Whole-Genome Sequencing of 117 Chromosome Segment Substitution Lines for Genetic Analyses of Complex Traits in Rice

Rice is one of the most important food crops in Asia. Genetic analyses of complex traits and molecular breeding studies in rice greatly rely on the construction of various genetic populations. Chromosome segment substitution lines (CSSLs) serve as a powerful genetic population for quantitative trait locus (QTL) mapping in rice. Moreover, CSSLs containing target genomic regions can be used as improved varieties in rice breeding. In this study, we developed a set of CSSLs consisting of 117 lines derived from the recipient ‘Huanghuazhan’ (HHZ) and the donor ‘Basmati Surkb 89–15’ (BAS). The 117 lines were extensively genotyped by whole-genome resequencing, and a high-density genotype map was constructed for the CSSL population. The 117 CSSLs covered 99.78% of the BAS genome. Each line contained a single segment, and the average segment length was 6.02 Mb. Using the CSSL population, we investigated three agronomic traits in Shanghai and Hangzhou, China, and a total of 25 QTLs were detected in both environments. Among those QTLs, we found that RFT1 was the causal gene for heading date variance between HHZ and BAS. RFT1 from BAS was found to contain a loss-of-function allele based on yeast two-hybrid assay, and its causal variation was a P to S change in the 94th amino acid of the RFT1 protein. The combination of high-throughput genotyping and marker-assisted selection (MAS) is a highly efficient way to construct CSSLs in rice, and extensively genotyped CSSLs will be a powerful tool for the genetic mapping of agronomic traits and molecular breeding for target QTLs/genes.

Ischnura praematura sp. nov. (Odonata: Zygoptera: Coenagrionidae): a species from Yunnan (China) whose females mate in the teneral state

Ischnura praematura sp. nov. (Holotype ♂, China, Yunnan, Lijiang, 26º31´03.54”N, 100º13’38.89”E, 2396 m, 04 xii 2015, I. Sanmartín-Villar & H. Zhang leg.) is morphologically described, illustrated and compared with close species of the genus. Ischnura praematura can be mainly distinguished from its congeners I. aurora, I. rubilio and I. asiatica by its abdominal and thoracic morphology and colouration. The posterior lobe of the prothorax is elevated in I. praematura and the mesostigmal plates possess dorsal triangular protuberances. Ischnura praematura shows pointed paraprocts, internalised wide cerci and lacks a dorsal tuberculum in the tenth abdominal segment. The blue abdominal colouration is present in the last three segments (incomplete for segment eight and ten in some individuals). No female polychromatism was detected and all females observed possessed different colouration than male (gynochrome). Morphological distinctiveness of the species is supported by genetic analyses, which show that I. praematura forms a well-supported, monophyletic clade, with I. asiatica, I. ezoin and I. pumilio as the most closely related species. In the field, mature females show strong reluctance to mate, and males were observed mating with newly emerged females.

Needle in a Whey-Stack: PhRACS as a Discovery Tool for Unknown Phage-Host Combinations

PhRACS aims to bridge the current divide between in silico genetic analyses (i.e., phageomic studies) and traditional culture-based methodology. Through the labeling of specific bacterial hosts with fluorescently tagged recombinant phage receptor binding proteins and the isolation of tagged cells using flow cytometry, PhRACS allows the full potential of phageomic data to be realized in the wet laboratory.

The genus Diaphanosoma (Diplostraca: Sididae) in Greece: morphological and molecular assessment

For the genus Diaphanosoma Fischer (Cladocera) the species’ name “D. brachyurum” has been widely used for many decades to identify other species belonging to this genus. To clarify the diversity of the genus in Greek lakes in the present study, we morphologically and genetically identified the Diaphanosoma species occurring in eight lakes. Three hundred twenty-nine Diaphanosoma individuals were morphologically examined, while for the genetic analyses the mtDNA COI gene was sequenced in 48 individuals. Combining the morphological and genetic results, we verified the occurrence of D. mongolianum, D. orghidani and D. macedonicum in our study area. We could not confirm prior records of D. brachyurum and D. lacustris while we provide the molecular identity of D. macedonicum. Furthermore, we highlight the need to check whether the European D. mongolianum populations are characterised of mitochondrial discordance and hybridization as the individuals from the Asian type locality of the species. Our results support the importance of combining both approaches to correctly identify taxonomic species, despite the extra effort and cost during the sample analysis.

