Identification of Ascochyta rabiei disease resistance in chickpea genotypes

Du, Weian; Zhao, Xiaochun; Raju, T. N.; Davies, Phil; Trethowan, Richard

doi:10.1007/s10681-011-0554-3

Cited by 7 publications

(4 citation statements)

References 11 publications

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“…However, none of the resistant sources is completely immune to A. rabiei pathotypes. Since the first recorded A. rabiei epidemic in Australia in 1998, extensive efforts have been made to develop resistant cultivars ( Du et al, 2012 ). The Australian chickpea breeding program (PBA, pulse breeding Australia; subsequently CBA, chickpea breeding Australia) has extensively deployed genetic resistance derived from an Iranian landrace, ICC3996 in several commercial chickpea cultivars ( Li et al, 2017 ).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Analyses Track Genomic Regions for Resistance to Ascochyta rabiei in Australian Chickpea Breeding Germplasm

et al. 2022

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Ascochyta blight (AB), caused by a necrotrophic fungus, Ascochyta rabiei (syn. Phoma rabiei) has the potential to destroy the chickpea industry worldwide, due to limited sources of genetic resistance in the cultivated gene pool, high evolutionary potential of the pathogen and challenges with integrated disease management. Therefore, the deployment of stable genetic resistance in new cultivars could provide an effective disease control strategy. To investigate the genetic basis of AB resistance, genotyping-by-sequencing based DArTseq-single nucleotide polymorphism (SNP) marker data along with phenotypic data of 251 advanced breeding lines and chickpea cultivars were used to perform genome-wide association (GWAS) analysis. Host resistance was evaluated seven weeks after sowing using two highly aggressive single spore isolates (F17191-1 and TR9571) of A. rabiei. GWAS analyses based on single-locus and multi-locus mixed models and haplotyping trend regression identified twenty-six genomic regions on Ca1, Ca4, and Ca6 that showed significant association with resistance to AB. Two haplotype blocks (HB) on chromosome Ca1; HB5 (992178–1108145 bp), and HB8 (1886221–1976301 bp) were associated with resistance against both isolates. Nine HB on the chromosome, Ca4, spanning a large genomic region (14.9–56.6 Mbp) were also associated with resistance, confirming the role of this chromosome in providing resistance to AB. Furthermore, trait-marker associations in two F3 derived populations for resistance to TR9571 isolate at the seedling stage under glasshouse conditions were also validated. Eighty-nine significantly associated SNPs were located within candidate genes, including genes encoding for serine/threonine-protein kinase, Myb protein, quinone oxidoreductase, and calmodulin-binding protein all of which are implicated in disease resistance. Taken together, this study identifies valuable sources of genetic resistance, SNP markers and candidate genes underlying genomic regions associated with AB resistance which may enable chickpea breeding programs to make genetic gains via marker-assisted/genomic selection strategies.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Analyses Track Genomic Regions for Resistance to Ascochyta rabiei in Australian Chickpea Breeding Germplasm

et al. 2022

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“…Chickpea ( Cicer arietinum L.) is a staple cool season food legume, important in the Indian sub-continent, West Asia, North Africa and grown as a high-return cash export crop in Australia and North America (Du et al, 2012). However, production is seriously constrained by fungal disease Ascochyta blight, which is the most frequent and devastating disease of chickpea crops worldwide (Sagi et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

“…Australia is the second largest global producer and exporter of chickpea (ABARE report from February 2, 2016), while India is the largest chickpea producer, whose production dwarfs that of all other countries. The first recorded A. rabiei epidemic in Australia occurred in 1998 (Du et al, 2012). With growing market demand and cash return, production in northern New South Wales and southern and central Queensland has recently increased.…”

