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Punniyamoorthy D, Souframanien J. Gamma-rays induced genome wide stable mutations in cowpea deciphered through whole genome sequencing. Int J Radiat Biol 2024:1-13. [PMID: 38683196 DOI: 10.1080/09553002.2024.2345087] [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: 07/07/2023] [Accepted: 03/30/2024] [Indexed: 05/01/2024]
Abstract
PURPOSE Gamma rays are the most widely exploited physical mutagen in plant mutation breeding. They are known to be involved in the development of more than 60% of global cowpea (Vigna unguiculata (L.) Walp.) mutant varieties. Nevertheless, the nature and type of genome-wide mutations induced by gamma rays have not been studied in cowpea and therefore, the present investigation was undertaken. MATERIALS AND METHODS Genomic DNAs from three stable gamma rays-induced mutants (large seed size, small seed size and disease resistant mutant) of cowpea cultivar 'CPD103' in M6 generation along with its progenitor were used for Illumina-based whole-genome resequencing. RESULTS Gamma rays induced a relatively higher frequency (88.9%) of single base substitutions (SBSs) with an average transition to transversion ratio (Ti/Tv) of 3.51 in M6 generation. A > G transitions, including its complementary T > C transitions, predominated the transition mutations, while all four types of transversion mutations were detected with frequencies over 6.5%. Indels (small insertions and deletions) constituted about 11% of the total induced variations, wherein small insertions (6.3%) were relatively more prominent than small deletions (4.8%). Among the indels, single-base indels and, in particular, those involving A/T bases showed a preponderance, albeit indels of up to three bases were detected in low proportions. Distributed across all 11 chromosomes, only a fraction of SBSs (19.45%) and indels (20.2%) potentially altered the encoded amino acids/peptides. The inherent mutation rate induced by gamma rays in cowpea was observed to be in the order of 1.4 × 10-7 per base pair in M6 generation. CONCLUSION Gamma-rays with a greater tendency to induce SBSs and, to a lesser extent, indels could be efficiently and effectively exploited in cowpea mutation breeding.
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Affiliation(s)
| | - Jegadeesan Souframanien
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, India
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2
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Sallam A, Dawood MFA, Jarquín D, Mohamed EA, Hussein MY, Börner A, Ahmed AAM. Genome-wide scanning to identify and validate single nucleotide polymorphism markers associated with drought tolerance in spring wheat seedlings. THE PLANT GENOME 2024:e20444. [PMID: 38476036 DOI: 10.1002/tpg2.20444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 03/14/2024]
Abstract
Unlike other growth stages of wheat, very few studies on drought tolerance have been done at the seedling stage, and this is due to the complexity and sensitivity of this stage to drought stress resulting from climate change. As a result, the drought tolerance of wheat seedlings is poorly understood and very few genes associated with drought tolerance at this stage were identified. To address this challenge, a set of 172 spring wheat genotypes representing 20 different countries was evaluated under drought stress at the seedling stage. Drought stress was applied on all tested genotypes by water withholding for 13 days. Two types of traits, namely morphological and physiological traits were scored on the leaves of all tested genotypes. Genome-wide association study (GWAS) is one of the effective genetic analysis methods that was used to identify target single nucleotide polymorphism (SNP) markers and candidate genes for later use in marker-assisted selection. The tested plant materials were genotyped using 25k Infinium iSelect array (25K) (herein after it will be identified as 25K) (for 172 genotypes) and genotyping-by-sequencing (GBS) (for 103 genotypes), respectively. The results of genotyping revealed 21,093 25K and 11,362 GBS-SNPs, which were used to perform GWAS analysis for all scored traits. The results of GWAS revealed that 131 and 55 significant SNPs were controlling morphological and physiological traits, respectively. Moreover, a total of eight and seven SNP markers were found to be associated with more than one morphological and physiological trait under drought stress, respectively. Remarkably, 10 significant SNPs found in this study were previously reported for their association with drought tolerance in wheat. Out of the 10 validated SNP markers, four SNPs were associated with drought at the seedling stage, while the remaining six SNPs were associated with drought stress at the reproductive stage. Moreover, the results of gene enrichment revealed 18 and six pathways as highly significant biological and molecular pathways, respectively. The selection based on drought-tolerant alleles revealed 15 genotypes with the highest number of different drought-tolerant alleles. These genotypes can be used as candidate parents in future breeding programs to produce highly drought-tolerant genotypes with high genetic diversity. Our findings in this study provide novel markers and useful information on the genetic basis of drought tolerance at early growth stages.
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Affiliation(s)
- Ahmed Sallam
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Germany
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt
| | - Mona F A Dawood
- Department of Botany and Microbiology, Faculty of Science, Assiut University, Assiut, Egypt
| | - Diego Jarquín
- Department of Agronomy, University of Florida, Gainesville, Florida, USA
| | - Elsayed A Mohamed
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt
| | - Mohamed Y Hussein
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Stadt Seeland, Germany
| | - Asmaa A M Ahmed
- Department of Genetics, Faculty of Agriculture, Assiut University, Assiut, 71526, Egypt
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3
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Zhou W, Yan Z, Zhang L. A comparative study of 11 non-linear regression models highlighting autoencoder, DBN, and SVR, enhanced by SHAP importance analysis in soybean branching prediction. Sci Rep 2024; 14:5905. [PMID: 38467662 PMCID: PMC10928191 DOI: 10.1038/s41598-024-55243-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/21/2024] [Indexed: 03/13/2024] Open
Abstract
To explore a robust tool for advancing digital breeding practices through an artificial intelligence-driven phenotype prediction expert system, we undertook a thorough analysis of 11 non-linear regression models. Our investigation specifically emphasized the significance of Support Vector Regression (SVR) and SHapley Additive exPlanations (SHAP) in predicting soybean branching. By using branching data (phenotype) of 1918 soybean accessions and 42 k SNP (Single Nucleotide Polymorphism) polymorphic data (genotype), this study systematically compared 11 non-linear regression AI models, including four deep learning models (DBN (deep belief network) regression, ANN (artificial neural network) regression, Autoencoders regression, and MLP (multilayer perceptron) regression) and seven machine learning models (e.g., SVR (support vector regression), XGBoost (eXtreme Gradient Boosting) regression, Random Forest regression, LightGBM regression, GPs (Gaussian processes) regression, Decision Tree regression, and Polynomial regression). After being evaluated by four valuation metrics: R2 (R-squared), MAE (Mean Absolute Error), MSE (Mean Squared Error), and MAPE (Mean Absolute Percentage Error), it was found that the SVR, Polynomial Regression, DBN, and Autoencoder outperformed other models and could obtain a better prediction accuracy when they were used for phenotype prediction. In the assessment of deep learning approaches, we exemplified the SVR model, conducting analyses on feature importance and gene ontology (GO) enrichment to provide comprehensive support. After comprehensively comparing four feature importance algorithms, no notable distinction was observed in the feature importance ranking scores across the four algorithms, namely Variable Ranking, Permutation, SHAP, and Correlation Matrix, but the SHAP value could provide rich information on genes with negative contributions, and SHAP importance was chosen for feature selection. The results of this study offer valuable insights into AI-mediated plant breeding, addressing challenges faced by traditional breeding programs. The method developed has broad applicability in phenotype prediction, minor QTL (quantitative trait loci) mining, and plant smart-breeding systems, contributing significantly to the advancement of AI-based breeding practices and transitioning from experience-based to data-based breeding.
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Affiliation(s)
- Wei Zhou
- Florida Agricultural and Mechanical University, Tallahassee, FL, 32307, USA.
| | - Zhengxiao Yan
- Florida State University, Tallahassee, FL, 32306, USA
| | - Liting Zhang
- Florida State University, Tallahassee, FL, 32306, USA
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4
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Rabieyan E, Darvishzadeh R, Mohammadi R, Gul A, Rasheed A, Akhar FK, Abdi H, Alipour H. Genetic diversity, linkage disequilibrium, and population structure of tetraploid wheat landraces originating from Europe and Asia. BMC Genomics 2023; 24:682. [PMID: 37964224 PMCID: PMC10644499 DOI: 10.1186/s12864-023-09768-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 10/26/2023] [Indexed: 11/16/2023] Open
Abstract
BACKGROUND Durum wheat is one of the most important crops, especially in the Mediterranean region. Insight into the genetic diversity of germplasm can improve the breeding program management in various traits. This study was done using single nucleotide polymorphisms (SNP) markers to characterize the genetic distinctiveness and differentiation of tetraploid wheat landraces collected from nine European and Asian countries. A sum of 23,334 polymorphic SNPs was detected in 126 tetraploid wheat landraces in relation to the reference genome. RESULTS The number of identified SNPs was 11,613 and 11,721 in A and B genomes, respectively. The highest and lowest diversity was on 6B and 6 A chromosomes, respectively. Structure analysis classified the landraces into two distinct subpopulations (K = 2). Evaluating the principal coordinate analysis (PCoA) and weighted pair-group method using arithmetic averages (WPGMA) clustering results demonstrated that landraces (99.2%) are categorized into one of the two chief subpopulations. Therefore, the grouping pattern did not clearly show the presence of a clear pattern of relationships between genetic diversity and their geographical derivation. Part of this result could be due to the historical exchange between different germplasms. Although the result did not separate landraces based on their region of origin, the landraces collected from Iran were classified into the same group and cluster. Analysis of molecular variance (AMOVA) also confirmed the results of population structure. Finally, Durum wheat landraces in some countries, including Turkey, Russia, Ukraine, and Afghanistan, were highly diverse, while others, including Iran and China, were low-diversity. CONCLUSION The recent study concluded that the 126 tetraploid wheat genotypes and their GBS-SNP markers are very appropriate for quantitative trait loci (QTLs) mapping and genome-wide association studies (GWAS). The core collection comprises two distinct subpopulations. Subpopulation II genotypes are the most diverse genotypes, and if they possess desired traits, they may be used in future breeding programs. The degree of diversity in the landraces of countries can provide the ground for the improvement of new cultivars with international cooperation. linkage disequilibrium (LD) hotspot distribution across the genome was investigated, which provides useful information about the genomic regions that contain intriguing genes.
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Affiliation(s)
- Ehsan Rabieyan
- Department of Agronomy and Plant Breeding, University of Tehran, Karaj, Iran
| | - Reza Darvishzadeh
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Reza Mohammadi
- Dryland Agricultural Research Institute (DARI), AREEO, Sararood branch, Iran
| | - Alvina Gul
- Atta-ur-Rahman School of Applied Biosciences, National University of Sciences and Technology, Islamabad, Pakistan
| | - Awais Rasheed
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China
- International Maize and Wheat Improvement Center (CIMMYT), c/o CAAS, Beijing, 100081, China
- Department of Plant Sciences, Quaid-I-Azam University, Islamabad, 45320, Pakistan
| | - Fatemeh Keykha Akhar
- Department of Plant Biotechnology, College of Agriculture, Jahrom University, Jahrom, Iran
| | - Hossein Abdi
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran
| | - Hadi Alipour
- Department of Plant Production and Genetics, Faculty of Agriculture, Urmia University, Urmia, Iran.
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5
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Villano C, Procino S, Blaiotta G, Carputo D, D’Agostino N, Di Serio E, Fanelli V, La Notte P, Miazzi MM, Montemurro C, Taranto F, Aversano R. Genetic diversity and signature of divergence in the genome of grapevine clones of Southern Italy varieties. FRONTIERS IN PLANT SCIENCE 2023; 14:1201287. [PMID: 37771498 PMCID: PMC10525710 DOI: 10.3389/fpls.2023.1201287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 08/21/2023] [Indexed: 09/30/2023]
Abstract
Sexual reproduction has contributed to a significant degree of variability in cultivated grapevine populations. However, the additional influence of spontaneous somatic mutations has played a pivotal role in shaping the diverse landscape of grapevine agrobiodiversity. These naturally occurring selections, termed 'clones,' represent a vast reservoir of potentially valuable traits and alleles that hold promise for enhancing grape quality and bolstering plant resilience against environmental and biotic challenges. Despite their potential, many of these clones remain largely untapped.In light of this context, this study aims to delve into the population structure, genetic diversity, and distinctive genetic loci within a collection of 138 clones derived from six Campanian and Apulian grapevine varieties, known for their desirable attributes in viticulture and winemaking. Employing two reduced representation sequencing methods, we extracted Single-Nucleotide Polymorphism (SNP) markers. Population structure analysis and fixation index (FST) calculations were conducted both between populations and at individual loci. Notably, varieties originating from the same geographical region exhibited pronounced genetic similarity.The resulting SNP dataset facilitated the identification of approximately two hundred loci featuring divergent markers (FST ≥ 0.80) within annotated exons. Several of these loci exhibited associations with essential traits like phenotypic adaptability and environmental responsiveness, offering compelling opportunities for grapevine breeding initiatives. By shedding light on the genetic variability inherent in these treasured traditional grapevines, our study contributes to the broader understanding of their potential. Importantly, it underscores the urgency of preserving and characterizing these valuable genetic resources to safeguard their intra-varietal diversity and foster future advancements in grapevine cultivation.
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Affiliation(s)
- Clizia Villano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Silvia Procino
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
- Institute of Biosciences and Bioresources (CNR-IBBR), Bari, Italy
| | - Giuseppe Blaiotta
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Domenico Carputo
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Nunzio D’Agostino
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
- Institute of Biosciences and Bioresources (CNR-IBBR), Bari, Italy
| | - Ermanno Di Serio
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Valentina Fanelli
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
| | - Pierfederico La Notte
- Support Unit Bari, Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Bari, Italy
| | | | - Cinzia Montemurro
- Department of Soil, Plant and Food Sciences, University of Bari Aldo Moro, Bari, Italy
- Support Unit Bari, Institute for Sustainable Plant Protection, National Research Council of Italy (CNR), Bari, Italy
- SINAGRI S.r.l., Spin Off of the University of Bari Aldo Moro, Bari, Italy
| | | | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
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6
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Chaurasiya A, Khilari AA, Kazi R, Jaiswal MR, Bhoite GM, Padwal MK, Momin AA, Shanmugam D, Kulkarni MJ. Nanopore Sequencing of RAGE Gene Polymorphisms and Their Association with Type 2 Diabetes. ACS OMEGA 2023; 8:25727-25738. [PMID: 37521601 PMCID: PMC10373474 DOI: 10.1021/acsomega.3c00297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 05/22/2023] [Indexed: 08/01/2023]
Abstract
The receptor for advanced glycation end products (RAGE) is a transmembrane protein that interacts with its ligands, advanced glycation end products (AGEs). AGEs are elevated in diabetes and diabetic complications, leading to increased oxidative stress and activation of pro-inflammatory pathways facilitated by AGE-RAGE signaling. Polymorphisms in the RAGE gene can potentially affect AGE-RAGE interaction and its downstream signaling, which plays a crucial role in the progression of diabetes and its complications. In this study, we used nanopore sequencing for genotyping of RAGE polymorphism and identified a maximum number of 33 polymorphisms, including two previously unreported novel mutations in a cohort of healthy, type 2 diabetics without nephropathy and type 2 diabetics with nephropathy in order to identify associations. Two novel RAGE polymorphisms in the intron 8 and 3'UTR region at genomic locations 32181834 and 32181132, respectively, were detected with a low frequency. For four previously reported polymorphisms, cross-validation by PCR-RFLP showed 99.75% concordance with nanopore sequencing. Analysis of genotype distribution and allele frequencies revealed that five single nucleotide polymorphisms, i.e., rs1800625, rs3131300, rs3134940, rs2070600, and rs9391855, were associated with an increased risk for type 2 diabetes.
