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ARS Home » Southeast Area » Baton Rouge, Louisiana » Honey Bee Lab » Research » Publications at this Location » Publication #413617
Research Project: Using Genetics to Improve the Breeding and Health of Honey Bees

Location: Honey Bee Breeding, Genetics, and Physiology Research

Title: Common signatures of selection reveal target loci for breeding across soybean populations

Author
item GOMES VIANA, JOAO PAULO - University Of Illinois
item Avalos, Arian
item ZHANG, ZHIHAI - University Of Illinois
item NELSON, RANDALL - University Of Illinois
item HUDSON, MATTHEW - University Of Illinois

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/21/2023
Publication Date: 1/23/2024
Citation: Gomes Viana, J., Avalos, A., Zhang, Z., Nelson, R., Hudson, M. 2024. Common signatures of selection reveal target loci for breeding across soybean populations. The Plant Genome. e20426. https://doi.org/10.1002/tpg2.20426.
DOI: https://doi.org/10.1002/tpg2.20426

Interpretive Summary: Understanding how plants achieve higher yields through selective breeding and distinguishing these changes from random genetic variations is crucial for advancing plant breeding. Soybeans play a vital role in global food security, but our knowledge of how selective breeding actually works is currently limited to just a few genes. In this study, we investigated the genome-wide signs of selection in soybean populations that underwent artificial selection for increased yield in multiple U.S. breeding programs. By comparing the USDA-ARS-created alternative soybean breeding population to conventional public soybean lines at different breeding stages, we aimed to identify common selection patterns and distinguish them from random genetic drift. Our findings revealed a strong preference for specific genetic variations in higher yielding soybeans derived from both the AGP and CGP, indicating that breeding programs favor the same key genetic variations even when starting from different plants.

Technical Abstract: Understanding the underlying genetic bases of yield-related selection and distinguishing these changes from genetic drift are critical for both improved understanding and future success of plant breeding. Soybean [Glycine max (L.) Merr.] is a key species for world food security, yet knowledge of the mechanism of selective breeding in soybean, such as the century-long program of artificial selection in U.S. soybean germplasm, is currently limited to certain genes and loci. Here, we identify genome-wide signatures of selection in separate populations of soybean subjected to artificial selection for increased yield by multiple breeding programs in the United States. We compared the alternative soybean breeding population (AGP) created by USDA-ARS to the conventional public soybean lines (CGP) developed at three different stages of breeding (ancestral, intermediate, and elite) to identify shared signatures of selection and differentiate these from drift. The results showed a strong selection for specific haplotypes identified by single site frequency and haplotype homozygosity methods. A set of common selection signatures was identified in both AGP and CGP that supports the hypothesis that separate breeding programs within similar environments coalesce on the fixation of the same key haplotypes. Signatures unique to each breeding program were observed. These results raise the possibility that selection analysis can allow the identification of favorable alleles to enhance directed breeding approaches.