Unlocking the almond genome: unraveling the secrets of heterozygosity

Almonds exhibit notable genetic diversity, crucial for agricultural advancements. Insights from the phased genome assembly of the ‘Texas’ cultivar illuminate the effects of structural variations on gene expression, broadening our comprehension of the almond’s genetic framework. The imperative for comprehensive investigations into these genetic details is apparent, as they are key to harnessing the genetic potential of almonds and enhancing cultivar traits through strategic breeding practices.

Published (DOI: 10.1093/hr/uhae106) in Horticulture Research on April 9, 2024, by the Centre for Research in Agricultural Genomics (CRAG), this study delves into the phased genome of the ‘Texas’ almond cultivar. It scrutinizes how high heterozygosity and structural variants modulate allele-specific expression. These revelations deepen our genetic understanding of almonds and lay the groundwork for future agricultural and breeding breakthroughs.

Leveraging advanced genomic sequencing techniques, researchers combined 260X PacBio long reads with 172X Hi-C Illumina short reads to construct a detailed phased genome of the ‘Texas’ almond. This methodology exposed the significant role of heterozygous transposable element insertions in regulating gene expression. The enhanced genome assembly, with a 13% increase in sequence data over previous versions, provides intricate insights into genetic interactions and functions. The study underscores the critical role of structural variants in trait variability, offering invaluable perspectives that could inform targeted almond breeding strategies to improve desirable traits.

Dr. Josep M. Casacuberta, a leading researcher in the study, emphasized, “This phased genome assembly represents a major leap in our comprehension of the almond genome. It not only clarifies the genetic complexity but also paves the way for new biotechnological applications in almond breeding and agriculture.”

The findings from this phased genome assembly carry significant implications for almond breeding programs, introducing innovative strategies to enhance traits such as disease resistance and yield. Furthermore, the study’s methods could be adapted to other crop species, potentially transforming agricultural genomics. By elucidating the specific interactions between structural variants and gene expression, researchers can more effectively devise interventions to boost crop resilience and productivity.

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References

DOI

10.1093/hr/uhae106

Original Source URL

https://doi.org/10.1093/hr/uhae106

Funding information

This work was supported by the Spanish Ministerio de Ciencia e Innovación PID2019-106374RB-I00 and PID2022-143167NB-I00 grants to J.C. and IJC2020-045949-I fellowship to R.C., and RTI2018-100795-B-I00 and PID2021-128885OB-I00 both funded by MCIN/AEI/10.13039/501100011033 and by ‘ERDF A way of making Europe’ to M.J.A. We also acknowledge the support from the CERCA Programme (‘Generalitat de Catalunya’) and the ‘Severo Ochoa Programme for Centres of Excellence in R&D’ 2016–2019 (SEV-2015-0533) and 2020–2023 (CEX2019-000902-S).

About Horticulture Research

Horticulture Research is an open access journal of Nanjing Agricultural University and ranked number one in the Horticulture category of the Journal Citation Reports ™ from Clarivate, 2022. The journal is committed to publishing original research articles, reviews, perspectives, comments, correspondence articles and letters to the editor related to all major horticultural plants and disciplines, including biotechnology, breeding, cellular and molecular biology, evolution, genetics, inter-species interactions, physiology, and the origination and domestication of crops.