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Bančič J, Odeny DA, Ojulong HF, Josiah SM, Buntjer J, Gaynor RC, Hoad SP, Gorjanc G, Dawson IK. Genomic and phenotypic characterization of finger millet indicates a complex diversification history. THE PLANT GENOME 2024; 17:e20392. [PMID: 37986545 DOI: 10.1002/tpg2.20392] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/10/2023] [Accepted: 08/16/2023] [Indexed: 11/22/2023]
Abstract
Advances in sequencing technologies mean that insights into crop diversification can now be explored in crops beyond major staples. We use a genome assembly of finger millet, an allotetraploid orphan crop, to analyze DArTseq single nucleotide polymorphisms (SNPs) at the whole and sub-genome level. A set of 8778 SNPs and 13 agronomic traits was used to characterize a diverse panel of 423 landraces from Africa and Asia. Through principal component analysis (PCA) and discriminant analysis of principal components, four distinct groups of accessions were identified that coincided with the primary geographic regions of finger millet cultivation. Notably, East Africa, presumed to be the crop's origin, exhibited the lowest genetic diversity. The PCA of phenotypic data also revealed geographic differentiation, albeit with differing relationships among geographic areas than indicated with genomic data. Further exploration of the sub-genomes A and B using neighbor-joining trees revealed distinct features that provide supporting evidence for the complex evolutionary history of finger millet. Although genome-wide association study found only a limited number of significant marker-trait associations, a clustering approach based on the distribution of marker effects obtained from a ridge regression genomic model was employed to investigate trait complexity. This analysis uncovered two distinct clusters. Overall, the findings suggest that finger millet has undergone complex and context-specific diversification, indicative of a lengthy domestication history. These analyses provide insights for the future development of finger millet.
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Affiliation(s)
- Jon Bančič
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Research Centre, Midlothian, UK
- Scotland's Rural College (SRUC), Kings Buildings, Edinburgh, UK
| | - Damaris A Odeny
- International Crops Research Institute for the Semi-Arid Tropics, ICRAF House, Gigiri Nairobi, Kenya
| | - Henry F Ojulong
- International Crops Research Institute for the Semi-Arid Tropics, ICRAF House, Gigiri Nairobi, Kenya
| | - Samuel M Josiah
- Department of Horticulture, University of Georgia, Athens, Georgia, USA
| | - Jaap Buntjer
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Research Centre, Midlothian, UK
| | - R Chris Gaynor
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Research Centre, Midlothian, UK
| | - Stephen P Hoad
- Scotland's Rural College (SRUC), Kings Buildings, Edinburgh, UK
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Research Centre, Midlothian, UK
| | - Ian K Dawson
- Scotland's Rural College (SRUC), Kings Buildings, Edinburgh, UK
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Jabari M, Golparvar A, Sorkhilalehloo B, Shams M. Investigation of genetic diversity of Iranian wild relatives of bread wheat using ISSR and SSR markers. J Genet Eng Biotechnol 2023; 21:73. [PMID: 37382843 DOI: 10.1186/s43141-023-00526-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 06/08/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND Wild relatives of wheat are one of the most important genetic resources to use in wheat breeding programs. Therefore, identifying wild relatives of wheat and being aware of their diversity, is undeniably effective in expanding the richness of the gene pool and the genetic base of new cultivars and can be a useful tool for breeders in the future. The present study was performed to evaluate the molecular diversity among 49 accessions of the genera Aegilops and Triticum in the National Plant Gene Bank of Iran using two DNA-based markers, i.e., SSR and ISSR. Also, the present study aimed to examine the relationships among the accessions studied belonging to different genetic backgrounds. RESULTS Ten SSR and tan ISSR primers produced 2065 and 1524 polymorphism bands, respectively. The number of Polymorphic Bands (NPB), the Polymorphism Information Content (PIC), Marker Index (MI), and Resolving Power (Rp) in SSR marker was 162 to 317, 0.830 to 0.919, 1.326 to 3.167, and 3.169 to 5.692, respectively, and in the ISSR marker, it was from 103 to 185, 0.377 to 0.441, 0.660 to 1.151, and 3.169 to 