The occurrence,inheritance,and segregation of complex genomic structural variation in synthetic Brassica napus

"Synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop improvement.Such synthetic allopolyploids often undergo rapid genomic structural variation(SV).However,how such SV arises,is inherited and fixed,and how it affects important traits,has rarely been comprehensively and quantitively studied in advanced generation synthetic lines.A better understanding of these processes will aid breeders in knowing how to best utilize synthetic allopolyploids in breeding programs.Here,we analyzed three genetic mapping populations(735 DH lines)derived from crosses between advanced synthetic and conventional Brassica napus(rapeseed)lines,using whole-genome sequencing to determine genome composition.We observed high tolerance of large structural variants,particularly toward the telomeres,and preferential selection for balanced homoeologous exchanges(duplication/deletion events between the A and C genomes resulting in retention of gene/chromosome dosage between homoeologous chromosome pairs),including stable events involving whole chromosomes("pseudoeuploidy").Given the experimental design(all three populations shared a common parent),we were able to observe that parental SV was regularly inherited,showed genetic hitchhiking effects on segregation,and was one of the major factors inducing adjacent novel and larger SV.Surprisingly,novel SV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic lines.However,incorporating genome-wide SV in linkage mapping explained significantly more genetic variance for traits.Our results provide a framework for detecting and understanding the occurrence and inheritance of genomic SV in breeding programs,and support the use of synthetic parents as an important source of novel trait variation.

Structural Variation Analysis of Mutated Nannochloropsis oceanica Caused by Zeocin Through Genome Re-Sequencing

Zeocin can cause double strand breaks of DNA and thus may be employed as a mutagen. In this study, two strains of Nannochloropsis oceanica, the wild and the Zeocin-tolerant strains, were re-sequenced to verify such function of Zeocin, The results showed that Zeocin can mutate the N. oceanica genome and cause the structural variation. Zeocin either swept away or selected the alleles of genes functioning in ubiquitin-mediated proteolysis, alpha-linolenic acid metabolism, ascorbate and aldarate metabolism, ribosome biogenesis, and circadian rhythm, indicating that N. oceanica may have adjusted its metabolic performances for protein, carbohydrate, and lipid, and changed its ribosome biosynthesis and living rhythm to survive in Zeocin containing medium. In addition, Zeocin caused mutation may have influenced the expression of a set of tanscription factors. It was concluded that Zeocin effectively caused the structural variation of the genome of N. oceanica, and forced the microalgae to select out the alleles of a set of genes around these variations in order to adapt to Zeocin containing medium. Further studies on the genetic basis of the phenotypic adaptation of this haploid and asexual microalga and the application of Zeocin to its genetic improvement are very important.

The role of genomic structural variation in the genetic improvement of polyploid crops

Many of our major crop species are polyploids, containing more than one genome or set of chromosomes. Polyploid crops present unique challenges, including difficulties in genome assembly, in discriminating between multiple gene and sequence copies, and in genetic mapping, hindering use of genomic data for genetics and breeding. Polyploid genomes may also be more prone to containing structural variation, such as loss of gene copies or sequences(presence–absence variation) and the presence of genes or sequences in multiple copies(copynumber variation). Although the two main types of genomic structural variation commonly identified are presence–absence variation and copy-number variation, we propose that homeologous exchanges constitute a third major form of genomic structural variation in polyploids. Homeologous exchanges involve the replacement of one genomic segment by a similar copy from another genome or ancestrally duplicated region, and are known to be extremely common in polyploids. Detecting all kinds of genomic structural variation is challenging, but recent advances such as optical mapping and long-read sequencing offer potential strategies to help identify structural variants even in complex polyploid genomes. All three major types of genomic structural variation(presence–absence, copy-number, and homeologous exchange) are now known to influence phenotypes in crop plants, with examples of flowering time, frost tolerance, and adaptive and agronomic traits. In this review,we summarize the challenges of genome analysis in polyploid crops, describe the various types of genomic structural variation and the genomics technologies and data that can be used to detect them, and collate information produced to date related to the impact of genomic structural variation on crop phenotypes. We highlight the importance of genomic structural variation for the future genetic improvement of polyploid crops.

