Genomic atlases of introgression and differentiation reveal breeding footprints in Chinese cultivated rice

The long history of cultivation and breeding has left a variety of footprints in the genomes of Asian cultivated rice (Oryza sativa L.). In this study, we focus on two types of genomic footprints, introgression and differentiation, in a population of more than 1200 Chinese rice accessions. We found that a Xian/indica and a temperate Geng/japonica accession respectively contained an average of 19.3-Mb and 6.8-Mb alien introgressed chromosomal segments, of which many contained functional sequence variants, quantitative trait loci, or genes controlling flowering, grain, and resistance traits. Notably, we found most introgressions, including the known heterotic loci Hd3a and TAC1, were distributed differentially between the female and male parents of three-line indica hybrid rice, indicating their potential contribution to heterosis. We also found many differentiated regions between subgroups within a subpopulation contained agronomically important loci, such as DTH7, Hd1 for heading date, and qCT7 for cold tolerance, providing new candidates for studying local adaptation or heterosis. Tracing these footprints allows us to better understand the genetic exchange or differentiation underlying agronomic traits in modern Chinese rice cultivars. These findings also provide potential targets for rice genetic research and breeding.     

Egg parasitoids (Hymenoptera: Mymaridae) of Amrasca biguttula (Ishida) (Hemiptera: Cicadellidae) on Okinawa Island,a pest of okra in Japan

The fairyfly Anagrus (Anagrus) japonicus Sahad (Hymenoptera: Mymaridae) is identified for the first time as an egg parasitoid of the okra leafhopper Amrasca (Sundapteryx) biguttula (Ishida) (Hemiptera: Cicadellidae) on Okinawa Island, Japan. Amrasca biguttula is a serious pest of okra, Abelmoschus esculentus (L.) Moench (Malvaceae), both in Okinawa and Bonin Islands. Female of A. japonicus is redescribed, and its previously unknown male is described, based on the reared specimens from Okinawa. Prior to this study, host associations of A. japonicus were unknown. Another species of Mymaridae, Arescon enocki (Subba Rao and Kaur), also emerged from eggs of A. biguttula on okra in Okinawa, albeit in much smaller numbers.     

The historical context of contemporary climatic adaptation: a case study in the climatically dynamic and environmentally complex southwestern United States

The process of adaptation can be highly dependent upon historical and contemporary factors, especially in environmentally and topographically complex regions affected by Pleistocene glaciations. Here, we investigate Hilaria jamesii (Poaceae), a dryland C₄ graminoid, to test how patterns of adaptive genetic variation are linked to its glacial and post-glacial history. We show that the species persisted in a single, southern refugium during the last glacial period and subsequently migrated throughout its current distribution concurrent with post-glacial warming. The species’ putative adaptive genetic variation correlates with climatic gradients (e.g. monsoon precipitation and mean diurnal temperature range) that covary with the species’ probable route of demographic expansion. The short timescale and multiple climatic dimensions of adaptation imply that natural selection acted primarily upon standing genetic variation. These findings suggest that restoration and conservation practices should prioritize the maintenance of standing genetic variation to ensure that species have the capacity to respond to future environmental changes.     

喀斯特次生林幼树更新空间分布格局及种间关联性

本研究以贵州省喀斯特典型区域紫云苗族布依族自治县撂荒30余年后自然恢复形成的次生林为对象,设置140 m×120 m固定样地,系统调查样地内幼树更新,并采用空间点格局分析方法分析幼树更新优势种群在不同空间尺度下的分布格局和种间关联性。结果表明: 调查样地中幼树共计1291株,包括39个树种,其中光皮桦、化香、马尾松、枫香和山杨5个树种的幼树个体数量总和达83.7%,重要值总和达77.8%,为幼树更新的优势树种。光皮桦、化香和枫香3个幼树优势种群的空间分布格局在0～60 m空间尺度上均呈现较强的聚集分布;马尾松和山杨2个幼树优势种群在小尺度上呈现聚集分布,大尺度上则随机分布。幼树优势种群空间关联性多呈现正关联,仅马尾松与枫香和山杨在小尺度呈现正关联,大尺度呈现不相关。调查样地5个幼树优势种群空间分布格局及种间关联性差别较大,可能与树种的生物学特性、生境及空间资源的利用密切相关。目前,林分多以先锋树种为主,群落结构不稳定;以马尾松和光皮桦为优势种群的松-桦混交林可能成为下一阶段演替方向,建议通过森林经营措施加快植被恢复进程。     

