, Rodovia Dourados/Itahum, Km 12, 79.804-970, Dourados, MS, Brazil
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Hromadová Z, Gálová Z, Mikolášová L, Balážová Ž, Vivodík M, Chňapek M. Efficiency of RAPD and SCoT Markers in the Genetic Diversity Assessment of the Common Bean. PLANTS (BASEL, SWITZERLAND) 2023; 12:2763. [PMID: 37570917 PMCID: PMC10420954 DOI: 10.3390/plants12152763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/13/2023]
Abstract
Knowledge about the genetic diversity of the available common bean germplasm can help breeders properly direct the choice of genetic material in the breeding process. The aim of the present work was to estimate the usefulness of 10 RAPD and 10 SCoT markers in genetic diversity detection among 33 common bean genotypes. Both molecular marker systems were able to generate high levels of polymorphism in the genetic material, which was supported by the relatively high polymorphic information content (PIC) values observed for the used markers. The Diversity Detection Index (DDI) and Marker Index (MI) were used to compare the effectiveness of RAPD and SCoT markers. For both techniques, high values of MI and DDI were calculated, representing their effectivity. The SCoT markers showed higher values of the parameters used (MI = 7.474, DI = 2.265) than the RAPD markers (MI = 5.323, DDI = 1.612), indicating their higher efficiency in the detection of molecular variability. Three constructed dendrograms and PCoA plots were created using RAPD and SCoT, and both methods combined confirmed sufficient separation of the bean genotypes from each other. At the same time, a higher efficiency of SCoT markers compared to RAPD markers in the detection of the genetic diversity of beans was also proven. The results may be of future interest in the choice of genetically distant material for breeding purposes.
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Affiliation(s)
| | | | | | | | | | - Milan Chňapek
- Institute of Biotechnology, Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, Tr. A. Hlinku 2, 949 76 Nitra, Slovakia; (Z.H.); (Z.G.); (L.M.); (Ž.B.); (M.V.)
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Mulugeta B, Ortiz R, Geleta M, Hailesilassie T, Hammenhag C, Hailu F, Tesfaye K. Harnessing genome-wide genetic diversity, population structure and linkage disequilibrium in Ethiopian durum wheat gene pool. FRONTIERS IN PLANT SCIENCE 2023; 14:1192356. [PMID: 37546270 PMCID: PMC10400094 DOI: 10.3389/fpls.2023.1192356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 08/08/2023]
Abstract
Yanyang Liu, Henan Academy of Agricultural Sciences (HNAAS), China; Landraces are an important genetic source for transferring valuable novel genes and alleles required to enhance genetic variation. Therefore, information on the gene pool's genetic diversity and population structure is essential for the conservation and sustainable use of durum wheat genetic resources. Hence, the aim of this study was to assess genetic diversity, population structure, and linkage disequilibrium, as well as to identify regions with selection signature. Five hundred (500) individuals representing 46 landraces, along with 28 cultivars were evaluated using the Illumina Infinium 25K wheat SNP array, resulting in 8,178 SNPs for further analysis. Gene diversity (GD) and the polymorphic information content (PIC) ranged from 0.13-0.50 and 0.12-0.38, with mean GD and PIC values of 0.34 and 0.27, respectively. Linkage disequilibrium (LD) revealed 353,600 pairs of significant SNPs at a cut-off (r2 > 0.20, P < 0.01), with an average r2 of 0.21 for marker pairs. The nucleotide diversity (π) and Tajima's D (TD) per chromosome for the populations ranged from 0.29-0.36 and 3.46-5.06, respectively, with genome level, mean π values of 0.33 and TD values of 4.43. Genomic scan using the Fst outlier test revealed 85 loci under selection signatures, with 65 loci under balancing selection and 17 under directional selection. Putative candidate genes co-localized with regions exhibiting strong selection signatures were associated with grain yield, plant height, host plant resistance to pathogens, heading date, grain quality, and phenolic content. The Bayesian Model (STRUCTURE) and distance-based (principal coordinate analysis, PCoA, and unweighted pair group method with arithmetic mean, UPGMA) methods grouped the genotypes into five subpopulations, where landraces from geographically non-adjoining environments were clustered in the same cluster. This research provides further insights into population structure and genetic relationships in a diverse set of durum wheat germplasm, which could be further used in wheat breeding programs to address production challenges sustainably.
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Affiliation(s)
- Behailu Mulugeta
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
- Sinana Agricultural Research Center, Oromia Agricultural Research Institute, Bale-Robe, Ethiopia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | - Faris Hailu
- Bio and Emerging Technology Institute, Addis Ababa, Ethiopia
| | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Department of Biology and Biotechnology, Wollo University, Dessie, Ethiopia
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Catarcione G, Paolacci AR, Alicandri E, Gramiccia E, Taviani P, Rea R, Costanza MT, De Lorenzis G, Puccio G, Mercati F, Ciaffi M. Genetic Diversity and Population Structure of Common Bean ( Phaseolus vulgaris L.) Landraces in the Lazio Region of Italy. PLANTS (BASEL, SWITZERLAND) 2023; 12:744. [PMID: 36840092 PMCID: PMC9968208 DOI: 10.3390/plants12040744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
Common bean cultivation has historically been a typical component of rural economies in Italy, particularly in mountainous and hilly zones along the Apennine ridge of the central and southern regions, where the production is focused on local landraces cultivated by small-scale farmers using low-input production systems. Such landraces are at risk of genetic erosion because of the recent socioeconomic changes in rural communities. One hundred fourteen accessions belonging to 66 landraces still being grown in the Lazio region were characterized using a multidisciplinary approach. This approach included morphological (seed traits), biochemical (phaseolin and phytohemagglutinin patterns), and molecular (microsatellite loci) analyses to investigate their genetic variation, structure, and distinctiveness, which will be essential for the implementation of adequate ex situ and in situ conservation strategies. Another objective of this study was to determine the original gene pool (Andean and Mesoamerican) of the investigated landraces and to evaluate the cross-hybridization events between the two ancestral gene pools in the P. vulgaris germplasm in the Lazio region. Molecular analyses on 456 samples (four for each of the 114 accessions) revealed that the P. vulgaris germplasm in the Lazio region exhibited a high level of genetic diversity (He = 0.622) and that the Mesoamerican and Andean gene pools were clearly differentiated, with the Andean gene pool prevailing (77%) and 12% of landraces representing putative hybrids between the two gene pools. A model-based cluster analysis based on the molecular markers highlighted three main groups in agreement with the phaseolin patterns and growth habit of landraces. The combined utilisation of morphological, biochemical, and molecular data allowed for the differentiation of all landraces and the resolution of certain instances of homonymy and synonymy. Furthermore, although a high level of homozygosity was found across all landraces, 32 of the 66 examined (49%) exhibited genetic variability, indicating that the analysis based on a single or few plants per landrace, as usually carried out, may provide incomplete information.