3D genome structural variations play important roles in regulating seed oil content of Brassica napus

Dissecting the complex regulatory mechanism of seed oil content(SOC)is one of the main research goals in Brassica napus.Increasing evidence suggests that genome architecture is linked to multiple biological functions.However,the effect of genome architecture on SOC regulation remains unclear.Here,we used high-throughput chromatin conformation capture to characterize differences in the three-dimen-sional(3D)landscape of genome architecture of seeds from two B.napus lines,N53-2(with high SOC)and Ken-C8(with low SOC).Bioinformatics analysis demonstrated that differentially accessible regions and differentially expressed genes between N53-2 and Ken-C8 were preferentially enriched in regions with quantitative trait loci(QTLs)/associated genomic regions(AGRs)for SOC.A multi-omics analysis demonstrated that expression of SOC-related genes was tightly correlated with genome structural varia-tions in QTLs/AGRs of B.napus.The candidate gene BnaA09g48250D,which showed structural variation in a QTL/AGR on chrA09,was identified byfine-mapping of a KN double-haploid population derived from hybridization of N53-2 and Ken-C8.Overexpression and knockout of BnaA09g48250D led to significant in-creases and decreases in SOC,respectively,in the transgenic lines.Taken together,our results reveal the 3D genome architecture of B.napus seeds and the roles of genome structural variations in SOC regulation,enriching our understanding of the molecular mechanisms of SOC regulation from the perspective of spatial chromatin structure.

Structural variation(SV)-based pan-genome and GWAS reveal the impacts of SVs on the speciation and diversification of allotetraploid cottons

Structural variations(SVs)have long been described as being involved in the origin,adaption,and domes-tication of species.However,the underlying genetic and genomic mechanisms are poorly understood.Here,we report a high-quality genome assembly of Gossypium barbadense acc.Tanguis,a landrace that is closely related to formation of extra-long-staple(ELS)cultivated cotton.An SV-based pan-genome(Pan-SV)was then constructed using a total of 182593 non-redundant SVs,including 2236 inversions,97398 insertions,and 82959 deletions from 11 assembled genomes of allopolyploid cotton.The utility of this Pan-sV was then demonstrated through population structure analysis and genome-wide association studies(GWASs).Using segregation mapping populations produced through crossing ELS cotton and the landrace along with an Sv-based GWAs,certain SVs responsible for speciation,domestication,and improvement in tetraploid cottons were identified.Importantly,some of the SVs presently identified as associated with the yield and fiber quality improvement had not been identified in previous SNP-based GWAS.In particular,a 9-bp insertion or deletion was found to associate with elimination of the interspecific reproductive isolation between Gossypium hirsutum and G.barbadense.Collectively,this study provides new insights into genome-wide,gene-scale SVs linked to important agronomic traits in a major crop spe-cies and highlights the importance of sVs during the speciation,domestication,and improvement of culti-vated crop species.

Analysis on Genomic Structure Changes and Diversity of Introgression Lines in Dongxiang Wild Rice(Oryza rufipogon Griff.)

[Objective] The aim of the study was to make research on genomic struc- ture variation and variety analysis of Dongxiang wild rice. [Method] Introgression groups of BC1F6 were based on donor of Oryza rufipogon Griff. and receptor of O. sativa sp. indica Kate. Strains of 239 in the group were analyzed on Polymor- phism with the help of 25 couples of SSR primers distributed in 12 pairs of chromo- somes. [Result] Gene fragments of O. rufipogon Griff. were found penetrated in the 25 microsatellite sites and most of the groups kept the parents of Xieqinzao B or DNA sequence of O. rufipogon Griff. The average rate of recurrent homozygous bands was 78.13% in the ILs, but the highest was 94.98% （amplified by primer RM131） and the lowest was 60.25% （RM171）. The average rate of donor homozy- gous bands was 13.37%, but the highest was 32.64% （RM171） and the lowest was 2.93% （RM1095）. There were numerous heterozygous sites in the population and the average heterozygosis rate was 5.62%, while the highest was 10.04%（RM401）. Moreover, we found some parental fragments were lost and some novel fragments were not detected in either parent in BC1F6 population. The average rate of lost bands was 2.88%, while the highest was 13.39% （RM311） and the lowest was 0 （RM401）. The average rate of new bands was 1%. The average of Nei＇s gene di- versity （He） and Shannon＇s Information index （I） were 0.276 and 0.457 respectively in high generation of introgression lines. [Conclusion] The study demonstrated that distant hybridization led to extensive genetic and epigenetic variations in high gener- ation of introgression lines, which expanded the base of genetic variation and laid an important foundation for rice improvement and germplasm innovation.

Structural variation in complex genome: detection, integration and function

Structural variations (SVs) are mutations with large-scale changes (generally>50 bp) in the genome. SVs are major sources of the genetic diversity of organisms and thus are of high relevance to phenotype variations, gene dosage and evolutionary genetics. Except detecting SVs through comparative genetic analyses, dozens of software had been developed based on the alignment of short-reads to a single linear genome in the past decades (Guan and Sung, 2016).

