How much effort is required to isolate nuclear microsatellites from plants?

Squirrell, J.; Hollingsworth, Peter M.; Woodhead, M.; Russell, Joanne; Lowe, Andrew J.; Gibby, Mary; Powell, W.

doi:10.1046/j.1365-294x.2003.01825.x

Cited by 284 publications

(217 citation statements)

References 64 publications

(14 reference statements)

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“…Unfortunately, the de novo development of SSRs is a costly and time-consuming endeavor (Zane et al, 2002;Squirrell et al, 2003), and these problems are often compounded by a paucity of resources in taxa that lack clear economic importance. Adding to this difficulty is the fact that the polymerase chain reaction primers used to amplify SSRs are frequently species-specific, meaning that markers developed in one taxon cannot be readily transferred to another.…”

Section: Introductionmentioning

confidence: 99%

EST-SSRs as a resource for population genetic analyses

2007

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Simple-sequence repeats (SSRs) have increasingly become the marker of choice for population genetic analyses. Unfortunately, the development of traditional 'anonymous' SSRs from genomic DNA is costly and time-consuming. These problems are further compounded by a paucity of resources in taxa that lack clear economic importance. However, the advent of the genomics age has resulted in the production of vast amounts of publicly available DNA sequence data, including large collections of expressed sequence tags (ESTs) from a variety of different taxa. Recent research has revealed that ESTs are a potentially rich source of SSRs that reveal polymorphisms not only within the source taxon, but in related taxa, as well. In this paper, we review what is known about the transferability of EST-SSRs from one taxon to another with particular reference to the potential of these markers to facilitate population genetic studies. As an example of the utility of these resources, we then cross-reference existing EST databases against lists of rare, endangered and invasive plant species and conclude that half of all suitable EST databases could be exploited for the population genetic analysis of species of conservation concern. We then discuss the advantages and disadvantages of EST-SSRs in the context of population genetic applications.

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Section: Introductionmentioning

confidence: 99%

EST-SSRs as a resource for population genetic analyses

2007

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“…However, the development of traditional 'anonymous' SSRs from genomic DNA is costly and timeconsuming (Squirrell et al, 2003;Ellis and Burke, 2007). Recently, with the development of functional genomics, a huge number of expressed sequence tags (ESTs) were deposited in a public sequence database (Kong et al, 2007), providing a potentially rich source of SSRs (Ellis and Burke, 2007).…”

Section: Introductionmentioning

confidence: 99%

Developing new SSR markers from ESTs of pea (Pisum sativum L.)

Gong

Mao

et al. 2010

J. Zhejiang Univ. Sci. B

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Abstract:The development of expressed sequence tags (ESTs) from pea has provided a useful source for mining novel simple sequence repeat (SSR) markers. In the present research, in order to find EST-derived SSR markers, 18 552 pea ESTs from the National Center for Biotechnology Information (NCBI) database were downloaded and assembled into 10 086 unigenes. A total of 586 microsatellites in 530 unigenes were identified, indicating that merely 5.25% of sequences contained SSRs. The most abundant SSRs within pea were tri-nucleotide repeat motifs, and among all the tri-nucleotide repeats, the motif GAA was the most abundant type. In total, 49 SSRs were used for primer design. EST-SSR loci were subsequently screened on 10 widely adapted varieties in China. Of these, nine loci showed polymorphic profiles that revealed two to three alleles per locus. The polymorphism information content value ranged from 0.18 to 0.58 with an average of 0.41. Furthermore, transferable analysis revealed that some of these loci showed transferability to faba bean. Because of their polymorphism and transferability, these nine novel EST-SSRs will be valuable tools for marker-assisted breeding and comparative mapping of pea in the future.

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“…Previous methods for identification of molecular markers, such as SSRs, insertions and deletions (InDels), and SNPs, were time-and cost-intensive because of the requirement for preparation and sequencing of genomic libraries and the limited information available regarding nucleotide sequences in the pear genome (Squirrell et al 2003;Eujayl et al 2004;Iniguez-Luy et al 2008;Yamamoto and Chevreau 2009;Kale et al 2012). However, recently developed NGS offer opportunities for high-throughput, time-saving, and costeffective marker development (Mardis 2008;Morozova and Marra 2008).…”

Section: Ngs In Pyrus Sppmentioning

confidence: 99%

Current Status of Knowledge and Research Perspectives in Korean Pear Genomics

Kim

2015

Plant Breed. Biotech.

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This is an Open-Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. ABSTRACT The pear (Pyrus spp.) is most important fruit crop in the world. The genus Pyrus belongs to the subfamily Maloideae in the Rosaceae family and contains at least 22 primary species; however, only a few species, including P. pyrifolia, P. ussuriensis, P. bretschneideri, and P. communis have been utilized for fruit production. In Korea, awareness of the importance of the fruit industry and fruit tree breeding is low, and there is little support for genetic and genomic studies of fruit trees. In foreign countries, studies have focused on obtaining genomic information of fruit crops and the development of important agronomic trait-related molecular markers, providing a genomic framework for fruit tree breeding. Although Korea does not actively participate in research on the genomics of fruit trees, it is not far behind other countries in terms of technology and is therefore still competitive in research and development. The resequencing of 'Whangkeumbae' and 'Minibae' pears has been performed using the Illumina Hiseq 2000 platform as a part of the Biogreen 21 project, offering novel, rapid methods for identification of molecular marker, such as single nucleotide polymorphisms, insertion-deletions, and simple sequence repeats, through next-generation sequencing (NGS) technology. These NGS-based molecular markers are useful for genetic studies of Asian pears, e.g., for construction of genetic linkage maps, mapping of quantitative trait loci, and marker-assisted selection.

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How much effort is required to isolate nuclear microsatellites from plants?

Cited by 284 publications

References 64 publications

EST-SSRs as a resource for population genetic analyses

EST-SSRs as a resource for population genetic analyses

Developing new SSR markers from ESTs of pea (Pisum sativum L.)

Current Status of Knowledge and Research Perspectives in Korean Pear Genomics

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