Efficient estimation for large-scale linkage disequilibrium patterns of the human genome.

In this study, we proposed an efficient algorithm (X-LD) for estimating linkage disequilibrium (LD) patterns for a genomic grid, which can be of inter-chromosomal scale or of small segments. Compared with conventional methods, the proposed method was significantly faster, dropped from O(nm2) to O(n2m)-n the sample size and m the number of SNPs, and consequently we were permitted to explore in depth unknown or reveal long-anticipated LD features of the human genome. Having applied the algorithm for 1000 Genome Project (1KG), we found (1) the extended LD, driven by population structure, universally existed, and the strength of inter-chromosomal LD was about 10% of their respective intra-chromosomal LD in relatively homogeneous cohorts, such as FIN, and to nearly 56% in admixed cohort, such as ASW. (2) After splitting each chromosome into upmost of more than a half million grids, we elucidated the LD of the HLA region was nearly 42 folders higher than chromosome 6 in CEU and 11.58 in ASW; on chromosome 11, we observed that the LD of its centromere was nearly 94.05 folders higher than chromosome 11 in YRI and 42.73 in ASW. (3) We uncovered the long-anticipated inversely proportional linear relationship between the length of a chromosome and the strength of chromosomal LD, and their Pearson's correlation was on average over 0.80 for 26 1KG cohorts. However, this linear norm was so far perturbed by chromosome 11 given its more completely sequenced centromere region. Uniquely chromosome 8 of ASW was found most deviated from the linear norm than any other autosomes. The proposed algorithm has been realized in C++ (called X-LD) and is available at https://github.com/gc5k/gear2, and can be applied to explore LD features in any sequenced populations.

Genomic insights into the genetic basis of cotton breeding in China.

The excellent Upland cotton (Gossypium hirsutum) cultivars developed since 1949 have made a huge contribution to cotton production in China, the world's largest producer and consumer of cotton. However, the genetic and genomic basis for the improvements of these cotton cultivars remains largely unclear. In this study, we selected 16 Upland cotton cultivars with important historical status in Chinese cotton breeding and constructed a multiparent, advanced generation, intercross (MAGIC) population comprising 920 recombinant inbred lines. A genome-wide association study using the MAGIC population identified 54 genomic loci associated with lint yield and fiber quality. Of them, 25 (46.30%) pleiotropic genomic loci cause simultaneous changes of lint yield and/or fiber quality traits, revealing complex trade-offs and linkage drags in Upland cotton agronomic traits. Deep sequencing data of 11 introduced ancestor cultivars and publicly available resequencing datasets of 839 cultivars developed in China during the past 70 years were integrated to explore the historical distribution and origin of the elite or selected alleles. Interestingly, 85% of these elite alleles were selected and fixed from different American ancestors, consistent with cotton breeding practices in China. However, seven elite alleles of native origin that are responsible for Fusarium wilt resistance, early maturing, good-quality fiber, and other characteristics were not found in American ancestors but have greatly contributed to Chinese cotton breeding and wide cultivation. Taken together, these results provide a genetic basis for further improving cotton cultivars and reveal that the genetic composition of Chinese cotton cultivars is narrow and mainly derived from early introduced American varieties.

Advanced genes expression pattern greatly contributes to divergence in Verticillium wilt resistance between Gossypium barbadense and Gossupium hirsutum.

Verticillium, representing one of the world's major pathogens, causes Verticillium wilt in important woody species, ornamentals, agricultural, etc., consequently resulting in a serious decline in production and quality, especially in cotton. Gossupium hirutum and Gossypium barbadense are two kinds of widely cultivated cotton species that suffer from Verticillium wilt, while G. barbadense has much higher resistance toward it than G. hirsutum. However, the molecular mechanism regarding their divergence in Verticillium wilt resistance remains largely unknown. In the current study, G. barbadense cv. Hai7124 and G. hirsutum acc. TM-1 were compared at 0, 12, 24, 48, 72, 96, 120, and 144 h post-inoculation (hpi) utilizing high throughput RNA-Sequencing. As a result, a total of 3,549 and 4,725 differentially expressed genes (DEGs) were identified, respectively. In particular, the resistant type Hai7124 displayed an earlier and faster detection and signaling response to the Verticillium dahliae infection and demonstrated higher expression levels of defense-related genes over TM-1 with respect to transcription factors, plant hormone signal transduction, plant-pathogen interaction, and nucleotide-binding leucine-rich repeat (NLR) genes. This study provides new insights into the molecular mechanisms of divergence in Verticillium wilt resistance between G. barbadense and G. hirsutum and important candidate genes for breeding V. dahliae resistant cotton cultivars.

Comparison of Mitochondrial Genomes between a Cytoplasmic Male-Sterile Line and Its Restorer Line for Identifying Candidate CMS Genes in Gossypium hirsutum.

As the core of heterosis utilization, cytoplasmic male sterility (CMS) has been widely used in hybrid seed production. Previous studies have shown that CMS is always closely related to the altered programming of mitochondrial genes. To explore candidate CMS genes in cotton (Gossypium hirsutum), sequencing and de novo assembly were performed on the mitochondrial genome of the G. hirsutum CMS line SI3A, with G. harknessii CMS-D2 cytoplasm, and the corresponding G. hirsutum restorer line 0-613-2R. Remarkable variations in genome structure and gene transcripts were detected. The mitochondrial genome of SI3A has three circle molecules, including one main circle and two sub-circles, while 0-613-2R only has one. RNA-seq and RT-qPCR analysis proved that orf606a and orf109a, which have a chimeric structure and transmembrane domain, were highly expressed in abortive anthers of SI3A. In addition, comparative analysis of RNA-seq and full-length transcripts revealed the complex I gene nad4 to be expressed at a lower level in SI3A than in its restorer and that it featured an intron retention splicing pattern. These two novel chimeric ORFs and nad4 are potential candidates that confer CMS character in SI3A. This study provides new insight into the molecular basis of the nuclear-cytoplasmic interaction mechanism, and that putative CMS genes might be important sources for future precise design cross-breeding of cotton.