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Affiliation(s)
- Arvindkumar
H. Chaurasiya
- Biochemical
Sciences Division, CSIR-National Chemical
Laboratory, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Ajinkya A. Khilari
- Biochemical
Sciences Division, CSIR-National Chemical
Laboratory, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rubina Kazi
- Biochemical
Sciences Division, CSIR-National Chemical
Laboratory, Pune 411008, India
| | - Meera R. Jaiswal
- Biochemical
Sciences Division, CSIR-National Chemical
Laboratory, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Gouri M. Bhoite
- Department
of Biochemistry, Bharati Vidyapeeth (DTU)
Dental College, Pune 411043, India
| | - Meghana K. Padwal
- Department
of Biochemistry, Bharati Vidyapeeth (DTU)
Medical College, Pune 411043, India
| | - Abdulrahaman A. Momin
- Department
of Biochemistry, Bharati Vidyapeeth (DTU)
Medical College, Pune 411043, India
| | - Dhanasekaran Shanmugam
- Biochemical
Sciences Division, CSIR-National Chemical
Laboratory, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Mahesh J. Kulkarni
- Biochemical
Sciences Division, CSIR-National Chemical
Laboratory, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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7
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Baloch FS, Altaf MT, Liaqat W, Bedir M, Nadeem MA, Cömertpay G, Çoban N, Habyarimana E, Barutçular C, Cerit I, Ludidi N, Karaköy T, Aasim M, Chung YS, Nawaz MA, Hatipoğlu R, Kökten K, Sun HJ. Recent advancements in the breeding of sorghum crop: current status and future strategies for marker-assisted breeding. Front Genet 2023; 14:1150616. [PMID: 37252661 PMCID: PMC10213934 DOI: 10.3389/fgene.2023.1150616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 04/17/2023] [Indexed: 05/31/2023] Open
Abstract
Sorghum is emerging as a model crop for functional genetics and genomics of tropical grasses with abundant uses, including food, feed, and fuel, among others. It is currently the fifth most significant primary cereal crop. Crops are subjected to various biotic and abiotic stresses, which negatively impact on agricultural production. Developing high-yielding, disease-resistant, and climate-resilient cultivars can be achieved through marker-assisted breeding. Such selection has considerably reduced the time to market new crop varieties adapted to challenging conditions. In the recent years, extensive knowledge was gained about genetic markers. We are providing an overview of current advances in sorghum breeding initiatives, with a special focus on early breeders who may not be familiar with DNA markers. Advancements in molecular plant breeding, genetics, genomics selection, and genome editing have contributed to a thorough understanding of DNA markers, provided various proofs of the genetic variety accessible in crop plants, and have substantially enhanced plant breeding technologies. Marker-assisted selection has accelerated and precised the plant breeding process, empowering plant breeders all around the world.
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Affiliation(s)
- Faheem Shehzad Baloch
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Tanveer Altaf
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Waqas Liaqat
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Mehmet Bedir
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Azhar Nadeem
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Gönül Cömertpay
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Nergiz Çoban
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ephrem Habyarimana
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | - Celaleddin Barutçular
- Department of Field Crops, Faculty of Agriculture, Çukurova University, Adana, Türkiye
| | - Ibrahim Cerit
- Eastern Mediterranean Agricultural Research Institute, Adana, Türkiye
| | - Ndomelele Ludidi
- Plant Stress Tolerance Laboratory, Department of Biotechnology, University of the Western Cape, Bellville, South Africa
- DSI-NRF Centre of Excellence in Food Security, University of the Western Cape, Bellville, South Africa
| | - Tolga Karaköy
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Muhammad Aasim
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, Jeju, Republic of Korea
| | | | - Rüştü Hatipoğlu
- Kırşehir Ahi Evran Universitesi Ziraat Fakultesi Tarla Bitkileri Bolumu, Kırşehir, Türkiye
| | - Kağan Kökten
- Faculty of Agricultural Sciences and Technologies, Sivas University of Science and Technology, Sivas, Türkiye
| | - Hyeon-Jin Sun
- Subtropical Horticulture Research Institute, Jeju National University, Jeju, Republic of Korea
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8
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Mudaki P, Wamalwa LN, Muui CW, Nzuve F, Muasya RM, Nguluu S, Kimani W. Genetic Diversity and Population Structure of Sorghum (Sorghum bicolor (L.) Moench) Landraces Using DArTseq-Derived Single-Nucleotide Polymorphism (SNP) Markers. J Mol Evol 2023:10.1007/s00239-023-10108-1. [PMID: 37147402 DOI: 10.1007/s00239-023-10108-1] [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: 12/07/2022] [Accepted: 04/02/2023] [Indexed: 05/07/2023]
Abstract
Genetic integrity of an accession should be preserved in the conservation of germplasm. Characterization of diverse germplasm based on a molecular basis enhances its conservation and use in breeding programs. The aim of this study was to assess the genetic diversity of 169 sorghum accessions using a total of 6977 SNP markers. The polymorphic information content of the markers was 0.31 which is considered to be moderately high. Structure analysis using ADMIXTURE program revealed a total of 10 subpopulations. Neighbor-joining tree revealed the presence of six main clusters among these subpopulations whereas in principal component analysis, seven clusters were identified. Cluster analysis grouped most populations depending on source of collection although other accessions originating from the same source were grouped under different clusters. Analysis of molecular variance (AMOVA) revealed 30% and 70% of the variation occurred within and among accessions, respectively. Gene flow within the populations was, however, limited indicating high differentiation within the subpopulation. Observed heterozygosity among accessions varied from 0.03 to 0.06 with a mean of 0.05 since sorghum is a self-pollinating crop. High genetic diversity among the subpopulations can be further explored for superior genes to develop new sorghum varieties.
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Affiliation(s)
- Phoebe Mudaki
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
| | - Lydia N Wamalwa
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
| | - Catherine W Muui
- Department of Agricultural Science and Technology, Kenyatta University, Nairobi, Kenya
| | - Felister Nzuve
- Department of Plant Science and Crop Protection, University of Nairobi, Nairobi, Kenya
| | | | - Simon Nguluu
- South Eastern Kenya University (SEKU), Kitui, Kenya
| | - Wilson Kimani
- International Livestock Research Institute (ILRI), Nairobi, Kenya.
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9
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Tympakianakis S, Trantas E, Avramidou EV, Ververidis F. Vitis vinifera genotyping toolbox to highlight diversity and germplasm identification. FRONTIERS IN PLANT SCIENCE 2023; 14:1139647. [PMID: 37180393 PMCID: PMC10169827 DOI: 10.3389/fpls.2023.1139647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2023] [Accepted: 03/27/2023] [Indexed: 05/16/2023]
Abstract
The contribution of vine cultivation to human welfare as well as the stimulation of basic social and cultural features of civilization has been great. The wide temporal and regional distribution created a wide array of genetic variants that have been used as propagating material to promote cultivation. Information on the origin and relationships among cultivars is of great interest from a phylogenetics and biotechnology perspective. Fingerprinting and exploration of the complicated genetic background of varieties may contribute to future breeding programs. In this review, we present the most frequently used molecular markers, which have been used on Vitis germplasm. We discuss the scientific progress that led to the new strategies being implemented utilizing state-of-the-art next generation sequencing technologies. Additionally, we attempted to delimit the discussion on the algorithms used in phylogenetic analyses and differentiation of grape varieties. Lastly, the contribution of epigenetics is highlighted to tackle future roadmaps for breeding and exploitation of Vitis germplasm. The latter will remain in the top of the edge for future breeding and cultivation and the molecular tools presented herein, will serve as a reference point in the challenging years to come.
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Affiliation(s)
- Stylianos Tympakianakis
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
| | - Emmanouil Trantas
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
- Institute of Agri-Food and Life Sciences, Research Center of the Hellenic Mediterranean University, Heraklion, Greece
| | - Evangelia V. Avramidou
- Institute of Mediterranean Forest Ecosystems, Hellenic Agricultural Organisation “DIMITRA“, Athens, Greece
| | - Filippos Ververidis
- Laboratory of Biological and Biotechnological Applications, Department of Agriculture, School of Agricultural Sciences, Hellenic Mediterranean University, Heraklion, Greece
- Institute of Agri-Food and Life Sciences, Research Center of the Hellenic Mediterranean University, Heraklion, Greece
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10
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La Borde N, Rajewski J, Dweikat I. Novel QTL for chilling tolerance at germination and early seedling stages in sorghum. Front Genet 2023; 14:1129460. [PMID: 37007950 PMCID: PMC10052408 DOI: 10.3389/fgene.2023.1129460] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/23/2023] [Indexed: 03/17/2023] Open
Abstract
Sorghum (Sorghum bicolor L.) a drought tolerant staple crop for half a billion people in Africa and Asia, an important source of animal feed throughout the world and a biofuel feedstock of growing importanceorghum’s originated from tropical regions rendering the crop to be cold sensitive. Low temperature stresses such as chilling and frost greatly affect the agronomic performance of sorghum and limit its geographical distribution, posing a major problem in temperate environments when sorghum is planted early. Understanding the genetic basis of wide adaptability and of sorghum would facilitate molecular breeding programs and studies of other C4 crops. The objective of this study is to conduct quantitative trait loci analysis using genotying by sequencing for early seed germination and seedling cold tolerance in two sorghum recombinant inbred lines populations. To accomplish that, we used two populations of recombinant inbred lines (RIL) developed from crosses between cold-tolerant (CT19, ICSV700) and cold-sensitive (TX430, M81E) parents. The derived RIL populations were evaluated for single nucleotide polymorphism (SNP) using genotype-by-sequencing (GBS) in the field and under controlled environments for their response to chilling stress. Linkage maps were constructed with 464 and 875 SNPs for the CT19 X TX430 (C1) and ICSV700 X M81 E (C2) populations respectively. Using quantitative trait loci (QTL) mapping, we identified QTL conferring tolerance to chilling tolerance at the seedling stage. A total of 16 and 39 total QTL were identified in the C1 and C2 populations, respectively. Two major QTL were identified in the C1 population, and three major QTL were mapped in the C2 population. Comparisons between the two populations and with previously identified QTL show a high degree of similarity in QTL locations. Given the amount of co-localization of QTL across traits and the direction of allelic effect supports that these regions have a pleiotropic effect. These QTL regions were also identified to be highly enriched for genes encoding chilling stress and hormonal response genes. This identified QTL can be useful in developing tools for molecular breeding of sorghums with improved low-temperature germinability.
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Esmail SM, Omar GE, Mourad AMI. In-Depth Understanding of the Genetic Control of Stripe Rust Resistance ( Puccinia striiformis f. sp. tritici) Induced in Wheat ( Triticum aestivum) by Trichoderma asperellum T34. PLANT DISEASE 2023; 107:457-472. [PMID: 36449539 DOI: 10.1094/pdis-07-22-1593-re] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Wheat stripe rust (caused by Puccinia striiformis f. tritici Erikss.) causes severe yield losses worldwide. Due to the continuous appearance of new stripe rust races, resistance has been broken in most of the highly resistant genotypes in Egypt and worldwide. Therefore, looking for new ways to resist such a severe disease is urgently needed. Trichoderma asperellum strain T34 has been known as an effective bioagent against many crop diseases. It exists naturally in Egyptian fields. Therefore, in our study, the effectiveness of strain T34 was tested as a bioagent against wheat stripe rust. For this purpose, 198 spring wheat genotypes were tested for their resistance against two different P. striiformis f. tritici populations collected from the Egyptian fields. The most highly aggressive P. striiformis f. tritici population was used to test the effectiveness of strain T34. Highly significant differences were found between strain T34 and stripe rust, suggesting the effectiveness of strain T34 in stripe rust resistance. A genome-wide association study identified 48 gene models controlling resistance under normal conditions and 46 gene models controlling strain T34-induced resistance. Of these gene models, only one common gene model was found, suggesting the presence of two different genetic systems controlling resistance under each condition. The pathways of the biological processes were investigated under both conditions. This study provided in-depth understanding of genetic control and, hence, will accelerate the future of wheat breeding programs for stripe rust resistance.
