Population structure and genetic diversity analysis in traditional rice landraces of Kerala

Abstract

The study entitled "Population structure and genetic diversity analysis in traditional rice landraces of Kerala" was undertaken during 2021-22 at the Department of Plant Biotechnology and Department of Plant Physiology, College of Agriculture, Vellayani. The study was undertaken for the genotyping of fifty rice landraces using SSR markers and population structure analysis. Fifty traditional rice landraces collected from RARS, Pattambi were raised in pots and the genomic DNA from one-month-old leaf samples were isolated by CTAB method. Fifty DNA samples were screened using thirty microsatellite primers and out of which five primers (RM431, RM154, RM85, RM5735, and RM104) did not show any amplification. Also, three SSR markers viz., RM554, RM246, and RM3825 amplified monomorphic banding patterns and hence they were not considered for further analysis. Twenty-two markers which yielded polymorphic bands were thus selected for final analysis. The Polymorphism Information Content (PIC) values for polymorphic markers ranged from 0.13 to 0.49. The primers which showed the highest PIC values were RM10793 (0.49) followed by RM310 (0.49) and RM5749 (0.48). The population structure of the fifty rice landraces performed using a software (STRUCTURE V2.3.4) divided the fifty rice landraces into four sub-populations. Phenotypic data of the same genotypes were collected from the Department of Plant Physiology, College of Agriculture, Vellayani and utilized to correlate the phenotypic data with genotypic data and to identify the tolerant landraces. Cluster analysis based phenotypic data resulted in four major clusters which was found to be similar with that of cluster produced by genotypic data. Phenotypic traits such as photosynthetic rate, transpiration rate, number of panicles per plant, and spikelet fertility per centage were used to identify the landraces that were tolerant to high temperature. According to the phenotypic data, the spikelet fertility of sub-population 1 ranged between 20-30% in high temperature condition, photosynthetic rate ranged between 15-30 µmolCO2m-2 s -1 , transpiration rate ranged between 8-15 mmolH2OCO2m-2 sec-1 , and number of panicles per plant ranged from 11-20, and this sub-population is considered to be moderately heat tolerant. The spikelet fertility of sub-population 2 ranged between 11-25% in high temperature condition, photosynthetic 117 rate ranged between 10-25 µmolCO2m-2 s -1 , transpiration rate ranged between 6-10 mmolH2OCO2m-2 sec-1 , and number of panicles per plant ranged from 7-15, and this sub-population is considered to be heat susceptible. The spikelet fertility of subpopulation 3 ranged between <25% in high temperature condition, photosynthetic rate ranged between 5-10 µmolCO2m-2 s -1 , transpiration rate ranged between 0-5 mmolH2OCO2m-2 sec-1 , and number of panicles per plant ranged from 5-10, and this sub-population is considered to be highly susceptible to heat. The spikelet fertility of sub-population 4 ranged between 11-20% in high temperature condition, photosynthetic rate ranged between 5-10 µmolCO2m-2 s -1 , transpiration rate ranged between 5-8 mmolH2OCO2m-2 sec-1 , and number of panicles per plant ranged from 5-10, and this sub-population is considered to be highly susceptible to heat. The phylogenetic tree was constructed using UPGMA (Un-weighted pair group method with arithmetic mean) using NTSYSpc cluster analysis software, and the dendrogram showed that all fifty rice landraces were divided into four major clusters. The pattern of grouping landraces into the clusters was similar to that obtained in the population structure analysis. Based on the interpretation of all the data obtained, among the fifty rice landraces; LB-2000-28-TCR-6985, Kuruva, Ittikandan, Champan, LN9937-Cherumallaram (Vatharam), Cheruvellari, Kokkan, Kurutha chitteni, Kathikannan, and Vellari were grouped as moderately tolerant to high temperature.