High-Quality Genome Assembly and Genome-Wide Association Study of Male Sterility Provide Resources for Flax Improvement

Abstract

Flax is an economic crop with a long history. It is grown worldwide and is mainly used for edible oil, industry, and textiles. Here, we reported a high-quality genome assembly for “Neiya No. 9”, a popular variety widely grown in China. Combining PacBio long reads, Hi-C sequencing, and a genetic map reported previously, a genome assembly of 473.55 Mb was constructed, which covers ~94.7% of the flax genome. These sequences were anchored onto 15 chromosomes. The N50 lengths of the contig and scaffold were 0.91 Mb and 31.72 Mb, respectively. A total of 32,786 protein-coding genes were annotated, and 95.9% of complete BUSCOs were found. Through morphological and cytological observation, the male sterility of flax was considered dominant nuclear sterility. Through GWAS analysis, the gene LUSG00017705 (cysteine synthase gene) was found to be closest to the most significant SNP, and the expression level of this gene was significantly lower in male sterile plants than in fertile plants. Among the significant SNPs identified in the GWAS analysis, only two were located in the coding region, and these two SNPs caused changes in the protein encoded by LUSG00017565 (cysteine protease gene). It was speculated that these two genes may be related to male sterility in flax. This is the first time the molecular mechanism of male sterility in flax has been reported. The high-quality genome assembly and the male sterility genes revealed, provided a solid foundation for flax breeding.

Genome of Linum usitatissimum convar. crepitans expands the view on the section Linum

“…Furthermore, the availability of several diverse genome Frontiers in Genetics frontiersin.org sequences for a species is key to the discovery of novel useful agricultural traits. For L. usitatissimum, seven genome sequences of different varieties were received earlier (You et al, 2018;Dmitriev et al, 2020b;Zhang et al, 2020;Sa et al, 2021;Dvorianinova et al, 2022;Zhao et al, 2023). In this work, we sequenced the genome of L. usitatissimum convar.…”

“…Genome sequences of flax representatives are useful sources of information for both basic and applied studies. Currently, seven L. usitatissimum assemblies are available in the databases (NCBI and Zenodo) (You et al, 2018;Dmitriev et al, 2020b;Zhang et al, 2020;Sa et al, 2021;Dvorianinova et al, 2022;Zhao et al, 2023). In the species of the section Linum, apart from L. usitatissimum, a genome of Linum bienne Mill.…”