Patterns of nuclear and chloroplast genetic diversity and structure of manioc along major Brazilian Amazonian rivers

Alves‐Pereira, Alessandro; Clement, Charles R.; Rodrigues, Doriane Picanço; Veasey, Elizabeth Ann; Dequigiovanni, Gabriel; Ramos, Santiago Linório Ferreyra; Pinheiro, José Baldin; Zucchi, Maria Imaculada

doi:10.1093/aob/mcx190

Cited by 33 publications

(32 citation statements)

References 77 publications

(110 reference statements)

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“…The absence of manioc starch grains in the 29 Massangana quartz flakes analyzed in this study rules these tools out as manioc grater teeth ( sensu [ 21 ]). This should not come as a surprise, however, since bitter manioc varieties that have a widespread distribution today, and which are grated and soaked to remove cyagenous toxins before consumption, were selected by people much later [ 53 – 55 ]. It was instead the sweet variety, which requires only boiling or roasting to be edible, that was originally domesticated in southwest Amazonia and spread rapidly throughout the neotropics [ 46 , 54 ].…”

Section: Discussionmentioning

confidence: 99%

Direct archaeological evidence for Southwestern Amazonia as an early plant domestication and food production centre

et al. 2018

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Southwestern Amazonia is considered an early centre of plant domestication in the New World, but most of the evidence for this hypothesis comes from genetic data since systematic archaeological fieldwork in the area is recent. This paper provides first-hand archaeobotanical evidence of food production from early and middle Holocene (ca. 9,000–5000 cal. BP) deposits at Teotonio, an open-air site located on a 40 m-high bluff on the south bank of the Madeira river. Such evidence includes the presence of local and exotic domesticates such as manioc (Manihot esculenta), squash (Cucurbita sp.) and beans (Phaseolus sp.), alongside edible fruits such as pequiá (Caryocar sp.) and guava (Psidium sp.) that point to the beginnings of landscape domestication. The results contribute to an ever-growing number of studies that posit southwest Amazonia as an important centre for early crop domestication and experimentation, and which highlight the longue-durée of human impacts on tropical forest biodiversity around the world.

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Section: Discussionmentioning

confidence: 99%

Direct archaeological evidence for Southwestern Amazonia as an early plant domestication and food production centre

et al. 2018

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“…(a) The signs of selection putatively related to the domestication and diversification of the crop. We identified considerable genetic divergence between wild and cultivated manioc, and between bitter and sweet manioc landraces with microsatellite (SSR) markers (Alves‐Pereira et al, ). Therefore, we expect to provide new information about possible signatures of genomic changes resulting from the selection of manioc landraces based on the identification of SNP markers putatively under selection.…”

Section: Introductionmentioning

confidence: 99%

A population genomics appraisal suggests independent dispersals for bitter and sweet manioc in Brazilian Amazonia

Alves‐Pereira

Clement

Rodrigues

et al. 2019

Evolutionary Applications

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Amazonia is a major world centre of plant domestication, but the genetics of domestication remains unclear for most Amazonian crops. Manioc (Manihot esculenta) is the most important staple food crop that originated in this region. Although manioc is relatively well-studied, little is known about the diversification of bitter and sweet landraces and how they were dispersed across Amazonia. We evaluated single nucleotide polymorphisms (SNPs) in wild and cultivated manioc to identify outlier SNPs putatively under selection and to assess the neutral genetic structure of landraces to make inferences about the evolution of the crop in Amazonia. Some outlier SNPs were in putative manioc genes possibly related to plant architecture, transcriptional regulation and responses to stress. The neutral SNPs revealed contrasting genetic structuring for bitter and sweet landraces. The outlier SNPs may be signatures of the genomic changes resulting from domestication, while the neutral genetic structure suggests independent dispersals for sweet and bitter manioc, possibly related to the earlier domestication and diversification of the former. Our results highlight the role of ancient peoples and current smallholders in the management and conservation of manioc genetic diversity, including putative genes and specific genetic resources with adaptive potential in the context of climate change.

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“…Therefore, it has a highly conserved tetrad structure, with a large single-copy (LSC) region, a small single-copy (SSC) region, and two inverse repeats (IRs) regions. As conserved matrilineal genetic information, chloroplasts play a part in cytoplasmic male sterility (CMS) [ 12 ], genetic diversity in populations [ 13 , 14 , 15 ], and especially, phylogenetic analysis [ 16 , 17 ]. In addition, the comparison of chloroplast sequences has been successfully used to study the evolution [ 18 ] and athentication markers to molecular identification at genus levels [ 19 ].…”

Section: Introductionmentioning

confidence: 99%

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Aster tataricus

et al. 2018

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We sequenced and analyzed the complete chloroplast genome of Aster tataricus (family Asteraceae), a Chinese herb used medicinally to relieve coughs and reduce sputum. The A. tataricus chloroplast genome was 152,992 bp in size, and harbored a pair of inverted repeat regions (IRa and IRb, each 24,850 bp) divided into a large single-copy (LSC, 84,698 bp) and a small single-copy (SSC, 18,250 bp) region. Our annotation revealed that the A. tataricus chloroplast genome contained 115 genes, including 81 protein-coding genes, 4 ribosomal RNA genes, and 30 transfer RNA genes. In addition, 70 simple sequence repeats (SSRs) were detected in the A. tataricus chloroplast genome, including mononucleotides (36), dinucleotides (1), trinucleotides (23), tetranucleotides (1), pentanucleotides (8), and hexanucleotides (1). Comparative chloroplast genome analysis of three Aster species indicated that a higher similarity was preserved in the IR regions than in the LSC and SSC regions, and that the differences in the degree of preservation were slighter between A. tataricus and A. altaicus than between A. tataricus and A. spathulifolius. Phylogenetic analysis revealed that A. tataricus was more closely related to A. altaicus than to A. spathulifolius. Our findings offer valuable information for future research on Aster species identification and selective breeding.

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Patterns of nuclear and chloroplast genetic diversity and structure of manioc along major Brazilian Amazonian rivers

Cited by 33 publications

References 77 publications

Direct archaeological evidence for Southwestern Amazonia as an early plant domestication and food production centre

Direct archaeological evidence for Southwestern Amazonia as an early plant domestication and food production centre

A population genomics appraisal suggests independent dispersals for bitter and sweet manioc in Brazilian Amazonia

Complete Chloroplast Genome Sequence and Phylogenetic Analysis of Aster tataricus

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