Molecular breeding lab in BGI Research focuses on many important crops breeding, especially the transformative progress from genomes to molecular breeding. The goal of the lab is to build a molecular breeding platform based on sequencing and genome analyzing, then supply the future breeding with new methods.

Progress in Rice

The Innovative Institute was established in September 2011, when the project to resequence 3000 core rice germplasm was initiated.

·  Resequencing 3000 core rice germplasm. To date, resequencing of 3200 rice has been finished, and a proportion of the data has been analyzed. The average sequencing coverage in each sample is up to 14X. Now, work is in progress to identify the SNP and construct the HapMap, which will be used for guiding the breeding of rice.

·  Molecular breeding of rice based on the genomics. With the resequencing data of 3000 rice germplasm, the highest density molecular marker system has been developed, which can be used for locating gene loci of certain important traits and screening rice population. Applying this key technique, population analysis of several super-rices were completed, many loci of important traits have been located successfully, such as the grain number per spike, setting rate, height, flag leave width, filled-grain percentage, pest resistance, grain length and so on. Now, we are trying to merge all of these traits to one crop to build a new super rice strain.

Progress in Millet

In the early 2010, BGI and Zhangjiakou Academy of Agriculture Science established collaboration on the Foxtail Millet Genome. The initial result was published in Nature Biotechnology, (Genome sequence of foxtail millet (Setariaitalica) provides insights into grass evolution and biofuel potential. Nature Biotechnology, 2012, 30(6):549-54.) In this project, the first draft of the whole genome was developed within 4.5 months and constructed a high density genetic linkage map within 2 months, which contains more than 700 molecular markers. Moreover, several genes were located with relations to male sterile, herbicide resistance and plant height, which could be used for breeding through transferring the targeted genes into strains and promoting the rapid, effective selection. Applying this method, the improved parental materials were obtained within 1 year, shortened the breeding period and increased the breeding efficiency significantly. 27 patents have been obtained in this project. The success of the foxtail millet project indicated that the technique of molecular breeding by whole genome-sequencing is applicable.

Progress in Super-rice

BGI and Hunan Hybrid Rice Research Center initiated a project of super-hybrid-rice together in the early 2012. This project will locate some main agronomic traits and improve the current rice directionally in short term to build a new super rice cultivar with technique of whole genome molecular breeding. 

To date, we have finished the gene location and population analysis of strains with high pest resistance or giant fringe. We finely located genes of some important agricultural traits, such as natural pest resistance, filled-grain percentage, length of rice grains, grain number per spike, number of first peduncle, number of second peduncle, setting percentage, plant height, period of sexual mature, seed holding, rice grain’s length-width ratio and so on. Moreover, we’ve explored more than 600,000 molecular markers through the whole genome of super rice. Based on these gene loci and molecular markers, we’ve built a genome-based breeding platform. We will finish the improvement of rice within 2 years, at the same time, add more other traits to cultivate new super-rice in short term. 

Progress in Potato

On July 11, 2011, the potato genome was drafted by the International Potato Genome Sequencing Consortium that constructed by 29 institutions including BGI, the Institute of Vegetables and Flowers in Chinese Academy of Agricultural Sciences and others. The result was published in Nature online. This is another breakthrough on this important tuber crop’s genomics since the framework of genome built in 2009. The genome will be valuable resource for the genetic improvement and breeding of potato.

In this research, BGI was in charge of the de novo sequencing, assembling and other bioinformatics analysis. The genome was sequenced in coverage of 123X, and the size assembled was 727Mb, which covered 86% of the whole genome. Potato is the first Asterids species to be sequenced. The group identified 39,031 protein coding genes, among which 2,642 are unique in the Asterids plants. The evolution of genome, tuber growth and resistance to pests were also characterized. BGI played an important role in this research with its powerful sequencing platform and extensive experience in bioinformatics analysis. 

Progress in goat

The result of first goat genome map, which is finished by BGI and Kunming Institute of Zoology CAS, was published on Nature Biotechnology On December 24, 2012. This research combined the technique of next-generation sequencing and whole-genome mapping, overcame the difficulty of assembly in goat genome and offered the reference genome of the first small ruminant. It will help to reveal the difference between ruminant and non-ruminant, and provide a new idea strategy for assembling large complex genomes.

Goat is one of the first domestic animals. Evidence indicates that the goat might have been domesticated from two wild Capris, and now is widely reared throughout the world, especially in China, India and other developing countries. Goats serve as an important source of meat, milk, fiber and pelts, and have also fulfilled agricultural, economic, cultural and even religious roles since very early times in human civilization.  Despite the agricultural and biological importance of goats, breeding and genetics studies have been hindered by the lack of a reference genome sequence. The de novo sequencing of goat will provide valuable resource to marker assisted breeding and improvement on the economic traits of goat. 

Progress in Oyster

The Oyster’s genome sequencing was carried out by BGI and Institute of Oceanology, CAS, and then the result was published in Nature on September 20, 2012 (The oyster genome reveals stress adaptation and complexity of shell formation. Nature, 2012, 490 (7418): 49-54). With next-generation sequencing technique and novel assembly strategy, Researchers constructed the genome map of oyster and the draft assembly provided insight into a molluscan genome characterized by high polymorphism, abundant repetitive sequences and active transposable elements. Genomic, transcriptomic and proteomic analyses showed unique adaptations of oysters to sessile life in a highly stressful intertidal environment and the complexity of shell formation.

As more and more oyster genome data was analyzed, it is hoped that the life habit of oyster could be changed to make it serves people better. For example, in the natural state, oyster will attach to the ship and the surface of some pipeline which would hinder the ship’s sailing and blocking the pipeline. Oyster’s sessile life nature makes it one of the marine fouling organisms. We may find out the key receptor of oyster’s sessile pathway, design a new drug which can change oyster to a swimming life, so the shipping hindering and pipeline blocking problem could be solved. With the results of transcriptome, miRNA, epigenetics and system biology research, researchers opened a new window for us to observe the oyster’s biological traits and its interaction with the environment, understand its characteristics of high fertility, high stress resistance and high heterozygosity, find out the omics mechanism of heterosis, species differentiation, sex determination, high mutation rate, high genetic load and sessile metamorphosis, then build an oyster genome-based breeding platform and theoretical research platform, improve the study of molluscsand marine genomics, and promote the healthy and sustainable development of molluscsculture industry.