Contrasting association of Leptin receptor polymorphisms and haplotypes with polycystic ovary syndrome in Bahraini and Tunisian women: a case–control study

Background: The present study examined the contribution of ethnicity to the association of leptin receptor gene (LEPR) gene variants with polycystic ovary syndrome (PCOS) in Tunisian and Bahraini Arabic-speaking women.Methods: Subjects consisted of 320 women with PCOS, and 446 eumenorrhic women from Tunisia, and 242 women with PCOS and 238 controls from Bahrain. Genotyping of (exonic) rs1137100 and rs1137101 and (intronic) rs2025804 LEPR variants was done by allelic exclusion.Results: The minor allele frequencies (MAFs) of rs1137100 and rs1137101 were significantly different between PCOS cases and control women from Bahrain but not Tunisia, and LEPR rs1137101 was associated with increased PCOS susceptibility only in Bahraini subjects. Furthermore, rs1137100 was associated with decreased PCOS risk among Bahrainis under codominant and recessive models; rs1137100 was negatively associated with PCOS in Tunisians after controlling for testosterone. In addition, rs2025804 was associated with increased PCOS risk among Tunisian but not Bahraini women, after adjusting for key covariates. Negative correlation was seen between rs1137101 and triglycerides in Tunisians, while homeostasis model assessment of insulin resistance (HOMA-IR) and insulin correlated with rs2025804 and rs1137101 among Bahraini subjects, and rs1137101 correlated with estradiol and prolactin. Taking TAG haplotype as common, positive association of TAA and negative association of TGG haplotype with PCOS was seen among Bahraini women; no three-locus PCOS-associated haplotypes were found in Tunisians.Conclusions: The present study is the first to demonstrate the contribution of ethnicity to the association of LEPR gene variants with PCOS, thereby highlighting the significance of controlling for ethnicity in gene association investigations.     

Evaluating human autosomal loci for sexually antagonistic viability selection in two large biobanks

Sex and sexual differentiation are pervasive across the tree of life. Because females and males often have substantially different functional requirements, we expect selection to differ between the sexes. Recent studies in diverse species, including humans, suggest that sexually antagonistic viability selection creates allele frequency differences between the sexes at many different loci. However, theory and population-level simulations indicate that sex-specific differences in viability would need to be very large to produce and maintain reported levels of between-sex allelic differentiation. We address this contradiction between theoretical predictions and empirical observations by evaluating evidence for sexually antagonistic viability selection on autosomal loci in humans using the largest cohort to date (UK Biobank, n = 487,999) along with a second large, independent cohort (BioVU, n = 93,864). We performed association tests between genetically ascertained sex and autosomal loci. Although we found dozens of genome-wide significant associations, none replicated across cohorts. Moreover, closer inspection revealed that all associations are likely due to cross-hybridization with sex chromosome regions during genotyping. We report loci with potential for mis-hybridization found on commonly used genotyping platforms that should be carefully considered in future genetic studies of sex-specific differences. Despite being well powered to detect allele frequency differences of up to 0.8% between the sexes, we do not detect clear evidence for this signature of sexually antagonistic viability selection on autosomal variation. These findings suggest a lack of strong ongoing sexually antagonistic viability selection acting on single locus autosomal variation in humans.     

HLA-A, -B, -C, -DRB1 and -DQB1 alleles associated with different hematological diseases in Chinese population

The purpose of this study was to explore the association between human leukocyte antigens (HLA)-A, -B, -C, -DRB1 and -DQB1 allele polymorphisms and different hematological diseases in Chinese groups. Retrospective analyses of HLA genotyping data in high-resolution for patients with acute myeloid leukemia (AML, 766 cases), chronic myeloid leukemia (CML, 330 cases), acute lymphoblastic leukemia (ALL, 605 cases), aplastic anemia (AA, 229 cases), myelodysplastic syndrome (MDS, 204 cases) were performed, and the susceptible or protective HLA alleles of the above-mentioned diseases were analyzed by Chi-square test and Fisher exact test with unrelated hematopoietic stem cell donors as control. The Results indicated that A*0201, B*4402, C*0701, DRB1*1201, DRB1*1401, and DQB1*0602 might be susceptible genes of AML, while A*1101, A*3303, B*5801, C*0302, DRB1*0301, DQB1*0201 and DQB1*0502 might be protective genes of AML. A*3303 might be a protective gene of CML, and DRB1*1401 might be a susceptible gene of CML. ALL's susceptible genes included A*0201, A*0210, B*5201, DRB1*1201, DRB1*1401 and DQB1*0602, but its protective genes included DQB1*0502. For AA, A*0201, A*0206, B*1511, DRB1*0901, DRB1*1401, DQB1*0303, DQB1*0602 might be susceptible genes, while A*3303, B*5801, C*0302, DRB1*1602 and DQB1*0502 might be protective genes. A*0201, A*0206, B*1511, DRB1*0901, DRB1*1401, DQB1*0303. A*0201, B*1558, B*4801, B*5201, DRB1*1401, DRB1*1501, and DQB1*0602 might be susceptible genes of MDS, and A*3303, B*4601, B*5801, C*0302, and DRB1*0901 might be protective genes of MDS. On the basis of HLA high-resolution genotyping for the first time, this study comprehensively analyzed HLA alleles associated with different hematological diseases in the Chinese population, which should provide clues for further study on the pathogenesis of these diseases.     

