1
|
Venkatesan J, Ramu V, Sethuraman T, Sivagnanam C, Doss G. Molecular marker for characterization of traditional and hybrid derivatives of Eleusine coracana (L.) using ISSR marker. J Genet Eng Biotechnol 2021; 19:178. [PMID: 34825986 PMCID: PMC8626548 DOI: 10.1186/s43141-021-00277-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 11/07/2021] [Indexed: 12/02/2022]
Abstract
BACKGROUND Finger millet is the most important food grain in the world for its nutritional benefits. Finger millet is genetically and geographically diverse and widely spread in the African and Asian sub-continent. Therefore, the present study was undertaken to analyze the genetic diversity using ISSR genetic markers using 15 ISSR primers. RESULTS About 23 genotypes of widely cultivated finger millet cultivars of economically important ones were characterized and the ISSR markers were critically analyzed for their performance with parameters such as polymorphic information content (PIC), effective multiplex ratio (EMR), marker index (MI), and resolving power (RP). In this study, 175 loci were scored across the 23 cultivars of finger millet, and out of these 173 loci (98%) were polymorphic, revealing the suitability of these loci for genetic diversity analysis with ISSR marker. The average number of polymorphic loci per primer was 11.50 with varying sizes from 100 bp to 2500 bp. ISSR primers that showed higher polymorphism were found to have higher EMR and MI values up to 15.30 and 13.44, respectively. CONCLUSION High degree of polymorphism supported with distinct differences of all the marker parameters revealed the suitability of ISSR markers for determining the genotypic differences based on ISSR markers among the 23 genotypes of finger millet. The possible application of the ISSR marker in the conservation and management of finger millet genetic resources is discussed.
Collapse
Affiliation(s)
- Jayalakshmi Venkatesan
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Palkalai Nagar, Madurai, Tamil Nadu, 625021, India.
| | - Vasuki Ramu
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Palkalai Nagar, Madurai, Tamil Nadu, 625021, India
| | - Thilaga Sethuraman
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Palkalai Nagar, Madurai, Tamil Nadu, 625021, India
| | - Chandrasekaran Sivagnanam
- Department of Plant Science, School of Biological Sciences, Madurai Kamaraj University, Palkalai Nagar, Madurai, Tamil Nadu, 625021, India
| | - Ganesh Doss
- Department of Plant Biotechnology, School of Biotechnology, Madurai Kamaraj University, Palkalai Nagar, Madurai, Tamil Nadu, 625021, India.
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Ravi RSD, Siril EA, Nair BR. The efficiency of Cytochrome P450 gene-based markers in accessing genetic variability of drumstick (Moringa oleifera Lam.) accessions. Mol Biol Rep 2020; 47:2929-2939. [PMID: 32236894 DOI: 10.1007/s11033-020-05391-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 03/24/2020] [Indexed: 11/24/2022]
Abstract
Drumstick (Moringa oleifera Lam.) is an important vegetable as well as forage crop of arid and semi-arid zones of the tropics. The leaves and pods of the plant are rich sources of minerals and vitamins. In the present work, genetic diversity study of 23 genotypes of M. oleifera collected from Kerala, Tamil Nadu and Karnataka states of India was carried out using seven cytochrome P450 (CytP450) markers. By using seven pairs of CytP450 gene-based markers, 88.25% of polymorphism was recorded among the 23 sampled genotypes. The Polymorphic Information Content (PI), Marker Index (MI) and Resolving Power obtained for seven primers were estimated 0.23, 2.96 and 9.83, respectively. The Unweighted Pair Group Method with Arithmetic mean (UPGMA) dendrogram based on this marker data indicate that genotypes from different geographical regions are placed in the same clusters. The dendrogram and Principal Coordinates Analysis (PCoA) plots derived from the binary data matrices were highly concordant. The investigation, in brief, proved that CytP450 based marker system is efficient in the elucidation of genetic diversity in M. oleifera accessions.