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Affiliation(s)
- Giulio Catarcione
- DIBAF, Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
| | - Anna Rita Paolacci
- DIBAF, Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
| | - Enrica Alicandri
- DIBAF, Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
| | - Elena Gramiccia
- DIBAF, Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
| | | | - Roberto Rea
- ARSIAL, Via Rodolfo Lanciani 38, 00162 Roma, Italy
| | | | | | | | | | - Mario Ciaffi
- DIBAF, Università degli Studi della Tuscia, Via San Camillo de Lellis, 01100 Viterbo, Italy
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Arriagada O, Arévalo B, Cabeza RA, Carrasco B, Schwember AR. Meta-QTL Analysis for Yield Components in Common Bean ( Phaseolus vulgaris L.). PLANTS (BASEL, SWITZERLAND) 2022; 12:117. [PMID: 36616246 PMCID: PMC9824219 DOI: 10.3390/plants12010117] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/15/2022] [Accepted: 12/17/2022] [Indexed: 06/17/2023]
Abstract
Common bean is one of the most important legumes produced and consumed worldwide because it is a highly valuable food for the human diet. However, its production is mainly carried out by small farmers, who obtain average grain yields below the potential yield of the species. In this sense, numerous mapping studies have been conducted to identify quantitative trait loci (QTL) associated with yield components in common bean. Meta-QTL (MQTL) analysis is a useful approach to combine data sets and for creating consensus positions for the QTL detected in independent studies. Consequently, the objective of this study was to perform a MQTL analysis to identify the most reliable and stable genomic regions associated with yield-related traits of common bean. A total of 667 QTL associated with yield-related traits reported in 21 different studies were collected. A total of 42 MQTL associated with yield-related traits were identified, in which the average confidence interval (CI) of the MQTL was 3.41 times lower than the CIs of the original QTL. Most of the MQTL (28) identified in this study contain QTL associated with yield and phenological traits; therefore, these MQTL can be useful in common bean breeding programs. Finally, a total of 18 candidate genes were identified and associated with grain yield within these MQTL, with functions related to ubiquitin ligase complex, response to auxin, and translation elongation factor activity.
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Affiliation(s)
- Osvin Arriagada
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
| | - Bárbara Arévalo
- Centro de Estudios en Alimentos Procesados, Talca 3460000, Chile
| | - Ricardo A. Cabeza
- Departamento de Producción Agrícola, Facultad de Ciencias Agrarias, Universidad de Talca, Talca 3460000, Chile
| | - Basilio Carrasco
- Centro de Estudios en Alimentos Procesados, Talca 3460000, Chile
| | - Andrés R. Schwember
- Departamento de Ciencias Vegetales, Facultad de Agronomía e Ingeniería Forestal, Pontificia Universidad Católica de Chile, Santiago 7820436, Chile
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Falcione M, Simiele M, Renella A, Scippa GS, Di Martino P, Trupiano D. A Multi-Level Approach as a Powerful Tool to Identify and Characterize Some Italian Autochthonous Common Bean ( Phaseolus vulgaris L.) Landraces under a Changing Environment. PLANTS (BASEL, SWITZERLAND) 2022; 11:2790. [PMID: 36297814 PMCID: PMC9609626 DOI: 10.3390/plants11202790] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 10/14/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
A prime role in matters of agrobiodiversity is held by landraces, which serve as a repository gene pool able to meet sustainable development goals and to face the ongoing challenges of climate change. However, many landraces are currently endangered due to environmental and socio-economic changes. Thus, effective characterization activities and conservation strategies should be undertaken to prevent their genetic and cultural erosion. In the current study, the morphological, genetic, and biochemical analyses were integrated with stress response-related studies to characterize the diversity of seven Italian autochthonous common bean landraces. The results showed that the morphological descriptors and the neutral molecular markers represent powerful tools to identify and distinguish diversity among landrace populations, but they cannot correlate with the stress tolerance pattern of genetically similar populations. The study also supported the use of proline as a biochemical marker to screen the most salt-sensitive bean landraces. Thus, to fully elucidate the future dynamics of agrobiodiversity and to establish the basis for safeguarding them while promoting their utilization, a multi-level approach should always be included in any local and national program for the characterization/conservation/use of genetic resources. This study should represent the basis for further joint research that effectively contributes to set/achieve Italian priorities towards sustainability in the framework of emerging environmental, societal, and economic challenges.