Contribution to the knowledge of Bulgarian serpentine grasslands and their relationships with Balkan serpentine syntaxa

Serpentine areas, including those in Bulgaria, are rich in endemic taxa, and still remain to be investigated phytocoenologically. We analyse the vegetation types in various sites and compare them with those in other Balkan countries. The main objectives were (1) to explore and describe the relationships between the vegetation in the serpentine areas investigated in Bulgaria with those in the Balkan Peninsula and (2) to explore and classify the diversity of vegetation in grasslands on serpentine rocks in eastern Rhodope, Bulgaria. The classic methodology of the Braun-Blanquet school was applied to the exploration of the vegetation. Average linkage method (unweighted pair group method with arithmetic mean) and principal coordinate analysis were used to evaluate floristic and synoptic similarities. As a result, the new endemic association Onosmo pavlovae-Festucetum dalmaticae was proposed. This association can be included in the alliance Alyssion heldreichii Bergmeier et al. 2009, newly described on serpentine rocks in northern Greece. Our data confirmed the existence of similar or vicariant endemic syntaxa (associations) on isolated serpentine terrains in northern Greece and south-eastern Bulgaria.     

Development of a Genotyping Microarray for Studying the Role of Gene-Environment Interactions in Risk for Lung Cancer

A microarray (LungCaGxE), based on Illumina BeadChip technology, was developed for high-resolution genotyping of genes that are candidates for involvement in environmentally driven aspects of lung cancer oncogenesis and/or tumor growth. The iterative array design process illustrates techniques for managing large panels of candidate genes and optimizing marker selection, aided by a new bioinformatics pipeline component, Tagger Batch Assistant. The LungCaGxE platform targets 298 genes and the proximal genetic regions in which they are located, using ∼13,000 DNA single nucleotide polymorphisms (SNPs), which include haplotype linkage markers with a minimum allele frequency of 1% and additional specifically targeted SNPs, for which published reports have indicated functional consequences or associations with lung cancer or other smoking-related diseases. The overall assay conversion rate was 98.9%; 99.0% of markers with a minimum Illumina design score of 0.6 successfully generated allele calls using genomic DNA from a study population of 1873 lung-cancer patients and controls.     

Development and Application of Microsatellites in Candidate Genes Related to Wood Properties in the Chinese White Poplar (Populus tomentosa Carr.)

Gene-derived simple sequence repeats (genic SSRs), also known as functional markers, are often preferred over random genomic markers because they represent variation in gene coding and/or regulatory regions. We characterized 544 genic SSR loci derived from 138 candidate genes involved in wood formation, distributed throughout the genome of Populus tomentosa, a key ecological and cultivated wood production species. Of these SSRs, three-quarters were located in the promoter or intron regions, and dinucleotide (59.7%) and trinucleotide repeat motifs (26.5%) predominated. By screening 15 wild P. tomentosa ecotypes, we identified 188 polymorphic genic SSRs with 861 alleles, 2–7 alleles for each marker. Transferability analysis of 30 random genic SSRs, testing whether these SSRs work in 26 genotypes of five genus Populus sections (outgroup, Salix matsudana), showed that 72% of the SSRs could be amplified in Turanga and 100% could be amplified in Leuce. Based on genotyping of these 26 genotypes, a neighbour-joining analysis showed the expected six phylogenetic groupings. In silico analysis of SSR variation in 220 sequences that are homologous between P. tomentosa and Populus trichocarpa suggested that genic SSR variations between relatives were predominantly affected by repeat motif variations or flanking sequence mutations. Inheritance tests and single-marker associations demonstrated the power of genic SSRs in family-based linkage mapping and candidate gene-based association studies, as well as marker-assisted selection and comparative genomic studies of P. tomentosa and related species.