The AVRDC - The World Vegetable Center mungbean (Vigna radiata) core and mini core collections

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Schafleitner, Roland ^a   Nair, Ramakrishnan Madhavan ^a   Rathore, Abhishek ^b   Wang, Yen Wei ^a   Lin, Chen Yu ^a   Chu, Shu Hui ^a   Lin, Pin Yun ^a   Chang, Jian Cheng ^a   Ebert, Andreas W ^a  

^a AVRDC THE WORLD VEGETABLE CENTER   (Taiwan)

^b INTERNATIONAL CROPS RESEARCH INSTITUTE FOR THE SEMI ARID TROPICS ICRISAT   (India)

Author keywords

Breeding; Core and mini core collection; Genetic diversity; Germplasm collection; Mungbean

Indexed keywords

ALLELE; ARTICLE; CLUSTER ANALYSIS; GENETIC VARIABILITY; GENOTYPE; GERMPLASM; MUNG BEAN; NONHUMAN; PHENOTYPIC VARIATION; PLANT BREEDING; SIMPLE SEQUENCE REPEAT; SPECIES DIVERSITY; BREEDING; COMPUTER INTERFACE; FABACEAE; FACTUAL DATABASE; GENETIC VARIATION; GENETICS; INTERNET; PHENOTYPE; PLANT GENOME;

VIGNA RADIATA;

MICROSATELLITE DNA;

BREEDING; CLUSTER ANALYSIS; DATABASES, FACTUAL; FABACEAE; GENETIC VARIATION; GENOME, PLANT; GENOTYPE; INTERNET; MICROSATELLITE REPEATS; PHENOTYPE; USER-COMPUTER INTERFACE;

EID: 84928795107     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-1556-7     Document Type: Article

References (39)

