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Nadeem S, Riaz Ahmed S, Luqman T, Tan DKY, Maryum Z, Akhtar KP, Muhy Ud Din Khan S, Tariq MS, Muhammad N, Khan MKR, Liu Y. A comprehensive review on Gossypium hirsutum resistance against cotton leaf curl virus. Front Genet 2024; 15:1306469. [PMID: 38440193 PMCID: PMC10909863 DOI: 10.3389/fgene.2024.1306469] [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: 10/03/2023] [Accepted: 02/01/2024] [Indexed: 03/06/2024] Open
Abstract
Cotton (Gossypium hirsutum L.) is a significant fiber crop. Being a major contributor to the textile industry requires continuous care and attention. Cotton is subjected to various biotic and abiotic constraints. Among these, biotic factors including cotton leaf curl virus (CLCuV) are dominant. CLCuV is a notorious disease of cotton and is acquired, carried, and transmitted by the whitefly (Bemisia tabaci). A cotton plant affected with CLCuV may show a wide range of symptoms such as yellowing of leaves, thickening of veins, upward or downward curling, formation of enations, and stunted growth. Though there are many efforts to protect the crop from CLCuV, long-term results are not yet obtained as CLCuV strains are capable of mutating and overcoming plant resistance. However, systemic-induced resistance using a gene-based approach remained effective until new virulent strains of CLCuV (like Cotton Leaf Curl Burewala Virus and others) came into existence. Disease control by biological means and the development of CLCuV-resistant cotton varieties are in progress. In this review, we first discussed in detail the evolution of cotton and CLCuV strains, the transmission mechanism of CLCuV, the genetic architecture of CLCuV vectors, and the use of pathogen and nonpathogen-based approaches to control CLCuD. Next, we delineate the uses of cutting-edge technologies like genome editing (with a special focus on CRISPR-Cas), next-generation technologies, and their application in cotton genomics and speed breeding to develop CLCuD resistant cotton germplasm in a short time. Finally, we delve into the current obstacles related to cotton genome editing and explore forthcoming pathways for enhancing precision in genome editing through the utilization of advanced genome editing technologies. These endeavors aim to enhance cotton's resilience against CLCuD.
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Affiliation(s)
- Sahar Nadeem
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Syed Riaz Ahmed
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
- Pakistan Agriculture Research Council (PARC), Horticulture Research Institute Khuzdar Baghbana, Khuzdar, Pakistan
| | - Tahira Luqman
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Daniel K. Y. Tan
- School of Life and Environmental Sciences, Plant Breeding Institute, Sydney Institute of Agriculture, Faculty of Science, The University of Sydney, Sydney, NSW, Australia
| | - Zahra Maryum
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Khalid Pervaiz Akhtar
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Sana Muhy Ud Din Khan
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Muhammad Sayyam Tariq
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
| | - Nazar Muhammad
- Agriculture and Cooperative Department, Quetta, Pakistan
| | - Muhammad Kashif Riaz Khan
- Nuclear Institute for Agriculture and Biology College, Pakistan Institute of Engineering and Applied Sciences (NIAB-C, PIEAS), Faisalabad, Pakistan
- Plant Breeding and Genetics Division, Cotton Group, Nuclear Institute for Agriculture and Biology, Faisalabad, Pakistan
| | - Yongming Liu
- National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, China
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Tesfaye M, Feyissa T, Hailesilassie T, Kanagarajan S, Zhu LH. Genetic Diversity and Population Structure in Ethiopian Mustard ( Brassica carinata A. Braun) as Revealed by Single Nucleotide Polymorphism Markers. Genes (Basel) 2023; 14:1757. [PMID: 37761897 PMCID: PMC10530317 DOI: 10.3390/genes14091757] [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: 08/11/2023] [Revised: 08/25/2023] [Accepted: 09/01/2023] [Indexed: 09/29/2023] Open
Abstract
Ethiopian mustard (Brassica carinata A. Braun) is currently one of the potential oilseeds dedicated to the production for biofuel and other bio-industrial applications. The crop is assumed to be native to Ethiopia where a number of diversified B. carinata germplasms are found and conserved ex situ. However, there is very limited information on the genetic diversity and population structure of the species. This study aimed to investigate the genetic diversity and population structure of B. carinata genotypes of different origins using high-throughput single nucleotide polymorphism (SNP) markers. We used Brassica 90K Illumina InfiniumTM SNP array for genotyping 90 B. carinata genotypes, and a total of 11,499 informative SNP markers were used for investigating the population structure and genetic diversity. The structure analysis, principal coordinate analysis (PcoA) and neighbor-joining tree analysis clustered the 90 B. carinata genotypes into two distinct subpopulations (Pop1 and Pop2). The majority of accessions (65%) were clustered in Pop1, mainly obtained from Oromia and South West Ethiopian People (SWEP) regions. Pop2 constituted dominantly of breeding lines and varieties, implying target selection contributed to the formation of distinct populations. Analysis of molecular variance (AMOVA) revealed a higher genetic variation (93%) within populations than between populations (7%), with low genetic differentiation (PhiPT = 0.07) and poor correlation between genetic and geographical distance (R = 0.02). This implies the presence of gene flow (Nm > 1) and weak geographical structure of accessions. Genetic diversity indices showed the presence of moderate genetic diversity in B. carinata populations with an average genetic diversity value (HE = 0.31) and polymorphism information content (PIC = 0.26). The findings of this study provide important and relevant information for future breeding and conservation efforts of B. carinata.
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Affiliation(s)
- Misteru Tesfaye
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, 234 22 Lomma, Sweden; (M.T.); (S.K.)
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (T.F.); (T.H.)
| | - Tileye Feyissa
- Institute of Biotechnology, Addis Ababa University, Addis Ababa P.O. Box 1176, Ethiopia; (T.F.); (T.H.)
| | | | - Selvaraju Kanagarajan
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, 234 22 Lomma, Sweden; (M.T.); (S.K.)
| | - Li-Hua Zhu
- Department of Plant Breeding, Swedish University of Agricultural Sciences, P.O. Box 190, 234 22 Lomma, Sweden; (M.T.); (S.K.)
