Allele-specific amplification for the detection of ascochyta blight resistance in chickpea

Madrid, Eva; Chen, W.; Rajesh, P. N.; Castro, P.; Millán, Teresa; Gil, J.

doi:10.1007/s10681-012-0753-6

Cited by 42 publications

(36 citation statements)

References 26 publications

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“…This region was also detected in the previous study as ar2b (Udupa and Baum, ), QTL_LG4 (Tar'an et al ., ) and QTL AR2 (Iruela et al ., ). A codominant SCAR marker (SCY17590) linked QTL AR2 has been used to trace the resistance alleles in 90% of resistant accessions in a collection of chickpea accessions from Spain, United States, Canada and ICARDA (Madrid et al ., ).…”

Section: Discussionmentioning

confidence: 97%

QTL sequencing strategy to map genomic regions associated with resistance to ascochyta blight in chickpea

Deokar

Sagi

Daba

et al. 2018

Plant Biotechnology Journal

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Whole-genome sequencing-based bulked segregant analysis (BSA) for mapping quantitative trait loci (QTL) provides an efficient alternative approach to conventional QTL analysis as it significantly reduces the scale and cost of analysis with comparable power to QTL detection using full mapping population. We tested the application of next-generation sequencing (NGS)-based BSA approach for mapping QTLs for ascochyta blight resistance in chickpea using two recombinant inbred line populations CPR-01 and CPR-02. Eleven QTLs in CPR-01 and six QTLs in CPR-02 populations were mapped on chromosomes Ca1, Ca2, Ca4, Ca6 and Ca7. The QTLs identified in CPR-01 using conventional biparental mapping approach were used to compare the efficiency of NGS-based BSA in detecting QTLs for ascochyta blight resistance. The QTLs on chromosomes Ca1, Ca4, Ca6 and Ca7 overlapped with the QTLs previously detected in CPR-01 using conventional QTL mapping method. The QTLs on chromosome Ca4 were detected in both populations and overlapped with the previously reported QTLs indicating conserved region for ascochyta blight resistance across different chickpea genotypes. Six candidate genes in the QTL regions identified using NGS-based BSA on chromosomes Ca2 and Ca4 were validated for their association with ascochyta blight resistance in the CPR-02 population. This study demonstrated the efficiency of NGS-based BSA as a rapid and cost-effective method to identify QTLs associated with ascochyta blight in chickpea.

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Section: Discussionmentioning

confidence: 97%

QTL sequencing strategy to map genomic regions associated with resistance to ascochyta blight in chickpea

Deokar

Sagi

Daba

et al. 2018

Plant Biotechnology Journal

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“…Transcriptional profiling using 756 microarray features identified 95 candidate genes differentially expressed during A. rabiei infection in four chickpea genotypes (Coram and Pang, 2006). However, the ETR-1 candidate characterized by Madrid et al (2013) was not identified as being differentially expressed in the study by Coram and Pang (2006). A recent published study by Leo et al (2016) examined the expression profiles of seventeen candidate genes.…”

Section: Introductionmentioning

confidence: 95%

Genome Analysis Identified Novel Candidate Genes for Ascochyta Blight Resistance in Chickpea Using Whole Genome Re-sequencing Data

Ruperao

Batley

et al. 2017

Front. Plant Sci.

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Ascochyta blight (AB) is a fungal disease that can significantly reduce chickpea production in Australia and other regions of the world. In this study, 69 chickpea genotypes were sequenced using whole genome re-sequencing (WGRS) methods. They included 48 Australian varieties differing in their resistance ranking to AB, 16 advanced breeding lines from the Australian chickpea breeding program, four landraces, and one accession representing the wild chickpea species Cicer reticulatum. More than 800,000 single nucleotide polymorphisms (SNPs) were identified. Population structure analysis revealed relatively narrow genetic diversity amongst recently released Australian varieties and two groups of varieties separated by the level of AB resistance. Several regions of the chickpea genome were under positive selection based on Tajima’s D test. Both Fst genome- scan and genome-wide association studies (GWAS) identified a 100 kb region (AB4.1) on chromosome 4 that was significantly associated with AB resistance. The AB4.1 region co-located to a large QTL interval of 7 Mb∼30 Mb identified previously in three different mapping populations which were genotyped at relatively low density with SSR or SNP markers. The AB4.1 region was validated by GWAS in an additional collection of 132 advanced breeding lines from the Australian chickpea breeding program, genotyped with approximately 144,000 SNPs. The reduced level of nucleotide diversity and long extent of linkage disequilibrium also suggested the AB4.1 region may have gone through selective sweeps probably caused by selection of the AB resistance trait in breeding. In total, 12 predicted genes were located in the AB4.1 QTL region, including those annotated as: NBS-LRR receptor-like kinase, wall-associated kinase, zinc finger protein, and serine/threonine protein kinases. One significant SNP located in the conserved catalytic domain of a NBS-LRR receptor-like kinase led to amino acid substitution. Transcriptional analysis using qPCR showed that some predicted genes were significantly induced in resistant lines after inoculation compared to non-inoculated plants. This study demonstrates the power of combining WGRS data with relatively simple traits to rapidly develop “functional makers” for marker-assisted selection and genomic selection.

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“…Using the SCAR marker SCY17 590 in combination with a co-dominant marker (CaETR) linked to QTL AR1 for resistance to Aschochyta in chickpea, it was possible to detect resistance alleles in 90% of resistant accessions in a collection of landraces [130]. Recently, efficient contribution of both markers in MAS of blight-resistant genotypes in different breeding programs in Tunisia and Spain have been reported [131,132].…”

Section: Marker-assisted Selection (Mas)mentioning

confidence: 99%

Fusarium Wilt Affecting Chickpea Crop

et al. 2017

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Chickpea (Cicer arietinum L.) contributes 18% of the global production of grain legume and serves as an important source of dietary protein. An important decrease in cropping area and production has been recorded during the last two decades. Several biotic and abiotic constraints underlie this decrease. Despite the efforts deployed in breeding and selection of several chickpea varieties with high yield potential that are tolerant to diseases, the situation has remained the same for the last decade. Fusarium wilt caused by Fusarium oxysporum f. sp. ciceris (Foc) is the major soil-borne fungus affecting chickpeas globally. Fusarium wilt epidemics can devastate crops and cause up to 100% loss in highly infested fields and under favorable conditions. To date, eight pathogenic races of Foc (races 0, 1A, 1B/C, 2, 3, 4, 5 and 6) have been reported worldwide. The development of resistant cultivars is the most effective method to manage this disease and to contribute to stabilizing chickpea yields. Development of resistant varieties to fusarium wilt in different breeding programs is mainly based on conventional selection. This method is time-consuming and depends on inoculum load and specific environmental factors that influence disease development. The use of molecular tools offers great potential for chickpea improvement, specifically by identifying molecular markers closely linked to genes/QTLs controlling fusarium wilt.

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Allele-specific amplification for the detection of ascochyta blight resistance in chickpea

Cited by 42 publications

References 26 publications

QTL sequencing strategy to map genomic regions associated with resistance to ascochyta blight in chickpea

QTL sequencing strategy to map genomic regions associated with resistance to ascochyta blight in chickpea

Genome Analysis Identified Novel Candidate Genes for Ascochyta Blight Resistance in Chickpea Using Whole Genome Re-sequencing Data

Fusarium Wilt Affecting Chickpea Crop

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