5.693, respectively. This indicates the efficiency of both markers in detecting polymorphism among the accessions studied. The ISSR marker had a higher polymorphism rate, MI, and Rp than the SSR marker. Molecular analysis of variance for both DNA-based markers showed that the genetic variation within the species was more than the genetic diversity between them. The high level of genomic diversity discovered in the Aegilops and Triticum species proved to provide an ideal gene pool for discovering genes useful for wheat breeding. The accessions were classified into eight groups based on SSR and ISSR markers using the UPGMA method of cluster analysis. According to the cluster analysis results, despite similarities between the accessions of a given province, in most cases, the geographical pattern was not in accordance with that observed using the molecular clustering. Based on the coordinate analysis, neighboring groups showed the maximum similarities, and distant ones revealed the maximum genetic distance from each other. The genetic structure analysis successfully separated accessions for their ploidy levels. CONCLUSIONS Both markers provided a comprehensive model of genetic diversity between Iranian accessions of Aegilops and Triticum genera. Primers used in the present study were effective, informative, and genome-specific which could be used in genome explanatory experiments.
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Affiliation(s)
- Maryam Jabari
- Department of Agronomy and Plant Breeding, College of Agriculture, Islamic Azad University, Isfahan (Khorasgan) Isfahan Branch, Iran
| | - Ahmadreza Golparvar
- Department of Agronomy and Plant Breeding, College of Agriculture, Islamic Azad University, Isfahan (Khorasgan) Isfahan Branch, Iran
| | - Behzad Sorkhilalehloo
- Genetic Research Department and the National Plant Genebank of Iran, Seed and Plant Improvement Institute, Agricultural Research, Education and Extension Organization, AREEO, Karaj, Iran.
| | - Majid Shams
- Department of Agronomy and Plant Breeding, College of Agriculture, Islamic Azad University, Isfahan (Khorasgan) Isfahan Branch, Iran
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Ahmadi AJ, Ahmadikhah A. Occurrence of simple sequence repeats in cDNA sequences of safflower ( Carthamus tinctorius) reveals the importance of SSR-containing genes for cell biology and dynamic response to environmental cues. FRONTIERS IN PLANT SCIENCE 2022; 13:991107. [PMID: 36466261 PMCID: PMC9714374 DOI: 10.3389/fpls.2022.991107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 10/17/2022] [Indexed: 06/17/2023]
Abstract
Safflower (Carthamus tinctorius) is a diploid crop plant belonging to the family Asteraceae and is well known as one of important oilseed crops due to edible oil containing unsaturated fatty acids. In recent years it is gaining increased attention for food, pharmaceutical and industrial uses, and hence the updating its breeding methods is necessary. Genic simple sequence repeats (SSRs) in addition of being desire molecular markers, are supposed to influence gene function and the respective phenotype. This study aimed to identify SSRs in cDNA sequences and further analysis of the functional features of the SSR-containing genes to elucidate their role in biological and cellular processes. We identified 1,841 SSR regions in 1,667 cDNA sequences. Among all types of repeats, trinucleotide repeats were the most abundant (35.7%), followed by hexanucleotide (29.6%) and dinucleotide repeats (22.0%). Thirty five SSR primer pairs were validated by PCR reaction, detected a high rate of polymorphism (>57%) among safflower accessions, physically mapped on safflower genome and could clearly discriminate the cultivated accessions from wild relatives. The cDNA-derived SSR markers are suitable for evaluation of genetic diversity, linkage and association mapping studies and genome-based breeding programmes. Occurrence of SSR repeats in biologically-important classes of proteins such as kinases, transferases and transcription factors was inferred from functional analyses, which along with variability of their repeat copies, can endow the cell and whole organism the flexibility of facing with continuously changing environment, and indicate a structure-based evolution mechanism of the genome which acts as an up-to-dating tool for the cell and whole origanism, which is realized in GO terms such as involvement of most SSR-containing genes in biological, cellular and metabolic processes, especially in response to stimulus, response to stress, interaction to other organisms and defense responses.
