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Maize (Zea mays L.) genome diversity as revealed by RNA-sequencing.

Hansey CN, Vaillancourt B, Sekhon RS, de Leon N, Kaeppler SM, Buell CR - PLoS ONE (2012)

Bottom Line: However, the transcribed gene set among the 21 lines varied, with 48.7% expressed in all of the lines, 27.9% expressed in one to 20 lines, and 23.4% expressed in none of the lines.De novo assembly of RNA-seq reads that did not map to the reference B73 genome sequence revealed 1,321 high confidence novel transcripts, of which, 564 loci were present in all 21 lines, including B73, and 757 loci were restricted to a subset of the lines.RT-PCR validation demonstrated 87.5% concordance with the computational prediction of these expressed novel transcripts.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America.

ABSTRACT
Maize is rich in genetic and phenotypic diversity. Understanding the sequence, structural, and expression variation that contributes to phenotypic diversity would facilitate more efficient varietal improvement. RNA based sequencing (RNA-seq) is a powerful approach for transcriptional analysis, assessing sequence variation, and identifying novel transcript sequences, particularly in large, complex, repetitive genomes such as maize. In this study, we sequenced RNA from whole seedlings of 21 maize inbred lines representing diverse North American and exotic germplasm. Single nucleotide polymorphism (SNP) detection identified 351,710 polymorphic loci distributed throughout the genome covering 22,830 annotated genes. Tight clustering of two distinct heterotic groups and exotic lines was evident using these SNPs as genetic markers. Transcript abundance analysis revealed minimal variation in the total number of genes expressed across these 21 lines (57.1% to 66.0%). However, the transcribed gene set among the 21 lines varied, with 48.7% expressed in all of the lines, 27.9% expressed in one to 20 lines, and 23.4% expressed in none of the lines. De novo assembly of RNA-seq reads that did not map to the reference B73 genome sequence revealed 1,321 high confidence novel transcripts, of which, 564 loci were present in all 21 lines, including B73, and 757 loci were restricted to a subset of the lines. RT-PCR validation demonstrated 87.5% concordance with the computational prediction of these expressed novel transcripts. Intriguingly, 145 of the novel de novo assembled loci were present in lines from only one of the two heterotic groups consistent with the hypothesis that, in addition to sequence polymorphisms and transcript abundance, transcript presence/absence variation is present and, thereby, may be a mechanism contributing to the genetic basis of heterosis.

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Related in: MedlinePlus

Neighbor-Joining tree of 21 diverse maize lines based on 351,710 single nucleotide polymorphisms (SNPs).Frequency based distances were calculated as pair-wise Rogers distances [53]. PowerMarker version 3.25 [54] was used to construct the tree.
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pone-0033071-g002: Neighbor-Joining tree of 21 diverse maize lines based on 351,710 single nucleotide polymorphisms (SNPs).Frequency based distances were calculated as pair-wise Rogers distances [53]. PowerMarker version 3.25 [54] was used to construct the tree.

Mentions: Cluster analysis using allele frequency based distances from the 350,710 SNPs revealed the expected grouping of SSS and NSS type germplasm, and of exotic lines (Figure 2). Studies using 511 random SNP markers [8] and 100 simple sequence repeat markers [41] in larger diversity panels have also demonstrated that pedigree based groups cluster together using genomic markers. Higher marker density in this study markedly improved the clustering, although fewer lines were included.


Maize (Zea mays L.) genome diversity as revealed by RNA-sequencing.

Hansey CN, Vaillancourt B, Sekhon RS, de Leon N, Kaeppler SM, Buell CR - PLoS ONE (2012)

Neighbor-Joining tree of 21 diverse maize lines based on 351,710 single nucleotide polymorphisms (SNPs).Frequency based distances were calculated as pair-wise Rogers distances [53]. PowerMarker version 3.25 [54] was used to construct the tree.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC3306378&req=5

pone-0033071-g002: Neighbor-Joining tree of 21 diverse maize lines based on 351,710 single nucleotide polymorphisms (SNPs).Frequency based distances were calculated as pair-wise Rogers distances [53]. PowerMarker version 3.25 [54] was used to construct the tree.
Mentions: Cluster analysis using allele frequency based distances from the 350,710 SNPs revealed the expected grouping of SSS and NSS type germplasm, and of exotic lines (Figure 2). Studies using 511 random SNP markers [8] and 100 simple sequence repeat markers [41] in larger diversity panels have also demonstrated that pedigree based groups cluster together using genomic markers. Higher marker density in this study markedly improved the clustering, although fewer lines were included.

Bottom Line: However, the transcribed gene set among the 21 lines varied, with 48.7% expressed in all of the lines, 27.9% expressed in one to 20 lines, and 23.4% expressed in none of the lines.De novo assembly of RNA-seq reads that did not map to the reference B73 genome sequence revealed 1,321 high confidence novel transcripts, of which, 564 loci were present in all 21 lines, including B73, and 757 loci were restricted to a subset of the lines.RT-PCR validation demonstrated 87.5% concordance with the computational prediction of these expressed novel transcripts.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology, Michigan State University, East Lansing, Michigan, United States of America.

ABSTRACT
Maize is rich in genetic and phenotypic diversity. Understanding the sequence, structural, and expression variation that contributes to phenotypic diversity would facilitate more efficient varietal improvement. RNA based sequencing (RNA-seq) is a powerful approach for transcriptional analysis, assessing sequence variation, and identifying novel transcript sequences, particularly in large, complex, repetitive genomes such as maize. In this study, we sequenced RNA from whole seedlings of 21 maize inbred lines representing diverse North American and exotic germplasm. Single nucleotide polymorphism (SNP) detection identified 351,710 polymorphic loci distributed throughout the genome covering 22,830 annotated genes. Tight clustering of two distinct heterotic groups and exotic lines was evident using these SNPs as genetic markers. Transcript abundance analysis revealed minimal variation in the total number of genes expressed across these 21 lines (57.1% to 66.0%). However, the transcribed gene set among the 21 lines varied, with 48.7% expressed in all of the lines, 27.9% expressed in one to 20 lines, and 23.4% expressed in none of the lines. De novo assembly of RNA-seq reads that did not map to the reference B73 genome sequence revealed 1,321 high confidence novel transcripts, of which, 564 loci were present in all 21 lines, including B73, and 757 loci were restricted to a subset of the lines. RT-PCR validation demonstrated 87.5% concordance with the computational prediction of these expressed novel transcripts. Intriguingly, 145 of the novel de novo assembled loci were present in lines from only one of the two heterotic groups consistent with the hypothesis that, in addition to sequence polymorphisms and transcript abundance, transcript presence/absence variation is present and, thereby, may be a mechanism contributing to the genetic basis of heterosis.

Show MeSH
Related in: MedlinePlus