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High-density QTLs mapping and transcriptome validation identify potential genes explain the genetic basis of Blister
Mohammed Saba Rahim1, Sangeeta Kumari2, Vishal Bhat1
1Molecular Genetic and Genomics Laboratory, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, India.
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Blister blight (BB) disease, caused by an obligate Exobasidium vexans, significantly impeded quality and yield characteristics in tea. Conventionally, tremendous use of fungicides has led to phytotoxicity and stunting plant growth. Despite various reports on pathogenesis and epidemiology, the genetic basis of BB lacks intensive study. To address this knowledge gap, identifying quantitative trait and protein-coding sequence variants in causal genes is the aim of this research to shorten the 20-year breeding cycle and implement modern breeding to improve trait efficiency. This study performed genotyping-by-sequencing on a pseudo-testcross progeny derived from a tolerant (SA6) crossed with a susceptible (Kangra-Asha) tea cultivar. This analysis identified 6650 high-quality single-nucleotide polymorphisms (SNPs) and constructed a high-density linkage map spanning 4637.4 cM of genetic distance. Furthermore, ICIM and MET modules identified 15 QTLs with 11 major QTLs for Blister blight, explaining 5-20 % of the phenotypic variation (PVE) across nine chromosomes of tea. Interestingly, validating 14 candidate genes within QTLs by transcriptional data exhibited significant differential expression in 'SA6' vs. 'Kangra-Asha'. Most influential, R-genes (WAK2, WAK5, alpha/beta hydrolase fold, NBS, TIR domain-containing gene), transcription factors (Trihelix-TF-GT2, MYB52, bZIP40), transposable elements (Tx1, Ty3-1, Ty5-1, T2-6), and RING-type E3-Ubiquitin Transferase (PUB29 and PUB28) were located within major QTLs, namely q_Bb_Cs_3.2, q_Bb_Cs_4.3, q_Bb_Cs_9.2, q_Bb_Cs_9.3, q_Bb_Cs_11 and q_Bb_Cs_13. Post-QTL analysis also identified quantitative traits of amino acid variation in four BB-associated genes, further solidifying the findings of this study. Indeed, novel QTLs harbouring significantly expressed genes hold translational utilization in genome editing and commercial breeding of tea cultivars tolerant to blister blight disease.
