Molecular Marker Validation for Grain Iron, Zinc, and Protein Content in Rice Using Single Marker Analysis Approach
K. S. SaiVenkat
Department of Genetics and Plant Breeding, S. V. Agricultural College, Tirupati, ANGRAU, Guntur, 522 034, India and ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad 500 030, India.
M. Reddi Sekhar
Department of Genetics and Plant Breeding, SMGR Agricultural College, Udayagiri, ANGRAU, Guntur, 522 034, India.
C. N. Neeraja
*
ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad 500 030, India.
P. Shanthi
Department of Genetics and Plant Breeding, S. V. Agricultural College, Tirupati, ANGRAU, Guntur, 522 034, India.
D. Sanjeeva Rao
ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad 500 030, India.
M. Sudha Rani
Department of Genetics and Plant Breeding, S. V. Agricultural College, Tirupati, ANGRAU, Guntur, 522 034, India.
*Author to whom correspondence should be addressed.
Abstract
Micronutrient malnutrition, particularly iron (Fe) and zinc (Zn) deficiencies, remains a major global health concern, highlighting the need for rice biofortification. Validating molecular markers linked to grain nutritional traits is essential for their effective use in marker-assisted breeding. In this study, a BC₁F₇ backcross inbred line (BIL) population comprising 158 lines derived from RNR15048 × Karuppunel was evaluated to validate simple sequence repeat (SSR) markers associated with grain Fe, Zn, and protein content (GPC) through single-marker analysis (SMA). A total of 196 SSR markers, including 118 previously reported QTL-linked markers, were screened for parental polymorphism; 89 polymorphic markers were subsequently used to genotype the BIL population. SMA identified 23 marker–trait associations across chromosomes 1, 2, 4, 6, 7, and 9, of which 18 exceeded the specified LOD threshold. Zinc content in polished rice had the highest number of significant associations (eight), followed by zinc content in brown rice (seven). Two markers, RM341 and RM11, were significantly associated with iron content in brown rice, while RM3524 was associated with GPC. The significant markers explained 3.83–10.68% of the phenotypic variation, indicating that these nutritional traits are influenced by multiple minor-effect loci. These validated SSR markers represent potentially useful molecular tools for marker-assisted selection aimed at developing rice cultivars with enhanced grain iron, zinc, and protein content for sustainable biofortification programmes.
Keywords: Rice biofortification, simple sequence repeat markers, single-marker analysis, backcross inbred lines, grain iron, grain zinc, grain protein content, marker-assisted selection, quantitative trait loci, parental polymorphism.