Geographic differences in patterns of genetic differentiation among bitter and sweet manioc (Manihot esculenta subsp. esculenta; Euphorbiaceae)

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

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.

Variation in production of cyanogenic glucosides during early plant development: A comparison of wild and domesticated sorghum

Domestication has narrowed the genetic diversity found in crop wild relatives, potentially reducing plasticity to cope with a changing climate. The tissues of domesticated sorghum (Sorghum bicolor), especially in younger plants, are cyanogenic and potentially toxic. Species of wild sorghum produce lower levels of the cyanogenic glucoside (CNglc) dhurrin than S. bicolor at maturity, but it is not known if this is also the case during germination and early growth. CNglcs play multiple roles in primary and specialised metabolism in domesticated sorghum and other crop plants. In this study, the temporal and spatial distribution of dhurrin in wild and domesticated sorghum at different growth stages was monitored in leaf, sheath and root tissues up to 35 days post germination using S. bicolor and the wild species S. brachypodum and S. macrospermum as the experimental systems. Growth parameters were also measured and allocation of plant total nitrogen (N%) to both dhurrin and nitrate (NO₃^-) was calculated. Negligible amounts of dhurrin were produced in the leaves of the two wild species compared to S. bicolor. The morphology of the two wild sorghums also differed from S. bicolor, with the greatest differences observed for the more distantly related S. brachypodum. S. bicolor had the highest leaf N% whilst the wild species had significantly higher root N%. Allocation of nitrogen to dhurrin in aboveground tissue was significantly higher in S. bicolor compared to the wild species but did not differ in the roots across the three species. The differences in plant morphology, dhurrin content and re-mobilisation, and nitrate/nitrogen allocation suggest that domestication has affected the functional roles of dhurrin in sorghum.

Large-scale genome-wide association study, using historical data, identifies conserved genetic architecture of cyanogenic glucoside content in cassava (Manihot esculenta Crantz) root

Manihot esculenta (cassava) is a root crop originating from South America that is a major staple in the tropics, including in marginal environments. This study focused on South American and African germplasm and investigated the genetic architecture of hydrogen cyanide (HCN), a major component of root quality. HCN, representing total cyanogenic glucosides, is a plant defense component against herbivory but is also toxic for human consumption. We genotyped 3354 landraces and modern breeding lines originating from 26 Brazilian states and 1389 individuals were phenotypically characterized across multi-year trials for HCN. All plant material was subjected to high-density genotyping using genotyping by sequencing. We performed genome-wide association mapping to characterize the genetic architecture and gene mapping of HCN. Field experiments revealed strong broad- and narrow-sense trait heritability (0.82 and 0.41, respectively). Two major loci were identified, encoding for an ATPase and a MATE protein, and contributing up to 7 and 30% of the HCN concentration in roots, respectively. We developed diagnostic markers for breeding applications, validated trait architecture consistency in African germplasm and investigated further evidence for the domestication of sweet and bitter cassava. Fine genomic characterization revealed: (i) the major role played by vacuolar transporters in regulating HCN content; (ii) the co-domestication of sweet and bitter cassava major alleles are dependent upon geographical zone; and (iii) the major loci allele for high HCN in M. esculenta Crantz seems to originate from its ancestor, M. esculenta subsp. flabellifolia. Taken together, these findings expand our insights into cyanogenic glucosides in cassava roots and its glycosylated derivatives in plants.

