Genetic relationship and nuclear dna content variation in Tef [Eragrostis tef (Zucc.) Trotter] accessions.
DNA
Flow cytometry
Ploidy
SSR
Tef
Journal
Molecular biology reports
ISSN: 1573-4978
Titre abrégé: Mol Biol Rep
Pays: Netherlands
ID NLM: 0403234
Informations de publication
Date de publication:
Jun 2020
Jun 2020
Historique:
received:
28
03
2020
accepted:
15
05
2020
pubmed:
25
5
2020
medline:
20
2
2021
entrez:
25
5
2020
Statut:
ppublish
Résumé
This study was initiated to reveal genetic relationship of 25 tef (Eragrostis tef (Zucc.) accessions by using 10 SSR markers and to determine DNA content variation by using flow cytometer analysis. Ten markers produced a total of 18 alleles and 11 of those were polymorphic. The mean polymorphism rate was 66.6%. The highest polymorphism information content value was obtained from marker CNLTs370 with 0.69 while markers CNTLs11 and CNTLs133 produced monomorphic bands only. UPGMA analysis divided 25 tef genotypes into three main clades. The accessions PI193511 and PI195934 were distinctly separated from the others. No ploidy differences were determined among the 25 tef accessions. 2C mean nuclear DNA content ranged from 1.406 pg to 1.510 with mean of 1.460 pg. The results of this study indicated that SSR markers successfully determined genetic relationship of 25 tef accession although they had a low rate of polymorphism. This study also revealed that available tef related SSR markers should be optimized before use and their efficiency may vary based on tef genotypes or accessions used.
Identifiants
pubmed: 32447499
doi: 10.1007/s11033-020-05537-w
pii: 10.1007/s11033-020-05537-w
doi:
Substances chimiques
Genetic Markers
0
DNA
9007-49-2
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
4455-4463Subventions
Organisme : Çanakkale Onsekiz Mart Üniversitesi
ID : FYL-2019-2834
Références
Chanyalew S, Ferede S, Damte T, Fikre T, Genet Y, Kebede W, Tolossa K, Tadele Z, Assefa K (2019) Significance and prospects of an orphan crop tef. Planta 250(3):753–767. https://doi.org/10.1007/s00425-019-03209-z
doi: 10.1007/s00425-019-03209-z
pubmed: 31222492
Cheng A, Mayes S, Dalle G, Demissew S, Massawe F (2017) Diversifying crops for food and nutrition security - a case of teff. Biol Rev Camb Philos Soc 92(1):188–198. https://doi.org/10.1111/brv.12225
doi: 10.1111/brv.12225
pubmed: 26456883
Tefera H, Assefa K, Hundera F, Kefyalew T, Teferra T (2003) Heritability and genetic advance in recombinant inbred lines of tef (Eragrostis tef). Euphytica 131(1):91–96
doi: 10.1023/A:1023009720870
Boechat SdC, Longhi-Wagner HM (2003) Ana´lise do fruto em espe´cies Eragrostis Wolf (Poaceae). Iheringia, Se´rie Botanica 58:131–168
Abraha MT, Shimelis H, Laing M, Assefa K, Amelework B (2016) Assessment of the genetic relationship of tef (Eragrostis tef) genotypes using SSR markers. South African Journal of Botany 105:106–110. https://doi.org/10.1016/j.sajb.2015.12.009
doi: 10.1016/j.sajb.2015.12.009
Girma D, Assefa K, Chanyalew S, Cannarozzi G, Kuhlemeier C, Tadele Z (2014) The origins and progress of genomics research on Tef (Eragrostis tef). Plant Biotechnol J 12(5):534–540. https://doi.org/10.1111/pbi.12199
doi: 10.1111/pbi.12199
pubmed: 24891040
Shumoy H, Raes K (2017) Tef: The Rising Ancient Cereal: What do we know about its Nutritional and Health Benefits? Plant Foods Hum Nutr 72(4):335–344. https://doi.org/10.1007/s11130-017-0641-2
doi: 10.1007/s11130-017-0641-2
pubmed: 29098639
Assefa K, Chanyalew S, Tadele Z (2016) Tef, Eragrostis tef (Zucc.) Trotter. In: Patil JV (ed) Millet and sorghum: biological and genetic improvement. Wiley-Black Well Publisher, New Jersey, pp 226–266
Kumar V, Sharma S, Sharma AK, Kumar M, Sharma S, Malik S, Singh KP, Sanger RS, Bhat KV (2008) Genetic diversity in Indian common bean (Phaseolus vulgaris L) using random amplified polymorphic DNA markers. Physiol Mol Biol Plants 14(4):383–387. https://doi.org/10.1007/s12298-008-0038-7
