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.

中文翻译：

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基于双消化限制性位点相关的DNA测序的三种巴西本土粮食作物的基因组多样性。

巴西的巨大生物多样性为许多作物物种的驯化创造了机会，其中包括一些在全球具有重要意义的物种。考虑到许多巴西本土农作物的经济价值，其种群的遗传特征对于支持其遗传资源的利用和保存至关重要，因为目前遗传资源正受到森林砍伐和外来农作物的加强栽培的威胁。DNA测序技术的最新进展促进了对非模型物种（包括仅具有局部重要性的物种）的快速基因组评估。在这种情况下，我们评估了三种巴西本土农作物的基因组多样性：木薯（Manihot esculenta），安纳托（Banna（Bixa orellana））和棕榈（juçara）（紫丁香（Euterpe edulis）。采用双消化酶切位点相关的DNA测序（ddRAD）来鉴定每种作物中的数千个SNP标记（木薯中的1952个，安纳托中的3362个和juçara中的1040个）。人口基因组分析确定了许多可能处于选择状态的基因座，但没有用于annatto和juçara的基因组序列阻碍了这些作物的进一步表征。尽管如此，所鉴定的SNP标记在表征基因组多样性和种群结构方面是有效的。基因组多样性和近交的水平与每个物种的生物学相容。尽管野生和栽培木薯的遗传差异显着，但野生和栽培安纳托的种质之间未观察到相同，并且在来自不同环境的juçara样品之间观察到遗传分化。种群基因组学方法的应用对于建立更好的管理这些作物的实践，促进巴西本土遗传资源的保护和增值可能是有价值的。