Abstract
The decreasing costs of next-generation sequencing and the improvements in de novo sequence assemblers have made it possible to obtain reference genomes for most eukaryotes, including minor crops such as the blueberry (Vaccinium corymbosum). Nevertheless, these genomes are at various levels of completeness and few have been anchored to chromosome scale and/or are haplotype-phased. We highlight the impact of a high-quality genome assembly for plant breeding and genetic research by showing how it affects our understanding of the genetic architecture of important traits and aids marker selection and candidate gene detection. We compared the results of genome-wide association studies and genomic selection that were already published using a blueberry draft genome as reference with the results using the recent released chromosome-scale and haplotype-phased blueberry genome. We believe that the benefits shown herein reinforce the importance of genome assembly projects for other non-model species.
Highlights
Assembling plant genomes using short-read–based sequencing is a challenging task, especially because most plant genomes are large, highly repetitive, and have undergone ancient and recent rounds of polyploidization
We highlight the impact of a high-quality genome assembly for plant breeding and genetic research by showing how it affects our understanding of the genetic architecture of important traits and aids marker selection and candidate gene detection
The draft genome assembly was performed for a diploid northern highbush (’W8520’) using short-reads from 454 pyrosequencing and Illumina platforms [3, 4]
Summary
Assembling plant genomes using short-read–based sequencing is a challenging task, especially because most plant genomes are large, highly repetitive, and have undergone ancient and recent rounds of polyploidization. GWAS can provide the first insights into the genetic architecture of a trait by identifying the number of significant loci, genomic position, mode of gene action, and effect on the phenotypic variation In this step, the high-resolution positioning of SNPs in the chromosome-scale assembly played an important role in unraveling the genetic architecture of the traits. The high-resolution positioning of SNPs in the chromosome-scale assembly played an important role in unraveling the genetic architecture of the traits Using this new pipeline, which included more accurate genotype calling using the updog R package [7], we were able to find significant SNPs with additive gene action mode (e.g., fruit pH), and novel associations (e.g., fruit firmness and scar size) that were not detected in our previous publication [2] (Fig. 1B). Similar predictive abilities in the same SHB population were reported by de Bem Oliveira et al [10] using the ’W8520’ genome
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