Directed yeast genome evolution by controlled introduction of trans-chromosomic structural variations

Naturally occurring structural variations(SVs)are a considerable source of genomic variation that can reshape the 3D architecture of chromosomes.Controllable methods aimed at introducing the complex SVs and their related molecular mechanisms have remained farfetched.In this study,an SV-prone yeast strain was developed using Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution(SCRaMbLE)technology with two synthetic chromosomes,namely synV and synX.The biosynthesis of astaxanthin is used as a readout and a proof of concept for the application of SVs in industries.Our findings showed that complex SVs,including a pericentric inversion and a trans-chromosome translocation between synV and synX,resulted in two neo-chromosomes and a 2.7-fold yield of astaxanthin.Also,genetic targets were mapped,which resulted in a higher astaxanthin yield,thus demonstrating the SVs’ability to reorganize genetic information along the chromosomes.The rational design of trans-chromosome translocation and pericentric inversion enabled precise induction of these phenomena.Collectively,this study provides an effective tool to not only accelerate the directed genome evolution but also to reveal the mechanistic insight of complex SVs for altering phenotypes.

Genome assembly of KA105,a new resource for maize molecular breeding and genomic research

Superior inbred lines are central to maize breeding as sources of natural variation.Although many elite lines have been sequenced,less sequencing attention has been paid to newly developed lines.We constructed a genome assembly of the elite inbred line KA105,which has recently been developed by an arti-ficial breeding population named Shaan A and has shown desirable characteristics for breeding.Its pedigree showed genetic divergence from B73 and other lines in its pedigree.Comparison with the B73 reference genome revealed extensive structural variation,58 presence/absence variation(PAV)genes,and 1023 expanded gene families,some of which may be associated with disease resistance.A network-based integrative analysis of stress-induced transcriptomes identified 13 KA105-specific PAV genes,of which eight were induced by at least one kind of stress,participating in gene modules responding to stress such as drought and southern leaf blight disease.More than 200,000 gene pairs were differentially correlated between KA105 and B73 during kernel development.The KA105 reference genome and transcriptome atlas are a resource for further germplasm improvement and surveys of maize genomic variation and gene function.

Structural and Expressional Variation Analyses of Mitochondrial Genomes Reveal Candidate Transcripts for the S^V Cytoplasmic Male Sterility in Wheat(Triticum aestivum L.)

Common wheat （Triticum aestivum L.） is one of the most important crops, and intra-specific wheat hybrids have obvious heterosis in yield and protein quality. Therefore, utilization of hybrid wheat varieties offers an effective way to increase yield and nutrition. Cytoplasmic male sterility （CMS） systems are a useful genetic tool for hybrid crop breeding, and are ideal models for studying the genetic interaction and cooperative function of mitochondrial and nuclear genomes in plants （Schnable and Wise, 1998; Hanson and Bentolila, 2004）.

Snapshot of Structural Variations in the Tibetan Wild Boar Genome at Single-Nucleotide Resolution

Genomic structural variations （SVs）, particularly insertions, deletions and inversions, can contribute to the heterogeneity of millions of nucleotides within a genome, and are likely to make an important contribution to biological diversity and phenotypic variation （Alkan et al., 2011; Bickhart and Liu, 2014）. With the rapid development of the next-generation sequencing technologies and the new assembly methodolo- gies, the multiple de novo assemblies of genomes within a species allow researchers to explore more detailed SV maps （Li et al., 2011）. Compared with the traditional read depth algorithm using the whole-genome resequencing approach and array-based technologies （Baker, 2012; Wang et al., 2012;

Genetic variation may play a crucial role in non-coding RNA biogenesis

Transcription, post-transcriptional modification, translation, post-translational modification, DNA replication, and signaling interaction of intra- and extra- cellular components are the relevant mechanisms in gene regulation. Transcription is one of the most important mechanisms in the control of gene expression. Further, post-transcriptional modifications play a crucial role after transcription which determine whether the transcribed gene is coding or non-coding RNA (ncRNAs). Genome-wide analysis of RNAs provides information about the coding RNAs, whereas the status of ncRNAs are still at large and must be discussed in detail as variations in the ncRNAs can lead to different phenotypes. In this short article, we discuss the role of genetic variation in ncRNA genes and how this variation may play a crucial role in ncRNA biogenesis that eventually leads to phenotypic variation and thus speciation.

Unraveling the puzzle of the origin and evolution of cotton A-genome

Gossypium hirsutum,the most widely planted cotton species,its evolution has long been an unsolved puzzle because of its hybrid origin from D-genome and A-genome species.To better understand the genetic component of cotton,Huang et al.recently sequenced and assembled the first A1-genome G.herbaceum,and updated the A2-genome G.arboreum and(AD)1-genome G.hirsutum.On the basis of the three reference genomes,they resolved existing controversial concepts and provided novel evolutionary insights surrounding the A-genome.