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Shao J, Hao Y, Wang L, Xie Y, Zhang H, Bai J, Wu J, Fu J. Development of a Model for Genomic Prediction of Multiple Traits in Common Bean Germplasm, Based on Population Structure. PLANTS (BASEL, SWITZERLAND) 2022; 11:1298. [PMID: 35631723 PMCID: PMC9144439 DOI: 10.3390/plants11101298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/08/2022] [Accepted: 05/09/2022] [Indexed: 06/15/2023]
Abstract
Due to insufficient identification and in-depth investigation of existing common bean germplasm resources, it is difficult for breeders to utilize these valuable genetic resources. This situation limits the breeding and industrial development of the common bean (Phaseolus vulgaris L.) in China. Genomic prediction (GP) is a breeding method that uses whole-genome molecular markers to calculate the genomic estimated breeding value (GEBV) of candidate materials and select breeding materials. This study aimed to use genomic prediction to evaluate 15 traits in a collection of 628 common bean lines (including 484 landraces and 144 breeding lines) to determine a common bean GP model. The GP model constructed by landraces showed a moderate to high predictive ability (ranging from 0.59-0.88). Using all landraces as a training set, the predictive ability of the GP model for most traits was higher than that using the landraces from each of two subgene pools, respectively. Randomly selecting breeding lines as additional training sets together with landrace training sets to predict the remaining breeding lines resulted in a higher predictive ability based on principal components analysis. This study constructed a widely applicable GP model of the common bean based on the population structure, and encouraged the development of GP models to quickly aggregate excellent traits and accelerate utilization of germplasm resources.
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Affiliation(s)
- Jing Shao
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China;
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (L.W.); (Y.X.); (H.Z.)
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China
| | - Yangfan Hao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (L.W.); (Y.X.); (H.Z.)
| | - Lanfen Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (L.W.); (Y.X.); (H.Z.)
| | - Yuxin Xie
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (L.W.); (Y.X.); (H.Z.)
| | - Hongwei Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (L.W.); (Y.X.); (H.Z.)
| | - Jiangping Bai
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China;
- Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China
| | - Jing Wu
- Department of Crop Genetics and Breeding, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China;
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (L.W.); (Y.X.); (H.Z.)
| | - Junjie Fu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (Y.H.); (L.W.); (Y.X.); (H.Z.)
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Yeken MZ, Emiralioğlu O, Çiftçi V, Bayraktar H, Palacioğlu G, Özer G. Analysis of genetic diversity among common bean germplasm by start codon targeted (SCoT) markers. Mol Biol Rep 2022; 49:3839-3847. [PMID: 35301653 DOI: 10.1007/s11033-022-07229-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 02/01/2022] [Accepted: 02/03/2022] [Indexed: 11/30/2022]
Abstract
BACKGROUND Breeding strategies to improve modern varieties having high yield, high nutritional value and resistance to biotic and abiotic stress, etc. is very important to make up for the food deficiencies. Molecular studies as a tool in breeding programs for the characterization of germplasm have been performed with several DNA marker systems. MATERIALS AND METHODS In the present study, the genetic diversity of 53 common bean landraces and 22 registered varieties from Turkey, and 12 genotypes from USDA was investigated using start codon targeted (SCoT) markers for the first time worldwide. The 8 primers having stronger and more polymorphic bands were used for PCR amplification. RESULTS The mean polymorphic band of all primers was found as 13.13. The average of polymorphic information content and resolving power values was 0.34 and 7.55, respectively. Analysis of molecular variance (AMOVA) explored the existence of higher genetic diversity within populations accounting for 92% compared to among populations variations. According to cluster analysis (UPGMA) and genetic structure based on SCoT data, accessions were separated into Andean (PopA) and Mesoamerican PopB) gene pools. Moreover, accessions were mostly placed in the same groups/subgroups according to their geographical origin. CONCLUSIONS A high level of genetic diversity was observed between the investigated accessions in this work. The findings will help to plant breeders to characterize common bean accessions.
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Affiliation(s)
- Mehmet Zahit Yeken
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Orkun Emiralioğlu
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Vahdettin Çiftçi
- Department of Field Crops, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey
| | - Harun Bayraktar
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Ankara, Turkey
| | - Gülsüm Palacioğlu
- Department of Plant Protection, Faculty of Agriculture, Ankara University, Ankara, Turkey
| | - Göksel Özer
- Department of Plant Protection, Faculty of Agriculture, Bolu Abant Izzet Baysal University, Bolu, Turkey.
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de Carvalho Paulino JF, de Almeida CP, Song Q, Carbonell SAM, Chiorato AF, Benchimol-Reis LL. Genetic diversity and inter-gene pool introgression of Mesoamerican Diversity Panel in common beans. J Appl Genet 2021; 62:585-600. [PMID: 34386968 DOI: 10.1007/s13353-021-00657-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/15/2021] [Accepted: 08/02/2021] [Indexed: 10/20/2022]
Abstract
Brazil is among the largest producers and consumers of common bean (Phaseolus vulgaris L.) and can be considered a secondary center of diversity for the species. The aim of this study was to estimate the genetic diversity, population structure, and relationships among 288 common bean accessions in an American Diversity Panel (ADP) genotyped with 4,042 high-quality single nucleotide polymorphisms (SNPs). The results showed inter-gene pool hybridization (hybrids) between the two main gene pools (i.e., Mesoamerican and Andean), based on principal component analysis (PCA), discriminant analysis of principal components (DAPC), and STRUCTURE analysis. The genetic diversity parameters showed that the Mesoamerican group has higher values of diversity and allelic richness in comparison with the Andean group. Considering the optimal clusters (K), clustering was performed according to the type of grain (i.e., market group), the institution of origin, the period of release, and agronomic traits. A new subset was selected and named the Mesoamerican Diversity Panel (MDP), with 205 Mesoamerican accessions. Analysis of molecular variance (AMOVA) showed low genetic variance between the two panels (i.e., ADP and MDP) with the highest percentage of the limited variance among accessions in each group. The ADP showed occurrence of high genetic differentiation between populations (i.e., Mesoamerican and Andean) and introgression between gene pools in hybrids based on a set of diagnostic SNPs. The MDP showed better linkage disequilibrium (LD) decay. The availability of genetic variation from inter-gene pool hybridizations presents a potential opportunity for breeders towards the development of superior common bean cultivars.
