Rice (Oryza sativa) is one of the most important crops in the world. Rice is considered a perfect model plant for plant genomics research because of its relatively small genome size (∼400 Mb), well-established and efficient transformation system, abundant genetic resources, and sequence homology with other cereal crops. Rice was the first crop genome to be sequenced, paving the way for the sequencing of other more complex crop genomes. Rice genomics has revolutionized the study of rice biology and has contributed significantly to rice breeding. Nonetheless, the size of the rice genome remains a daunting task for whole-genome sequencing, the third largest public genome project undertaken to date, after human and mouse genomes.

CD Genomics is a leading service provider for agricultural genomics research, offering reliable rice genome sequencing services to support research and breeding efforts in the field of rice genomics for clients worldwide. Our services help improve yield, disease resistance, and nutritional content of rice varieties.

Our rice genome sequencing service

CD Genomics offers comprehensive and customizable rice genome sequencing services using cutting-edge technology and expertise to characterize the rice genome at the cytogenetic, genetic, and molecular levels. Our services cover all stages of the sequencing process, from library preparation to data analysis, ensuring high-quality and accurate results.

With our advanced next-generation sequencing and long-read sequencing technology platforms, as well as bioinformatics tools, our highly skilled experts can generate high-quality whole genome sequences for a wide range of rice varieties. Our high-throughput sequencing technology allows for the identification and characterization of genetic variants, including single nucleotide polymorphisms (SNPs), insertions/deletions (indels), and structural variants.

To ensure the accuracy and reliability of sequencing data, we follow strict quality control measures throughout the process. Our bioinformatics analysis pipeline is designed to process large-scale genomic data and provide comprehensive annotation of genes, regulatory elements, and repetitive sequences within the rice genome.

CD Genomics offers a wide range of rice genomes and their annotations, including but not limited to:

What we offer

CD Genomics uses a shotgun approach to seqence bacterial artificial chromosomes (BAC) or P1-derived artificial chromosome (PAC) clones. With this procedure, individual PAC/BAC clones (100 to 200 kb) With this procedure, individual PAC/BAC clones (100 to 200 kb) from a sequence-ready contig are shattered by sonication or nebulization, and the fragments are subcloned to produce a shotgun library with an average Clones from the shotgun library are then sequenced at random to provide the desired degree of "coverage" of the total sequence. In addition, we provide cloning and functional analysis of rice agronomy-related genes and QTL.

We aim to provide the scientific community with accurate and timely sequence annotation of the rice genome and to facilitate comprehensive analysis of the structure and function of the rice genome based on the annotation. CD Genomics provides comprehensive rice genomics research:

• Rice structural genomics: genome sequencing to construct a complete sequence map of the rice genome.
• Functional genomics: decoding the functions of rice genes.
• Quantitative genomics: large-scale sequence and statistics-based studies aimed at analyzing quantitative traits and genetic characteristics of rice populations.

Applications of rice genome sequencing

• Uncovering the genetic basis of rice traits

By comparing the genomes of different rice varieties, we help you identify genes associated with important agronomic traits such as yield, disease resistance, and tolerance to environmental stress. These data can support breeders in developing improved rice varieties with desirable traits through marker-assisted selection and genetic engineering techniques.

• Accelerating gene discovery and functional genomics

Using the reference genome as a blueprint, we help you identify and characterize specific genes responsible for important biological processes in rice. In addition, we provide transcriptomics, proteomics, and metabolomics analyses to help you gain insights into gene expression patterns, protein functions, and metabolic pathways in rice.

• Comparative genomics and crop improvement

Sequencing the rice genome not only facilitates rice research but also promotes comparative genomics between different cereal crops. By comparing the rice genome with the genomes of other crops, such as maize and wheat, we help you identify conserved genomic regions and gene families. In addition, data from comparative genomics can be used to improve rice through targeted breeding strategies and genetic engineering.

Case study of rice genome sequencing

The rice genome sequence was published in 2005 and was the first cereal plant genome. In addition to its relatively small genome size, one of the original motivations for sequencing rice was that it could be used as a model for other cereal crops with larger genomes, such as corn and wheat. This is partly based on the small genome size of rice and the implementation of molecular mapping (e.g. RFLP) of conserved markers and marker sequences.

Researchers have successfully resequenced the whole genome of three traditional Basmati varieties at a coverage of more than 25X using Illumina HiSeq2500 and mapped the obtained sequences to the reference genome sequences of Nipponbare (japonica rice), Kasalath (aus rice), and Zhenshan 97 ( indica rice).

Fig. 1. Phenotypic comparison of Basmati 370, Dahrdun Basmati, and Rato Basmati. (Kishor et al., 2020)

• Genetic Diversity and Evolution: Identification of specific genetic variants and classification of basmati rice varieties into different groups based on whole-genome sequencing data facilitated targeted breeding programs to improve rice quality and agronomic traits.
• Functional elements and genomic features: Functional annotation of the rice genome revealed important insights into the functional elements and genomic features of the crop.
• Agronomic traits and grain quality: By analyzing key traits such as grain aspect ratio, panicle length, and amylose content, this study identified the genetic variation associated with these traits.

CD Genomics offers cutting-edge rice genome sequencing services to provide comprehensive genomic information to researchers and breeders for their studies. We aim to provide data to support basic research on the genetics of important rice traits and to promote rice improvement. If you are interested, please feel free to contact us.

Reference

1. Kishor, D. S., et al. Evaluation of whole-genome sequence, genetic diversity, and agronomic traits of Basmati rice (Oryza sativa L.). Frontiers in Genetics. 11 (2020): 86.