Gene Flow from Wild to Managed Colonies in the Stingless Bee Scaptotrigona Mexicana and an Update on its Mating Frequency

Researchers have hypothesized that wild stingless bee colonies are a repository of genes for managed populations via the mating of managed virgin queens with males from wild colonies. We tested this hypothesis with the stingless bee, Scaptotrigona mexicana, a culturally important species in the study region. Each of ten colonies were split into two colonies and placed in a meliponary, which resulted in ten queen-right mother colonies and ten queenless daughter colonies. We allowed daughter colonies to produce gynes, which then naturally mated with males of unknown origins. Six months later, five third-instar larvae from each colony were genotyped at six microsatellite loci. Four new alleles (12% of 33 alleles) were found in daughter colonies that were not present in any other mother colony. The Fst index showed no overall significant differences between mother and daughter colonies, indicating that they belonged to the same population despite the new alleles. Interestingly, nine queens were estimated to be polyandrous, with an average mating frequency of 1.3, unlike previous reports for this species. These results have implications for the fitness of managed stingless bee colonies and suggest that a better understanding of how gene flow is affected by human management practices would be beneficial.

High molecular weight glutenin gene diversity in Aegilops tauschii demonstrates unique origin of superior wheat quality

Central to the diversity of wheat products was the origin of hexaploid bread wheat, which added the D-genome of Aegilops tauschii to tetraploid wheat giving rise to superior dough properties in leavened breads. The polyploidization, however, imposed a genetic bottleneck, with only limited diversity introduced in the wheat D-subgenome. To understand genetic variants for quality, we sequenced 273 accessions spanning the known diversity of Ae. tauschii. We discovered 45 haplotypes in Glu-D1, a major determinant of quality, relative to the two predominant haplotypes in wheat. The wheat allele 2 + 12 was found in Ae. tauschii Lineage 2, the donor of the wheat D-subgenome. Conversely, the superior quality wheat allele 5 + 10 allele originated in Lineage 3, a recently characterized lineage of Ae. tauschii, showing a unique origin of this important allele. These two wheat alleles were also quite similar relative to the total observed molecular diversity in Ae. tauschii at Glu-D1. Ae. tauschii is thus a reservoir for unique Glu-D1 alleles and provides the genomic resource to begin utilizing new alleles for end-use quality improvement in wheat breeding programs.

Genetic Differentiation for Gene Diversity among Pearl Millet (Pennisetum glaucum (L.) R. Br.) Landraces As Revealed by SSR Markers

Pearl millet (Pennisetum glaucum) is one the most important crops in Burkina Faso. Knowledge of the genetic parameters of different pearl millet landraces grown in Burkina Faso is of great importance for improvement and breeding programs of pearl millet. In this study, 20 pairs of SSR markers were used to compare and analyze the genetic diversity of 86 landrace populations. Results show a total of 67 alleles detected and each locus varies between 2 and 6 with an average of 4 alleles per marker. The probability to having two different alleles per locus was 0.61. The values of genetic diversity parameters of pearl millet populations from the northern region of the country were higher than those from the others regions. The analysis indicates that, over time, alleles are lost and new alleles are added. Analysis of molecular variance showed genetic variation was primarily a function of differences in cultivated populations. Most pairwise FST comparisons between provenances were at a statistically significant level. Our study will provide a scientific basis for the effective management and utilization of germplasm resources of pearl millet populations.

Gene editing in Brassica napus for basic research and trait development

The genome of Brassica napus L. is the result of several polyploidization events that occurred during the history of B. napus. Due to its relatively short domestication history, diversity is relatively limited. An increasing number of loci in this crop’s genome have been gene-edited using various technologies and reagent delivery methods for basic research as well as for trait development. New alleles have been developed as edits in single, 2, 4, or more homologous loci in this important oilseed crop. This comprehensive review will summarize new alleles that have been developed as they relate to weed control, flowering, self-incompatibility, plant hormone biology, disease resistance, grain composition, and pod shatter reduction. These new alleles have significantly augmented our understanding of both plant growth and development for basic research as well as for their potential commercial impacts.

Newly identified parasitic nematode beta-tubulin alleles confer resistance to benzimidazoles

Infections by parasitic nematodes cause large health and economic burdens worldwide. We use anthelmintic drugs to reduce these infections. However, resistance to anthelmintic drugs is extremely common and increasing worldwide. It is essential to understand the mechanisms of resistance to slow its spread. Recently, four new parasitic nematode beta-tubulin alleles have been identified in benzimidazole (BZ) resistant parasite populations: E198I, E198K, E198T, and E198stop. These alleles have not been tested for the ability to confer resistance or for any effects that they might have on organismal fitness. We introduced these four new alleles into the sensitive C. elegans laboratory-adapted N2 strain and exposed these genome-edited strains to both albendazole and fenbendazole. We found that all four alleles conferred resistance to both BZ drugs. Additionally, we tested for fitness consequences in both control and albendazole conditions over seven generations in competitive fitness assays. We found that none of the edited alleles had deleterious effects on fitness in control conditions and that all four alleles conferred strong and equivalent fitness benefits in BZ drug conditions. Because it is unknown if previously validated alleles confer a dominant or recessive BZ resistance phenotype, we tested the phenotypes caused by five of these alleles and found that none of them conferred a dominant BZ resistance phenotype. Accurate measurements of resistance, fitness effects, and dominance caused by the resistance alleles allow for the generation of better models of population dynamics and facilitate control practices that maximize the efficacy of this critical anthelmintic drug class.

