Development of Genome-wide Simple Sequence Repeat Markers Using Whole-genome Shotgun Sequences of Sorghum (Sorghum bicolor (L.) Moench)

Yonemaru, Jun‐ichi; Ando, Tsuyu; Mizubayashi, Tatsumi; Kasuga, Shigemitsu; Matsumoto, Takashi; Yano, Masahiro

doi:10.1093/dnares/dsp005

Cited by 96 publications

(80 citation statements)

References 27 publications

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“…This is higher than EST-SSRs reported in wheat (25%), sorghum (45%) and cultivated flax (40.7%) (Eujayl et al 2002;Cloutier et al 2009, Yonemaru et al 2009), but lower than another study in L. usitatissimum (62.2%) (Roose-Amsaleg et al 2006). Differences in polymorphism might be attributable to the genomic origin of the SSRs developed by Roose-Amsaleg et al (2006) considered more polymorphic than EST-SSRs.…”

Section: Distribution Of Est-ssrs and Polymorphismcontrasting

confidence: 56%

Characterization of novel genic SSR markers in Linum usitatissimum (L.) and their transferability across eleven Linum species

Soto‐Cerda¹,

Saavedra²,

Navarro³

et al. 2011

Electro Journal of Biotech

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Little is known about the evolutionary relationships among Linum species, basically because of the lack of transferable molecular markers. Currently, expressed sequence tags available in public databases provide an opportunity for the rapid and inexpensive development of simple sequence repeat (SSR) markers in wild flax species. In this regard, fifty expressed sequence tag-derived microsatellite markers (EST-SSRs) were evaluated for polymorphism and transferability in 50 Linum usitatissimum cultivars/accessions and 11 Linum species. Among them 23 EST-SSRs were polymorphic in L. usitatissimum, while 2-4 alleles were detected (average 2.26 per locus). The polymorphism information content value ranged from 0.08 to 0.55 (average 0.38). Forty one genic markers (95.3%) produced strong amplicons in at least two of the 11 Linum species. The percentage of cross amplification ranged from 34.1% to 92.7% in L. tauricum and L. bienne, respectively. Moreover, the rate of transferability was associated positively with the botanical section. Our results suggest that the high degree of EST-SSRs transferability to Linum species can be a useful enhancement of the current database of SSR markers for future genetic and evolutionary studies.

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Section: Distribution Of Est-ssrs and Polymorphismcontrasting

confidence: 56%

Characterization of novel genic SSR markers in Linum usitatissimum (L.) and their transferability across eleven Linum species

Soto‐Cerda¹,

Saavedra²,

Navarro³

et al. 2011

Electro Journal of Biotech

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“…Lagercrantz et al (1993) reported the frequent occurrence of (AT) n motif among dinucleotides as the peculiar feature of most plant genomes. This is in accordance with the present study and other studies such as microsatellite detection in cpDNA of 12 Brassicaceae family members (Sumit et al 2010) and whole genome sequences of Sorghum bicolor (Yonemaru et al 2009) and pine genomic sequences (Chagne et al 2004).…”

Section: Ssr Distribution In Date Palm Genomesupporting

confidence: 94%

Microsatellites mining in date palm (Phoenix dactylifera L.) and their cross transferability across Arecaceae family

Manju¹,

Manimekalai²,

Naganeeswaran³

et al. 2016

Plant Omics

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Phoenix dactylifera L. (date palm) is the first publicly available nuclear genome sequence under Arecaceae family and indeed under the entire order Arecales. These genomic sequences were mined for microsatellites which could be used for marker assisted selection for important traits. We have developed an integrated, configurable and time effective microsatellite mining and annotation pipeline for this purpose. Microsatellite survey of date palm whole genome shotgun sequences using the developed pipeline detected a total of 166,760 perfect repeats with an average of one SSR per 2.2kb. Putative functions of these SSR-containing sequences within the proximity of genic regions were predicted. Primers targeting the functionally important SSR regions were designed and a set of eight SSR primers synthesized and were validated in vitro across five members of the Arecaceae family (coconut, arecanut, oilpalm, date palm and palmyrah palm). We have found that 28.6% of the SSRs are common among the members of arecaceae family. Those SSRs could be used in molecular marker analysis of less studied palm family members like arecanut and palmyrah palm.

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“…Compared to SNP marker system, SSR markers requires just the primer sequences which are usually available once published. This is the primary reason why so much effort has been devoted to developing SSR markers (Kong et al 2000;Li et al 2009;Ramu et al 2009;Srinivas et al 2009;Yonemaru et al 2009) and to using SSR markers in genetic mapping (Bhattramakki et al 2000;Haussmann et al 2002;Wu and Huang 2006), diversity studies (Abu Assar et al 2005;Agrama and Tuinstra 2003;Ali et al 2008;Anas and Yoshida 2004;Barnaud et al 2007;Caniato et al 2007;Casa et al 2005;Deu et al 2008;Dillon et al 2005;Folkertsma et al 2005;Ghebru et al 2002;Menz et al 2004;Pei et al 2010;Shehzad et al 2009b;Smith et al 2000;Wang et al 2009b) and molecular breeding (Knoll and Ejeta 2008) in sorghum. The objective of this study was to identify SSR markers associated with sorghum stem height using the aforementioned poolbased genome-wide association mapping technique.…”

Section: Introductionmentioning

confidence: 99%

Identification of SSR markers associated with height using pool-based genome-wide association mapping in sorghum

et al. 2011

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Sorghum has been proposed as a potential energy crop. However, it has been traditionally bred for grain yield and forage quality, not traits related to bioenergy production. To develop tools for genetic improvement of bioenergy-related traits such as height, genetic markers associated with these traits have to be identified first. Association mapping has been extensively used in humans and in some crop plants for this purpose. However, genome-wide association mapping using the whole association panel is costly and time-consuming. A variation of this method called pool-based genome-wide association mapping has been extensively used in humans. In this variation, pools of individuals with contrasting phenotypes, instead of the whole panel, are screened with genetic markers and polymorphic markers are confirmed by screening the individuals in the pools. Here we identified several new simple sequence repeats (SSR) markers associated with height using this pool-based genome-wide association mapping in sorghum.After screening the tall and short pools of sorghum accessions from the sorghum mini core collection developed at the International Crops Research Institute for the Semi-Arid Tropics with 703 SSR markers, we have identified four markers that are closely associated with sorghum height on chromosomes 2, 6, and 9. Comparison with published maps indicates that all four markers are clustered with markers previously mapped to height or height-related traits and with candidate genes involved in regulating plant height such as FtsZ, Ugt, and GA 2-oxidase. The mapping method can be applied to other crop plants for which a high throughput genome-wide association mapping platform is not yet available.

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Development of Genome-wide Simple Sequence Repeat Markers Using Whole-genome Shotgun Sequences of Sorghum (Sorghum bicolor (L.) Moench)

Cited by 96 publications

References 27 publications

Characterization of novel genic SSR markers in Linum usitatissimum (L.) and their transferability across eleven Linum species

Characterization of novel genic SSR markers in Linum usitatissimum (L.) and their transferability across eleven Linum species

Microsatellites mining in date palm (Phoenix dactylifera L.) and their cross transferability across Arecaceae family

Identification of SSR markers associated with height using pool-based genome-wide association mapping in sorghum

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