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Background <p><i>Handroanthus chrysanthus</i> is a remarkable landscape tree species with significant research and development potential. However, it remains unclear whether the varieties introduced to China are one species or two species. Since the morphological characteristics of seeds are extremely valuable in plant systematics research, in this work, 126 germplasm samples of <i>H. chrysanthus</i> were genotyped by genotyping-by-sequencing (GBS) for the first time. Subsequently, the phylogenetic tree, kinship and population structure were analyzed. Additionally, a genome-wide association analysis study (GWAS) was performed to identify candidate genes for seed morphology traits in <i>H. chrysanthus</i>.</p> Results <p>After applying various filtering criteria, 124 574 high-quality single-nucleotide polymorphisms (SNPs) were obtained. Most germplasms showed no obvious genetic relationship. The phenotypic analysis indicated that the four seed morphology-related traits had high variability. The coefficients of variance ranged from 9.50 to 12.07%, and they followed a continuous normal distribution. A total of 29 significant SNPs were identified by GWAS based on mixed linear model (MLM (QK)), and the number of significant SNPs associated with NWL, NWW, WL and WW were 14, 16, 2 and 9, respectively, among which 9 were pleiotropic loci. Within a 50-kb range of the flanking sequence of these significant SNP loci, 68 candidate genes potentially related to seed morphological traits were identified. Then, 29 candidate genes were screened by integrating expression level and functional annotation. Combined with quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis, CDL12_15522, CDL12_15254, CDL12_11100, CDL12_11105 were ultimately selected as the important candidate gene.</p> Conclusions <p>This study reveals the genetic basis of seed traits in <i>H. chrysanthus</i>, offering new perspectives on into its introduction history. The identification of markers closely related to these seed traits can be utilized for classification and breeding programs, thereby providing a theoretical basis for the genetic background and classification of <i>H. chrysanthus</i>.</p>

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Population structure, genetic diversity and genome-wide association analysis of the seed morphology traits in Handroanthus chrysanthus (Jacq.) s.o.grose

  • 期刊论文

  • 出版模式：

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  • 发表日期：

    2025年9月30日

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  • Xiuhua Shang,
  • Zhihua Wu,
  • Guowu Zhang,
  • Youshuang Wang,
  • Xiaoming Li,
  • Peijian Zhang

摘要

Background

Handroanthus chrysanthus is a remarkable landscape tree species with significant research and development potential. However, it remains unclear whether the varieties introduced to China are one species or two species. Since the morphological characteristics of seeds are extremely valuable in plant systematics research, in this work, 126 germplasm samples of H. chrysanthus were genotyped by genotyping-by-sequencing (GBS) for the first time. Subsequently, the phylogenetic tree, kinship and population structure were analyzed. Additionally, a genome-wide association analysis study (GWAS) was performed to identify candidate genes for seed morphology traits in H. chrysanthus.

Results

After applying various filtering criteria, 124 574 high-quality single-nucleotide polymorphisms (SNPs) were obtained. Most germplasms showed no obvious genetic relationship. The phenotypic analysis indicated that the four seed morphology-related traits had high variability. The coefficients of variance ranged from 9.50 to 12.07%, and they followed a continuous normal distribution. A total of 29 significant SNPs were identified by GWAS based on mixed linear model (MLM (QK)), and the number of significant SNPs associated with NWL, NWW, WL and WW were 14, 16, 2 and 9, respectively, among which 9 were pleiotropic loci. Within a 50-kb range of the flanking sequence of these significant SNP loci, 68 candidate genes potentially related to seed morphological traits were identified. Then, 29 candidate genes were screened by integrating expression level and functional annotation. Combined with quantitative reverse-transcription polymerase chain reaction (qRT-PCR) analysis, CDL12_15522, CDL12_15254, CDL12_11100, CDL12_11105 were ultimately selected as the important candidate gene.

Conclusions

This study reveals the genetic basis of seed traits in H. chrysanthus, offering new perspectives on into its introduction history. The identification of markers closely related to these seed traits can be utilized for classification and breeding programs, thereby providing a theoretical basis for the genetic background and classification of H. chrysanthus.