Progress and Prospect of Breeding Utilization of Green Revolution Gene SD1 in Rice

Rice (Oryza sativa L.) is one of the most important cereal crops in the world. The identification of sd1 mutants in rice resulted in a semi-dwarf phenotype that was used by breeders to improve yields. Investigations of sd1 mutants initiated the “green revolution” for rice and staved off famine for many people in the 1960s. The smaller plant height conferred by sd1 allele gives the plants lodging resistance even with a high amount of nitrogen fertilizer. Guang-chang-ai-carrying sd1 was the first high-yielding rice variety that capitalized on the semi-dwarf trait, aiming to significantly improve the rice yield in China. IR8, known as the miracle rice, was also bred by using sd1. The green revolution gene sd1 in rice has been used for decades, but was not identified for a long time. The SD1 gene encodes the rice Gibberellin 20 oxidase-2 (GA20ox2). As such, the SD1 gene is instrumental in uncovering the molecular mechanisms underlying gibberellin biosynthesis There are ten different alleles of SD1. These alleles are identified by genome sequencing within several donor lines in breeding for semi-dwarf rice. Apart from breeding applications and the molecular mechanism of GA biosynthesis, the SD1 gene is also involved in the molecular regulation of other important agronomic traits, like nitrogen fertilizer utilization. The dentification of new alleles of SD1 can be obtained by mutagenesis and genome editing. These new alleles will play an important role in improving the resource diversity of semi-dwarf breeding in the future.

Molecular Characterization of German Acinetobacter baumannii Isolates and Multilocus Sequence Typing (MLST) Analysis Based on WGS Reveals Novel STs

Acinetobacter baumannii (A. baumannii) is a major cause of severe nosocomial infections worldwide. The emergence of infections associated with A. baumannii poses a significant health risk in Germany. A. baumannii is part of the ACB complex and is difficult to distinguish from other species phenotypically, necessitating its reliable identification. The current study analyzed 89 A. baumannii strains from human and non-human origins by matrix-assisted laser desorption/ionization (MALDI–TOF) and PCR detection of intrinsic blaOXA-51-like carbapenemase, blaOXA-23-like, blaOXA-24-like, blaOXA-58-like, and ISAba 1 genes. Whole-genome sequencing (WGS) was applied for species confirmation and strain type determination. Combining the molecular detection of the intrinsic blaOXA-51-like carbapenemase gene together with MALDI–TOF with a score value of >2.300 proved to be a suitable tool for A. baumannii identification. WGS data for all of the sequenced strains confirmed the identity of all A. baumannii strains. The Pasteur scheme successfully assigned 79.7% of the strains into distinct STs, while the Oxford scheme succeeded in allocating only 42.7% of isolates. Multilocus sequence typing (MLST) analysis based on the Pasteur scheme identified 16 STs. ST/241 was the most prevalent in samples from non-human origin, whereas ST/2 was predominant in human samples. Furthermore, eight isolates of non-human origin were allocated to seven new STs (ST/1410, ST/1414, ST/1416, ST/1417, ST/1418, ST/1419, and ST/1421). Ten isolates from non-human origin could not be typed since new alleles were observed in the loci Pas_cpn60, Pas_rpoB, and Pas_gltA. MLST analysis based on the Pasteur scheme was more appropriate than the Oxford scheme for the current group of A. baumannii.

A genetic screen for regulators of muscle morphogenesis in Drosophila

The mechanisms that determine the final topology of skeletal muscles remain largely unknown. We have been developing Drosophila body wall musculature as a model to identify and characterize the pathways that control muscle size, shape, and orientation during embryogenesis (Johnson et al., 2013; Williams et al., 2015; Yang et al., 2020a; Yang et al., 2020b). Our working model argues muscle morphogenesis is regulated by (1) extracellular guidance cues that direct muscle cells toward muscle attachment sites, and (2) contact dependent interactions between muscles and tendon cells. While we have identified several pathways that regulate muscle morphogenesis, our understanding is far from complete. Here we report the results of a recent EMS-based forward genetic screen that identified a myriad of loci not previously associated with muscle morphogenesis. We recovered new alleles of known muscle morphogenesis genes, including back seat driver, kon-tiki, thisbe, and tumbleweed, arguing our screen had the depth and precision to uncover myogenic genes. We also identified new alleles of spalt-major, barren, and patched that presumably disrupt independent muscle morphogenesis pathways. Equally as important, our screen shows that at least 11 morphogenetic loci remain to be mapped and characterized. Our screen has developed exciting new tools to study muscle morphogenesis, which may provide future insights into the mechanisms that regulate skeletal muscle topology.

Evaluation of the S-locus in Prunus domestica, characterization, phylogeny and 3D modelling

Self-compatibility has become the primary objective of most prune (Prunus domestica) breeding programs in order to avoid the problems related to the gametophytic self-incompatibility (GSI) system present in this crop. GSI is typically under the control of a specific locus., known as the S-locus., which contains at least two genes. The first gene encodes glycoproteins with RNase activity in the pistils., and the second is an SFB gene expressed in the pollen. There is limited information on genetics of SI/SC in prune and in comparison., with other Prunus species, cloning., sequencing and discovery of different S-alleles is very scarce. Clear information about S-alleles can be used for molecular identification and characterization of the S-haplotypes. We determined the S-alleles of 36 cultivars and selections using primers that revealed 17 new alleles. In addition, our study describes for the first time the association and design of a molecular marker for self-compatibility in P. domestica. Our phylogenetic tree showed that the S-alleles are spread across the phylogeny, suggesting that like previous alleles detected in the Rosaceae., they were of trans-specific origin. We provide for the first time 3D models for the P. domestica SI RNase alleles as well as in other Prunus species, including P. salicina (Japanese plum), P. avium (cherry), P. armeniaca (apricot), P. cerasifera and P. spinosa.