doi: 10.1007/s12298-008-0038-7
pubmed: 23572906
Jamali SH, Cockram J, Hickey LT (2019) Insights into deployment of DNA markers in plant variety protection and registration. Theoretical and Applied Genetics 132(7):1911–1929. https://doi.org/10.1007/s00122-019-03348-7
doi: 10.1007/s00122-019-03348-7
pubmed: 31049631
Bai GH, Ayele M, Tefera H, Nguyen HT (2000) Genetic diversity in tef [Eragrostis tef (Zucc) Trotter] and its relatives as revealed by random amplified polymorphic DNAs. Euphytica 112:15–22
doi: 10.1023/A:1003802207158
Zhang D, Ayele M, Tefera H, Nguyen HT (2001) RFLP linkage map of the Ethiopian cereal tef [Eragrostis tef (Zucc)Trotter]. TheorApplGenet 102:957–964
Bai G, Tefera H, Ayele M, Nguyen HT (1999) A genetic linkage map of tef [Eragrostis tef (Zucc) Trotter] based on amplified fragment length polymorphism. Theor Appl Genet 99(3–4):599–604. https://doi.org/10.1007/s001220051274
doi: 10.1007/s001220051274
pubmed: 22665195
Ayele M, Tefera H, Assefa K, Nguyen HT (1999) Genetic characterization of two Eragrostis species using AFLP and morphological traits. Hereditas 130(1):33–40. https://doi.org/10.1111/j.1601-5223.1999.00033.x
doi: 10.1111/j.1601-5223.1999.00033.x
pubmed: 10364827
Ayele M, Nguyen HT (2000) Evaluation of amplified fragment length polymorphism markers in tef, Eragrostis tef (Zucc.) Trotter, and related species. Plant Breeding 119:403–409
doi: 10.1046/j.1439-0523.2000.00512.x
Yu JK, Sun Q, Rota ML, Edwards H, Tefera H, Sorrells ME (2006) Expressed sequence tag analysis in tef (Eragrostis tef (Zucc) Trotter). Genome 49(4):365–372. https://doi.org/10.1139/g05-118
doi: 10.1139/g05-118
pubmed: 16699556
Zeid M, Yu JK, Goldowitz I, Denton ME, Costich DE, Jayasuriya CT, Saha M, Elshire R, Benscher D, Breseghello F, Munkvold J, Varshney RK, Belay G, Sorrells ME (2010) Cross-amplification of EST-derived markers among 16 grass species. Field Crops Research 118:28–35
doi: 10.1016/j.fcr.2010.03.014
Assefa K, Merker A, Tefera H (2003) Inter simple sequence repeat (ISSR) analysis of genetic diversity in tef [Eragrostis tef (Zucc) Trotter]. Hereditas 139(3):174–183. https://doi.org/10.1111/j.1601-5223.2003.01800.x
doi: 10.1111/j.1601-5223.2003.01800.x
pubmed: 15061798
Zeid M, Assefa K, Haddis A, Chanyalew S, Sorrells ME (2012) Genetic diversity in tef [Eragrostis tef (Zucc.) Trotter] germplasm using SSR markers. Field Crops Research 127:64–70
doi: 10.1016/j.fcr.2011.10.013
Nadeem MA, Nawaz MA, Shahid MQ, Dogan Y, Comertpay G, Yildiz M, Hatipoglu R, Ahmad F, Alsaleh A, Labhane N, Ozkan H, Chung GW, Baloch FS (2018) DNA molecular markers in plant breeding: current status and recent advancements in genomic selection and genome editing. Biotechnol Biotechnol Equip 32(2):261–285. https://doi.org/10.1080/13102818.2017.1400401
doi: 10.1080/13102818.2017.1400401
Cannarozzi G, Plaza-Wuthrich S, Esfeld K, Larti S, Wilson YS, Girma D, de Castro E, Chanyalew S, Blosch R, Farinelli L, Lyons E, Schneider M, Falquet L, Kuhlemeier C, Assefa K, Tadele Z (2014) Genome and transcriptome sequencing identifies breeding targets in the orphan crop tef (Eragrostis tef). BMC Genomics 15:581. https://doi.org/10.1186/1471-2164-15-581
doi: 10.1186/1471-2164-15-581
pubmed: 25007843
pmcid: 4119204
Tiryaki I, Tuna M (2012) Determination of intraspecific nuclear DNA content variation in common vetch (Vicia sativa L.) lines and cultivars based on two distinct internal reference standards. Turkish Journal of Agriculture and Forestry 36(6):645–653
Bennett MD, Leitch IJ (2011) Nuclear DNA amounts in angiosperms: targets, trends and tomorrow. Ann Bot 107(3):467–590. https://doi.org/10.1093/aob/mcq258
doi: 10.1093/aob/mcq258
pubmed: 21257716
pmcid: 3043933