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Kumar M, Sirohi U, Yadav MK, Chaudhary V. In Vitro Culture Technology and Advanced Biotechnology Tools Toward Improvement in Gladiolus (Gladiolus species): Present Scenario and Future Prospects. Mol Biotechnol 2023:10.1007/s12033-023-00818-8. [PMID: 37528332 DOI: 10.1007/s12033-023-00818-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Accepted: 07/07/2023] [Indexed: 08/03/2023]
Abstract
In the world's flower trade, gladiolus (Gladiolus spp.) is ranked first among bulbous flowers and eighth among cut flowers, with more than 30,000 different cultivars being grown. Mass multiplication and commercialization are restricted by the traditional propagation methods. However, the large-scale proliferation and improvement of the gladiolus have been accomplished with the aid of plant tissue culture and other biotechnological techniques. The current review includes a thorough examination of the growth and development parameters required for successful in vitro gladiolus development as well as cormel formation. Moreover, focus is being given to various techniques and methods such as in vitro cytogenetic stability and modification of chromosome number, in vitro mutagenesis and selection of pest resistance, in vitro identification and selection to develop virus-free germplasm, cryopreservation, synthetic seed technology, identifying virus diseases by RT-PCR, somaclonal variation, and protoplast and somatic hybridization. Molecular markers and their applications for genetic diversity analysis, relationships between different genotypes, and clonal stability analysis in Gladiolus species have been conducted by several research groups worldwide and are also being discussed. The article also covers efforts to enhance the functionality of plant phenotypes through genetic transformation. Future prospects for further improvement of ornamental gladiolus are also explored. Overall, the current review provides insight into the applications of basic and advanced biotechnological tools for gladiolus improvement.
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Affiliation(s)
- Mukesh Kumar
- College of Horticulture, SVPUAT, Meerut, UP, 250110, India.
| | - Ujjwal Sirohi
- NIPGR, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Manoj Kumar Yadav
- Department of Agriculture Biotechnology, College of Agriculture, SVPUAT, Meerut, UP, 250110, India
| | - Veena Chaudhary
- Department of Chemistry, Meerut College, Meerut, 250002, India
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Dmitriev AA, Pushkova EN, Melnikova NV. Plant Genome Sequencing: Modern Technologies and Novel Opportunities for Breeding. Mol Biol 2022. [DOI: 10.1134/s0026893322040045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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Thidiazuron Induced In Vitro Clonal Propagation of Lagerstroemia speciosa (L.) Pers.—An Important Avenue Tree. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8050359] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
A high throughput regeneration protocol has been developed for Lagerstroemia speciosa through node explants under the regime of various plant growth regulators (PGRs). This protocol can provide an alternative mode to seed-grown plants and minimize the cost–time of regeneration, significantly. Murashige and Skoog (MS) medium containing various combinations of PGRs exhibited a marked stimulatory effect on morphogenesis. Of the various combinations tried, node explant pretreated with thidiazuron (TDZ; 5.0 µM) for 4 weeks and followed with transfer into MS medium containing 1.0 μM 6-benzyladenine (BA) and 0.25 μM α-naphthalene acetic acid (NAA) was reported to be the best treatment as it resulted in a maximum number of 24.5 shoots with an average shoot length of 7.1 cm per explant in 90% of cultures after 12 weeks of incubation. The in vitro-generated shoots rooted satisfactorily in the adopted ex vitro method of rooting, which saves time and cost. Among the different treatments, the greatest rooting percentage (85%) was observed in the 200 μM IBA-treated shoots, with the highest root number (8.7) and length (3.4 cm) occurring after 4 weeks. Four months after being transferred to ex vitro, some of the physiological attributes of the in vitro-propagated plants were examined and compared to the ex vitro plants. Further, analysis of the genetic integrity in tissue culture-raised plantlets along with the parental tree was accomplished through DNA-based RAPD technique. The monomorphic banding pattern obtained by the RAPD primers resulted in a high level of genetic uniformity in regenerated plants.
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The Genetic Differences and Structure of Selected Important Populations of the Endangered Taxus baccata in the Czech Republic. FORESTS 2022. [DOI: 10.3390/f13020137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Taxus baccata L. (common yew) is an endangered tree species in the Czech Republic. However, its natural occurrence has not been adequately protected in all areas of the country. The aim of this study is to determine whether the yew population in the newly established Mařeničky seed orchard (TS_L) enables mixing with other Czech yew populations. Using a set of nuclear microsatellites, the genetic diversity in the Lužické Mountains (TS_L) and in selected wild-provenance populations from the Czech Republic (Jílovské yews, TS_J; Březinské yews, TS_B, and yews from Moravský Karst, TS_M) was studied, as they could be donor sources for potential translocation activities. We observed that the level of genetic diversity within the four Czech yew units that were investigated was high. An analysis of the molecular variance (AMOVA) showed 7% variation among populations, and the genetic differentiation values were low to moderate (FST = 0.042–0.108). According to a STRUCTURE analysis, high genetic similarity was observed between the TS_L and TS_B units. Our results provide important genetic suggestions on how conservation management can be designed to maximize its success.
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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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9
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Ramzan F, Kim HT, Younis A, Ramzan Y, Lim KB. Genetic assessment of the effects of self-fertilization in a Lilium L. hybrids using molecular cytogenetic methods (FISH and ISSR). Saudi J Biol Sci 2020; 28:1770-1778. [PMID: 33732061 PMCID: PMC7938132 DOI: 10.1016/j.sjbs.2020.12.019] [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: 10/05/2019] [Revised: 12/06/2020] [Accepted: 12/09/2020] [Indexed: 11/28/2022] Open
Abstract
Self-fertilization (also termed selfing) is a mode of reproduction that occurs in hermaphrodites and has evolved several times in various plant and animal species. A transition from outbreeding to selfing in hermaphroditic flowers is typically associated with changes in flower morphology and functionality. This study aimed to identify genetic effects of selfing in the F2 progeny of F1 hybrid developed by crossing Lilium lancifolium with the Asiatic Lilium hybrid ‘Dreamland.’ Fluorescence in situ hybridization (FISH) and inter-simple sequence repeats (ISSR) techniques were used to detect genetic variations in plants produced by selfing. The FISH results showed that F1 hybrid were similar to the female parent (L. lancifolium) regarding the 45S loci, but F2 individuals showed variation in the number and location of the respective loci. In F2 progeny, F2-2, F2-3, F2-4, F2-5, and F2-8 hybrids expressed two strong and one weak 5S signal on chromosome 3, whereas F2-7 and F2-9 individuals expressed one strong and two weak signals. Only two strong 5S signals were detected in an F2-1 plant. The ISSR results showed a maximum similarity value of 0.6269 between the female parent and the F2-2 hybrid. Regarding similarity to the male parent, a maximum value of 0.6119 was found in the F2-1 and F2-2 hybrids. The highest genetic distance from L. lancifolium and the Asiatic Lilium hybrid ‘Dreamland’ was observed in the F2-4 progeny (0.6352 and 0.7547, respectively). Phylogenetic relationships showed that the F2 progeny were closer to the male parent than to the female parent. Self-fertilization showed effects on variation among the F2 progeny, and effects on the genome were confirmed using FISH and ISSR analyses.
