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Ramesh P, Juturu VN, Yugandhar P, Pedersen S, Hemasundar A, Yolcu S, Chandra Obul Reddy P, Chandra Mohan Reddy CV, Veerabramha Chari P, Mohan R, Chandra Sekhar A. Molecular genetics and phenotypic assessment of foxtail millet ( Setaria italica (L.) P. Beauv.) landraces revealed remarkable variability of morpho-physiological, yield, and yield-related traits. Front Genet 2023; 14:1052575. [PMID: 36760993 PMCID: PMC9905688 DOI: 10.3389/fgene.2023.1052575] [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: 09/24/2022] [Accepted: 01/09/2023] [Indexed: 01/26/2023] Open
Abstract
Foxtail millet (Setaria italica (L.) P. Beauv.) is highly valued for nutritional traits, stress tolerance and sustainability in resource-poor dryland agriculture. However, the low productivity of this crop in semi-arid regions of Southern India, is further threatened by climate stress. Landraces are valuable genetic resources, regionally adapted in form of novel alleles that are responsible for cope up the adverse conditions used by local farmers. In recent years, there is an erosion of genetic diversity. We have hypothesized that plant genetic resources collected from the semi-arid climatic zone would serve as a source of novel alleles for the development of climate resilience foxtail millet lines with enhanced yield. Keeping in view, there is an urgent need for conservation of genetic resources. To explore the genetic diversity, to identify superior genotypes and novel alleles, we collected a heterogeneous mixture of foxtail millet landraces from farmer fields. In an extensive multi-year study, we developed twenty genetically fixed foxtail millet landraces by single seed descent method. These landraces characterized along with four released cultivars with agro-morphological, physiological, yield and yield-related traits assessed genetic diversity and population structure. The landraces showed significant diversity in all the studied traits. We identified landraces S3G5, Red, Black and S1C1 that showed outstanding grain yield with earlier flowering, and maturity as compared to released cultivars. Diversity analysis using 67 simple sequence repeat microsatellite and other markers detected 127 alleles including 11 rare alleles, averaging 1.89 alleles per locus, expected heterozygosity of 0.26 and an average polymorphism information content of 0.23, collectively indicating a moderate genetic diversity in the landrace populations. Euclidean Ward's clustering, based on the molecular markers, principal coordinate analysis and structure analysis concordantly distinguished the genotypes into two to three sub-populations. A significant phenotypic and genotypic diversity observed in the landraces indicates a diverse gene pool that can be utilized for sustainable foxtail millet crop improvement.
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Affiliation(s)
- Palakurthi Ramesh
- Molecular Genetics and Functional Genomics Laboratory, Department of Biotechnology, School of Life Sciences, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | - Vijaya Naresh Juturu
- Molecular Genetics and Functional Genomics Laboratory, Department of Biotechnology, School of Life Sciences, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | - Poli Yugandhar
- Plant Molecular Biology Laboratory, Indian Institute of Rice Research, Hyderabad, Telangana, India
| | - Sydney Pedersen
- Department of Biology, Mercyhurst University, Erie, PA, United States
| | - Alavilli Hemasundar
- Department of Bioresources Engineering, Sejong University, Seoul, South Korea
| | - Seher Yolcu
- Department of Life Sciences, Sogang University, Seoul, South Korea
| | - Puli Chandra Obul Reddy
- Plant Molecular Biology Laboratory, Department of Botany, School of Life Sciences, Yogi Vemana University, Kadapa, Andhra Pradesh, India
| | | | - P. Veerabramha Chari
- Department of Biotechnology, Krishna University, Machilipatnam, Andhra Pradesh, India
| | - Rajinikanth Mohan
- Department of Biology, Mercyhurst University, Erie, PA, United States,*Correspondence: Akila Chandra Sekhar, , ; Rajinikanth Mohan,
| | - Akila Chandra Sekhar
- Molecular Genetics and Functional Genomics Laboratory, Department of Biotechnology, School of Life Sciences, Yogi Vemana University, Kadapa, Andhra Pradesh, India,*Correspondence: Akila Chandra Sekhar, , ; Rajinikanth Mohan,
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Chander S, Bhat KV, Kumari R, Sen S, Gaikwad AB, Gowda MVC, Dikshit N. Analysis of spatial distribution of genetic diversity and validation of Indian foxtail millet core collection. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:663-673. [PMID: 28878504 PMCID: PMC5567709 DOI: 10.1007/s12298-017-0448-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 05/02/2017] [Accepted: 05/12/2017] [Indexed: 05/28/2023]
