Construction and Genetic Analysis of a Worldwide Core Collection of Rapeseed

Rapeseed (Brassica napus) is an important oilseed crop, which is widely planted in the world. In a previous study, we collected 991 accessions of rapeseed from the worldwide germplasm and revealed genetic polymorphisms within these germplasm by whole-genome resequencing. However, management of such a large amount of accessions is time-consuming, laborious and costly. Therefore, we constructed a core collection of rapeseed consisting of 300 worldwide accessions based on their genetic diversity. Compared with 991 accessions, the worldwide core collection showed similar geographic distribution, the proportion of three ecotypes, nucleotide diversity and the associated SNPs of flowering time. Besides, we identified FT ortholog (BnaA02g12130D) and FLC ortholog (BnaA10g22080D) responsible for flowering time and ecotype differentiation through selective sweep analysis and genome-wide association analysis (GWAS) of flowering time using the rapeseed core collection. FT and FLC are two well-known genes regulating flowering time in Arabidopsis. These results indicate that the worldwide core collection can represent the genetic diversity of 991 worldwide accessions, which could be more efficiently used for phenotypic and genetic studies in rapeseed.

Resprouters Versus Reseeders: Are Wild Rooibos Ecotypes Genetically Distinct?

Aspalathus linearis (Burm. F.) R. Dahlgren (Fabaceae) or rooibos, is a strict endemic species, limited to areas of the Cederberg (Western Cape) and the southern Bokkeveld plateau (Northern Cape) in the greater Cape Floristic Region (CFR) of South Africa. Wild rooibos, unlike the cultivated type, is variable in morphology, biochemistry, ecology and genetics, and these ecotypes are broadly distinguished into two main groups, namely, reseeders and resprouters, based on their fire-survival strategy. No previous assessment of genetic diversity or population structure using microsatellite markers has been conducted in A. linearis. This study aimed to test the hypothesis that wild rooibos ecotypes are distinct in genetic variability and that the ecotypes found in the Northern Cape are differentiated from those in the Cederberg that may be linked to a fire-survival strategy as well as distinct morphological and phytochemical differences. A phylogeographical and population genetic analyses of both chloroplast (trnLF intergenic region) and newly developed species-specific nuclear markers (microsatellites) was performed on six geographically representative wild rooibos populations. From the diversity indices, it was evident that the wild rooibos populations have low-to-moderate genetic diversity (He: 0.618–0.723; Ho: 0.528–0.704). The Jamaka population (Cederberg, Western Cape) had the lowest haplotype diversity (H = 0.286), and the lowest nucleotide diversity (π = 0.006) even though the data revealed large variations in haplotype diversity (h = 0.286–0.900) and nucleotide diversity (π = 0.006–0.025) between populations and amongst regions where wild rooibos populations are found. Our data suggests that populations of rooibos become less diverse from the Melkkraal population (Suid Bokkeveld, Northern Cape) down towards the Cederberg (Western Cape) populations, possibly indicative of clinal variation. The largest genetic differentiation was between Heuningvlei (Cederberg, Western Cape) and Jamaka (FST = 0.101) localities within the Cederberg mountainous region, and, Blomfontein (Northern Cape) and Jamaka (Cederberg) (FST = 0.101). There was also a significant isolation by distance (R2 = 0.296, p = 0.044). The presence of three main clusters is also clearly reflected in the discriminant analysis of principal components (DAPC) based on the microsatellite marker analyses. The correct and appropriate management of wild genetic resources of the species is urgently needed, considering that the wild Cederberg populations are genetically distinct from the wild Northern Cape plants and are delineated in accordance with ecological functional traits of reseeding or resprouting, respectively. The haplotype divergence of the ecotypes has also provided insights into the genetic history of these populations and highlighted the need for the establishment of appropriate conservation strategies for the protection of wild ecotypes.