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Affiliation(s)
- Fahad Ramzan
- Deptartment of Horticulture, Kyungpook National University, Daegu 41566, South Korea
| | - Hyoung Tae Kim
- Deptartment of Horticulture, Kyungpook National University, Daegu 41566, South Korea
| | - Adnan Younis
- Institute of Horticultural Sciences, University of Agriculture, Faisalabad 38040, Pakistan
| | - Yasir Ramzan
- Wheat Research Institute, AARI, Faisalabad, Pakistan
| | - Ki-Byung Lim
- Deptartment of Horticulture, Kyungpook National University, Daegu 41566, South Korea
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Liu L, Song W, Wang L, Sun X, Qi Y, Wu T, Sun S, Jiang B, Wu C, Hou W, Ni Z, Han T. Allele combinations of maturity genes E1-E4 affect adaptation of soybean to diverse geographic regions and farming systems in China. PLoS One 2020; 15:e0235397. [PMID: 32628713 PMCID: PMC7337298 DOI: 10.1371/journal.pone.0235397] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 06/15/2020] [Indexed: 11/25/2022] Open
Abstract
Appropriate flowering and maturity time are important for soybean production. Four maturity genes E1, E2, E3 and E4 have been molecularly identified and found to play major roles in the control of flowering and maturity of soybean. Here, to further investigate the effect of different allele combinations of E1-E4, we performed Kompetitive Allele Specific PCR (KASP) assays based on single nucleotide polymorphisms (SNPs) at these four E loci, and genotyped E1-E4 genes across 308 Chinese cultivars with a wide range of maturity groups. In total, twenty-one allele combinations for E1-E4 genes were identified across these Chinese cultivars. Various combinations of mutations at four E loci gave rise to the diversity of flowering and maturity time, which were associated with the adaptation of soybean cultivars to diverse geographic regions and farming systems. In particular, the cultivars with mutations at all four E loci reached flowering and maturity very early, and adapted to high-latitude cold regions. The allele combinations e1-as/e2-ns/e3-tr/E4, E1/e2-ns/E3/E4 and E1/E2/E3/E4 played important roles in the Northeast China, Huang-Huai-Hai (HHH) Rivers Valley and South China regions, respectively. Notably, E1 and E2, especially E2, affected flowering and maturity time of soybean significantly. Our study will be beneficial for germplasm evaluation, cultivar improvement and regionalization of cultivation in soybean production.
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Affiliation(s)
- Luping Liu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Wenwen Song
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Liwei Wang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xuegang Sun
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yanping Qi
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Tingting Wu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Shi Sun
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Bingjun Jiang
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Cunxiang Wu
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Wensheng Hou
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zhongfu Ni
- State Key Laboratory of Agrobiotechnology, Key Laboratory of Crop Heterosis and Utilization (MOE), College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Tianfu Han
- Ministry of Agriculture and Rural Affairs Key Laboratory of Soybean Biology (Beijing), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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Salgotra RK, Stewart CN. Functional Markers for Precision Plant Breeding. Int J Mol Sci 2020; 21:E4792. [PMID: 32640763 PMCID: PMC7370099 DOI: 10.3390/ijms21134792] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 06/19/2020] [Accepted: 07/02/2020] [Indexed: 01/24/2023] Open
Abstract
Advances in molecular biology including genomics, high-throughput sequencing, and genome editing enable increasingly faster and more precise cultivar development. Identifying genes and functional markers (FMs) that are highly associated with plant phenotypic variation is a grand challenge. Functional genomics approaches such as transcriptomics, targeting induced local lesions in genomes (TILLING), homologous recombinant (HR), association mapping, and allele mining are all strategies to identify FMs for breeding goals, such as agronomic traits and biotic and abiotic stress resistance. The advantage of FMs over other markers used in plant breeding is the close genomic association of an FM with a phenotype. Thereby, FMs may facilitate the direct selection of genes associated with phenotypic traits, which serves to increase selection efficiencies to develop varieties. Herein, we review the latest methods in FM development and how FMs are being used in precision breeding for agronomic and quality traits as well as in breeding for biotic and abiotic stress resistance using marker assisted selection (MAS) methods. In summary, this article describes the use of FMs in breeding for development of elite crop cultivars to enhance global food security goals.
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Affiliation(s)
- Romesh K. Salgotra
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences & Technology of Jammu, Chatha, Jammu 190008, India
| | - C. Neal Stewart
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996, USA
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Dheer P, Rautela I, Sharma V, Dhiman M, Sharma A, Sharma N, Sharma MD. Evolution in crop improvement approaches and future prospects of molecular markers to CRISPR/Cas9 system. Gene 2020; 753:144795. [PMID: 32450202 DOI: 10.1016/j.gene.2020.144795] [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: 04/10/2020] [Revised: 05/07/2020] [Accepted: 05/19/2020] [Indexed: 01/03/2023]
Abstract
The advent of genetic selection and genome modification method assure about a real novel reformation in biotechnology and genetic engineering. With the extensive capabilities of molecular markers of them being stable, cost-effective and easy to use, they ultimately become a potent tool for variety of applications such a gene targeting, selection, editing, functional genomics; mainly for the improvisation of commercially important crops. Three main benefits of molecular marker in the field of agriculture and crop improvement programmes first, reduction of the duration of breeding programmes, second, they allow creation of new genetic variation and genetic diversity of plants and third most promising benefit is help in production of engineered plant for disease resistance, or resistance from pathogen and herbicides. This review is anticipated to present an outline how the techniques have been evolved from the simple conventional applications of DNA based molecular markers to highly throughput CRISPR technology and geared the crop yield. Techniques like using Zinc Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9) systems have revolutionised in the field of genome editing. These have been promptly accepted in both the research and commercial industry. On the whole, the widespread use of molecular markers with their types, their appliance in plant breeding along with the advances in genetic selection and genome editing together being a novel strategy to boost crop yield has been reviewed.