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Affiliation(s)
- Ahmad Jawid Ahmadi
- Agronomy Department, Faculty of Agriculture, Higher Education Institute of Samangan, Samangan, Afghanistan
| | - Assadollah Ahmadikhah
- Department of Cell and Molecular Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
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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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Brhane H, Haileselassie T, Tesfaye K, Hammenhag C, Ortiz R, Abreha KB, Geleta M. Novel Expressed Sequence Tag-Derived and Other Genomic Simple Sequence Repeat Markers Revealed Genetic Diversity in Ethiopian Finger Millet Landrace Populations and Cultivars. FRONTIERS IN PLANT SCIENCE 2021; 12:735610. [PMID: 34630485 PMCID: PMC8495221 DOI: 10.3389/fpls.2021.735610] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 08/26/2021] [Indexed: 06/02/2023]
Abstract
Finger millet (Eleusine coracana (L.) Geartn.) is a self-pollinating amphidiploid crop cultivated with minimal input for food and feed, as well as a source of income for small-scale farmers. To efficiently assess its genetic diversity for conservation and use in breeding programs, polymorphic DNA markers that represent its complex tetraploid genome have to be developed and used. In this study, 13 new expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were developed based on publicly available finger millet ESTs. Using 10 polymorphic SSR markers (3 genomic and 7 novel EST-derived), the genetic diversity of 55 landrace accessions and 5 cultivars of finger millet representing its major growing areas in Ethiopia was assessed. In total, 26 alleles were detected across the 10 loci, and the average observed number of alleles per locus was 5.6. The polymorphic information content (PIC) of the loci ranged from 0.045 (Elco-48) to 0.71 (UGEP-66). The level of genetic diversity did not differ much between the accessions with the mean gene diversity estimates ranging only from 0.44 (accession 216054) to 0.68 (accession 237443). Similarly, a narrow range of variation was recorded at the level of regional states ranging from 0.54 (Oromia) to 0.59 (Amhara and Tigray). Interestingly, the average gene diversity of the landrace accessions (0.57) was similar to that of the cultivars (0.58). The analysis of molecular variance (AMOVA) revealed significant genetic variation both within and among accessions. The variation among the accessions accounted for 18.8% of the total variation (F ST = 0.19; P < 0.001). Similarly, significant genetic variation was obtained among the geographic regions, accounting for 6.9% of the total variation (P < 0.001). The results of the cluster, principal coordinate, and population structure analyses suggest a poor correlation between the genetic makeups of finger millet landrace populations and their geographic regions of origin, which in turn suggests strong gene flow between populations within and across geographic regions. This study contributed novel EST-SSR markers for their various applications, and those that were monomorphic should be tested in more diverse finger millet genetic resources.
