Co-location of QTL for Sclerotinia stem rot resistance and flowering time in Brassica napus

Sclerotinia stem rot(SSR) caused by Sclerotinia sclerotiorum(Lib.) de Bary is one of the most devastating diseases of Brassica napus worldwide. Both SSR resistance and flowering time(FT) adaptation are major breeding goals in B. napus. However, early maturing rapeseed varieties, which are important for rice-rapeseed rotation in China, are often highly susceptible to SSR. Here, we found that SSR resistance was significantly negatively correlated with FT in a natural population containing 521 rapeseed inbred lines and a double haploid(DH) population with 150 individual lines, both of which had great variation in FT. Four chromosomal regions on A2, A6, C2, and C8 affecting both SSR resistance and FT were identified using quantitative trait loci(QTL) mapping after constructing a high-density genetic map based on single nucleotide polymorphism markers in the DH population.Furthermore, we aligned QTL for the two traits identified in the present and previous studies to the B. napus reference genome, and identified four colocalized QTL hotspots of SSR resistance and FT on A2(0–7.7 Mb), A3(0.8–7.5 Mb), C2(0–15.2 Mb), and C6(20.2–36.6 Mb). Our results revealed a genetic link between SSR resistance and FT in B.napus, which should facilitate the development of effective strategies in both early maturing and SSR resistance breeding and in map-based cloning of SSR resistance QTL.

An integrated rice panicle phenotyping method based on X-ray and RGB scanning and deep learning

Rice panicle phenotyping is required in rice breeding for high yield and grain quality.To fully evaluate spikelet and kernel traits without threshing and hulling,using X-ray and RGB scanning,we developed an integrated rice panicle phenotyping system and a corresponding image analysis pipeline.We compared five methods of counting spikelets and found that Faster R-CNN achieved high accuracy(R~2 of 0.99)and speed.Faster R-CNN was also applied to indica and japonica classification and achieved 91%accuracy.The proposed integrated panicle phenotyping method offers benefit for rice functional genetics and breeding.

AraENCODE:A comprehensive epigenomic database of Arabidopsis thaliana

Dear Editor,Arabidopsis thaliana is an important model organism in plant biology and genetics.The genome of Arabidopsis ecotype Columbia-0 has been sequenced and completely annotated(Cheng et al.,2017),which facilitates the genomics research of plants.Over the past two decades,advances in the gene regulation studies have elucidated a spectrum of epigenetic molecular phenomena,including DNA methylation,histone modification,chromatin accessibility,and chromatin interaction,which collectively form an additional layer of information based on DNA sequence(Law and Jacobsen,2010).The epigenome landscape has been characterized in Arabidopsis as more high-throughput analyses were developed(Zhao et al.,2022).Without a doubt,in-depth studies of gene expression regulation heavily rely on such epigenomic information.However,the utilization of this knowledge poses a challenge for certain groups lacking bioinformatics analysts or adequate computing resources.

RiceENCODE:A comprehensive epigenomicdatabase as a rice Encyclopedia of DNA Elements

Dear Editor,Rice(Oryza sativa)is one of the most important crops in the worldand a common model plant for genomic research.The genomesofXian/IndicaandGeng/Japonicahave been completelysequenced and annotated with accurate genome information.Over the past few years,epigenomic information,including DNAmethylation,histone modification,and chromatin accessibility,has been characterized in theXian/IndicaandGeng/Japonicage-nomes(Zhao et al.,2020).Quite a few rice three-dimensionalgenome studies have been published in the meantime(Zhaoet al.,2019).However,it is still a big challenge for many groupsthat lack dedicated bioinformatic personnel or sufficientcomputational resources to utilize such epigenetic data.

De Novo Plant Genome Assembly Based on Chromatin Interactions： A Case Study of Arabidopsis thaliana

Dear Editor,Genome assembly is typically a two-stage process： paired sequencing reads are joined into contigs, and contigs are assem- bled into scaffolds. Over the past 10 years, next-generation sequencing （NGS） technologies have become inexpensive, routine, and widespread. As a result, most plant genomes that are sequenced by NGS produce “drafts” that are always contig or scaffold maps remaining in a more or less advanced stage of completion （Claros et al., 2012）. Slow advances in the technology for the de novo assembly of scaffolds into chromosome-scale scaffolds have become the main restriction to the completion of and high-quality genome sequence acquisition.

Rice Information GateWay： A Comprehensive Bioinformatics Platform for Indica Rice Genomes

Dear Editor,Oryza sativa subsp, indica and japonica are two subspecies of Asian cultivated rice, among which indica rice is much more widely grown and genetically diverse. Over the past years, the Rice Annotation Project Database （RAP-DB） （Ohyanagi et al., 2006） and Michigan State University Rice Genome Annotation Project （MSU-RGAP） （Ouyang et al., 2007） are two popular databases that have been developed to manage rice genomic and transcriptomic data based on the unified reference genome of japonica cultivar Nipponbare （International Rice Genome Sequencing Project, 2005）. Beijing Genomics Institute Rice Information System （BGI-RIS） （Zhao et ai., 2004） is an available resource for indica rice cultivar 93-11;