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Affiliation(s)
- Pallavi Dheer
- Department of Life Sciences, Shri Guru Ram Rai Institute of Technology & Science, Patel Nagar, Dehradun, Uttarakhand, India
| | - Indra Rautela
- Department of Biotechnology, SALS, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Vandana Sharma
- Department of Botany, K.L.DAV (PG) College, Roorkee,Uttarakhand, India
| | - Manjul Dhiman
- Department of Botany, K.L.DAV (PG) College, Roorkee,Uttarakhand, India
| | - Aditi Sharma
- Department of Biotechnology, Graphic Era University, Dehradun, Uttarakhand, India
| | - Nishesh Sharma
- Department of Biotechnology, SALS, Uttaranchal University, Dehradun, Uttarakhand, India
| | - Manish Dev Sharma
- Department of Biotechnology, School of Basic and Applied Sciences, Shri Guru Ram Rai University, Patel Nagar, Dehradun, Uttarakhand, India.
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Mekonnen T, Haileselassie T, Goodwin SB, Tesfayea K. Genetic diversity and population structure of Zymoseptoria tritici in Ethiopia as revealed by microsatellite markers. Fungal Genet Biol 2020; 141:103413. [PMID: 32442667 DOI: 10.1016/j.fgb.2020.103413] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 02/02/2020] [Accepted: 05/15/2020] [Indexed: 11/17/2022]
Abstract
Septoria tritici blotch (STB), caused by Zymoseptoria tritici (formerly: Mycosphaerella graminicola or Septoria tritici), is one of the most devastating diseases of wheat globally. Understanding genetic diversity of the pathogen has supreme importance in developing best management strategies. However, there is dearth of information on the genetic structure of Z. tritici populations in Ethiopia. Therefore, the present study was targeted to uncover the genetic diversity and population structure of Z. tritici populations from the major wheat-growing areas of Ethiopia. Totally, 182 Z. tritici isolates representing eight populations were analyzed with 14 microsatellite markers. All the microsatellite loci were polymorphic and highly informative, and hence useful genetic tools to depict the genetic diversity and population structure of the pathogen. A wide range of diversity indices including number of observed alleles, effective number of alleles, Shannon's diversity index, number of private alleles, Nei's gene diversity and percentage of polymorphic loci (PPL) were computed to determine genetic variation within populations. A high within-populations genetic diversity was confirmed with gene diversity index and PPL values ranging from 0.34 - 0.58 and 79-100% with overall mean of 0.45 and 94%, respectively. Analysis of molecular variance (AMOVA) revealed a moderate genetic differentiation where 92% of the total genetic variation resides within populations, leaving only 8% among populations. Cluster (UPGMA), PCoA and STRUCTURE analyses did not group the populations into sharply genetically distinct clusters according to their geographical origins, likely due to high gene flow (Nm = 5.66) and reproductive biology of the pathogen. All individual samples shared alleles from two subgroups (K = 2) evidencing high potential of genetic admixture. In conclusion, the microsatellite markers used in the present study were highly informative and thus, helped to dissect the genetic structures of Z. tritici populations in Ethiopia. Among the studied populations, those of East Shewa, Arsi, South West Shewa and Bale showed a high genetic diversity, and hence these areas can be considered as hot spots for investigations planned on the pathogen and host-pathogen interactions. Therefore, the present study not only enriches missing information in Ethiopia but also provides new insights into the epidemiology and genetic structure of Z. tritici in Africa where the agro-climatic conditions and the wheat cropping systems are different from other parts of the world. Such baseline information is useful for designing and implementing durable and effective management strategies.
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Affiliation(s)
- Tilahun Mekonnen
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia.
| | | | - Stephen B Goodwin
- USDA-Agricultural Research Service, Department of Botany and Plant Pathology, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054, USA.
| | - Kassahun Tesfayea
- Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia; Ethiopian Biotechnology Institute. Affiliated with Institute of Biotechnology, Addis Ababa University, Addis Ababa, Ethiopia.
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Development and utilization of an InDel marker linked to the fertility restorer genes of CMS-D8 and CMS-D2 in cotton. Mol Biol Rep 2020; 47:1275-1282. [PMID: 31894465 DOI: 10.1007/s11033-019-05240-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 12/17/2019] [Indexed: 01/12/2023]
Abstract
The cytoplasmic male sterility (CMS) system is a useful tool for commercial hybrid cotton seed production. Two main CMS systems, CMS-D8 and CMS-D2, have been recognized with Rf2 and Rf1 as the restorer genes, respectively. The development of molecular markers tightly linked with restorer genes can facilitate the breeding of restorer lines. In this study, the InDel-1892 marker was developed to distinguish Rf2 and Rf1 simultaneously. Sequence alignment implied that CMS-D8-Rf2 has a 32 bp insertion and that CMS-D2-Rf1 has a 186 bp insertion at the InDel-1892 locus. The codominant marker was co-segregated with Rf1 and Rf2. Hence, this marker can be used for tracing Rf1 and Rf2 simultaneously and identifying the allele status at the restorer gene locus. The results of this study will facilitate efficient marker-assisted selection for restorer lines and hybrids of CMS systems.
