Simple Sequence Repeat Markers in Genetic Divergence and Marker-Assisted Selection of Rice Cultivars: A Review

Kaur, Shubhneet; Panesar, Parmjit S.; Bera, Manab Bandhu; Kaur, Varinder

doi:10.1080/10408398.2011.646363

Cited by 70 publications

(43 citation statements)

References 60 publications

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“…Simple sequence repeats (SSRs) in the cp genome can be highly variable at the intra-specific level, and are therefore often used as genetic markers in population genetics and evolutionary studies (Dong et al, 2013, 2016; Kaur et al, 2015; Suo et al, 2016; Yang et al, 2016). We analyzed the simple sequence repeats (SSRs) in the cp genomes (Tables 2, 3, Tables S2, S3).…”

Section: Resultsmentioning

confidence: 99%

Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes

Dong

Li³

et al. 2017

Front. Plant Sci.

123

101

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Crape myrtles are economically important ornamental trees of the genus Lagerstroemia L. (Lythraceae), with a distribution from tropical to northern temperate zones. They are positioned phylogenetically to a large subclade of rosids (in the eudicots) which contain more than 25% of all the angiosperms. They commonly bloom from summer till fall and are of significant value in city landscape and environmental protection. Morphological traits are shared inter-specifically among plants of Lagerstroemia to certain extent and are also influenced by environmental conditions and different developmental stages. Thus, classification of plants in Lagerstroemia at species and cultivar levels is still a challenging task. Chloroplast (cp) genome sequences have been proven to be an informative and valuable source of cp DNA markers for genetic diversity evaluation. In this study, the complete cp genomes of three Lagerstroemia species were newly sequenced, and three other published cp genome sequences of Lagerstroemia were retrieved for comparative analyses in order to obtain an upgraded understanding of the application value of genetic information from the cp genomes. The six cp genomes ranged from 152,049 bp (L. subcostata) to 152,526 bp (L. speciosa) in length. We analyzed nucleotide substitutions, insertions/deletions, and simple sequence repeats in the cp genomes, and discovered 12 relatively highly variable regions that will potentially provide plastid markers for further taxonomic, phylogenetic, and population genetics studies in Lagerstroemia. The phylogenetic relationships of the Lagerstroemia taxa inferred from the datasets from the cp genomes obtained high support, indicating that cp genome data may be useful in resolving relationships in this genus.

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Section: Resultsmentioning

confidence: 99%

Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes

Dong

Li³

et al. 2017

Front. Plant Sci.

123

101

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“…The popularity of SSR markers can be ascribed to a number of desirable genetic attributes including co-dominant inheritance, high reproducibility, robust amplification, multi-allelic nature, and wide genomic distribution in different coding and non-coding sequence components of genome (Li et al, 2004; Varshney et al, 2005; Parida et al, 2006; Miah et al, 2013). Furthermore, amenability of these markers to multiplex high-throughput genotyping makes them the prime choice for various plant structural, functional and comparative genomics applications (Ashkani et al, 2011; Luo et al, 2013; Zhang et al, 2014; Kaur et al, 2015). …”

Section: Introductionmentioning

confidence: 99%

An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice

et al. 2016

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Development and use of genome-wide informative simple sequence repeat (SSR) markers and novel integrated genomic strategies are vital to drive genomics-assisted breeding applications and for efficient dissection of quantitative trait loci (QTLs) underlying complex traits in rice. The present study developed 6244 genome-wide informative SSR markers exhibiting in silico fragment length polymorphism based on repeat-unit variations among genomic sequences of 11 indica, japonica, aus, and wild rice accessions. These markers were mapped on diverse coding and non-coding sequence components of known cloned/candidate genes annotated from 12 chromosomes and revealed a much higher amplification (97%) and polymorphic potential (88%) along with wider genetic/functional diversity level (16–74% with a mean 53%) especially among accessions belonging to indica cultivar group, suggesting their utility in large-scale genomics-assisted breeding applications in rice. A high-density 3791 SSR markers-anchored genetic linkage map (IR 64 × Sonasal) spanning 2060 cM total map-length with an average inter-marker distance of 0.54 cM was generated. This reference genetic map identified six major genomic regions harboring robust QTLs (31% combined phenotypic variation explained with a 5.7–8.7 LOD) governing grain weight on six rice chromosomes. One strong grain weight major QTL region (OsqGW5.1) was narrowed-down by integrating traditional QTL mapping with high-resolution QTL region-specific integrated SSR and single nucleotide polymorphism markers-based QTL-seq analysis and differential expression profiling. This led us to delineate two natural allelic variants in two known cis-regulatory elements (RAV1AAT and CARGCW8GAT) of glycosyl hydrolase and serine carboxypeptidase genes exhibiting pronounced seed-specific differential regulation in low (Sonasal) and high (IR 64) grain weight mapping parental accessions. Our genome-wide SSR marker resource (polymorphic within/between diverse cultivar groups) and integrated genomic strategy can efficiently scan functionally relevant potential molecular tags (markers, candidate genes and alleles) regulating complex agronomic traits (grain weight) and expedite marker-assisted genetic enhancement in rice.

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“…Its use has involved studies of quantification and determination of gene diversity (Cardoso et al, 2014); characterization of Value for Cultivation and Use (VCU) (Cardoso et al, 2013), assisted selection (Alzate-Marian et al, 2005), among others. The SSRs have been widely used in recent years and had selected population studies and use of genetic resources in plants for breeding purposes because of their hypervariability and ease polymorphism detection (Li et al, 2015a;Li et al, 2015b;Kaur et al, 2015;Zhai et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

In silico identification of putative expressed sequence tag (EST)-simple sequence repeats (SSRs) markers of resistance to Meloidogyne spp. in common bean

Vieira¹,

Silva²,

Pereira³

et al. 2016

Afr. J. Agric. Res.

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Expressed sequences are important sources in the development of functional heterologous microsatellite markers in phylogenetic related groups, that is, soybean and commom bean. The objective of this work was to identify and characterize expressed sequence tag (EST)-simple sequence repeats (SSRs) in silico candidates of resistance to Meloidogyne spp. in common bean. Seven DNA sequences from soybean associated with genetic resistance have been identified and obtained in the NCBI database. Its homology in common bean genome was verified using the BLAST tool. The cellular processes involved were also checked using the Blast2GO program. The identification of microsatellite markers and design of the primer pairs was performed using the SSRLocator and Primer3 programs, respectively. The transferability rate of common beans the target sequences identified was 86%, demonstrating the power of success of this method. All the cellular processes involved in the original DNA sequences were verified from EST on beans, with E-value between 0 and 2.9×10 -168. Fifteen ESTSSRs candidates for common bean resistance were identified, which have proved to be suitable for their amplification by PCR. The transferability analysis of ESTs related to resistance to Meloidogyne spp., especially among soybeans and common beans is efficient. Based on this study, 15 EST-SSRs candidates are available for validation and later use.

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Simple Sequence Repeat Markers in Genetic Divergence and Marker-Assisted Selection of Rice Cultivars: A Review

Cited by 70 publications

References 60 publications

Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes

Comparative Analysis of Six Lagerstroemia Complete Chloroplast Genomes

An Efficient Strategy Combining SSR Markers- and Advanced QTL-seq-driven QTL Mapping Unravels Candidate Genes Regulating Grain Weight in Rice

In silico identification of putative expressed sequence tag (EST)-simple sequence repeats (SSRs) markers of resistance to Meloidogyne spp. in common bean

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