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Rice Production & Heterosis – The Future of the Hybrid Technology and its relationship with Genome Sequencing

Date: 18/02/2021 | Animal & Plant Whole Genome Sequencing | De novo

Global predictions indicate the human population will continue to rise. Sustaining food or agriculture production is a concerning matter that must be addressed. In the mid-20th century, hybrid technology gave rise to the “green revolution” that increased agricultural production. The core of the hybrid technologies lies at the genome of these plants. Genomic sequencing companies are endlessly improving their technological capacities, allowing researchers to dig deep into the genome of rice plants and explain why certain offspring are able to outperform their parents.

Agriculture and population growth

Rice (Oryza. sativa) is one of the most important foods on a global scale, a staple for many countries, especially amongst Asian countries. Throughout the years, rice productivity has increased twofold. However, global demand has exponentially increased, as well. Rice production must be increased as well to meet these demands and it needs to be done under rigorous environmental conditions, due to climate changes and many other factors.

This can be done by increasing a crop’s stability and the grain’s quality. To do this more research needs to be conducted to understand the distinctive genetic diversity of the O. sativa gene pool and its diverse alleles. Genome sequencing companies provide researchers with knowledge-based tools, to allow for DNA sequencing and other techniques, such as resequencing.

The utility of genome sequencing in the field of rice breeding

By using DNA sequencing services, researchers can provide a clearer picture of these changes that yield a higher grain quality. This results in longer reads and higher total genomic output, due the higher number of bases covered. Novogene, a trustworthy company, provides researchers with the latest next-generation sequencing technology and bioinformatics expertise required for these complex tasks.

Resequencing is a procedure that utilizes different structural variations, such as Single Nucleotide Variations and Single Nucleotide Polymorphisms (SNVs and SNPs, respectively), as well as insertion and deletion mutations (InDels). The importance of these molecular changes is highlighted in heterosis, where the first filial generation of hybrids possess higher quality traits than its progenitors.

A hybrid is born when the egg of a rice plant is fertilized by the pollen of another rice plant but from a different variety or line. In heterosis, the resultant hybrid rice seed shows superiority to both parents in agronomic traits or yield. The genes involved in the development of better traits are still being studied, but certain candidates have been identified, such as the fertility and sterility genes, determined by the nuclear genome. Thus, understanding how a hybrid descendant differs from its parents, from a genetic point of view, is key to understanding the underlying complexity of heterosis, in turn, this would allow for improvement and innovation in breeding strategies[1].

Novogene blog Rice Sequencing

Research Background

Multiple studies[2, 3, 4] have been released in the field of rice genomics, but most of them focus on the japonica Nipponbare genome, which has become the reference sequencing genome. Because of this, it has allowed researchers to gain a certain insight on the diversity among thousands of rice cultivars. This is partly due because the japonica subtype is mainly distributed in the northern regions of China, the most rice cultivated areas of the country[5].  The others are indica and japonica. Other studies [6] used the indica subtype as the reference genome, to understand the variations of SNPs and InDels that give rise to superior hybrids.

Research Material

Researchers acquire thousands of conventional rice (CR) or germplasm rice (GR) accessions through a variety of different organizations, such as the International Rice Research Institute (IRRI) or the China National Crop Gene Bank (CNCGB), to name a few. The total DNA was extracted from the leaves of 1-month-old rice plants. Afterwards, they were sequenced utilizing Illumina NovaSeq technology. The nuclear, mitochondrial and chloroplast genomes of these plants were mapped. As expected, these large samples yield equally higher sequencing libraries, with datasets that can easily go up to a few terabytes of information.

Research Result

By identifying the SNPs and InDel variations, the phylogenetic and kinship relationships between the accessions, the genetic distances between the different lines (i.e. how conserved or distinctive rice genomes are across different generations or subgroups) and the identification of the loci involved in the heterosis of rice plants, through the use of next-generation sequencing technology, allowed researchers to shed some light on this widely studied subject.

More genes than previously reported might be involved in the yield heterosis through the 3- and 2-line hybrid technology. Results show the loci associated with heterosis is different between these two breeding techniques, probably as a result of the differences in the flexibility of the two hybrid systems and their history. The 2-line hybrid system was developed 20 years after the 3-line system, which would explain why there is less diversity in hybrids born out of the former system than the latter[6].

Phylogenetic analyses show that, between the indica and japonica subtypes, the former is the largest and most diverse group, showing a clear differentiation between both[3]. Plus, it’s also shown that, across different chromosomes, the distribution of the identifiable SNPs varies considerably. Thus, determining how conserved or distanced the chromosome genome is between parents’ lines and their hybrid offspring (through the use of phylogenetic and kinship analyses), is very important. Answering many questions regarding the hybrid rice crosses will facilitate the innovation of breeding techniques, improving crop yield to sustain an ever-growing population.


[1] Scanlon M, Timmermans M. Growth and development: from genes to networks and a mechanistic understanding of plant development. Curr Opin Plant Biol. 2013 Feb;16(1):1-4. [Curr Opin Plant Biol]
[2] Wang W., et al., Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature. 2018 May;557(7703):43-49. [Nature]
[3] The 3,000 rice genomes project, The 3,000 rice genomes project, GigaScience, Volume 3, Issue 1, December 2014, 2047–217X–3–7, 7. [GigaScience]
[4] Huang X, et al., Genomic architecture of heterosis for yield traits in rice. Nature. 2016 Sep 29;537(7622):629-633. [Nature]
[5] Jiang S, Sun S, Bai L, Ding G, Wang T, et al. (2017) Resequencing and variation identification of whole genome of the japonica rice variety “Longdao24” with high yield. PLOS ONE 12(7): e0181037 [Plos One]
[6] Lv, Q., Li, W., Sun, Z. et al. Resequencing of 1,143 indica rice accessions reveals important genetic variations and different heterosis patterns. Nat Commun 11, 4778 (2020). [Nature Communicates]