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15
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Wilt and Root Rot Complex of Important Pulse Crops: Their Detection and Integrated Management. Fungal Biol 2020. [DOI: 10.1007/978-3-030-35947-8_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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16
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Valadez-Moctezuma E, Cabrera-Hidalgo AJ. Easy strategy used to detect the genetic variability in chickpea ( Cicer arietinum L.). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2018; 24:921-928. [PMID: 30150866 PMCID: PMC6103936 DOI: 10.1007/s12298-018-0548-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 04/17/2018] [Accepted: 05/03/2018] [Indexed: 06/08/2023]
Abstract
A priority in the management and use of elite plant materials for breeding has been based on molecular markers or DNA sequencing of entire genomes, in order to perform genetic differentiation which is still quite costly. Chickpea (Cicer arietinum) is one of the species with genomic monotony and very low polymorphism, and its detection even with DNA markers has not been easy. In germplasm banks, the genetic distinction is a priority in order to use properly selected lines. In this study, 57 chickpea accessions from a germplasm bank were analyzed by using nrRAMP (non-radioactive Random Amplified Microsatellite Polymorphism) markers, and their genetic variability was determined. Our results showed DNA polymorphisms, which are enough to differentiate between the accessions and between C. arietinum and Cicer reticulatum (out-group); this last wild species is closely related to chickpea. We concluded that the nrRAMP technique was an effective and a highly useful method to assess the genetic diversity and variability among closely related plants, such as chickpea; in addition, this technique can be easily implemented in laboratories.
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Affiliation(s)
- E. Valadez-Moctezuma
- Laboratorio de Biología Molecular, Departamento de Fitotecnia, Universidad Autónoma Chapingo, Carr. México-Texcoco km 38.5, C.P. 56230 Chapingo, Edo. México Mexico
| | - A. J. Cabrera-Hidalgo
- Laboratorio de Biología Molecular, Departamento de Fitotecnia, Universidad Autónoma Chapingo, Carr. México-Texcoco km 38.5, C.P. 56230 Chapingo, Edo. México Mexico
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17
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Pradeep AR, Jingade AH, Urs RS. Molecular Markers for Biomass Traits: Association, Interaction and Genetic Divergence in Silkworm Bombyx mori. Biomark Insights 2017. [DOI: 10.1177/117727190700200032] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Improvement of high yielding, disease resistant silkworm strains became imminent to increase production of silk, which is a major revenue earner for sericulturists. Since environment interacts with phenotype, conventional breeding did not result in commendable yield improvement in synthetic strains of silkworm, Bombyx mori. Identification of DNA markers associated with different economically important biomass traits and its introgression could assist molecular breeding and expression of stabilized high yielding characters, but genetic basis of most quantitative traits in silkworm is poorly understood due to its polygenic control. Correlation analysis (R = 0.9) revealed significant interrelation among biomass traits viz., larval duration (TLD), larval weight (LWT), cocoon weight (CWT), shell weight (SWT), shell ratio (SR) and floss content. PCR using inter simple sequence repeat (ISSR) primers revealed 92% polymorphism among 14 tropical and temperate strains of B. mori, with average diversity index of 0.747. Stepwise multiple regression analysis (MRA) selected 35 ISSR markers positively or negatively correlated with different biomass traits, illustrated polygenic control. ISSR marker 830.81050bp was significantly associated with LWT, CWT, SWT, SR and floss content, indicated its pleiotropic role. Two ISSR markers, 835.51950bp and 825.9710bp showed significant association with floss content and TLD. These markers were segregated in F2 generation and Chi-square test confirmed (χ2 = ~45; P < 0.05) its genetic contribution to the associated biomass traits. Strains, with both positively and negatively correlated markers, had intermediate mean value for biomass traits (eg. SWT = 0.17 ± 0.014 g in GNM and Moria) indicated interaction of loci in natural populations. Low yielding Indian strains grouped together by Hierarchical clustering. Chinese and Japanese strains were distributed in the periphery of ALSCAL matrix indicated convergence of genetic characters in Indian strains. Average genetic distance between Chinese strains and Indian strains (0.193) significantly ( P < 0.01) varied from that between Chinese and Japanese strains. Interaction of loci and allelic substitutions induced phenotypic plasticity in temperate B. mori populations on tropic adaptation in India. These outcomes show possibility to combine favorable alleles at different QTL to increase larval, cocoon and shell weight.
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Affiliation(s)
- Appukuttannair R Pradeep
- Seribiotech Research Laboratory, Central Silk Board, CSB Campus, Kodathi, Carmelram. P.O; Bangalore, Karnataka, India. Pin - 560 035
| | - Anuradha H Jingade
- Seribiotech Research Laboratory, Central Silk Board, CSB Campus, Kodathi, Carmelram. P.O; Bangalore, Karnataka, India. Pin - 560 035
| | - Raje S Urs
- Seribiotech Research Laboratory, Central Silk Board, CSB Campus, Kodathi, Carmelram. P.O; Bangalore, Karnataka, India. Pin - 560 035
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Adhikari S, Saha S, Biswas A, Rana TS, Bandyopadhyay TK, Ghosh P. Application of molecular markers in plant genome analysis: a review. THE NUCLEUS 2017. [DOI: 10.1007/s13237-017-0214-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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19
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Amallah L, Taghouti M, Rhrib K, Gaboun F, Arahou M, Hassikou R, Diria G. Validation of simple sequence repeats associated with quality traits in durum wheat. ACTA ACUST UNITED AC 2016. [DOI: 10.1007/s12892-016-0096-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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20
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Sairkar PK, Sharma A, Shukla NP. SCAR Marker for Identification and Discrimination of Commiphora wightii and C. myrrha. Mol Biol Int 2016; 2016:1482796. [PMID: 27069687 PMCID: PMC4812406 DOI: 10.1155/2016/1482796] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2015] [Revised: 01/28/2016] [Accepted: 02/01/2016] [Indexed: 11/17/2022] Open
Abstract
Commercially important Commiphora species are drought-tolerant plants and they are leafless for most of the year. Therefore, it is necessary to develop some molecular marker for the identification. Intended for that, in the present study, species-specific, sequence-characterized amplified regions (SCAR) markers were developed for proficient and precise identification of closely related species Commiphora wightii and C. myrrha, which may ensure the quality, safety, and efficacy of medicines made from these plants through adulterous mixing of these plants. Two species-specific RAPD amplicons were selected, gel-purified, cloned, and sequenced after screening of 20 RAPD primers. The sequence of 979 and 590 nucleotides (Genebank accession numbers K90051 and K90052) was used for development of 4 SCAR markers, namely, Sc1P, Sc1Pm, Sc2P, and Sc2Pm. Out of them, the Sc1Pm was specific for C. wightii, while Sc2P discriminated both the Commiphora species. These markers are first reported and will be useful for rapid identification of closely related Commiphora wightii and C. myrrha species.
