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The History of Wheat Breeding Revealed by Plant Whole Genome Sequencing

The advancement in next-generation sequencing (NGS) technologies has revolutionized the biological sciences, enabling researchers to study biological systems at a level that has never before been possible. NGS is a type of high-throughput sequencing that is fast, widely available and has significantly reduced the cost of DNA sequencing, making it more accessible. This advancement in sequencing technologies has paved the way for whole genome sequencing which has enabled researchers to address questions that were previously too difficult to explore.

Plant whole genome sequencing using NGS has enabled researchers to obtain a whole host of new information which has given scientists a deeper understanding of plant biology. The information gained from NGS a plant genome can help researchers to study the evolution of the plants, as well as help them to identify genes and other elements. This information is of particular value to agriculture and crop sciences, where information can be used to understand how important agronomic traits are controlled, presenting new opportunities for plant improvements through better plant breeding and plant improvement programs. This advancement in sequencing technologies has even enabled researched to examine crop genomes, including wheat and barley, which were previously thought to be unattainable due to their large and complex nature.

Discovery and Utilization of Wheat Gene Resources

Wheat is an important cereal crop that has been bred all over the world, with production exceeding 600 million tons per year. China is one of the world’s largest wheat producers, accounting for about 17% of the global wheat production. Chinese wheat breeders have been developing and releasing new and improved varieties of wheat since the 1940s.

Owing to its agricultural and economical value, wheat has been at the forefront of scientific studies for a long time. Wheat genetic resources were first used in 1876 when Stephen Wilson produced the first hybrid involving wheat and rye in Scotland. More recently, in 2018, scientists sequenced and assembled the genome of the Chinese Spring wheat model cultivar. Combined with early published wheat gene resources, this has which has paved the way for more advanced studies into the quantitative genetics and functional genomics of various wheat crops.

Researchers at the Chinese Academy of Agriculture Science, Novogene Co. Ltd., and collaborators investigated how selection has affected the wheat genome by resequencing 145 varieties of wheat found in China. The researchers used Animal & Plant Whole Genome Sequencing to resequence these varieties or cultivars using the Chinese Spring Refseq (V. 1.0) as the reference. The varieties of wheat examined included: 100 modern Chinese cultivars, 25 Chinese landraces, and 20 elite cultivars from other national breeding programs which have been introduced to China. The authors used the Illumina Novaseq platform to generate ~43.75 Tb of raw sequences with a 150-bp read length. The sequence data was then taken and mapped against the bread wheat reference genome to look for variations in the genomic information.

Selection Affects Plant Genomes

While it is well recognized that intensive selection in crop breeding usually results in a lower genetic diversity, this is not the case for the modern wheat varieties found in China.

The primary goals of wheat breeding have changed over time, from breeding rust-resistant crops to semi-dwarf breeds and breeding for higher yield cultivars. Today the cultivator’s primary goals are to produce crops that have a high yield and improved grain quality. The nature of breeding-driven selection has resulted in dramatic changes in some of the plants’ physical properties, including those related to grain yield. These changes in physical properties, or the plant’s phenotype, are reflected in the genome, providing genome-scale historical evidence for the distinct genomic regions and phenotypes that the different breeders have targeted across decades.

By sequencing the entire set of genes for the different varieties of wheat, researchers can examine the genome level diversity and provide a comprehensive summary of the gene pool available for breeding. From the sequencing data, researchers were able to identify where genes had been retained or replaced over generations, and which genes had been newly assembled and could have potential value in breeding. From this, the researchers proposed a strategy for evaluating the breeding value of the varieties based on the accumulation of beneficial haplotypes.

Wheat is one of the most important crops globally, providing the most calories and protein of any food source to the world’s growing population. Genetic resources are fundamental to sustaining and increasing, global wheat production to support the world’s population both now and in the future. By characterizing the wheat genome and increasing our understanding of these plants, researchers may be able to identify specific genes related to highly desired traits. This valuable information could be used to further improve wheat production in the future, improving both the yield and quality while increasing the tolerance to environmental stressors and its resilience to weather extremes.


Hao C., Jiao C., Hou J., Li T., Liu H., Wang Y., Zheng J., Liu H., Bi Z., Xu F., Zhao J., Ma L., Wang Y., Majeed U., Liu X., Appels R., Maccaferri M., Tuberosa R., Lu H., and Zhang X. (2020). Resequencing of 145 Cultivars Reveals Asymmetric Sub-Genome Selection and Strong Founder Genotype Effects on Wheat Breeding in China. Mol. Plant. doi: j.molp.2020.09.001.