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<p>Caucasian clover (<i>Trifolium ambiguum</i>) is a long-lived forage legume with a wide range of adaptations and nutritive values. However, its inheritance information remains largely unknown. Here, a de novo whole-genome survey of Caucasian clovers was conducted using next-generation sequencing. K-mer analysis showed that the preliminary estimated genome size of Caucasian clover was 4.36&#xa0;Gb, and its heterozygosity and repeat sequence content were 0.44% and 94.41%, respectively. Based on the genomic data, 546,107 simple sequence repeat (SSR) loci were developed. The most frequent repeat motifs were mononucleotides (62.0%), followed by dinucleotides (18.8%), trinucleotides (6.8%), tetranucleotides (1.1%), hexanucleotides (0.4%), and pentanucleotides (0.3%). 120 SSR primer pairs were developed, 20 polymorphic SSRs were selected for testing 12 Caucasian clover accessions, and 93 alleles were successfully amplified. The average polymorphic information content value was 0.56, indicating a high degree of polymorphism for these SSR markers. The genomic data obtained in this study could provide a reference basis for genome sequencing and assembly of Caucasian clover in the future.</p>

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Genome survey and identification of simple sequence repeat markers for Caucasian clover (Trifolium ambiguum Bieb.)

  • 期刊论文

  • 发表日期：

    2025年8月29日

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  • Jin Gao,
  • Pengcheng Ni,
  • Xiaojing Qiang,
  • Lei Liu,
  • Fan Huang

摘要

Caucasian clover (Trifolium ambiguum) is a long-lived forage legume with a wide range of adaptations and nutritive values. However, its inheritance information remains largely unknown. Here, a de novo whole-genome survey of Caucasian clovers was conducted using next-generation sequencing. K-mer analysis showed that the preliminary estimated genome size of Caucasian clover was 4.36 Gb, and its heterozygosity and repeat sequence content were 0.44% and 94.41%, respectively. Based on the genomic data, 546,107 simple sequence repeat (SSR) loci were developed. The most frequent repeat motifs were mononucleotides (62.0%), followed by dinucleotides (18.8%), trinucleotides (6.8%), tetranucleotides (1.1%), hexanucleotides (0.4%), and pentanucleotides (0.3%). 120 SSR primer pairs were developed, 20 polymorphic SSRs were selected for testing 12 Caucasian clover accessions, and 93 alleles were successfully amplified. The average polymorphic information content value was 0.56, indicating a high degree of polymorphism for these SSR markers. The genomic data obtained in this study could provide a reference basis for genome sequencing and assembly of Caucasian clover in the future.