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Affiliation(s)
- Pramod Kumar Sairkar
- Centre of Excellence in Biotechnology, M. P. Council of Science & Technology, Bhopal, Madhya Pradesh, India
| | - Anjana Sharma
- Bacteriology Laboratory, Department of Post Graduate Studies & Research in Biological Science, Rani Durgawati University, Jabalpur, Madhya Pradesh, India
| | - N. P. Shukla
- Centre of Excellence in Biotechnology, M. P. Council of Science & Technology, Bhopal, Madhya Pradesh, India
- Madhya Pradesh Pollution Control Board, Bhopal, Madhya Pradesh, India
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21
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Hamza NB, Sharma N, Tripathi A, Sanan-Mishra N. MicroRNA expression profiles in response to drought stress in Sorghum bicolor. Gene Expr Patterns 2016; 20:88-98. [PMID: 26772909 DOI: 10.1016/j.gep.2016.01.001] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Revised: 12/18/2015] [Accepted: 01/04/2016] [Indexed: 01/08/2023]
Abstract
The regulatory role of small non-coding RNAs that are 20-24 nucleotides in length has become the foremost area of research for biologists. A major class of small RNAs represented by the microRNAs (miRNAs), has been implicated in various aspects of plant development including leaf pattering, meristem function, root patterning etc. Recent findings support that miRNAs are regulated by drought and other abiotic stresses in various plant species. In this study, were report the expression profiling of 8 known abiotic stress deregulated miRNAs in 11 elite sorghum genotypes, under watered and drought conditions. Significant deregulation was observed with miR396, miR393, miR397-5p, miR166, miR167 and miR168. Among these, the expression levels of sbi-miR396 and sbi-miR398 were the highest in all the genotypes. The expression of sbi-miR396 was maximum in the grain sorghum HSD3226 under well-watered conditions and the profile shifted towards HSD3221 under drought stress. Forage accessions, N98 and Atlas, showed an opposite behavior in expression patterns of miR397-5p in drought physiologies. Such dynamic expression patterns could be indicative of prevailing drought tolerant mechanisms present in these sorghum accessions. This data provides insights into sorghum miRNAs which may have potential use in improving drought tolerance in sorghum and other cereal crops.
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Affiliation(s)
- Nada Babiker Hamza
- Department of Molecular Biology, Commission for Biotechnology and Genetic Engineering, National Center for Research, P.O. Box: 2404, Khartoum, Sudan.
| | - Neha Sharma
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, ArunaAsaf Ali Marg, New Delhi, 110067, India
| | - Anita Tripathi
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, ArunaAsaf Ali Marg, New Delhi, 110067, India
| | - Neeti Sanan-Mishra
- Plant RNAi Biology Group, International Centre for Genetic Engineering and Biotechnology, ArunaAsaf Ali Marg, New Delhi, 110067, India.
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22
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Govindaraj M, Vetriventhan M, Srinivasan M. Importance of genetic diversity assessment in crop plants and its recent advances: an overview of its analytical perspectives. GENETICS RESEARCH INTERNATIONAL 2015; 2015:431487. [PMID: 25874132 PMCID: PMC4383386 DOI: 10.1155/2015/431487] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Revised: 11/24/2014] [Accepted: 11/27/2014] [Indexed: 11/17/2022]
Abstract
The importance of plant genetic diversity (PGD) is now being recognized as a specific area since exploding population with urbanization and decreasing cultivable lands are the critical factors contributing to food insecurity in developing world. Agricultural scientists realized that PGD can be captured and stored in the form of plant genetic resources (PGR) such as gene bank, DNA library, and so forth, in the biorepository which preserve genetic material for long period. However, conserved PGR must be utilized for crop improvement in order to meet future global challenges in relation to food and nutritional security. This paper comprehensively reviews four important areas; (i) the significance of plant genetic diversity (PGD) and PGR especially on agriculturally important crops (mostly field crops); (ii) risk associated with narrowing the genetic base of current commercial cultivars and climate change; (iii) analysis of existing PGD analytical methods in pregenomic and genomic era; and (iv) modern tools available for PGD analysis in postgenomic era. This discussion benefits the plant scientist community in order to use the new methods and technology for better and rapid assessment, for utilization of germplasm from gene banks to their applied breeding programs. With the advent of new biotechnological techniques, this process of genetic manipulation is now being accelerated and carried out with more precision (neglecting environmental effects) and fast-track manner than the classical breeding techniques. It is also to note that gene banks look into several issues in order to improve levels of germplasm distribution and its utilization, duplication of plant identity, and access to database, for prebreeding activities. Since plant breeding research and cultivar development are integral components of improving food production, therefore, availability of and access to diverse genetic sources will ensure that the global food production network becomes more sustainable. The pros and cons of the basic and advanced statistical tools available for measuring genetic diversity are briefly discussed and their source links (mostly) were provided to get easy access; thus, it improves the understanding of tools and its practical applicability to the researchers.
