Genomic sequence and copy number evolution during hybrid crop development in sunflowers

Area of Science:

• Plant genetics
• Agricultural science
• Crop breeding

Background:

• Hybrid crops depend on distinct male and female heterotic gene pools.
• Sunflower breeding utilizes crop-wild relatives to develop cytoplasmic male sterile female lines and fertility-restoring male lines.

Purpose of the Study:

• To investigate genetic alterations in sunflower improvement using genomic data.
• To understand the genetic basis of heterotic gene pool development in sunflowers.

Main Methods:

• Analysis of genomic data from a diversity panel of sunflower lines (male, female, and open-pollinated).
• Exploration of genetic differentiation and introgression from wild relatives.
• Examination of gene content differences between male and female lines.

Main Results:

• Sunflower male lines show the greatest divergence from open-pollinated progenitors.
• Genetic differentiation is concentrated in chromosomes 8, 10, and 13, driven by introgressions from wild relatives.
• Gene content varies significantly between male and female lines, especially in regions with high genetic differentiation (high F_ST).

Conclusions:

• Introgression from wild relatives introduced different gene content, including gene removal, during sunflower improvement.
• Parallel evolution of ancestral variation in both male and female lines suggests limited selection for heterotic overdominance.
• While genomewide gene complementation doesn't explain heterosis, absent genes in specific lines, particularly those related to pathogen defense, may be functionally relevant for breeders.