Experimental evolution in maize with replicated divergent selection identifies two plant-height-associated regions

Area of Science:

• Agricultural Science
• Evolutionary Biology
• Genetics

Background:

• Experimental evolution, or long-term selection, is crucial in agricultural research for understanding adaptation.
• Selection mapping aims to identify genomic regions under selection, but robust significance thresholds are challenging, especially in unreplicated crop studies.
• Previous methods often use empirical distributions, risking false positives or negatives, and single-marker statistics can identify linked neutral loci.

Purpose of the Study:

• To conduct divergent, replicated selection for plant height in a maize population under field conditions.
• To develop and apply robust significance thresholds for selection mapping using replicated data.
• To identify genomic regions and genes associated with selection for plant height in maize.

Main Methods:

• Divergent selection for extreme plant height (shortest and tallest 5%) was applied for three generations in a random-mating maize population.
• A window-based statistic (FSTSum) leveraging replicated selection was used.
• Significance thresholds were determined using the false discovery rate for selection (FDRfS).

Main Results:

• Two significant genomic regions were identified as putatively under selection.
• One region on chromosome 3 is located near known plant height genes (Dwarf1 and iAA8).
• Haplotype block analysis revealed strong selection patterns in short plant height subpopulations on chromosome 3.

Conclusions:

• Replicated field selection combined with FDRfS provides a robust method for accurate selection mapping in crops.
• The study identified specific genomic regions associated with selection for plant height in maize.
• Findings highlight the importance of specific genes and chromosomal regions in maize plant height evolution.