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Affiliation(s)
- M. Govindaraj
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641 003, India
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana 502324, India
| | - M. Vetriventhan
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore 641 003, India
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana 502324, India
| | - M. Srinivasan
- School of Life Science, Bharathidasan University, Tiruchirappalli 620 024, India
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23
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Adhikari S, Biswas A, Bandyopadhyay TK, Ghosh PD. A preliminary report on the genetic variation in pointed gourd (Trichosanthes dioica Roxb.) as assessed by random amplified polymorphic DNA. ACTA BIOLOGICA HUNGARICA 2014; 65:156-64. [PMID: 24873909 DOI: 10.1556/abiol.65.2014.2.4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Pointed gourd (Trichosanthes dioica Roxb.) is an economically important cucurbit and is extensively propagated through vegetative means, viz vine and root cuttings. As the accessions are poorly characterized it is important at the beginning of a breeding programme to discriminate among available genotypes to establish the level of genetic diversity. The genetic diversity of 10 pointed gourd races, referred to as accessions was evaluated. DNA profiling was generated using 10 sequence independent RAPD markers. A total of 58 scorable loci were observed out of which 18 (31.03%) loci were considered polymorphic. Genetic diversity parameters [average and effective number of alleles, Shannon's index, percent polymorphism, Nei's gene diversity, polymorphic information content (PIC)] for RAPD along with UPGMA clustering based on Jaccard's coefficient were estimated. The UPGMA dendogram constructed based on RAPD analysis in 10 pointed gourd accessions were found to be grouped in a single cluster and may represent members of one heterotic group. RAPD analysis showed promise as an effective tool in estimating genetic polymorphism in different accessions of pointed gourd.
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Affiliation(s)
- S Adhikari
- University of Kalyani Department of Botany Kalyani 741235 West Bengal India
| | - A Biswas
- University of Kalyani Department of Botany Kalyani 741235 West Bengal India
| | - T K Bandyopadhyay
- University of Kalyani Department of Molecular Biology and Biotechnology Kalyani 741235 West Bengal India
| | - P D Ghosh
- University of Kalyani Department of Botany Kalyani 741235 West Bengal India
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24
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GUPTA MAMTA, VERMA BHAWNA, KUMAR NARESH, CHAHOTA RAKESHK, RATHOUR RAJEEV, SHARMA SHYAMK, BHATIA SABHYATA, SHARMA TILAKR. Construction of intersubspecific molecular genetic map of lentil based on ISSR, RAPD and SSR markers. J Genet 2012; 91:279-87. [DOI: 10.1007/s12041-012-0180-4] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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25
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Rayhan MU, Van K, Kim DH, Kim SI, Kim MY, Lee YH, Lee SH. Identification of Gy4 nulls and development of multiplex PCR-based co-dominant marker for Gy4 and α’ subunit of β-conglycinin in soybean. Genes Genomics 2011. [DOI: 10.1007/s13258-010-0158-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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26
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Boopathi NM, Thiyagu K, Urbi B, Santhoshkumar M, Gopikrishnan A, Aravind S, Swapnashri G, Ravikesavan R. Marker-assisted breeding as next-generation strategy for genetic improvement of productivity and quality: can it be realized in cotton? INTERNATIONAL JOURNAL OF PLANT GENOMICS 2011; 2011:670104. [PMID: 21577317 PMCID: PMC3092514 DOI: 10.1155/2011/670104] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2010] [Accepted: 01/22/2011] [Indexed: 05/29/2023]
Abstract
The dawdling development in genetic improvement of cotton with conventional breeding program is chiefly due to lack of complete knowledge on and precise manipulation of fiber productivity and quality. Naturally available cotton continues to be a resource for the upcoming breeding program, and contemporary technologies to exploit the available natural variation are outlined in this paper for further improvement of fiber. Particularly emphasis is given to application, obstacles, and perspectives of marker-assisted breeding since it appears to be more promising in manipulating novel genes that are available in the cotton germplasm. Deployment of system quantitative genetics in marker-assisted breeding program would be essential to realize its role in cotton. At the same time, role of genetic engineering and in vitro mutagenesis cannot be ruled out in genetic improvement of cotton.
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Affiliation(s)
- N. Manikanda Boopathi
- Department of Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - K. Thiyagu
- Department of Cotton, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - B. Urbi
- Department of Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - M. Santhoshkumar
- Department of Cotton, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - A. Gopikrishnan
- Department of Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - S. Aravind
- Department of Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - Gat Swapnashri
- Department of Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641003, India
| | - R. Ravikesavan
- Department of Cotton, Tamil Nadu Agricultural University, Coimbatore 641003, India
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Molecular and morphological characterization of advanced breeding lines from diverse cross in mung bean (Vigna radiata (L.) Wilczek). J Genet 2010; 88:341-4. [PMID: 20086302 DOI: 10.1007/s12041-009-0050-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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30
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Sethy NK, Shokeen B, Edwards KJ, Bhatia S. Development of microsatellite markers and analysis of intraspecific genetic variability in chickpea (Cicer arietinum L.). TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2006; 112:1416-28. [PMID: 16534564 DOI: 10.1007/s00122-006-0243-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2005] [Accepted: 02/13/2006] [Indexed: 05/07/2023]
Abstract
Paucity of polymorphic molecular markers in chickpea (Cicer arietinum L.) has been a major limitation in the improvement of this important legume. Hence, in an attempt to develop sequence-tagged microsatellite sites (STMS) markers from chickpea, a microsatellite enriched library from the C. arietinum cv. Pusa362 nuclear genome was constructed for the identification of (CA/GT)n and (CT/GA)n microsatellite motifs. A total of 92 new microsatellites were identified, of which 74 functional STMS primer pairs were developed. These markers were validated using 9 chickpea and one C. reticulatum accession. Of the STMS markers developed, 25 polymorphic markers were used to analyze the intraspecific genetic diversity within 36 geographically diverse chickpea accessions. The 25 primer pairs amplified single loci producing a minimum of 2 and maximum of 11 alleles. A total of 159 alleles were detected with an average of 6.4 alleles per locus. The observed and expected heterozygosity values averaged 0.32 (0.08-0.91) and 0.74 (0.23-0.89) respectively. The UPGMA based dendrogram was able to distinguish all the accessions except two accessions from Afghanistan establishing that microsatellites could successfully detect intraspecific genetic diversity in chickpea. Further, cloning and sequencing of size variant alleles at two microsatellite loci revealed that the variable numbers of AG repeats in different alleles were the major source of polymorphism. Point mutations were found to occur both within and immediately upstream of the long tracts of perfect repeats, thereby bringing about a conversion of perfect motifs into imperfect or compound motifs. Such events possibly occurred in order to limit the expansion of microsatellites and also lead to the birth of new microsatellites. The microsatellite markers developed in this study will be useful for genetic diversity analysis, linkage map construction as well as for depicting intraspecific microsatellite evolution.