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Affiliation(s)
- Samar M Esmail
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Ghady E Omar
- Wheat Disease Research Department, Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
| | - Amira M I Mourad
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Germany
- Department of Agronomy, Faculty of Agriculture, Assiut University, Assiut, Egypt
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Gohar IMA, Alyamani A, Shafi ME, Mohamed EAE, Ghareeb RY, Desoky EM, Hasan ME, Zaitoun AF, Abdelsalam NR, El-Tarabily KA, Elnahal ASM. A quantitative and qualitative assessment of sugar beet genotype resistance to root-knot nematode, Meloidogyne incognita. FRONTIERS IN PLANT SCIENCE 2023; 13:966377. [PMID: 36714787 PMCID: PMC9881751 DOI: 10.3389/fpls.2022.966377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/28/2022] [Indexed: 06/18/2023]
Abstract
Sugar beet productivity is highly constrained by the root-knot nematode (RKN) Meloidogyne incognita. Eight sugar beet genotypes were screened under greenhouse conditions for their susceptibility to M. incognita according to an adapted quantitative scheme for assignment Canto-Saenz's host suitability (resistance) designations (AQSCS). Besides, the degree of susceptibility or tolerance of the examined genotypes was recorded by the modified host-parasite index (MHPI) scale based on yield performance. In addition, single nucleotide polymorphism (SNP) was also determined. Sugar beet genotypes have been classified into four categories for their susceptibility or tolerance according to the AQSCS scale. The first category, the moderately resistant (MR) group implies only one variety named SVH 2015, which did not support nematode reproduction (RF≤1), and had less root damage (GI≈2). Second, the tolerant group (T) involving Lilly and Halawa KWS supported fairly high nematode reproduction (RF>1) with relatively plant damage (GI≤2). Whereas the susceptible (S) category involved four varieties, FARIDA, Lammia KWS, Polat, and Capella, which supported nematode reproduction factor (RF>1) with high plant damage (GI>2). The fourth category refers to the highly susceptible (HYS) varieties such as Natura KWS that showed (RF≤1) and very high plant damage (GI>2). However, the MHPI scale showed that Lammia KWS variety was shifted from the (S) category to the (T) category. Results revealed significant differences among genotypes regarding disease severity, yield production, and quality traits. The SVH 2015 variety exhibited the lowest disease index values concerning population density with 800/250 cm3 soils, RF=2, root damage/gall index (GI=1.8), gall size (GS=2.3), gall area (GA=3.7), damage index (DI=3.4), susceptibility rate (SR=2.4), and MHP index (MHPI=2.5). However, Lammia KWS showed the highest disease index values regarding population density with 8890/250 cm3 soils, RF= 22.2, GI= 4.8, and SR= 14.1. Meanwhile, Natura KWS the highest GS, GA and MHPI with 7.1, 8 and 20.9, respectively. The lowest DI was achieved by Capella (DI= 6) followed by Lammia KWS (DI= 5.9). For yield production, and quality traits, SVH 2015 exhibited the lowest reductions of sugar yields/beet's root with 11.1%. While Natura KWS had the highest reduction with 79.3%, as well as it showed the highest reduction in quality traits; including sucrose, T.S.S, and purity with 65, 27.3, and 51.9%, respectively. The amino acid alignment and prediction of the DNA sequences revealed the presence of five SNPs among all sugar beet verities.
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Affiliation(s)
- Ibrahim M. A. Gohar
- Sugar Crops Research Institute, Department of Sugar Crops Disease and Pests Research, Agricultural Research Center, Giza, Egypt
| | - Amal Alyamani
- Department of Biotechnology, Faculty of Sciences, Taif University, Taif, Saudi Arabia
| | - Manal E. Shafi
- Department of Biological Sciences, Zoology, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Elshaimaa A. E. Mohamed
- Sugar Crops Research Institute, Department of Genetic and Breeding, Agricultural Research Center, Giza, Egypt
| | - Rehab Y. Ghareeb
- Plant Protection and Biomolecular Diagnosis Department, Arid Lands Cultivation Research Institute, The City of Scientific Research and Technological Applications, New Borg El Arab, Alexandria, Egypt
| | - Elsayed M. Desoky
- Botany Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Mohamed E. Hasan
- Bioinformatic Department, Genetic Engineering and Biotechnology Research Institute, University of Sadat City, Sadat City, Egypt
| | - Amera F. Zaitoun
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Nader R. Abdelsalam
- Agricultural Botany Department, Faculty of Agriculture (Saba Basha), Alexandria University, Alexandria, Egypt
| | - Khaled A. El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain, United Arab Emirates
- Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Ahmed S. M. Elnahal
- Plant Pathology Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
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Capo-chichi LJA, Elakhdar A, Kubo T, Nyachiro J, Juskiw P, Capettini F, Slaski JJ, Ramirez GH, Beattie AD. Genetic diversity and population structure assessment of Western Canadian barley cooperative trials. FRONTIERS IN PLANT SCIENCE 2023; 13:1006719. [PMID: 36699829 PMCID: PMC9868428 DOI: 10.3389/fpls.2022.1006719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 11/25/2022] [Indexed: 06/17/2023]
Abstract
Studying the population structure and genetic diversity of historical datasets is a proposed use for association analysis. This is particularly important when the dataset contains traits that are time-consuming or costly to measure. A set of 96 elite barley genotypes, developed from eight breeding programs of the Western Canadian Cooperative Trials were used in the current study. Genetic diversity, allelic variation, and linkage disequilibrium (LD) were investigated using 5063 high-quality SNP markers via the Illumina 9K Barley Infinium iSelect SNP assay. The distribution of SNPs markers across the barley genome ranged from 449 markers on chromosome 1H to 1111 markers on chromosome 5H. The average polymorphism information content (PIC) per locus was 0.275 and ranged from 0.094 to 0.375. Bayesian clustering in STRUCTURE and principal coordinate analysis revealed that the populations are differentiated primarily due to the different breeding program origins and ear-row type into five subpopulations. Analysis of molecular variance based on PhiPT values suggested that high values of genetic diversity were observed within populations and accounted for 90% of the total variance. Subpopulation 5 exhibited the most diversity with the highest values of the diversity indices, which represent the breeding program gene pool of AFC, AAFRD, AU, and BARI. With increasing genetic distance, the LD values, expressed as r2, declined to below the critical r2 = 0.18 after 3.91 cM, and the same pattern was observed on each chromosome. Our results identified an important pattern of genetic diversity among the Canadian barley panel that was proposed to be representative of target breeding programs and may have important implications for association mapping in the future. This highlight, that efforts to identify novel variability underlying this diversity may present practical breeding opportunities to develop new barley genotypes.
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Affiliation(s)
- Ludovic J. A. Capo-chichi
- Department of Renewable Resources, Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Ammar Elakhdar
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
- Field Crops Research Institute, Agricultural Research Center, Giza, Egypt
| | - Takahiko Kubo
- Institute of Genetic Resources, Faculty of Agriculture, Kyushu University, Fukuoka, Japan
| | - Joseph Nyachiro
- Field Crop Development Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada
| | - Patricia Juskiw
- Field Crop Development Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada
| | - Flavio Capettini
- Field Crop Development Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada
| | - Jan J. Slaski
- Ecosystems and Plant Sciences, InnoTech Alberta Inc., Vegreville, AB, Canada
| | - Guillermo Hernandez Ramirez
- Department of Renewable Resources, Faculty of Agriculture, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Aaron D. Beattie
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK, Canada
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Liang W, Du H, Pang B, Cheng J, He B, Hu F, Lv Y, Zhang Y. High-density genetic mapping identified QTLs for anaerobic germination tolerance in rice. FRONTIERS IN PLANT SCIENCE 2022; 13:1076600. [PMID: 36618635 PMCID: PMC9822775 DOI: 10.3389/fpls.2022.1076600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
The tolerance of rice anaerobic germination (AG) is the main limiting factor for direct seeding application, yet the genetics mechanism is still in its infancy. In the study, recombinant inbred lines population of TD70 Japonica cultivar and Kasalath Indica cultivar, was employed to construct a high-density genetic map by whole genome re-sequencing. As a result, a genetic map containing 12,328 bin-markers was constructed and a total of 50 QTLs were then detected for CL(coleoptile length), CD (coleoptile diameter), CSA (coleoptile surface area) and CV (coleoptile volume) related traits in the two stages of anaerobic treatment using complete interval mapping method (inclusive composite interval mapping, ICIM). Among the four traits associated with coleoptile, coleoptile volume had the largest number of QTLs (17), followed by coleoptile diameter (16), and coleoptile length had 5 QTLs. These QTLs could explain phenotypic contribution rates ranging from 0.34% to 11.17% and LOD values ranging from 2.52 to 11.57. Combined with transcriptome analysis, 31 candidate genes were identified. Furthermore, 12 stable QTLs were used to detect the aggregation effect analysis. Besides, It was found that individuals with more aggregation synergistic alleles had higher phenotypic values in different environments. Totally, high-density genetic map, QTL mapping and aggregation effect analysis of different loci related to the anaerobic germination of rice seeds were conducted to lay a foundation for the fine mapping of related genes in subsequent assisted breeding.
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Affiliation(s)
- Wenhua Liang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hongyang Du
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
- Key Laboratory of Rice Genetic Breeding of Anhui Province, Rice Research Institute, Anhui Academy of Agricultural Science, Hefei, China
| | - Bingwen Pang
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Junjie Cheng
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Bing He
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Fengqin Hu
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Yuanda Lv
- Excellence and Innovation Center, Jiangsu Academy of Agricultural, Sciences, Nanjing, China
| | - Yadong Zhang
- Institute of Food Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
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Wei Y, He S, Wang J, Fan P, He Y, Hu K, Chen Y, Zhou G, Zhong D, Zheng X. Genome-wide SNPs reveal novel patterns of spatial genetic structure in Aedes albopictus (Diptera Culicidae) population in China. Front Public Health 2022; 10:1028026. [PMID: 36438226 PMCID: PMC9685676 DOI: 10.3389/fpubh.2022.1028026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022] Open
Abstract
Introduction Since the second half of the 20th century, Aedes albopictus, a vector for more than 20 arboviruses, has spread worldwide. Aedes albopictus is the main vector of infectious diseases transmitted by Aedes mosquitoes in China, and it has caused concerns regarding public health. A comprehensive understanding of the spatial genetic structure of this vector species at a genomic level is essential for effective vector control and the prevention of vector-borne diseases. Methods During 2016-2018, adult female Ae. albopictus mosquitoes were collected from eight different geographical locations across China. Restriction site-associated DNA sequencing (RAD-seq) was used for high-throughput identification of single nucleotide polymorphisms (SNPs) and genotyping of the Ae. albopictus population. The spatial genetic structure was analyzed and compared to those exhibited by mitochondrial cytochrome c oxidase subunit 1 (cox1) and microsatellites in the Ae. albopictus population. Results A total of 9,103 genome-wide SNP loci in 101 specimens and 32 haplotypes of cox1 in 231 specimens were identified in the samples from eight locations in China. Principal component analysis revealed that samples from Lingshui and Zhanjiang were more genetically different than those from the other locations. The SNPs provided a better resolution and stronger signals for novel spatial population genetic structures than those from the cox1 data and a set of previously genotyped microsatellites. The fixation indexes from the SNP dataset showed shallow but significant genetic differentiation in the population. The Mantel test indicated a positive correlation between genetic distance and geographical distance. However, the asymmetric gene flow was detected among the populations, and it was higher from south to north and west to east than in the opposite directions. Conclusions The genome-wide SNPs revealed seven gene pools and fine spatial genetic structure of the Ae. albopictus population in China. The RAD-seq approach has great potential to increase our understanding of the spatial dynamics of population spread and establishment, which will help us to design new strategies for controlling vectors and mosquito-borne diseases.
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Affiliation(s)
- Yong Wei
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China,Clinical Laboratory, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Song He
- Clinical Laboratory, Shenzhen Qianhai Shekou Free Trade Zone Hospital, Shenzhen, China
| | - Jiatian Wang
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Peiyang Fan
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yulan He
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Ke Hu
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Yulan Chen
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China
| | - Guofa Zhou
- Program in Public Health, College of Health Sciences, University of California, Irvine, Irvine, CA, United States
| | - Daibin Zhong
- Program in Public Health, College of Health Sciences, University of California, Irvine, Irvine, CA, United States
| | - Xueli Zheng
- Department of Pathogen Biology, School of Public Health, Southern Medical University, Guangzhou, China,*Correspondence: Xueli Zheng
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Best NB, McSteen P. Mapping Maize Mutants Using Bulked-Segregant Analysis and Next-Generation Sequencing. Curr Protoc 2022; 2:e591. [PMID: 36350247 DOI: 10.1002/cpz1.591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Forward genetics is used to identify the genetic basis for a phenotype. The approach involves identifying a mutant organism exhibiting a phenotype of interest and then mapping the causative locus or gene. Bulked-segregant analysis (BSA) is a quick and effective approach to map mutants using pools of mutants and wild-type plants from a segregating population to identify linkage of the mutant phenotype, and this approach has been successfully used in plants. Traditional linkage mapping approaches are outdated and time intensive, and can be very difficult. With the highly evolved development and reduction in cost of high-throughput sequencing, this new approach combined with BSA has become extremely effective in multiple plant species, including Zea mays (maize). While the approach is incredibly powerful, careful experimental design, bioinformatic mapping techniques, and interpretation of results are important to obtain the desired results in an effective and timely manner. Poor design of a mapping population, limitations in bioinformatic experience, and inadequate understanding of sequence data are limitations of these approaches for the researcher. Here, we describe a straightforward protocol for mapping mutations responsible for a phenotype of interest in maize, using high-throughput sequencing and BSA. Specifically, we discuss relevant aspects of developing a mutant mapping population. This is followed by a detailed protocol for DNA preparation and analysis of short-read sequences to map and identify candidate causative mutations responsible for the mutant phenotype of interest. We provide command-line and perl scripts to complete the bioinformatic analysis of the mutant sequence data. This protocol lays out the design of the BSA, bioinformatic approaches, and interpreting the sequencing data. These methods are very adaptable to any forward genetics experiment and provide a step-by-step approach to identifying the genetic basis of a maize mutant phenotype. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol: Bulked-segregant analysis and high-throughput sequencing to map maize mutants.
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Affiliation(s)
- Norman B Best
- USDA-ARS, Plant Genetics Research Unit, Columbia, Missouri
| | - Paula McSteen
- Division of Biological Sciences, Bond Life Sciences Center, University of Missouri, Columbia, Missouri
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Zafar S, You H, Zhang F, Zhu SB, Chen K, Shen C, Wu H, Zhu F, Zhang C, Xu J. Genetic dissection of grain traits and their corresponding heterosis in an elite hybrid. FRONTIERS IN PLANT SCIENCE 2022; 13:977349. [PMID: 36275576 PMCID: PMC9581170 DOI: 10.3389/fpls.2022.977349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 09/14/2022] [Indexed: 06/16/2023]
Abstract
Rice productivity has considerably improved due to the effective employment of heterosis, but the genetic basis of heterosis for grain shape and weight remains uncertain. For studying the genetic dissection of heterosis for grain shape/weight and their relationship with grain yield in rice, quantitative trait locus (QTL) mapping was performed on 1,061 recombinant inbred lines (RILs), which was developed by crossing xian/indica rice Quan9311B (Q9311B) and Wu-shan-si-miao (WSSM). Whereas, BC1F1 (a backcross F1) was developed by crossing RILs with Quan9311A (Q9311A) combined with phenotyping in Hefei (HF) and Nanning (NN) environments. Overall, 114 (main-effect, mQTL) and 359 (epistatic QTL, eQTL) were identified in all populations (RIL, BC1F1, and mid-parent heterosis, HMPs) for 1000-grain weight (TGW), grain yield per plant (GYP) and grain shape traits including grain length (GL), grain width (GW), and grain length to width ratio (GLWR). Differential QTL detection revealed that all additive loci in RILs population do not show heterotic effects, and few of them affect the performance of BC1F1. However, 25 mQTL not only contributed to BC1F1's performance but also contributed to heterosis. A total of seven QTL regions was identified, which simultaneously affected multiple grain traits (grain yield, weight, shape) in the same environment, including five regions with opposite directions and two regions with same directions of favorable allele effects, indicating that partial genetic overlaps are existed between different grain traits. This study suggested different approaches for obtaining good grain quality with high yield by pyramiding or introgressing favorable alleles (FA) with the same direction of gene effect at the QTL regions affecting grain shape/weight and grain yield distributing on different chromosomes, or introgressing or pyramiding FA in the parents instead of fixing additive effects in hybrid as well as pyramiding the polymorphic overdominant/dominant loci between the parents and eliminating underdominant loci from the parents. These outcomes offer valuable information and strategy to develop hybrid rice with suitable grain type and weight.
