Sequencing of the Urochloa ruziziensis genome enhances genetic improvement of forage species

Knowledge should accelerate the improvement of the species, better known as brachiaria. Currently, the process of developing a new cultivar takes more than a decade

05.04.2022 | 13:59 (UTC -3)
Embrapa
Experiment with brachiaria grass (Urochloa ruziziensis) at Embrapa Cerrados, in the Federal District. - Photo: Marco Pessoa
Experiment with brachiaria grass (Urochloa ruziziensis) at Embrapa Cerrados, in the Federal District. - Photo: Marco Pessoa

Using state-of-the-art DNA sequencing and bioinformatics technologies, Embrapa researchers assembled the genome of Urochloa ruziziensis, one of the most used forage grasses in tropical agriculture, especially in integration systems. The information generated from the genome of this brachiaria species will support the development of forage cultivars in a more precise and dynamic way. In this way, forage genetic improvement programs will be able to solve agricultural problems with greater efficiency and agility by making improved cultivars available in less time. 

Marco Pessoa Filho, researcher at Embrapa Cerrados (DF), explains that U. ruziziensis is evolutionary close to the other species of the Urochloa genus most used in cultivated tropical pastures – U. brizantha, U. decumbens and U. humidicola. But while these species are apomictic, that is, they reproduce asexually, generating clonal seeds without exchanging genetic material, U. ruziziensis has a sexual mode of reproduction, through the exchange of pollen.

Due to this characteristic, an advantage of U. ruziziensis, according to the researcher, is the possibility of recombining the genetic diversity of the species through crossings and selecting the best combinations through classical genetic improvement, without the limitations of apomictic species, whose cultivars are generally obtained from accessions (samples collected in the field and representing the genetic variation of a population or individual propagated by clones), which limits genetic variability; or by crossing between different species, which in some cases can result in compatibility and seed production problems.

Furthermore, U. ruziziensis has a diploid genome, that is, the plant's DNA is organized into two sets of chromosomes (in the case of this species, nine pairs), while the other cultivated brachiarias are polyploid, presenting four, six or more sets of chromosomes. The species was also chosen for study because it has a relatively small genome. “It’s a simpler genome to work with when compared to other brachiaria”, explains Pessoa.

“By genetically improving U. ruziziensis, we can both obtain good materials for the development of cultivars of this species (intraspecific recombination) and also support the improvement of apomictic species, providing good sexual individuals that can be crossed with good apomictic individuals (interspecific recombination) ”, adds the researcher.

He recalls that the reduction in costs of new genomic technologies has allowed research groups to act independently, without the need to establish large networks. In the case of assembling the U. ruziziensis genome, the team relied on external sequencing services, carrying out most of the computational work at Embrapa itself.

Use

The genome obtained in this work can be used in research on genomics, advanced biology, genetics, characterization and use of genetic resources in support of tropical forage grass improvement programs.

It will serve as a basis for the discovery of genomic variants (positions in the genome that vary between individuals, which may be mutations, insertions or deletions) that can be applied in genotyping platforms for genomic selection, association studies between genotype (gene composition of the individual ) and phenotype (physical characteristics of the individual), characterization of germplasm (genetic material) and genetic mapping, and for the application of new gene editing technologies, such as CRISPR.

“The genome itself is no longer the ultimate goal of research. Today, it is the starting point for the development of tools to support improvement”, analyzes the researcher. Thus, after genome sequencing, genomic variants have been discovered in a new research project for future application in genotyping platforms. “Our expectation is that we will soon be able to calibrate prediction models based on genomic information for characteristics of interest such as biomass and seed productivity”, explains Pessoa in the case of forage species.

Furthermore, the expertise obtained with the genomic sequencing of U. ruziziensis could be transferred to research groups in genetics and improvement of other forage species at Embrapa, encouraging the obtaining of new genomes and further amplifying the impact and benefits provided by the technology .

“We are producing solid knowledge bases to support genetic improvement work in the medium and long term. The discovery of variants anchored in quality reference genomes will allow an informed choice of markers for implementing genotyping platforms with specific purposes”, says the researcher, adding that this approach has already been used successfully by Embrapa in species such as eucalyptus.

The U. ruziziensis genomic sequencing research received resources of R$ 187,8 thousand from the Federal District Research Support Foundation (FAPDF) and had contributions from researchers from Embrapa Genetic Resources and Biotechnology and Embrapa Dairy Cattle.

Genomic data is publicly available for download from the National Center for Biotechnology Information (NCBI). Gene prediction and annotation data and the location of single base polymorphisms (SNPs) are stored in an internal database, implemented on the Machado platform, developed by researchers from Embrapa Agricultura Digital.

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