Collapse
Affiliation(s)
- R S Drisya Ravi
- Department of Biotechnology, University of Kerala, Kariavattom, Trivandrum, 695581, India
| | - E A Siril
- Department of Botany, University of Kerala, Kariavattom, Trivandrum, 695581, India.
| | - Bindu R Nair
- Department of Botany, University of Kerala, Kariavattom, Trivandrum, 695581, India
| |
Collapse
|
4
|
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.
Collapse
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.
| |
Collapse
|
5
|
Pandian S, Satish L, Rameshkumar R, Muthuramalingam P, Rency AS, Rathinapriya P, Ramesh M. Analysis of population structure and genetic diversity in an exotic germplasm collection of Eleusine coracana (L.) Gaertn. using genic-SSR markers. Gene 2018; 653:80-90. [DOI: 10.1016/j.gene.2018.02.018] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 01/22/2018] [Accepted: 02/07/2018] [Indexed: 11/30/2022]
|
6
|
Vinoth A, Ravindhran R. Biofortification in Millets: A Sustainable Approach for Nutritional Security. FRONTIERS IN PLANT SCIENCE 2017; 8:29. [PMID: 28167953 PMCID: PMC5253353 DOI: 10.3389/fpls.2017.00029] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/05/2017] [Indexed: 05/04/2023]
Abstract
Nutritional insecurity is a major threat to the world's population that is highly dependent on cereals-based diet, deficient in micronutrients. Next to cereals, millets are the primary sources of energy in the semi-arid tropics and drought-prone regions of Asia and Africa. Millets are nutritionally superior as their grains contain high amount of proteins, essential amino acids, minerals, and vitamins. Biofortification of staple crops is proved to be an economically feasible approach to combat micronutrient malnutrition. HarvestPlus group realized the importance of millet biofortification and released conventionally bred high iron pearl millet in India to tackle iron deficiency. Molecular basis of waxy starch has been identified in foxtail millet, proso millet, and barnyard millet to facilitate their use in infant foods. With close genetic-relatedness to cereals, comparative genomics has helped in deciphering quantitative trait loci and genes linked to protein quality in finger millet. Recently, transgenic expression of zinc transporters resulted in the development of high grain zinc while transcriptomics revealed various calcium sensor genes involved in uptake, translocation, and accumulation of calcium in finger millet. Biofortification in millets is still limited by the presence of antinutrients like phytic acid, polyphenols, and tannins. RNA interference and genome editing tools [zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR)] needs to be employed to reduce these antinutrients. In this review paper, we discuss the strategies to accelerate biofortification in millets by summarizing the opportunities and challenges to increase the bioavailability of macro and micronutrients.
Collapse
Affiliation(s)
- A Vinoth
- T. A. Lourdusamy Unit for Plant Tissue Culture and Molecular Biology, Department of Plant Biology and Biotechnology, Loyola College Chennai, India
| | - R Ravindhran
- T. A. Lourdusamy Unit for Plant Tissue Culture and Molecular Biology, Department of Plant Biology and Biotechnology, Loyola College Chennai, India
| |
Collapse
|
7
|
Rajendran HAD, Muthusamy R, Stanislaus AC, Krishnaraj T, Kuppusamy S, Ignacimuthu S, Al-Dhabi NA. Analysis of molecular variance and population structure in southern Indian finger millet genotypes using three different molecular markers. JOURNAL OF CROP SCIENCE AND BIOTECHNOLOGY 2016; 19:275-283. [DOI: 10.1007/s12892-016-0015-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/30/2023]
|
8
|
Kumar A, Metwal M, Kaur S, Gupta AK, Puranik S, Singh S, Singh M, Gupta S, Babu BK, Sood S, Yadav R. Nutraceutical Value of Finger Millet [Eleusine coracana (L.) Gaertn.], and Their Improvement Using Omics Approaches. FRONTIERS IN PLANT SCIENCE 2016; 7:934. [PMID: 27446162 PMCID: PMC4925701 DOI: 10.3389/fpls.2016.00934] [Citation(s) in RCA: 81] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Accepted: 06/13/2016] [Indexed: 05/22/2023]
Abstract
The science of nutritional biology has progressed extensively over the last decade to develop food-based nutraceuticals as a form of highly personalized medicine or therapeutic agent. Finger millet [Eleusine coracana (L.) Gaertn.] is a crop with potentially tremendous but under-explored source of nutraceutical properties as compared to other regularly consumed cereals. In the era of growing divide and drawback of nutritional security, these characteristics must be harnessed to develop finger millet as a novel functional food. In addition, introgression of these traits into other staple crops can improve the well-being of the general population on a global scale. The objective of this review is to emphasize the importance of biofortification of finger millet in context of universal health and nutritional crisis. We have specifically highlighted the role that recent biotechnological advancements have to offer for enrichment of its nutritional value and how these developments can commission to the field of nutritional biology by opening new avenues for future research.
