Structural variations in plant genomes

Saxena, Rachit K.; Edwards, David; Varshney, Rajeev K.

doi:10.1093/bfgp/elu016

Cited by 186 publications

(154 citation statements)

References 85 publications

(120 reference statements)

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“…However, genome wide patterns of structural variation in plant genomes are difficult to assess 27 , and previous efforts have relied on short read mapping, which misses the vast majority of intergenic spaces where most rearrangements are likely to occur 10 . To investigate structural variation at a genome wide scale, we generated optical maps (Extended Data Table 1) for two additional maize inbred lines: the tropical line Ki11, one of the founders of the maize nested association mapping (NAM) population 28 , and W22, which has served as a foundation for studies of maize genetics 29 .…”

Section: Openmentioning

confidence: 99%

Improved maize reference genome with single-molecule technologies

Jiao

Peluso

Shi

et al. 2017

Nature

1,033

1,087

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Complete and accurate reference genomes and annotations provide fundamental tools for characterization of genetic and functional variation 1 . These resources facilitate the determination of biological processes and support translation of research findings into improved and sustainable agricultural technologies. Many reference genomes for crop plants have been generated over the past decade, but these genomes are often fragmented and missing complex repeat regions 2 . Here we report the assembly and annotation of a reference genome of maize, a genetic and agricultural model species, using single-molecule real-time sequencing and high-resolution optical mapping. Relative to the previous reference genome 3 , our assembly features a 52-fold increase in contig length and notable improvements in the assembly of intergenic spaces and centromeres. Characterization of the repetitive portion of the genome revealed more than 130,000 intact transposable elements, allowing us to identify transposable element lineage expansions that are unique to maize. Gene annotations were updated using 111,000 full-length transcripts obtained by single-molecule real-time sequencing 4 . In addition, comparative optical mapping of two other inbred maize lines revealed a prevalence of deletions in regions of low gene density and maize lineage-specific genes.

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Section: Openmentioning

confidence: 99%

Improved maize reference genome with single-molecule technologies

Jiao

Peluso

Shi

et al. 2017

Nature

1,033

1,087

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“…In Arabidopsis, SV deletions were found to affect more than 2000 protein coding genes (Cao et al, 2011), and in maize, SVs were found to be enriched at loci associated with important agronomical traits including leaf development and disease resistance (Chia et al, 2012). Despite these findings, the formation mechanisms of plant SVs and their functional impact still remain largely unexplored (Saxena et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

et al. 2015

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Structural variations (SVs) represent a major source of genetic diversity. However, the functional impact and formation mechanisms of SVs in plant genomes remain largely unexplored. Here, we report a nucleotide-resolution SV map of cucumber (Cucumis sativas) that comprises 26,788 SVs based on deep resequencing of 115 diverse accessions. The largest proportion of cucumber SVs was formed through nonhomologous end-joining rearrangements, and the occurrence of SVs is closely associated with regions of high nucleotide diversity. These SVs affect the coding regions of 1676 genes, some of which are associated with cucumber domestication. Based on the map, we discovered a copy number variation (CNV) involving four genes that defines the Female (F) locus and gives rise to gynoecious cucumber plants, which bear only female flowers and set fruit at almost every node. The CNV arose from a recent 30.2-kb duplication at a meiotically unstable region, likely via microhomology-mediated breakinduced replication. The SV set provides a snapshot of structural variations in plants and will serve as an important resource for exploring genes underlying key traits and for facilitating practical breeding in cucumber.

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“…of PAVs proves their connection with ancestral evolution and domestication [34]. PAVs are also found in mitochondrial DNA of maize [2,33]. CIMMYT, China and Brazil [21].…”

mentioning

confidence: 80%

Structural architecture of genome of corn

Сатарова¹

2016

Visnyk agrarnoi nauky

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T. Satarova, doctor of biological sciences Institute of grain crops of NAAS STRUCTURAL ARCHITECTURE OF GENOME OF CORNThe purpose. Analysis of modern state of researches of genome of corn, in particular structural architecture of kernel DNA and infraspecific polymorphy of the genome caused by emersion transposon, indels, microsatellites, one-nucleotide substitutions. Conclusions. The high level of scrutiny of structural architecture of genome of corn enables to identify molecular markers for assessment of polymorphy of selection specimens, to search functional markers of valuable economic attributes and to use them in programs of marker-associate selection.

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Structural variations in plant genomes

Cited by 186 publications

References 85 publications

Improved maize reference genome with single-molecule technologies

Improved maize reference genome with single-molecule technologies

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

Structural architecture of genome of corn

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