Rakha, M. | bioRxiv Science

bioRxiv2024

Near-complete telomere-to-telomere de novo genome assemblies of Egyptian clover (Trifolium alexandrinum)

Egyptian clover (Trifolium alexandrinum L.), also known as berseem clover, is an important forage crop to semi-arid conditions that was domesticated in ancient Egypt and introduced and well adapted to numerous countries. Despite its agricultural importance, genomic research on Egyptian clover has been limited to developing efficient modern breeding programs. In the present study, we constructed near-complete telomere-to-telomere-level genome assemblies for two Egyptian clover cultivars, Helaly and Fahl. Initial assemblies were established by using highly-fidelity long-read technology. To extend sequence contiguity, we developed a gap-targeted sequencing (GAP-Seq) method, in which contig ends are targeted for sequencing to obtain long reads bridging two contigs. The total length of the resultant chromosome-level assemblies was 547.7 Mb for Helaly and 536.3 Mb for Fahl. These differences in sequence length can be attributed to the expansion of DNA transposons. Population genomic analysis using single-nucleotide polymorphisms revealed 38 highly conserved genomic regions within Helaly. Growth- and stress response-associated gene ontologies were enriched in the 38 regions, indicating that these genes may determine the unique characteristics of Helaly. Comprehensive genomic resources can provide valuable insights into genetic improvements in Egyptian clover and legume genomics.

genomics↗

bioRxiv2019

Understanding patterns of abiotic and biotic stress resilience to unleash the potential of crop wild relatives for climate-smart legume breeding

Although new varieties are urgently needed for climate-smart legume production, legume breeding lags behind with cereals and underutilizes wild relatives. This paper provides insights in patterns of abiotic and biotic stress resilience of legume crops and wild relatives to enhance the use and conservation of these genetic resources for climate-smart legume breeding. We focus on Vigna, a pantropical genus with more than 88 taxa including important crops such as cowpea and mung bean. Sources of pest and disease resistance occur in more than 50 percent of the Vigna taxa, which were screened while sources of abiotic stress resilience occur in less than 20 percent of the taxa, which were screened. This difference suggests that Vigna taxa co-evolve with pests and diseases while taxa are more conservative to adapt to climatic changes and salinization. Twenty-two Vigna taxa are poorly conserved in genebanks or not at all. This germplasm is not available for legume breeding and requires urgent germplasm collecting before these taxa extirpate on farm and in the wild. Vigna taxa, which tolerate heat and drought stress are rare compared with taxa, which escape these stresses or tolerate salinity. These rare Vigna taxa should be prioritized for conservation and screening for multifunctional traits of combined abiotic and biotic stress resilience. The high presence of salinity tolerance compared with drought stress tolerance, suggests that Vigna taxa are good at developing salt-tolerant traits compared with drought-tolerant traits. Vigna taxa are therefore of high value for legume production in areas that suffer from salinization.

plant biology↗