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Key message <p>Genome-wide analyses revealed signals of selection in specific genomic regions, distinct temporal shifts in genetic structure, and the maintenance of genetic diversity across barley and wheat breeding in Uruguay.</p> <p>A key challenge in plant breeding is to increase the frequency of desirable alleles while preserving sufficient genetic diversity for long-term crop improvement. We assessed temporal changes in genetic diversity and structure in the Uruguayan spring malting barley and bread wheat breeding programs. Using high-throughput genotyping—skim-sequencing for 280 barley genotypes and genotyping-by-sequencing (GBS) for 131 wheat genotypes, we identified 2,859,257 and 110,388 SNPs, respectively. Genotypes were grouped by historical breeding periods spanning pre-1980 to 2022 in barley and 1916 to 2022 in wheat. ADMIXTURE and principal coordinate analyses revealed distinct genetic groupings, with clearer temporal shifts in barley than wheat. Despite significant differentiation between breeding periods, no consistent genome-wide trend of diversity loss was observed in either crop. In barley, genetic diversity peaked during the 1990s–2000s, followed by a modest decline, with chromosomes 2H and 5H showing major shifts in allele frequency in recent periods, likely reflecting the introgression of European germplasm for malt quality. In wheat, the earliest group (1916–1958) exhibited the greatest genetic divergence, while modern genotypes showed increased diversity in the D sub-genome. Genomic regions on chromosomes 1H and 5H in barley and 2A and 6A in wheat showed signs of selection or introgression. Our findings highlight how breeding strategies, germplasm exchange, and selection pressures have shaped crop diversity over time and underscore the importance of managing genetic resources to sustain breeding progress.</p>

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The impact of breeding on barley and wheat genetic diversity and the identification of genomic regions that have undergone selection

  • 期刊论文

  • 发表日期：

    2025年12月26日

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  • Bettina Lado,
  • Monika Kavanová,
  • Ariel Castro,
  • Silvina Baraibar,
  • Jesse Poland,
  • Federico Condón,
  • Martin Quincke,
  • Paula Silva

摘要

Key message

Genome-wide analyses revealed signals of selection in specific genomic regions, distinct temporal shifts in genetic structure, and the maintenance of genetic diversity across barley and wheat breeding in Uruguay.

A key challenge in plant breeding is to increase the frequency of desirable alleles while preserving sufficient genetic diversity for long-term crop improvement. We assessed temporal changes in genetic diversity and structure in the Uruguayan spring malting barley and bread wheat breeding programs. Using high-throughput genotyping—skim-sequencing for 280 barley genotypes and genotyping-by-sequencing (GBS) for 131 wheat genotypes, we identified 2,859,257 and 110,388 SNPs, respectively. Genotypes were grouped by historical breeding periods spanning pre-1980 to 2022 in barley and 1916 to 2022 in wheat. ADMIXTURE and principal coordinate analyses revealed distinct genetic groupings, with clearer temporal shifts in barley than wheat. Despite significant differentiation between breeding periods, no consistent genome-wide trend of diversity loss was observed in either crop. In barley, genetic diversity peaked during the 1990s–2000s, followed by a modest decline, with chromosomes 2H and 5H showing major shifts in allele frequency in recent periods, likely reflecting the introgression of European germplasm for malt quality. In wheat, the earliest group (1916–1958) exhibited the greatest genetic divergence, while modern genotypes showed increased diversity in the D sub-genome. Genomic regions on chromosomes 1H and 5H in barley and 2A and 6A in wheat showed signs of selection or introgression. Our findings highlight how breeding strategies, germplasm exchange, and selection pressures have shaped crop diversity over time and underscore the importance of managing genetic resources to sustain breeding progress.