Unraveling a genetic roadmap for improved taste in the domesticated apple

Although taste is an important aspect of fruit quality, an understanding of its genetic control remains elusive in apple and other fruit crops. In this study, we conducted genomic sequence analysis of 497 Malus accessions and revealed erosion of genetic diversity caused by apple breeding and possible independent domestication events of dessert and cider apples. Signatures of selection for fruit acidity and size, but not for fruit sugar content, were detected during the processes of both domestication and improvement. Furthermore, we found that single mutations in major genes affecting fruit taste, including Ma1, MdTDT, and MdSOT2, dramatically decrease malate, citrate, and sorbitol accumulation, respectively, and correspond to important domestication events. Interestingly, Ma1 was identified to have pleiotropic effects on both organic acid content and sugar:acid ratio, suggesting that it plays a vital role in determining fruit taste. Fruit taste is unlikely to have been negatively affected by linkage drag associated with selection for larger fruit that resulted from the pyramiding of multiple genes with minor effects on fruit size. Collectively, our study provides new insights into the genetic basis of fruit quality and its evolutionary roadmap during apple domestication, pinpointing several candidate genes for genetic manipulation of fruit taste in apple.

Nondestructive 3D Image Analysis Pipeline to Extract Rice Grain Traits Using X-Ray Computed Tomography

The traits of rice panicles play important roles in yield assessment,variety classification,rice breeding,and cultivation management.Most traditional grain phenotyping methods require threshing and thus are time-consuming and labor-intensive;moreover,these methods cannot obtain 3D grain traits.In this work,based on X-ray computed tomography,we proposed an image analysis method to extract twenty-two 3D grain traits.After 104 samples were tested,the R^(2) values between the extracted and manual measurements of the grain number and grain length were 0.980 and 0.960,respectively.We also found a high correlation between the total grain volume and weight.In addition,the extracted 3D grain traits were used to classify the rice varieties,and the support vector machine classifier had a higher recognition accuracy than the stepwise discriminant analysis and random forest classifiers.In conclusion,we developed a 3D image analysis pipeline to extract rice grain traits using X-ray computed tomography that can provide more 3D grain information and could benefit future research on rice functional genomics and rice breeding.

Advances in technologies for 3D genomics research

The spatial structure of the orderly organized chromatin in the nucleus has important roles in maintaining normal cell function and in regulation of gene expression, and the high-throughput Hi-C and Ch IA-PET methods have been widely used in various biological studies for determining potential spatial genome structures and their functions. However, there are still great difficulties and challenges in three-dimensional(3D) genomics research. More efficient, economical, and unbiased approaches to studying 3D genomics need to be developed for more widespread and easier applications. Here, we review the most recent studies on new 3D genomics research technologies, such as improvements of the traditional Hi-C and Ch IA-PET methods, new approaches based on non-proximal-ligation strategies, and imaging-based methods improved in recent years. Especially, we review the CRISPR-based methods for functional validations in 3D genomics, which could be the forthcoming directions. We hope this review can show some insights into the potential improvements for future 3D genomics.

HPV-CCDC106 integration alters local chromosome architecture and hijacks an enhancer by three-dimensional genome structure remodeling in cervical cancer

Integration of human papillomavirus(HPV)DNA into the human genome is a reputed key driver of cervical cancer.However,the effects of HPV integration on chromatin structural organization and gene expression are largely unknown.We studied a cohort of 61 samples and identified an integration hot spot in the CCDC106 gene on chromosome 19.We then selected fresh cancer tissue that contained the unique integration loci at CCDC106 with no HPV episomal DNA and performed whole-genome,RNA,chromatin immunoprecipitation and high-throughput chromosome conformation capture(Hi-C)sequencing to identify the mechanisms of HPV integration in cervical carcinogenesis.Molecular analyses indicated that chromosome 19 exhibited significant genomic variation and differential expression densities,with correlation found between three-dimensional(3D)structural change and gene expression.Importantly,HPV integration divided one topologically associated domain(TAD)into two smaller TADs and hijacked an enhancer from PEG3 to CCDC106,with a decrease in PEG3 expression and an increase in CCDC106 expression.This expression dysregulation was further confirmed using 10 samples from our cohort,which exhibited the same HPV-CCDC106 integration.In summary,we found that HPV-CCDC106 integration altered local chromosome architecture and hijacked an enhancer via 3D genome structure remodeling.Thus,this study provides insight into the 3D structural mechanism underlying HPV integration in cervical carcinogenesis.

3RISPR-P 2.0： An Improved CRISPR-Cas9 Too For Genome Editing in Plants

The clustered regularly interspaced short palindromic repeat （CRISPR） - CRISPR-associated protein 9 （CRISPR-Cas9） system has emerged as a versatile molecular tool for genome editing in various organisms in recent years （Tsai and Joung, 2016）. In this system, the endonuclease of Cas9 is directed to DNA targets by a synthetic guide RNA （sgRNA）.

Robust capturing chromosome conformation using the DLO Hi-C 2.0 method

The human genome contains around 20,000 protein-coding genes and a vast of transcriptional regulatory elements(ENCODE Project Consortium,2012;Roadmap Epigenomics Consortium et al.,2015;Stunnenberg and Hirst,2016).It still remains elusive how these regulatory elements regulate their target genes across genomic distances of millions of bases.