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Affiliation(s)
- Sundus Zafar
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hui You
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fan Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shuang Bin Zhu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Kai Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Congcong Shen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Hezhou Wu
- Hunan Tao-Hua-Yuan Agricultural Technologies Co., LTD., Hunan, China
| | - Fangjin Zhu
- Hunan Tao-Hua-Yuan Agricultural Technologies Co., LTD., Hunan, China
| | | | - Jianlong Xu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
- The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Hainan Yazhou Bay Seed Lab/National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
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Chang M, Kim JY, Lee H, Lee EJ, Lee WH, Moon S, Choe S, Choung CM. Development of diagnostic SNP markers and a novel SNP genotyping assay for distinguishing opium poppies. Forensic Sci Int 2022; 339:111416. [DOI: 10.1016/j.forsciint.2022.111416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/14/2022] [Accepted: 08/02/2022] [Indexed: 11/04/2022]
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Goyal M, Pelegrin AC, Jaillard M, Saharman YR, Klaassen CHW, Verbrugh HA, Severin JA, van Belkum A. Whole Genome Multi-Locus Sequence Typing and Genomic Single Nucleotide Polymorphism Analysis for Epidemiological Typing of Pseudomonas aeruginosa From Indonesian Intensive Care Units. Front Microbiol 2022; 13:861222. [PMID: 35910643 PMCID: PMC9329958 DOI: 10.3389/fmicb.2022.861222] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 06/17/2022] [Indexed: 11/13/2022] Open
Abstract
We have previously studied carbapenem non-susceptible Pseudomonas aeruginosa (CNPA) strains from intensive care units (ICUs) in a referral hospital in Jakarta, Indonesia (Pelegrin et al., 2019). We documented that CNPA transmissions and acquisitions among patients were variable over time and that these were not significantly reduced by a set of infection control measures. Three high risk international CNPA clones (sequence type (ST)235, ST823, ST357) dominated, and carbapenem resistance was due to carbapenemase-encoding genes and mutations in the porin OprD. Pelegrin et al. (2019) reported core genome analysis of these strains. We present a more refined and detailed whole genome-based analysis of major clones represented in the same dataset. As per our knowledge, this is the first study reporting Single Nucleotide Polymorphisms (wgSNP) analysis of Pseudomonas strains. With whole genome-based Multi Locus Sequence Typing (wgMLST) of the 3 CNPA clones (ST235, ST357 and ST823), three to eleven subgroups with up to 200 allelic variants were observed for each of the CNPA clones. Furthermore, we analyzed these CNPA clone clusters for the presence of wgSNP to redefine CNPA transmission events during hospitalization. A maximum number 35350 SNPs (including non-informative wgSNPs) and 398 SNPs (ST-specific_informative-wgSNPs) were found in ST235, 34,570 SNPs (including non-informative wgSNPs) and 111 SNPs (ST-specific_informative-wgSNPs) in ST357 and 26,443 SNPs (including non-informative SNPs) and 61 SNPs (ST-specific_informative-wgSNPs) in ST823. ST-specific_Informative-wgSNPs were commonly noticed in sensor-response regulator genes. However, the majority of non-informative wgSNPs was found in conserved hypothetical proteins or in uncharacterized proteins. Of note, antibiotic resistance and virulence genes segregated according to the wgSNP analyses. A total of 8 transmission chains for ST235 strains followed by 9 and 4 possible transmission chains for ST357 and ST823 were traceable on the basis of pairwise distances of informative-wgSNPs (0 to 4 SNPs) among the strains. The present study demonstrates the value of detailed whole genome sequence analysis for highly refined epidemiological analysis of P. aeruginosa.
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Affiliation(s)
- Manisha Goyal
- bioMérieux Open Innovation and Partnerships, Macry-LÉtoile, France
| | | | | | - Yulia Rosa Saharman
- Department of Clinical Microbiology, Faculty of Medicine, Dr. Cipto Mangunkusumo General Hospital, Universitas Indonesia, Jakarta, Indonesia
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Corné H. W. Klaassen
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Henri A. Verbrugh
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Juliëtte A. Severin
- Department of Medical Microbiology and Infectious Diseases, Erasmus MC University Medical Center, Rotterdam, Netherlands
| | - Alex van Belkum
- bioMérieux Open Innovation and Partnerships, Macry-LÉtoile, France
- *Correspondence: Alex van Belkum,
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20
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Bello SF, Adeola AC, Nie Q. The study of candidate genes in the improvement of egg production in ducks – a review. Poult Sci 2022; 101:101850. [PMID: 35544958 PMCID: PMC9108513 DOI: 10.1016/j.psj.2022.101850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 11/01/2022] Open
Abstract
Duck is the second-largest poultry species aside from chicken. The rate of egg production is a major determinant of the economic income of poultry farmers. Among the reproductive organs, the ovary is a major part of the female reproductive system which is highly important for egg production. Based on the importance of this organ, several studies have been carried out to identify candidate genes at the transcriptome level, and also the expression level of these genes at different tissues or egg-laying conditions, and single nucleotide polymorphism (SNPs) of genes associated with egg production in duck. In this review, expression profile and association study analyses at SNPs level of different candidate genes with egg production traits of duck were highlighted. Furthermore, different studies on transcriptome analysis, Quantitative Trait Loci (QTL) mapping, and Genome Wide Association Study (GWAS) approach used to identify potential candidate genes for egg production in ducks were reported. This review would widen our knowledge on molecular markers that are associated or have a positive correlation to improving egg production in ducks, for the increasing world populace.
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21
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Lee S, Chakma N, Joung S, Lee JM, Lee J. QTL Mapping for Resistance to Bacterial Wilt Caused by Two Isolates of Ralstonia solanacearum in Chili Pepper (Capsicum annuum L.). PLANTS 2022; 11:plants11121551. [PMID: 35736702 PMCID: PMC9229654 DOI: 10.3390/plants11121551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/08/2022] [Accepted: 06/08/2022] [Indexed: 11/16/2022]
Abstract
Bacterial wilt caused by the β-proteobacterium Ralstonia solanacearum is one of the most destructive soil-borne pathogens in peppers (Capsicum annuum L.) worldwide. Cultivated pepper fields in Korea face a continuous spread of this pathogen due to global warming. The most efficient and sustainable strategy for controlling bacterial wilt is to develop resistant pepper varieties. Resistance, which is quantitatively inherited, occurs differentially depending on R. solanacearum isolates. Therefore, in this study, we aimed to identify resistance quantitative trait loci (QTLs) in two F2 populations derived from self-pollination of a highly resistant pepper cultivar ‘Konesian hot’ using a moderately pathogenic ‘HS’ isolate and a highly pathogenic ‘HWA’ isolate of R. solanacearum for inoculation, via genotyping-by-sequencing analysis. QTL analysis revealed five QTLs, Bwr6w-7.2, Bwr6w-8.1, Bwr6w-9.1, Bwr6w-9.2, and Bwr6w-10.1, conferring resistance to the ‘HS’ isolate with R2 values of 13.05, 12.67, 15.07, 10.46, and 9.69%, respectively, and three QTLs, Bwr6w-5.1, Bwr6w-6.1, and Bwr6w-7.1, resistant to the ‘HWA’ isolate with phenotypic variances of 19.67, 16.50, and 12.56%, respectively. Additionally, six high-resolution melting (HRM) markers closely linked to the QTLs were developed. In all the markers, the mean disease index of the paternal genotype was significantly lower than that of the maternal genotype. The QTLs and HRM markers are expected to be useful for the development of pepper varieties with high resistance to bacterial wilt.
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Affiliation(s)
- Saeyoung Lee
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea; (S.L.); (N.C.); (S.J.)
| | - Nidhi Chakma
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea; (S.L.); (N.C.); (S.J.)
| | - Sunjeong Joung
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea; (S.L.); (N.C.); (S.J.)
| | - Je Min Lee
- Department of Horticultural Science, College of Agriculture and Life Sciences, Kyungpook National University, Daegu 41566, Korea;
| | - Jundae Lee
- Department of Horticulture, Institute of Agricultural Science & Technology, Jeonbuk National University, Jeonju 54896, Korea; (S.L.); (N.C.); (S.J.)
- Correspondence: ; Tel.: +82-63-270-2560
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22
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Brhane H, Haileselassie T, Tesfaye K, Ortiz R, Hammenhag C, Abreha KB, Geleta M. Novel GBS-Based SNP Markers for Finger Millet and Their Use in Genetic Diversity Analyses. Front Genet 2022; 13:848627. [PMID: 35559011 PMCID: PMC9090224 DOI: 10.3389/fgene.2022.848627] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 03/21/2022] [Indexed: 12/04/2022] Open
Abstract
Eleusine coracana (L.) Gaertn., commonly known as finger millet, is a multipurpose crop used for food and feed. Genomic tools are required for the characterization of crop gene pools and their genomics-led breeding. High-throughput sequencing-based characterization of finger millet germplasm representing diverse agro-ecologies was considered an effective method for determining its genetic diversity, thereby suggesting potential candidates for breeding. In this study, the genotyping-by-sequencing (GBS) method was used to simultaneously identify novel single nucleotide polymorphism (SNP) markers and genotype 288 finger millet accessions collected from Ethiopia and Zimbabwe. The accessions were characterized at individual and group levels using 5,226 bi-allelic SNPs, with a minimum allele frequency (MAF) of above 0.05, distributed across 2,500 scaffolds of the finger millet reference genome. The polymorphism information content (PIC) of the SNPs was 0.23 on average, and a quarter of them have PIC values over 0.32, making them highly informative. The grouping of the 288 accessions into seven populations based on geographic proximity and the potential for germplasm exchange revealed a narrow range of observed heterozygosity (Ho; 0.09–0.11) and expected heterozygosity (He) that ranged over twofold, from 0.11 to 0.26. Alleles unique to the different groups were also identified, which merit further investigation for their potential association with desirable traits. The analysis of molecular variance (AMOVA) revealed a highly significant genetic differentiation among groups of accessions classified based on the geographic region, country of origin, days to flowering, panicle type, and Al tolerance (p < 0.01). The high genetic differentiation between Ethiopian and Zimbabwean accessions was evident in the AMOVA, cluster, principal coordinate, and population structure analyses. The level of genetic diversity of finger millet accessions varies moderately among locations within Ethiopia, with accessions from the northern region having the lowest level. In the neighbor-joining cluster analysis, most of the improved cultivars included in this study were closely clustered, probably because they were developed using genetically less diverse germplasm and/or selected for similar traits, such as grain yield. The recombination of alleles via crossbreeding genetically distinct accessions from different regions of the two countries can potentially lead to the development of superior cultivars.
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Affiliation(s)
- Haftom Brhane
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia.,Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | | | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia.,Ethiopian Biotechnology Institute, Ministry of Science and Technology, Addis Ababa, Ethiopia
| | - Rodomiro Ortiz
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Kibrom B Abreha
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Mulatu Geleta
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
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23
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Genome-wide SNPs detect fine-scale genetic structure in threatened populations of squirrel glider Petaurus norfolcensis. CONSERV GENET 2022. [DOI: 10.1007/s10592-022-01435-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
AbstractAustralian arboreal mammals are experiencing significant population declines, particularly due to land clearing and resulting habitat fragmentation. The squirrel glider, Petaurus norfolcensis, is a threatened species in New South Wales, with a stronghold population in the Lake Macquarie Local Government Area (LGA) where fragmentation due to urbanization is an ongoing problem for the species conservation. Here we report on the use of squirrel glider mitochondrial (385 bp cytochrome b gene, 70 individuals) and nuclear DNA (6,834 SNPs, 87 individuals) markers to assess their population genetic structure and connectivity across 14 locations sampled in the Lake Macquarie LGA. The mitochondrial DNA sequences detected evidence of a historical genetic bottleneck, while the genome-wide SNPs detected significant population structure in the Lake Macquarie squirrel glider populations at scales as fine as one kilometer. There was no evidence of inbreeding within patches, however there were clear effects of habitat fragmentation and biogeographical barriers on gene flow. A least cost path analysis identified thin linear corridors that have high priority for conservation. These areas should be protected to avoid further isolation of squirrel glider populations and the loss of genetic diversity through genetic drift.
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24
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Razzaq A, Zafar MM, Ali A, Hafeez A, Sharif F, Guan X, Deng X, Pengtao L, Shi Y, Haroon M, Gong W, Ren M, Yuan Y. The Pivotal Role of Major Chromosomes of Sub-Genomes A and D in Fiber Quality Traits of Cotton. Front Genet 2022; 12:642595. [PMID: 35401652 PMCID: PMC8988190 DOI: 10.3389/fgene.2021.642595] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 10/25/2021] [Indexed: 02/02/2023] Open
Abstract
Lack of precise information about the candidate genes involved in a complex quantitative trait is a major obstacle in the cotton fiber quality improvement, and thus, overall genetic gain in conventional phenotypic selection is low. Recent molecular interventions and advancements in genome sequencing have led to the development of high-throughput molecular markers, quantitative trait locus (QTL) fine mapping, and single nucleotide polymorphisms (SNPs). These advanced tools have resolved the existing bottlenecks in trait-specific breeding. This review demonstrates the significance of chromosomes 3, 7, 9, 11, and 12 of sub-genomes A and D carrying candidate genes for fiber quality. However, chromosome 7 carrying SNPs for stable and potent QTLs related to fiber quality provides great insights for fiber quality-targeted research. This information can be validated by marker-assisted selection (MAS) and transgene in Arabidopsis and subsequently in cotton.
