Next-generation sequencing (NGS) approaches are widely used in genome-wide genetic marker discovery and genotyping. However, current NGS approaches are not easy to apply to general outbred populations (human and some major farm animals) for SNP identification because of the high level of heterogeneity and phase ambiguity in the haplotype. Here, we reported a new method for SNP genotyping, called genotyping by genome reducing and sequencing (GGRS) to genotype outbred species. Through an improved procedure for library preparation and a marker discovery and genotyping pipeline, the GGRS approach can genotype outbred species cost-effectively and high-reproducibly. We also evaluated the efficiency and accuracy of our approach for high-density SNP discovery and genotyping in a large genome pig species (2.8 Gb), for which more than 70,000 single nucleotide polymorphisms (SNPs) can be identified for an expenditure of only $80 (USD)/sample.

The Arabidopsis thaliana WRKY proteins are characterized by a sequence of 60 amino acids including WRKY domain. It is well established that these proteins are involved in the regulation of various physiological programs unique to plants including pathogen defense, senescence and response to environmental stresses, which attracts attention of the scientific community as to how this family might have evolved. We tried to satisfy this curiosity and analyze reasons for duplications of these gene sequences leading to their diversified gene actions. The WRKY sequences available in Arabidopsis thaliana were used to evaluate selection pressure following duplication events. A phylogenetic tree was constructed and the WRKY family was divided into five sub-families. After that, tests were conducted to decide whether positive or purified selection played key role in these events. Our results suggest that purifying selection played major role during the evolution of this family. Some amino acid changes were also detected in specific branches of phylogeny suggesting that relaxed constraints might also have contributed to functional divergence among sub-families. Sites relaxed from purifying selection were identified and mapped onto the structural and functional regions of the WRKY1 protein. These analyses will enhance our understanding of the precise role played by natural selection to create functional diversity in WRKY family.

Bi2O2Se is emerging as a photosensitive functional material for optoelectronics, and its photodetection mechanism is mostly considered to be a photoconductive regime in previous reports. Here, the bolometric effect is discovered in Bi2O2Se photodetectors. The coexistence of photoconductive effect and bolometric effect is generally observed in multiwavelength photoresponse measurements and then confirmed with microscale local heating experiments. The unique photoresponse of Bi2O2Se photodetectors may arise from a change of hot electrons during temperature rises instead of photoexcited holes and electrons. Direct proof of the bolometric effect is achieved by real‐time temperature tracking of Bi2O2Se photodetectors under time evolution after light excitation. Moreover, the Bi2O2Se bolometer shows a high temperature coefficient of resistance (−1.6% K−1), high bolometric coefficient (−31 nA K−1), and high bolometric responsivity (>320 A W−1). These findings offer a new approach to develop bolometric photodetectors based on Bi2O2Se layered materials.

Jinhua pig, a well-known Chinese indigenous breed, has evolved as a pig breed with excellent meat quality, greater disease resistance, and higher prolificacy. The reduction in the number of Jinhua pigs over the past years has raised concerns about inbreeding. Runs of homozygosity (ROH) along the genome have been applied to quantify individual autozygosity to improve the understanding of inbreeding depression and identify genes associated with traits of interest. Here, we investigated the occurrence and distribution of ROH using next-generation sequencing data to characterize autozygosity in 202 Jinhua pigs, as well as to identify the genomic regions with high ROH frequencies within individuals. The average inbreeding coefficient, based on ROH longer than 1 Mb, was 0.168 ± 0.052. In total, 18,690 ROH were identified in all individuals, among which shorter segments (1–5 Mb) predominated. Individual ROH autosome coverage ranged from 5.32 to 29.14% in the Jinhua population. On average, approximately 16.8% of the whole genome was covered by ROH segments, with the lowest coverage on SSC11 and the highest coverage on SSC17. A total of 824 SNPs (about 0.5%) and 11 ROH island regions were identified (occurring in over 45% of the samples). Genes associated with reproduction ( HOXA3, HOXA7, HOXA10 , and HOXA11 ), meat quality ( MYOD1, LPIN3 , and CTNNBL1 ), appetite ( NUCB2 ) and disease resistance traits ( MUC4, MUC13, MUC20, LMLN, ITGB5, HEG1, SLC12A8 , and MYLK ) were identified in ROH islands. Moreover, several quantitative trait loci for ham weight and ham fat thickness were detected. Genes in ROH islands suggested, at least partially, a selection for economic traits and environmental adaptation, and should be subject of future investigation. These findings contribute to the understanding of the effects of environmental and artificial selection in shaping the distribution of functional variants in the pig genome.

