Identification of near-isogenic lines: an innovative approach, validated for root and shoot morphological characters in a mapping population of rice (Oryza sativa L.)

• Published in: Euphytica Vol. 160; no. 3; pp. 357 - 368
• Main Authors: Prabuddha, H. R, Manjunatha, K, Venuprasad, R, Vinod, M. S, Jureifa, J. H, Shashidhar, H. E
• Format: Journal Article
• Language: English
• Published: Dordrecht Dordrecht : Springer Netherlands 01-04-2008; Springer Netherlands; Springer; Springer Nature B.V
• Subjects: Adaptation to environment and cultivation conditions; Agronomy. Soil science and plant productions; Biological and medical sciences; Biomedical and Life Sciences; Biotechnology; Correlation coefficient; Drought; drought tolerance; Fundamental and applied biological sciences. Psychology; genes; genetic markers; Genetics and breeding of economic plants; genome; Genotypes; genotypically closely related pairs; Life Sciences; lines; Moisture stress; Morphology; near-isogenic lines; Oryza sativa; Plant breeding; plant genetics; Plant Genetics and Genomics; plant morphology; Plant Pathology; Plant Physiology; Plant reproduction; Plant resistance; Plant Sciences; Population genetics; Rice; roots; shoots; Varietal selection. Specialized plant breeding, plant breeding aims; water stress; Candidate gene; Mapping population; Near-isogenic lines; L; Drought resistance; Cartography; Monocotyledones; Root; Oryza sativa L; Cereal crop; Oryza sativa; Innovation; Gramineae; Morphology; Angiospermae; Genetic improvement; Near isogenic line; Population; Spermatophyta; Shoot
• ISSN: 0014-2336; 1573-5060
• DOI: 10.1007/s10681-007-9546-8

Near-isogenic lines (NILs) constitute valuable tools in genetic investigations and plant breeding programs. Conventional methods for developing these are time consuming and tedious. An innovative method for identifying NILs is proposed and validated. The method involves computation of simple correlation coefficients of all possible pairs of genotypes within a mapping population using molecular marker data, and phenotypic characterization of those pairs with very high positive correlation. The pairs having both genomic and phenotypic similarity except for a single trait are considered as NILs. This strategy was tested with a doubled haploid mapping population involving CT9993 and IR62266. This population was saturated with 315 markers and comprised 154 lines. The pairs showing very high correlation coefficients (0.70-0.97) and differing for less than 10% of the markers were considered as Genotypically Closely Related Pairs (GCRPs). Graphical genotyping was employed to visualize the genome of the closely related lines. A total of 39 such pairs were subjected to rigorous evaluation for root and shoot morphological traits in two contrasting moisture regimes. Four GCRPs under well-watered condition and ten GCRPs under low moisture stress condition are statistically significant for a single phenotypic trait and are considered as NILs for their respective traits and would be the valuable materials for genetic studies. Mapped QTLs and candidate genes were employed to explain the probable cause of phenotypic difference in NILs.