High-resolution genetic mapping of maize pan-genome sequence anchors

Lü, Fei; Romay, M. Cinta; Glaubitz, Jeffrey C.; Bradbury, Peter J.; Elshire, Robert J.; Wang, Tianyu; Yu, Li; Li, Yongxiang; Semagn, Kassa; Zhang, Xuecai; Hernandez, Alvaro G.; Mikel, Mark A.; Soifer, Ilya; Barad, Omer; Buckler, Edward S.

doi:10.1038/ncomms7914

Cited by 202 publications

(184 citation statements)

References 43 publications

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“…There have been two approaches to study its diversity. Survey short-read sequencing has been performed on a large number of inbred lines to achieve a global overview of genome structural variation (37). BAC libraries have been constructed and DNA fingerprinting has been used to reconstruct chromosomal regions with overlaps so that the sequences of these regions could be obtained from sequencing these BAC clones (21,38).…”

Section: Discussionmentioning

confidence: 99%

Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads

Dong

Feng

Kumar

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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Haplotype variation not only involves SNPs but also insertions and deletions, in particular gene copy number variations. However, comparisons of individual genomes have been difficult because traditional sequencing methods give too short reads to unambiguously reconstruct chromosomal regions containing repetitive DNA sequences. An example of such a case is the protein gene family in maize that acts as a sink for reduced nitrogen in the seed. Previously, 41-48 gene copies of the alpha zein gene family that spread over six loci spanning between 30-and 500-kb chromosomal regions have been described in two Iowa Stiff Stalk (SS) inbreds. Analyses of those regions were possible because of overlapping BAC clones, generated by an expensive and labor-intensive approach. Here we used singlemolecule real-time (Pacific Biosciences) shotgun sequencing to assemble the six chromosomal regions from the Non-Stiff Stalk maize inbred W22 from a single DNA sequence dataset. To validate the reconstructed regions, we developed an optical map (BioNano genome map; BioNano Genomics) of W22 and found agreement between the two datasets. Using the sequences of full-length cDNAs from W22, we found that the error rate of PacBio sequencing seemed to be less than 0.1% after autocorrection and assembly. Expressed genes, some with premature stop codons, are interspersed with nonexpressed genes, giving rise to genotype-specific expression differences. Alignment of these regions with those from the previous analyzed regions of SS lines exhibits in part dramatic differences between these two heterotic groups.shotgun DNA sequencing | haplotype variation | gene copy number | transposable elements | maize genome U ltimately all traits are manifested in the gene content of the genome. Despite the complex nature of the regulation of mRNA synthesis and turnover, cDNA sequencing had been used as an economic approach to determine the gene content of the human genome (1). However, to achieve a better overview of all genes and their chromosomal organization, whole-genome sequencing of the human genome became essential (2). Still, the identification of all genes and their order in chromosomes of eukaryotic species has been hampered by the presence of repetitive DNA in large-size genomes. The portion of repetitive DNA in genomes is not only composed of transposable elements but also of gene families, which can vary in copy number even within the same species, generating haplotypes with changes in gene expression (3,4).It also has become clear that the distribution of genes and transposable elements is intermixed and one cannot sequence one or the other separately; they are contiguous in nature. This has been overcome by the construction of genomic libraries in the form of yeast and bacterial artificial chromosomes used to make physical maps before sequencing them individually (5, 6). An advantage was that such clone collections could be sequenced by large consortiums and organized as community efforts (7). A disadvantage was the lack of completion and the enor...

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Section: Discussionmentioning

confidence: 99%

Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads

Dong

Feng

Kumar

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

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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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“…TEs are now recognized as an abundant and unexplored natural source of regulatory sequences for host genes, and TE biology has become an active research area in recent years [5][6][7][8][9][10] . Sequencing technologies such as Illumina HiSeq X Ten and PacBio RS II sequencing, and new library construction methods such as 10x Genomics, as well as new assembly techniques such as DeNovoMAGIC2 11,12 , are now significantly accelerating the progress of wheat genome sequencing efforts. Common wheat is a hexaploid species with A, B and D subgenomes.…”

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confidence: 99%

The Aegilops tauschii genome reveals multiple impacts of transposons

Zhao¹,

Zou²,

et al. 2017

Nature Plants

165

112

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Wheat is an important global crop with an extremely large and complex genome that contains more transposable elements (TEs) than any other known crop species. Here, we generated a chromosome-scale, high-quality reference genome of Aegilops tauschii, the donor of the wheat D genome, in which 92.5% sequences have been anchored to chromosomes. Using this assembly, we accurately characterized genic loci, gene expression, pseudogenes, methylation, recombination ratios, microRNAs and especially TEs on chromosomes. In addition to the discovery of a wave of very recent gene duplications, we detected that TEs occurred in about half of the genes, and found that such genes are expressed at lower levels than those without TEs, presumably because of their elevated methylation levels. We mapped all wheat molecular markers and constructed a high-resolution integrated genetic map corresponding to genome sequences, thereby placing previously detected agronomically important genes/ quantitative trait loci (QTLs) on the Ae. tauschii genome for the first time. NaTuRe PLaNTs

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High-resolution genetic mapping of maize pan-genome sequence anchors

Cited by 202 publications

References 43 publications

Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads

Analysis of tandem gene copies in maize chromosomal regions reconstructed from long sequence reads

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

The Aegilops tauschii genome reveals multiple impacts of transposons

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