Genetic Diversity and Selection Criteria for Yield and Aroma in Rice (Oryza sativa L.) Germplasm of the Eastern Democratic Republic of Congo

Abstract

Improving yield and aroma are among significant objectives of many plant breeding programs, since they are two critical parameters that determine farmers’ and consumers’ variety acceptability and consequently the productivity and market value of rice, respectively. This study aimed to evaluate the genetic diversity and population structure of rice germplasm from the Eastern DRC, determine key parameters associated with high grain yield, classify genotypes and establish the volatile compounds associated with the rice grain aroma. Therefore, 8389 high-quality filtered SNPs generated from 94 rice genotypes using the DArTseq method, were used for genetic diversity and population structure evaluation. The ADMIXTURE program, used for structure analysis, revealed five sub-populations with admixtures. Analysis of molecular variance revealed significant variation between sub-populations (36.09%) and within genotypes (34.04%). The low overall number of migrants (Nm = 0.23) and high fixation index (Fst = 0.52) indicated limited gene flow and significant differentiation between the sub-populations. Observed heterozygosity (Ho = 0.08) was lower than expected heterozygosity (He = 0.14) because of the high inbreeding (Fis = 0.52) nature of rice. A high average Euclidean genetic distance (0.87) revealed the existence of genetic diversity among the 94 genotypes. Selection criteria for grain yield was determined using a set of 49 genotypes. The field experiment was conducted following a 7x7 Triple lattice design in two locations, each with three replicates. Data were collected on fourteen morphological traits. Grain yield reflected a significant and positive correlation with the number of productive tillers/hill, panicle weight, number of primary branches/panicle, number of filled grains/panicle, and number of spikelets/panicle. The sensory test conducted by five panelists, along with the 2-Acetyl-1-Pyrroline (2-AP) profiles classified 49 non-aromatic, 32 semi-aromatic and five aromatic rice genotypes. The classification confirmed Basmati 370, ARS563-425-1-B-2-3 genotypes with strong aroma and high 2-AP contents (1.4 and 1.11 mg/kg, respectively). Furthermore, the untargeted metabolomics revealed 22 major compounds co-detected and positively associated to 2-AP in rice samples. These findings offer additional tools and information to breeding programs for enhancing rice productivity and aroma in the region and beyond, that would ultimately benefit both farmers and consumers.