Genome-wide genetic changes during modern breeding of maize

• Published in: Nature genetics Vol. 44; no. 7; pp. 812 - 815
• Main Authors: Jiao, Yinping, Zhao, Hainan, Ren, Longhui, Song, Weibin, Zeng, Biao, Guo, Jinjie, Wang, Baobao, Liu, Zhipeng, Chen, Jing, Li, Wei, Zhang, Mei, Xie, Shaojun, Lai, Jinsheng
• Format: Journal Article
• Language: English
• Published: New York Nature Publishing Group US 01.07.2012; Nature Publishing Group
• Subjects: 631/1647/334/2244/1401; 631/208/205/2138; 631/208/2491/711; 631/449/447/8; Agriculture; Alleles; Animal Genetics and Genomics; Biological and medical sciences; Biomedical and Life Sciences; Biomedicine; Breeding; Breeding - methods; Cancer Research; Corn; DNA Copy Number Variations; Fundamental and applied biological sciences. Psychology; Gene Function; Gene mapping; Genes; Genetic aspects; Genetics; Genetics of eukaryotes. Biological and molecular evolution; Genome, Plant; Genome-Wide Association Study - methods; Genomes; Genomics; Human Genetics; letter; Physiological aspects; Plant breeding; Polymorphism, Single Nucleotide; Selection, Genetic; Studies; Zea mays; Zea mays - genetics; China; United States > US; Genetics
• ISSN: 1061-4036; 1546-1718
• DOI: 10.1038/ng.2312

Jinsheng Lai and colleagues report the resequencing of 278 inbred maize lines and perform a genome-wide analysis of genetic changes during modern breeding. Using SNP imputation, the authors also perform a genome-wide association study for cob color, silk color and date to anthesis. The authors identified association signals with significant P values near known targets. The success of modern maize breeding has been demonstrated by remarkable increases in productivity over the last four decades. However, the underlying genetic changes correlated with these gains remain largely unknown. We report here the sequencing of 278 temperate maize inbred lines from different stages of breeding history, including deep resequencing of 4 lines with known pedigree information. The results show that modern breeding has introduced highly dynamic genetic changes into the maize genome. Artificial selection has affected thousands of targets, including genes and non-genic regions, leading to a reduction in nucleotide diversity and an increase in the proportion of rare alleles. Genetic changes during breeding happen rapidly, with extensive variation (SNPs, indels and copy-number variants (CNVs)) occurring, even within identity-by-descent regions. Our genome-wide assessment of genetic changes during modern maize breeding provides new strategies as well as practical targets for future crop breeding and biotechnology.