Genomics of long-and short-term adaptation in maize and teosinte

Maize is an excellent model for the study of plant adaptation. Indeed, post domestication maize quickly adapted to a host of new environments across the globe. And work over the last decade has begun to highlight the role of the wild relatives of maize-the teosintes Zea mays ssp. parviglumis and ssp. mexicana-as excellent models for dissecting long-term local adaptation. Although human-driven selection associated with maize domestication has been extensively studied, the genetic bases of natural variation is still poorly understood. Here we review studies on the genetic basis of adaptation and plasticity in maize and its wild relatives. We highlight a range of different processes that contribute to adaptation and discuss evidence from natural, cultivated, and experimental populations. From an applied perspective, understanding the genetic bases of adaptation and the contribution of plasticity will provide us with new tools to both better understand and mitigate the effect of climate changes on natural and cultivated populations. PeerJ Preprints | https://doi.org/10.7287/peerj.preprints.27190v1 | CC BY 4.0 Open Access | re

Les mélanges de variétés ont contribué à l’expansion géographique mondiale d’une espèce cultivée, le maïs

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Whose Needs Does Service Serve? Complicating the Citizen Soldier Narrative

The growth of conscript militaries was integral to the creation of civil rights in European nation-states, which established militaries as a key site of claims-making. However, the United States military has diverged from these models, and most cases of inclusion or integration of social groups are not directly connected with claims-making. What has influenced the U.S. military’s responsiveness to pressures, both internal and external, and how has this changed over time? I employ a comparative historical approach to three cases—African-Americans, women, and non-heterosexuals—to unpack the U.S. military as a state institution and a site of claims-making. By incorporating elements unique to American institutions into existing models of militaries, I find that the U.S. military has become increasingly vulnerable to domestic political, international political, internal economic, and internal and external cultural pressures since the World War period. Despite its enormous economic and physical strength, the U.S. military is more responsive now than ever before to internal and external demands

Transcriptomic response to divergent selection for flowering times reveals convergence and key players of the underlying gene regulatory network

International audienceArtificial selection experiments are designed to investigate phenotypic evolution of complex traits and its genetic basis. Here we focused on flowering time, a trait of key importance for plant adaptation and life-cycle shifts. We undertook divergent selection experiments from two maize inbred lines. After 13 generations of selection, we obtained a time-lag of roughly two weeks between Early-and Late-populations. We used this material to characterize the genome-wide transcriptomic response to selection in the shoot apical meristem before, during and after floral transition in field conditions during two consecutive years. We validated the reliability of performing RNA-sequencing in uncontrolled conditions. We found that roughly half of maize genes were expressed in the shoot apical meristem, 59.3% of which were differentially expressed. We detected a majority of genes with differential expression between inbreds and across meristem status, and retrieved a subset of 2,451 genes involved in the response to selection. Among these, we found a significant enrichment for genes with known function in maize flowering time. Furthermore, they were more often shared between inbreds than expected by chance, suggesting convergence of gene expression. We discuss new insights into the expression pattern of key players of the underlying gene regulatory network including the Zea mays genes CENTRORADIALIS (ZCN8), RELATED TO AP2.7 (RAP2.7), MADS4 (ZMM4), KNOTTED1 (KN1), GIBBERELLIN2-OXIDASE1 (GA2ox1), as well as alternative scenarios for genetic convergence

Standing variation and new mutations both contribute to a fast response to selection for flowering time in maize inbreds