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Affiliation(s)
| | - Caléo Panhoca de Almeida
- Common Bean Genetic Group, Natural Center of Plant Genetics, Agronomic Institute (IAC), Campinas, SP, Brazil
| | - Qijian Song
- Soybean Genomics and Improvement Lab, USDA-ARS, Beltsville, MD, USA
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Assessment of the Origin and Diversity of Croatian Common Bean Germplasm Using Phaseolin Type, SSR and SNP Markers and Morphological Traits. PLANTS 2021; 10:plants10040665. [PMID: 33808489 PMCID: PMC8066053 DOI: 10.3390/plants10040665] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/25/2021] [Accepted: 03/28/2021] [Indexed: 11/18/2022]
Abstract
Landraces represent valuable genetic resources for breeding programmes to produce high-yielding varieties adapted to stressful environmental conditions. Although the common bean (Phaseolus vulgaris L.) is an economically important food legume for direct human consumption worldwide, common bean production in Croatia is based almost exclusively on landraces and there is no common bean breeding program. Information on phaseolin type and results of population structure and genetic diversity obtained by analysis of SSR and SNP markers, in combination with the morphological characterization of 174 accessions of 10 common bean landraces (morphotypes), enabled thorough classification of accessions. The accessions were classified into phaseolin type H1 (“S”) of Mesoamerican origin and phaseolin types H2 (“H” or “C”) and H3 (“T”) of Andean origin. By applying distance- and model-based clustering methods to SSR markers, the accessions were classified into two clusters at K = 2 separating the accessions according to the centres of origin, while at K = 3, the accessions of Andean origin were further classified into two clusters of accessions that differed in phaseolin type (H2 and H3). Using SNP markers, model-based analysis of population structure was performed, the results of which were consistent with those of SSR markers. In addition, 122 accessions were assigned to 14 newly formed true-type morphogenetic groups derived from three different domestication events: (1) Mesoamerican (H1A) (“Biser”, “Kukuruzar”, “Tetovac”, “Trešnjevac”), (2) Andean—indeterminate type (H2B1) (“Dan noć”, “Sivi”, “Puter”, ”Sivi prošarani”, “Trešnjevac”) and (3) Andean—determinate type (H3B2) (“Bijeli”, “Dan noć”, “Puter”, “Trešnjevac”, “Zelenčec”). The rest of the accessions could represent putative hybrids between morphogenetic groups. The differences between the true-type groups of accessions were further analysed based on nine quantitative traits, and the subsets of traits that best distinguish among centres of origin (A: Mesoamerican, B: Andean) and genetic groups (H1A, H2B1, H3B2) were proposed.
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Gunjača J, Carović-Stanko K, Lazarević B, Vidak M, Petek M, Liber Z, Šatović Z. Genome-Wide Association Studies of Mineral Content in Common Bean. FRONTIERS IN PLANT SCIENCE 2021; 12:636484. [PMID: 33763096 PMCID: PMC7982862 DOI: 10.3389/fpls.2021.636484] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/09/2021] [Indexed: 05/15/2023]
Abstract
Micronutrient malnutrition is one of the main public health problems in many parts of the world. This problem raises the attention of all valuable sources of micronutrients for the human diet, such as common bean (Phaseolus vulgaris L.). In this research, a panel of 174 accessions representing Croatian common bean landraces was phenotyped for seed content of eight nutrients (N, P, K, Ca, Mg, Fe, Zn, and Mn), and genotyped using 6,311 high-quality DArTseq-derived SNP markers. A genome-wide association study (GWAS) was then performed to identify new genetic sources for improving seed mineral content. Twenty-two quantitative trait nucleotides (QTN) associated with seed nitrogen content were discovered on chromosomes Pv01, Pv02, Pv03, Pv05, Pv07, Pv08, and Pv10. Five QTNs were associated with seed phosphorus content, four on chromosome Pv07, and one on Pv08. A single significant QTN was found for seed calcium content on chromosome Pv09 and for seed magnesium content on Pv08. Finally, two QTNs associated with seed zinc content were identified on Pv06 while no QTNs were found to be associated with seed potassium, iron, or manganese content. Our results demonstrate the utility of GWAS for understanding the genetic architecture of seed nutritional traits in common bean and have utility for future enrichment of seed with macro- and micronutrients through genomics-assisted breeding.