Subsampling Technique to Estimate Variance Component for UK-Biobank Traits.

The estimation of heritability has been an important question in statistical genetics. Due to the clear mathematical properties, the modified Haseman-Elston regression has been found a bridge that connects and develops various parallel heritability estimation methods. With the increasing sample size, estimating heritability for biobank-scale data poses a challenge for statistical computation, in particular that the calculation of the genetic relationship matrix is a huge challenge in statistical computation. Using the Haseman-Elston framework, in this study we explicitly analyzed the mathematical structure of the key term tr( K T K ), the trace of high-order term of the genetic relationship matrix, a component involved in the estimation procedure. In this study, we proposed two estimators, which can estimate tr( K T K ) with greatly reduced sampling variance compared to the existing method under the same computational complexity. We applied this method to 81 traits in UK Biobank data and compared the chromosome-wise partition heritability with the whole-genome heritability, also as an approach for testing polygenicity.

EigenGWAS: An online visualizing and interactive application for detecting genomic signatures of natural selection.

Detecting genetic regions under selection in structured populations is of great importance in ecology, evolutionary biology and breeding programmes. We recently proposed EigenGWAS, an unsupervised genomic scanning approach that is similar to F ST but does not require grouping information of the population, for detection of genomic regions under selection. The original EigenGWAS is designed for the random mating population, and here we extend its use to inbred populations. We also show in theory and simulation that eigenvalues, the previous corrector for genetic drift in EigenGWAS, are overcorrected for genetic drift, and the genomic inflation factor is a better option for this adjustment. Applying the updated algorithm, we introduce the new EigenGWAS online platform with highly efficient core implementation. Our online computational tool accepts plink data in a standard binary format that can be easily converted from the original sequencing data, provides the users with graphical results via the R-Shiny user-friendly interface. We applied the proposed method and tool to various data sets, and biologically interpretable results as well as caveats that may lead to an unsatisfactory outcome are given. The EigenGWAS online platform is available at www.eigengwas.com, and can be localized and scaled up via R (recommended) or docker.

(3R)-5,6,7-trihydroxy-3-isopropyl-3-methylisochroman-1-one reduces lipoteichoic acid-induced damage in rat cardiomyoblast cells.

OBJECTIVE: Infective endocarditis is usually caused by Streptococcus sanguinis and characterized by inflammatory responses in the endocardium. This study aimed to investigate if the new compound (3R)-5,6,7-trihydroxy-3-isopropyl-3-methylisochroman-1-one (TIM) isolated from Alpinia katsumadai Hayata could provide protection against lipoteichoic acid (LTA)-induced cell damage in embryonic rat heart cells (H9c2). METHODS: LTA-induced cell damage was established in H9c2, and the protective effects of TIM against the cell damage were examined at different concentrations (0.1-2.5 µM). The inflammatory response and oxidative stress in H9c2 cells were also measured. RESULTS: Treatment with TIM (0.1-2.5 µM) significantly decreased LTA-induced toxicity in H9c2 cells, which was indicated by increase in cell viability, elevation in the mitochondrial membrane potential, decrease in the release of cytochrome-c and DNA damage, inhibition of caspase-3/9 activities, and change in apoptosis-related protein expression in LTA-treated H9c2 cells. TIM treatment also significantly attenuated the redox imbalance in H9c2 cells by decreasing malondialdehyde and intracellular reactive oxygen species levels as well as by enhancing superoxide dismutase activities and glutathione levels by increasing nuclear factor (erythroid-derived 2)-like 2 protein expression. Moreover, TIM treatment decreased interleukin 1 ß, interleukin 12, and tumor necrosis factor α levels by inhibiting nuclear factor kappa B protein expression. CONCLUSION: Our data indicated that TIM protected H9c2 cells against LTA-induced toxicity, at least partially through inhibiting the inflammatory response and oxidative stress, providing scientific rational to develop TIM to treat infective endocarditis.

Short-term pretreatment with atorvastatin attenuates left ventricular dysfunction, reduces infarct size and apoptosis in acute myocardial infarction rats.

BACKGROUND: Atorvastatin showed a number of cardiovascular benefits, however, the role and underlying molecular mechanisms of short-term atorvastatin-mediated protection remain unclear. METHODS: 30 rats were randomly divided into 3 groups: sham group, acute myocardial infarction model group and atorvastatin group. The rats of acute myocardial infarction model were established by ligation of the left anterior descending of coronary arteries. Before surgery, rats in the atorvastatin group received 20 mg/kg/d atorvastatin for 7 days in atorvastatin group. After 4 hours of model established, changes in hemodynamics parameters were recorded and myocardial infarct size was achieved by Evans blue-TTC staining. Myocardium apoptosis was evaluated by TUNEL. The expression of FAS, FAS-L, Bcl-2, Bax, p-BAD, Caspase-8 and Caspase-3 in myocardium were examined by Western blot. RESULTS: In the atorvastatin group, left ventricular function was elevated and infarct size was decreased compared with the model group. Moreover, in the atorvastatin group, the cell apoptosis index was reduced in response to myocardial infarction. The expressions of Bcl-2 were increased and Bax, p-BAD, Fas, Fas-L, caspase-8 and caspase-3 in myocardium were decreased in atorvastatin group. CONCLUSIONS: Short-term atorvastatin pretreatment restored left ventricular function and limited infarct size in acute myocardial infarction, which were associated with reduction of the apoptosis in myocardium through Bcl-2 and Fas pathway.