Genetic diversity in the IZUMO1-JUNO protein-receptor pair involved in human reproduction

Fertilization in mammals begins with the union of egg and sperm, an event that starts a cascade of cellular processes. The molecular-level understanding of these processes can guide the development of new strategies for controlling and/or promoting fertilization, and inform researchers and medical professional on the best choice of interventions. The proteins encoded by the IZUMO1 and JUNO genes form a ligand-receptor protein pair involved in the recognition of sperm and egg. Due to their role in the fertilization process, these proteins are potential targets for the development of novel anti-contraceptive, as well as infertility treatments. Here we present a comprehensive analysis of these gene sequences, with the objective of identifying evolutionary patterns that may support their relevance as targets for preventing or improving fertility among humans. JUNO and IZUMO1 gene sequences were identified within the genomes of over 2,000 humans sequenced in the 1000 Genomes Project. The human sequences were subjected to analyses of nucleotide diversity, deviation from neutrality of genetic variation, population-based differentiation (FST), haplotype inference, and whole chromosome scanning for signals of positive or of balancing selection. Derived alleles were determined by comparison to archaic hominin and other primate genomes. The potential effect of common non-synonymous variants on protein-protein interaction was also assessed. IZUMO1 displays higher variability among human individuals than JUNO. Genetic differentiation between continental population pairs was within whole-genome estimates for all but the JUNO gene in the African population group with respect to the other 4 population groups (American, East Asian, South Asian, and European). Tajima’s D values demonstrated deviation from neutrality for both genes in comparison to a group of genes identified in the literature as under balancing or positive selection. Tajima’s D for IZUMO1 aligns with values calculated for genes presumed to be under balancing selection, whereas JUNO’s value aligned with genes presumed to be under positive selection. These inferences on selection are both supported by SNP density, nucleotide diversity and haplotype analysis. A JUNO haplotype carrying 3 derived alleles out of 5, one of which is a missense mutation implicated in polyspermy, was found to be significant in a population of African ancestry. Polyspermy has a disadvantageous impact on fertility and its presence in approximately 30% of the population of African ancestry may be associated to a potentially beneficial role of this haplotype. This role has not been established and may be related to a non-reproductive role of JUNO. The high degree of conservation of the JUNO sequence combined with a dominant haplotype across multiple population groups supports JUNO as a potential target for the development of contraceptive treatments. In addition to providing a detailed account of human genetic diversity across these 2 important and related genes, this study also provides a framework for large population-based studies investigating protein-protein interactions at the genome level.

Distribution of Two Strains of Leptoglossus zonatus (Dallas) (Hemiptera: Coreidae) in the Western Hemisphere: Is L. zonatus a Potential Invasive Species in California?

The leaffooted plant bug, Leptoglossus zonatus (Dallas) (Hemiptera: Coreidae) is polyphagous and widely distributed in the Western Hemisphere. Although it has been recorded in California since around 1900, it has become a more common pest in almonds in the last decade. Other studies have shown that an established insect can become a pest when a new genotype is introduced. This study investigated the distribution of two lineages (strains) of L. zonatus in the Western Hemisphere. Specimens from the Leptoglossus collection in the national insect collection in Mexico were used to extract DNA and sequence the mitochondrial DNA cytochrome oxidase I (mtDNA COI) gene, for use in population genetic and phylogenetic analyses. New sequences from Mexico, Central and South America were combined with those available in GenBank, from California and Brazil. Two lineages (strains) of L. zonatus were uncovered. One lineage occurs in California, Mexico and Ecuador. The second lineage is more widespread and found in California, Mexico, Guatemala, Nicaragua, Bolivia and Brazil. The haplotype number and diversity, and nucleotide diversity, were found for samples from California, Mexico, and Brazil, for the two lineages, and for all 118 sequences combined. All sequences combined produced five haplotypes, and a haplotype diversity of 0.54. California and Brazil had 3 haplotypes each, with one haplotype shared (5 total). Haplotype diversity in California and in Brazil were 0.526 and 0.505, respectively. A haplotype network found that one haplotype was most abundant and widespread. The small number of haplotypes, a range expansion, and economic pest status of L. zonatus in California, all contribute to this insect being a potentially invasive insect pest.