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Affiliation(s)
- Abdul Razzaq
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore, Pakistan
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
| | - Muhammad Mubashar Zafar
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Arfan Ali
- FB Genetics Four Brothers Group, Lahore, Pakistan
| | - Abdul Hafeez
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Faiza Sharif
- University Institute of Physical Therapy, The University of Lahore, Lahore, Pakistan
| | | | - Xiaoying Deng
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Li Pengtao
- School of Biotechnology and Food Engineering, Anyang Institute of Technology, Anyang, China
| | - Yuzhen Shi
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Muhammad Haroon
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
| | - Wankui Gong
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
| | - Maozhi Ren
- State Key Laboratory of Cotton Biology, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
| | - Youlu Yuan
- Key Laboratory of Biological and Genetic Breeding of Cotton, The Ministry of Agriculture, Institute of Cotton Research, Chinese Academy of Agricultural Science, Anyang, China
- Zhengzhou Research Base, State Key Laboratory of Cotton Biology, Zhengzhou University, Zhengzhou, China
- *Correspondence: Abdul Razzaq, ; Youlu Yuan , ; Maozhi Ren,
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25
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Alemu A, Brantestam AK, Chawade A. Unraveling the Genetic Basis of Key Agronomic Traits of Wrinkled Vining Pea ( Pisum sativum L.) for Sustainable Production. FRONTIERS IN PLANT SCIENCE 2022; 13:844450. [PMID: 35360298 PMCID: PMC8964273 DOI: 10.3389/fpls.2022.844450] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Abstract
Estimating the allelic variation and exploring the genetic basis of quantitatively inherited complex traits are the two foremost breeding scenarios for sustainable crop production. The current study utilized 188 wrinkled vining pea genotypes comprising historical varieties and breeding lines to evaluate the existing genetic diversity and to detect molecular markers associated with traits relevant to vining pea production, such as wrinkled vining pea yield (YTM100), plant height (PH), earliness (ERL), adult plant resistance to downy mildew (DM), pod length (PDL), numbers of pods per plant (PDP), number of peas per pod (PPD), and percent of small wrinkled vining peas (PSP). Marker-trait associations (MTAs) were conducted using 6902 quality single nucleotide polymorphism (SNP) markers generated from the diversity arrays technology sequencing (DArTseq) and Genotyping-by-sequencing (GBS) sequencing methods. The best linear unbiased prediction (BLUP) values were estimated from the two-decades-long (1999-2020) unbalanced phenotypic data sets recorded from two private breeding programs, the Findus and the Birds eye, now owned by Nomad Foods. Analysis of variance revealed a highly significant variation between genotypes and genotype-by-environment interactions for the ten traits. The genetic diversity and population structure analyses estimated an intermediate level of genetic variation with two optimal sub-groups within the current panel. A total of 48 significant (P < 0.0001) MTAs were identified for eight different traits, including five for wrinkled vining pea yield on chr2LG1, chr4LG4, chr7LG7, and scaffolds (two), and six for adult plant resistance to downy mildew on chr1LG6, chr3LG5 (two), chr6LG2, and chr7LG7 (two). We reported several novel MTAs for different crucial traits with agronomic importance in wrinkled vining pea production for the first time, and these candidate markers could be easily validated and integrated into the active breeding programs for marker-assisted selection.
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Affiliation(s)
- Admas Alemu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
| | | | - Aakash Chawade
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Alnarp, Sweden
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26
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de Aquino SO, Kiwuka C, Tournebize R, Gain C, Marraccini P, Mariac C, Bethune K, Couderc M, Cubry P, Andrade AC, Lepelley M, Darracq O, Crouzillat D, Anten N, Musoli P, Vigouroux Y, de Kochko A, Manel S, François O, Poncet V. Adaptive potential of
Coffea canephora
from Uganda in response to climate change. Mol Ecol 2022; 31:1800-1819. [DOI: 10.1111/mec.16360] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 11/12/2021] [Accepted: 01/06/2022] [Indexed: 11/28/2022]
Affiliation(s)
| | - Catherine Kiwuka
- NARO Kampala Uganda
- Centre for Crop Systems Analysis Wageningen Univ. Wageningen Netherlands
| | | | - Clément Gain
- U. Grenoble‐Alpes, TIMC‐IMAG, CNRS UMR 5525, Grenoble, France and LJK, Inria, CNRS UMR 5224 Grenoble France
| | | | - Cédric Mariac
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | - Kévin Bethune
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | - Marie Couderc
- DIADE, Univ. Montpellier, CIRAD, IRD Montpellier France
| | | | | | | | | | | | - Niels Anten
- Centre for Crop Systems Analysis Wageningen Univ. Wageningen Netherlands
| | | | | | | | - Stéphanie Manel
- CEFE, Univ Montpellier, CNRS, EPHE‐PSL University, IRD Montpellier France
| | - Olivier François
- U. Grenoble‐Alpes, TIMC‐IMAG, CNRS UMR 5525, Grenoble, France and LJK, Inria, CNRS UMR 5224 Grenoble France
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27
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Insights into opium poppy (Papaver spp.) genetic diversity from genotyping-by-sequencing analysis. Sci Rep 2022; 12:111. [PMID: 34997061 PMCID: PMC8741915 DOI: 10.1038/s41598-021-04056-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 12/14/2021] [Indexed: 12/02/2022] Open
Abstract
Opium poppy (Papaver somniferum) is one of the world’s oldest medicinal plants and a versatile model system to study secondary metabolism. However, our knowledge of its genetic diversity is limited, restricting utilization of the available germplasm for research and crop improvement. We used genotyping-by-sequencing to investigate the extent of genetic diversity and population structure in a collection of poppy germplasm consisting of 91 accessions originating in 30 countries of Europe, North Africa, America, and Asia. We identified five genetically distinct subpopulations using discriminate analysis of principal components and STRUCTURE analysis. Most accessions obtained from the same country were grouped together within subpopulations, likely a consequence of the restriction on movement of poppy germplasm. Alkaloid profiles of accessions were highly diverse, with morphine being dominant. Phylogenetic analysis identified genetic groups that were largely consistent with the subpopulations detected and that could be differentiated broadly based on traits such as number of branches and seed weight. These accessions and the associated genotypic data are valuable resources for further genetic diversity analysis, which could include definition of poppy core sets to facilitate genebank management and use of the diversity for genetic improvement of this valuable crop.
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28
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Park JS, Kang MY, Shim EJ, Oh J, Seo KI, Kim KS, Sim SC, Chung SM, Park Y, Lee GP, Lee WS, Kim M, Jung JK. Genome-wide core sets of SNP markers and Fluidigm assays for rapid and effective genotypic identification of Korean cultivars of lettuce ( Lactuca sativa L.). HORTICULTURE RESEARCH 2022; 9:uhac119. [PMID: 35928401 PMCID: PMC9343917 DOI: 10.1093/hr/uhac119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 05/04/2022] [Indexed: 05/08/2023]
Abstract
Lettuce is one of the economically important leaf vegetables and is cultivated mainly in temperate climate areas. Cultivar identification based on the distinctness, uniformity, and stability (DUS) test is a prerequisite for new cultivar registration. However, DUS testing based on morphological features is time-consuming, labor-intensive, and costly, and can also be influenced by environmental factors. Thus, molecular markers have also been used for the identification of genetic diversity as an effective, accurate, and stable method. Currently, genome-wide single nucleotide polymorphisms (SNPs) using next-generation sequencing technology are commonly applied in genetic research on diverse plant species. This study aimed to establish an effective and high-throughput cultivar identification system for lettuce using core sets of SNP markers developed by genotyping by sequencing (GBS). GBS identified 17 877 high-quality SNPs for 90 commercial lettuce cultivars. Genetic differentiation analyses based on the selected SNPs classified the lettuce cultivars into three main groups. Core sets of 192, 96, 48, and 24 markers were further selected and validated using the Fluidigm platform. Phylogenetic analyses based on all core sets of SNPs successfully discriminated individual cultivars that have been currently recognized. These core sets of SNP markers will support the construction of a DNA database of lettuce that can be useful for cultivar identification and purity testing, as well as DUS testing in the plant variety protection system. Additionally, this work will facilitate genetic research to improve breeding in lettuce.
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Affiliation(s)
- Jee-Soo Park
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Min-Young Kang
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Eun-Jo Shim
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - JongHee Oh
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Kyoung-In Seo
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Kyung Seok Kim
- Department of Natural Resource Ecology and Management, Iowa State University, Ames IA 50011, USA
| | - Sung-Chur Sim
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Republic of Korea
| | - Sang-Min Chung
- Department of Life Sciences, Dongguk University, Seoul 04620, Republic of Korea
| | - Younghoon Park
- Department of Horticultural Bioscience, Pusan National University, Miryang 50463, South Korea
| | - Gung Pyo Lee
- Department of Plant Science and Technology, Chung-Ang University, Ansung 17546, South Korea
| | - Won-Sik Lee
- Seed Testing and Research Center, Korea Seed & Variety Service, Gimcheon 39660, Republic of Korea
| | - Minkyung Kim
- Department of Bioresources Engineering, Sejong University, Seoul 05006, Republic of Korea
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29
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Ortiz M, Jauset-Rubio M, Skouridou V, Machado D, Viveiros M, Clark TG, Simonova A, Kodr D, Hocek M, O’Sullivan CK. Electrochemical Detection of Single-Nucleotide Polymorphism Associated with Rifampicin Resistance in Mycobacterium tuberculosis Using Solid-Phase Primer Elongation with Ferrocene-Linked Redox-Labeled Nucleotides. ACS Sens 2021; 6:4398-4407. [PMID: 34797987 PMCID: PMC8715531 DOI: 10.1021/acssensors.1c01710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
Here, we report the
electrochemical detection of single-point mutations
using solid-phase isothermal primer elongation with redox-labeled
oligonucleotides. A single-base mutation associated with resistance
to rifampicin, an antibiotic commonly used for the treatment of Mycobacterium tuberculosis, was used as a model system
to demonstrate a proof-of-concept of the approach. Four 5′-thiolated
primers, designed to be complementary with the same fragment of the
target sequence and differing only in the last base, addressing the
polymorphic site, were self-assembled via chemisorption on individual
gold electrodes of an array. Following hybridization with single-stranded
DNA, Klenow (exo-) DNA polymerase-mediated primer extension with ferrocene-labeled
2′-deoxyribonucleoside triphosphates (dNFcTPs) was
only observed to proceed at the electrode where there was full complementarity
between the surface-tethered probe and the target DNA being interrogated.
We tested all four ferrocenylethynyl-linked dNTPs and optimized the
ratio of labeled/natural nucleotides to achieve maximum sensitivity.
Following a 20 min hybridization step, Klenow (exo-) DNA polymerase-mediated
primer elongation at 37 °C for 5 min was optimal for the enzymatic
incorporation of a ferrocene-labeled nucleotide, achieving unequivocal
electrochemical detection of a single-point mutation in 14 samples
of genomic DNA extracted from Mycobacterium tuberculosis strains. The approach is rapid, cost-effective, facile, and can
be extended to multiplexed electrochemical single-point mutation genotyping.
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Affiliation(s)
- Mayreli Ortiz
- Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Miriam Jauset-Rubio
- Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Vasso Skouridou
- Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
| | - Diana Machado
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisbon, Portugal
| | - Miguel Viveiros
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisbon, Portugal
| | - Taane G. Clark
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, Rua da Junqueira, 100, 1349-008 Lisbon, Portugal
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, WC1E 7HT London, U.K
| | - Anna Simonova
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam.2, 16610 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843 Prague 2, Czech Republic
| | - David Kodr
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam.2, 16610 Prague 6, Czech Republic
| | - Michal Hocek
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, Flemingovo nam.2, 16610 Prague 6, Czech Republic
- Department of Organic Chemistry, Faculty of Science, Charles University, Hlavova 8, 12843 Prague 2, Czech Republic
| | - Ciara K. O’Sullivan
- Departament d’Enginyeria Química, Universitat Rovira i Virgili, Avinguda Països Catalans 26, 43007 Tarragona, Spain
- Institució Catalana de Recerca i Estudis Avançats, Passeig Lluis Companys 23, 08010 Barcelona, Spain
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30
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Thant AA, Zaw H, Kalousova M, Singh RK, Lojka B. Genetic Diversity and Population Structure of Myanmar Rice (Oryza sativa L.) Varieties Using DArTseq-Based SNP and SilicoDArT Markers. PLANTS 2021; 10:plants10122564. [PMID: 34961035 PMCID: PMC8707408 DOI: 10.3390/plants10122564] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 11/18/2021] [Accepted: 11/20/2021] [Indexed: 11/25/2022]
Abstract
Myanmar is well known as a primary center of plant genetic resources for rice. A considerable number of genetic diversity studies have been conducted in Myanmar using various DNA markers. However, this is the first report using DArTseq technology for exploring the genetic diversity of Myanmar rice. In our study, two ultra-high-throughput diversity array technology markers were employed to investigate the genetic diversity and population structure of local rice varieties in the Ayeyarwady delta, the major region of rice cultivation. The study was performed using 117 rice genotypes with 7643 SNP and 4064 silicoDArT markers derived from the DArT platform. Genetic variance among the genotypes ranged from 0 to 0.753 in SNPs, and from 0.001 to 0.954 in silicoDArT. Two distinct population groups were identified from SNP data analysis. Cluster analysis with both markers clearly separated traditional Pawsan varieties and modern high-yielding varieties. A significant divergence was found between populations according to the Fst values (0.737) obtained from the analysis of molecular variance, which revealed 74% genetic variation at the population level. These findings support rice researchers in identifying useful DNA polymorphisms in genes and pinpointing specific genes conferring desirable phenotypic traits for further genome-wide association studies and parental selection for recombination breeding to enhance rice varietal development and release.
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Affiliation(s)
- Aye Aye Thant
- Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6 Suchdol, 165 00 Prague, Czech Republic;
- Correspondence: (A.A.T.); (B.L.); Tel.: +420-773495976 (A.A.T.); +420-224382171 or +420-734170763 (B.L.)
| | - Hein Zaw
- Plant Biotechnology Center, Pale Myothit, Shwe Nanthar, Mingaladon, Yangon 110 23, Myanmar;
| | - Marie Kalousova
- Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6 Suchdol, 165 00 Prague, Czech Republic;
| | - Rakesh Kumar Singh
- International Center for Biosaline Agriculture, Crop Diversification and Genetics, Al Rwayyah 2, Academic City, Dubai P.O. Box 14660, United Arab Emirates;
| | - Bohdan Lojka
- Department of Crop Sciences and Agroforestry, Faculty of Tropical AgriSciences, Czech University of Life Sciences Prague, Kamýcká 129, Praha 6 Suchdol, 165 00 Prague, Czech Republic;
- Correspondence: (A.A.T.); (B.L.); Tel.: +420-773495976 (A.A.T.); +420-224382171 or +420-734170763 (B.L.)
