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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, Corrensstra├če 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

Bar plots of the STRUCTURE analysis.Each of the 21 maize inbred lines is represented by a vertical bar, partitioned into K = 8 colored segments that designate the fraction of each population estimated to belong to the inferred subgroups (Population ID corresponds to S1 Table).
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pone.0132120.g004: Bar plots of the STRUCTURE analysis.Each of the 21 maize inbred lines is represented by a vertical bar, partitioned into K = 8 colored segments that designate the fraction of each population estimated to belong to the inferred subgroups (Population ID corresponds to S1 Table).

Mentions: STRUCTURE analysis predicted K = 8 as the optimum number of sub-populations, revealing that at least eight distinct groups exist in the studied inbred lines (Fig 4 and S4 Fig). Some groups displayed heterogeneity, comprising a sizable portion of another group; however, most inbred lines originating from the USA clustered together in one group (yellow-filled bar). In regards to the two main gene pools (Dent and Flint), the majority of flints, except those originating from France, were classified into four distinct groups, each consisting of an individual inbred line. The flints originating from France contained a significant portion of USA dent materials. On the other hand, dent materials (except F7059, originating from France) display heterogeneity, comprising a portion from at least one of the four dent groups.


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)

Bar plots of the STRUCTURE analysis.Each of the 21 maize inbred lines is represented by a vertical bar, partitioned into K = 8 colored segments that designate the fraction of each population estimated to belong to the inferred subgroups (Population ID corresponds to S1 Table).
© Copyright Policy
Related In: Results  -  Collection

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

pone.0132120.g004: Bar plots of the STRUCTURE analysis.Each of the 21 maize inbred lines is represented by a vertical bar, partitioned into K = 8 colored segments that designate the fraction of each population estimated to belong to the inferred subgroups (Population ID corresponds to S1 Table).
Mentions: STRUCTURE analysis predicted K = 8 as the optimum number of sub-populations, revealing that at least eight distinct groups exist in the studied inbred lines (Fig 4 and S4 Fig). Some groups displayed heterogeneity, comprising a sizable portion of another group; however, most inbred lines originating from the USA clustered together in one group (yellow-filled bar). In regards to the two main gene pools (Dent and Flint), the majority of flints, except those originating from France, were classified into four distinct groups, each consisting of an individual inbred line. The flints originating from France contained a significant portion of USA dent materials. On the other hand, dent materials (except F7059, originating from France) display heterogeneity, comprising a portion from at least one of the four dent groups.

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, Corrensstra├če 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