YUCA: PAN Y CARNE, UNA ALTERNATIVA POTENCIAL PARA HACER FRENTE AL HAMBRE OCULTA

Uno de los retos que encara la humanidad es asegurar la alimentación y la adecuada nutrición para los cerca de ocho billones de habitantes del planeta. Las raíces de yuca constituyen la cuarta fuente más importante de calorías para la población humana siendo uno de los pilares de la seguridad alimentaria. Las raíces de yuca no poseen atributos nutricionales adecuados. Aunque existen variedades con valores relativamente altos de estos compuestos, sus valores están lejos de los necesarios para asegurar los requerimientos mínimos de la población humana. Las hojas de yuca poseen valores altos de contenido proteico, minerales y vitaminas, por lo que representan una fuente nutricional alternativa. Sin embargo, el consumo de hojas de yuca en América Latina es escaso o nulo como consecuencia de los altos niveles de cianuro que poseen. En algunos países de África y Asia las hojas se consumen a través de diversas recetas que incluye su cocción, eliminando así una gran cantidad del contenido cianógeno. En esta revisión se presenta un panorama general de la importancia nutricional de la yuca, las diferentes estrategias de mejoramiento genético clásico y no convencional destinados a incrementar los contenidos nutricionales de raíces y la importancia de la explotación de la variabilidad intrínseca de la yuca como una fuente de variedades y genes que puedan contribuir a la implementación de estrategias encaminadas a desarrollar materiales con los requerimientos nutricionales adecuados. Finalmente, se presenta el potencial que tienen las hojas de yuca para ser empleadas dentro de programas complementarios destinados a mejorar la calidad nutricional de la población humana.

Cassava breeding and agronomy in Asia: 50 years of history and future directions

In Asia, cassava (Manihot esculenta) is cultivated by more than 8 million farmers, driving the rural economy of many countries. The International Center for Tropical Agriculture (CIAT), in partnership with national agricultural research institutes (NARIs), instigated breeding and agronomic research in Asia, 1983. The breeding program has successfully released high-yielding cultivars resulting in an average yield increase from 13.0 t ha-1 in 1996 to 21.3 t ha-1 in 2016, with significant economic benefits. Following the success in increasing yields, cassava breeding has turned its focus to higher-value traits, such as waxy cassava, to reach new market niches. More recently, building resistance to invasive pests and diseases has become a top priority due to the emergent threat of cassava mosaic disease (CMD). The agronomic research involves driving profitability with advanced technologies focusing on better agronomic management practices thereby maintaining sustainable production systems. Remote sensing technologies are being tested for trait discovery and large-scale field evaluation of cassava. In summary, cassava breeding in Asia is driven by a combination of food and market demand with technological innovations to increase the productivity. Further, exploration in the potential of data-driven agriculture is needed to empower researchers and producers for sustainable advancement.

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

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.

Conservación de la diversidad de yuca en los sistemas tradicionales de cultivo de la Amazonía

La yuca es determinante para la seguridad alimentaria de cientos de millones de personas alrededor del mundo. A pesar de que el principal medio de propagación del cultivo es a través de semilla asexual por estacas (tallos maduros) se ha revelado una relativamente alta diversidad intraespecífica, principalmente en los sistemas de cultivo de manejo tradicional. En esta revisión se documentan algunos estudios realizados sobre la diversidad de la yuca, tanto por marcadores moleculares como morfológicos, centrándose en aquellos realizados en el Amazonas. También se exponen los principales factores que han determinado el aprovechamiento y conservación de esta diversidad, tales como la aparición espontánea de semillas de origen sexual, el sistema de chagras indígenas, la memoria biocultural y la facilidad de intercambio de semilla entre comunidades. Finalmente, se pone de manifiesto que en los sistemas de manejo tradicional la conservación y uso de la diversidad intraespecífica se constituye en un elemento prioritario que se ha perdido en los sistemas de cultivo a gran escala. En los sistemas de manejo tradicional existe un vínculo etnobotánico que pervive e invita a buscar prácticas alternativas que aseguran un mantenimiento de la diversidad, permitiendo una productividad eficiente e incluso se hace un mejor manejo para disminuir los riesgos de incidencia de algunas plagas y enfermedades.

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

Background and Aims

Amazonia is a major world centre of plant domestication, but little is known about how the crops were dispersed across the region. Manioc (Manihot esculenta) was domesticated in the south-western Amazon basin, and is the most important staple food crop that originated in Amazonia. Current contrasting distributions may reflect distinct histories of dispersal of bitter and sweet manioc landraces. To produce new insights into the evolutionary history of the crop, we investigated the contemporary genetic diversity and structure of bitter and sweet manioc along major Amazonian rivers.

Methods

The patterns of genetic structure and diversity of wild and cultivated sweet and bitter manioc with four chloroplast and 14 nuclear microsatellite markers were evaluated. Results were interpreted in terms of the crop's dispersal.