Collapse
Affiliation(s)
- Anil Kumar
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and TechnologyPantnagar, India
| | - Mamta Metwal
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and TechnologyPantnagar, India
| | - Sanveen Kaur
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and TechnologyPantnagar, India
| | - Atul K. Gupta
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and TechnologyPantnagar, India
| | - Swati Puranik
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| | - Sadhna Singh
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and TechnologyPantnagar, India
| | - Manoj Singh
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and TechnologyPantnagar, India
| | - Supriya Gupta
- Department of Molecular Biology and Genetic Engineering, G.B. Pant University of Agriculture and TechnologyPantnagar, India
| | - B. K. Babu
- ICAR–Vivekananda Institute of Hill AgricultureAlmora, India
| | - Salej Sood
- ICAR–Vivekananda Institute of Hill AgricultureAlmora, India
| | - Rattan Yadav
- Institute of Biological, Environmental and Rural Sciences, Aberystwyth UniversityAberystwyth, UK
| |
Collapse
|
9
|
Radio-tolerance of finger millet Eleusine coracana (L.) Gaertn cultivars to ionizing radiation. THE NUCLEUS 2016. [DOI: 10.1007/s13237-016-0163-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
|
10
|
Ramakrishnan M, Antony Ceasar S, Duraipandiyan V, Al-Dhabi NA, Ignacimuthu S. Assessment of genetic diversity, population structure and relationships in Indian and non-Indian genotypes of finger millet (Eleusine coracana (L.) Gaertn) using genomic SSR markers. SPRINGERPLUS 2016; 5:120. [PMID: 26900542 PMCID: PMC4749518 DOI: 10.1186/s40064-015-1626-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 12/16/2015] [Indexed: 12/01/2022]
Abstract
We evaluated the genetic variation and population structure in Indian and non-Indian genotypes of finger millet using 87 genomic SSR primers. The 128 finger millet genotypes were collected and genomic DNA was isolated. Eighty-seven genomic SSR primers with 60–70 % GC contents were used for PCR analysis of 128 finger millet genotypes. The PCR products were separated and visualized on a 6 % polyacrylamide gel followed by silver staining. The data were used to estimate major allele frequency using Power Marker v3.0. Dendrograms were constructed based on the Jaccard’s similarity coefficient. Statistical fitness and population structure analyses were performed to find the genetic diversity. The mean major allele frequency was 0.92; the means of polymorphic alleles were 2.13 per primer and 1.45 per genotype; the average polymorphism was 59.94 % per primer and average PIC value was 0.44 per primer. Indian genotypes produced an additional 0.21 allele than non-Indian genotypes. Gene diversity was in the range from 0.02 to 0.35. The average heterozygosity was 0.11, close to 100 % homozygosity. The highest inbreeding coefficient was observed with SSR marker UGEP67. The Jaccard’s similarity coefficient value ranged from 0.011 to 0.836. The highest similarity value was 0.836 between genotypes DPI009-04 and GPU-45. Indian genotypes were placed in Eleusine coracana major cluster (EcMC) 1 along with 6 non-Indian genotypes. AMOVA showed that molecular variance in genotypes from various geographical regions was 4 %; among populations it was 3 % and within populations it was 93 %. PCA scatter plot analysis showed that GPU-28, GPU-45 and DPI009-04 were closely dispersed in first component axis. In structural analysis, the genotypes were divided into three subpopulations (SP1, SP2 and SP3). All the three subpopulations had an admixture of alleles and no pure line was observed. These analyses confirmed that all the genotypes were genetically diverse and had been grouped based on their geographic regions.
