Biology subjects

Dillon, N. L.

Publications and source records attributed to Dillon, N. L..

3 recordsLinked to original sources

bioRxiv2025

Chromosome-scale haplotype genome assemblies for the Australian mango 'Kensington Pride' 1 and a wild relative, Mangifera laurina, provide insights into anthracnose-resistance and volatile 2 compound biosynthesis genes

Mango (Mangifera indica) is one of the most popular fruits cultivated in tropical and subtropical regions of the world. The availability of reference genomes helps to identify the genetic basis of important traits. Here we report assembled high-quality chromosome-level genomes for the Australian mango cultivar Kensington Pride, and M. laurina; a wild relative, which shows resistance to anthracnose disease. PacBio HiFi sequencing with higher genome coverage enabled the assembly of both genomes with 100% completeness. Genome sizes of Kensington Pride and M. laurina were 367 Mb and 379 Mb, respectively, with all 20 chromosomes in both genomes having telomeres at both ends. K-mer analysis revealed that these genomes are highly heterozygous and significant structural variations were identified between Kensington Pride, M. laurina, and the recently published genome of the cultivar Irwin. Functional annotation identified key genes involved in carotenoid, anthocyanin, and terpenoid biosynthesis, responsible for fruit color and flavour in mango. Furthermore, the presence of a SNP in {beta}-1,3-glucanase 2 gene associated with anthracnose resistance was analyzed. Whole genome duplication analysis confirmed that mangoes have undergone two polyploidization events during their evolution. Analysis revealed a conserved pattern of colinear genes, although many colinear blocks were also identified on non-homologous chromosomes. Practitioner PointsO_LIPacBio HiFi sequencing and high coverage produced genomes for Kensington Pride mango and M. laurina with 100% completeness, identifying all the telomeres in the assembled chromosomes. C_LIO_LISignificant structural variations were identified between Kensington Pride, M. laurina, and the published Irwin genome. C_LIO_LIGenes linked in the biosynthesis of unique terpenoids were identified, and the structural differences in the annotated {beta}-1,3-glucanase 2 genes associated with anthracnose resistance provide a resource for gene expression analysis in susceptible and resistant cultivars. C_LI

plant biology↗

bioRxiv2024

Centromeres are Hotspots for Chromosomal Inversions and Breeding Traits in Mango

Chromosomal inversions can preserve combinations of favorable alleles by suppressing recombination. Simultaneously, they reduce the effectiveness of purifying selection enabling deleterious alleles to accumulate. This study explores how areas of low recombination, including centromeric regions and chromosomal inversions, contribute to the accumulation of deleterious and favorable loci in 225 Mangifera indica genomes from the Australian Mango Breeding Program. Here, we identify 17 chromosomal inversions that cover 7.7% (29.7Mb) of the M. indica genome: eight pericentric (inversion includes the centromere) and nine paracentric (inversion is on one arm of the chromosome). Our results show that these large pericentric inversions are accumulating deleterious loci, while the paracentric inversions show deleterious levels above and below the genome wide average. We find that despite their deleterious load, chromosomal inversions contain small effect loci linked to variation in crucial breeding traits, indicating that chromosomal inversions have likely facilitated their selection. The results from this study have important implications for selective breeding of favorable combinations of alleles in regions of low recombination. Significance StatementChromosomal inversions and other low recombination regions of the genome can drive trait evolution. Fewer recombination events can assist in maintaining favorable combinations of alleles, but it can also make disentangling favorable and deleterious alleles difficult. Understanding whether these low recombination regions contain favorable or deleterious loci could drive our decision to increase or decrease the frequency of these regions in target breeding populations. Breeding for large segments of the genome based on presence or absence of an inversion can rapidly drive large trait differences within few generations. Harnessing the impact of large low recombination regions of the genome could have major implications for future genetic improvement in breeding.

genomics↗

bioRxiv2022

The influence of genetic structure on phenotypic diversity in the Australian mango (Mangifera indica) gene pool

Genomic selection is a promising breeding technique for tree crops to accelerate the development of new cultivars. However, factors such as genetic structure can create spurious associations between genotype and phenotype due to the shared history between populations with different trait values. Genetic structure can therefore reduce the accuracy of the genotype to phenotype map, a fundamental requirement of genomic selection models. Here, we employed 272 single nucleotide polymorphisms from 208 Mangifera indica cultivars to explore whether the genetic structure of the Australian mango gene pool explained variation in tree size, fruit blush colour and intensity. Our results show that genetic structure is weak, but cultivars imported from Southeast Asia (mainly those from Thailand) were genetically differentiated across multiple population genetic analyses. We find that genetic structure was strongly associated with phenotypic diversity in M. indica, suggesting that the history of these cultivars could drive spurious associations between loci and key mango phenotypes in the Australian mango gene pool. Incorporating such genetic structure in associations between genotype and phenotype has the potential to improve the accuracy of genomic selection, which can assist the development of new cultivars.

evolutionary biology↗