Important genomic regions zinc, grain, yield, and agronomic traits in rice (Oryza sativa L.) unveiled using connected populations

Micronutrient mainutrition is a serious nutritional problem that affects billions of people around the world. Breeding for rice varieties with increased micronutrient content is one of the sustainable approaches to address micronutrient malnutrition. Hence, developing rice with high Zn and Fe content along with desirable agronomic characters are the main targets in biofortification breeding. In this study, we tested four connected recombinant inbred populations derived from the crosses of Kaliboro (donor parent) with IR14M141, IR14M110, IR14M125, and IR95044:8-B-5-22-19-GBS (recipient parents) to detect QTL affecting grain Zn content, Fe content, grain yield, and agronomic traits. The multi-cross QTL analysis using the connected populations effectively identified 156 QTL with two major QTL (plant height and grain Zn content) for agronomic and biofortification traits distributed in all 12 chromosomes where some of them have overlapping genomic regions. Fourteen and 27 QTL were detected for grain Fe and grain Zn, respectively that were located across 12 chromosomes. A major QTL (qZn sub 5.1) for grain Zn content that accounted for 13% of phenotypic variation was detected using MC-QTL analysis and was verified by genome wide association analysis mapping in multiple populations and inclusive interval mapping of individual populations. Genomic region of qZn sub 5.1 was studied through in-silico candidate gene analysis, gene prediction, and cis-regulatory analysis. A number primary putative genes OsZIP5, OsZIP9, and LOC_OS50G40490 were found harboring this important genomic region, OsZIP5, OsZIP9, LOC-O50G40490 showed also functional SNP polymorphisms when the genome of the parents were compared. These predicted genes where further analyzed for cis-regulatory elements found in their promoter and coding regions. Results revealed a robust number of regulatory elements involve in seed storage, photoperoidism, light-regulation, alpha-amylase expression and disease resistance. Findings suggest the possible association of genes involve in Zn uptake and transport with other physiological functions. The information of QTL affecting agronomic traits and qZn5.1 can provide the genetic basis and would be useful in marker-aided breeding for rice with high Zn coupled with desirable agronomic characteristics. Major QTL qZn sub 5.1 can be used for marker-aided breeding for high grain Zn content in rice.