A PRELIMINARY COMPARISON OF MITOCHONDRIAL D-LOOP REGION OF FUNAAB ALPHA AND NIGERIAN INDIGENOUS CHICKENS

Nigerian indigenous chickens possess immunity from endemic diseases and have a better survival rate than commercial hybrid strains under local production conditions. FUNAAB Alpha chicken was developed by improving Nigerian indigenous chickens through crossbreeding and selection. This study compared the mitochondrial d-loop of FUNAAB Alpha and Nigerian indigenous chickens to check likely genetic erosion and loss of diversity in development of FUNAAB Alpha breed. Blood samples were collected from Nigerian indigenous (n=23) and FUNAAB Alpha (n=20) chickens sampled from farms and houses in Ogun state, Nigeria. The Hypervariable 1 (HV1) of the mitochondrial d-loop region was amplified and sequenced. Single nucleotide polymorphisms present in HV1 of chickens were identified using Clustal W. Genetic diversity of the region was determined using DnaSp v5 while selective forces acting on the chickens were predicted using HyPhy software implemented inside MEGA 6 software. Phylogenetic relationship among FUNAAB Alpha, Nigerian indigenous and other chicken breeds was determined using MEGA 6 software. Five polymorphisms were identified in FUNAAB Alpha chickens while twelve were identified in Nigerian indigenous chickens. All the polymorphisms identified in FUNAAB Alpha chickens were also observed in Nigerian indigenous chickens while seven polymorphisms were unique to Nigerian indigenous chickens. Higher diversity indices were observed in Nigerian indigenous chickens (number of haplotype: 4; haplotype diversity: 0.743±0.012; nucleotide diversity: 0.014±0.0013 and average number of nucleotide differences: 4.332) compared with FUNAAB Alpha chickens (number of haplotype: 2; haplotype diversity: 0.485±0.001; nucleotide diversity: 0.008±0.0001 and average number of nucleotide differences: 2.424). Positive selective forces were acting on FUNAAB Alpha chickens while negative selective forces were acting on Nigerian indigenous chickens. Phylogenetic analysis revealed that FUNAAB Alpha chickens clustered with Nigerian indigenous and South American chickens. It can be concluded that there was likely genetic erosion and loss of diversity in development of FUNAAB Alpha breed. Breeding programmes aimed at improvement of genetic diversity and reduction of genetic erosion should be applied in subsequent improvement of FUNAAB Alpha chickens.

Tajima D test accurately forecasts Omicron / COVID-19 outbreak

On 26 November 2021, the World Health Organization designated the SARS-CoV-2 variant B.1.1.529, Omicron, a variant of concern. However, the phylogenetic and evolutionary dynamics of this variant remain unclear. An analysis of the 131 Omicron variant sequences from November 9 to November 28, 2021 reveals that variants have diverged into at least 6 major subgroups. 86.3% of the cases have an insertion at amino acid 214 (INS214EPE) of the spike protein. Neutrality analysis of DH (−2.814, p<0.001) and Zeng’s E (0.0583, p=1.0) tests suggested that directional selection was the major driving force of Omicron variant evolution. The synonymous (Dsyn) and nonsynonymous (Dnonsyn) polymorphisms of the Omicron variant spike gene were estimated with Tajima’s D statistic to eliminate homogenous effects. Both D ratio (Dnonsyn/Dsyn, 1.57) and ΔD (Dsyn-Dnonsyn, 0.63) indicate that purifying selection operates at present. The low nucleotide diversity (0.00008) and Tajima D value (−2.709, p<0.001) also confirms that Omicron variants had already spread in human population for more than the 6 weeks than has been reported. These results, along with our previous analysis of Delta and Lambda variants, also supports the validity of the Tajima’s D test score, with a threshold value as −2.50, as an accurate predictor of new COVID-19 outbreaks.

Two divergent haplogroups of a sacsin-like gene in Acropora corals

Reef-building corals are declining due to environmental changes. Sacsin is a member of the heat shock proteins and has been reported as a candidate protein associated with the stress response in Acropora corals. Recently, high nucleotide diversity and the persistence of two divergent haplogroups of sacsin-like genes in Acropora millepora have been reported. While it was not clear when the two haplogroups have split and whether the haplogroups have persisted in only A. millepora or the other lineages in the genus Acropora. In this study, we analyzed a genomic region containing a sacsin-like gene from Acropora and Montipora species. Higher nucleotide diversity in the sacsin-like gene compared with that of surrounding regions was also observed in A. digitifera. This nucleotide diversity is derived from two divergent haplogroups of a sacsin-like gene, which are present in at least three Acropora species. The origin of these two haplogroups can be traced back before the divergence of Acropora and Montipora (119 Ma). Although the link between exceptionally high genetic variation in sacsin-like genes and functional differences in sacsin-like proteins is not clear, the divergent haplogroups may respond differently to envionmental stressors and serve in the adaptive phsiological ecology of these keystone species.

