Genetic diversity and structure of Benin pineapple (Ananas comosus (L) Merr.) germplasm collection using Simple Sequence Repeat (SSR) markers.

Document Type : Original research paper

Authors
Charlotte Adje 1
Antoine Abel Missihoun 2
Paulin Sedah 2
Hubert Adoukonou Sagbadja 2
Enoch Achigan Dako 1
Clément Agbangla 2
1 Faculty of Agronomic Sciences (FSA), University of Abomey-Calavi, Cotonou, Republic of Benin
2 Faculty of Sciences and Techniques (FAST), University of Abomey-Calavi, Cotonou, Republic of Benin
10.22058/jpmb.2024.2024521.1297
Abstract
Pineapple stands as a cornerstone among Benin's vital fruit crops, playing a pivotal role in enhancing both household food security and income. This delectable fruit is prominently featured among the key crops advocated for cultivation within the country. Despite the critical role this crop plays, our understanding of the diversity within genetic resources is remains limited. This study aimed to assess genetic variation and infer the population structure of 57 pineapple accessions collected from Benin's national core collection, using 10 simple sequences repeat (SSR) markers. The result showed a total of 23 alleles, ranging from 2 to 4, with a mean of 2.3 alleles per locus. The polymorphic information content was 0.34 whereas the mean expected heterozygosity was 0.43. The UPGMA dendrogram revealed two main clusters. The collection was determined to exhibit a structured composition comprising two distinct groups based on genetic analysis. This grouping was further validated by AMOVA, affirming its existence. Our work offers valuable insights into the genetic diversity within Beninese pineapple germplasm, thereby guiding strategic conservation efforts. Moreover, these findings open avenues for leveraging the genetic variation present in Benin’s pineapple germplasm for future pineapple breeding programs, thereby enhancing pineapple cultivation and resilience.
Keywords
Ananas comosus
SSR
structure
germplasm
Benin
Subjects
Adjé, C., Achigan-Dako, E., and Agbangla, C. (2016). Optimizing genomic DNA isolation in pineapple (Ananas comosus L.) J Plant Breed Genet 4: 11-18.
Adje, C., Achigan-Dako, E., d’Eeckenbrugge, G., Hounnankpon, Y., and Agbangla, C. (2019). Morphological characterization of pineapple (Ananas comosus) genetic resources from Benin. Fruits 74(4): 167-179.
Ali, M., Rajewski, J., Baenziger, P., Gill, K., Eskridge, K., and Dweikat, I. (2008). Assessment of genetic diversity and relationship among a collection of US sweet sorghum germplasm by SSR markers. Mol Breed 21(4): 497-509.
Baafi, E., Osei, M.K., Agyeman, A., and Afriyie, J. (2015). Diversity studies on sugarloaf pineapple variety. Int J Sci Knowl 4(1): 14-25.
Bartholomew, D.P., and Sinclair, E. (1993). "Key to pest and disorders," in Pineapple pests and disorders, eds. R.H. Broadley, R.C.I. Wassman & E. Sinclair.  (Brisbane: Department of Primary Industries), 1-7.
Brat, P., Hoang, L.N., Soler, A., Reynes, M., and Brillouet, J.M. (2004). Physicochemical characterization of a new pineapple hybrid (FLHORAN41 Cv.). J Agric Food Chem 52(20): 6170-6177. doi: 10.1021/jf0492621.
Collins, J.L. (1960). The Pineapple: Botany, Cultivation and Utilization. New York: Interscience Publishers Inc.
Coppens d'Eeckenbrugge, G., Leal, F., and Duval, M.-F. (1997). "Germplasm resources of pineapple," in Horticultural Reviews, ed. J. Janick.  (New York: John Wiley & Sons, Inc.), 133-175.
DDAEP, ATL, and 7, A. (2021). Production d’ananas par commune campagne 2014-2015, 2020-2021. Rapports d'activités.
Duval, M.F., Coppens d'Eeckenbrugge, G., Ferreira, R.F., Cabral, J.R.S., and Bianchetti, B. (1997). First results from joint EMBRAPA-CIRAD Ananas germplasm collecting in Brazil and French Guyana. Acta Hort 425: 137-144.
Fassinou Hotegni, V., Lommen, W., Agbossou, E., and Struik, P. (2015). Selective plants pruning as a means to reduce heterogeneity in pineapple fruit quality. SpringerPlus 4(129 ): Doi 10.1186/s40064-40015-40907-40069.
Fassinou Hotegni, V., Lommen, W.J.M., Vorst, J.G.A.J.v.d., Agbossou, E.K., and Struik, P.C. (2012). Analysis of pineapple production systems in Benin. Acta Hortic 928: 47-58.
Feng, S., Tong, H., Chen, Y., Wang, J., Chen, Y., Sun, G., He, J., and Wu, Y. (2013). Development of pineapple microsatellite markers and germplasm genetic diversity analysis. Biomed Res Int 2013: 317912. doi: 10.1155/2013/317912.
Gioia, T., Logozzo, G., Marzario, S., Spagnoletti Zeuli, P., and Gepts, P.J.P.O. (2019). Evolution of SSR diversity from wild types to US advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris). PLoS One 14(1): e0211342.