Statistical analysis for genome-wide association study

In the past few years, genome-wide association study （GWAS） has made great successes in identifying genetic susceptibility loci underlying many complex diseases and traits. The findings provide important genetic insights into understanding pathogenesis of diseases. In this paper, we present an overview of widely used approaches and strategies for analysis of GWAS, offered a general consideration to deal with GWAS data. The issues regarding data quality control, population structure, association analysis, multiple comparison and visual presentation of GWAS results are discussed; other advanced topics including the issue of missing heritability, meta-analysis, setbased association analysis, copy number variation analysis and GWAS cohort analysis are also briefly introduced.

Incidence,genomic diversity,and evolution of strawberry mottle virus in China

Strawberry mottle virus(SMoV)is one of the most common viruses infecting strawberries,causing losses to fruit yield and quality.In this study,165 strawberry leaf samples were collected from six provinces of China,46 of which tested positive for SMoV.The complete genome sequences of 11 SMoV isolates were obtained from Liaoning(DGHY3,DGHY16-2,DGHY17,DGHY20-2,DGHY21,DGHY26-2),Shandong(SDHY1,SDHY5,SDHY31-2,SDHY33-2),and Beijing(BJMX7).The RNA1 and RNA2 nucleotide identities between the 11 Chinese isolates were 95.4-99.3%and 96.3-99.6%,respectively,and they shared 78.4-96.6%and 84.8-93.5%identities with the available SMoV isolates in GenBank.Recombination analysis revealed that Chinese isolate SDHY33-2 and Canadian isolates Ontario and Simcoe were recombinants,and recombination events frequently occurred in the 3’UTR of SMoV.Phylogenetic analysis showed that in an RNA1 tree,most Chinese isolates clustered into the same group while isolate DGHY17 clustered into another group together with Czech isolate C and three Canadian isolates.In an RNA2 tree,all Chinese isolates clustered into a single group.The phylogenetic analysis based on nucleotide sequences was consistent with the results based on coat protein(CP)and RNA-dependent RNA polymerase(RdRp).Further evolutionary analysis indicated that negative selection drives SMoV evolution,and gene flow plays a major role in genetic differentiation.Additionally,reassortment and recombination also influence the evolution of SMoV.To our knowledge,this is the first report of the complete genome of SMoV isolates from China and a detailed analysis of the SMoV population structure.

The identification of presence/absence variants associated with the apparent differences of growth period structures between cultivated and wild soybeans

The cultivated soybean（Glycine max（L.） Merr.） was distinguished from its wild progenitor Glycine soja Sieb.＆ Zucc.in growth period structure,by a shorter vegetative phase（V）,a prolonged reproductive phase（R） and hence a larger R/V ratio.However,the genetic basis of the domestication of soybean from wild materials is unclear.Here,a panel of 123 cultivated and 97 wild accessions were genotyped using a set of 24 presence/absence variants（PAVs） while at the same time the materials were phenotyped with respect to flowering and maturity times at two trial sites located at very different latitudes.The major result of this study showed that variation at PAVs is informative for assessing patterns of genetic diversity in Glycine spp.The genotyping was largely consistent with the taxonomic status,although a few accessions were intermediate between the two major clades identified.Allelic diversity was much higher in the wild germplasm than in the cultivated materials.A significant domestication signal was detected at 11 of the PAVs at 0.01 level.In particular,this study has provided information for revealing the genetic basis of photoperiodism which was a prominent feature for the domestication of soybean.A significant marker-trait association with R/V ratio was detected at 14 of the PAVs,but stripping out population structure reduced this to three.These results will provide markers information for further finding of R/V related genes that can help to understand the domestication process and introgress novel genes in wild soybean to broaden the genetic base of modern soybean cultivars.