Background: Forkhead box, class O (FoxO) belongs to the large family of forkhead transcription factors that are characterized by a conserved forkhead box DNA-binding domain. To date, the FoxO group has four mammalian members: FoxO1, FoxO3a, FoxO4 and FoxO6, which are orthologs of DAF16, an insulin-responsive transcription factor involved in regulating longevity of worms and flies. The degree of homology between these four members is high, especially in the forkhead domain, which contains the DNA-binding interface. Yet, mouse FoxO knockouts have revealed that each FoxO gene has its unique role in the physiological process. Whether the functional divergences are primarily due to adaptive selection pressure or relaxed selective constraint remains an open question. As such, this study aims to address the evolutionary mode of FoxO, which may lead to the functional divergence.

We report a novel algorithm, iBLUP, to impute missing genotypes by simultaneously and comprehensively using identity by descent and linkage disequilibrium information. The simulation studies showed that the algorithm exhibited drastically tolerance to high missing rate, especially for rare variants than other common imputation methods, e.g. BEAGLE and fastPHASE. At a missing rate of 70%, the accuracy of BEAGLE and fastPHASE dropped to 0.82 and 0.74 respectively while iBLUP retained an accuracy of 0.95. For minor allele, the accuracy of BEAGLE and fastPHASE decreased to −0.1 and 0.03, while iBLUP still had an accuracy of 0.61.We implemented the algorithm in a publicly available software package also named iBLUP. The application of iBLUP for processing real sequencing data in an outbred pig population was demonstrated.

The insulin/insulin growth factor-1(IGF1)/FOXO (IIF) signal transduction pathway plays a core role in the endocrine system. Although the components of this pathway have been well characterized, the evolutionary pattern remains poorly understood. Here, we perform a comprehensive analysis to study whether the differences of signaling transduction elements exist as well as to determine whether the genes are subject to equivalent evolutionary forces and how natural selection shapes the evolution pattern of proteins in an interacting system. Our results demonstrate that most IIF pathway components are present throughout all animal phyla investigated here, and they are under strong selective constraint. Remarkably, we detect that the components in the middle of the pathway undergo stronger purifying selection, which is different from previous similar reports. We also find that the dN/dS may be influenced by quite complicated factors including codon bias, protein length among others.

2D materials with low-symmetry exhibit anisotropic physical properties, making them promising candidates for various applications. However, the lack of matured synthesis methods in anisotropic 2D materials is still the main obstacle to their future applications. Given the mature synthesis method of transition metal dichalcogenides (TMDCs), manipulating anisotropy in 2D TMDCs becomes a promising way to tune or trigger functional properties. Herein, for the first time, a van der Waals symmetry engineering is reported to introduce in-plane polarization in MoS 2 through contact with low-symmetric CrOCl. The emergence of asymmetric second harmonic generation pattern in MoS 2 /CrOCl heterojunction indicates the variation of lattice symmetry in MoS 2 . Furthermore, the theoretical simulation shows that such change stems from lattice-mismatch-induced uniaxial strain because of the strong interlayer interactions. The angle-dependent Raman and photoluminescence spectra further identify that the uniaxial strain gives rise to the in-plane polarization in MoS 2 . In addition, the polarized MoS 2 exhibits excellent orientation-sensitive electrical characteristics with a conductance anisotropy ratio of ≈1.5. More importantly, the strong linear polarization-sensitive photodetection is realized, and the anisotropic ratio reached 1.25 with 532 nm. The results suggest that symmetric engineering potentially opens up a new field to endow high-symmetry 2D materials with anisotropic functionalities.