BGI, the world's largest genomics organization, together with other 17 international institutes, announced that it completed the second generation of maize HapMap (Maize HapMap2) and genomics studies on maize domestication and improvement. The two separate studies were published online in the same issue of Nature Genetics.
The studies mark an important milestone in Maize (Zeamays) genomics research, providing an unprecedented glimpse into maize's 'wonderful diversity' and revealing new insights into the evolutionary history of maize genome. These studies will provide valuable insights for botanists and breeders worldwide and facilitate the genetic engineering of this vital cereal crop in the world.
In addition to BGI, the other collaborative organizations include U.S. Department of Agriculture (USDA), Cold Spring Harbor Laboratory, University of California Davis, Cornell University, the International Maize and Wheat Improvement Center (CIMMYT), and others.
Characterizing Maize's Impressive Diversity
Maize's impressive diversity has been attracting much attention in the academic community and agricultural sector. However, characterizing this diversity- in particular at high levels- has been technically challenging. In this study, researchers developed a novel population-genetics scoring model for comprehensively characterizing the genetic variations, including single nucleotide polymorphisms (SNPs), small insertion-deletions, and structural variations (SVs). Through the comprehensive analysis, about 55 million SNPs were identified across 103 inbred lines of wild and domesticated maize. They also found that SVs were prevalent throughout the maize genome and were associated with some important agronomic traits, such as those involved in leaf development and disease resistance.
The researchers also investigated the major factors that influence the maize genome size. The results showed the genome size variations between maize and Gama grass (Tripsacum dactyloides), maize's sister genus, are mostly driven by the abundance of transposable elements (TE). In contrast with the fact that the intra-species genome size variation is influenced by the DNA structure known aschromosomal knobs. In addition to the differences, there is tremendous unity of gene content between maize relatives, suggesting that the adaptations, such as frost and drought tolerance, amongst all of maize's relatives are likely integratable in maize.
Tracing Maize's Evolution and Improvement
Since maize was domesticated approximately 10,000 year ago, its wild progenitor went through a particular transformation that had radically altered maize's wild species to meet human's needs. To comprehensively trace maize's evolution process, researchers sequenced 75 wild, landrace and modern maize lines. Through the comparative population genomics analysis, they found the evidence of new genetic diversity that has arisen since domestication, maybe due to the introgression from wild relatives. They also identified a number of genes that obviously had played important roles in the transition from wild to domesticated maize.
More importantly, the results demonstrated that the selection applied by ancient farmers seemed to play a stronger impact on maize evolution than the breeding techniques adopted by modern breeders. Hybridization in agriculture is vitally important to maintain genetic diversity, and sustains the quality and yield of a crop. In this study, researchers found that many of the changes in the patterns of gene expression had been concentrated in the genes selected for heterosis by modern breeding techniques. These findings suggest that modern breeders should devote more efforts to make effective improvement on candidates by introducing more diversity at the regions linked with selection.
Xun Xu, Ph.D., deputy director of BGI, said, "Genetic improvement of crops is the key output of breeding research. The two studies provide a new way to comprehensively understand maize's genetic diversity and evolutionary history as well as offer an invaluable guidance for botanists and breeders to improve this vital crop."
Gengyun Zhang, Ph.D., vice president of BGI, said, "Maize is one of the world's most important crops. The two studies will provide a valuable foundation for accelerating the improvement of maize towards meeting the world's increasing demands for food, livestock feed and biofuel. We look forward to achieve more breakthrough for solving the food security challenges and environmental problems in the near future."