SPAR Markers-Assisted Assessment of Genetic Diversity and Population Structure in Finger Millet (Eleusine Coracana (L.) Gaertn) Mini-Core Collection

다국어 초록 (Multilingual Abstract)

Finger millet is an important staple food crop of semi-arid tropics also known as “super cereal” and has a higher calcium content than any other crops. Thousands of germplasm are being maintained and its genetic characterization is essential for further utilization in crop improvement. This research was performed to estimate the diversity and population genetic structure in the mini-core collection of finger millet by using SPAR markers, namely RAPD, ISSR, and DAMD markers. Altogether, 32 primers were used in this study, which produced 408 bands among which 344 were polymorphic. Analysis by combining all three marker systems revealed 84.31% of polymorphism among 90 genotypes of finger millet. Average polymorphism information content (PIC) produced by the ISSR, RAPD, and DAMD markers were 0.79, 0.81, 0.62, and average Rp values were 12.84, 8.17, and 8.53, respectively. The Jaccard's similarity value ranged from 0.233-0.861. IE 6059 and IE 5870 genotypes showed the highest Jaccard's similarity value of 0.861 in UPGMA analysis. Neighbor joining-based phylogenetic analysis produced two major clusters and the genotypes were grouped based on their geographical region of origin. Principal component analysis and principal coordinates analysis also confirmed the results. In population STRUCTURE analysis, the genotypes were divided into two subpopulations (P1and P2). These results confirmed that the genotypes we have assessed were genetically diverse and were clustered based on their geographic region of origin. The information obtained from this study will be useful in population management strategies and selection of genotypes for an effective breeding program in the future.

참고문헌 (Reference)

1 Ramakrishnan M, "Using molecular markers to assess the genetic diversity and population structure of finger millet (Eleusine coracana (L.) Gaertn.) from various geographical regions" 63 : 361-376, 2016

2 Arya L, "Use of genomic and genic SSR markers for assessing genetic diversity and population structure in Indian and African finger millet (Eleusine coracana (L.) Gaertn.) germplasm" 299 : 1395-1401, 2013

3 Ramakrishnan M, "Tracing QTLs for leaf blast resistance and agronomic performance of finger millet (Eleusine coracana (L.) Gaertn.) genotypes through association mapping and in silico comparative genomics analyses" 11 : e0159264-, 2016

4 Dida MM, "The genetic map of finger millet, Eleusine coracana" 114 : 321-332, 2007

5 Hema R, "Stable expression of mtlD gene imparts multiple stress tolerance in finger millet" 9 : e99110-, 2014

6 Comino C, "Selection in Artemisia umbelliformis Lam. Piedmont ecotypes to improve cultivation in alpine environment" 62 : 567-577, 2015

7 Bhatt D, "Responses to drought induced oxidative stress in five finger millet varieties differing in their geographical distribution" 17 : 347-353, 2011

8 Souza E, "Relationships among 70 North American oat germplasms: II. Cluster analysis using qualitative characters" 31 : 605-612, 1991

9 Kumar H, "RAPD and ISSR marker-based comparative evaluation of genetic diversity among indian germplasms of euryale ferox: an aquatic food plant" 180 : 1345-1360, 2016

10 Latha MA, "Production of transgenic plants resistant to leaf blast disease in finger millet (Eleusine coracana (L.) Gaertn.)" 169 : 657-667, 2005

11 Dida MM, "Population structure and diversity in finger millet Eleusine coracana germplasm" 1 : 131-141, 2008

12 Gupta S, "Population structure and association mapping of yield contributing agronomic traits in foxtail millet" 33 : 881-893, 2014

13 Hammer Ø, "PAST: paleontological statistics software package for education and data analysis" 4 : 9-, 2001

14 Tehrim S, "Molecular characterization of traditional and improved rice cultivars based on random amplified polymorphic DNAs (RAPDs) markers" 11 : 10297-10304, 2012

15 Yaman H, "Molecular characterization of the wild relatives of safflower (Carthamustinctorius L.) in Turkey as revealed by ISSRs" 61 : 595-602, 2014

16 Liu Q, "Low-copy nuclear gene and McGISH resolves polyploidy history of Eleusine coracana and morphological character evolution in Eleusine" 38 : 1-12, 2014

17 Doyle JJ, "Isolation of plant DNA from fresh tissue" 12 : 13-15, 1990

18 Pritchard JK, "Inference of population structure using multilocus genotype data" 155 : 945-959, 2000

19 Lande R, "Genetics and demography in biological conservation" 241 : 1455-1460, 1988

20 Frankham, R, "Genetics and conservation biology" 326 : 22-29, 2003

21 Uma S, "Genetic variability in recovery growth and synthesis of stress proteins in response to polyethylene glycol and salt stress in finger millet" 76 : 43-49, 1995

22 Das S, "Genetic variability and relationships among thirty genotypes of finger millet (Eleusine coracana L. Gaertn.) using RAPD markers" 62 : 116-122, 2007

