Scholarlink

<p>Diploid potato breeding is frequently challenged by residual heterozygosity, which impedes the generation of pure inbred lines for F1 hybrid production. The Fixation-Restitution Breeding strategy, which employs residual heterozygosity to avoid inbreeding depression, is a promising alternative for true seed F1 hybrids, as maintaining heterozygosity throughout the fixation process is crucial to its success. In this study, we used a multiplex amplicon-sequencing assay (PotatoMASH), in conjunction with read-backed haplotyping, as an effective tool for tracing homozygosity in diploid germplasm. Utilising a collection of 271 inbred diploid clones from the Wageningen diploid breeding programme, we obtain a “snapshot” of the genetic composition shaped by over 40 years of breeding efforts. Furthermore, we examined a self-compatible individual lineage from the programme to identify key hotspots of homozygosity across chromosomes. Our results demonstrate that multiplex amplicon sequencing with read-backed haplotyping, through haplotag construction, provides a more accurate and reliable measure of homozygosity compared to traditional SNP-based methods, without the requirement for parental genomic data. In S3 progenies, we observed average homozygosity levels of 82–83.4% for Identity-by-State (IBS) and 72.6–74.8% for Identity-by-Descent (IBD), which were lower than anticipated. Hotspots of heterozygosity were detected across all chromosomes, with chromosome 5 entirely heterozygous across three generations of selfing and chromosome 11 reaching full homozygosity in one S3 progeny. This absence of homozygosity on chromosome 5 may be associated with reproduction-related QTLs and genes that favour the heterozygous state due to potentially deleterious alleles. These findings demonstrate the potential of assays such as PotatoMASH to effectively track and optimise heterozygosity in Fixation-Restitution breeding programmes.</p>

错误：搜索内容不能为空，请输入英文关键词
错误：关键词超出字数限制，请精简
高级检索

Utilising Multiplex Amplicon Sequencing and Read-Backed Haplotyping to Track Homozygosity and Residual Heterozygosity in Diploid Potato Breeding

  • 期刊论文

  • 发表日期：

    2026年7月1日

查看全文
  • Lea Vexler,
  • Dan Milbourne,
  • Ronald C. B. Hutten,
  • Vanessa Prigge,
  • Christel Engelen,
  • Stephen Byrne,
  • Maria de la O. Leyva-Perez,
  • Denis Griffin,
  • Richard G. F. Visser,
  • Herman J. van Eck

摘要

Diploid potato breeding is frequently challenged by residual heterozygosity, which impedes the generation of pure inbred lines for F1 hybrid production. The Fixation-Restitution Breeding strategy, which employs residual heterozygosity to avoid inbreeding depression, is a promising alternative for true seed F1 hybrids, as maintaining heterozygosity throughout the fixation process is crucial to its success. In this study, we used a multiplex amplicon-sequencing assay (PotatoMASH), in conjunction with read-backed haplotyping, as an effective tool for tracing homozygosity in diploid germplasm. Utilising a collection of 271 inbred diploid clones from the Wageningen diploid breeding programme, we obtain a “snapshot” of the genetic composition shaped by over 40 years of breeding efforts. Furthermore, we examined a self-compatible individual lineage from the programme to identify key hotspots of homozygosity across chromosomes. Our results demonstrate that multiplex amplicon sequencing with read-backed haplotyping, through haplotag construction, provides a more accurate and reliable measure of homozygosity compared to traditional SNP-based methods, without the requirement for parental genomic data. In S3 progenies, we observed average homozygosity levels of 82–83.4% for Identity-by-State (IBS) and 72.6–74.8% for Identity-by-Descent (IBD), which were lower than anticipated. Hotspots of heterozygosity were detected across all chromosomes, with chromosome 5 entirely heterozygous across three generations of selfing and chromosome 11 reaching full homozygosity in one S3 progeny. This absence of homozygosity on chromosome 5 may be associated with reproduction-related QTLs and genes that favour the heterozygous state due to potentially deleterious alleles. These findings demonstrate the potential of assays such as PotatoMASH to effectively track and optimise heterozygosity in Fixation-Restitution breeding programmes.