In vitro performance in cotton plants with different genetic backgrounds: the case of Gossypium hirsutum in Mexico, and its implications for germplasm conservation

Multiple domestication events explain the origin of Gossypium hirsutum landraces in Mexico

Several Mesoamerican crops constitute wild-to-domesticated complexes generated by multiple initial domestication events, and continuous gene flow among crop populations and between these populations and their wild relatives. It has been suggested that the domestication of cotton (Gossypium hirsutum) started in the northwest of the Yucatán Peninsula, from where it spread to other regions inside and outside of Mexico. We tested this hypothesis by assembling chloroplast genomes of 23 wild, landraces, and breeding lines (transgene-introgressed and conventional). The phylogenetic analysis showed that the evolutionary history of cotton in Mexico involves multiple events of introgression and genetic divergence. From this, we conclude that Mexican landraces arose from multiple wild populations. Our results also revealed that their structural and functional chloroplast organizations had been preserved. However, genetic diversity decreases as a consequence of domestication, mainly in transgene-introgressed (TI) individuals (π = 0.00020, 0.00001, 0.00016, 0, and 0, of wild, TI-wild, landraces, TI-landraces, and breeding lines, respectively). We identified homologous regions that differentiate wild from domesticated plants and indicate a relationship among the samples. A decrease in genetic diversity associated with transgene introgression in cotton was identified for the first time, and our outcomes are therefore relevant to both biosecurity and agrobiodiversity conservation.

Eco-Geography of Feral Cotton: A Missing Piece in the Puzzle of Gene Flow Dynamics Among Members of Gossypium hirsutum Primary Gene Pool

Mexico is the center of origin and genetic diversity of upland cotton (Gossypium hirsutum L.), the most important source of natural fiber in the world. Currently, wild and domesticated populations (including genetically modified [GM] varieties) occur in this country and gene flow among them has shaped the species’ genetic diversity and structure, setting a complex and challenging scenario for its conservation. Moreover, recent gene flow from GM cultivars to wild Mexican cotton populations has been reported since 2011. In situ conservation of G. hirsutum requires knowledge about the extent of its geographic distribution, both wild and domesticated, as well as the possible routes and mechanisms that contribute to gene flow between the members of the species wild-to-domesticated continuum (i.e., the primary gene pool). However, little is known about the distribution of feral populations that could facilitate gene flow by acting as bridges. In this study, we analyzed the potential distribution of feral cotton based on an ecological niche modeling approach and discussed its implications in the light of the distribution of wild and domesticated cotton. Then, we examined the processes that could be leading to the escape of seeds from the cultivated fields. Our results indicate that the climatic suitability of feral plants in the environmental and geographic space is broad and overlaps with areas of wild cotton habitat and crop fields, suggesting a region that could bridge cultivated cotton and its wild relatives by allowing gene flow between them. This study provides information for management efforts focused on the conservation of wild populations, native landraces, and non-GM domesticated cotton at its center of origin and genetic diversity.

Host genotype explains rhizospheric microbial community composition: the case of wild cotton metapopulations (Gossypium hirsutum L.) in Mexico

The rhizosphere provides several benefits to the plant host being a strong determinant for its health, growth and productivity. Nonetheless, the factors behind the assembly of the microbial communities associated with the rhizosphere such as the role of plant genotypes are not completely understood. In this study, we tested the role that intraspecific genetic variation has in rhizospheric microbial community assemblages, using genetically distinct wild cotton populations as a model of study. We followed a common garden experiment including five wild cotton populations, controlling for plant genotypes, environmental conditions and soil microbial community inoculum, to test for microbial differences associated with genetic variation of the plant hosts. Microbial communities of the treatments were characterized by culture-independent 16S rRNA gene amplicon sequencing with Illumina MiSeq platform. We analyzed microbial community diversity (alpha and beta), and diversity structure of such communities, determined by co-occurrence networks. Results show that different plant genotypes select for different and specific microbial communities from a common inoculum. Although we found common amplicon sequence variants (ASVs) to all plant populations (235), we also found unique ASVs for different populations that could be related to potential functional role of such ASVs in the rhizosphere.

Ongoing ecological and evolutionary consequences by the presence of transgenes in a wild cotton population

After 25 years of genetically modified cotton cultivation in Mexico, gene flow between transgenic individuals and their wild relatives represents an opportunity for analysing the impacts of the presence of novel genes in ecological and evolutionary processes in natural conditions. We show comprehensive empirical evidence on the physiological, metabolic, and ecological effects of transgene introgression in wild cotton, Gossypium hirsutum. We report that the expression of both the cry and cp4-epsps genes in wild cotton under natural conditions altered extrafloral nectar inducibility and thus, its association with different ant species: the dominance of the defensive species Camponotus planatus in Bt plants, the presence of cp4-epsps without defence role of Monomorium ebeninum ants, and of the invasive species Paratrechina longicornis in wild plants without transgenes. Moreover, we found an increase in herbivore damage to cp4-epsps plants. Our results reveal the influence of transgene expression on native ecological interactions. These findings can be useful in the design of risk assessment methodologies for genetically modified organisms and the in situ conservation of G. hirsutum metapopulations.