Hidden Rice Diversity in the Guianas

Abstract

Traditional crop varieties are an important source of genetic diversity for crop adaptation and modern breeding. Landraces of Asian (Oryza sativa) and African (Oryza glaberrima) rice have been well studied on the continents where they were domesticated. However, their history of cultivation in northern South America is poorly understood. Here, we reveal the rice diversity that is maintained by Maroons, descendants of enslaved Africans who fled to the interior forests of the Guianas ca. 300 years ago. We interviewed subsistence farmers who practice shifting cultivation along the Maroni and Lawa rivers that form the natural border between French Guiana and Suriname, and used ethnobotanical and morphological methods to identify around 50 varieties, of which 15 were previously undocumented. The genetic origin of these varieties was explored using the Angiosperms353 universal probe set. Despite the large distances between sites and relative inaccessibility of the area, phenotypic and genetic diversity did not display any geographic structure, which is consistent with knowledge of seed exchange among members of the same ethnolinguistic group. Although improved US cultivars were introduced in Maroon villages in the 1940s, these have not displaced the traditional landraces, which are cherished for their taste and nutritious qualities and for their importance in Maroon spiritual life. The unique agricultural and ritual practices of Maroons confirm their role as custodians of rice diversity, a role that is currently under threat from external pressures and encroaching globalization. We expect that the rice diversity uncovered in this study represents only a fraction of the total diversity in the Guianas and may constitute a large untapped resource that holds promise for future rice improvement. Further efforts to inventory and preserve these landraces will help to protect a precious cultural heritage and local food security.

Reconstructing the Complex Evolutionary History of the Papuasian Schefflera Radiation Through Herbariomics

“…Whereas Kadlec et al (2017) argued that high sequence variability across angiosperm orders precluded the usefulness of universal probes in resolving species-level relationships, Chau et al (2018) found that general purpose probes can be as effective as taxon-specific ones. While we do not compare these alternative probes, the results from our study, Larridon et al (2020) and Murphy et al (2020) suggest that an appropriately designed universal probe set can capture adequate phylogenomic information to resolve relationships at the species-level and even at the population-level (Van Andel et al, 2019). Liu et al (2019) showed experimentally that when probes are <30% divergent from regions targeted, enrichment worked adequately (see Figure 6 and Supplementary Figure S6 in Liu et al, 2019).…”

“…To overcome this design and optimization hurdle, the Angiosperms-353 probe set was developed from available transcriptome and genome data (One Thousand Plant Transcriptomes Initiative, 2019)including twelve Apiales representatives, three of them (Hedera, Hydrocotyle, and Polyscias) in Araliaceae -with universal probes that capture 353 nuclear single-copy loci shared across all angiosperms (Johnson et al, 2018). By using the Angiosperms-353 sequence capture probes, our study is among the first to test the efficacy of this probe set to resolve species-level relationships from either historical herbarium specimens (Brewer et al, 2019;Larridon et al, 2020;Murphy et al, 2020) or fresh tissue (Van Andel et al, 2019).…”

Relative performance of customized and universal probe sets in target enrichment: A case study in subtribe Malinae

“…The Angiosperms353 markers seem to resolve the phylogenies of rapidly radiating groups well (Larridon et al, 2020;Shee et al, 2020) and show potential for resolving from deep (Johnson et al, 2019) to shallow phylogenetic scales, even resolving within-species relationships (Van Andel et al, 2019;Murphy et al, 2020), but their utility has not yet been fully evaluated. To date, only one study has compared the benefits of Angiosperms353 with those of a custom probe set (Larridon et al, 2020).…”

Lineage‐specific vs. universal: A comparison of the Compositae1061 and Angiosperms353 enrichment panels in the sunflower family

“…Johnson et al (2019) showed an average recovery of ~283 loci per species for the Angiosperms353 probe set, and at least 100 loci for over 600 angiosperm species, but this can be increased further using the pipeline recently described by McLay et al (2021). It has been successfully implemented with low-quality material such as herbarium specimens (Brewer et al, 2019;Shee et al, 2020) and performed well for resolving shallow-level relationships (e.g., radiations [Larridon et al, 2020;Shee et al, 2020] and even at the intraspecific level [Van Andel et al, 2020;Beck et al, 2021;Slimp et al, 2021]). A few studies have compared the performance of Angiosperms353 with other taxon-specific probe sets (e.g., in Cyperus L. [Larridon et al, 2020], in the subtribe Malinae of the Rosaceae [Ufimov et al, 2021], and in the Ochnaceae [Shah et al, 2021]), but only Larridon et al (2020) directly tested the mergeability of different data sets.…”