Simple sequence repeat marker development from bacterial artificial chromosome end sequences and expressed sequence tags of flax (Linum usitatissimum L.)

Abstract

Flax is an important oilseed crop in North America and is mostly grown as a fibre crop in Europe. As a self-pollinated diploid with a small estimated genome size of ~370 Mb, flax is well suited for fast progress in genomics. In the last few years, important genetic resources have been developed for this crop. Here, we describe the assessment and comparative analyses of 1,506 putative simple sequence repeats (SSRs) of which, 1,164 were derived from BAC-end sequences (BESs) and 342 from expressed sequence tags (ESTs). The SSRs were assessed on a panel of 16 flax accessions with 673 (58 %) and 145 (42 %) primer pairs being polymorphic in the BESs and ESTs, respectively. With 818 novel polymorphic SSR primer pairs reported in this study, the repertoire of available SSRs in flax has more than doubled from the combined total of 508 of all previous reports. Among nucleotide motifs, trinucleotides were the most abundant irrespective of the class, but dinucleotides were the most polymorphic. SSR length was also positively correlated with polymorphism. Two dinucleotide (AT/TA and AG/GA) and two trinucleotide (AAT/ATA/TAA and GAA/AGA/AAG) motifs and their iterations, different from those reported in many other crops, accounted for more than half of all the SSRs and were also more polymorphic (63.4 %) than the rest of the markers (42.7 %). This improved resource promises to be useful in genetic, quantitative trait loci (QTL) and association mapping as well as for anchoring the physical/genetic map with the whole genome shotgun reference sequence of flax.Electronic supplementary materialThe online version of this article (doi:10.1007/s00122-012-1860-4) contains supplementary material, which is available to authorized users.

Genetic diversity, population structure and association analysis in linseed (Linum usitatissimum L.)

“…In the present investigation, we applied 50 widely distributed SSRs to evaluate the genetic diversity and identify diverseaccessions/groupofaccessionsamongalargesetof168 accessionsoflinseed.Atotalof337allelesweredetectedfrom50 SSRswithanaverageof6.74allelesperSSRs.Thisaverageallele numberwasfoundtobehigherthanthatreportedearlier (RooseAmsalegetal.2006;Dengetal.2011;Palietal.2014;Soto-Cerda etal.2012Cloutieretal.2012b).Thehigherallelenumber mightbeduetothelargeanddiversesetofaccessionsandwidely distributed SSRs used in the present study. The three markers namelyLU_2332,LUSc_38_01andLuSc_196_02having13, 12 and 12 alleles with PIC value above 0.80 seems to be highly informativeandcouldbefurtherutilizedinevaluatingothersets oflinseedgermplasm.TheaveragePICvalue(0.47)wasfoundto be higher than those reported by Soto-Cerda et al (2011, Cloutier et al (2009Cloutier et al ( , 2012b. While Deng et al (2010) reported slightly higher average PIC value (0.56) than found in the present study.…”

Development of Novel SSR Markers for Flax (Linum usitatissimum L.) Using Reduced-Representation Genome Sequencing

“…In flax, large numbers of genomic SSR markers have already been developed (Cloutier et al, 2009, 2012a; Deng et al, 2010; Sandip et al, 2012). Three microsatellite isolation methods, all utilizing next-generation sequencing methodologies, have rapidly pinpointed SSR markers for evaluation of diverse oilseed flax genotypes.…”

“…Such rapid advances demonstrate the value of this sequencing technology for SSR marker discovery (Sandip et al, 2012) and recent characterization among almost all fiber and oilseed flax cultivars (Roose-Amsaleg et al, 2006; Deng et al, 2010). Notably, 1506 putative simple sequence repeats have recently been assessed using a panel of 16 flax accessions, resulting in discovery of 818 novel polymorphic SSR primer pairs (Cloutier et al, 2012a). However, specific progress using these SSR makers toward the development of flax breeding programs must first await development of other necessary genetic and genomic resources.…”

“…Other recent advances in DNA sequencing have increased the availability of molecular markers, including genomic SSRs (Wiesner et al, 2001; Roose-Amsaleg et al, 2006; Deng et al, 2010; Soto-Cerda et al, 2011a; Cloutier et al, 2012a; Sandip et al, 2012) and SSRs from expressed sequence tags (EST-SSRs) (Cloutier et al, 2009, 2012a; Soto-Cerda et al, 2011b). Moreover, with the development of low-cost next generation sequencing technologies, RRGS has become a popular method for genotyping (Sun et al, 2013).…”

Validation and Transferability of Simple Sequence Repeats (Ssr’s) From Some Species of Acacia Genus to Acacia Nilotica L.

“…Codominant markers usually have a PIC value from 0.5 to 1 [54]. It implies that selected SSR loci were highly informative.…”