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Genetic marker discovery, intraspecific linkage map construction and quantitative trait locus analysis of ascochyta blight resistance in chickpea (Cicer arietinum L.)

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Abstract

Ascochyta blight, caused by the fungus Ascochyta rabiei (Pass.) Labr., is a highly destructive disease of chickpea (Cicer arietinum L.) on a global basis, and exhibits considerable natural variation for pathogenicity. Different sources of ascochyta blight resistance are available within the cultivated species, suitable for pyramiding to improve field performance. Robust and closely linked genetic markers are desirable to facilitate this approach. A total of 4,654 simple sequence repeat (SSR) and 1,430 single nucleotide polymorphism (SNP) markers were identified from a chickpea expressed sequence tag (EST) database. Subsets of 143 EST–SSRs and 768 SNPs were further used for validation and subsequent high-density genetic mapping of two intraspecific mapping populations (Lasseter × ICC3996 and S95362 × Howzat). Comparison of the linkage maps to the genome of Medicago truncatula revealed a high degree of conserved macrosynteny. Based on field evaluation of ascochyta blight incidence performed over 2 years, two genomic regions containing resistance determinants were identified in the Lasseter × ICC3996 family. In the S95362 × Howzat population, only one quantitative trait locus (QTL) region was identified for both phenotypic evaluation trials, which on the basis of bridging markers was deduced to coincide with one of the Lasseter × ICC3996 QTLs. Of the two QTL-containing regions identified in this study, one (ab_QTL1) was predicted to be in common with QTLs identified in prior studies, while the other (ab_QTL2) may be novel. Markers in close linkage to ascochyta blight resistance genes that have been identified in this study can be further validated and effectively implemented in chickpea breeding programs.

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Acknowledgments

This work was supported by funding from the Victorian Department of Environment and Primary Industries and the Grains Research and Development Council, Australia.

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Author notes

  1. Kristy Hobson

    Present address: NSW Department of Primary Industries, 4 Marsden Park Rd, Tamworth, NSW, 2340, Australia

Authors and Affiliations

  1. Biosciences Research Division, Department of Environment and Primary Industries, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC, 3083, Australia

    Amber Stephens, Maria Lombardi, Noel O. I. Cogan, John W. Forster & Sukhjiwan Kaur

  2. Biosciences Research Division, Department of Environment and Primary Industries, Grains Innovation Park, Horsham, VIC, 3401, Australia

    Kristy Hobson & Michael Materne

  3. La Trobe University, Bundoora, VIC, 3086, Australia

    John W. Forster

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Correspondence to John W. Forster.

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Amber Stephens and Maria Lombardi have contributed equally to this work.

Electronic supplementary material

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11032_2013_9950_MOESM1_ESM.xls

Details of all SSR markers used in linkage mapping analysis: This file contains a list of all SSR marker assays including those that are public and those developed as part of the present study, along with statistics on amplification efficiency and polymorphism rate (XLS 45 kb)

11032_2013_9950_MOESM2_ESM.xls

Sequence information of all of the SSR primer pairs identified and designed using BatchPrimer3: This file contains all of the information (sequence information, orientation, sequence length, expected product length, expected position on Mt genome, Tm, GC content and SSR motif length) on SSR primer pairs designed using BatchPrimer 3 (XLS 2282 kb)

11032_2013_9950_MOESM3_ESM.xls

Details of the 768plex SNP-OPA design: This file contains names and sequence information for all SNP markers used for linkage mapping (XLS 199 kb)

11032_2013_9950_MOESM4_ESM.txt

Consensus sequences of 454 assembled contigs: The data represents the consensus sequences of 20,846 assembled contigs generated as a result of de novo assembly of chickpea ESTs (TXT 17941 kb)

11032_2013_9950_MOESM5_ESM.txt

Sequence information of 454 singletons: The data represents the sequence information on all the singletons generated from de novo assembly of chickpea ESTs. (TXT 21148 kb)

11032_2013_9950_MOESM6_ESM.xls

Characterization of a sub-set of EST-SSRs on wild and cultivated genotypes of chickpea. The table presents data on number and size of alleles amplified from screening of 96 EST-SSR primer pairs on 5 genotypes of chickpea (XLS 22 kb)

11032_2013_9950_MOESM7_ESM.emf

Representative clustering patterns generated by the Illumina GoldenGate® SNP Genotyping assay: The file contains an example of clustering patterns obtained from SNP genotyping assay on two mapping populations. The data point colour codes represent: red, AA (homozygous); blue, BB (homozygous); purple, AB (heterozygous); black, no call (missing data). (EMF 1068 kb)

11032_2013_9950_MOESM8_ESM.xls

Linkage map statistics from Lasseter x ICC3996 and S95362 x Howzat populations: This file contains details of different markers (SSRs and SNPs) and their corresponding positions on different LGs (XLS 80 kb)

11032_2013_9950_MOESM9_ESM.pptx

Comparison between genetic linkage maps of Lasseter x ICC3996 and S95362 x Howzat: This file shows the visual representation of all LGs from both Lasseter x ICC3996 and S95362 x Howzat maps, and the common marker loci between them (PPTX 283 kb)

11032_2013_9950_MOESM10_ESM.pptx

Synteny between genetic linkage maps of Lasseter x ICC3996 and S95362 x Howzat and Medicago truncatula chromosomes: This file shows the visual representation of all LGs from both Lasseter x ICC3996 and S95362 x Howzat maps and their syntenic relationships with Medicago truncatula (PPTX 189 kb)

11032_2013_9950_MOESM11_ESM.jpg

Frequency distribution of ascochyta blight disease score for two mapping populations: This file contains frequency histograms generated from ascochyta blight disease score from RILs of mapping populations A. S95362 x Howzat in 2005, B. Lasseter x ICC3996 in 2005, C. S95362 x Howzat in 2005, Howzat in 2009 and D. Lasseter x ICC3996 in 2009 (JPEG 150 kb)

11032_2013_9950_MOESM12_ESM.doc

Summary statistics for ascochyta blight resistance QTLs in chickpea: This table represents the data on QTL identification of ascochyta blight resistance in Lasseter x ICC3996 and S95362 X Howzat populations using simple interval mapping (SIM) and composite interval mapping (CIM) (DOC 37 kb)

11032_2013_9950_MOESM13_ESM.xlsx

BLAST analysis of SNP marker sequences flanking QTL regions to chickpea reference genome: This file contains the BLAST analysis data for sequences underpinning SNP loci flanking ab_QTL1 and ab_QTL2 against the chickpea reference genome (XLSX 12 kb)

11032_2013_9950_MOESM14_ESM.docx

Sequences of predicted candidate genes from comparison of flanking markers to reference genome of chickpea: This file contains the sequence information for three candidate genes predicted from the ascochyta blight resistance QTL-containing regions (DOCX 16 kb)

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Stephens, A., Lombardi, M., Cogan, N.O.I. et al. Genetic marker discovery, intraspecific linkage map construction and quantitative trait locus analysis of ascochyta blight resistance in chickpea (Cicer arietinum L.). Mol Breeding 33, 297–313 (2014). https://doi.org/10.1007/s11032-013-9950-9

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