基于全基因组重测序数据的新疆褐牛基因组结构变异检测及群体结构分析

旨在鉴定新疆褐牛基因组结构变异(structure variation,SVs)特征,并在此基础上探索新疆褐牛培育过程中受到影响的结构变异。本研究基于全基因组重测序数据,利用Manta、Delly、Lumpy三款软件对新疆褐牛及其父母本(瑞士褐牛、哈萨克牛)以及中国西门塔尔牛基因组结构变异进行检测,之后利用主成分分析、构建系统发育树和遗传分化指数(F_(ST))将新疆褐牛基因组与其余3个品种进行比较分析。结果显示,4个牛品种共检测出54969个SVs,缺失型变异占比最高(56.59%),插入型变异占比最少(0.03%)。从数量上看,这些SVs在染色体上的分布呈现出随染色体号变大而逐渐减少的趋势。不同品种间存在共有变异和品种特有变异,其中地方品种哈萨克牛拥有的特有SVs数量最多。主成分分析和系统发育树结果发现,新疆褐牛同哈萨克牛和瑞士褐牛具有较近的亲缘关系。经选择信号分析、基因注释和富集分析,挖掘出了一批与产奶性状(PI 4K2A、ELOVL3、ECHS1、SCD、TCF 7L2、PNLIPRP2、BTRC、PLCE 1)、生长发育(BMP6、TLL2、MAPK9、ROR 2)、适应性(PRKC B)以及免疫(GSTO2、GSTO 1)相关的关键基因。本研究从结构变异上解析新疆褐牛的特征,并揭示一些新疆褐牛培育过程中高度分化的基因,为推动新疆褐牛的遗传改良提供了基础资料。

大豆泛基因组研究进展

人工驯化为农业发展提供了原始驱动力,也深刻地改变了许多动植物的遗传背景。伴随组学大数据理论和技术体系的发展,作物基因组研究已迈入泛基因组时代。借助泛基因组的研究思路,通过多基因组间的比较和整合,能够评估物种遗传信息上界和下界,认知物种的遗传多样性全貌。此外,将泛基因组与染色体大尺度结构变异、群体高通量测序及多层次组学数据相结合,可以进行更为深入的性状-遗传机制解析。大豆(Glycine max(L.)Merr.)是重要的粮油经济作物,大豆产能关乎国家粮食安全。对大豆遗传背景形成、重要农艺性状关键位点的解析,是实现更高效的大豆育种改良的前提。本文首先对泛基因组学的核心问题进行了阐述,解释了从头组装/比对组装、迭代式组装和图基因组等泛基因组研究策略的演变历程和各自特征;接着对作物泛基因组研究的热点问题进行了概括,并且以大豆为例详细阐释了包括类群选择、泛基因组构建、数据挖掘等方面在内的泛基因组研究的开展思路,着重说明染色体结构变异在大豆演化/驯化历程中的贡献及其在农艺性状遗传基础挖掘上的价值;最后讨论了图泛基因组在数据整合、结构变异计算方面的应用前景。本文对作物泛基因组未来的发展趋势进行了展望,以期为作物基因组学及数据科学研究提供参考。

基于全基因组重测序分析大尾寒羊基因组变异特征和群体结构

旨在了解大尾寒羊基因组遗传变异特征和群体结构,可以为更好地保护和利用大尾寒羊提供指导。本研究对170只(66只公羊,104只母羊)大尾寒羊进行了全基因组重测序,利用GATK、Manta、Plink等软件对大尾寒羊基因组遗传变异、群体结构和连锁不平衡等进行了分析,以期了解大尾寒羊基因组变异特征和群体结构。测序共获得1599.56 G高质量数据(平均9.409 G·只^(-1))。大尾寒羊群体中共发现50276079个SNPs和7240540个InDel,它们多分布于基因间和内含子区域。群体的基因组结构性变异(SV)最多的类型为染色体间的易位(CTX),平均每只羊有415.82个CTX,主要分布在基因间区域;发生拷贝数变异(CNV)最多的区域在外显子,平均每只羊有175个。主成分分析显示,大尾寒羊个体较分散,聚集不集中。结合亲缘关系、系统发育树和群体结构,将大尾寒羊分为6个家系,各家系含量差别较大,体型有差异。群体聚类分析中发现有些个体祖先成分较为单一。群体连锁不平衡(LD)分析显示LD衰减速度快,群体遗传多样性较高。驯化中受选择的基因主要与脂质代谢和产热有关。综上,大尾寒羊群体包含6个家系,遗传多样性较丰富,保种效果良好,建议对小家系进行扩繁,大家系注意减少近交,确保家系结构平衡,同时注重大尾寒羊的开发和利用。

The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies.Poplars,among the world’s most widely distributed and cultivated trees,exhibit extensive phenotypic diversity and environmental adaptability.In this study,we present a genus-level super-pangenome comprising 19 Populus genomes,revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation.Through the integration of pangenomes with transcriptomes,methylomes,and chromatin accessibility mapping,we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures,notably CG methylation in gene-body regions.Further comparative genomic analyses have enabled the identification of 142202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence.We have experimentally validated a∼180-bp presence/absence variant affecting the expression of the CUC2 gene,crucial for leaf serration formation.Finally,we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome(http://www.populus-superpangenome.com).Together,the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.