Analysis of historical selection in winter wheat

Area of Science:

• Plant genetics and breeding
• Quantitative genetics
• Agricultural science

Background:

• Winter wheat (Triticum aestivum) is a vital global crop with extensive breeding history.
• Genetic gains in traits like yield are well-documented, driven by selective breeding.
• Understanding historical selection is crucial for optimizing future crop improvement strategies.

Purpose of the Study:

• To develop and apply a novel selection mapping approach, Regression of Alleles on Years (RALLY), to identify loci under historical selection in winter wheat.
• To analyze allele frequency distributions over time in large winter wheat collections.
• To characterize the impact of historical selection on key agronomic and quality traits.

Main Methods:

• Analysis of two large winter wheat collections (Triticeae Genome and WAGTAIL panels) with historical release data.
• Development and application of the RALLY method, a logistic regression of allele counts on variety release year.
• Implementation of a hybrid genomic and delta control strategy to mitigate drift effects on allele frequencies.

Main Results:

• Identification of 22 significant RALLY quantitative selection loci (QSLs) in the Triticeae Genome panel.
• Estimation of local heritabilities for 12 traits across identified QSLs.
• Demonstration that alleles increasing in frequency over time are strongly associated with positive yield effects but negative effects on flowering time, lodging, plant height, and grain protein content.

Conclusions:

• The RALLY method effectively identifies selected genomic regions while controlling for genetic drift.
• Historical selection in winter wheat has systematically favored yield-enhancing alleles at the expense of other important traits.
• These findings provide insights into past breeding patterns and offer guidance for future winter wheat breeding programs.