Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

Hirsch, Candice N.; Hirsch, Cory D.; Brohammer, Alex B.; Bowman, Megan J.; Soifer, Ilya; Barad, Omer; Shem-Tov, Doron; Baruch, Kobi; Lü, Fei; Hernandez, Alvaro G.; Fields, Christopher J.; Wright, Chris; Koehler, Klaus L.; Springer, Nathan M.; Buckler, Edward S.; Buell, C. Robin; León, Natalia de; Kaeppler, Shawn M.; Childs, Kevin L.; Mikel, Mark A.

doi:10.1105/tpc.16.00353

Cited by 181 publications

(210 citation statements)

References 91 publications

(134 reference statements)

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“…2c). The new maize B73 reference genome has 240 fold higher contiguity than the recently published short read genome assembly of maize cultivar PH207 (contig N50: 1,180 kb versus 5 kb) 13 .…”

Section: Openmentioning

confidence: 80%

Improved maize reference genome with single-molecule technologies

Jiao

Peluso

Shi

et al. 2017

Nature

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1,036

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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: 80%

Improved maize reference genome with single-molecule technologies

Jiao

Peluso

Shi

et al. 2017

Nature

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1,036

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“…For example, by a conservative estimate, at least 180 putative single-copy genes were present in one inbred but absent in the other, and >400 instances of putative sequence copy number variation between the two inbreds were observed (Springer et al, 2009). Likewise, a comparison (Hirsch et al, 2016) between B73 and PH207 found >2500 genes present only in one of those inbreds.…”

Section: Conventional Plant Breeding Sources Of Genetic Variation Usementioning

confidence: 96%

“…This germplasm is adapted for breeding in Maize proteins (300-400 amino acids long) from 2 alleles differ by 3-4 amino acids Tenaillon et al (2001) Maize genome has 55 million SNPs Gore et al (2009) Green Revolution gene has 2 SNPs for dwarf wheat Peng et al (1999) One SNP caused loss of shattering in domestic rice Konishi et al (2006) Tall or short pea plants (Mendel) Ellis et al (2011) Silva et al (2013) Only 81% of Brassica genes are always present in the same number Golicz et al (2016) 2500 genes found only in either B73 or PH207 Hirsch et al (2016) G. soja genotypes can vary by 1000 to 3000 gene families from each other Li et al (2014) 1992). Nevertheless, breeders are shifting from using these random methods of introducing genetic diversity over the past couple of decades to newer, more predictable methods like genetic engineering.…”

Section: Conventional Plant Breeding Sources Of Genetic Variation Usementioning

confidence: 99%

Bringing New Plant Varieties to Market: Plant Breeding and Selection Practices Advance Beneficial Characteristics while Minimizing Unintended Changes

et al. 2017

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Commercial‐scale plant breeding is a complex process in which new crop varieties are continuously being developed to improve yield and agronomic performance over current varieties. A wide array of naturally occurring genetic changes are sources of new characteristics available to plant breeders. During conventional plant breeding, genetic material is exchanged that has the potential to beneficially or adversely affect plant characteristics. For this reason, commercial‐scale breeders have implemented extensive plant selection practices to identify the top‐performing candidates with the desired characteristics while minimizing the advancement of unintended changes. Selection practices in maize (Zea mays L.) breeding involve phenotypic assessments of thousands of candidate lines throughout hundreds of different environmental conditions over many years. Desirable characteristics can also be introduced through genetic modification. For genetically modified (GM) crops, molecular analysis is used to select transformed plants with a single copy of an intact DNA insert and without disruption of endogenous genes. All the while, GM crops go through the same extensive phenotypic characterization as conventionally bred crops. Data from both conventional and GM maize breeding programs are presented to show the similarities between these two processes.

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“…Such questions will best be approached through a comparative analysis of maize cell types, developmental states, and genetic variants. With the rapidly growing resources available for other maize lines (Lu et al, 2015;Andorf et al, 2016;Hirsch et al, 2016;Jiao et al, 2017), the ability to integrate the multiple kinds of information represented in replication timing profiles will greatly facilitate comparative analyses of the maize pan-genome.…”

Section: Models For Maize Dna Replication Timingmentioning

confidence: 99%

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

Wear

Song²,

Zynda³

et al. 2017

Plant Cell

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All plants and animals must replicate their DNA, using a regulated process to ensure that their genomes are completely and accurately replicated. DNA replication timing programs have been extensively studied in yeast and animal systems, but much less is known about the replication programs of plants. We report a novel adaptation of the "Repli-seq" assay for use in intact root tips of maize (Zea mays) that includes several different cell lineages and present whole-genome replication timing profiles from cells in early, mid, and late S phase of the mitotic cell cycle. Maize root tips have a complex replication timing program, including regions of distinct early, mid, and late S replication that each constitute between 20 and 24% of the genome, as well as other loci corresponding to ;32% of the genome that exhibit replication activity in two different time windows. Analyses of genomic, transcriptional, and chromatin features of the euchromatic portion of the maize genome provide evidence for a gradient of early replicating, open chromatin that transitions gradually to less open and less transcriptionally active chromatin replicating in mid S phase. Our genomic level analysis also demonstrated that the centromere core replicates in mid S, before heavily compacted classical heterochromatin, including pericentromeres and knobs, which replicate during late S phase.

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Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize

Cited by 181 publications

References 91 publications

Improved maize reference genome with single-molecule technologies

Improved maize reference genome with single-molecule technologies

Bringing New Plant Varieties to Market: Plant Breeding and Selection Practices Advance Beneficial Characteristics while Minimizing Unintended Changes

Genomic Analysis of the DNA Replication Timing Program during Mitotic S Phase in Maize (Zea mays) Root Tips

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