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Affiliation(s)
- Haftom Brhane
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
| | | | - Kassahun Tesfaye
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia
- Ethiopian Biotechnology Institute, Ministry of Science and Technology, Addis Ababa, Ethiopia
| | - Cecilia Hammenhag
- Department of Plant Breeding, Swedish University of Agricultural Sciences, Lomma, Sweden
| | - Rodomiro Ortiz
- 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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Backiyalakshmi C, Vetriventhan M, Deshpande S, Babu C, Allan V, Naresh D, Gupta R, Azevedo VCR. Genome-Wide Assessment of Population Structure and Genetic Diversity of the Global Finger Millet Germplasm Panel Conserved at the ICRISAT Genebank. FRONTIERS IN PLANT SCIENCE 2021; 12:692463. [PMID: 34489996 PMCID: PMC8417690 DOI: 10.3389/fpls.2021.692463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 06/16/2021] [Indexed: 06/13/2023]
Abstract
Finger millet [Eleusine coracana (L.) Gaertn.] is an important climate-resilient nutrient-dense crop grown as a staple food grain in Asia and Africa. Utilizing the full potential of the crop mainly depends on an in-depth exploration of the vast diversity in its germplasm. In this study, the global finger millet germplasm diversity panel of 314 accessions was genotyped, using the DArTseq approach to assess genetic diversity and population structure. We obtained 33,884 high-quality single nucleotide polymorphism (SNP) markers on 306 accessions after filtering. Finger millet germplasm showed considerable genetic diversity, and the mean polymorphic information content, gene diversity, and Shannon Index were 0.110, 0.114, and 0.194, respectively. The average genetic distance of the entire set was 0.301 (range 0.040 - 0.450). The accessions of the race elongata (0.326) showed the highest average genetic distance, and the least was in the race plana (0.275); and higher genetic divergence was observed between elongata and vulgaris (0.320), while the least was between compacta and plana (0.281). An average, landrace accessions had higher gene diversity (0.144) and genetic distance (0.299) than the breeding lines (0.117 and 0.267, respectively). A similar average gene diversity was observed in the accessions of Asia (0.132) and Africa (0.129), but Asia had slightly higher genetic distance (0.286) than African accessions (0.276), and the distance between these two regions was 0.327. This was also confirmed by a model-based STRUCTURE analysis, genetic distance-based clustering, and principal coordinate analysis, which revealed two major populations representing Asia and Africa. Analysis of molecular variance suggests that the significant population differentiation was mainly due to within individuals between regions or between populations while races had a negligible impact on population structure. Finger millet diversity is structured based on a geographical region of origin, while the racial structure made negligible contribution to population structure. The information generated from this study can provide greater insights into the population structure and genetic diversity within and among regions and races, and an understanding of genomic-assisted finger millet improvement.
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Affiliation(s)
- C. Backiyalakshmi
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Mani Vetriventhan
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Santosh Deshpande
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - C. Babu
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - V. Allan
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University (TNAU), Coimbatore, India
| | - D. Naresh
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Rajeev Gupta
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Vania C. R. Azevedo
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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Analysis of genetic diversity and population structure using SSR markers and validation of a Cleavage Amplified Polymorphic Sequences (CAPS) marker involving the sodium transporter OsHKT1;5 in saline tolerant rice (Oryza sativa L.) landraces. Gene 2019; 713:143976. [PMID: 31306715 DOI: 10.1016/j.gene.2019.143976] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/11/2019] [Accepted: 07/11/2019] [Indexed: 11/21/2022]
Abstract
Naturally evolved saline tolerant rice landraces found along the coastline of India are a valuable genomic resource to explore the complex, polygenic nature of salinity tolerance. In the present study, a set of 28 genome wide SSR markers, 11 salt responsive genic SSR markers and 8 Saltol QTL linked SSR markers were used to estimate genetic relatedness and population structure within a collection of 47 rice landraces (including a tolerant and 2 sensitive checks) originating from geographically divergent coastal regions of India. All three marker types identified substantial genetic variation among the landraces, as evident from their higher PIC values (0.53 for genomic SSRs, 0.43 for Genic SSRs and 0.59 for Saltol SSRs). The markers RM431, RM484 (Genomic SSRs), OsCAX (D), OsCAX (T) (Genic SSRs) and RM562 (Saltol SSR) were identified as good candidates to be used in breeding programs for improving salinity tolerance in rice. STRUCTURE analysis divided the landraces into five distinct populations, with classification correlating with their geographical locations. Principal coordinate and hierarchical cluster analyses (UPGMA and neighbor joining) are in close agreement with STRUCTURE results. AMOVA analysis indicated a higher magnitude of genetic differentiation within individuals of groups (58%), than among groups (42%). We also report the development and validation of a new Cleavage Amplified Polymorphic Sequence (CAPS) marker (OsHKT1;5V395) that targets a codon in the sodium transporter gene OsHKT1;5 (Saltol/SKC1 locus) that is associated with sodium transport rates in the above rice landraces. The CAPS marker was found to be present in all landraces except in IR29, Kamini, Gheus, Matla 1 and Matla 2. Significant molecular genetic diversity established among the analyzed salt tolerant rice landraces will aid in future association mapping; the CAPS marker, OsHKT1;5V395 can be used to map rice landraces for the presence of the SNP (Single Nucleotide Polymorphism) associated with increased sodium transport rates and concomitant salinity tolerance in rice.