Ostrich eggshell beads reveal 50,000-year-old social network in Africa

Humans evolved in a patchwork of semi-connected populations across Africa1,2; understanding when and how these groups connected is critical to interpreting our present-day biological and cultural diversity. Genetic analyses reveal that eastern and southern African lineages diverged sometime in the Pleistocene epoch, approximately 350–70 thousand years ago (ka)3,4; however, little is known about the exact timing of these interactions, the cultural context of these exchanges or the mechanisms that drove their separation. Here we compare ostrich eggshell bead variations between eastern and southern Africa to explore population dynamics over the past 50,000 years. We found that ostrich eggshell bead technology probably originated in eastern Africa and spread southward approximately 50–33 ka via a regional network. This connection breaks down approximately 33 ka, with populations remaining isolated until herders entered southern Africa after 2 ka. The timing of this disconnection broadly corresponds with the southward shift of the Intertropical Convergence Zone, which caused periodic flooding of the Zambezi River catchment (an area that connects eastern and southern Africa). This suggests that climate exerted some influence in shaping human social contact. Our study implies a later regional divergence than predicted by genetic analyses, identifies an approximately 3,000-kilometre stylistic connection and offers important new insights into the social dimension of ancient interactions.

Nesobasis rito sp. nov. (Zygoptera: Coenagrionidae), a new species of forest damselfly from Vanua Levu, Fiji

Nesobasis rito sp. nov. (Holotype ♂, Fiji, Vanua Levu, Drawa, 31 v 2018, A. Rivas-Torres leg.) from the comosa group is here described, illustrated, diagnosed, and compared with morphologically close species of the genus. Nesobasis rito can be distinguished from its related congeners by the shape of the caudal appendages and the ligula. The most similar species are N. comosa and N. heteroneura, which, like N. rito, have the caudal appendages covered by dense setae (especially the first species), but the shape differs clearly in lateral view, with N. rito having longer and more slender appendages, and a basal tooth clearly seen in dorsal view, absent in other members of the comosa group. The specific status of the collected specimens is also supported by the results of genetic analyses, where N. rito appears as a well-supported monophyletic clade. Nesobasis rito also has a distinct distribution from its most similar congeners: it is found on Vanua Levu, while N. comosa is found on Viti Levu and the closely related N. heteroneura is found on Viti Levu and Ovalau. All species of this group are found in streams with native forest riparian vegetation on their respective islands.

Shared genetic influences on depression and menopause symptoms

Background Women experience major depression and post-traumatic stress disorder (PTSD) approximately twice as often as men. Estrogen is thought to contribute to sex differences in these disorders, and reduced estrogen is also known to be a key driver of menopause symptoms such as hot flashes. Moreover, estrogen is used to treat menopause symptoms. In order to test for potential shared genetic influences between menopause symptoms and psychiatric disorders, we conducted a genome-wide association study (GWAS) of estrogen medication use (as a proxy for menopause symptoms) in the UK Biobank. Methods The analysis included 232 993 women aged 39–71 in the UK Biobank. The outcome variable for genetic analyses was estrogen medication use, excluding women using hormonal contraceptives. Trans-ancestry GWAS meta-analyses were conducted along with genetic correlation analyses on the European ancestry GWAS results. Hormone usage was also tested for association with depression and PTSD. Results GWAS of estrogen medication use (compared to non-use) identified a locus in the TACR3 gene, which was previously linked to hot flashes in menopause [top rs77322567, odds ratio (OR) = 0.78, p = 7.7 × 10−15]. Genetic correlation analyses revealed shared genetic influences on menopause symptoms and depression (rg = 0.231, s.e.= 0.055, p = 2.8 × 10−5). Non-genetic analyses revealed higher psychiatric symptoms scores among women using estrogen medications. Conclusions These results suggest that menopause symptoms have a complex genetic etiology which is partially shared with genetic influences on depression. Moreover, the TACR3 gene identified here has direct clinical relevance; antagonists for the neurokinin 3 receptor (coded for by TACR3) are effective treatments for hot flashes.