Abstract
Foxtail millet [Setaria italica (L.) P. Beauv.] is an important small millet, grown as a short duration, drought tolerant crop across the world. This crop can be grown on wide ranges of soil conditions and has an immense potential for food and fodder in rainfed and arid regions of the India. In the present study, 31 primer pairs (27 SSR and 4 EST-SSR) were used to analyse the genetic diversity in 223 core collection accessions. Analysis resulted in detection of a total of 136 alleles with an average of 4.38 alleles per locus. Among these 136 alleles, 22 were rare, 70 were common and 44 were frequent. The PIC value ranged from 0.01 to 0.86 with an average of 0.31. The average number of observed alleles ranged from 2.0 (northern hills of India accessions) to 4.06 (exotic) with an average of 2.72. The mean Shannon's Information Index ranged from 0.44 (northern hills of India) to 0.69 (exotic) with an average of 0.52. Pair-wise Fst values indicated little to moderate genetic differentiation among the group of accessions. UPGMA clustering grouped the accessions into two major groups while analysis for population substructure indicated presence of four subpopulations. However there was no statistically well supported grouping of the accessions based on eco-geographic specificities. The core collection designated here represented substantial genetic diversity at molecular level, hence may be a good source of diversity for use in foxtail improvement programs in the region.
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Affiliation(s)
| | - K. V. Bhat
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110 012 India
| | - Ratna Kumari
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110 012 India
| | - Sanjay Sen
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110 012 India
| | - A. B. Gaikwad
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110 012 India
| | - M. V. C. Gowda
- All India Co-ordinated Small Millets Improvement Project, GKVK, Bengaluru, 560 065 India
| | - N. Dikshit
- ICAR-National Bureau of Plant Genetic Resources, Regional Station, Akola, 444 104 India
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Exploring Identity-By-Descent Segments and Putative Functions Using Different Foundation Parents in Maize. PLoS One 2016; 11:e0168374. [PMID: 27997600 PMCID: PMC5172581 DOI: 10.1371/journal.pone.0168374] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 11/29/2016] [Indexed: 02/06/2023] Open
Abstract
Maize foundation parents (FPs) play no-alternative roles in hybrid breeding because they were widely used in the development of new lines and hybrids. The combination of different identity-by-descent (IBD) segments and genes could account for the formation patterns of different FPs, and knowledge of these IBD regions would provide an extensive foundation for the development of new candidate FP lines in future maize breeding. In this paper, a panel of 304 elite lines derived from FPs, i.e., B73, 207, Mo17, and Huangzaosi (HZS), was collected and analyzed using 43,252 single nucleotide polymorphism (SNP) markers. Most IBD segments specific to particular FP groups were identified, including 116 IBD segments in B73, 105 in Mo17, 111 in 207, and 190 in HZS. In these regions, 423 quantitative trait nucleotides (QTNs) associated with 15 agronomic traits and 804 candidate genes were identified. Some known adaptation-related genes, e.g., dwarf8 and vgt1 in HZS, zcn8 and epc in Mo17, and ZmCCT in 207, were validated as being tightly linked to particular IBD segments. In addition, numerous new candidate genes were also identified. For example, GRMZM2G154278 in HZS, which belongs to the cell cycle control family, was closely linked to a QTN of the ear height/plant height (EH/PH) trait; GRMZM2G051943 in 207, which encodes an endochitinase precursor (EP) chitinase, was closely linked to a QTN for kernel density; and GRMZM2G170586 in Mo17 was closely linked to a QTN for ear diameter. Complex correlations among these genes were also found. Many IBD segments and genes were included in the formation of FP lines, and complex regulatory networks exist among them. These results provide new insights on the genetic basis of complex traits and provide new candidate IBD regions or genes for the improvement of special traits in maize production.
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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.
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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
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