Association of molecular markers with physio-biochemical traits related to seed vigour in rice

Abstract

Eighteen physio-biochemical traits influencing seed vigour were studied for their association with molecular markers using a mini core set constituted from 120 germplasm lines. High genetic variation was detected in the parameters namely chlrophyll a, Chlrophyll b, total chlorophyll, carotenoids, total anthocyanin content, gamma-oryzanols, total phenolics content, superoxide dismutase, catalase, guaicol peroxidase, total soluble sugar, total protein, seed vigour index -I and seed vigour index -II. Strong positive correlation of seed vigour index II was observed with amylose content, total anthocyanin content, catalase, total phenolic content and total flavonoid content while a negative association was observed for gamma-oryzanol content. High gene diversity (0.7169) and informative markers value (0.6789) were estimated from the investigation. Three genetic structure groups were observed in the panel population and genotypes were grouped in the subpopulations based on the seed vigour trait. Differences in the fixation indices of the three sub populations indicated existence of linkage disequilibrium in the studied panel population. Association of the traits namely total flavonoids, superoxide dismutase, catalase, chlorophyll a, Chlorophyll b, total chlorophyll, carotenoids, starch, amylose, total anthocyanin, gamma-oryzanol, total phenolics with the molecular markers were detected by Generalized Linear Model and Mixed Linear Model showing > 0.10 R² value. Association of the trait, total flavonoids with marker RM7364 located on chromosome 8 reported in earlier study was validated in this investigation. The validated markers and the novel markers detected showing higher R² value will be useful for improvement of seed vigour in rice.

Keywords: Biochemical traits; Marker-trait association; Molecular markers; Physiological traits; Rice; Seed vigour.

Fig. 1

Heat map showing Pearson’s correlation coefficients for physio-biochemical traits. Chl a: chlorophyll a; Chl b; chlorophyll b; Total chl: total chlorophyll; TAC: total anthocyamin content; TPC: total phenolic content; TFC: total flavonoid content; SOD: superoxide dismutase; CAT: catalase; PEROX: peroxidase; TSS: total soluble sugar; SVI-I:seed vigour index I; SVI- II: seed vigour index II; Significant correlations are colored either in red (positive: dark red at 0.01 and light red at 0.05 level) or blue (negative: dark blue at 0.01 and light blue at 0.05 level) hues, while correlations that were not significant are shown in gray

Fig. 2

Cluster Analysis of 48 genotypes based 18 biochemical traits. The name of each genotype is listed in the Table 1

Fig. 3

a Graph of ∆K value for estimation peak value between successive K values for measuring the highest ∆K and b population structure obtained based on inferred ancestry value on the basis 50 molecular markers (K = 3)

Fig. 4

Quantile–Quantile (Q–Q) plot and distribution of marker-trait association from MLM analysis for biochemical traits related to seed vigour at p < 0.05