Screening of rice germplasms (Oryza sativa L.) for seedling stage cold tolerance utilizing morphological and molecular markers

Cold temperature is a devastating abiotic stress for rice production, especially in the areas where low temperature prevails throughout the crop duration or in particular growth stages. Boro cultivation season in eastern India is such a replica of rice cultivation under occasional colder climate. Therefore, it is imperative to study a large collection of germplasms for potential cold tolerant stocks. In this study, 106 germplasms from eastern India were cultivated during Boro season in field as well as under 10 °C and 28 °C temperature conditions inside plant growth chamber. Six seedling growth parameters were used as phenotypic markers and 56 cold tolerance quantitative trait loci linked simple sequence repeats (SSRs) were utilized as molecular markers. Leaf yellowing and germination index were also incorporated within the framework of cold tolerance screening to enrich the multidimensional approach. Based on the k-means clustering for each morphological parameter in each condition, the genotypes were ranked and the resulting total ranks for each genotype eventually grouped them into four clusters, i.e. highly susceptible, susceptible, moderately tolerant and tolerant as different level of cold tolerance. Among the screened SSRs, only 33 were polymorphic and most informative were RM336, RM566 and RM1349 due to higher marker efficiency threshold. Combining both morphology and molecular analysis, highly tolerant landraces such as Neera, Barnamali, Khaiya Boro and genotypes such as Purbachi, CB1, Gotra, UPR 103-80 were identified which may be of greater use in development of high yielding cold tolerant genotypes.