Table_8_Genome-Wide Association Analyses Track Genomic Regions for Resistance to Ascochyta rabiei in Australian Chickpea Breeding Germplasm.xlsx

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.

由坏死性真菌 Ascochyta rabiei（同义词 Phoma rabiei）引起的 Ascochyta blight（AB）病，具有摧毁全球鹰嘴豆产业的潜力。鉴于栽培基因库中遗传抗性的来源有限、病原体的进化潜力巨大以及综合病害管理的挑战，因此，在新品种中部署稳定的遗传抗性可能提供一种有效的病害控制策略。为了探究 AB 抗性的遗传基础，本研究利用基于测序的基因分型技术 DArTseq 单核苷酸多态性（SNP）标记数据以及 251 个高级育种系和鹰嘴豆品种的表型数据，进行了全基因组关联（GWAS）分析。宿主抗性在播种后七周使用两种高度侵袭性的单孢子分离株（F17191-1 和 TR9571）的 A. rabiei 进行评估。基于单位点和多位点混合模型以及单倍型趋势回归的 GWAS 分析，在 Ca1、Ca4 和 Ca6 染色体上确定了与 AB 抗性显著相关的二十六个基因组区域。位于 Ca1 染色体上的两个单倍型块（HB5，992178–1108145 bp；HB8，1886221–1976301 bp）与对两种分离株的抗性相关。在 Ca4 染色体上，跨越一个庞大的基因组区域（14.9–56.6 Mbp）的九个单倍型块也与抗性相关，进一步证实了该染色体在提供 AB 抗性中的作用。此外，在温室条件下对 TR9571 分离株的幼苗阶段进行抗性验证的两个 F3 衍生群体中的性状-标记关联也得到了证实。在候选基因中定位了 89 个与显著相关的单核苷酸多态性（SNPs），包括编码丝氨酸/苏氨酸蛋白激酶、Myb 蛋白、醌氧化还原酶和钙调蛋白结合蛋白的基因，这些基因均与抗病性有关。综合来看，本研究识别了宝贵的遗传抗性来源、与 AB 抗性相关的基因组区域的 SNP 标记和候选基因，这或许能够使鹰嘴豆育种计划通过标记辅助/基因组选择策略实现遗传上的突破。