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Affiliation(s)
- Jerko Gunjača
- Department of Plant Breeding, Genetics and Biometrics, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Zagreb, Croatia
| | - Klaudija Carović-Stanko
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Zagreb, Croatia
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
- *Correspondence: Klaudija Carović-Stanko,
| | - Boris Lazarević
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Zagreb, Croatia
- Department of Plant Nutrition, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Monika Vidak
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Zagreb, Croatia
| | - Marko Petek
- Department of Plant Nutrition, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Zlatko Liber
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Zagreb, Croatia
- Department of Biology, Faculty of Science, University of Zagreb, Zagreb, Croatia
| | - Zlatko Šatović
- Centre of Excellence for Biodiversity and Molecular Plant Breeding (CoE CroP-BioDiv), Zagreb, Croatia
- Department of Seed Science and Technology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
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Valdisser PAMR, Müller BSF, de Almeida Filho JE, Morais Júnior OP, Guimarães CM, Borba TCO, de Souza IP, Zucchi MI, Neves LG, Coelho ASG, Brondani C, Vianello RP. Genome-Wide Association Studies Detect Multiple QTLs for Productivity in Mesoamerican Diversity Panel of Common Bean Under Drought Stress. FRONTIERS IN PLANT SCIENCE 2020; 11:574674. [PMID: 33343591 PMCID: PMC7738703 DOI: 10.3389/fpls.2020.574674] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/22/2020] [Indexed: 05/26/2023]
Abstract
Drought stress is an important abiotic factor limiting common bean yield, with great impact on the production worldwide. Understanding the genetic basis regulating beans' yield and seed weight (SW) is a fundamental prerequisite for the development of superior cultivars. The main objectives of this work were to conduct genome-wide marker discovery by genotyping a Mesoamerican panel of common bean germplasm, containing cultivated and landrace accessions of broad origin, followed by the identification of genomic regions associated with productivity under two water regimes using different genome-wide association study (GWAS) approaches. A total of 11,870 markers were genotyped for the 339 genotypes, of which 3,213 were SilicoDArT and 8,657 SNPs derived from DArT and CaptureSeq. The estimated linkage disequilibrium extension, corrected for structure and relatedness (r 2 sv ), was 98.63 and 124.18 kb for landraces and breeding lines, respectively. Germplasm was structured into landraces and lines/cultivars. We carried out GWASs for 100-SW and yield in field environments with and without water stress for 3 consecutive years, using single-, segment-, and gene-based models. Higher number of associations at high stringency was identified for the SW trait under irrigation, totaling ∼185 QTLs for both single- and segment-based, whereas gene-based GWASs showed ∼220 genomic regions containing ∼650 genes. For SW under drought, 18 QTLs were identified for single- and segment-based and 35 genes by gene-based GWASs. For yield, under irrigation, 25 associations were identified, whereas under drought the total was 10 using both approaches. In addition to the consistent associations detected across experiments, these GWAS approaches provided important complementary QTL information (∼221 QTLs; 650 genes; r 2 from 0.01% to 32%). Several QTLs were mined within or near candidate genes playing significant role in productivity, providing better understanding of the genetic mechanisms underlying these traits and making available molecular tools to be used in marker-assisted breeding. The findings also allowed the identification of genetic material (germplasm) with better yield performance under drought, promising to a common bean breeding program. Finally, the availability of this highly diverse Mesoamerican panel is of great scientific value for the analysis of any relevant traits in common bean.
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Affiliation(s)
- Paula Arielle Mendes Ribeiro Valdisser
- Biotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, Brazil
- Genetics and Molecular Biology Graduate Program, Institute of Biology, UNICAMP, Campinas, Brazil
| | - Bárbara S. F. Müller
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, United States
| | | | | | | | - Tereza C. O. Borba
- Biotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, Brazil
| | - Isabela Pavanelli de Souza
- Biotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, Brazil
- Postgraduate Program in Biological Sciences, Institute of Biological Sciences, Federal University of Goiás, Goiânia, Brazil
| | - Maria Imaculada Zucchi
- Genetics and Molecular Biology Graduate Program, Institute of Biology, UNICAMP, Campinas, Brazil
- Agribusiness Technology Agency of São Paulo State, Agriculture and Food Supply Secretary of São Paulo, Piracicaba, Brazil
| | | | | | - Claudio Brondani
- Biotechnology Laboratory, EMBRAPA Arroz e Feijão, Santo Antônio de Goiás, Brazil
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Costa EN, Martins LO, Reis LC, Fernandes MG, de Paula Quintão Scalon S. Resistance of Cowpea Genotypes to Spodoptera frugiperda (Lepidoptera: Noctuidae) and Its Relationship to Resistance-Related Enzymes. JOURNAL OF ECONOMIC ENTOMOLOGY 2020; 113:2521-2529. [PMID: 32841343 DOI: 10.1093/jee/toaa179] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Indexed: 06/11/2023]
Abstract
Spodoptera frugiperda (J.E. Smith) can attack cowpea plants (Vigna unguiculata [L.] Walp.) (Fabales: Fabaceae) in any growth stage but attacks primarily in the first days after plant emergence, when the plants are more sensitive to defoliation. This study was carried out to evaluate the resistance to S. frugiperda in six cowpea genotypes, of which four were cultivars (BRS Tapahium, BRS Tumucumaque, Fradinho, and Miranda), and two were landraces (Juti and Nioaque), in three different experiments. In the first experiment, adult emergence, adult weight, adult longevity, larva to adult period, numbers of injured leaves per plant canopy (upper, middle, and lower), and reduction in plant dry matter were assessed. In the second experiment, the oviposition preference of S. frugiperda for the different cowpea genotypes was evaluated under free-choice conditions. In the third experiment, levels of peroxidase (POD), superoxide dismutase (SOD), and protein content in cowpea leaves were assessed. Insects fed on landrace Juti plants showed low adult emergence, yielded a lower fitness index, and caused less plant dry matter reduction. In addition, plants of landrace Juti were less preferred for oviposition. Overall, Juti plants showed higher resistance levels in all three resistance categories and higher levels of POD and SOD in S. frugiperda injured leaves, in addition to a lower protein content. Juti will be tested in field conditions, followed by molecular characterization. This will provide additional information about its potential as an S. frugiperda resistance source in plant breeding programs.