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Ahmar S, Ballesta P, Ali M, Mora-Poblete F. Achievements and Challenges of Genomics-Assisted Breeding in Forest Trees: From Marker-Assisted Selection to Genome Editing. Int J Mol Sci 2021; 22:10583. [PMID: 34638922 PMCID: PMC8508745 DOI: 10.3390/ijms221910583] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/26/2021] [Accepted: 09/27/2021] [Indexed: 12/23/2022] Open
Abstract
Forest tree breeding efforts have focused mainly on improving traits of economic importance, selecting trees suited to new environments or generating trees that are more resilient to biotic and abiotic stressors. This review describes various methods of forest tree selection assisted by genomics and the main technological challenges and achievements in research at the genomic level. Due to the long rotation time of a forest plantation and the resulting long generation times necessary to complete a breeding cycle, the use of advanced techniques with traditional breeding have been necessary, allowing the use of more precise methods for determining the genetic architecture of traits of interest, such as genome-wide association studies (GWASs) and genomic selection (GS). In this sense, main factors that determine the accuracy of genomic prediction models are also addressed. In turn, the introduction of genome editing opens the door to new possibilities in forest trees and especially clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR/Cas9). It is a highly efficient and effective genome editing technique that has been used to effectively implement targetable changes at specific places in the genome of a forest tree. In this sense, forest trees still lack a transformation method and an inefficient number of genotypes for CRISPR/Cas9. This challenge could be addressed with the use of the newly developing technique GRF-GIF with speed breeding.
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Affiliation(s)
- Sunny Ahmar
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile;
| | - Paulina Ballesta
- The National Fund for Scientific and Technological Development, Av. del Agua 3895, Talca 3460000, Chile
| | - Mohsin Ali
- Department of Forestry and Range Management, University of Agriculture Faisalabad, Faisalabad 38000, Pakistan;
| | - Freddy Mora-Poblete
- Institute of Biological Sciences, University of Talca, 1 Poniente 1141, Talca 3460000, Chile;
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Chen AYA, Huang CW, Liu SH, Liu AC, Chaung HC. Single Nucleotide Polymorphisms of Immunity-Related Genes and Their Effects on Immunophenotypes in Different Pig Breeds. Genes (Basel) 2021; 12:genes12091377. [PMID: 34573362 PMCID: PMC8471458 DOI: 10.3390/genes12091377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 11/16/2022] Open
Abstract
Enhancing resistance and tolerance to pathogens remains an important selection objective in the production of livestock animals. Single nucleotide polymorphisms (SNPs) vary gene expression at the transcriptional level, influencing an individual's immune regulation and susceptibility to diseases. In this study, we investigated the distribution of SNP sites in immune-related genes and their correlations with cell surface markers of immune cells within purebred (Taiwan black, Duroc, Landrace and Yorkshire) and crossbred (Landrace-Yorkshire) pigs. Thirty-nine SNPs of immune-related genes, including 11 cytokines, 5 chemokines and 23 Toll-like receptors (TLRs) (interferon-α and γ (IFN-α, γ), tumor necrosis factor-α (TNF-α), granulocyte-macrophage colony-stimulating factor (GM-CSF), Monocyte chemoattractant protein-1 (MCP-1) and TLR3, TLR4, TLR7, TLR8, and TLR9) were selected, and the percentages of positive cells with five cell surface markers of CD4, CD8, CD80/86, MHCI, and MHCII were analyzed. There were 28 SNPs that were significantly different among breeds, particularly between Landrace and Taiwan black. For instance, the frequency of SNP1 IFN-α -235A/G in Taiwan black and Landrace was 11.11% and 96.15%, respectively. In addition, 18 SNPs significantly correlated with the expression of cell surface markers, including CD4, CD8, CD80/86, and MHCII. The percentage of CD4+ (39.27%) in SNP33 TLR-8 543C/C was significantly higher than those in A/C (24.34%), at p < 0.05. Together, our findings show that Taiwan black pigs had a unique genotype distribution, whereas Landrace and Yorkshire had a more similar genotype distribution. Thus, an understanding of the genetic uniqueness of each breed could help to identify functionally important SNPs in immunoregulation.
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Affiliation(s)
- Ann Ying-An Chen
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan; (A.Y.-A.C.); (A.-C.L.)
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan
| | - Chao-Wei Huang
- Department of Tropical Agriculture and International Cooperation, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan;
| | - Shyh-Hwa Liu
- Department of Animal Science, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan;
| | - An-Chi Liu
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan; (A.Y.-A.C.); (A.-C.L.)
| | - Hso-Chi Chaung
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan; (A.Y.-A.C.); (A.-C.L.)
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Neipu, Pingtung 912, Taiwan
- Correspondence:
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Galal-Khallaf A, Hussein D, El-Sayed Hassab El-Nabi S. Single nucleotide polymorphism-based methodology for authentication of bovine, caprine, ovine, camel, and donkey meat cuts. J Food Sci 2021; 86:4444-4456. [PMID: 34431103 DOI: 10.1111/1750-3841.15885] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 12/21/2022]
Abstract
To guarantee food safetyand sustainability, it is necessary to verify meat authenticity. This study focused on the development of single nucleotide polymorphism-based polymerase chain reaction-restriction fragment length polymorphism (SNP-based PCR-RFLP) and forensically informative nucleotide sequence (FINS) methodologies based on PCR amplification of the mitochondrial 12S rRNA gene for discrimination of six red meat species, that is, cattle, buffalo, goat, sheep, camel, and donkey. FINS allowed the unambiguous identification of all species analyzed. In addition, six SNPs, where a restriction site for TasI could be localized using a preliminary in silico analysis, gave a unique RFLP pattern for each species. The results revealed a low level of species substitution (8%) in the tested meat samples. In particular, one buffalo and goat samples have been substituted with cow and sheep, respectively. Finally, the developed techniques herein showed high potentials to be routinely used as reliable and fast tools to avoid meat species substitutions. PRACTICAL APPLICATION: This research deals with genetic techniques to trace meats. This kind of research helps the concerned agencies to build capacity to safeguard consumer sentiments as well as providing better market access and better food price and quality for the consumer.
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Affiliation(s)
- Asmaa Galal-Khallaf
- Genetic Engineering and Molecular Biology Division, Department of Zoology, Faculty of Science, Menoufia University, Shebin El-Kom, Egypt
| | - Doaa Hussein
- Department of Zoology, Faculty of Science, Menoufia University, Shebin El-Kom, Egypt
| | - Sobhy El-Sayed Hassab El-Nabi
- Genetic Engineering and Molecular Biology Division, Department of Zoology, Faculty of Science, Menoufia University, Shebin El-Kom, Egypt
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Sharma B, Hussain T, Khan MA, Jaiswal V. Exploring AT2R and its polymorphism in different diseases: An approach to develop AT2R as a drug target beyond hypertension. Curr Drug Targets 2021; 23:99-113. [PMID: 34365920 DOI: 10.2174/1389450122666210806125919] [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: 02/01/2021] [Revised: 05/30/2021] [Accepted: 06/02/2021] [Indexed: 11/22/2022]
Abstract
The Angiotensin II type 2 receptor (AT2R) is one of the critical components of the renin-angiotensin system (RAS), which performs diverse functions like inhibiting cell differentiation, cell proliferation, vasodilatation, reduces oxidative stress and inflammation. AT2R is relatively less studied in comparison to other components of RAS despite its uniqueness (sex-linked) and diverse functions. The AT2R is differentially expressed in different tissues, and its gene polymorphisms are associated with several diseases. The molecular mechanism behind the association of AT2R and its gene polymorphisms with the diseases remains to be fully understood, which hinders the development of AT2R as a drug target. Single nucleotide polymorphisms (SNPs) in AT2R are found at different locations (exons, introns, promoter, and UTR regions) and were studied for association with different diseases. There may be different mechanisms behind these associations as some AT2R SNP variants were associated with differential expression, the SNPs (A1675G/A1332G) affect the alternate splicing of AT2R mRNA, A1332G genotype results in shortening of the AT2R mRNA and subsequently defective protein. Few SNPs were found to be associated with the diseases in either females (C4599A) or males (T1334C). Several other SNPs were expected to be associated with other similar/related diseases, but studies have not been done yet. The present review emphasizes on the significance of AT2R and its polymorphisms associated with the diseases to explore the precise role of AT2R in different diseases and the possibility to develop AT2R as a potential drug target.
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Affiliation(s)
- Bhanu Sharma
- Faculty of Applied Sciences and Biotechnology Shoolini University of Biotechnology and Management Sciences, Post Box No. 9, Head post Office, Solan, Himachal Pradesh. India
| | - Tahir Hussain
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, Texas. United States
| | - Mohammed Azhar Khan
- Faculty of Applied Sciences and Biotechnology Shoolini University of Biotechnology and Management Sciences, Post Box No. 9, Head post Office, Solan, Himachal Pradesh. India
| | - Varun Jaiswal
- Department of Food and Nutrition, College of BioNano Technology, Gachon University, Gyeonggi-do 13120. South Korea
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Roy NS, Ban YW, Yoo H, Ramekar RV, Cheong EJ, Park NI, Na JK, Park KC, Choi IY. Analysis of genome variants in dwarf soybean lines obtained in F6 derived from cross of normal parents (cultivated and wild soybean). Genomics Inform 2021; 19:e19. [PMID: 34261303 PMCID: PMC8261272 DOI: 10.5808/gi.21024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 04/21/2021] [Indexed: 11/20/2022] Open
Abstract
Plant height is an important component of plant architecture and significantly affects crop breeding practices and yield. We studied DNA variations derived from F5 recombinant inbred lines (RILs) with 96.8% homozygous genotypes. Here, we report DNA variations between the normal and dwarf members of four lines harvested from a single seed parent in an F6 RIL population derived from a cross between Glycine max var. Peking and Glycine soja IT182936. Whole genome sequencing was carried out, and the DNA variations in the whole genome were compared between the normal and dwarf samples. We found a large number of DNA variations in both the dwarf and semi-dwarf lines, with one single nucleotide polymorphism (SNP) per at least 3.68 kb in the dwarf lines and 1 SNP per 11.13 kb of the whole genome. This value is 2.18 times higher than the expected DNA variation in the F6 population. A total of 186 SNPs and 241 SNPs were discovered in the coding regions of the dwarf lines 1282 and 1303, respectively, and we discovered 33 homogeneous nonsynonymous SNPs that occurred at the same loci in each set of dwarf and normal soybean. Of them, five SNPs were in the same positions between lines 1282 and 1303. Our results provide important information for improving our understanding of the genetics of soybean plant height and crop breeding. These polymorphisms could be useful genetic resources for plant breeders, geneticists, and biologists for future molecular biology and breeding projects.
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Affiliation(s)
- Neha Samir Roy
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
| | - Yong-Wook Ban
- Department of Forest Environmental System, Kangwon National University, Chuncheon 24341, Korea
| | - Hana Yoo
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
| | - Rahul Vasudeo Ramekar
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
| | - Eun Ju Cheong
- Department of Forest Environmental System, Kangwon National University, Chuncheon 24341, Korea
| | - Nam-Il Park
- Department of Plant Science, Gangneung-Wonju National University, Gangneung 25457, Korea
| | - Jong Kuk Na
- Department of Controlled Agriculture, Kangwon National University, Chuncheon 24341, Korea
| | - Kyong-Cheul Park
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
| | - Ik-Young Choi
- Department of Agriculture and Life Industry, Kangwon National University, Chuncheon 24341, Korea
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Sica P, Scariolo F, Galvao A, Battaggia D, Nicoletto C, Maucieri C, Palumbo F, Franklin D, Cabrera M, Borin M, Sambo P, Barcaccia G. Molecular Hallmarks, Agronomic Performances and Seed Nutraceutical Properties to Exploit Neglected Genetic Resources of Common Beans Grown by Organic Farming in Two Contrasting Environments. FRONTIERS IN PLANT SCIENCE 2021; 12:674985. [PMID: 34113370 PMCID: PMC8185351 DOI: 10.3389/fpls.2021.674985] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/29/2021] [Indexed: 06/12/2023]
Abstract
Common bean (Phaseolus vulgaris L.) is an essential source of food proteins and an important component of sustainable agriculture systems around the world. Thus, conserving and exploiting the genetic materials of this crop species play an important role in achieving global food safety and security through the preservation of functional and serependic opportunities afforded by plant species diversity. Our research aimed to collect and perform agronomic, morpho-phenological, molecular-genetic, and nutraceutical characterizations of common bean accessions, including lowland and mountain Venetian niche landraces (ancient farmer populations) and Italian elite lineages (old breeder selections). Molecular characterization with SSR and SNP markers grouped these accessions into two well-separated clusters that were linked to the original Andean and Mesoamerican gene pools, which was consistent with the outputs of ancestral analysis. Genetic diversity in the two main clusters was not distributed equally the Andean gene pool was found to be much more uniform than the Mesoamerican pool. Additional subdivision resulted in subclusters, supporting the existence of six varietal groups. Accessions were selected according to preliminary investigations and historical records and cultivated in two contrasting Venetian environments: sea-level and mountain territories. We found that the environment significantly affected some nutraceutical properties of the seeds, mainly protein and starch contents. The antioxidant capacity was found significantly greater at sea level for climbing accessions and in the mountains for dwarf accessions. The seed yield at sea level was halved than mountain due to a seeds reduction in weight, volume, size and density. At sea level, bean landraces tended to have extended flowering periods and shorter fresh pod periods. The seed yield was positively correlated with the length of the period during which plants had fresh pods and negatively correlated with the length of the flowering period. Thus, the agronomic performance of these genetic resources showed their strong connection and adaptation to mountainous environments. On the whole, the genetic-molecular information put together for these univocal bean entries was combined with overall results from plant and seed analyses to select and transform the best accessions into commercial varieties (i.e., pure lines) suitable for wider cultivation.
