Molecular Markers for Sweet Sorghum Based on Microarray Expression Data

Calviño, Martín; Miclaus, Mihai; Bruggmann, Rémy; Messing, Joachim

doi:10.1007/s12284-009-9029-8

Cited by 19 publications

(18 citation statements)

References 27 publications

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“…Our comparative analysis from re-sequencing data showed that genes with functionally divergent genes between BT×623 and Keller might not be directly involved in sugar accumulation. Interestingly, screening of sorghum genes linked to high sugar content indicated that 80% of differentially expressed genes between sweet and grain sorghum had their orthologs in rice suggesting limited contribution of their gene content for differentiating sorghum sugar accumulation [8,9]. Thus, our data and others [8,9,28] suggested that expression divergence should play important roles in the divergence of sugar accumulation between sweet and grain sorghum lines.…”

Section: Discussionmentioning

confidence: 53%

“…Interestingly, screening of sorghum genes linked to high sugar content indicated that 80% of differentially expressed genes between sweet and grain sorghum had their orthologs in rice suggesting limited contribution of their gene content for differentiating sorghum sugar accumulation [8,9]. Thus, our data and others [8,9,28] suggested that expression divergence should play important roles in the divergence of sugar accumulation between sweet and grain sorghum lines. In fact, changes of gene expression in eukaryotes often give rise to new phenotypes and the changes were frequently used as a proxy indicator of functional divergence of genes [29].…”

Section: Discussionmentioning

confidence: 53%

“…The chips were used for detecting the expression of only 12,982 unique genes. Calviño et al (2008; 2009) identified 154 differentially expressed genes between grain and sweet sorghum lines by using an Affymetrix sugarcane genechip [8,9]. However, only conserved sorghum genes could be detectable using the sugarcane chip.…”

Section: Introductionmentioning

confidence: 99%

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Genetic variation and expression diversity between grain and sweet sorghum lines

Jiang

Jeevanandam

et al. 2013

BMC Genomics

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BackgroundBiological scientists have long sought after understanding how genes and their structural/functional changes contribute to morphological diversity. Though both grain (BT×623) and sweet (Keller) sorghum lines originated from the same species Sorghum bicolor L., they exhibit obvious phenotypic variations. However, the genome re-sequencing data revealed that they exhibited limited functional diversity in their encoding genes in a genome-wide level. The result raises the question how the obvious morphological variations between grain and sweet sorghum occurred in a relatively short evolutionary or domesticated period.ResultsWe implemented an integrative approach by using computational and experimental analyses to provide a detail insight into phenotypic, genetic variation and expression diversity between BT×623 and Keller lines. We have investigated genome-wide expression divergence between BT×623 and Keller under normal and sucrose treatment. Through the data analysis, we detected more than 3,000 differentially expressed genes between these two varieties. Such expression divergence was partially contributed by differential cis-regulatory elements or DNA methylation, which was genetically determined by functionally divergent genes between these two varieties. Both tandem and segmental duplication played important roles in the genome evolution and expression divergence.ConclusionSubstantial differences in gene expression patterns between these two varieties have been observed. Such an expression divergence is genetically determined by the divergence in genome level.

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Section: Discussionmentioning

confidence: 53%

Section: Discussionmentioning

confidence: 53%

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Genetic variation and expression diversity between grain and sweet sorghum lines

Jiang

Jeevanandam

et al. 2013

BMC Genomics

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“…The juice from three internodes of the main stem was harvested at the time of flowering and the Brix degree measured as previously described [30,31]. The average Brix degree from three internodes per plant was used.…”

Section: Methodsmentioning

confidence: 99%

Characterization of the small RNA component of the transcriptome from grain and sweet sorghum stems