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Affiliation(s)
- Eduardo Neves Costa
- Programa de Pós-Graduação em Agronomia (Produção Vegetal), Faculdade de Ciências Agrárias
| | - Lucas Ortega Martins
- Programa de Pós-Graduação em Entomologia e Conservação da Biodiversidade, Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados, Dourados, Brazil
| | - Lucas Coutinho Reis
- Programa de Pós-Graduação em Agronomia (Produção Vegetal), Faculdade de Ciências Agrárias
| | - Marcos Gino Fernandes
- Programa de Pós-Graduação em Agronomia (Produção Vegetal), Faculdade de Ciências Agrárias
- Programa de Pós-Graduação em Entomologia e Conservação da Biodiversidade, Faculdade de Ciências Biológicas e Ambientais, Universidade Federal da Grande Dourados, Dourados, Brazil
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Fiore MC, Raimondo FM, Mercati F, Digangi I, Sunseri F, Scialabba A. Preserving Biodiversity in Marginal Rural Areas: Assessment of Morphological and Genetic Variability of a Sicilian Common Bean Germplasm Collection. PLANTS (BASEL, SWITZERLAND) 2020; 9:E989. [PMID: 32759817 PMCID: PMC7463873 DOI: 10.3390/plants9080989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Revised: 07/31/2020] [Accepted: 08/01/2020] [Indexed: 11/17/2022]
Abstract
The historical cultivation of common bean (Phaseolus vulgaris L.) has resulted in the development of local populations/cultivars in restricted Italian rural areas. Many common bean landraces, still cultivated in small mountain areas from Sicily, have become outdated and endangered due to the commercial varieties spreading. These accessions are poorly known but often represent a genetic heritage to be preserved and enhanced. The ex situ conservation of fifty-seven Sicilian common bean landraces was carried out at the "Living Plants Germplasm Bank" at Ucria (Messina, Italy), founded by the Nebrodi Regional Park, together with the "Sicilian Plant Germplasm Repository" of University of Palermo (SPGR/PA). To assess the germplasm genetic diversity, nineteen morphological traits and eight Simple Sequence Repeats (SSRs) were used. Genetic distances among landraces were calculated to construct a clustering tree by using unweighted pair group method arithmetic (UPGMA). Seed germplasm diversity of Sicilian common bean varied from 80.7% to 93.3%, based on six seed descriptors and six leaf, flower, and pod descriptors, respectively, while cluster genetic analysis depicted a clear separation among all the 57 landraces. Principal coordinates (PCoA) and STRUCTURE analyses showed a prevalent rate of admixture between Mesoamerican and Andean gene pools in Sicilian common bean collection, confirming its heterogeneity. The observed high level of diversity evidenced the needs to adopt accurate criterion to plan a definitive ex situ germplasm collection to share agrobiodiversity with local farmers and to avoid any further loss of genetic resources in rural and protected areas.
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Affiliation(s)
- Maria Carola Fiore
- Council for Agricultural Research and Economics Research Centre for Plant Protection and Certification (S.S. 113 km 245,500), 90011 Bagheria, Italy
| | | | - Francesco Mercati
- Institute of Biosciences and Bioresources (IBBR), National Research Council, Corso Calatafimi 414, 90129 Palermo, Italy;
| | - Ignazio Digangi
- Living Plants Germplasm Bank of Nebrodi, Contrada Pirato, 98060 Ucria (ME), Italy;
| | - Francesco Sunseri
- Department of Agraria, University Mediterranea of Reggio Calabria, Località Feo di Vito snc, 89124 Reggio Calabria, Italy;
| | - Anna Scialabba
- Department of Biological, Chemical and Pharmaceutical Science and Technologies (STEBICEF), University of Palermo, Via Archirafi 38, 90123 Palermo, Italy;
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15
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Lei L, Wang L, Wang S, Wu J. Marker-Trait Association Analysis of Seed Traits in Accessions of Common Bean ( Phaseolus vulgaris L.) in China. Front Genet 2020; 11:698. [PMID: 32714377 PMCID: PMC7344293 DOI: 10.3389/fgene.2020.00698] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 06/08/2020] [Indexed: 01/22/2023] Open
Abstract
Seed weight and seed size are the key agronomic traits that determine yield in common bean. To investigate the genetic architecture of four seed traits (100-seed weight, seed length, seed width, and seed height) of common bean in China, marker-trait association analysis of these seed traits was performed in a nationwide population of 395 common bean accessions using 116 polymorphic SSR markers. The four seed traits were evaluated in six trials across three environments. Seed size varied among the environments. Population structure was evaluated based on SSR markers and phaseolin, which divided the accessions into two main subpopulations representing the two known gene pools. Seed weight and seed size had a strong relationship with population clustering. In addition, in a Genome-wide association studies (GWAS), 21 significantly associated markers were identified for the four seed traits with two models, namely, general linear model (GLM) and mixed linear model (MLM). Some markers had pleiotropic effects, i.e., controlled more than one trait. The significant quantitative trait loci identified in this study could be used in marker-assisted breeding to accelerate the genetic improvement of yield in common bean.
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Affiliation(s)
- Lei Lei
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lanfen Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shumin Wang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jing Wu
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, China
- CAAS-CIAT Joint Laboratory in Advanced Technologies for Sustainable Agriculture, Beijing, China
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16
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Zhang M, Zhang S, Ye M, Jiang L, Vallejos CE, Wu R. The genetic control of leaf allometry in the common bean, Phaseolus vulgaris. BMC Genet 2020; 21:29. [PMID: 32169029 PMCID: PMC7071654 DOI: 10.1186/s12863-020-00838-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 03/05/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND To maximize photosynthetic efficiency, plants have evolved a capacity by which leaf area scales allometrically with leaf mass through interactions with the environment. However, our understanding of genetic control of this allometric relationship remains limited. RESULTS We integrated allometric scaling laws expressed at static and ontogenetic levels into genetic mapping to identify the quantitative trait loci (QTLs) that mediate how leaf area scales with leaf mass and how such leaf allometry, under the control of these QTLs, varies as a response to environment change. A major QTL detected by the static model constantly affects the allometric growth of leaf area vs. leaf mass for the common bean (Phaseolus vulgaris) in two different environments. The ontogenetic model identified this QTL plus a few other QTLs that determine developmental trajectories of leaf allometry, whose expression is contingent heavily upon the environment. CONCLUSIONS Our results gain new insight into the genetic mechanisms of how plants program their leaf morphogenesis to adapt to environmental perturbations.