Key results

No phylogeographic patterns among rivers were detected, and genetic structure among rivers was confounded by the bitter-sweet divergence. However, differences in the distribution of nuclear diversity and somewhat distinctive patterns of genetic structure across rivers were observed within bitter and sweet manioc.

Conclusions

Various pre-Columbian and post-European conquest events in the history of Amazonian occupation may explain the absence of clearer patterns of genetic structure. However, the wide distribution of the most common chloroplast haplotype agrees with an early dispersal of manioc across Brazilian Amazonia. Furthermore, differences in genetic structure and in the spatial distribution of genetic diversity suggest that bitter and sweet manioc had distinct dispersal histories. Knowledge about how prehistoric and contemporary Amazonian peoples manage their crops is valuable for the maintenance and conservation of the impressive diversity of their native crops.

High genetic diversity among and within bitter manioc varieties cultivated in different soil types in Central Amazonia

Although manioc is well adapted to nutrient-poor Oxisols of Amazonia, ethnobotanical observations show that bitter manioc is also frequently cultivated in the highly fertile soils of the floodplains and Amazonian dark earths (ADE) along the middle Madeira River. Because different sets of varieties are grown in each soil type, and there are agronomic similarities between ADE and floodplain varieties, it was hypothesized that varieties grown in ADE and floodplain were more closely related to each other than either is to varieties grown in Oxisols. We tested this hypothesis evaluating the intra-varietal genetic diversity and the genetic relationships among manioc varieties commonly cultivated in Oxisols, ADE and floodplain soils. Genetic results did not agree with ethnobotanical expectation, since the relationships between varieties were variable and most individuals of varieties with the same vernacular name, but grown in ADE and floodplain, were distinct. Although the same vernacular name could not always be associated with genetic similarities, there is still a great amount of variation among the varieties. Many ecological and genetic processes may explain the high genetic diversity and differentiation found for bitter manioc varieties, but all contribute to the maintenance and amplification of genetic diversity within the manioc in Central Amazonia.

Food Aversions and Cravings during Pregnancy on Yasawa Island, Fiji

Women often experience novel food aversions and cravings during pregnancy. These appetite changes have been hypothesized to work alongside cultural strategies as adaptive responses to the challenges posed by pregnancy (e.g., maternal immune suppression). Here, we report a study that assessed whether data from an indigenous population in Fiji are consistent with the predictions of this hypothesis. We found that aversions focus predominantly on foods expected to exacerbate the challenges of pregnancy. Cravings focus on foods that provide calories and micronutrients while posing few threats to mothers and fetuses. We also found that women who experience aversions to specific foods are more likely to crave foods that meet nutritional needs similar to those provided by the aversive foods. These findings are in line with the predictions of the hypothesis. This adds further weight to the argument that appetite changes may function in parallel with cultural mechanisms to solve pregnancy challenges.

Effect of genotype and genotype by environment interaction on total cyanide content, fresh root, and starch yield in farmer-preferred cassava landraces in Tanzania

High starch yield is the most important trait for commercialized cassava starch production. Furthermore, cyanide present in cassava roots poses a health challenge in the use of cassava for food. Cassava genotypes have varying maturity periods that are also environmental dependent. This study aimed at identifying suitable cultivars and optimum time of harvest to maximize starch production across three environments. The study found significant difference between genotypes, locations, harvest period, and all the interactions (P ≤ 0.001) for all traits analyzed. Kiroba recorded high starch yields of 17.4, 12.7, and 8.2 t ha-1 at Chambezi, Amani, and Magadu, respectively. Kilusungu recorded highest cyanide content of 300-400 ppm across all locations but Kiroba recorded highest values of 800 ppm, 15 months after planting at Chambezi. Genotype by environment (GGE) biplot analysis revealed that Kiroba was a superior cultivar in terms of starch yield. Kilusungu recorded highest cyanide content and average starch yield, therefore suitable for use in starch production. The study confirmed effect of genotype and genotype by environment interaction, Kiroba cultivar was superior in terms of starch yield and maximum starch yield was obtained at 9 months after planting. Nyamkagile and Kibandameno had the lowest cyanide content across all environments.