23 Verma S, "Genetic relationships among wild and cultivated accessions of curry leaf plant (Murraya koenigii (L.) Spreng.), as revealed by DNA fingerprinting methods" 53 : 139-149, 2013

24 Rahman SN, "Genetic polymorphism in rice (Oryza sativa L.) through RAPD analysis" 6 : 224-229, 2007

25 Fakrudin B, "Genetic diversity assessment of finger millet, (Eleusine coracana (Gaertn.), germplasm through RAPD analysis" 138 : 50-54, 2004

26 Ayres DR, "Genetic diversity and structure of the narrow endemic Wyethia reticulata and its congener W. bolanderi (Asteraceae) using RAPD and allozyme techniques" 86 : 344-353, 1999

27 Saker MM, "Genetic analysis of some Egyptian rice genotypes using RAPD, SSR and AFLP" 1 : 4-, 2005

28 Weir BS., "Genetic Data Analysis: Methods for Discrete Population Genetic Data" Sinauer Assoc Inc. Pub 377-, 1990

29 Peakall R, "GenAlEx 6.5: genetic analysis in excel. Population genetic software for teaching and research -an update" 28 : 2537-2539, 2012

30 Hilu KW, "Evolution of finger millet: evidence from random amplified polymorphic DNA" 38 : 232-238, 1995

31 Panwar P, "Efficiency of RAPD, SSR and cytochrome P450 gene based markers in accessing genetic variability amongst finger millet (Eleusine coracana) accessions" 37 : 4075-4082, 2010

32 Hilu KW, "Domestication of Eleusine coracana" 30 : 199-208, 1976

33 Aruna C, "Diversity analysis using ISSR markers for resistance to shoot pests in sorghum" 35 : 110-117, 2012

34 Satish L, "Direct plant regeneration from in vitro-derived shoot apical meristems of finger millet (Eleusine coracana (L.) Gaertn.)" 51 : 192-200, 2015

35 Evanno G, "Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study" 14 : 2611-2620, 2005

36 Laurentin H, "Data analysis for molecular characterization of plant genetic resources" 56 : 277-292, 2009

37 Williams JG, "DNA polymorphisms amplified by arbitrary primers are useful as genetic markers" 18 : 6531-6535, 1990

38 Reed DH, "Correlation between fitness and genetic diversity" 17 : 230-237, 2003

39 Botstein D, "Construction of a genetic linkage map in man using restriction fragment length polymorphisms" 32 : 314-331, 1980

40 Babu BK, "Comparative genomics and association mapping approaches for blast resistant genes in finger millet using SSRs" 9 (9): e99182-, 2014

41 Liu WL, "Characterization of genomic inheritance of intergeneric hybrids between Ascocenda and Phalaenopsis cultivars by GISH, PCR-RFLP and RFLP" 11 : e0153512-, 2016

42 Verma S, "Assessment of genetic diversity in indigenous turmeric (Curcuma longa) germplasm from India using molecular markers" 21 : 233-242, 2015

43 Shilpha J, "Assessment of genetic diversity in Solanum trilobatum L., an important medicinal plant from South India using RAPD and ISSR markers" 60 : 807-818, 2013

44 Babu B, "Assessment of genetic diversity among finger millet (Eleusine coracana (L) Gaertn) accessions using molecular markers" 54 : 399-404, 2007

45 Gupta R, "Assessment of Genetic Relatedness among Three Varieties of Finger Millet with Variable Seed Coat Color Using RAPD and ISSR Markers" 2 : 19-, 2010

46 Eva M. Sehr, "Assessment of Genetic Diversity Amongst Ugandan Sesame (Sesamum indicum L.) Landraces Based on Agromorphological Traits and Genetic Markers" 한국작물학회 19 (19): 117-129, 2016

47 Pandian S, "Analysis of population structure and genetic diversity in an exotic germplasm collection of Eleusine coracana (L.) Gaertn. using genic-SSR markers" 653 : 80-90, 2018

48 Satish L, "Analysis of genetic variation in sorghum (Sorghum bicolor (L.) Moench)genotypes with various agronomical traits using SPAR methods" 576 : 581-585, 2016

49 Host Antony David Rajendran, "Analysis of Molecular Variance and Population Structure in Southern Indian Finger Millet Genotypes Using Three Different Molecular Markers" 한국작물학회 19 (19): 275-283, 2016

50 Pandian S, "An amazing nutritional value in wonderful finger millet makes this 'The Most Lovable Food Crop' to the world" 3 : 034-036, 2017

51 Kumar A, "Allele mining for resistance gene analogs (RGAs) in crop plants: A special emphasis on blast resistance in finger millet (Eleusine coracana L.)" 76 : 1-9, 2016

52 Prevost A, "A new system of comparing PCR primers applied to ISSR fingerprinting of potato cultivars" 98 : 107-112, 1999