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

The Crop Journal 2024年第2期12卷 515-528页

作者： Dandan Hu Jin Lu Wenwen Li Yinghui Yang Junxiong Xu Han Qin Hao Wang Yan Niu Huaiqi Zhang Qingqing Liu Xiangxiang He annaliese s.mason JChris Pires Zhiyong Xiong Jun Zou National Key Laboratory of Crop Genetic Improvement College of Plant Science and TechnologyHuazhong Agricultural UniversityWuhan 430070HubeiChina College of Agronomy Henan Agricultural UniversityZhengzhou 450002HenanChina Key Laboratory of Herbage and Endemic Crop Biotechnology Inner Mongolia UniversityHohhot 010070Inner MongoliaChina Plant Breeding Department University of BonnBonn 53115Germany Department of soil and Crop sciences Colorado State UniversityFort CollinsCO 80523USA

"synthetic"allopolyploids recreated by interspecific hybridization play an important role in providing novel genomic variation for crop *** 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 ***,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 *** 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 ***,novel sV occurred at low frequencies with no significant impacts on observed fertility and yield-related traits in the advanced generation synthetic ***,incorporating genome-wide sV in linkage mapping explained significantly more genetic variance for *** 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.

关键词： Allopolyploid Large Genome structural variation Linkage mapping synthetic polyploids Inheritance and segregation

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

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The Crop Journal 2019年第2期7卷 127-140页

作者： sarah-Veronica schiessl Elvis Katche Elizabeth Ihien Harmeet singh Chawla annaliese s.mason Department of Plant Breeding Justus Liebig University

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.

关键词： Presence–absence variation Copy-number variation Homeologous exchanges Genome structure Pan-genome

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Fertility,genome stability,and homozygosity in a diverse set of resynthesized rapeseed lines

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The Crop Journal 2023年第2期11卷 468-477页

作者： Elizabeth Ihien Katche Antje schierholt Heiko C.Becker Jacqueline Batley annaliese s.mason Plant Breeding Department The University of Bonn53115 BonnGermany Department of Plant Breeding Justus Liebig University35392 GiessenGermany Department of Crop sciences Division of Plant Breeding MethodologyGeorg-August University Göttingen37073 GöttingenGermany school of Biological sciences The University of Western AustraliaPerthWA 6009Australia

Rapeseed(Brassica napus,AACC)was formed by hybridization between progenitor species Brassica rapa(AA)and Brassica oleracea(CC).As a result of a limited number of hybridization events between specific progenitor genotypes and strong breeding selection for oil quality traits,rapeseed has limited genetic *** production of resynthesized *** lines via interspecific hybridization of the diploid progenitor species *** and *** is one possible way to increase genetic variation in ***,most resynthesized lines produced so far have been reported to be meiotically unstable and infertile,in contrast to established *** *** hinders both maintenance and use of this germplasm in breeding *** characterized a large set of 140 resynthesized lines produced by crosses between *** and ***,as well as between *** and wild C genome species(***,***,***,***,*** and ***)for purity(homozygosity),fertility,and genome ***-pollinated seed set,seeds per ten pods as well as percentage pollen viability were used to estimate *** genotyping was performed using the Illumina Infinium Brassica 60K array for 116 genotypes,with at least three individuals per *** of the material which had been advanced through multiple generations was no longer pure,with heterozygosity detected corresponding to unknown parental contributions via *** and genome stability were both *** lines had high numbers of copy number variants(CNVs),indicative of meiotic instability,and high numbers of CNVs were significantly associated with reduced *** putatively stable resynthesized *** lines were *** investigation of these lines may reveal the mechanisms underlying this *** results suggest that selection of stable resynthesized lines for breeding purposes is possible.

关键词： Fertility Genome stability Copy number variants sNP genotyping Resynthesized lines

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New Insights into Nested Long Terminal Repeat Retrotransposons in Brassica species

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Molecular Plant 2013年第2期6卷 470-482页

作者： Lijuan Wei Meili Xiaoa Zeshan An Bi Ma annaliese s. mason Wei Qian Jiana Li Donghui Fu Chongqing Engineering Research Center for Rapeseed College of Agronomy and Biotechnology Southwest University Chongqing 400716 China school of Agriculture and Food sciences and centre for Integrative I~egume-Research The University of Queensland 1:he Universit'y of QueenslandBrisbane 4072 Australia Key Laboratory of Crop Physiology Ecology and Genetic Breeding Ministry of Education Agronomy College Jiangxi Agricultural University Nanchang330045 China