<p>Abstract</p> <p>Background</p> <p>In order to investigate the rate and limits of the response to selection from highly inbred genetic material and evaluate the respective contribution of standing variation and new mutations, we conducted a divergent selection experiment from maize inbred lines in open-field conditions during 7 years. Two maize commercial seed lots considered as inbred lines, <it>F</it>252 and <it>MBS</it>847, constituted two biological replicates of the experiment. In each replicate, we derived an Early and a Late population by selecting and selfing the earliest and the latest individuals, respectively, to produce the next generation.</p> <p>Results</p> <p>All populations, except the Early <it>MBS</it>847, responded to selection despite a short number of generations and a small effective population size. Part of the response can be attributed to standing genetic variation in the initial seed lot. Indeed, we identified one polymorphism initially segregating in the <it>F</it>252 seed lot at a candidate locus for flowering time, which explained 35% of the trait variation within the Late <it>F</it>252 population. However, the model that best explained our data takes into account both residual polymorphism in the initial seed lots and a constant input of heritable genetic variation by new (epi)mutations. Under this model, values of mutational heritability range from 0.013 to 0.025, and stand as an upper bound compare to what is reported in other species.</p> <p>Conclusions</p> <p>Our study reports a long-term divergent selection experiment for a complex trait, flowering time, conducted on maize in open-field conditions. Starting from a highly inbred material, we created within a few generations populations that strikingly differ from the initial seed lot for flowering time while preserving most of the phenotypic characteristics of the initial inbred. Such material is unique for studying the dynamics of the response to selection and its determinants. In addition to the fixation of a standing beneficial mutation associated with a large phenotypic effect, a constant input of genetic variance by new mutations has likely contributed to the response. We discuss our results in the context of the evolution and mutational dynamics of populations characterized by a small effective population size.</p

Genome Size and Transposable Element Content as Determined by High-Throughput Sequencing in Maize and Zea luxurians

The genome of maize (Zea mays ssp. mays) consists mostly of transposable elements (TEs) and varies in size among lines. This variation extends to other species in the genus Zea: although maize and Zea luxurians diverged only ∼140,000 years ago, their genomes differ in size by ∼50%. We used paired-end Illumina sequencing to evaluate the potential contribution of TEs to the genome size difference between these two species. We aligned the reads both to a filtered gene set and to an exemplar database of unique repeats representing 1,514 TE families; ∼85% of reads mapped against TE repeats in both species. The relative contribution of TE families to the B73 genome was highly correlated with previous estimates, suggesting that reliable estimates of TE content can be obtained from short high-throughput sequencing reads, even at low coverage. Because we used paired-end reads, we could assess whether a TE was near a gene by determining if one paired read mapped to a TE and the second read mapped to a gene. Using this method, Class 2 DNA elements were found significantly more often in genic regions than Class 1 RNA elements, but Class 1 elements were found more often near other TEs. Overall, we found that both Class 1 and 2 TE families account for ∼70% of the genome size difference between B73 and luxurians. Interestingly, the relative abundance of TE families was conserved between species (r = 0.97), suggesting genome-wide control of TE content rather than family-specific effects

QTL Mapping Combined With Comparative Analyses Identified Candidate Genes for Reduced Shattering in Setaria italica

Setaria (L.) P. Beauv is a genus of grasses that belongs to the Poaceae (grass) family, subfamily Panicoideae. Two members of the Setaria genus, Setaria italica (foxtail millet) and S. viridis (green foxtail), have been studied extensively over the past few years as model species for C4-photosynthesis and to facilitate genome studies in complex Panicoid bioenergy grasses. We exploited the available genetic and genomic resources for S. italica and its wild progenitor, S. viridis, to study the genetic basis of seed shattering. Reduced shattering is a key trait that underwent positive selection during domestication. Phenotyping of F2:3 and recombinant inbred line (RIL) populations generated from a cross between S. italica accession B100 and S. viridis accession A10 identified the presence of additive main effect quantitative trait loci (QTL) on chromosomes V and IX. As expected, enhanced seed shattering was contributed by the wild S. viridis. Comparative analyses pinpointed Sh1 and qSH1, two shattering genes previously identified in sorghum and rice, as potentially underlying the QTL on Setaria chromosomes IX and V, respectively. The Sh1 allele in S. italica was shown to carry a PIF/Harbinger MITE in exon 2, which gave rise to an alternatively spliced transcript that lacked exon 2. This MITE was universally present in S. italica accessions around the world and absent from the S. viridis germplasm tested, strongly suggesting a single origin of foxtail millet domestication. The qSH1 gene carried two MITEs in the 5′UTR. Presence of one or both MITEs was strongly associated with cultivated germplasm. If the MITE insertion(s) in qSH1 played a role in reducing shattering in S. italica accessions, selection for the variants likely occurred after the domestication of foxtail millet

New Insight into the History of Domesticated Apple: Secondary Contribution of the European Wild Apple to the Genome of Cultivated Varieties

