For more than 10,000 years, the selection of plant and animal traits that are better tailored for human use has shaped the development of civilizations. During this period, bread wheat (Triticum aestivum) emerged as one of the world's most important crops. We used exome sequencing of a world-wide panel of almost 500 genotypes selected from across the geographical range of the wheat species complex to explore how 10,000 years of hybridization, selection, adaptation and plant breeding shaped the genetic makeup of modern bread wheats. We observed considerable genetic variations at the genic, chromosomal and subgenomic levels deciphering the likely origins of modern day wheats, the consequences of range expansion and allelic variants selected since its domestication. Our data supports a reconciled model of wheat evolution and provides novel avenues for future breeding improvement.
In this study, the phylogenetic relationships of 164 species of the family Drosophilidae are discussed, using the Amyrel gene, a member of the a-amylase multigene family. This study focuses on numerous species groups in the subgenera Sophophora and Drosophila of the genus Drosophila but also includes other closely related genera. Nucleotide data were analysed by several methods: maximum parsimony, neighbour joining, maximum likelihood and Bayesian inference. Heterogeneity of base composition (mainly low GC contents in the species groups willistoni and saltans) has been addressed. In all analyses, the genus Drosophila appeared paraphyletic. The subgenus Sophophora clearly appeared to be a monophyletic group, showing well-resolved clades, with the Neotropical groups arising in a basal position. Here, it is proposed to raise the species subgroups ananassae and montium to the rank of species group, and to restrict the melanogaster species group to the melanogaster subgroup plus the ÔOrientalÕ subgroups, among which the suzukii subgroup is polyphyletic. Some related genera such as Zaprionus, Liodrosophila, Scaptomyza and Hirtodrosophila are clustered with, or inside the subgenus Drosophila, which is therefore paraphyletic and should be reviewed.
Alpha-amylases are present in all kingdoms of the living world. Despite strong conservation of the tertiary structure, only a few amino acids are conserved in interkingdom comparisons. Animal alpha-amylases are characterized by several typical motifs and biochemical properties. A few cases of such alpha-amylases have been previously reported in some eubacterial species. We screened the bacterial genomes available in the sequence databases for new occurrences of animal-like alpha-amylases. Three novel cases were found, which belong to unrelated bacterial phyla: Chloroflexus aurantiacus, Microbulbifer degradans, and Thermobifida fusca. All the animal-like alpha-amylases in Bacteria probably result from repeated horizontal gene transfer from animals. The M. degradans genome also contains bacterial-type and plant-type alpha-amylases in addition to the animal-type one. Thus, this species exhibits alpha-amylases of animal, plant, and bacterial origins. Moreover, the similarities in the extra C-terminal domains (different from both the alpha-amylase domain C and the starch-binding domain), when present, also suggest interkingdom as well as intragenomic shuffling.
Genomic selection offers several routes for increasing the genetic gain or efficiency of plant breeding programmes. In various species of livestock, there is empirical evidence of increased rates of genetic gain from the use of genomic selection to target different aspects of the breeder’s equation. Accurate predictions of genomic breeding value are central to this, and the design of training sets is in turn central to achieving sufficient levels of accuracy. In summary, small numbers of close relatives and very large numbers of distant relatives are expected to enable predictions with higher accuracy. To quantify the effect of some of the properties of training sets on the accuracy of genomic selection in crops, we performed an extensive field-based winter wheat trial. In summary, this trial involved the construction of 44 F 2:4 bi- and tri-parental populations, from which 2992 lines were grown on four field locations and yield was measured. For each line, genotype data were generated for 25 K segregating SNP markers. The overall heritability of yield was estimated to 0.65, and estimates within individual families ranged between 0.10 and 0.85. Genomic prediction accuracies of yield BLUEs were 0.125–0.127 using two different cross-validation approaches and generally increased with training set size. Using related crosses in training and validation sets generally resulted in higher prediction accuracies than using unrelated crosses. The results of this study emphasise the importance of the training panel design in relation to the genetic material to which the resulting prediction model is to be applied. Electronic supplementary material The online version of this article (10.1007/s00122-019-03327-y) contains supplementary material, which is available to authorized users.
To date, the International Maize and Wheat Improvement Center (CIMMYT) has produced more than 1000 synthetic hexaploid wheats (SHWs), using diverse accessions of the D genome donor species (Aegilops tauschii). Many of these SHWs produced from many different Ae. tauschii have shown resistance or tolerance to various biotic and abiotic stresses, indicating the potential importance of the Ae. tauschii gene pool for breeding purposes. SHWs were backcrossed to CIMMYT improved germplasm to produce synthetic backcross-derived lines (SBLs), which are agronomically similar to the improved parents, but retain the introgressed traits of interest under selection and thereby new diversity. Molecular studies show that SHWs and SBLs are genetically diverse at the DNA level when compared with traditional bread wheat cultivars and preferential transmission of some alleles from the SHW parent has been seen in all genomes, indicating positive selection. Marker analyses of wheat cultivars released over time indicate that SBLs are ideal materials to simultaneously increase yield and diversity for other traits. Following successful diversification of the wheat D genome, CIMMYT has shifted to target improvement of hexaploid wheat via the A and B genomes, focusing on specific traits. Screening the CIMMYT germplasm collection of T. turgidum subsp. dicoccum for Russian wheat aphid resistance and drought tolerance revealed varying levels of phenotypic expression. Promising accessions will be used for the production of new SHWs for future introgressions into elite bread wheat backgrounds.
BackgroundAt the very end of the larval stage Drosophila expectorate a glue secreted by their salivary glands to attach themselves to a substrate while pupariating. The glue is a mixture of apparently unrelated proteins, some of which are highly glycosylated and possess internal repeats. Because species adhere to distinct substrates (i.e. leaves, wood, rotten fruits), glue genes are expected to evolve rapidly.ResultsWe used available genome sequences and PCR-sequencing of regions of interest to investigate the glue genes in 20 Drosophila species. We discovered a new gene in addition to the seven glue genes annotated in D. melanogaster. We also identified a phase 1 intron at a conserved position present in five of the eight glue genes of D. melanogaster, suggesting a common origin for those glue genes. A slightly significant rate of gene turnover was inferred. Both the number of repeats and the repeat sequence were found to diverge rapidly, even between closely related species. We also detected high repeat number variation at the intrapopulation level in D. melanogaster.ConclusionMost conspicuous signs of accelerated evolution are found in the repeat regions of several glue genes.Electronic supplementary materialThe online version of this article (10.1186/s12862-019-1364-9) contains supplementary material, which is available to authorized users.
We have used two paralogous genes (Amyrel and Amy) of the amylase multigene family to reconstruct the phylogeny of the nine Drosophila melanogaster subgroup sister species, including D. santomea, the newly discovered endemic from São Tomé island. The evolutionary divergence of these genes is of special interest as it is suspected to result from physiological evolution via gene duplication. This paper describes the relationship between the geographical origin of the various strains and the patterns of mating and phylogeny, focusing on the evolution of D. santomea and its relationship to other species and their niches. The Amyrel and Amy data indicate that, contrary to expectations, the sympatric insular D. yakuba population is less closely related to D. santomea than allopatric mainland ones, suggesting that the extant insular D. yakuba population on São Tomé results from a recent secondary colonization. Data for sympatric and allopatric D. yakuba suggest that D. santomea arose from a mainland D. yakuba parental stock when montane habitats of the Cameroon volcanic line extended to lower altitudes during colder and less humid periods. Despite their different modes of evolution and different functions, the Amyrel and Amy genes provide remarkably consistent topologies and hence reflect the same history, that of the species.
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