Characterization of heterogeneity in popular rice landrace through field and molecular evaluation

Abstract

Context Identification and purification of the landrace Chittimuthyalu using stability and molecular heterozygosity can be useful for rice diversity.

Objectives The present study reports the characterization of 12 genotypic variants of Chittimuthyalu in terms of (i) variation and correlation among agromorphological, grain quality and nutrient traits, viz., Zn and Fe; (ii) stability across years; and (iii) characterization and heterozygosity.

Methods A total of twelve genotypic variants were identified based on field-level agromorphological observations in the Chittimuthyalu landrace. For identification of a stable genotypic variant for grain Zn, genotype by environment (G × E) interaction was analyzed across three years using additive main effects and multiplicative interaction (AMMI) model and genotype main effects plus G × E (GGE) model for multienvironment data analysis along with principal component analysis (PCA). Correspondingly, twenty-five high polymorphism information content (PIC) RM markers were used for the identification of molecular heterozygosity in landrace.

Results Stepwise regression analysis of phenotype revealed the interdependence of zinc in polished rice (ZPR), iron in polished rice (IPR), and single plant yield (SPY) and the positive association of grain Zn with IPR and SPY. Based on GGE and AMMI analyses of the variants, MCM3 was found to be stable across the environments for ZPR. Out of 46% polymorphic RM markers, seven markers (RM10149, RM13347, RM21749, RM13263, RM10361, RM12276 and RM474) were heterozygous. Heterozygous alleles were observed in eight variants (MCM2, MCM3, MCM5, MCM6 MCM7, MCM8, MCM10 and MCM12). The polymorphic information content (PIC) of the markers ranged from 0.58 to 0.88, with an average of 0.64. The percentage of the most common allele frequencies ranged from 4.2 to 95.8 across the markers. RM13347 showed nine markersingle bondtrait associations with P ≤ 0.05 and R2 ranging from 2.3% to 14.3% with a mean of 7.74%.

Conclusions The present study has revealed the inherent heterogeneity in landraces in terms of their agromorphological, yield-related and nutritional quality traits. A promising genetic stock (MCM3) was identified as a donor for high grain ZPR and was registered as genetic stock.

Implications The identified genetic stock is being shared with breeders in the breeding programme and farmers for the multiplication of high grain Zn rice.