Current status of genomic resources on wild relatives of rice

Abstract

Rice is a food crop of global importance, cultivated in diverse agro-climatic zones of the world. However, in the process of domestication many beneficial alleles have been eroded from the gene pool of the rice cultivated globally and eventually has made it vulnerable to a plethora of stresses. In contrast, the wild relatives of rice, despite being agronomically inferior, have inherited a potential of surviving in a range of geographical habitats. These adaptations enrich them with novel traits that upon introgression to modern cultivated varieties offer tremendous potential of increasing yield and adaptability. But, due to the unavailability of their genetic as well as genomic resources, identification and characterisation of these novel beneficial alleles has been a challenging task. Nevertheless, with the unprecedented surge in the area of conservation genomics, researchers have now shifted their focus towards these natural repositories of beneficial traits. Presently, there are several generic and specialized databases harboring genome-wide information on wild species of rice, and are acting as a useful resource for identification of novel genes and alleles, designing of molecular markers, comparative analysis and evolutionary biology studies. In this review, we introduce the key features of these databases focusing on their utility in rice breeding programs.

DNA-Based Tools to Certify Authenticity of Rice Varieties—An Overview

“…Another relevant tool is the Rice SNP-Seek database [95,96] that includes the phenotypic, genotypic and varietal information of rice and SNP genotyping data from the 3K Rice Genome project. Ultimately, this paved the way for the identification of millions of SNPs and InDels that assisted in rice genomics research.…”

“…A major step towards the advancement of DNA barcoding technology in rice was the 3K Rice Genome Project (3K-RG) initiative [4], since it allowed for the identification and exploration of allelic/haplotype variation [105]. From the 3K-RG project, several databases arose such as RPAN genome browser and the already-mentioned Rice SNP-Seek database [95,96]. RPAN genome browser represents the union of all the genes present in rice species, providing a new dimension to the genome complexity based on the presence or absence of variation in a genome [106].…”

Challenges and opportunities in productivity and sustainability of rice cultivation system: a critical review in Indian perspective

“…Genomic information of 3,010 diverse Asian cultivated rice including 3000 rice accessions of 3 K rice genome project was used to identify 29 million SNPs, 2.4 million small indels, 10,000 novel full-length protein-coding genes and more than 90 thousand structural variations, which will serve as an extremely important genetic resource for breeding and biotechnology research (Wang et al 2018). Several databases and genomic resources of rice are available in public domain for gene/allele discovery, molecular marker designing and basic studies (Kamboj et al 2020). These resources have facilitated the QTL discovery and gene cloning for marker-assisted breeding programs and transgenic research.…”

Leveraging the 3000 Rice Genome Data for Computational Design of Polymorphic Markers in a Local Rice Variety Lacking Sequence Data

“…Although the SNP pre-screening method can reduce our fine-mapping program's cost and time, we also noted that this approach currently has some undesirable characteristics that may hinder its wider adoption by other researchers. Firstly, this approach relies on the abundant availability of genomic data in rice, where high-quality reference genome and wholegenome sequence data are already available for thousands of rice accessions that represent the worldwide genetic diversity of rice [39]. Researchers working on other crops may not have such luxury [40], making this approach difficult to apply for such crops.…”