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Targeted Sequencing Reveals Large-Scale Sequence Polymorphism in Maize Candidate Genes for Biomass Production and Composition.

Muraya MM, Schmutzer T, Ulpinnis C, Scholz U, Altmann T - PLoS ONE (2015)

Bottom Line: We found that substantial sequence variation exists among genomic regions targeted in this study, which was particularly evident within coding regions.Further, annotated SNPs identified here will serve as useful genetic tools and as candidates in searches for phenotype-altering DNA variation.In summary, we demonstrated that sequencing of captured DNA is a powerful approach for variant discovery in maize genes.

View Article: PubMed Central - PubMed

Affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Stadt Seeland, Germany; Department of Plant Science, Chuka University, P.O. Box, 109-60400, Chuka, Kenya.

ABSTRACT
A major goal of maize genomic research is to identify sequence polymorphisms responsible for phenotypic variation in traits of economic importance. Large-scale detection of sequence variation is critical for linking genes, or genomic regions, to phenotypes. However, due to its size and complexity, it remains expensive to generate whole genome sequences of sufficient coverage for divergent maize lines, even with access to next generation sequencing (NGS) technology. Because methods involving reduction of genome complexity, such as genotyping-by-sequencing (GBS), assess only a limited fraction of sequence variation, targeted sequencing of selected genomic loci offers an attractive alternative. We therefore designed a sequence capture assay to target 29 Mb genomic regions and surveyed a total of 4,648 genes possibly affecting biomass production in 21 diverse inbred maize lines (7 flints, 14 dents). Captured and enriched genomic DNA was sequenced using the 454 NGS platform to 19.6-fold average depth coverage, and a broad evaluation of read alignment and variant calling methods was performed to select optimal procedures for variant discovery. Sequence alignment with the B73 reference and de novo assembly identified 383,145 putative single nucleotide polymorphisms (SNPs), of which 42,685 were non-synonymous alterations and 7,139 caused frameshifts. Presence/absence variation (PAV) of genes was also detected. We found that substantial sequence variation exists among genomic regions targeted in this study, which was particularly evident within coding regions. This diversification has the potential to broaden functional diversity and generate phenotypic variation that may lead to new adaptations and the modification of important agronomic traits. Further, annotated SNPs identified here will serve as useful genetic tools and as candidates in searches for phenotype-altering DNA variation. In summary, we demonstrated that sequencing of captured DNA is a powerful approach for variant discovery in maize genes.

No MeSH data available.


Related in: MedlinePlus

Distribution of 4,785 candidate genes over 10 maize chromosomes.Selected genes are predicted to control various aspects of plant growth, biomass production, and composition; bar graph depicts their distribution in the maize genome.
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pone.0132120.g007: Distribution of 4,785 candidate genes over 10 maize chromosomes.Selected genes are predicted to control various aspects of plant growth, biomass production, and composition; bar graph depicts their distribution in the maize genome.

Mentions: A BLAST of the candidate genes from different species (maize, rice, barley, and Arabidopsis) was carried out against maize CDS (maize genome project: www.maizesequence.org, version ZmB73_4a.53). Maize gene identifiers were checked for uniqueness, and genomic sequences (exons, including introns) were extracted. All genes were extended by 1 kb at the 5′ and 3′ ends, and the primary target regions to be placed on the maize array were determined. This yielded a set of sequences having an L50 of 6,583 bp, with the largest contig covering 77 kb. Using this information, and eliminating redundancy, the number of genes was reduced to 4,758 (S12 Table), corresponding to 99% of the 2.1 M NimbleGen microarray capacity. These genes were well distributed across all the maize chromosomes (Fig 7). The gene coordinates genes were then sent to Roche NimbleGen to facilitate the design of a custom 2.1 NimbleGen sequence capture microarray.


Targeted Sequencing Reveals Large-Scale Sequence Polymorphism in Maize Candidate Genes for Biomass Production and Composition.

Muraya MM, Schmutzer T, Ulpinnis C, Scholz U, Altmann T - PLoS ONE (2015)

Distribution of 4,785 candidate genes over 10 maize chromosomes.Selected genes are predicted to control various aspects of plant growth, biomass production, and composition; bar graph depicts their distribution in the maize genome.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4495061&req=5

pone.0132120.g007: Distribution of 4,785 candidate genes over 10 maize chromosomes.Selected genes are predicted to control various aspects of plant growth, biomass production, and composition; bar graph depicts their distribution in the maize genome.
Mentions: A BLAST of the candidate genes from different species (maize, rice, barley, and Arabidopsis) was carried out against maize CDS (maize genome project: www.maizesequence.org, version ZmB73_4a.53). Maize gene identifiers were checked for uniqueness, and genomic sequences (exons, including introns) were extracted. All genes were extended by 1 kb at the 5′ and 3′ ends, and the primary target regions to be placed on the maize array were determined. This yielded a set of sequences having an L50 of 6,583 bp, with the largest contig covering 77 kb. Using this information, and eliminating redundancy, the number of genes was reduced to 4,758 (S12 Table), corresponding to 99% of the 2.1 M NimbleGen microarray capacity. These genes were well distributed across all the maize chromosomes (Fig 7). The gene coordinates genes were then sent to Roche NimbleGen to facilitate the design of a custom 2.1 NimbleGen sequence capture microarray.

Bottom Line: We found that substantial sequence variation exists among genomic regions targeted in this study, which was particularly evident within coding regions.Further, annotated SNPs identified here will serve as useful genetic tools and as candidates in searches for phenotype-altering DNA variation.In summary, we demonstrated that sequencing of captured DNA is a powerful approach for variant discovery in maize genes.

View Article: PubMed Central - PubMed

Affiliation: Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Corrensstraße 3, D-06466, Stadt Seeland, Germany; Department of Plant Science, Chuka University, P.O. Box, 109-60400, Chuka, Kenya.

ABSTRACT
A major goal of maize genomic research is to identify sequence polymorphisms responsible for phenotypic variation in traits of economic importance. Large-scale detection of sequence variation is critical for linking genes, or genomic regions, to phenotypes. However, due to its size and complexity, it remains expensive to generate whole genome sequences of sufficient coverage for divergent maize lines, even with access to next generation sequencing (NGS) technology. Because methods involving reduction of genome complexity, such as genotyping-by-sequencing (GBS), assess only a limited fraction of sequence variation, targeted sequencing of selected genomic loci offers an attractive alternative. We therefore designed a sequence capture assay to target 29 Mb genomic regions and surveyed a total of 4,648 genes possibly affecting biomass production in 21 diverse inbred maize lines (7 flints, 14 dents). Captured and enriched genomic DNA was sequenced using the 454 NGS platform to 19.6-fold average depth coverage, and a broad evaluation of read alignment and variant calling methods was performed to select optimal procedures for variant discovery. Sequence alignment with the B73 reference and de novo assembly identified 383,145 putative single nucleotide polymorphisms (SNPs), of which 42,685 were non-synonymous alterations and 7,139 caused frameshifts. Presence/absence variation (PAV) of genes was also detected. We found that substantial sequence variation exists among genomic regions targeted in this study, which was particularly evident within coding regions. This diversification has the potential to broaden functional diversity and generate phenotypic variation that may lead to new adaptations and the modification of important agronomic traits. Further, annotated SNPs identified here will serve as useful genetic tools and as candidates in searches for phenotype-altering DNA variation. In summary, we demonstrated that sequencing of captured DNA is a powerful approach for variant discovery in maize genes.

No MeSH data available.


Related in: MedlinePlus