Overriding Mendelian inheritance in Arabidopsis with a CRISPR toxin-antidote gene drive that impairs pollen germination.

Synthetic gene drives, inspired by natural selfish genetic elements and transmitted to progeny at super-Mendelian (>50%) frequencies, present transformative potential for disseminating traits that benefit humans throughout wild populations, even facing potential fitness costs. Here we constructed a gene drive system in plants called CRISPR-Assisted Inheritance utilizing NPG1 (CAIN), which uses a toxin-antidote mechanism in the male germline to override Mendelian inheritance. Specifically, a guide RNA-Cas9 cassette targets the essential No Pollen Germination 1 (NPG1) gene, serving as the toxin to block pollen germination.

A designer synthetic chromosome fragment functions in moss.

Rapid advances in DNA synthesis techniques have enabled the assembly and engineering of viral and microbial genomes, presenting new opportunities for synthetic genomics in multicellular eukaryotic organisms. These organisms, characterized by larger genomes, abundant transposons and extensive epigenetic regulation, pose unique challenges. Here we report the in vivo assembly of chromosomal fragments in the moss Physcomitrium patens, producing phenotypically virtually wild-type lines in which one-third of the coding region of a chromosomal arm is replaced by redesigned, chemically synthesized fragments.

Analysis of genetic architecture and favorable allele usage of agronomic traits in a large collection of Chinese rice accessions.

Genotyping and phenotyping large natural populations provide opportunities for population genomic analysis and genome-wide association studies (GWAS). Several rice populations have been re-sequenced in the past decade; however, many major Chinese rice cultivars were not included in these studies. Here, we report large-scale genomic and phenotypic datasets for a collection mainly comprised of 1,275 rice accessions of widely planted cultivars and parental hybrid rice lines from China.

Systematic discovery of novel and valuable plant gene modules by large-scale RNA-seq samples.

Motivation: The complex cellular networks underlying phenotypes are formed by the interacting gene modules. Building and analyzing genome-wide and high-quality Gene Co-expression Networks (GCNs) is useful for uncovering these modules and understanding the phenotypes of an organism.

Results: Using large-scale RNA-seq samples, we constructed high coverage and confident GCNs in two monocot species rice and maize, and two eudicot species Arabidopsis and soybean, and subdivided them into co-expressed gene modules.

NetMiner-an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples.

Accurately reconstructing gene co-expression network is of great importance for uncovering the genetic architecture underlying complex and various phenotypes. The recent availability of high-throughput RNA-seq sequencing has made genome-wide detecting and quantifying of the novel, rare and low-abundance transcripts practical. However, its potential merits in reconstructing gene co-expression network have still not been well explored.