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8
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Sood S, Joshi DC, Chandra AK, Kumar A. Phenomics and genomics of finger millet: current status and future prospects. PLANTA 2019; 250:731-751. [PMID: 30968267 DOI: 10.1007/s00425-019-03159-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 04/02/2019] [Indexed: 06/09/2023]
Abstract
Diverse gene pool, advanced plant phenomics and genomics methods enhanced genetic gain and understanding of important agronomic, adaptation and nutritional traits in finger millet. Finger millet (Eleusine coracana L. Gaertn) is an important minor millet for food and nutritional security in semi-arid regions of the world. The crop has wide adaptability and can be grown right from high hills in Himalayan region to coastal plains. It provides food grain as well as palatable straw for cattle, and is fairly climate resilient. The crop has large gene pool with distinct features of both Indian and African germplasm types. Interspecific hybridization between Indian and African germplasm has resulted in greater yield enhancement and disease resistance. The crop has shown numerous advantages over major cereals in terms of stress adaptation, nutritional quality and health benefits. It has indispensable repository of novel genes for the benefits of mankind. Although rapid strides have been made in allele mining in model crops and major cereals, the progress in finger millet genomics is lacking. Comparative genomics have paved the way for the marker-assisted selection, where resistance gene homologues of rice for blast and sequence variants for nutritional traits from other cereals have been invariably used. Transcriptomics studies have provided preliminary understanding of the nutritional variation, drought and salinity tolerance. However, the genetics of many important traits in finger millet is poorly understood and need systematic efforts from biologists across disciplines. Recently, deciphered finger millet genome will enable identification of candidate genes for agronomically and nutritionally important traits. Further, improvement in genome assembly and application of genomic selection as well as genome editing in near future will provide plethora of information and opportunity to understand the genetics of complex traits.
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Affiliation(s)
- Salej Sood
- ICAR-Central Potato Research Institute, Shimla, HP, India.
| | - Dinesh C Joshi
- ICAR-Vivekananda Institute of Hill Agriculture, Almora, Uttarakhand, India
| | - Ajay Kumar Chandra
- GB Pant University of Agricultural Sciences and Technology, Pantnagar, Uttarakhand, India
| | - Anil Kumar
- GB Pant University of Agricultural Sciences and Technology, Pantnagar, Uttarakhand, India.
- Rani Lakshmi Bai Central Agricultural University, Jhanshi, UP, India.
