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Detection of genetic integrity of conserved maize (Zea mays L.) germplasm in genebanks using SNP markers

Abstract

Twenty maize landrace accessions regenerated and conserved in five maize genebanks were investigated for genetic integrity using 1,150 Single Nucleotide Polymorphisms (SNPs) and 235 SNP haplotypes. The genetic diversity of three accessions changed significantly in terms of the average number of alleles per locus. Ten out of twenty accessions had significantly different SNP allelic frequencies, either after regeneration or in the same accession held in different genebanks. The proportion of loci with significant changes in SNP allelic frequency was very low (37/1,150). Changes in the major allelic frequency (MAF) for the majority of SNP loci (60.2–75.2%) were less than 0.05. For SNP haplotypes, the genetic diversity of four accessions changed significantly in terms of average number of haplotype alleles and polymorphic information content (PIC) per locus. The proportion of SNP haplotype alleles lost in the later generations ranged between 0 and 22.6%, and at the same time 0–19.9% of the SNP haplotype alleles appeared in later generations, however, these were absent in the earlier generations. Dynamic changes in genetic integrity, in terms of presence and absence of genes (alleles), by both SNP and SNP haplotype analysis were detected during regeneration. A suboptimum number of ears harvested in one generation can be combined with those from another, repeated regeneration to capture the diversity of the previous generation. Use of molecular markers during regeneration of accessions can help in understanding the extent of genetic integrity of the maize accessions in ex situ genebanks and in recommending the best practice for maintaining the original genetic diversity of the genebank accessions.

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Acknowledgments

The authors would like to thank Ramu Punna, contract editor Debra Eaton Mullan, and CIMMYT editor Mike Listman for their help in improving the manuscript. We acknowledge the full financial support received from The International Rice Research Institute, Philippines (IRRI) in conjunction with The Consultative Group on International Agricultural Research (CGIAR) genebank rehabilitation projects of The World Bank, coordinated by System-wide Genetic Resources Programme (SGRP). We also would like to express our sincere thanks to the cooperators of Latin American maize regeneration projects and International Institute of Tropical Agriculture, Nigeria (IITA) for germplasm introductions at CIMMYT maize genebank.

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Correspondence to Jianbing Yan.

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Wen, W., Taba, S., Shah, T. et al. Detection of genetic integrity of conserved maize (Zea mays L.) germplasm in genebanks using SNP markers. Genet Resour Crop Evol 58, 189–207 (2011). https://doi.org/10.1007/s10722-010-9562-8

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Keywords

  • Conservation
  • Genebank
  • Genetic integrity
  • Maize
  • Regeneration
  • SNP
  • Zea mays