Collapse
Affiliation(s)
- M Ramakrishnan
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600 034 India
| | - S Antony Ceasar
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600 034 India ; Faculty of Biological Sciences, Centre for Plant Sciences and School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT UK
| | - V Duraipandiyan
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600 034 India ; Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P.O.Box. 2455, Riyadh, 11451 Kingdom of Saudi Arabia
| | - N A Al-Dhabi
- Department of Botany and Microbiology, Addiriyah Chair for Environmental Studies, College of Science, King Saud University, P.O.Box. 2455, Riyadh, 11451 Kingdom of Saudi Arabia
| | - S Ignacimuthu
- Division of Plant Biotechnology, Entomology Research Institute, Loyola College, Chennai, 600 034 India ; Visiting Professor Program, Deanship of Scientific Research, College of Science, King Saud University, P.O.Box. 2455, Riyadh, 11451 Kingdom of Saudi Arabia
| |
Collapse
|
11
|
Sood S, Kumar A, Babu BK, Gaur VS, Pandey D, Kant L, Pattnayak A. Gene Discovery and Advances in Finger Millet [ Eleusine coracana (L.) Gaertn.] Genomics-An Important Nutri-Cereal of Future. FRONTIERS IN PLANT SCIENCE 2016; 7:1634. [PMID: 27881984 PMCID: PMC5101212 DOI: 10.3389/fpls.2016.01634] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 10/17/2016] [Indexed: 05/22/2023]
Abstract
The rapid strides in molecular marker technologies followed by genomics, and next generation sequencing advancements in three major crops (rice, maize and wheat) of the world have given opportunities for their use in the orphan, but highly valuable future crops, including finger millet [Eleusine coracana (L.) Gaertn.]. Finger millet has many special agronomic and nutritional characteristics, which make it an indispensable crop in arid, semi-arid, hilly and tribal areas of India and Africa. The crop has proven its adaptability in harsh conditions and has shown resilience to climate change. The adaptability traits of finger millet have shown the advantage over major cereal grains under stress conditions, revealing it as a storehouse of important genomic resources for crop improvement. Although new technologies for genomic studies are now available, progress in identifying and tapping these important alleles or genes is lacking. RAPDs were the default choice for genetic diversity studies in the crop until the last decade, but the subsequent development of SSRs and comparative genomics paved the way for the marker assisted selection in finger millet. Resistance gene homologs from NBS-LRR region of finger millet for blast and sequence variants for nutritional traits from other cereals have been developed and used invariably. Population structure analysis studies exhibit 2-4 sub-populations in the finger millet gene pool with separate grouping of Indian and exotic genotypes. Recently, the omics technologies have been efficiently applied to understand the nutritional variation, drought tolerance and gene mining. Progress has also occurred with respect to transgenics development. This review presents the current biotechnological advancements along with research gaps and future perspective of genomic research in finger millet.
