A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement - PubMed (original) (raw)

A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement

Masanori Yamasaki et al. Plant Cell. 2005 Nov.

Abstract

Maize (Zea mays subsp mays) was domesticated from teosinte (Z. mays subsp parviglumis) through a single domestication event in southern Mexico between 6000 and 9000 years ago. This domestication event resulted in the original maize landrace varieties, which were spread throughout the Americas by Native Americans and adapted to a wide range of environmental conditions. Starting with landraces, 20th century plant breeders selected inbred lines of maize for use in hybrid maize production. Both domestication and crop improvement involved selection of specific alleles at genes controlling key morphological and agronomic traits, resulting in reduced genetic diversity relative to unselected genes. Here, we sequenced 1095 maize genes from a sample of 14 inbred lines and chose 35 genes with zero sequence diversity as potential targets of selection. These 35 genes were then sequenced in a sample of diverse maize landraces and teosintes and tested for selection. Using two statistical tests, we identified eight candidate genes. Extended gene sequencing of these eight candidate loci confirmed that six were selected throughout the gene, and the remaining two exhibited evidence of selection in the 3' portion of each gene. The selected genes have functions consistent with agronomic selection for nutritional quality, maturity, and productivity. Our large-scale screen for artificial selection allows identification of genes of potential agronomic importance even when gene function and the phenotype of interest are unknown.

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Figures

Figure 1.

Figure 1.

Effect of Domestication and Plant Breeding on Genetic Diversity of Maize Genes. The colored circles represent different alleles. The shaded areas indicate bottleneck effects placed on all genes by the processes of domestication and improvement (plant breeding). Our model assumes that there will be three types of genes: neutral genes that show reduction of diversity by the general bottleneck effects, domestication genes in which diversity is greatly reduced by selection between the teosintes and landraces, and improvement genes in which diversity is greatly reduced by selection between the landraces and inbreds.

Figure 2.

Figure 2.

Distribution of Genetic Diversity π for 1095 Maize Genes. The genes were sequenced in the panel of 14 diverse maize inbreds (Table 1).

Figure 3.

Figure 3.

The Genetic Diversity π in Landraces and Teosintes for Each of 35 Genes with Zero Diversity in Inbred Lines. The black bars indicate genetic diversity in the teosintes, and the white bars indicate genetic diversity in the landraces. Where no white bars are present, the genetic diversity in the landraces was zero. Inbreds are not shown as all are π = zero. The two rows under the figure indicate the test results for selection by HKA and CS analyses. The “-” indicates no significance; n = not tested in the HKA test due to inability to amplify a T. dactyloides orthologous sequence; I, improvement candidate; D, domestication candidate. The GenBank accession of the original Maize Mapping Project/DuPont unigene sequence is indicated under the bar.

Figure 4.

Figure 4.

Sliding-Window Analysis of the Genetic Diversity π in Maize Inbreds and Teosintes. For sliding-window analysis, π was calculated for segments of 100 bp at 10-bp intervals. Horizontal and vertical axes on the graphs indicate DNA sequence position and genetic diversity π, respectively. Red lines indicate genetic diversity in the inbreds, whereas blue lines indicate genetic diversity in the teosintes. For gene structure under the sliding-window graphs, white bars indicate the predicted exons, and black lines indicate introns or genomic regions. Left arrows and right arrows indicate the positions for predicted start codons and stop codons, respectively. The lines with two arrows under the gene structure indicate the sequencing regions in our initial screening. (A) AY108876; (B) AY107195; (C) AY110109; (D) AY105060; (E) AY108178; (F) AY106616; (G) AY107952; (H) AY106371.

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