Mapping and validating quantitative trait loci (QTL) for anthocyanin-related genes, coupled with marker analysis for pericarp pigmentation and yield traits in a black and white rice cross

Abstract

This study explores the genetic mechanisms underpinning pigmentation traits in rice, with emphasis on the Kala4 gene responsible for black pigmentation which offers several health benefits. The Kala4 trait was incorporated into the Improved White Ponni variety to develop a black rice introgression line. Comprehensive genomic analysis identified specific chromosomal regions related to black pigmentation and yield traits. The study evaluated 200 F₂ plants derived from a cross between Manipur Black rice and Improved White Ponni, using 81 distinct polymorphism markers. The results confirmed the crucial role of the Kala4 loci in black pigmentation and identified key genes regulating anthocyanin synthesis and the PURPLE PERICARP trait. This enhanced our understanding of rice pigmentation and its genetic intricacies. The study also evaluated yield-associated traits in the F₂ population, identifying eleven QTLs related to yield, most notably on chromosome 4. These QTLs contribute significantly to phenotypic variance, suggesting their potential for marker-assisted selection in breeding programs. Continued exploration of the Kala4 gene on chromosome 4 can provide further insights into QTLs for hybrid rice, expediting future rice improvement strategies and allowing for targeted selection in breeding programs, thereby enhancing future rice crop development strategies.