Assessment of genetic diversity of local rice accessions cultivated in Guinea revealed by SNPs markers, and identification of markers associated with tolerance to iron toxicity

Abstract

Rice is the staple food in the Republic of Guinea. However, its production is seriously hampered by iron toxicity. The fight against this stress necessarily involves the search for tolerant or resistant varieties. The study aims to determine quantitative trait locus (QTL) associated with tolerance to iron toxicity and to identify genotypes tolerant or resistant to iron toxicity. Thus, 90 local rice accessions collected in two regions of Guinea with high iron toxicity were evaluated using 33,537 single nucleotide polymorphism (SNP) markers. Seventy of the SNP markers expressed a polymorphism rate of 100%. Diversity analysis of the entire collection with these markers revealed a total of 140 alleles, a moderate Nei genetic diversity of 0.426, a fairly high Shannon diversity index of 0.610 and an organization of the accessions into four genetic groups. The study also identified 12 potentially iron-tolerant accessions and five QTLs associated with iron-toxicity tolerance located on chromosomes 1, 2, 3, 11, and 12. The 12 genotypes identified could be exploited in the lowland rice breeding program.

Genetic variation and population structure of Oryza sativa accessions in the AfricaRice collection and development of the AfricaRice O. sativa Core Collection

“…Furthermore, Worede et al. (2013) used SSR markers to successfully group NERICA 3 and NERICA 4, upland accessions, into the Japonica cluster with Azucena, a tropical japonica (Laho et al., 2022; D. Wang et al., 2018). L. Barry et al.…”

“…This was confirmed by W. , where NER-ICA 1, 2, 8, and 9 were classified as tropical japonica and NERICA-L-1, -20 and, -27 as indica-1B, the subpopulation that includes modern cultivars of diverse origins. Furthermore, Worede et al (2013) used SSR markers to successfully group NERICA 3 and NERICA 4, upland accessions, into the Japonica cluster with Azucena, a tropical japonica (Laho et al, 2022;. L. Barry et al (2022) reported NERICA-L-19 clustered with IR64 and Bouake 189, which were identified as indica2 by D. .…”