Assessment of Genetic Diversity in Traditional Landraces and Improved Cultivars of Rice

Abstract

Background: Rice is the staple food for more than half of the world's population. Rice cultivation needs expansion to meet the increasing food demands across the globe. Genetic diversity is desired for crop breeding because it serves as the backbone for improving cultivars. The process of domestication and modern plant breeding technologies applied to rice has contributed to the erosion of genetic diversity. Current breeding programs have extensively shaped the genetic diversity of elite rice cultivars to no small extent. Results: We explored the genetic diversity of traditional landraces and improved cultivars by inspecting the whole genome SNP markers of 20 rice accessions. We found a higher number of genetic variations (76.70%) and observed heterozygosity (0.024) in landraces than improved cultivars. The principal component analysis also revealed the higher genetic diversity among the landraces. While population structure based on the phylogenetic tree suggested the population's structure according to rice subspecies. The genetic diversity parameter, FST, was applied to estimate the genetic differentiation of rice, which revealed week genetic differentiation (0.121) and nucleotide diversity (0.314) in modern rice cultivars. Genome-wide genetic differentiation (FST) analysis identified the two domesticated genes: Kala4 (pericarp color) and Ghd7 (heading date), and eight improvement genes: Sd1, Ghd8, GW2, NRT1.1b, GW6a, and Hd3a, that coincide with the candidate selective sweeps. Inbreeding depression (0.68617) among the modern cultivars suggests no genetic gain in future breeding efforts and compels exotic material utilization in the breeding programs. Conclusion: These findings demonstrate that modern cultivars have a narrow genetic base compared to landraces. Therefore, exploring the genome of landraces at a large scale to identify the genes responsible for stability and adaptation to abiotic stresses can help design varieties that can survive vulnerable climates.

Exploration of traditional rice (Oryza sativa L.) land races: Scope for the future sustainable food production

“…So, the utmost importance should be given to these characters during the selection for yield improvement in rice. Zahra et al (2020) [36] found that modern cultivars have a narrow genetic base compared to landraces. Therefore, exploring the genome of landraces at a large scale to identify the genes responsible for stability and adaptation to abiotic stresses can help design varieties that can survive vulnerable climates.…”

Genetic variability for micronutrients under an aerobic condition in local landraces of rice from different agro-ecological regions of Karnataka, India

“…Landraces that endowed with tremendous genetic variability support the adaptation of landraces to wide agro-ecological niches. Landraces are precious genetic resources because they contain rich variability of agronomical important and complex quantitative traits, which have not been widely utilized or incorporated into modern varieties (Rao et al 2018;Zahra et al 2020). Assessing genetic variability for growth, yield, and grain quality characters among the local landraces is an important step before starting a crop breeding program to incorporate traits of interest.…”