Collapse
Affiliation(s)
- Salej Sood
- Indian Council of Agricultural Research, Vivekananda Institute of Hill AgricultureAlmora, India
- *Correspondence: Salej Sood ;
| | - Anil Kumar
- Molecular Biology and Genetic Engineering, Govind Ballabh Pant University of Agriculture and TechnologyPantnagar, India
- Anil Kumar
| | - B. Kalyana Babu
- Indian Council of Agricultural Research, Indian Institute of Oil Palm ResearchPedavegi, India
| | | | - Dinesh Pandey
- Molecular Biology and Genetic Engineering, Govind Ballabh Pant University of Agriculture and TechnologyPantnagar, India
| | - Lakshmi Kant
- Indian Council of Agricultural Research, Vivekananda Institute of Hill AgricultureAlmora, India
| | - Arunava Pattnayak
- Indian Council of Agricultural Research, Vivekananda Institute of Hill AgricultureAlmora, India
| |
Collapse
|
12
|
Oxidative stress and non-linear threshold (NLT) genotoxic dose responses to ionizing radiation in niger, Guizotia abyssinica (L.f.) Cass. THE NUCLEUS 2014. [DOI: 10.1007/s13237-014-0126-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
|
13
|
Zhang D, Xia T, Yan M, Dai X, Xu J, Li S, Yin T. Genetic introgression and species boundary of two geographically overlapping pine species revealed by molecular markers. PLoS One 2014; 9:e101106. [PMID: 24977711 PMCID: PMC4076219 DOI: 10.1371/journal.pone.0101106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 06/02/2014] [Indexed: 12/04/2022] Open
Abstract
Gene introgression and hybrid barriers have long been a major focus of studies of geographically overlapping species. Two pine species, Pinus massoniana and P. hwangshanensis, are frequently observed growing adjacent to each other, where they overlap in a narrow hybrid zone. As a consequence, these species constitute an ideal system for studying genetic introgression and reproductive barriers between naturally hybridizing, adjacently distributed species. In this study, we sampled 270 pine trees along an elevation gradient in Anhui Province, China and analyzed these samples using EST-SSR markers. The molecular data revealed that direct gene flow between the two species was fairly low, and that the majority of gene introgression was intermediated by backcrossing. On the basis of empirical observation, the on-site distribution of pines was divided into a P. massoniana zone, a hybrid zone, and a P. hwangshanensis zone. STRUCTURE analysis revealed the existence of a distinct species boundary between the two pine species. The genetic boundary of the hybrid zone, on the other hand, was indistinct owing to intensive backcrossing with parental species. Compared with P. massoniana, P. hwangshanensis was found to backcross with the hybrids more intensively, consistent with the observation that morphological and anatomical characteristics of trees in the contact zone were biased towards P. hwangshanensis. The introgression ability of amplified alleles varied across species, with some being completely blocked from interspecific introgression. Our study has provided a living example to help explain the persistence of adjacently distributed species coexisting with their interfertile hybrids.
Collapse
Affiliation(s)
- Defang Zhang
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, China
| | - Tao Xia
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, China
| | - Maomao Yan
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, China
| | - Xiaogang Dai
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, China
| | - Jin Xu
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, China
| | - Shuxian Li
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, China
| | - Tongming Yin
- The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, China
- * E-mail:
| |
Collapse
|
14
|
Nirgude M, Babu BK, Shambhavi Y, Singh UM, Upadhyaya HD, Kumar A. Development and molecular characterization of genic molecular markers for grain protein and calcium content in finger millet (Eleusine coracana (L.) Gaertn.). Mol Biol Rep 2014; 41:1189-200. [PMID: 24477581 DOI: 10.1007/s11033-013-2825-7] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2013] [Accepted: 10/25/2013] [Indexed: 11/29/2022]
Abstract
Finger millet (Eleusine coracana (L.) Gaertn), holds immense agricultural and economic importance for its high nutraceuticals quality. Finger millets seeds are rich source of calcium and its proteins are good source of essential amino acids. In the present study, we developed 36 EST-SSR primers for the opaque2 modifiers and 20 anchored-SSR primers for calcium transporters and calmodulin for analysis of the genetic diversity of 103 finger millet genotypes for grain protein and calcium contents. Out of the 36 opaque2 modifiers primers, 15 were found polymorphic and were used for the diversity analysis. The highest PIC value was observed with the primer FMO2E33 (0.26), while the lowest was observed FMO2E27 (0.023) with an average value of 0.17. The gene diversity was highest for the primer FMO2E33 (0.33), however it was lowest for FMO2E27 (0.024) at average value of 0.29. The percentage polymorphism shown by opaque2 modifiers primers was 68.23%. The diversity analysis by calcium transporters and calmodulin based anchored SSR loci revealed that the highest PIC was observed with the primer FMCA8 (0.30) and the lowest was observed for FMCA5 (0.023) with an average value of 0.18. The highest gene diversity was observed for primer FMCA8 (0.37), while lowest for FMCA5 (0.024) at an average of 0.21. The opaque2 modifiers specific EST-SSRs could able to differentiate the finger millet genotypes into high, medium and low protein containing genotypes. However, calcium dependent candidate gene based EST-SSRs could broadly differentiate the genotypes based on the calcium content with a few exceptions. A significant negative correlation between calcium and protein content was observed. The present study resulted in identification of highly polymorphic primers (FMO2E30, FMO2E33, FMO2-18 and FMO2-14) based on the parameters such as percentage of polymorphism, PIC values, gene diversity and number of alleles.