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Affiliation(s)
- Niroj Kumar Sethy
- National Centre for Plant Genome Research, Jawaharlal Nehru University Campus, Post Box No. 10531, New Delhi, 110067, India
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Vlácilová K, Ohri D, Vrána J, Cíhalíková J, Kubaláková M, Kahl G, Dolezel J. Development of flow cytogenetics and physical genome mapping in chickpea (Cicer arietinum L.). Chromosome Res 2003; 10:695-706. [PMID: 12575797 DOI: 10.1023/a:1021584914931] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Procedures for flow cytometric analysis and sorting of mitotic chromosomes (flow cytogenetics) have been developed for chickpea (Cicer arietinum). Suspensions of intact chromosomes were prepared from root tips treated to achieve a high degree of metaphase synchrony. The optimal protocol consisted of a treatment of roots with 2 mmol/L hydroxyurea for 18 h, a 4.5-h recovery in hydroxyurea-free medium, 2 h incubation with 10 micromol/L oryzalin, and ice-water treatment overnight. This procedure resulted in an average metaphase index of 47%. Synchronized root tips were fixed in 2% formaldehyde for 20 min, and chromosome suspensions prepared by mechanical homogenization of fixed root tips. More than 4 x 10(5) morphologically intact chromosomes could be isolated from 15 root tips. Flow cytometric analysis of DAPI-stained chromosomes resulted in histograms of relative fluorescence intensity (flow karyotypes) containing eight peaks, representing individual chromosomes and/or groups of chromosomes with a similar relative DNA content. Five peaks could be assigned to individual chromosomes (A, B, C, G, H). The parity of sorted chromosome fractions was high, and chromosomes B and H could be sorted with 100% purity. PCR on flow-sorted chromosome fractions with primers for sequence-tagged microsatellite site (STMS) markers permitted assignment of the genetic linkage group LG8 to the smallest chickpea chromosome H. This study extends the number of legume species for which flow cytogenetics is available, and demonstrates the potential of flow cytogenetics for genome mapping in chickpea.
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Affiliation(s)
- K Vlácilová
- Laboratory of Molecular Cytogenetics and Cytometry, Institute of Experimental Botany, Sokolovská 6, CZ-77200 Olomouc, Czech Republic
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Benko-Iseppon AM, Winter P, Huettel B, Staginnus C, Muehlbauer FJ, Kahl G. Molecular markers closely linked to fusarium resistance genes in chickpea show significant alignments to pathogenesis-related genes located on Arabidopsis chromosomes 1 and 5. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2003; 107:379-386. [PMID: 12709786 DOI: 10.1007/s00122-003-1260-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2002] [Accepted: 01/10/2003] [Indexed: 05/24/2023]
Abstract
A population of 131 recombinant inbred lines from a wide cross between chickpea ( Cicer arietinum L., resistant parent) and Cicer reticulatum (susceptible parent) segregating for the closely linked resistances against Fusarium oxysporum f.sp. ciceri races 4 and 5 was used to develop DNA amplification fingerprinting markers linked to both resistance loci. Bulked segregant analysis revealed 19 new markers on linkage group 2 of the genetic map on which the resistance genes are located. Closest linkage (2.0 cM) was observed between marker R-2609-1 and the race 4 resistance locus. Seven other markers flanked this locus in a range from 4.1 to 9.0 cM. These are the most closely linked markers available for this locus up to date. The sequences of the linked markers were highly similar to genes encoding proteins involved in plant pathogen response, such as a PR-5 thaumatin-like protein and an important regulator of the phytoalexin pathway, anthranilate N-hydroxycinnamoyl-benzoyltransferase. Others showed significant alignments to genes encoding housekeeping enzymes such as the MutS2 DNA-mismatch repair protein. In the Arabidopsis genome, similar genes are located on short segments of chromosome 1 and 5, respectively, suggesting synteny between the fusarium resistance gene cluster of chickpea and the corresponding regions in the Arabidopsis genome. Three marker sequences were similar to retrotransposon-derived and/or satellite DNA sequences. The markers developed here provide a starting point for physical mapping and map-based cloning of the fusarium resistance genes and exploration of synteny in this highly interesting region of the chickpea genome.
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Affiliation(s)
- A-M Benko-Iseppon
- Universidade Federal de Pernambuco, UFPE, CCB, Genética, Av. Prof. Moraes Rego, s/no., 50732-970, Recife - PE, Brazil
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Pfaff T, Kahl G. Mapping of gene-specific markers on the genetic map of chickpea (Cicer arietinum L.). Mol Genet Genomics 2003; 269:243-51. [PMID: 12756536 DOI: 10.1007/s00438-003-0828-0] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2002] [Accepted: 01/06/2003] [Indexed: 11/25/2022]
Abstract
With the exception of the fact that it is made up of eight different chromosomes, the physical organization of the 738-Mb genome of the important legume crop chickpea (Cicer arietinum L.) is unknown. In an attempt to increase our knowledge of the basic structure of this genome, we determined the map positions of a series of genes involved in plant defence responses (DR) by genetic linkage analysis. Exploiting the sequence data available in GenBank, we selected genes known to be induced in chickpea and other plants by pathogen attack. Gene-specific primers were designed based on conserved regions, and used to detect the corresponding gene sequences in a segregating population derived from an interspecific cross between Cicer arietinum and C. reticulatum. Forty-seven gene-specific markers were integrated into an existing map based on STMS, AFLP, DAF and other anonymous markers. The potential of this approach is discussed.
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Affiliation(s)
- T Pfaff
- Plant Molecular Biology, Biocenter, University of Frankfurt, Marie-Curie-Str. 9, Germany
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Shavrukov Y, Yonemoto-Kurihara S, Tanaka M. Analysis of restriction fragment length polymorphism of Japanese sugar beet lines with incomplete monogermity. Genes Genet Syst 1997. [DOI: 10.1266/ggs.72.163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
- Yuri Shavrukov
- Institute of Cytology and Genetics, Russian Academy of Sciences
| | | | - Masakatsu Tanaka
- Upland Agriculture Research Center, Hokkaido National Agricutural Experiment Station
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