Rice is one of the most ancient and extensively consumed staple food crops. Its cultivation and domestication have a significant role in the rise of agricultural civilization in Asia. Rice is considered to have been domesticated from Asian wild rice, O. rufipogon, 10,000 years ago [10, 59, 60, 61]. The split between two progenitors, indica, and japonica from which both cultivated types originated, occurred 800,000 years ago [10]. This separation shows long before the origin of agriculture. While aus/boro lineage split from indica appears to be more recent as ~ 540,000 years ago [10].
During the process of domestication, rice has experienced significant phenotypic changes like grain size, color, shattering, seed dormancy, and tillering, as recently identified and verified through quantitative trait loci mapping [21, 22, 62, 63]. Since the domestication of rice, a series of artificial selection procedures have been applied in rice breeding programs that have led to a decline in genetic variability [64]. After the domestication, rice breeders mainly focused on selecting lines with long grain, more tillering, and high yield potential, except for other biotic and abiotic stress tolerant and quality traits. Such unidirectional selection of varieties resulted in a narrow genetic base among the modern cultivars. The present study assessed 20 rice accession genetic diversity, including landraces and modern cultivars, using SNP markers.
Our results revealed that modern cultivars have a narrow genetic base compared to landraces. Like the previous study, the genetic bottleneck caused a limited diversity in cultivated varieties [15]. There is an urgent need to harnessing genetic variation for further improvement and enhance the crop yield's genetic gains. Higher heterozygosity was observed in landraces (HT = 0.02444) than improved varieties (HT =0.01671), as also observed by Alvarez et al. (2007) [65]. Low FST values between these sub-populations and increased observed homozygosity in varieties suggest high inbreeding depression. Thus, the genetic diversity within landraces will be significant for designing new commercial varieties to broaden the new genotypes' variability.
Genetic diversity is desired for crop breeding because it serves as the backbone for improving cultivars. It assists in designing varieties capable of coping with changing climatic conditions by manipulating genetic makeup [66]. Developing elite rice cultivars with increased genetic variability has become a leading challenge for crop breeders, which can implicate recent advances in breeding technologies. The collection of diverse and valuable germplasm in the gene bank is one of the keys to enhancing genetic diversity [14, 67].
Modern crop breeding techniques and advances in crop management practices significantly improve the annual gain of 0.8–1.2% in crop productivity [68]. Genomic breeding is one of the modern breeding technologies, integrating diverse accessions, genomic resources, and molecular technology and breeding tools. Large scale dense genotyping of various germplasm resources has become an essential part of crop germplasm characterization and its further utilization. Based on the genetic and morphological characterization of germplasm, additional help dissect the genetic basis of quantitative traits and identify the novel genes [16, 41, 69]. Utilization of critical genetic loci and pyramiding of these loci through breeding, leading to the development of new germplasm. This advanced breeding approach is named "genome-based breeding by design." Genome-based breeding by design strategy successfully develops green super rice (GSR) cultivars [70, 71, 72].
Genomic selection is one of the most crucial breeding strategies to increase genetic gains and have advantages over the traditional approaches [73]. It can be improved by incorporating the high-throughput SNP chips and next-generation sequencing (NGS)-based platforms and high-throughput phenotyping technologies. This advanced technology helps identify suitable parents for breeding programs, ultimately resulting in a genetic gain of future crops. A genome-wide association study is another genomic strategy using in rice crops [14, 15, 17]. This technique is used to decipher the genetic basis of important quantitative traits, identifying the novel genes underlying study traits, and providing knowledge about the valuable haplotypes. With the implementing such beneficial haplotypes in breeding program result in a genetic gain of advanced cultivars. A haplotype is consisting of two or more SNPs with strong linkage disequilibrium. Sometimes one SNP linked with an undesirable trait causes linkage drag. In this regard, gene-editing technology plays a vital role in reducing linkage drag and regulating critical genes' gene expression. CRISPR-Cas9 tool enabled multiplex-gene editing and was considered a non-GMO approach [74]. This advanced genome editing technique helps breed the new cultivars by activating the homeo-alleles of a gene or deactivating the alleles causing the linkage drag.
In the future, diverse germplasm collection, especially early domesticated cultivars (landraces), enriches the gene pools with multiple genetic backgrounds. Traditional landraces are a rich source of genetic variability and adaptable to stressful environmental conditions. 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. Further, effective implementation of these advanced breeding techniques at one platform will bring the next-generation crops with higher genetic gains. These next-generation crops will help to meet the food security demands for the projected global population in 2050.