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Affiliation(s)
- Pietro Sica
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Padua, Italy
| | - Francesco Scariolo
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Aline Galvao
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Domiziana Battaggia
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Carlo Nicoletto
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Carmelo Maucieri
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Fabio Palumbo
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Dorcas Franklin
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Padua, Italy
| | - Miguel Cabrera
- Department of Agronomy Food Natural Resources Animals and Environment (DAFNAE), University of Padova, Padua, Italy
| | - Maurizio Borin
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Paolo Sambo
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - Gianni Barcaccia
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
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Gao J, Ning XL. SNP detection and population structure evaluation of Salix gordejevii Y. L. Chang et Skv. in Hunshandake Sandland, Inner Mongolia, China. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:997-1005. [PMID: 34108824 PMCID: PMC8140056 DOI: 10.1007/s12298-021-00994-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 03/20/2021] [Accepted: 04/09/2021] [Indexed: 06/12/2023]
Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant and richest form of genomic polymorphism and, hence, are highly favorable markers for genetic map construction and genome-wide association studies. Based on the DNA specific-locus amplified fragment sequencing (SLAF-seq) for large-scale SNP detection, the genetic diversity and population structure of Salix gordejevii Y. L. Chang et Skv., a valuable sand-fixing shrub, was assessed in 199 accessions from 20 populations in Hunshandake Sandland of northern China. A total of 623.15 M reads resulted in 30.49 × sequencing depth on average and a mean Q30 of 95.70%, and 2,287,715 SNPs in 178,509 polymorphic SLAF tags were obtained. By discarding minor allele frequency > 0.05 and integrity > 0.8, a total of 93,600 SNPs were retained for population genetic analyses, which revealed that 199 individuals could be divided into six groups based on cross-validation errors. However, this grouping pattern did not match the geographical distribution, indicating that there is no apparent geographic barrier in the blank areas where S. gordejevii was not distributed in Hunshandake Sandland. In addition, the physical distance of linkage disequilibrium decay in the analyzed S. gordejevii individuals was 18.5 kb when r 2 = 0.1. The linkage disequilibrium decay distances for different chromosomes varied from 4.6 kb (chromosome 16) to 37.8 kb (chromosome 3). The obtained SNPs offer suitable marker resources for further genetic and genomic studies and will benefit S. gordejevii breeding programs.
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Affiliation(s)
- Jian Gao
- Faculty of Resources and Environment, Baotou Teachers’ College, Inner Mongolia University of Science and Technology, Baotou, 014030 China
| | - Xiao-Li Ning
- Faculty of Resources and Environment, Baotou Teachers’ College, Inner Mongolia University of Science and Technology, Baotou, 014030 China
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Kim SJ, Park JS, Shin YH, Park YD. Identification and Validation of Genetic Variations in Transgenic Chinese Cabbage Plants ( Brassica rapa ssp. pekinensis) by Next-Generation Sequencing. Genes (Basel) 2021; 12:genes12050621. [PMID: 33922022 PMCID: PMC8143544 DOI: 10.3390/genes12050621] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 04/16/2021] [Accepted: 04/19/2021] [Indexed: 01/24/2023] Open
Abstract
Transgenic plants are usually produced through tissue culture, which is an essential step in Agrobacterium-mediated plant transformation. However, genomic variations, termed somaclonal variations, have been detected in transgenic plants cultured in vitro. The occurrence of these variations should be as low as possible to secure the stability of transgenic crops. Determining the cause and mechanism of somaclonal variations in tissue culture-derived plants will help reduce the rate of variation and promote the stable expression of genes in transgenic plants. In order to determine the genetic variability in transgenic Chinese cabbage plants, we performed whole-genome resequencing and compared the sequencing data with the ‘CT001’ reference genome. The variation candidates that were expected to consistently occur in the transgenic lines were selected and validated. The single nucleotide polymorphism (SNP) and insertion and deletion (InDel) candidates were identified using the resequencing data and validated by reverse transcription (RT)-PCR analysis. The deduced amino acid sequences were used to determine whether the variations caused changes in the resulting polypeptide, and the annotations of the mutated genes were analyzed to predict the possible effects of the SNPs on gene function. In conclusion, we selected and validated the genetic variations identified in transgenic Chinese cabbage plants. Their genomes were expected to be affected by the process of Agrobacterium-mediated transformation. The findings of our study will provide a genetic basis for transgenic plant research.
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Affiliation(s)
| | | | | | - Young-Doo Park
- Correspondence: ; Tel.: +82-10-3338-9344; Fax: +82-31-202-8395
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Islam M, Abdullah, Zubaida B, Amin N, Khan RI, Shafqat N, Masood R, Waseem S, Tahir J, Ahmed I, Naeem M, Ahmad H. Agro-Morphological, Yield, and Genotyping-by-Sequencing Data of Selected Wheat ( Triticum aestivum) Germplasm From Pakistan. Front Genet 2021; 12:617772. [PMID: 34163518 PMCID: PMC8216712 DOI: 10.3389/fgene.2021.617772] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 03/19/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Madiha Islam
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Abdullah
- Department of Biochemistry, Quaid-i-Azam University, Islamabad, Pakistan
| | - Bibi Zubaida
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
| | - Nageena Amin
- Institute of Molecular Biology and Biotechnology, Bahauddin Zakariya University, Multan, Pakistan
| | - Rashid Iqbal Khan
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Noshin Shafqat
- Department of Agriculture, Hazara University, Mansehra, Pakistan
| | - Rabia Masood
- Department of Botany, Hazara University, Mansehra, Pakistan
| | | | - Jibran Tahir
- Terrestrial Bioscience New Zealand Limited, Auckland, New Zealand
| | - Ibrar Ahmed
- Alpha Genomics Private Limited, Islamabad, Pakistan
| | - Muhammad Naeem
- Federal Seed Certification and Registration Department, Islamabad, Pakistan
| | - Habib Ahmad
- Department of Biotechnology and Genetic Engineering, Hazara University, Mansehra, Pakistan
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Negisho K, Shibru S, Pillen K, Ordon F, Wehner G. Genetic diversity of Ethiopian durum wheat landraces. PLoS One 2021; 16:e0247016. [PMID: 33596260 PMCID: PMC7888639 DOI: 10.1371/journal.pone.0247016] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Accepted: 01/30/2021] [Indexed: 01/27/2023] Open
Abstract
Genetic diversity and population structure assessment in crops is essential for marker trait association, marker assisted breeding and crop germplasm conservation. We analyzed a set of 285 durum wheat accessions comprising 215 Ethiopian durum wheat landraces, 10 released durum wheat varieties, 10 advanced durum wheat lines from Ethiopia, and 50 durum wheat lines from CIMMYT. We investigated the genetic diversity and population structure for the complete panel as well as for the 215 landraces, separately based on 11,919 SNP markers with known physical positions. The whole panel was clustered into two populations representing on the one hand mainly the landraces, and on the other hand mainly released, advanced and CIMMYT lines. Further population structure analysis of the landraces uncovered 4 subgroups emphasizing the high degree of genetic diversity within Ethiopian durum landraces. Population structure based AMOVA for both sets unveiled significant (P < 0.001) variation between populations and within populations. Total variation within population accessions (81%, 76%) was higher than total variation between populations (19%, 24%) for both sets. Population structure analysis based genetic differentiation (FST) and gene flow (Nm) for the whole set and the Ethiopian landraces were 0.19 and 0.24, 1.04, and 0.81, respectively indicating high genetic differentiation and limited gene flow. Diversity indices verify that the landrace panel was more diverse with (I = 0.7, He = 0.46, uHe = 0.46) than the advanced lines (I = 0.6, He = 0.42, uHe = 0.42). Similarly, differences within the landrace clusters were observed. In summary a high genetic diversity within Ethiopian durum wheat landraces was detected, which may be a target for national and international wheat improvement programs to exploit valuable traits for biotic and abiotic stresses.
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Affiliation(s)
- Kefyalew Negisho
- Ethiopian Institute of Agricultural Research (EIAR), National Agricultural Biotechnology Research Center, Holeta, Ethiopia
| | - Surafel Shibru
- Ethiopian Institute of Agricultural Research (EIAR), Melkassa Research Center, Melkassa, Ethiopia
| | - Klaus Pillen
- Martin-Luther-University, Institute of Agricultural and Nutritional Sciences, Halle (Saale), Germany
| | - Frank Ordon
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
| | - Gwendolin Wehner
- Julius Kühn Institute (JKI), Institute for Resistance Research and Stress Tolerance, Quedlinburg, Germany
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Pirrello C, Zeilmaker T, Bianco L, Giacomelli L, Moser C, Vezzulli S. Mining Grapevine Downy Mildew Susceptibility Genes: A Resource for Genomics-Based Breeding and Tailored Gene Editing. Biomolecules 2021; 11:181. [PMID: 33525704 PMCID: PMC7912118 DOI: 10.3390/biom11020181] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/13/2022] Open
Abstract
Several pathogens continuously threaten viticulture worldwide. Until now, the investigation on resistance loci has been the main trend to understand the interaction between grapevine and the mildew causal agents. Dominantly inherited gene-based resistance has shown to be race-specific in some cases, to confer partial immunity, and to be potentially overcome within a few years since its introgression. Recently, on the footprint of research conducted in Arabidopsis, putative genes associated with downy mildew susceptibility have been discovered also in the grapevine genome. In this work, we deep-sequenced four putative susceptibility genes-namely VvDMR6.1, VvDMR6.2, VvDLO1, VvDLO2-in 190 genetically diverse grapevine genotypes to discover new sources of broad-spectrum and recessively inherited resistance. Identified Single Nucleotide Polymorphisms were screened in a bottleneck analysis from the genetic sequence to their impact on protein structure. Fifty-five genotypes showed at least one impacting mutation in one or more of the scouted genes. Haplotypes were inferred for each gene and two of them at the VvDMR6.2 gene were found significantly more represented in downy mildew resistant genotypes. The current results provide a resource for grapevine and plant genetics and could corroborate genomic-assisted breeding programs as well as tailored gene editing approaches for resistance to biotic stresses.
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Affiliation(s)
- Carlotta Pirrello
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Via delle Scienze 206, 33100 Udine, Italy
| | - Tieme Zeilmaker
- SciENZA Biotechnologies B.V., Sciencepark 904, 1098 XH Amsterdam, The Netherlands;
| | - Luca Bianco
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
| | - Lisa Giacomelli
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
- SciENZA Biotechnologies B.V., Sciencepark 904, 1098 XH Amsterdam, The Netherlands;
| | - Claudio Moser
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
| | - Silvia Vezzulli
- Research and Innovation Centre, Edmund Mach Foundation, Via E. Mach 1, 38010 San Michele all’Adige, Italy; (C.P.); (L.B.); (L.G.); (C.M.)
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Zeng J, Dong M, Zhu B, Gao X, Chen D, Li Y. Label-Free Detection of C–T Mutations by Surface-Enhanced Raman Spectroscopy Using Thiosulfate-Modified Nanoparticles. Anal Chem 2021; 93:1951-1956. [DOI: 10.1021/acs.analchem.0c04052] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Jiayu Zeng
- College of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City, Guizhou Province 550025, China
| | - Meiyu Dong
- College of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City, Guizhou Province 550025, China
| | - Bixue Zhu
- College of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City, Guizhou Province 550025, China
| | - Xin Gao
- School of Physics, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City, Guizhou Province 550025, China
| | - Dongmei Chen
- College of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City, Guizhou Province 550025, China
| | - Yang Li
- College of Chemistry and Chemical Engineering, Guizhou University, No. 2708, South Section of Huaxi Avenue, Guiyang City, Guizhou Province 550025, China
- College of Pharmacy, Harbin Medical University, No. 157, Health Road, Nangang District, Harbin City, Heilongjiang Province 150086, China
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Muturi PW, Mgonja M, Rubaihayo P, Mwololo JK. QTL Mapping of Traits Associated with Dual Resistance to the African Stem Borer ( Busseola fusca) and Spotted Stem Borer ( Chilo partellus) in Sorghum ( Sorghum bicolor). Int J Genomics 2021; 2021:7016712. [PMID: 33532486 PMCID: PMC7834829 DOI: 10.1155/2021/7016712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 10/14/2020] [Accepted: 11/16/2020] [Indexed: 11/21/2022] Open
Abstract
Sorghum (Sorghum bicolor (L.) Moench) is an important food crop in semi-arid tropics. The crop grain yield ranges from 0.5 t/ha to 0.8 t/ha compared to potential yields of 10 t/ha. The African stem borer Busseola fusca Fuller (Noctuidae) and the spotted stem borer Chilo partellus Swinhoe (Crambidae), are among the most economically important insect pests of sorghum. The two borers can cause 15% - 80% grain yield loss in sorghum. Mapping of QTLs associated with resistance traits to the two stem borers is important towards marker-assisted breeding. The objective of this study was to map QTLs associated with resistance traits to B. fusca and C. partellus in sorghum. 243 F9:10 sorghum RILs derived from ICSV 745 (S) and PB 15520-1 (R) were selected for the study with 4,955 SNP markers. The RILs were evaluated in three sites. Data was collected on leaf feeding, deadheart, exit holes, stem tunnels, leaf toughness, seedling vigour, bloom waxiness, and leaf glossiness. ANOVA for all the traits was done using Genstat statistical software. Insect damage traits and morphological traits were correlated using Pearson's correlation coefficients. Genetic mapping was done using JoinMap 4 software, while QTL analysis was done using PLABQTL software. A likelihood odds ratio (LOD) score of 3.0 was used to declare linkage. Joint analyses across borer species and sites revealed 4 QTLs controlling deadheart formation; 6 controlling leaf feeding damage; 5 controlling exit holes and stem tunneling damages; 2 controlling bloom waxiness, leaf glossiness, and seedling vigour; 4 conditioning trichome density; and 6 conditioning leaf toughness. Joint analyses for B. fusca and C. partellus further revealed that marker CS132-2 colocalised for leaf toughness and stem tunneling traits on QTLs 1 and 2, respectively; thus, the two traits can be improved using the same linked marker. This study recommended further studies to identify gene(s) underlying the mapped QTLs.