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Affiliation(s)
- Miaomiao Zhang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Shilong Zhang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Meixia Ye
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Libo Jiang
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - C Eduardo Vallejos
- Department of Horticultural Sciences, University of Florida, Gainesville, FL, 326511, USA
| | - Rongling Wu
- Center for Computational Biology, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China. .,Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, 17033, USA.
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17
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Braglia L, Gavazzi F, Morello L, Gianì S, Nick P, Breviario D. On the applicability of the Tubulin-Based Polymorphism (TBP) genotyping method: a comprehensive guide illustrated through the application on different genetic resources in the legume family. PLANT METHODS 2020; 16:86. [PMID: 32536963 PMCID: PMC7291473 DOI: 10.1186/s13007-020-00627-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 05/30/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Plant discrimination is of relevance for taxonomic, evolutionary, breeding and nutritional studies. To this purpose, evidence is reported to demonstrate TBP (Tubulin-Based-Polymorphism) as a DNA-based method suitable for assessing plant diversity. RESULTS Exploiting one of the most valuable features of TBP, that is the convenient and immediate application of the assay to groups of individuals that may belong to different taxa, we show that the TBP method can successfully discriminate different agricultural species and their crop wild relatives within the Papilionoideae subfamily. Detection of intraspecific variability is demonstrated by the genotyping of 27 different accessions of Phaseolus vulgaris. CONCLUSIONS These data illustrate TBP as a useful and versatile tool for plant genotyping. Since its potential has not yet been fully appreciated by the scientific community, we carefully report all the experimental details of a successful TBP protocol, while describing different applications, so that the method can be replicated in other laboratories.
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Affiliation(s)
- Luca Braglia
- CNR- National Research Council, Institute of Agricultural Biology and Biotechnology-IBBA, Via Alfonso Corti 12, 20133 Milan, Italy
| | - Floriana Gavazzi
- CNR- National Research Council, Institute of Agricultural Biology and Biotechnology-IBBA, Via Alfonso Corti 12, 20133 Milan, Italy
| | - Laura Morello
- CNR- National Research Council, Institute of Agricultural Biology and Biotechnology-IBBA, Via Alfonso Corti 12, 20133 Milan, Italy
| | - Silvia Gianì
- CNR- National Research Council, Institute of Agricultural Biology and Biotechnology-IBBA, Via Alfonso Corti 12, 20133 Milan, Italy
| | - Peter Nick
- Department of Molecular Cell Biology, Botanical Institute, Karlsruhe Institute of Technology (KIT), Fritz-Haber-Weg 4, 76131 Karlsruhe, Baden-Württemberg Germany
| | - Diego Breviario
- CNR- National Research Council, Institute of Agricultural Biology and Biotechnology-IBBA, Via Alfonso Corti 12, 20133 Milan, Italy
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18
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Pipan B, Meglič V. Diversification and genetic structure of the western-to-eastern progression of European Phaseolus vulgaris L. germplasm. BMC PLANT BIOLOGY 2019; 19:442. [PMID: 31646962 PMCID: PMC6813049 DOI: 10.1186/s12870-019-2051-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 09/23/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Common bean (Phaseolus vulgaris L.) is the most important food legume for direct human consumption around the world, as it represents a valuable source of components with nutritional and health benefits. RESULTS We conducted a study to define and explain the genetic relatedness and diversification level of common bean (Phaseolus vulgaris L.) germplasm from Portugal to Ukraine, along a western-to-eastern line of southern European countries, including Poland. This was based on the P. vulgaris genetic structure, and was designed to better describe its distribution and domestication pathways in Europe. Using the multi-crop passport descriptors that include geographic origin and different phaseolin types (corresponding to the Mesoamerican and Andean gene pools), 782 accessions were obtained from nine gene banks and 12 geographic origins. We selected 33 genome/ gene-related/ gene-pool-related nuclear simple sequence repeat markers that covered the genetic diversity across the P. vulgaris genome. The overall polymorphic information content was 0.800. Without specifying geographic origin, global structure cluster analysis generated 10 genetic clusters. Among the PvSHP1 markers, the most informative for gene pool assignment of the European P. vulgaris germplasm was PvSHP1-B. Results of AMOVA show that 89% of the molecular variability is shared within the 782 accessions, with 4% molecular variability among the different geographic origins along this western-to-eastern line of southern Europe (including Poland). CONCLUSIONS This study shows that the diversification line of the European P. vulgaris germplasm followed from the western areas of southern Europe (Portugal, Spain, Italy, Slovenia) to the more eastern areas of southern Europe. This progression defines three geographically separated subgroups, as the northern (Poland, Ukraine, Romania), southern (Albania, Bulgaria), and central (Bosnia and Herzegovina, Serbia, Hungary) areas of eastern Europe.
