Recently, researchers from Biotechnology Research Institute (BRI) of Chinese Academy of Agricultural Sciences (CAAS), in collaboration with South China Agricultural University, Peking University and several other institutions reported their research results in a paper entitled “Genome-wide selection and genetic improvement during modern maize breeding” published in the internationally reputed journal “Nature Genetics”.
Maize (Zea mays ssp. mays L.) is a major staple crop worldwide. Its sufficient supply is of critical importance to securing food safety in China and worldwide. Since the advent of modern breeding in the 1930s, maize yields have increased > 7 folds. However, the genomic bases that associated with this improvement remain largely unexplored. Thus, the researchers conducted a comprehensive analysis of the genomic and phenotypic changes associated with modern maize breeding through chronological sampling of 350 elite inbred lines representing multiple eras of germplasm from both China and the United States. They documented several convergent phenotypic changes in both countries, including continuous reduced ear height, more erect leaves, reduced tassel branch number and accelerated flowering. Using genome-wide association methods, they identified a total of 233 loci associated with 15 key agronomic traits, and 160 of them underlying the four adaptive morphological traits. Using genome-wide selection scan methods, they identified 1,888 genomic regions representing the targets of selection during modern breeding (called “breeding signatures”). Dozens of genes in responses to biotic and abiotic stress, response to light, biosynthesis or signaling processes of auxin and other phytohormones were identified as strong candidates of breeding selection. Moreover, they verified the function of two selected candidates, ZmPIF3.3 and TSH4, in regulating ear height and tassel branch number, respectively, using CRISPR-knockout mutants.
This study provides a genomic overview of the selection targets during modern maize breeding and a valuable source for high-density tolerant superior allele mining. More broadly, this work demonstrates the utility of breeding-era approach for identifying breeding signatures and lays the foundation for future genomics-enabled breeding for maize and other plants.
Dr. Baobao Wang from the Innovation Team of Maize Functional Genomics of BRI, Dr. Zechuan Lin from Peking University, and Ph. D student Xin Li from BRI are the co-first authors of this research. Professor Haiyang Wang (South China Agricultural University) and associate professor Hang He (Peking University) are the co-corresponding authors. Researchers from several other institutions also participated in this study. This research was funded by National Key R&D Program of China (2016YFD0101001), the Major Program of Guangdong Basic and Applied Research (2019B030302006), National Transgenic Science and Technology Program (2019ZX08010003-002-004), National Natural Science Foundation of China (31801377, 31430008, 31921004), the Agricultural Science and Technology Innovation Program of CAAS, and Jilin Provincial Science and Technology Key Project (20170204007NY).

More information can be found through the link:https://doi.org/10.1038/s41588-020-0616-3