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Affiliation(s)
- Phyllis W. Muturi
- Department of Agricultural Resource Management, University of Embu, P.O. Box 60100, Embu, Kenya
| | - Mary Mgonja
- Alliance for a Green Revolution in Africa, P.O. Box 34441, Dar es Salaam, Tanzania
| | - Patrick Rubaihayo
- Department of Agricultural Production, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - James K. Mwololo
- East and South African Research Program, International Crops Research Institute of the Semi-Arid Tropics (ICRISAT), P.O. Box 1096 Lilongwe, Malawi
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Kalendar R, Baidyussen A, Serikbay D, Zotova L, Khassanova G, Kuzbakova M, Jatayev S, Hu YG, Schramm C, Anderson PA, Jenkins CLD, Soole KL, Shavrukov Y. Modified "Allele-Specific qPCR" Method for SNP Genotyping Based on FRET. FRONTIERS IN PLANT SCIENCE 2021; 12:747886. [PMID: 35082803 PMCID: PMC8784781 DOI: 10.3389/fpls.2021.747886] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 10/22/2021] [Indexed: 05/02/2023]
Abstract
The proposed method is a modified and improved version of the existing "Allele-specific q-PCR" (ASQ) method for genotyping of single nucleotide polymorphism (SNP) based on fluorescence resonance energy transfer (FRET). This method is similar to frequently used techniques like Amplifluor and Kompetitive allele specific PCR (KASP), as well as others employing common universal probes (UPs) for SNP analyses. In the proposed ASQ method, the fluorophores and quencher are located in separate complementary oligonucleotides. The ASQ method is based on the simultaneous presence in PCR of the following two components: an allele-specific mixture (allele-specific and common primers) and a template-independent detector mixture that contains two or more (up to four) universal probes (UP-1 to 4) and a single universal quencher oligonucleotide (Uni-Q). The SNP site is positioned preferably at a penultimate base in each allele-specific primer, which increases the reaction specificity and allele discrimination. The proposed ASQ method is advanced in providing a very clear and effective measurement of the fluorescence emitted, with very low signal background-noise, and simple procedures convenient for customized modifications and adjustments. Importantly, this ASQ method is estimated as two- to ten-fold cheaper than Amplifluor and KASP, and much cheaper than all those methods that rely on dual-labeled probes without universal components, like TaqMan and Molecular Beacons. Results for SNP genotyping in the barley genes HvSAP16 and HvSAP8, in which stress-associated proteins are controlled, are presented as proven and validated examples. This method is suitable for bi-allelic uniplex reactions but it can potentially be used for 3- or 4-allelic variants or different SNPs in a multiplex format in a range of applications including medical, forensic, or others involving SNP genotyping.
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Affiliation(s)
- Ruslan Kalendar
- National Laboratory Astana, Nazarbayev University, Nur-Sultan, Kazakhstan
- Institute of Biotechnology HiLIFE, University of Helsinki, Helsinki, Finland
- *Correspondence: Ruslan Kalendar
| | - Akmaral Baidyussen
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Dauren Serikbay
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Lyudmila Zotova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Gulmira Khassanova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Marzhan Kuzbakova
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Satyvaldy Jatayev
- Faculty of Agronomy, S. Seifullin Kazakh AgroTechnical University, Nur-Sultan, Kazakhstan
| | - Yin-Gang Hu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Carly Schramm
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Peter A. Anderson
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Colin L. D. Jenkins
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Kathleen L. Soole
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
| | - Yuri Shavrukov
- College of Science and Engineering, Biological Sciences, Flinders University, Adelaide, SA, Australia
- Yuri Shavrukov
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McClure T, Goh SK, Cox D, Muralidharan V, Dobrovic A, Testro AG. Donor-specific cell-free DNA as a biomarker in liver transplantation: A review. World J Transplant 2020; 10:307-319. [PMID: 33312892 PMCID: PMC7708879 DOI: 10.5500/wjt.v10.i11.307] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 10/09/2020] [Accepted: 10/30/2020] [Indexed: 02/05/2023] Open
Abstract
Due to advances in modern medicine, liver transplantation has revolutionised the prognosis of many previously incurable liver diseases. This progress has largely been due to advances in immunosuppressant therapy. However, despite the judicious use of immunosuppression, many liver transplant recipients still experience complications such as rejection, which necessitates diagnosis via invasive liver biopsy. There is a clear need for novel, minimally-invasive tests to optimise immunosuppression and improve patient outcomes. An emerging biomarker in this ''precision medicine'' liver transplantation field is that of donor-specific cell free DNA. In this review, we detail the background and methods of detecting this biomarker, examine its utility in liver transplantation and discuss future research directions that may be most impactful.
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Affiliation(s)
- Tess McClure
- Liver Transplant Unit, Austin Health, Heidelberg 3084, VIC, Australia
| | - Su Kah Goh
- Department of Surgery, Austin Health, Heidelberg 3084, VIC, Australia
| | - Daniel Cox
- Department of Surgery, Austin Health, Heidelberg 3084, VIC, Australia
| | | | - Alexander Dobrovic
- Department of Surgery, The University of Melbourne, Heidelberg 3084, VIC, Australia
| | - Adam G Testro
- Liver Transplant Unit, Austin Health, Heidelberg 3084, VIC, Australia
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Khadka K, Torkamaneh D, Kaviani M, Belzile F, Raizada MN, Navabi A. Population structure of Nepali spring wheat (Triticum aestivum L.) germplasm. BMC PLANT BIOLOGY 2020; 20:530. [PMID: 33225886 PMCID: PMC7682013 DOI: 10.1186/s12870-020-02722-8] [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: 02/27/2020] [Accepted: 10/26/2020] [Indexed: 05/04/2023]
Abstract
BACKGROUND Appropriate information about genetic diversity and population structure of germplasm improves the efficiency of plant breeding. The low productivity of Nepali bread wheat (Triticum aestivum L.) is a major concern particularly since Nepal is ranked the 4th most vulnerable nation globally to climate change. The genetic diversity and population structure of Nepali spring wheat have not been reported. This study aims to improve the exploitation of more diverse and under-utilized genetic resources to contribute to current and future breeding efforts for global food security. RESULTS We used genotyping-by-sequencing (GBS) to characterize a panel of 318 spring wheat accessions from Nepal including 166 landraces, 115 CIMMYT advanced lines, and 34 Nepali released varieties. We identified 95 K high-quality SNPs. The greatest genetic diversity was observed among the landraces, followed by CIMMYT lines, and released varieties. Though we expected only 3 groupings corresponding to these 3 seed origins, the population structure revealed two large, distinct subpopulations along with two smaller and scattered subpopulations in between, with significant admixture. This result was confirmed by principal component analysis (PCA) and UPGMA distance-based clustering. The pattern of LD decay differed between subpopulations, ranging from 60 to 150 Kb. We discuss the possibility that germplasm explorations during the 1970s-1990s may have mistakenly collected exotic germplasm instead of local landraces and/or collected materials that had already cross-hybridized since exotic germplasm was introduced starting in the 1950s. CONCLUSION We suggest that only a subset of wheat "landraces" in Nepal are authentic which this study has identified. Targeting these authentic landraces may accelerate local breeding programs to improve the food security of this climate-vulnerable nation. Overall, this study provides a novel understanding of the genetic diversity of wheat in Nepal and this may contribute to global wheat breeding initiatives.
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Affiliation(s)
- Kamal Khadka
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada.
| | - Davoud Torkamaneh
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
- Département de Phytologie, Université Laval, Québec City, QC, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
| | - Mina Kaviani
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Francois Belzile
- Département de Phytologie, Université Laval, Québec City, QC, G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC, Canada
| | - Manish N Raizada
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
| | - Alireza Navabi
- Department of Plant Agriculture, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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Yang X, Tan B, Liu H, Zhu W, Xu L, Wang Y, Fan X, Sha L, Zhang H, Zeng J, Wu D, Jiang Y, Hu X, Chen G, Zhou Y, Kang H. Genetic Diversity and Population Structure of Asian and European Common Wheat Accessions Based on Genotyping-By-Sequencing. Front Genet 2020; 11:580782. [PMID: 33101397 PMCID: PMC7545058 DOI: 10.3389/fgene.2020.580782] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Accepted: 09/03/2020] [Indexed: 12/17/2022] Open
Abstract
Obtaining information on the genetic diversity and population structure of germplasm facilitates its use in wheat breeding programs. Recently, with the development of next-generation sequencing technology, genotyping-by-sequencing (GBS) has been used as a high-throughput and cost-effective molecular tool for examination of the genetic diversity of wheat breeding lines. In this study, GBS was used to characterize a population of 180 accessions of common wheat originating from Asia and Europe between the latitudes 30° and 45°N. In total, 24,767 high-quality single-nucleotide polymorphism (SNP) markers were used for analysis of genetic diversity and population structure. The B genome contained the highest number of SNPs, followed by the A and D genomes. The polymorphism information content was in the range of 0.1 to 0.4, with a mean of 0.26. The distribution of SNPs markers on the 21 chromosomes ranged from 243 on chromosome 4D to 2,337 on chromosome 3B. Structure and cluster analyses divided the panel of accessions into two subgroups (G1 and G2). G1 principally consisted of European and partial Asian accessions, and G2 comprised mainly accessions from the Middle East and partial Asia. Molecular analysis of variance showed that the genetic variation was greater within groups (99%) than between groups (1%). Comparison of the two subgroups indicated that G1 and G2 contained a high level of genetic diversity. The genetic diversity of G2 was slightly higher as indicated by the observed heterozygosity (H o) = 0.23, and unbiased diversity index (uh) = 0.34. The present results will not only help breeders to understand the genetic diversity of wheat germplasm on the Eurasian continent between the latitudes of 30° and 45°N, but also provide valuable information for wheat genetic improvement through introgression of novel genetic variation in this region.
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Affiliation(s)
- Xiu Yang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Binwen Tan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Haijiao Liu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Wei Zhu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lili Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
| | - Yi Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xing Fan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Lina Sha
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Haiqin Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Jian Zeng
- College of Resources, Sichuan Agricultural University, Chengdu, China
| | - Dandan Wu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Xigui Hu
- Center of Wheat Research, Henan Institute of Science and Technology, Xinxiang, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Yonghong Zhou
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
| | - Houyang Kang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, China
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, China
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Critical Analysis of Genome-Wide Association Studies: Triple Negative Breast Cancer Quae Exempli Causa. Int J Mol Sci 2020; 21:ijms21165835. [PMID: 32823908 PMCID: PMC7461549 DOI: 10.3390/ijms21165835] [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: 07/15/2020] [Revised: 08/10/2020] [Accepted: 08/11/2020] [Indexed: 12/14/2022] Open
Abstract
Genome-wide association studies (GWAS) are useful in assessing and analyzing either differences or variations in DNA sequences across the human genome to detect genetic risk factors of diseases prevalent within a target population under study. The ultimate goal of GWAS is to predict either disease risk or disease progression by identifying genetic risk factors. These risk factors will define the biological basis of disease susceptibility for the purposes of developing innovative, preventative, and therapeutic strategies. As single nucleotide polymorphisms (SNPs) are often used in GWAS, their relevance for triple negative breast cancer (TNBC) will be assessed in this review. Furthermore, as there are different levels and patterns of linkage disequilibrium (LD) present within different human subpopulations, a plausible strategy to evaluate known SNPs associated with incidence of breast cancer in ethnically different patient cohorts will be presented and discussed. Additionally, a description of GWAS for TNBC will be presented, involving various identified SNPs correlated with miRNA sites to determine their efficacies on either prognosis or progression of TNBC in patients. Although GWAS have identified multiple common breast cancer susceptibility variants that individually would result in minor risks, it is their combined effects that would likely result in major risks. Thus, one approach to quantify synergistic effects of such common variants is to utilize polygenic risk scores. Therefore, studies utilizing predictive risk scores (PRSs) based on known breast cancer susceptibility SNPs will be evaluated. Such PRSs are potentially useful in improving stratification for screening, particularly when combining family history, other risk factors, and risk prediction models. In conclusion, although interpretation of the results from GWAS remains a challenge, the use of SNPs associated with TNBC may elucidate and better contextualize these studies.
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Genetic Mapping in Autohexaploid Sweet Potato with Low-Coverage NGS-Based Genotyping Data. G3-GENES GENOMES GENETICS 2020; 10:2661-2670. [PMID: 32482727 PMCID: PMC7407471 DOI: 10.1534/g3.120.401433] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing (NGS)-based genotyping methods can generate numerous genetic markers in a single experiment and have contributed to plant genetic mapping. However, for high precision genetic analysis, the complicated genetic segregation mode in polyploid organisms requires high-coverage NGS data and elaborate analytical algorithms. In the present study, we propose a simple strategy for the genetic mapping of polyploids using low-coverage NGS data. The validity of the strategy was investigated using simulated data. Previous studies indicated that accurate allele dosage estimation from low-coverage NGS data (read depth < 40) is difficult. Therefore, we used allele dosage probabilities calculated from read counts in association analyses to detect loci associated with phenotypic variations. The allele dosage probabilities showed significant detection power, although higher allele dosage estimation accuracy resulted in higher detection power. On the contrary, differences in the segregation patterns between the marker and causal genes resulted in a drastic decrease in detection power even if the marker and casual genes were in complete linkage and the allele dosage estimation was accurate. These results indicated that the use of a larger number of markers is advantageous, even if the accuracy of allele dosage estimation is low. Finally, we applied the strategy for the genetic mapping of autohexaploid sweet potato (Ipomoea batatas) populations to detect loci associated with agronomic traits. Our strategy could constitute a cost-effective approach for preliminary experiments done performed to large-scale studies.
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50
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Genetic Diversity, Population Structure, and Parentage Analysis of Croatian Grapevine Germplasm. Genes (Basel) 2020; 11:genes11070737. [PMID: 32630730 PMCID: PMC7397172 DOI: 10.3390/genes11070737] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/25/2020] [Accepted: 06/25/2020] [Indexed: 12/29/2022] Open
Abstract
Croatian viticulture was most extensive at the beginning of the 20th century, when about 400 varieties were in use. Autochthonous varieties are the result of spontaneous hybridization from the pre-phylloxera era and are still cultivated today on about 35 % of vineyard area, while some exist only in repositories. We present what is the most comprehensive genetic analysis of all major Croatian national repositories, with a large number of microsatellite, or simple sequence repeat (SSR) markers, and it is also the first study to apply single nucleotide polymorphism (SNP) markers. After 212 accessions were fingerprinted, 95 were classified as unique to Croatian germplasm. Genetic diversity of Croatian germplasm is rather high considering its size. SNP markers proved useful for fingerprinting but less informative and practical than SSRs. Analysis of the genetic structure showed that Croatian germplasm is predominantly part of the Balkan grape gene pool. A high number of admixed varieties and synonyms is a consequence of complex pedigrees and migrations. Parentage analysis confirmed 24 full parentages, as well as 113 half-kinships. Unexpectedly, several key genitors could not be detected within the present Croatian germplasm. The low number of reconstructed parentages (19%) points to severe genetic erosion and stresses the importance of germplasm repositories.
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