Simulated vector transmission differentially influences dynamics of two viral variants of deformed wing virus in honey bees (Apis mellifera)

Understanding how vectors alter the interactions between viruses and their hosts is a fundamental question in virology and disease ecology. In honey bees, transmission of deformed wing virus (DWV) by parasitic Varroa mites has been associated with elevated disease and host mortality, and Varroa transmission has been hypothesized to lead to increased viral titres or select for more virulent variants. Here, we mimicked Varroa transmission by serially passaging a mixed population of two DWV variants, A and B, by injection through in vitro reared honey bee pupae and tracking these viral populations through five passages. The DWV-A and DWV-B variant proportions shifted dynamically through passaging, with DWV-B outcompeting DWV-A after one passage, but levels of both variants becoming equivalent by Passage 5. Sequencing analysis revealed a dominant, recombinant DWV-B strain (DWV-A derived 5′ IRES region with the rest of the genome DWV-B), with low nucleotide diversity that decreased through passaging. DWV-A populations had higher nucleotide diversity compared to DWV-B, but this also decreased through passaging. Selection signatures were found across functional regions of the DWV-A and DWV-B genomes, including amino acid mutations in the putative capsid protein region. Simulated vector transmission differentially impacted two closely related viral variants which could influence viral interactions with the host, demonstrating surprising plasticity in vector-host-viral dynamics.

Comparative analysis of twelve mitogenomes of Caliscelidae (Hemiptera: Fulgoromorpha) and their phylogenetic implications

Here, the complete mitochondrial genomes (mitogenomes) of 12 Caliscelidae species, Augilina tetraina, Augilina triaina, Symplana brevistrata, Symplana lii, Neosymplana vittatum, Pseudosymplanella nigrifasciata, Symplanella brevicephala, Symplanella unipuncta, Augilodes binghami, Cylindratus longicephalus, Caliscelis shandongensis, and Peltonotellus sp., were determined and comparatively analyzed. The genomes varied from 15,424 to 16,746 bp in size, comprising 37 mitochondrial genes and an A+T-rich region. The typical gene content and arrangement were similar to those of most Fulgoroidea species. The nucleotide compositions of the mitogenomes were biased toward A/T. All protein-coding genes (PCGs) started with a canonical ATN or GTG codon and ended with TAN or an incomplete stop codon, single T. Among 13 PCGs in 16 reported Caliscelidae mitogenomes, cox1 and atp8 showed the lowest and highest nucleotide diversity, respectively. All PCGs evolved under purifying selection, with atp8 considered a comparatively fast-evolving gene. Phylogenetic relationships were reconstructed based on 13 PCGs in 16 Caliscelidae species and five outgroups using maximum likelihood and Bayesian inference analyses. All species of Caliscelidae formed a steadily monophyletic group with high support. Peltonotellini was present at the basal position of the phylogenetic tree. Augilini was the sister group to Caliscelini and Peltonotellini.

Dosage of duplicated and antifunctionalized homeobox proteins influences spikelet development in barley

Illuminating the mechanisms of inflorescence architecture of grain crops that feed our world may strengthen the goal towards sustainable agriculture. Lateral spikelet development of barley (Hordeum vulgare L.) is such an example of a floral architectural trait regulated by VRS1 (Vulgare Row-type Spike 1 or Six-rowed Spike 1, syn. HvHOX1). The mechanistic function of this gene and its paralog HvHOX2 on spikelet development is still fragmentary. Here, we show that these duplicated transcription factors (TFs) have contrasting nucleotide diversity in various barley genotypes and several Hordeum species. Despite this difference, both proteins retain their basic properties of the homeodomain leucine zipper class I family of TFs. During spikelet development, these genes exhibit similar spatiotemporal expression patterns yet with anticyclic expression levels. A gene co-expression network analysis suggested that both have an ancestral relationship but their functions appear antagonistic to each other, i.e., HvHOX1 suppresses whereas HvHOX2 rather promotes spikelet development. Our transgenic promoter-swap analysis showed that HvHOX2 can restore suppressed lateral spikelets when expression levels are increased; however, at its low endogenous expression level, HvHOX2 appears dispensable for spikelet development. Collectively, this study proposes that the dosage of the two antagonistic TFs, HvHOX1 and HvHOX2, influence spikelet development in barley.