Section: Introductionmentioning

confidence: 99%

Determination of the Key Resistance Gene Analogs Involved in Ascochyta rabiei Recognition in Chickpea

et al. 2019

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Chickpea ( Cicer arietinum L.) is an important cool season food legume, however, its production is severely constrained by the foliar disease Ascochyta blight caused by the fungus Ascochyta rabiei (syn. Phoma rabiei ). Several disease management options have been developed to control the pathogen, including breeding for host plant resistance. However, the pathogen population is evolving to produce more aggressive isolates. For host resistance to be effective, the plant must quickly recognize the pathogen and instigate initial defense mechanisms, optimally at the point of contact. Given that the most resistant host genotypes display rapid pathogen recognition and response, the approach taken was to assess the type, speed and pattern of recognition via Resistance Gene Analog (RGA) transcription among resistant and susceptible cultivated chickpea varieties. RGAs are key factors in the recognition of plant pathogens and the signaling of inducible defenses. In this study, a suite of RGA loci were chosen for further investigation from both published literature and from newly mined homologous sequences within the National Center for Biotechnology Information (NCBI) database. Following their validation in the chickpea genome, 10 target RGAs were selected for differential expression analysis in response to A. rabiei infection. This was performed in a set of four chickpea varieties including two resistant cultivars (ICC3996 and PBA Seamer), one moderately resistant cultivar (PBA HatTrick) and one susceptible cultivar (Kyabra). Gene expression at each RGA locus was assessed via qPCR at 2, 6, and 24 h after A. rabiei inoculation with a previously characterized highly aggressive isolate. As a result, all loci were differentially transcribed in response to pathogen infection in at least one genotype and at least one time point after inoculation. Among these, the differential expression of four RGAs was significant and consistently increased in the most resistant genotype ICC3996 immediately following inoculation, when spore germination began and ahead of penetration into the plant’s epidermal tissues. Further in silico analyses indicated that the differentially transcribed RGAs function through ADP-binding within the pathogen recognition pathway. These represent clear targets for future functional validation and potential for selective resistance breeding for introgression into elite cultivars.

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“…The development of blight tolerant lines has made the introduction of winter sowing possible in the Mediterranean region, notably increasing chickpea production that could be doubled (Millan et al, 2015). Thus, a number of AB resistant sources have been identified and used in breeding programs although complete resistance is not available yet (Collard et al, 2003;Du et al, 2012;Gayacharan et al, 2020;Newman et al, 2021;Shah et al, 2021).…”

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confidence: 99%

Four haplotype blocks linked to Ascochyta blight disease resistance in chickpea under Mediterranean conditions

et al. 2023

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Ascochyta blight, caused by the fungal pathogen Ascochyta blight, caused by the fungal pathogen Ascochyta rabiei, is a devastating biotic stress that poses a significant threat to chickpea cultivation worldwide. To combat this disease, breeding programs have focused on developing cultivars with resistance to Ascochyta blight. However, a comprehensive understanding of the underlying plant defense mechanism is still lacking. To identify genomic regions associated with resistance, a recombinant inbred line (RIL) population was created by crossing ILC3279 (kabuli, resistant) and WR315 (desi, susceptible), which was then phenotyped and sequenced using a tuneable genotyping-by-sequencing (tGBS) protocol to obtain single nucleotide polymorphisms (SNPs). We further validated the association of genomic regions with Ascochyta blight resistance in a second recombinant inbred line\population derived from the cross between JG62 (desi, susceptible) and ILC72 (kabuli, resistant). Our analysis identified four genomic regions associated with Ascochyta blight resistance in chromosomes 2 and 4, among which a region spanning from 3.52 to 8.20 Mb in chromosome 4 was the most robust candidate for resistance, being associated with resistance in both years and populations. A total of 30 genes from the identified regions were selected as robust candidates, and LOC101507066, which encodes a leucine-rich repeat receptor-like protein kinase, was the most robust candidate gene, as it plays critical roles in plant stress responses and immunity. Our findings have potential to accelerate marker-assisted genetic improvement and facilitate the development of integrated strategies for crop protection.

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Identification of Ascochyta rabiei disease resistance in chickpea genotypes

Cited by 7 publications

References 11 publications

Genome-Wide Association Analyses Track Genomic Regions for Resistance to Ascochyta rabiei in Australian Chickpea Breeding Germplasm

Genome-Wide Association Analyses Track Genomic Regions for Resistance to Ascochyta rabiei in Australian Chickpea Breeding Germplasm

Determination of the Key Resistance Gene Analogs Involved in Ascochyta rabiei Recognition in Chickpea

Four haplotype blocks linked to Ascochyta blight disease resistance in chickpea under Mediterranean conditions

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