Genomic Diversity of Three Brazilian Native Food Crops Based on Double-Digest Restriction Site-Associated DNA Sequencing

Abstract

The megabiodiversity of Brazil created opportunities for the domestication of a number of crop species, including some of major global importance. Considering the economic value of many Brazilian native crops, the genetic characterization of their populations is fundamental to support the utilization and conservation of their genetic resources, currently threatened by deforestation and the intensification of monuculture of exotic crops. Recent advances in DNA sequencing technologies have promoted the rapid genomic evaluation of non-model species, including those of only local importance. In this context, we evaluated the genomic diversity of three native Brazilian crops: manioc (Manihot esculenta), annatto (Bixa orellana) and the juçara palm (Euterpe edulis). Double-digest restriction site-associated DNA sequencing (ddRAD) was employed to identify thousands of SNP markers in each crop species (1952 in manioc, 3362 in annatto and 1040 in juçara). Population genomic analyses identified many loci putatively under selection, but the unavailability of genome sequences for annatto and juçara hampers further characterization for these crops. Nonetheless, the SNP markers identified were effective in the characterization of the genomic diversity and population structure. The levels of genomic diversity and inbreeding were compatible with the biology of each species. While wild and cultivated manioc were remarkably genetically divergent, the same was not observed between accessions of wild and cultivated annatto, and genetic differentiation was observed among juçara samples from different environments. The application of population genomic approaches may be valuable for the establishment of better practices of management of these crops, promoting the conservation and valorization of Brazilian native genetic resources.

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Data Availability

The ddRAD sequences generated and analyzed during the current study will be available after publication as FASTQ files (.fq.gz) in the Sequence Read Archive (SRA) repository of the National Center for Biotechnology Information (NCBI), accession PRJNA493823 (https://www.ncbi.nlm.nih.gov/sra/PRJNA493823).

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Acknowledgments

This study was funded by Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES – BioComputacional 051/2013), and Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP – 2012/08307-5, 2013/00003-0). AA-P thanks CAPES and FAPESP (2018/00036-9) for post-doctoral scholarships. MN (2013/17354-0) and GD (2013/08884-5) thank FAPESP for doctoral scholarships. MIZ, JBP, CRC, PHSB and APS thank the National Council for Scientific and Technological Development (CNPq) for research fellowships and a post-doctoral scholarship (grant # 150297/2018-1) of GD. The authors thank Danilo Augusto Sforça and Aline C.L. Moraes for laboratory assistance.

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AA-P, MN, GD, APS and MIZ designed the research. AA-P, MN, GD, PHSB, EAV, and CRC performed sample collections. AA-P, MN and GD prepared the ddRAD genomic libraries. AA-P, MN, GD, JBP, EAV, PHSB, CRC and MIZ performed analyses and discussed results. All coauthors prepared the manuscript.

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Correspondence to Maria Imaculada Zucchi.

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Alves-Pereira, A., Novello, M., Dequigiovanni, G. et al. Genomic Diversity of Three Brazilian Native Food Crops Based on Double-Digest Restriction Site-Associated DNA Sequencing. Tropical Plant Biol. 12, 268–281 (2019). https://doi.org/10.1007/s12042-019-09229-z

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Keywords

  • Bixa orellana
  • Euterpe edulis
  • Manihot esculenta
  • Population genomics
  • SNP