2011

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BackgroundSorghum belongs to the tribe of the Andropogoneae that includes potential biofuel crops like switchgrass, Miscanthus and successful biofuel crops like corn and sugarcane. However, from a genomics point of view sorghum has compared to these other species a simpler genome because it lacks the additional rounds of whole genome duplication events. Therefore, it has become possible to generate a high-quality genome sequence. Furthermore, cultivars exists that rival sugarcane in levels of stem sugar so that a genetic approach can be used to investigate which genes are differentially expressed to achieve high levels of stem sugar.ResultsHere, we characterized the small RNA component of the transcriptome from grain and sweet sorghum stems, and from F2 plants derived from their cross that segregated for sugar content and flowering time. We found that variation in miR172 and miR395 expression correlated with flowering time whereas variation in miR169 expression correlated with sugar content in stems. Interestingly, genotypic differences in the ratio of miR395 to miR395* were identified, with miR395* species expressed as abundantly as miR395 in sweet sorghum but not in grain sorghum. Finally, we provided experimental evidence for previously annotated miRNAs detecting the expression of 25 miRNA families from the 27 known and discovered 9 new miRNAs candidates in the sorghum genome.ConclusionsSequencing the small RNA component of sorghum stem tissue provides us with experimental evidence for previously predicted microRNAs in the sorghum genome and microRNAs with a potential role in stem sugar accumulation and flowering time.

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“…We discovered allelic variation in miR169 expression between grain and sweet sorghum, suggesting that miR169 could also play a role in the sugar content of sorghum stems (Calvino et al 2011). Although high sugar content in stems is a trait shared by sorghum and sugarcane (Calvino et al 2008, 2009), this trait seems to be silent in other grasses (Calvino and Messing 2011). This prompted us to investigate the evolution and dynamic amplification of miR169 gene copies in grass genomes.…”

Section: Introductionmentioning

confidence: 99%

Discovery of MicroRNA169 Gene Copies in Genomes of Flowering Plants through Positional Information

Calviño

Messing

2013

Genome Biology and Evolution

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Expansion and contraction of microRNA (miRNA) families can be studied in sequenced plant genomes through sequence alignments. Here, we focused on miR169 in sorghum because of its implications in drought tolerance and stem-sugar content. We were able to discover many miR169 copies that have escaped standard genome annotation methods. A new miR169 cluster was found on sorghum chromosome 1. This cluster is composed of the previously annotated sbi-MIR169o together with two newly found MIR169 copies, named sbi-MIR169t and sbi-MIR169u. We also found that a miR169 cluster on sorghum chr7 consisting of sbi-MIR169l, sbi-MIR169m, and sbi-MIR169n is contained within a chromosomal inversion of at least 500 kb that occurred in sorghum relative to Brachypodium, rice, foxtail millet, and maize. Surprisingly, synteny of chromosomal segments containing MIR169 copies with linked bHLH and CONSTANS-LIKE genes extended from Brachypodium to dictotyledonous species such as grapevine, soybean, and cassava, indicating a strong conservation of linkages of certain flowering and/or plant height genes and microRNAs, which may explain linkage drag of drought and flowering traits and would have consequences for breeding new varieties. Furthermore, alignment of rice and sorghum orthologous regions revealed the presence of two additional miR169 gene copies (miR169r and miR169s) on sorghum chr7 that formed an antisense miRNA gene pair. Both copies are expressed and target different set of genes. Synteny-based analysis of microRNAs among different plant species should lead to the discovery of new microRNAs in general and contribute to our understanding of their evolution.

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Molecular Markers for Sweet Sorghum Based on Microarray Expression Data

Abstract: Using an Affymetrix sugarcane genechip, we previously identified 154 genes differentially expressed between grain and sweet sorghum. Although many of these genes have functions related to sugar and cell wall metabolism, dissection of the trait requires genetic analysis.

Cited by 19 publications

References 27 publications

Genetic variation and expression diversity between grain and sweet sorghum lines

Genetic variation and expression diversity between grain and sweet sorghum lines

Characterization of the small RNA component of the transcriptome from grain and sweet sorghum stems

Discovery of MicroRNA169 Gene Copies in Genomes of Flowering Plants through Positional Information

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