Genome-Wide Development and Use of Microsatellite Markers for Large-Scale Genotyping Applications in Foxtail Millet [Setaria italica (L.)]

Pandey, Garima; Misra, Gopal; Kumari, Kajal; Gupta, Sarika; Parida, Swarup K.; Chattopadhyay, Debasis; Prasad, Manoj

doi:10.1093/dnares/dst002

Cited by 151 publications

(123 citation statements)

References 32 publications

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“…It has been previously documented that some microsatellites could be transferable between species or even between genera (Chagne et al, 2004; Mnejja et al, 2005; Guo et al, 2006; Pandey et al, 2013), In this study, we tried to develop a large number of conserved microsatellites which can be used for genetic analyses in different palm species. A total of 7 265 conserved microsatellite markers were identified between E. guineensis and P. dactylifera .…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Transferability of Microsatellite Markers between Palmae Species

Xiao

Xia

et al. 2016

Front. Plant Sci.

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The Palmae family contains 202 genera and approximately 2800 species. Except for Elaeis guineensis and Phoenix dactylifera, almost no genetic and genomic information is available for Palmae species. Therefore, this is an obstacle to the conservation and genetic assessment of Palmae species, especially those that are currently endangered. The study was performed to develop a large number of microsatellite markers which can be used for genetic analysis in different Palmae species. Based on the assembled genome of E. guineensis and P. dactylifera, a total of 814 383 and 371 629 microsatellites were identified. Among these microsatellites identified in E. guineensis, 734 509 primer pairs could be designed from the flanking sequences of these microsatellites. The majority (618 762) of these designed primer pairs had in silico products in the genome of E. guineensis. These 618 762 primer pairs were subsequently used to in silico amplify the genome of P. dactylifera. A total of 7 265 conserved microsatellites were identified between E. guineensis and P. dactylifera. One hundred and thirty-five primer pairs flanking the conserved SSRs were stochastically selected and validated to have high cross-genera transferability, varying from 16.7 to 93.3% with an average of 73.7%. These genome-wide conserved microsatellite markers will provide a useful tool for genetic assessment and conservation of different Palmae species in the future.

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Section: Discussionmentioning

confidence: 99%

Genome-Wide Identification and Transferability of Microsatellite Markers between Palmae Species

Xiao

Xia

et al. 2016

Front. Plant Sci.

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“…The first foxtail millet restriction fragment length polymorphism (RFLP)-based map consisting of 160 loci was constructed in an intervarietal cross (Wang et al, 1998) which was further proven to be useful in creating comparative genetic maps of foxtail millet and rice (Devos et al, 1998). Since then several groups reported on development of various genomic or EST based simple sequence repeat (SSR) markers to be used in diverse genotyping applications, phylogenetic and transferability studies in foxtail millet and other grass species (Jia et al, 2007;Jia et al, 2009;Heng et al, 2011;Gupta et al, 2012;Gupta et al, 2013). Considering the importance of intron length polymorphic (ILP) markers as genomic resources, Gupta et al (2011) andMuthamilarasan et al (2014a) developed 98 and 5123 ILP markers respectively in foxtail millet.…”

Section: Foxtail Milletmentioning

confidence: 99%

“…Xu et al (2013) developed a total of 9,576 and 7,056 SSR markers from 42,754 transcripts generated from referenced based assembly using foxtail millet genome and 60,751 transcripts from de novo assembly, respectively. Several other researchers also reported on identification of several microsatellite repeat motifs (Pandey et al, 2013;Zhang et al, 2014), eSSRs , and transposable elements (TE)-based markers (Yadav et al, 2014a) using Setaria genome sequence data. In another interesting study, 176 microRNA (miRNA)-based molecular markers have been developed (Yadav et al, 2014b) from a set of 335 mature miRNAs (Khan et al, 2014).…”

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confidence: 99%

Advances in Omics for Enhancing Abiotic Stress Tolerance in Millets

Lata¹

2015

Proceedings of the Indian National Science Academy

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Millets are small-seeded annual cereal crops which are mostly grown in marginal soils of arid and semi-arid regions, and consequently have to face several abiotic constraints that lead to reduction in the yield. Advanced biotechnological applications, particularly 'omics' approaches could serve as the most immediate and prospective strategies for improving abiotic stress tolerance in millet crops. Omics approaches lead to understand the mechanism of stress response and tolerance at molecular level through insights into gene, protein or metabolite profile and their phenotypic effects. Among millet crops, foxtail millet has been more intensively studied and characterized under abiotic stress conditions owing to its small genome size and diploidy. Genome-wide investigation and expression profiling studies have been extensively carried out in foxtail millet. However proteomic and metabolomic studies in response to abiotic stress in millets are still very limited. Some of the major quantitative trait loci (QTLs) controlling abiotic stress tolerance in millets have also been identified and mapped as for instance a major QTL for terminal drought tolerance in pearl millet and a major QTL for dehydration tolerance in foxtail millet. Gene manipulation for enhanced abiotic stress tolerance involving regulatory genes have proved to be more useful than using single or multiple stress responsive genes. Consequently, the recent advances in 'omics' technologies and accessibility to the genome sequences extend huge potential to enhance stress tolerance of millets. This review thus attempts to summarize various omics strategies and their applications in abiotic stress research in important millet crops namely foxtail millet, pearl millet and finger millet.

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“…The past decade has witnessed continuous efforts towards developing both conventional and EST-SSR markers in finger millet [7,8,5,9]. Studies on comparative genomics have indicated high genomic colinearity between rice and finger millet [10] and cross-transferability of SSR markers from major cereal crops to E. coracana indicated 57% reproducible cross-species/genus amplicons [11] and 73-95% cross-amplification in finger millet from pearl millet SSRs [12].…”

Section: Introductionmentioning

confidence: 99%

Inter-species Transferability of Microsatellite Markers Derived from Wild Relatives to Cultivated Species of Finger Millet

Kotrappa¹

2017

IJGG

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Abstract:The accessibility to public sequence information has paved the way for development of new genomic resources and its cross transferability among closely related genera. In the present study, the nucleotide and EST sequences derived from nine different species of Eleusine were utilized for identifying microsatellite markers and their transferability in E. coracana. The frequency and distribution of repeat motifs of Di, tri, tetra and penta-nucleotide repeats were compared across species. The nucleotide/EST sequences, classified based on their function, were majorly involved in abiotic stress followed by carbohydrate biosynthesis in all the species. Of 2133 primers designed, tri-nucleotide repeats were more abundant (1043) followed by repeats in compound format (963). A highest number of 1660 primer pairs were identified in E. coracana subsp. coracana and nearly 50% of which contained compound repeats, majorly comprising of di-nucleotides. The frequency of microsatellite repeats and the number of primers designed per sequence were maximum in E. kigeziensis (138%) followed by E. floccifolia (126%) while the same was minimum in E. coracana subsp. africana (53%). While the transferability of microsatellites derived from other Eleusine species to cultivated coracana species ranged from 50 to 100%, the primers derived from cultivated species were more informative than from that of wild relatives.

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Genome-Wide Development and Use of Microsatellite Markers for Large-Scale Genotyping Applications in Foxtail Millet [Setaria italica (L.)]

Cited by 151 publications

References 32 publications

Genome-Wide Identification and Transferability of Microsatellite Markers between Palmae Species

Genome-Wide Identification and Transferability of Microsatellite Markers between Palmae Species

Advances in Omics for Enhancing Abiotic Stress Tolerance in Millets

Inter-species Transferability of Microsatellite Markers Derived from Wild Relatives to Cultivated Species of Finger Millet

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