ArticleMolecular breeding : new strategies in plant improvement2026
Genome-wide signatures of selection and genetic diversity reveal the impact of modern breeding on Brazilian soybean.
Article in Molecular breeding : new strategies in plant improvement, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
Soybean (Glycine max (L.) Merr.) breeding in Brazil has driven remarkable gains in yield and adaptation; however, intensive selection raises concerns regarding the erosion of genetic diversity in modern cultivars. Here, we conducted a genome-wide analysis of genetic diversity, population structure, linkage disequilibrium, and selection signatures in Brazilian soybean germplasm using high-density SNP genotyping. Ninety-five genotypes from the Soybean Breeding Program for Quality Traits at UFV, including commercial cultivars and advanced breeding lines from both in-house and external sources, representing different breeding periods were genotyped with the 180K Axiom® Soybean SNP array, and 61,712 high-quality SNPs were retained after quality control. Population structure analyses consistently identified two main genetic groups largely corresponding to older and modern cultivars, along with an admixed group. Modern cultivars exhibited reduced nucleotide diversity and lower Tajima's D values compared with older genotypes, while AMOVA, Fst, and Nei genetic distance estimates indicated moderate genetic differentiation between populations. Genome-wide linkage disequilibrium was extensive, with slow LD decay, reflecting the effects of self-pollination, domestication bottlenecks, and strong directional selection. BayeScan analysis detected 581 SNPs exhibiting signatures of positive directional selection (α > 0), indicating elevated genetic differentiation between groups, many of which overlapped with previously reported QTLs related to yield components, seed composition, and plant architecture. A pronounced selection hotspot on chromosome 19 showed near-complete haplotype differentiation between older and modern cultivars, highlighting a genomic region repeatedly targeted during recent breeding cycles. Together, these results demonstrate that contemporary soybean breeding in Brazil has reshaped genome-wide diversity by intensifying selection at key loci while maintaining a narrow genetic base, providing important insights for future breeding strategies aimed at sustaining long-term genetic gain. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-026-01679-0.
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