Hossain, M.F., Akhtar, S., and Anwar, M. (2015). Nutritional value and medicinal benefits of pineapple. Int J Food Sci Nutr 4(1): 84-88.
Ismail, S.N., Ghani, N.S.A., Ab Razak, S.F., Abidin, R.A.Z., Mohd Yusof, M.F., Zubir, M.N., and Zainol, R. (2020). Genetic Diversity of Pineapple (Ananas comosus) Germplasm in Malaysia Using Simple Sequence Repeat (SSR) Markers. Trop Life Sci Res 31(3): 15-27. doi: 10.21315/tlsr2020.31.3.2.
Kato, C.Y., Nagai, C., Moore, P.H., Zee, F., Kim, M.S., Steiger, D.L., and Ming, R. (2004). Intra-specific DNA polymorphism in pineapple (Ananas comosus (L.) Merr.) assessed by AFLP markers. Genet Resour Crop Evol 51(8): 815-825.
Kinsuat, M., and Kumar, V. (2007). Polymorphic microsatellite and cryptic simple repeat sequence markers in pineapples (Ananas comosus var. comosus). Mol Ecol Notes 7: 1032–1035.
Leal, F., and Antoni, M.G. (1981). Description and key to the pineapple varieties in Venezuela. Rev Facultad Agron, Univ Venezuela 51-79.
Liu, K. (2005). PowerMarker: new genetic data analysis software. Version 3.0. http://www.powermarker.net.
Malézieux, E., Cote, F., and Bartholomew, D.P. (2003). "Crop environment, and vegetative physiology and growth " in The Pineapple: Botany, Production and Uses, eds. D.P. Bartholomew, R. Paull & K.G. Rohrbach.  (Wallingford: CABI Publishing), 69-107.
Mallor, C., Arnedo-Andrés, M., and Garcés-Claver, A. (2014). Assessing the genetic diversity of Spanish Allium cepa landraces for onion breeding using microsatellite markers. Sci Hortic 170: 24-31.
Missihoun, A., Adoukonou-Sagbadja, H., Sedah, P., Agbangla, C., Ahanhanzo, C., and Dagba, R.A. (2015). Genetic diversity of Sorghum bicolor (L.) Moench landraces from Northwestern Benin as revealed by microsatellite markers. Afr J Biotechnol 14(16): 1342-1353.
Noyer, J.L., and Lanaud, C. (1997). RFLP analysis of rDNA variability in Ananas genus. Acta Hortic 425: 153-160.
Peakall, R., and Smouse, P.E. (2006). GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6(1): 288-295.
Py, C., Lacoeuilhe, J.J., and Teisson, C. (1987). The pineapple, cultivation and uses. Paris: Editions G.-P. Maisonneuve.
Rakshit, S., Gomashe, S., Ganapathy, K., Elangovan, M., Ratnavathi, C., Seetharama, N., and Patil, J. (2012). Morphological and molecular diversity reveal wide variability among sorghum Maldandi landraces from India. Plant Biotechnol J 21: 145-156
Rodrígueza, D., Grajal-Martín, M.J., Isidrón, M., Petit, S., and Hormaza, J.I. (2013). Polymorphic microsatellite markers in pineapple (Ananas comosus (L.) Merrill). Sci Hortic 156: 127-130. doi: 10.1016/j.scienta.2013.03.026.
Salehi, M., A. , Arzani, M.T., and A., R. (2018). Genetic diversity of wheat wild relatives using SSR markers. Genetika 50: 131-141.
Samouelian, F., Gaudin, V., and Boccara, M. (2009). Génétique moléculaire des plantes. Editions Quae.
Shahbandeh, M. (2022). Global pineapple production by leading countries 2020. Agriculture Farming https://www.statista.com/statistics/298517: October, 04 2022.
Sharma, P., Mehta, G., Shefali, Muthusamy, S.K., Singh, S.K., and Singh, G.P. (2021). Development and validation of heat-responsive candidate gene and miRNA gene based SSR markers to analysis genetic diversity in wheat for heat tolerance breeding. Mol Biol Rep 48(1): 381-393. doi: 10.1007/s11033-020-06059-1.
Shoda, M., Urasaki, N., Sakiyama, S., Terakami, S., Hosaka, F., Shigeta, N., Nishitani, C., and Yamamoto, T. (2012). DNA profiling of pineapple cultivars in Japan discriminated by SSR markers. Breed Sci 62(4): 352-359. doi: 10.1270/jsbbs.62.352.
Tossou, C.C., Capo-Chichi, D.B.E., and Yedomonhan, H. (2015). Diversity and morphological characterization varieties of pineapple (Ananas comosus (L.) Merrill ) grown in Benin. J Appl Biosci 87: 8113-8120.
Van Oosterhout, C., Hutchinson, W., Wills, D., and Shipley, P. (2004). MICRO-CHECKER: software for identifying and correcting genotyping errors in microsatellite data. Mol Ecol Notes 4: 535 - 538.
Zhang, J., Liu, J., and Ming, R. (2014). Genomic analyses of the CAM plant pineapple. J Exp Bot 65(13): 3395-3404. doi: 10.1093/jxb/eru101.
Zhao, H., and Qin, Y. (2018). "Genetic Diversity of Pineapple," in Genetics and Genomics of Pineapple. Springer), 51-59.
 
Journal of Plant Molecular Breeding
Volume 11, Issue 2
December 2023
Pages 94-106

  • Receive Date 09 March 2024
  • Revise Date 06 April 2024
  • Accept Date 01 April 2024
  • First Publish Date 01 April 2024