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Abstract Detail



Genetics Section

Xue, Shiming [1], Zantinge, Jennifer [1], Juskiw, Patricia [2], Xi, Kequan [3], Holtz, Michael [1].

Identifying SNP markers for multiple leaf scald resistance in barley through restriction-site associated sequencing with the Ion Torrent PGM.

Scald, caused by Rhynchosporium commune, is an economically important foliar disease of barley. Over the past decades, ‘Seebe’, a 2-row feed barley cv. registered in 1992 by the Field Crop Development Centre (FCDC), has shown scald field resistance. ‘Shyri’ also has scald resistance and it is thought to be the result of different resistance genes. We carried out the present study in a hope to identify SNP markers from different resistance sources for gene pyramiding breeding program. Eighty lines were randomly selected from a ‘Seebe’/’Shyri’ F7 recombinant inbreed line (RIL) population, and analysed by genotyping by sequencing (GBS) according to protocols developed by Mascher et al. (2013) with modifications. Libraries were created by digesting sample DNA with restriction enzymes PstI and MspI followed by ligation of adapters to the fragment ends and PCR amplification. The amplified libraries from ten lines were then pooled, purified using a PCR purification kit. The amplified libraries from two parents were purified separately from six 25-µl volume PCR reactions. 2% agarose e-gels (Invitrogen) were used to select 200-300bp/300-500bp fragments by multiple collections. Following library quantification of the size-selections, eight sequencing runs were performed on Ion PGM sequencer using 318 v2 chips and Ion PGM 200 Seq Kit. Total reads from a sequencing run ranged from 3.7 to 5.25 million, and median read length varied from 138 to 237bp. From 2974 SNPs revealed by TASSEL GBS analysis pipeline, 41 SNPs showed R2 values of over 10% in single marker analysis using WinQTL2.5. Interval mapping (IM) revealed two scald resistance QTLs on 2H and one QTL on 6H, all associated with alleles from ‘Seebe’. A resistance QTL on 3H and 5H were also revealed by interval mapping, and they are associated with alleles from ‘Shyri’. The closest SNPs markers with linkage to these QTLs could explain 10.0% to 20.5% of the phenotypic variation among the 80 lines inoculated in 2012 in fields. These markers will be further validated by high-resolution melt curve analysis, cleaved amplified polymorphic sequences (CAPS) or Taqman allele discrimination assays.


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1 - Field Crop Development Center, Alberta Agriculture and Rural Development, 5030 - 50 Street, Lacombe, AB, T4L1W8, Canada
2 - Field Crop Development Centre, Alberta Agriculture and Rural Development, 5030 50th Street, Lacombe, AB, T4L 1W8, Canada
3 - Alberta Agriculture, Field Crop Development Centre, 6000 C and E Trail, Lacombe, AB, T4L 1W1, Canada

Keywords:
barley
SNPs
GBS.

Presentation Type: Poster:Posters for Sections
Session: P
Location: Hall D/The Shaw Conference Centre
Date: Monday, July 27th, 2015
Time: 5:30 PM
Number: PGN014
Abstract ID:1186
Candidate for Awards:None


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