Selective signatures and high genome-wide diversity in traditional Brazilian manioc (Manihot esculenta Crantz) varieties

Alessandro Alves-Pereira,José Baldin Pinheiro,Charles R Clement,João Paulo Gomes Viana,Anete Pereira De Souza,Maria Imaculada Zucchi,Elizabeth Ann Veasey

doi:10.1038/s41598-022-05160-8

Abstract

Knowledge about genetic diversity is essential to promote effective use and conservation of crops, because it enables farmers to adapt their crops to specific needs and is the raw material for breeding. Manioc (Manihot esculenta ssp. esculenta) is one of the world’s major food crops and has the potential to help achieve food security in the context of on-going climate changes. We evaluated single nucleotide polymorphisms in traditional Brazilian manioc varieties conserved in the gene bank of the Luiz de Queiroz College of Agriculture, University of São Paulo. We assessed genome-wide diversity and identified selective signatures contrasting varieties from different biomes with samples of manioc’s wild ancestor M. esculenta ssp. flabellifolia. We identified signatures of selection putatively associated with resistance genes, plant development and response to abiotic stresses that might have been important for the crop’s domestication and diversification resulting from cultivation in different environments. Additionally, high neutral genetic diversity within groups of varieties from different biomes and low genetic divergence among biomes reflect the complexity of manioc’s evolutionary dynamics under traditional cultivation. Our results exemplify how smallholder practices contribute to conserve manioc’s genetic resources, maintaining variation of potential adaptive significance and high levels of neutral genetic diversity.

Highlights

Food security—the regular access to enough high-quality food with sufficient protein and energy—is one of the major goals of the United Nations’ 2030 Agenda for Sustainable Development to promote a fairer w orld[1]
There are many methods for the detection of selective signatures based on the significant deviation of outlier markers from the distribution of a given statistic measured under a specific m odel[53]
The reduction of genetic diversity associated with domestication bottlenecks, or resulting from multiple founding effects during crops’ d ispersals[59,60], might have affected plant defense and resistance m echanisms[61]

Summary

Introduction

Food security—the regular access to enough high-quality food with sufficient protein and energy—is one of the major goals of the United Nations’ 2030 Agenda for Sustainable Development to promote a fairer w orld[1] It is, an enormous challenge due to the accelerated increase in the world’s human population and on-going global climate c hanges[2,3]. The crop has an immense diversity of varieties which are cultivated around the Tropics, mainly by low-income smallholder farmers[13,14], and it is considered one of the most promising crops to promote food security in developing c ountries[14] This is because manioc is well-adapted to marginal areas with poor soils and can be produced efficiently even on small scales, with low inputs and without mechanization[14]. Sweet and bitter manioc cannot be separated by morphological traits, they are genetically divergent and farmers’ traditional knowledge categorize them clearly[13]

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Conclusion