The apple is the most common and culturally important fruit crop of temperate areas. The elucidation of its origin and domestication history is therefore of great interest. The wild Central Asian species Malus sieversii has previously been identified as the main contributor to the genome of the cultivated apple (Malus domestica), on the basis of morphological, molecular, and historical evidence. The possible contribution of other wild species present along the Silk Route running from Asia to Western Europe remains a matter of debate, particularly with respect to the contribution of the European wild apple. We used microsatellite markers and an unprecedented large sampling of five Malus species throughout Eurasia (839 accessions from China to Spain) to show that multiple species have contributed to the genetic makeup of domesticated apples. The wild European crabapple M. sylvestris, in particular, was a major secondary contributor. Bidirectional gene flow between the domesticated apple and the European crabapple resulted in the current M. domestica being genetically more closely related to this species than to its Central Asian progenitor, M. sieversii. We found no evidence of a domestication bottleneck or clonal population structure in apples, despite the use of vegetative propagation by grafting. We show that the evolution of domesticated apples occurred over a long time period and involved more than one wild species. Our results support the view that self-incompatibility, a long lifespan, and cultural practices such as selection from open-pollinated seeds have facilitated introgression from wild relatives and the maintenance of genetic variation during domestication. This combination of processes may account for the diversification of several long-lived perennial crops, yielding domestication patterns different from those observed for annual species

Sélection et coévolution de gènes paralogues impliqués dans la synthèse d'amidon au cours de la radiation des angiospermes et chez le maïs, depuis sa domestication

La duplication permet à un gène d'être présent en plusieurs copies dans un génome (gènes paralogues) et peut, à ce titre, conduire à des innovations génétiques. L ADPglucose pyrophosphorylase (AGPase), composée de deux petites sous-unités (SSU) et de deux grandes sous-unités (LSU), est codée par une famille multigénique chez les angiospermes. Elle catalyse une réaction limitante dans la voie de biosynthèse de l amidon et représente ainsi une cible potentielle de la sélection. L objectif de ma thèse a été d étudier l évolution de cette famille à l échelle de la radiation des Angiospermes d une part, et d autre part à une échelle intra-spécifique depuis la domestication du maïs. A l échelle des Angiospermes, les LSUs présentent des sites qui ont évolué sous sélection positive, certains d entre eux appartenant à des domaines fonctionnels importants (liaison au substrat, domaine d interaction entre sous-unités). Au contraire, les SSUs ont évolué sous forte contrainte sélective et montrent des traces de coévolution. Chez le maïs, l AGPase est majoritairement exprimée au niveau de l albumen (gènes SSUend et LSUend), l embryon (SSUemb et LSUemb) et les feuilles (SSUleaf et LSUleaf). La combinaison de plusieurs statistiques ainsi que la prise en compte de la démographie suggèrent des histoires évolutives contrastées, les paralogues ayant évolué sous sélection directionnelle (LSUleaf, LSUend, LSUemb), balancée (SSUemb) ou diversifiante (SSUleaf). Ces résultats illustrent le rôle important de la redondance génétique dans la réponse à la sélection et l évolution des espèces.Gene duplication allows the emergence of multiple copies of a gene in a genome (paralogs) and can ultimately trigger genetic innovation. The AGPase (ADPglucose pyrophosphorylase) encompasses two small subunits (SSU) and two large subunits (LSU). This enzyme is encoded by a multigenic family in Angiosperms. AGPase catalyses a limiting reaction of the starch synthesis pathway and has therefore been likely targeted by selection. During my PhD I studied the evolution of the AGPase multigenic family at an interspecific, during Angiosperm radiation, and at an intraspecific scale since maize domestication. In Angiosperms, a handful of sites in LSUs exhibited signs of positive selection, some of which belong to functional domains such as the interaction domain between subunits and the substrate-binding domain. In contrast, SSUs have evolved under strong selective constraints without convincing evidence of positive selection. Signs of coevolution however were detected within SSUs. In maize, AGPase is expressed mostly in the endosperm (genes SSUend and LSUend), the embryo (SSUemb and LSUemb) and the leaves (SSUleaf and LSUleaf). Using multiple neutrality statistics and accounting for demography, I have shown that the 6 paralogs have evolved under contrasted selective pressures during or after domestication including positive selection (LSUleaf, LSUend, LSUemb), balancing selection (SSUemb) and diversifying selection (SSUleaf). These results illustrate the importance of genetic redundancy in the response to selection and more generally, in species evolution.ORSAY-PARIS 11-BU Sciences (914712101) / SudocSudocFranceF