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Current IssueEditorial BoardOnline First ArticlesArchive

Research Article

volume 42 issue 6 (december 2019) : 743-749,   Doi: 10.18805/LR-451

Construction and validation of core collections in Pisum sp. using different methodologies

E
Espósito
M
María Andrea
G
Gatti
I
Ileana
C
Cointry
E
Enrique
1Cátedra de Mejoramiento Vegetal y Producción de Semillas, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Santa Fe, Argentina.

  • Submitted30-08-2018|

  • Accepted07-02-2019|

  • First Online 30-04-2019|

  • doi 10.18805/LR-451

Cite article:- Espósito, Andrea María, Gatti, Ileana, Cointry, Enrique (2019). Construction and validation of core collections in Pisum sp. using different methodologies. Legume Research. 42(6): 743-749. doi: 10.18805/LR-451.

ABSTRACT

Core collections contribute to a better utilization of accessions in breeding programs. Eighty-five accessions from a collection of Pisum germplasm were evaluated during 2015 and 2016. Phenotypic values of 12 morphological traits were measured and genotypic values (BLUP) were calculated. Molecular characterization was performed assaying a total of 15 SSR and 25 SRAP primer combinations. Four Cluster Analysis (phenotypic values, genotypic values, molecular markers and consensus) and four strategies to determine the number of accessions selected (constant, logarithmic, proportional and maximization strategies) were applied to construct 16 core collections. Validation of the core collections were performed through Mean difference percentage (MD), Variance difference percentage (VD), Coincidence rate of range (CR) Variable rate of coefficient of variation (VR), Shannon diversity index (SW) and the Taxonomy coverage (TC). The logarithmic strategy with data on genotypic values was the best strategy, while the least  strategy was the proportional strategy with molecular marker data.

REFERENCES

  1. Alvarado, G., López, M., Vargas, M., Pacheco, A., Rodríguez, F., Burgueño, J., Crossa, J. (2016) META-R (Multi Environment Trial Analysis whit R for Windows.) Version 6.0 http://hdl.handle.net/11529/10201 International Maize and Wheat Improvement Center.
  2. Balzarini, M., Di Renzo, J. (2003) Info-Gen: Software para análisis estadístico de datos genéticos. Facultad de Ciencias Agropecuarias. Universidad Nacional de Córdoba. Argentina.
  3. Balzarini, M., Bruno, C., Peña, A., Teich, I., Di Renzo, J. (2010) Estadística en Biotecnología. Aplicaciones en Info-Gen. Encuentro Grupo Editor. Córdoba, Argentina.
  4. Diwan, N., McIntosh, M.S., Bauchan, G.R. (1995) Methods of developing a core collection of annual Medicago species. Theor Appl Genet 90:755-761.
  5. Espósito, M.A., Martin, E.A., Cravero, V.P., López Anido, F.S., Cointry, E. (2007) Characterization of pea accessions by SRAP’s markers. Sci Hortic 113:329-335.
  6. Frankel, O.H., Brown, A.H.D. (1984) Plant genetic resources today: a critical appraisal. In: Crop Genetic Resources: Conservation & Evaluation. [Holden JHW, Williams JT (eds)]. George Alien & Unwin Ltd., London, pp 249-257. 
  7. Gower, J.C. (1975) Generalized Procrustes Analysis. Physchometrika 40:33-51.
  8. Hanci, F., Cebeci, E. (2018) Determination of morphological variability of different pisum genotypes using principal component analysis. Legume Res DOI: 10.18805/LR-438. On line: 30/10/2018.
  9. Hu, J.J., Zhu, J., Xu, H.H.M. (2000) Methods of constructing core collections by stepwise clustering with three sampling strategies based on the genotypic values of crops. Theor Appl Genet 101(1-2):264-268.
  10. Hutcheson, K. (1970) A test for comparing diversities based on the Shannon formula. J Theor Biol 29:151-154. https://doi.org/    10.1016/0022-5193(70)90124-4.
  11. Jaggal, L.G., Patil, B.R., Naik, P.M., Priya, K. (2016) Genetic diversity of selected accessions for seed protein among pigeonpea minicore collection. Legume Res 39(5):704-708.
  12. Kim, K.W., Chung, H.K., Cho, G.T., Ma, K.H., Chandrabalan, D., Gwag, J.G., Kim, T.S., Cho, E.G., Park, Y.J. (2007) PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets. Bioinformatics 23(16):2155-62.
  13. Peric, V., Nikoliæ, A.,Babiæ, V., Sudariæ, A.,Srebriæ, M., Ðorðeviæ, V., Mladenoviæ Driniæ, S. (2014) Genetika 46 (3):839-854.
  14. Piepho, H.P., Möhring, J., Melchinger, A.E., Büchse, A. (2008) BLUP for phenotypic selection in plant breeding and variety testing. Euphytica 161:209-228.
  15. Semwal D.P., Ahlawat, S.P., Pradheep, K. (2018) Pigeonpea (Cajanus cajan (L.) Millsp.) and its wild spp. germplasm collection status, diversity distribution and trait-specific germplasm mapping using GIS tools in India. Legume Res 41 (5):656-662.
  16. Shannon, C.E., Weaver, W. (1949) The mathematical theory of communication. The University of Illinois Press, Urbana, 117p.
  17. Smýkal, P., Hýbl, M., Corander, J., Jarkovský, J., Flavell, A., Griga, M. (2008) Genetic diversity and population structure of pea (Pisum sativum L.) varieties derived from combined retrotransposon, microsatellite and morphological marker analysis. Theor Appl Genet 117:413-424.
  18. Snedecor, G.W., Cochran, W.G. (1980) Statistical Methods, 7ed, Iowa State University, Ames: 507 p.
  19. Sokal, R.R., Michener, C.D. (1958) A Statistical Methods for Evaluating Systematic Relationships. University of Kansas Science Bulletin 38:1409-1438.
  20. Van Hintum, T.J.L., Brown, A.H.D., Spillane, C., Hodgkin, T. (2003) Colecciones núcleo de recursos fitogenéticos. Boletín Técnico No. 3del IPGRI. Instituto Internacional de Recursos Fitogenéticos, Roma, Italia. 
  21. Zhang, J., Wang, Y., Zhang, X.Z., Li, T.H., Wang, K., Xu, X.F., Han, Z.H. (2010) Sampling strategy to develop a primary core collection of apple cultivars based on fruit traits. Afr J Biotechnol 9:123-127. 
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    Research Article

