Genomic variation analysis and discovery of stable heterozygous loci in Loquat (Eriobotrya japonica)

Background The high heterozygosity of the loquat (Eriobotrya japonica Lindl.) genome has hindered the efficient application of modern breeding strategies. Although several genome assemblies have been published, comprehensive analyses of gene haplotypes, locus-specific variation, and the inheritance of heterozygous loci remain limited. Result To investigate genomic variation in loquat, 28 accessions were subjected to whole-genome resequencing, and the resulting reads were aligned to the reference genome for variant identification. Single nucleotide polymorphisms (SNPs), insertions and deletions (InDels), copy number variations (CNVs), and structural variants (SVs) were detected. A total of 196 heterozygous InDel loci and 182 heterozygous SNP loci were identified. Based on 48 InDel loci, 48 primer pairs were designed, and two pairs consistently amplified heterozygous genotypes across diverse loquat materials. These loci were stably heterozygous in wild, semi-wild, and cultivated accessions, as well as in progeny derived from self-pollination or hybridization, regardless of ploidy level or geographic origin. Finally, gene expression at these two loci differed significantly among various organs, including roots, stems, flowers, fruits, and leaves. Conclusion The consistent heterozygosity of these loci, which are located on different chromosomes, suggests a deviation from Mendelian segregation and implies the involvement of a gamete-selective or pre-fertilization recognition mechanism. These findings enhanced the understanding of the genetic mechanisms underlying the loquat genome, provided useful molecular tools for breeding, and offered new insights into loquat reproductive biology and improvement.