1. Zukovskij PM. Cultivated plants and their wild relatives. Farnham Royal, UK: Commonwealth Agricultural Bureaux; 1962.
2. Nair RM, Schafleitner R, Kenyon L, Srinivasan R, Easdown W, Ebert AW, et al. Genetic improvement of mungbean. SABRAO J Breed Genet. 2012;44:177-90.
3. Chitra U, Vimala V, Singh U, Geervani P. Variability in phytic acid content and protein digestibility of grain legumes. Plant Food Hum Nutr. 1995;1995(47):163-72.
4. Sandhu KS, Lim S-T. Digestibility of legume starches as influenced by their physical and structural properties. Carbohyd Polym. 2008;71:245-52.
5. Yaqub M, Mahmood T, Akhtar M, Iqbal MM, Ali S. Induction of mungbean [Vigna radiata (L.) Wilczek] as a grain legume in the annual rice-wheat double cropping system. Pakistan J Bot. 2010;42:3125-35.
6. DFID. 2010. https://www.gov.uk/government/case-studies/dfid-research-farmers-benefit-from-new-mungbean-varieties.
7. Kang YJ, Kim S, Kim MY, Lestari P, Kim KH, Ha B-K, et al. Genome sequence of mungbean and insights into evolution within Vigna species. Nature Comm. 2014;5. doi:10.1038/ncomms6443.
8. AVRDC Vegetable Genetic Resources Information System AVGRIS [ http://203.64.245.173/search_result.asp?VINO=&ACCNO=&TEMPNO=&SPECIE=VIGNARADIATA&PEDCUL = &SUBTAX = &COUNTR = &NOTES=;] accessed 23 October 2014.
9. Ebert AW. Ex situ conservation of plant genetic resources 1 of major vegetables. In: Normah MN, Chin HF, Reed BM, editors. Conservation of tropical plant species. New York: Springer Science+Business Media; 2013. p. 373-417.
10. Liu C, Wang S, Wang L, Sun L, Mei L, Xu N, et al. Establishment of candidate core collection in Chinese mungbean germplasm resources. Acta Agron Sin. 2008;34:700.
11. Bisht IS, Mahajan RK, Patel DP. The use of characterisation data to establish the Indian mungbean core collection and assessment of genetic diversity. Genet Resour Crop Ev. 1998;45:127-33.
12. Barkley NA, Wang ML, Gillaspie AG, Dean RE, Pederson GA, Jenkins TM. Discovering and verifying DNA polymorphisms in a mung bean [V. radiata (L.) R. Wilczek] collection by EcoTILLING and sequencing. BMC Res Notes. 2008;1:28.
13. Moe KT, Gwag JG, Park YJ. Efficiency of PowerCore in core set development using amplified fragment length polymorphic markers in mungbean. Plant Breed. 2012;131:110-7.
14. Sangiri C, Kaga A, Tomooka N, Vaughan D, Srinives P. Genetic diversity of the mungbean (Vigna radiata, Leguminosae) genepool on the basis of microsatellite analysis. Aus J Bot. 2008;55:837-47.
15. Nei M. Genetic distance between populations. Am Nat. 1972;106:283-92.
16. Frankel OH. Genetic perspectives of germplasm conservation. In: Arber W, Illmensee K, Peacock JW, Starlinger P, editors. Genetic manipulation: impact on man and society. Cambridge: Cambridge University Press; 1984. p. 161-70.
17. Frankel OH, Brown AHD. Plant genetic resources today: a critical appraisal. In: Holden JHW, Williams JT, editors. Crop genetic resources: conservation and evaluation. London: Allen and Unwin; 1984. p. 249-57.
18. VanHintum TJL, Brown AHD, Spillane C, Hodgkin T. Core collections of plant genetic resources. In: IPGRI Technical Bulletin No. 3. Rome, Italy: International Plant Genetic Resources Institute; 2000.
19. Hu J, Zhu J, Xu HM. Methods of constructing core collections by stepwise clustering with three sampling strategies based on the genotypic values of crops. Theor Appl Genet. 2000;101:264-8.
20. Balfourier F, Roussel V, Strelchenko P, Exbrayat-Vinson F, Sourdille P, Boutet G, et al. A worldwide bread wheat core collection arrayed in a 384-well plate. Theor Appl Genet. 2007;114:1265-75.
21. Odong TL, Jansen J, van Eeuwijk FA, van Hintum TJL. Quality of core collections for effective utilisation of genetic resources review, discussion and interpretation. Theor Appl Genet. 2013;126:289-305.
22. Hennink S, Zeven AC. The interpretation of Nei and Shannon-Weaver within population variation indices. Euphytica. 1990;51:235-40.
23. Kim KW, Chung HK, Cho GT, Ma KH, Chandrabalan D, Gwag JG, et al. PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets. Bioinformatics. 2007;23:2155-62.
24. Ward J. Hierarchical grouping to optimize an objective function. J Am Stat Assoc. 1963;38:236-44.
25. Fulton TM, Chunwongse J, Tanksley SD. Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Mol Biol Rep. 1995;13:207-9.
26. Somta P, Seehalak W, Srinives P. Development, characterization and cross-species amplification of mungbean (Vigna radiata) genic microsatellite markers. Conserv Genet. 2009;10:1939-43.
27. Tangphatsornruang S, Somta P, Uthaipaisanwong P, Chanprasert J, Sangsrakru D, Seehalak W, et al. Characterization of microsatellites and gene contents from genome shotgun sequences of mungbean (Vigna radiata (L.) Wilczek). BMC Plant Biol. 2009;9:137.
28. Moe KT, Chung J-W, Cho Y-I, Moon J-K, Ku Y-H, Jung J-K, et al. Sequence information on simple sequence repeats and single nucleotide polymorphisms through transcriptome analysis of mungbean. J Integr Plant Biol. 2011;53:63-73.
29. Huang X. A contig assembly program based on sensitive detection of fragment overlaps. Genomics. 1992;14:18-25.
30. Maia LCD, Palmieri DA, Souza VQD, Kopp MM, Carvalho FIFD, Costa de Oliveira A. SSR Locator: tool for simple sequence repeat discovery integrated with primer design and PCR simulation. Int J Plant Genomics. 2008;412696. doi:10.1155/2008/412696.
31. Liu K, Muse SV. PowerMarker: an integrated analysis environment for genetic marker analysis. Bioinformatics. 2005;21:2128-9.
32. National Center for Biotechnology Information (US). BLAST+. [ http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download ]
33. Yeh FC, Yang RC, Boyle T, Ye ZH, Mao JX. POPGENE, version 1.32: the user friendly software for population genetic analysis. [ http://www.ualberta.ca/~fyeh/popgene_info.html ]
34. Mantel NA. The detection of disease clustering and a generalized regression approach. Cancer Res. 1967;27:209-20.
35. Peakall R, Smouse PE. GenAlEx 6.5: genetic analysis in Excel. Population genetic software for teaching and research-an update. Bioinformatics. 2012;28:2537-9.
36. Pritchard JK, Stephens M, Donnelly P. Inference of population structure using multilocus genotype data. Genetics. 2000;155:945-59.
37. Earl DA, von Holdt BM. Structure Harvester: a website and program for visualizing STRUCTURE output and implementing the Evanno method. Conserv Genet Res. 2012;4:359-61.
38. De Beukelaer H, Smýkal P, Davenport GF, Fack V. Core Hunter 1 II: fast core subset selection based on multiple genetic diversity measures using Mixed Replica search. BMC Bioinformatics. 2012;13:312.
39. Cao L, Grabchak M. EntropyEstimation-package. Tools for the Estimation of Entropy and Related Quantities. [ http://cran.rproject.org/web/packages/EntropyEstimation/EntropyEstimation.pdf ]