    volume 42 issue 6 (december 2019) : 743-749,   Doi: 10.18805/LR-451

    Construction and validation of core collections in Pisum sp. using different methodologies

    E
    Espósito
    M
    María Andrea
    G
    Gatti
    I
    Ileana
    C
    Cointry
    E
    Enrique
    1Cátedra de Mejoramiento Vegetal y Producción de Semillas, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, Santa Fe, Argentina.

    • Submitted30-08-2018|

    • Accepted07-02-2019|

    • First Online 30-04-2019|

    • doi 10.18805/LR-451

    Cite article:- Espósito, Andrea María, Gatti, Ileana, Cointry, Enrique (2019). Construction and validation of core collections in Pisum sp. using different methodologies. Legume Research. 42(6): 743-749. doi: 10.18805/LR-451.

    ABSTRACT

    Core collections contribute to a better utilization of accessions in breeding programs. Eighty-five accessions from a collection of Pisum germplasm were evaluated during 2015 and 2016. Phenotypic values of 12 morphological traits were measured and genotypic values (BLUP) were calculated. Molecular characterization was performed assaying a total of 15 SSR and 25 SRAP primer combinations. Four Cluster Analysis (phenotypic values, genotypic values, molecular markers and consensus) and four strategies to determine the number of accessions selected (constant, logarithmic, proportional and maximization strategies) were applied to construct 16 core collections. Validation of the core collections were performed through Mean difference percentage (MD), Variance difference percentage (VD), Coincidence rate of range (CR) Variable rate of coefficient of variation (VR), Shannon diversity index (SW) and the Taxonomy coverage (TC). The logarithmic strategy with data on genotypic values was the best strategy, while the least  strategy was the proportional strategy with molecular marker data.