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Xie P, Zhao G, Niu J, Wang J, Zhou Q, Guo Y, Ma X. Comprehensive analysis of population genetics of Phoxinus phoxinus ujmonensis in the Irtysh River: Abiotic and biotic factors. Ecol Evol 2019; 9:7997-8012. [PMID: 31380067 PMCID: PMC6662318 DOI: 10.1002/ece3.5320] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2019] [Revised: 05/14/2019] [Accepted: 05/15/2019] [Indexed: 12/25/2022] Open
Abstract
As a widely distributed species along the Irtysh River, Phoxinus phoxinus ujmonensis (Kaschtschenko, 1899) was used as a model to investigate genetic diversity and population structure as well as the influence of environmental factors on population genetics. In this study, we specifically developed 12 polymorphic microsatellite loci. The analysis of microsatellite and mtDNA markers revealed a high and a moderate genetic diversity across seven populations, respectively. Moderate differentiation was also detected among several populations, indicating the impact of habitat fragmentation and divergence. The absence of isolation by distance implied an extensive gene flow, while the presence of isolation by adaptation implied that these populations might be in the process of adapting to divergent habitats. Correlation analysis showed that abiotic factors like dissolved oxygen, pH, total dissolved solids, and conductivity in water as well as biotic factors like plankton diversity and fish species diversity had impact on genetic diversity and divergence in P. phoxinus ujmonensis populations. The results of this study will provide an insight into the effect of environmental factors on genetic diversity and contribute to the study of population genetics of sympatric species.
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Affiliation(s)
- Peng Xie
- College of FisheriesHuazhong Agricultural UniversityWuhanChina
| | - Guang Zhao
- College of FisheriesHuazhong Agricultural UniversityWuhanChina
| | - Jian‐Gong Niu
- Fisheries Research Institute of Xinjiang Uygur Autonomous RegionUrumqiChina
| | - Jun Wang
- Institute of International Rivers and Eco‐securityYunnan UniversityKunmingChina
| | - Qiong Zhou
- College of FisheriesHuazhong Agricultural UniversityWuhanChina
| | - Yan Guo
- Fisheries Research Institute of Xinjiang Uygur Autonomous RegionUrumqiChina
| | - Xu‐Fa Ma
- College of FisheriesHuazhong Agricultural UniversityWuhanChina
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10
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Guo Q, Li X, Yang S, Yang Z, Sun Y, Zhang J, Cao S, Dong L, Uddin S, Li Y. Evaluation of the Genetic Diversity and Differentiation of Black Locust ( Robinia pseudoacacia L.) Based on Genomic and Expressed Sequence Tag-Simple Sequence Repeats. Int J Mol Sci 2018; 19:ijms19092492. [PMID: 30142921 PMCID: PMC6164529 DOI: 10.3390/ijms19092492] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 08/19/2018] [Accepted: 08/20/2018] [Indexed: 11/16/2022] Open
Abstract
Understanding the genetic diversity and differentiation of the genetic resources of a species is important for the effective use and protection of forest tree resources. Ex situ development is a common method for the protection of genetic diversity and an essential resource for users who require ready access to a species’ germplasm. In this study, we collected seeds of black locust (Robinia pseudoacacia L.) from 19 provenances, covering most of its natural distribution; we randomly selected 367 tender leaves with well-grown and different maternal strains from this group for further analysis. Forty-eight simple sequence repeat (SSR) primers were successfully selected from 91 pairs of SSR primers using native-deformation polyacrylamide gel electrophoresis. In addition, we identified identical genotypes among all individuals and evaluated the quality of the markers. From this, 35 loci were confirmed for analyses of genetic diversity and differentiation of the black locust provenances, which contained 28 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and 7 genomic DNA-derived simple sequence repeats (G-SSRs). We observed high genetic diversity among the native black locust provenances, from which Wright’s fixation index and molecular variance suggested that a majority of the genetic differentiation variation could be attributed to within-provenance differences. The genetic distance and identity results indicated that geographic distance was not a dominating factor influencing the distribution of black locust. This is the first study to evaluate provenance genetic variation in native black locust samples using two types of SSR markers, which provides a comprehensive theoretical basis for ex situ conservation and utilization of genetic resources, with an emphasis on breeding applications.
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Affiliation(s)
- Qi Guo
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Xiuyu Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Shuhong Yang
- Henan Academy of Forestry, Zhengzhou 450008, China.
| | - Zhiheng Yang
- State-Owned Linghai Hongqi Forest, Jinzhou 121228, China.
| | - Yuhan Sun
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | | | - Sen Cao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Li Dong
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Saleem Uddin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Yun Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China.
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