Ohri D, Bhargava A, Chatterjee A (2004) Nuclear DNA amounts in 112 species of tropical hardwoods - new estimates. Plant Biol (Stuttg) 6(5):555–561. https://doi.org/10.1055/s-2004-821235
doi: 10.1055/s-2004-821235
Ohri D (2005) Climate and growth form: the consequences for genome size in plants. Plant Biol (Stuttg) 7(5):449–458. https://doi.org/10.1055/s-2005-865878
doi: 10.1055/s-2005-865878
Borsch T, Hilu KW, Quandt D, Wilde V, Neinhuis C, Barthlott W (2004) Non–coding plastid trnT–trnF sequences reveal a well resolved phylogeny of basal angiosperms. J Evol Biol 16:558–576. https://doi.org/10.1046/j.1420-9101.2003.00577.x
doi: 10.1046/j.1420-9101.2003.00577.x
Zeid M, Belay G, Mulkey S, Poland J, Sorrells ME (2011) QTL mapping for yield and lodging resistance in an enhanced SSR-based map for tef. Theor Appl Genet 122:77–93
doi: 10.1007/s00122-010-1424-4
Kang HW, Park DS, Go SJ, Eun MY (2002) Fingerprinting of diverse genomes using PCR with universal rice primers generated from repetitive sequence of Korean weedy rice. Mol Cells 13(2):281–287
pubmed: 12018851
SAS I (1997) SAS/STAT software: Changes and enhancements through release 6.12. SAS Inst., Cary, NC.,
Dawson IK, Simons AJ, Waugh R, Powell W (1996) Detection and pattern of interspecific hybridization between Gliricida sepium and G maculata in Meso-America revealed by PCR-based assays. Mol Ecol 5(1):89–98
doi: 10.1111/j.1365-294X.1996.tb00294.x
Powell W, Morgante M, Doyle JJ, McNicol JW, Tingey SV, Rafalski AJ (1996) Genepool variation in genus Glycine subgenus Soja revealed by polymorphic nuclear and chloroplast microsatellites. Genetics 144(2):793–803
pubmed: 8889540
pmcid: 1207570
Dice LR (1945) Measures of the amount of ecological association between species. Ecology 26:297–307
doi: 10.2307/1932409
Dolezel J, Bartos J, Voglmayr H, Greilhuber J (2003) Nuclear DNA content and genome size of trout and human. Cytometry A. 51(2):127–128. https://doi.org/10.1002/cyto.a.10013
doi: 10.1002/cyto.a.10013
pubmed: 12541287
Roman B, Satovic Z, Pozarkova D, Macas J, Dolezel J, Cubero JI, Torres AM (2003) Development of a composite map in Vicia faba, breeding applications and future prospects. Theor Appl Genet 108:1079–1088
doi: 10.1007/s00122-003-1515-6
Fikre T, Tesfaye K, Assefa K (2018) Genetic diversity of Ethiopian tef [(Eragrostis tef (Zucc.) Trotter] released and selected farmers’ varieties along with two wild relatives as revealed by microsatellite markers. Journal of Crop Science and Biotechnology 21:367–374
doi: 10.1007/s12892-018-0066-0
Abraha MT (2016) Assessment of the genetic relationship of tef (Eragrostis tef) genotypes using SSR markers. South African J of Botany. https://doi.org/10.1016/j.sajb.2015.12.009
doi: 10.1016/j.sajb.2015.12.009
Ayele M, Dolezel J, VanDuren M, Brunner H, ZapataArias FJ (1996) Flow cytometric analysis of nuclear genome of the Ethiopian cereal Tef [Eragrostis tef (Zucc) Trotter]. Genetica 98:211–215
doi: 10.1007/BF00121369
Girma D, Cannarozzi G, Weichert A, Tadele Z (2018) Genotyping by Sequencing Reasserts the Close Relationship between Tef and Its Putative Wild Eragrostis Progenitors. Diveristy 10:17. https://doi.org/10.3390/d10020017
doi: 10.3390/d10020017
Hundera F, Arumuganathan K, Baenziger PS (2000) Determination of relative nuclear DNA content of tef [Eragrostis tef (Zucc.) Trotter] using flow cytometry. Journal of Genetics and Breeding 54:165–168
Ingram A, Doyle J (2007) Eragrostis (Poaceae): Monophyly and infrageneric classification. J Syst Evolut Bot 23
Ketema S (1993) Tef (Eragrostis tef): Breeding, Genetic Resources, Agronomy. Utilization and Role in Ethiopian Agriculture, Institute of Agricultural Research, Addis Ababa, Ethiopia
Girma D, Canarozzi G, Weichert A, Tadele Z (2020) Restriction Site Associated DNA Sequencing based Single Nucleotide Polymorphism Discovery in Selected Tef (Eragrostis tef) and Wild Eragrostis Species. Ethiop J Agric Sci 30(1):49–68