Genetic dissection of Septoria tritici blotch and Septoria nodorum blotch resistance in wheat using GWAS

Alma Kokhmetova^1*Nagenahalli Dharmegowda Rathan^2*Deepmala Sehgal^3*Yuliya Zeleneva⁴Madina Kumarbayeva¹Ardak Bolatbekova¹Gopalareddy Krishnappa^5*Zhenis Keishilov¹Asia Kokhmetova¹Kanat Mukhametzhanov¹Kanat Bakhytuly¹

• ¹Institute of Plant Biology and Biotechnology (IPBB), Almaty, Kazakhstan
• ²Coverta Agriscience, Hyderabad, Telangana, India., Hyderabad, India
• ³Syngenta, Jealott's Hill International Research Centre, Bracknell, Berkshire, United Kingdom., Berkshire, United Kingdom
• ⁴Laboratory of Mycology and Phytopathology, All Russian Institute of Plant Protection., St. Petersburg-Pushkin, Russia
• ⁵Sugarcane Breeding Institute, Indian Council of Agricultural Research, Coimbatore, Coimbatore, Kerala, India

For identifying genomic regions associated with resistance to Septoria tritici blotch (STB) and Septoria nodorum blotch (SNB) in wheat, a genome-wide association study (GWAS) was conducted using a diverse panel of 191 spring and winter wheat genotypes. The panel was genotyped using DArTseq TM technology and phenotyped under natural field conditions for three cropping seasons (2019-2020, 2020-2021, and 2021-2022) and under artificially inoculated field conditions for two cropping seasons (2020-2021 and 2021-2022). Additionally, the panel was phenotyped under greenhouse condition for five mixed isolates of Zymoseptoria triticiSTB (five mixed isolates in a single experiment) and SNB, (four independent isolates, and a purified toxin in five different independent experiments) of Parastagonospora nodorum under greenhouse conditions. GWAS identified nine marker -trait associations (MTAs), including six MTAs for different isolates under greenhouse conditions, two MTAs under natural field conditions, and one MTA under artificially inoculated field conditions. A pleiotropic SNP MTA (100023665) was identified on chromosome 5B governing resistance against SNB isolate Pn Sn2K_USA and SNB purified toxin Pn ToxA_USA and, explaining 30.73% and 46.94% of phenotypic variation, respectively. In silico analysis identified important candidates genes belonging to the leucine-rich repeat (LRR) domain superfamily, Zinc finger GRF-type transcription factors, potassium transporters, nucleotide-binding site (NBS) domain superfamily, disease resistance protein, P-loop containing nucleoside triphosphate hydrolase, virus X resistance proteinApoptotic proteaseactivating factors, and NB-ARC domains.