Collapse
Affiliation(s)
- M Nirgude
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences & Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, 263 145, India
| | | | | | | | | | | |
Collapse
|
15
|
Kumar A, Sharma N, Panwar P, Gupta AK. Use of SSR, RAPD markers and protein profiles based analysis to differentiate Eleusine coracana genotypes differing in their protein content. Mol Biol Rep 2011; 39:4949-60. [PMID: 22167326 DOI: 10.1007/s11033-011-1291-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2011] [Accepted: 11/30/2011] [Indexed: 11/26/2022]
Abstract
Fifty-two genotypes of Eleusine coracana collected from Uttarakhand hills were subjected to simple sequence repeat (SSR), random amplified polymorphic DNA (RAPD)-PCR and protein profiling analysis to investigate the variation in protein content. The main objective of the present study was to detect variability among E. coracana and also assess the discriminating ability of these three molecular methods. A total of 21 RAPD and 24 SSR primers were assayed for their specificity in detecting genetic variability in E. coracana, of which 20 RAPD and 21 SSR primers were highly reproducible and were found suitable for use in PCR analysis. Assessing genetic diversity among E. coracana genotypes by RAPD-PCR using 20 polymorphic primers yielded 56 different RAPD markers which clustered the genotypes into different groups on the basis of protein content. Similarly, SSR-PCR with 21 polymorphic primers clustered the genotypes into different groups. On the other hand, biochemical typing of E. coracana using whole seed proteins generated profiles that showed no major difference indicating the technique to be not useful in typing genotypes of this crop. However, a few of the genotypes showed the presence of a unique band of 32 kDa that needs to be further investigated to understand the role of the protein from nutritional point of view, if any. In the present study, significant negative correlation (r = -0.69*) was found between the protein and calcium content of finger millet genotypes. Sodium Dodecyl Sulphate Polyacrylamide Gel Electrophoresis based seed storage proteins generated profiles showed no major differences in banding pattern among 52 finger millet genotypes while quantitative estimation of seed storage protein fractions using Lowry method revealed that glutelin was highest followed by prolamin, globulin and albumin.
Collapse
Affiliation(s)
- Anil Kumar
- Department of Molecular Biology and Genetic Engineering, College of Basic Sciences & Humanities, G.B. Pant University of Agriculture and Technology, Pantnagar, 263 145, India,
| | | | | | | |
Collapse
|
16
|
Phylogeny of kangaroo apples (Solanum subg. Archaesolanum, Solanaceae). Mol Biol Rep 2011; 38:5243-59. [PMID: 21258867 DOI: 10.1007/s11033-011-0675-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2010] [Accepted: 01/10/2011] [Indexed: 10/18/2022]
Abstract
Kangaroo apples, subgenus Archaesolanum, are a unique and still poorly known group within the genus Solanum. Here we aimed to reveal phylogeny, historical biogeography and age of diversification of Archaesolanum. We sampled all recognized species of the group and sequenced three chloroplast regions, the trnT-trnL spacer, trnL intron and trnL-trnF spacer to calibrate a molecular clock to estimate the age of the group. Distributional data were combined with the results of phylogenetic analysis to track the historical processes responsible for the current range of the group. Our analysis supported the monophyly of the kangaroo apples and the biogeographical disjunction between the two subclades within the group. Based on the divergence time estimates the most recent common ancestor of kangaroo apples is from the late Miocene age (~9 MYA). Based on the age estimate the common ancestors of the kangaroo apples are presumed to have arrived in Australia by long-distance dispersal. The two distinct lineages within the group have separated during the aridification of the continent and further speciated in the brief resurgence of rainforests during the Pliocene.
Collapse
|