In silico mapping of 1758 new SSR markers developed from public genomic sequences for sorghum

Li, Manli; Yuyama, Nana; Luo, Le; Hirata, Masaharu; Cai, Hongwei

doi:10.1007/s11032-009-9270-2

Cited by 55 publications

(33 citation statements)

References 23 publications

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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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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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“…A total of 639 pairs of sorghum simple sequence repeat (SSR) markers (Li et al 2009;Yonemaru et al 2009) distributed across the sorghum genome were used to screen for polymorphisms in the parental lines, and 127 polymorphic SSR primer pairs were used to genotype the F 2 populations. For the ATx623 × SA2313 population, we genotyped six polymorphic SSR markers on chromosome 1 (the qGW1 region), nine markers on chromosome 2 (the qGW2 region), and one marker on chromosome 4 (sorghum homolog of rice grain weight gene GW2).…”

Section: Molecular Marker Analysismentioning

confidence: 99%

“…To fine-map qGW1, additional SSR primers in the target region were identified (Li et al 2009;Yonemaru et al 2009), as well as designing four new SSR markers on the basis of the sorghum genome sequence (http://www. gramene.org/Sorghum_bicolor/Location).…”

Section: Molecular Marker Analysismentioning

confidence: 99%

“…PCR reactions were carried out using an M13-tagged forward primer (Rampling et al 2001) as previously described (Li et al 2009). The reaction mixture (10 μl) contained 20 ng template DNA, 1 pmol forward primer, 5 pmol reverse primer, 5 pmol M13 (−29) primer, 1 μl of 10 × PCR buffer, 0.8 μl of 2.5 mM dNTPs, and 0.5 U Taq polymerase.…”

Section: Molecular Marker Analysismentioning

confidence: 99%

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Fine mapping of qGW1, a major QTL for grain weight in sorghum

Han

Chen

Mace³

et al. 2015

Theor Appl Genet

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We detected seven QTLs for 100-grain weight in sorghum using an F 2 population, and delimited qGW1 to a 101-kb region on the short arm of chromosome 1, which contained 13 putative genes. Sorghum is one of the most important cereal crops. Breeding high-yielding sorghum varieties will have a profound impact on global food security. Grain weight is an important component of grain yield. It is a quantitative trait controlled by multiple quantitative trait loci (QTLs); however, the genetic basis of grain weight in sorghum is not well understood. In the present study, using an F2 population derived from a cross between the grain sorghum variety SA2313 (Sorghum bicolor) and the Sudan-grass variety Hiro-1 (S. bicolor), we detected seven QTLs for 100-grain weight. One of them, qGW1, was detected consistently over 2 years and contributed between 20 and 40 % of the phenotypic variation across multiple genetic backgrounds. Using extreme recombinants from a fine-mapping F3 population, we delimited qGW1 to a 101-kb region on the short arm of chromosome 1, containing 13 predicted gene models, one of which was found to be under purifying selection during domestication. However, none of the grain size candidate genes shared sequence similarity with previously cloned grain weight-related genes from rice. This study will facilitate isolation of the gene underlying qGW1 and advance our understanding of the regulatory mechanisms of grain weight. SSR markers linked to the qGW1 locus can be used for improving sorghum grain yield through marker-assisted selection.

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“…CAP3 and BLASTN are used for clustering and alignment, while SSRIT and MISA are used for the identifi cation of microsatellites. During the last 5 years, about 1758 new SSR markers from genomic sequence contigs (Li et al 2009a ), 109 and 600 SSR markers from ESTs (Ramu et al 2009 ;Srinivas et al 2009 ), 1519 SSR markers from unigenes (Nagaraja Reddy et al 2012 ), and 5599 SSR and 110 (GATA) n motif-based SSR markers from whole-genome sequences (Yonemaru et al 2009 ;Jaikishan et al 2013 ) were developed through in silico approaches.…”

Section: Bioinformatics For Molecular Marker Developmentmentioning

confidence: 99%

Molecular Marker Development Using Bioinformatic Tools

Rajendrakumar

2015

Sorghum Molecular Breeding

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In silico mapping of 1758 new SSR markers developed from public genomic sequences for sorghum

Cited by 55 publications

References 23 publications

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

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

Fine mapping of qGW1, a major QTL for grain weight in sorghum

Molecular Marker Development Using Bioinformatic Tools

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