Dissection of epistatic inferaction's for agronomic, grain zinc and iron concentration in a recombinant inbred population of rice (Oryza sativa)

Biofortification breeding of rice with good agronomic and high grain zinc (Zn) is one of the sustainable and cost-effective approaches in alleviating Zn malnutrition. Grain Zn is a genetically complex trait and significantly influenced by environmental factors resulting in slow progress in breeding for high Zn rice. Hence, genetic dissection of agronomic and grain Zn can assist in more precise and faster development of high Zn rice variaties. Epistasis makes a substantial contribution to the genetic control of quantitative traits. In this study, genetic linkage map was constructed based on 458 polymorphic SNP markers in 197 recombinant inbred lines (RILs) derived from a cross between 'IR14M141' and 'Jamir' (AUS type cultivar) to investigate the epistatic interactions for days to flowering (DF), plant height (PH), number of tillers (NT), number of panicles (NP), panicle length (PL), thousand grain weight (TGW), grain length (GL), grain width (GW), grain yield (YLD), grain iron (Fe) and Zn, Epistatic interactions between marker loci was performed for single and multi-environment analyses with stringent threshold LOD of 5.0 using the ICIM-EPI method of ICIM v.4.1 software. The single environment analysis detected 14 significant di-genic interactions: ten in 2017 Dry Season and four in 2017 Wet Season. Three, one, four, two, two, one, and one di-genic interactions were identified for DF, PH, PL, YLD, TGW, GL, GW, and Zn, respectively, whose phenotypic variance explained (PVE) ranged from 9.54 to 31.34% in 2017 DS and from 16.33 to 46.76% in 2017 WS. Moreover, epistatic multi-environment analysis identified 126 di-genic interactions for all traits distributed on all the 12 chromosomes. Each of the interactions individually accounted for 1.85 – 12.22% of the phenotypic variation. These results indicate that epistatic interaction plays an important role in controlling the expression of complex traits. Thus, utilization of marker assisted selection in rice breeding must take epistatic effects into consideration.