Linkage mapping and quantitative trait loci detection for seedling vigor and grain size in advanced backcross introgression lines from wild accessions of Oryza nivara

Detection of beneficial genes from wild accessions of cultivated crops is becoming increasingly important for crop improvement, especially for traits lost during domestication. A set of wild introgression lines derived from advanced back cross breeding of Swarna with Oryza nivara species were characterized for grain size and seedling vigor related traits. Grain length in the population varied between 7.23 and 8.22 mm, while width varied from 2.66 to 3.13 mm. The length-to-width ratio (LWR) ranged from 2.41 to 3.06 mm, showing various grain shapes in the population. Simultaneously, seedling vigor-related traits were studied, and a significant correlation was observed between seedling vigor traits and grain size parameters. Further mapping of quantitative trait loci (QTL) using simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) genotyping identified 18 QTL for seedling vigor- and grain size-related traits. Among these QTL, three major QTL ( qAS7.1 , qPL7.1 and qL7.1 ) were detected for grain size-related traits on chromosome 7, explaining 21.44%, 19.11% and 22.60% of phenotypic variation, respectively. Similarly, for seedling vigor traits, seven major QTL, viz., qSDW3.1 , qTDW3.1 , qSVI2-3.1 , qSL3.1 , qTL3.1 , qSVI1-6.1 , and qRDW8 . 1 , were detected, explaining 18.3–26.38% of phenotypic variation. These QTL were on chromosomes 6 and 7 for seedling vigor and grain size traits and were collocated with common flanking markers. Hence, the results are useful for marker assisted breeding programmes for introgression and simultaneous improvement of seedling vigor and grain size, and further fine mapping of the related genes.