High resolution genetic mapping and identification of a candidate gene(s) for the purple sheath color and plant height in an interspecific F 2 population derived from Oryza nivara Sharma & Shastry × Oryza sativa L. cross

Wild relatives of rice ( Oryza sativa L.) represent enormous genetic diversity for many traits. Many domestication related traits found only in wild species that are lost from cultivated species during domestication. In this study, we report high-resolution mapping of two domestications related quantitative trait locus (QTL) controlling purple sheath color and plant height using high-density SNP based linkage map in an interspecific F 2 population derived from a cross between O. nivara Sharma & Shastry and O. sativa . The segregation ratio of purple sheath color fit into 3:1 indicated that the presence of a dominant gene. The segregation of plant height trait exhibited a normal distribution in F 2 and F 2:3 generations. QTL analysis showed the identification of two QTLs controlling purple sheath color (designated as qPsh6.1 and qPsh6.2 ) on chromosome 6 explaining 27.12% and 14% phenotypic variance, respectively. The only plant height QTL (tentatively designated as qPh1.9 ) was mapped on chromosome 1 contributing 18.3% phenotypic variance. The qPsh6.1 covers 25.17 Kb region flanked by AX-95928721 and AX-95954573 containing five open reading frames (ORFs) while qPsh6.2 spanned in 118.2 Kb region containing 19 ORFs flanked by markers AX-95956260 and AX-95928295. The qPh1.9 gene controlling plant height was mapped between two SNP markers, AX-95944819 and AX-95964796 co-segregated with the locus LOC_Os01g66690 encoding for ZIP4/SPO22 protein. The detailed genetic study of the location of these genes will be useful for the map-based cloning.