American Journal of Botany最新文献

The potential roles of genomic structural variations (SVs) in the control of phenotypic traits and in evolution were suggested as early as the 20th century. However, they were then overshadowed by the emphasis put on single nucleotide polymorphisms (SNPs). Recently, SVs have received renewed attention in evolutionary research due to advancements in sequencing technologies and analytical methods.

At the macroevolutionary scale, plant genomes tend to evolve faster than those of other eukaryotes, due to the prevalence of whole genome duplication events (Wendel et al., 2016). Unlike other types of structural variants, such as inversions, copy number variations (CNVs) result from unbalanced mutations that affect the dosage, or amount, of a DNA sequence. When genes are involved, the number of copies of a gene varies from one individual to another. In plants, gene copy number variations (gCNVs) are likely to be abundant due to events such as mating system shifts (the efficacy of purifying selection is reduced in selfing species), hybridization and subsequent genome rearrangements, and whole genome duplications followed by biased retention (Panchy et al., 2016; Wendel et al., 2016; Van de Peer et al., 2017). For example, in Arabidopsis thaliana (L.) Heynh. (Brassicaceae) 10 to 18% of all genes display CNVs (Zmienko et al., 2020; Jaegle et al., 2023). In the genus Picea Mill. (Pinaceae), at least 10% of the protein-coding genes display CNVs (P. abies (L.) H. Karst and P. obovata Ledeb., Q. Zhou et al., 2025; and P. glauca (Moench) Voss and P. mariana (Mill.) Britton, Sterns & Poggenburg, Prunier et al., 2017).

Gene duplications have primarily been studied for their roles in long-term evolution. However, a change in gene dosage usually results in a change in the amount of gene products, such as RNA or proteins (e.g., Shao et al., 2019). Therefore, gCNVs have a unique, multiallelic, and quantitative nature. Fully apprehending their role in short-term evolutionary processes requires studying them as quantitative genotypes rather than in a presence/absence (or biallelic) manner, as is most often done (Figure 1, top panel). Unlike SNPs, the accuracy and resolution of gCNV genotyping are usually dependent on the platform used. From short-read sequencing data, one can use biased allelic ratios (Figure 2A) and changes in the depth of coverage (DoC) caused by the mis-mapping of reads from duplicated regions to the same locus in the reference genome to identify CNVs (Figure 2). However, short reads often fail to capture the underlying genetic structure of gCNVs, and changes in DoC can only be interpreted as relative copy numbers across homologous chromosomes (Figure 1, middle panel). Long-read sequencing is a promising alternative that allows for the phasing of the various alleles to obtain

Many perennial fruit crops are clonally propagated, resulting in uniform fruit quality but increasing vulnerability to pests, diseases, and climate change. In contrast, closely related crop wild relatives (CWRs) continue to evolve in response to these pressures and are a valuable source of adaptive traits. Despite their potential, CWRs are underutilized in perennial fruit breeding. Efficient and accurate introgression of traits from CWRs during perennial fruit breeding will require the use of genomics. Genomics-assisted breeding begins with genetic mapping, such as genome-wide association studies, to identify markers predictive of traits of interest. For diverse species such as CWRs, a pangenomic approach that incorporates multiple species as a reference is often necessary. Continued use of CWRs in fruit breeding also depends on their conservation, both in situ (in natural habitats) and ex situ (off-site). Ex situ collections can also be used for genetic mapping, further supporting genomics-assisted plant breeding efforts. Ultimately, breeding and conservation of perennial fruit crops are complementary goals that benefit from the development and application of genomic resources.