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Affiliation(s)
- Barbara Pipan
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia
| | - Vladimir Meglič
- Crop Science Department, Agricultural Institute of Slovenia, Hacquetova ulica 17, SI-1000 Ljubljana, Slovenia
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Rajnovic I, Ramírez-Bahena MH, Sánchez-Juanes F, González-Buitrago JM, Kajic S, Peix Á, Velázquez E, Sikora S. Phylogenetic diversity of rhizobia nodulating Phaseolus vulgaris in Croatia and definition of the symbiovar phaseoli within the species Rhizobium pisi. Syst Appl Microbiol 2019; 42:126019. [PMID: 31635886 DOI: 10.1016/j.syapm.2019.126019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/23/2019] [Accepted: 07/25/2019] [Indexed: 11/27/2022]
Abstract
Phaseolus vulgaris is a legume indigenous to America which is currently cultivated in Europe including countries located at the Southeast of this continent, such as Croatia, where several local landraces are cultivated, most of them of Andean origin. In this work we identify at species and symbiovar levels several fast-growing strains able to form effective symbiosis with P. vulgaris in different Croatian soils. The identification at species level based on MALDI-TOF MS and core gene sequence analysis showed that most of these strains belong to the species R. leguminosarum, R. hidalgonense and R. pisi. In addition, several strains belong to putative new species phylogenetically close to R. ecuadorense and R. sophoriradicis. All Croatian strains belong to the symbiovar phaseoli and harbour the α and γ nodC alleles typical for American strains of this symbiovar. Nevertheless, most of Croatian strains harboured the γ nodC gene allele supporting its Andean origin since it is also dominant in other European countries, where Andean cultivars of P. vulgaris are traditionally cultivated, as occurs in Spain. The only strains harbouring the α nodC allele belong to R. hidalgonense and R. pisi, this last only containing the symbiovars viciae and trifolii to date. This is the first report about the presence in Europe of the species R. hidalgonense, the nodulation of P. vulgaris by R. pisi and the existence of the symbiovar phaseoli within this species. These results significantly increase the knowledge of the biogeography of Rhizobium-P. vulgaris symbiosis.
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Affiliation(s)
- Ivana Rajnovic
- Department of Microbiology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | | | - Fernando Sánchez-Juanes
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain; Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Spain
| | - José-Manuel González-Buitrago
- Instituto de Investigación Biomédica de Salamanca (IBSAL), Salamanca, Spain; Departamento de Bioquímica y Biología Molecular, Universidad de Salamanca, Spain
| | - Sanja Kajic
- Department of Microbiology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
| | - Álvaro Peix
- Instituto de Recursos Naturales y Agrobiología, IRNASA-CSIC, Salamanca, Spain; Unidad Asociada Grupo de Interacción Planta-Microorganismo (Universidad de Salamanca-IRNASA-CSIC), Salamanca, Spain.
| | - Encarna Velázquez
- Unidad Asociada Grupo de Interacción Planta-Microorganismo (Universidad de Salamanca-IRNASA-CSIC), Salamanca, Spain; Departmento de Microbiología y Genética and CIALE, Universidad de Salamanca, Salamanca, Spain
| | - Sanja Sikora
- Department of Microbiology, Faculty of Agriculture, University of Zagreb, Zagreb, Croatia
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Nadeem MA, Habyarimana E, Çiftçi V, Nawaz MA, Karaköy T, Comertpay G, Shahid MQ, Hatipoğlu R, Yeken MZ, Ali F, Ercişli S, Chung G, Baloch FS. Characterization of genetic diversity in Turkish common bean gene pool using phenotypic and whole-genome DArTseq-generated silicoDArT marker information. PLoS One 2018; 13:e0205363. [PMID: 30308006 PMCID: PMC6181364 DOI: 10.1371/journal.pone.0205363] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 09/20/2018] [Indexed: 12/31/2022] Open
Abstract
Turkey presents a great diversity of common bean landraces in farmers' fields. We collected 183 common bean accessions from 19 different Turkish geographic regions and 5 scarlet runner bean accessions to investigate their genetic diversity and population structure using phenotypic information (growth habit, and seed weight, flower color, bracteole shape and size, pod shape and leaf shape and color), geographic provenance and 12,557 silicoDArT markers. A total of 24.14% markers were found novel. For the entire population (188 accessions), the expected heterozygosity was 0.078 and overall gene diversity, Fst and Fis were 0.14, 0.55 and 1, respectively. Using marker information, model-based structure, principal coordinate analysis (PCoA) and unweighted pair-group method with arithmetic means (UPGMA) algorithms clustered the 188 accessions into two main populations A (predominant) and B, and 5 unclassified genotypes, representing 3 meaningful heterotic groups for breeding purposes. Phenotypic information clearly distinguished these populations; population A and B, respectively, were bigger (>40g/100 seeds) and smaller (<40g/100 seeds) seed-sized. The unclassified population was pure and only contained climbing genotypes with 100 seed weight 2-3 times greater than populations A and B. Clustering was mainly based on A: seed weight, B: growth habit, C: geographical provinces and D: flower color. Mean kinship was generally low, but population B was more diverse than population A. Overall, a useful level of gene and genotypic diversity was observed in this work and can be used by the scientific community in breeding efforts to develop superior common bean strains.
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Affiliation(s)
- Muhammad Azhar Nadeem
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Ephrem Habyarimana
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria–Centro di ricerca cerealicoltura e colture industriali, Bologna, Italy
| | - Vahdettin Çiftçi
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Muhammad Amjad Nawaz
- Department of Biotechnology, Chonnam National University, Chonnam, Republic of Korea
| | - Tolga Karaköy
- Organic Agriculture Program, Vocational School of Sivas, University of Cumhuriyet, Sivas, Turkey
| | - Gonul Comertpay
- Eastern Mediterranean Agricultural Research Institute, Turkey
| | - Muhammad Qasim Shahid
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bio resources, South China Agricultural University, Guangzhou, China
| | - Rüştü Hatipoğlu
- Department of Field Crops, Faculty of Agricultural, University of Cukurova, Adana, Turkey
| | - Mehmet Zahit Yeken
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Fawad Ali
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
| | - Sezai Ercişli
- Department of Horticulture, Faculty of Agriculture, Ataturk University, Erzurum, Turkey
| | - Gyuhwa Chung
- Department of Biotechnology, Chonnam National University, Chonnam, Republic of Korea
| | - Faheem Shehzad Baloch
- Department of field crops, Faculty of Agricultural and Natural Science, Abant Izzet Baysal University, Bolu, Turkey
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