Long terminal repeat （LTR） retrotransposons, one of the foremost types of transposons, continually change or modify gene function and reorganize the genome through bursts of dramatic proliferation. Many LTR-TEs preferen-tially insert within other LTR-TEs, but the cause and evolutionary significance of these nested LTR-TEs are not well under-stood. In this study, a total of 1.52 Gb of Brassica sequence containing 2020 bacterial artificial chromosomes （BACs） was scanned, and six bacterial artificial chromosome （BAC） clones with extremely nested LTR-TEs （LTR-TEs density： 7.24/kb） were selected for further analysis. The majority of the LTR-TEs in four of the six BACs were found to be derived from the rapid proliferation of retrotransposons originating within the BAC regions, with only a few LTR-TEs originating from the proliferation and insertion of retrotransposons from outside the BAC regions approximately 5-23 Mya. LTR-TEs also pref-erably inserted into TA-rich repeat regions. Gene prediction by Genescan identified 207 genes in the 0.84Mb of total BAC sequences. Only a few genes （3/207） could be matched to the Brassica expressed sequence tag （EsT） database, indicating that most genes were inactive after retrotransposon insertion. Five of the six BACs were putatively centromeric. Hence, nested LTR-TEs in centromere regions are rapidly duplicated, repeatedly inserted, and act to suppress activity of genes and to reshuffle the structure of the centromeric sequences. Our results suggest that LTR-TEs burst and proliferate on a local scale to create nested LTR-TE regions, and that these nested LTR-TEs play a role in the formation of centromeres.

关键词： LTR retrotransposons Brassica centromere retrotransposon-rich transposon burst.

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Research progress and strategies for multifunctional rapeseed： A case study of China

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Journal of Integrative Agriculture 2016年第8期15卷 1673-1684页

作者： FU Dong-hui JIANG Ling-yan annaliese s mason XIAO Mei-li ZHU Long-rong LI Li-zhi ZHOU Qing-hong sHEN Chang-jian HUANG Chun-hui Key Laboratory of Crop Physiology Ecology and Genetic Breeding Ministry of Education/Agronomy College Jiangxi Agricultural University Nanchang 330045 P.R.China Department of Biochemistry University of Missouri Columbia 65211 USA Department of Plant Breeding IFZ Research Centre for Biosystems Land Use and Nutrition Justus Liebig University Heinrich- Buff-Ring 26-32 Giessen 35392 Germany Jiangxi Province Key Laboratory of Animal Nutrition/Engineering Research Center of Feed Development Jiangxi Agricultural University Nanchang 330045 P.R. China Linli County Rural Practical Technology Research Institute Changde 415000 P.R. China

financially supported by the Key R＆D Program of Jiangxi Province of China （20152ACF60010）;the Key Projects of Hunan science and Technology support Program of China （Application research of Guiye A male sterile line）;the Research Project of Humanities and social sciences in Universities of Jiangxi Province, China（JC1315）;supported by Emmy Noether DFG grant MA 6473/1-1

关键词： multifunctional rapeseed sightseeing rapeseed remediation of cadmium pollution rapeseed oil fodder vegetables

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

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The Crop Journal 2024年第2期 515页

作者： Dandan Hu Jin Lu Wenwen Li Yinghui Yang Junxiong Xu Han Qin Hao Wang Yan Niu Huaiqi Zhang Qingqing Liu Xiangxiang He annaliese s.mason J.Chris Pires Zhiyong Xiong Jun Zou

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Characterization and evolution of conserved miRNA through duplication events in date palm(Phoenix dactylifera)

Characterization and evolution of conserved miRNA through du...

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第十四届全国植物基因组学大会

作者： Wei Xia Yong Xiao Yaodong Yang annaliese s.mason Xintao Lei Zilong Ma Hainan Key Laboratory of Tropical Oil Crops Biology Coconuts Research InstituteChinese Academy of Tropical Agricultural Sciences

MicroRNAs(miRNAs) are important regulators of gene expression at the post-transcriptional level in a wide range of *** conserved miRNAs regulate ancestral transcription factors common to all plants,and control importa... 详细信息

关键词： Phoenix dactylifera microRNA genomic duplication

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RNA-seq analysis of Cocos nucifera:transcriptome sequencing and de novo assembly for subsequent functional genomics approaches

RNA-Seq analysis of Cocos nucifera:transcriptome sequencing ...

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第十四届全国植物基因组学大会

作者： Yong Xiao Haikuo Fan Yaodong Yang Wei Xia annaliese s.mason Zhihui Xia songlin Zhao Hainan Key Laboratory of Tropical Oil Crops Biology Coconut Research InstituteChinese Academy of Tropical Agricultural Sciences

Cocos nucifera(coconut),a member of the Arecaceae family,is an economically important woody palm grown in tropical *** its agronomic importance, previous germplasm assessment studies have relied solely on morphologica... 详细信息

关键词： Cocos nucifera L. RNA-seq denovo assemble transcriptome fatty acid

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Efficient isolation of high quality RNA from tropical palms for RNA-seq analysis

Efficient isolation of high quality RNA from tropical palms ...

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第十四届全国植物基因组学大会

作者： Lixia Zhou Yong Xiao Yaodong Yang Hongxing Cao Haikuo Fan Zilong Ma Xintao Lei annaliese s.mason Zhihui Xia Xi Huang Coconuts Research Institute Chinese Academy of Tropical Agricultural Sciences

Currently,RNA-seq as a high throughput technology is being widely applied to various species to elucidate the complexity of the transcriptome and to discover large number of novel ***,the technology has had poor succe... 详细信息

关键词： RNA isolation RNA-seq Cocos nucifera Palmaceace rRNA

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

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The Crop Journal 2019年第2期

作者： sarah-Veronica schiessl Elvis Katche Elizabeth Ihien Harmeet singh Chawla annaliese s.mason

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