Genomics-informed elucidation of trait phenotype and MABB approaches deliver major gene resistance in aromatic rice landrace Mushk Budji

Asif Bashir Shikari^1*Raheel Shafeeq Khan¹Noor ul Ain¹FAYAZ MOHIDDIN²Gazala Hassan Khan²Najeebul Rehman Sofi²Dr Zahoor Ahmed Dar³M. Ashraf Ahangar⁴Gowhar Ali³AFLAQ HAMID WANI³Bilal A. Padder⁵

• ¹1Division of Genetics and Plant Breeding, Faculty of Agriculture, Wadura Campus, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
• ²2Mountain Research Centre for Field Crops, Khudwani, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
• ³3National Seed project, Shalimar Campus, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
• ⁴2Mountain Research Centre for Field Crops, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India
• ⁵4Division of Plant Pathology, Shalimar Campus, Sher-e-Kashmir University of Agricultural Sciences and Technology of Kashmir, Srinagar, India

Abstract Introduction: A novel set of pyramided lines for durable blast resistance was developed using marker-assisted backcross breeding (MABB) strategy in the genetic background of aromatic landrace Mushk Budji (MB). Methods: Simultaneous-but-stepwise transfer of the blast resistance genes Pi54 and Pi9 was effected through integration of foreground and background genome recovery process, expedited through selection aided by genome-wide SSRs and >1500 KASP markers. MABB, whole genome re-sequencing coupled with stringent phenotypic selection for aroma, amylose content, kernel dimensions and cooking quality helped to minimize the linkage drag and to achieve early recurrent parent genome (RPG) recovery in inter-cross BC2F2:3 generation. Results: The two-gene lines carrying Pi9+Pi54 were developed through inter-crossing corresponding near-isogenic lines (NILs) with RPG of around 90%. With the help of sequencing of derived NILs, we could first time establish the role of major alleles underlying rice quality and stress resilience in MB. In a process we confirmed retention of favourable alleles at key genetic loci, such as, BADH2 (aroma), Wx (amylose content), Rc (white pericarp), Hd1/Hd4/Hd5 (heading date) and COLD1/COLD6 (cold tolerance) in the derived NILs. GGE biplot analysis revealed stable performance of five advanced lines across target ecologies. Discussion: A set of NILs was useful in elucidating the phenotypic effect of 11 genes related to grain type, quality and adaptability traits in landrace MB. Multi-environment screening for blast resistance, at hotspot locations, besides, artificial inoculation validated the resistance response of lines for leaf and neck blast. This study demonstrates the successful integration of genomics-assisted breeding and phenotypic selection to improve a heritage rice variety for enhanced disease resistance and ecological adaptation. The development of improved MB lines is a rare endeavour of targeted improvement of traditional rice landraces, which would help in its area expansion and enable us to preserve the heritage rice landrace.