    REFERENCES

    1. Alvarado, G., López, M., Vargas, M., Pacheco, A., Rodríguez, F., Burgueño, J., Crossa, J. (2016) META-R (Multi Environment Trial Analysis whit R for Windows.) Version 6.0 http://hdl.handle.net/11529/10201 International Maize and Wheat Improvement Center.
    2. Balzarini, M., Di Renzo, J. (2003) Info-Gen: Software para análisis estadístico de datos genéticos. Facultad de Ciencias Agropecuarias. Universidad Nacional de Córdoba. Argentina.
    3. Balzarini, M., Bruno, C., Peña, A., Teich, I., Di Renzo, J. (2010) Estadística en Biotecnología. Aplicaciones en Info-Gen. Encuentro Grupo Editor. Córdoba, Argentina.
    4. Diwan, N., McIntosh, M.S., Bauchan, G.R. (1995) Methods of developing a core collection of annual Medicago species. Theor Appl Genet 90:755-761.
    5. Espósito, M.A., Martin, E.A., Cravero, V.P., López Anido, F.S., Cointry, E. (2007) Characterization of pea accessions by SRAP’s markers. Sci Hortic 113:329-335.
    6. Frankel, O.H., Brown, A.H.D. (1984) Plant genetic resources today: a critical appraisal. In: Crop Genetic Resources: Conservation & Evaluation. [Holden JHW, Williams JT (eds)]. George Alien & Unwin Ltd., London, pp 249-257. 
    7. Gower, J.C. (1975) Generalized Procrustes Analysis. Physchometrika 40:33-51.
    8. Hanci, F., Cebeci, E. (2018) Determination of morphological variability of different pisum genotypes using principal component analysis. Legume Res DOI: 10.18805/LR-438. On line: 30/10/2018.
    9. Hu, J.J., Zhu, J., Xu, H.H.M. (2000) Methods of constructing core collections by stepwise clustering with three sampling strategies based on the genotypic values of crops. Theor Appl Genet 101(1-2):264-268.
    10. Hutcheson, K. (1970) A test for comparing diversities based on the Shannon formula. J Theor Biol 29:151-154. https://doi.org/    10.1016/0022-5193(70)90124-4.
    11. Jaggal, L.G., Patil, B.R., Naik, P.M., Priya, K. (2016) Genetic diversity of selected accessions for seed protein among pigeonpea minicore collection. Legume Res 39(5):704-708.
    12. Kim, K.W., Chung, H.K., Cho, G.T., Ma, K.H., Chandrabalan, D., Gwag, J.G., Kim, T.S., Cho, E.G., Park, Y.J. (2007) PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets. Bioinformatics 23(16):2155-62.
    13. Peric, V., Nikoliæ, A.,Babiæ, V., Sudariæ, A.,Srebriæ, M., Ðorðeviæ, V., Mladenoviæ Driniæ, S. (2014) Genetika 46 (3):839-854.
    14. Piepho, H.P., Möhring, J., Melchinger, A.E., Büchse, A. (2008) BLUP for phenotypic selection in plant breeding and variety testing. Euphytica 161:209-228.
    15. Semwal D.P., Ahlawat, S.P., Pradheep, K. (2018) Pigeonpea (Cajanus cajan (L.) Millsp.) and its wild spp. germplasm collection status, diversity distribution and trait-specific germplasm mapping using GIS tools in India. Legume Res 41 (5):656-662.
    16. Shannon, C.E., Weaver, W. (1949) The mathematical theory of communication. The University of Illinois Press, Urbana, 117p.
    17. Smýkal, P., Hýbl, M., Corander, J., Jarkovský, J., Flavell, A., Griga, M. (2008) Genetic diversity and population structure of pea (Pisum sativum L.) varieties derived from combined retrotransposon, microsatellite and morphological marker analysis. Theor Appl Genet 117:413-424.
    18. Snedecor, G.W., Cochran, W.G. (1980) Statistical Methods, 7ed, Iowa State University, Ames: 507 p.
    19. Sokal, R.R., Michener, C.D. (1958) A Statistical Methods for Evaluating Systematic Relationships. University of Kansas Science Bulletin 38:1409-1438.
    20. Van Hintum, T.J.L., Brown, A.H.D., Spillane, C., Hodgkin, T. (2003) Colecciones núcleo de recursos fitogenéticos. Boletín Técnico No. 3del IPGRI. Instituto Internacional de Recursos Fitogenéticos, Roma, Italia. 
    21. Zhang, J., Wang, Y., Zhang, X.Z., Li, T.H., Wang, K., Xu, X.F., Han, Z.H. (2010) Sampling strategy to develop a primary core collection of apple cultivars based on fruit traits. Afr J Biotechnol 9:123-127. 
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