Genetic loci and functional genes conferring deep-sowing tolerance across multiple environments in soybean

Deep-sowing is an effective strategy to ensure uniform seedling emergence and yield under drought stress condition for plants, which mainly depends on the mesocotyl or hypocotyl elongation in the monocots or dicots plants. In view of this, the hypocotyl lengths of 500 soybean accessions were evaluated under the deep-sowing conditions in nine environments, and the genetic loci and functional genes were discovered by combining with the deep re-sequencing genotypes (20 ×). The results showed that a total of 2,007 SNPs/SVs on 19 chromosomes were identified to associate with the hypocotyl length, of which 1,165 SNPs/SVs (58.05%) located on chromosome 14, and 706 SNPs/SVs (35.18%) located on chromosome 5. Moreover, 630 consistent SNPs/SVs on chromosomes 14 and 90 consistent SNPs/SVs on chromosomes 5 were detected across more than five environments. Furtherly, two causal genes, GmHYL05 and GmHYL14, were screened out in the consistent loci. Transgenic analyses revealed that the overexpression of GmHYL05 significantly enhanced the hypocotyl elongation in Arabidopsis, while the CRISPR/Cas9-mediated knockout of GmHYL05 resulted in decreasing of hypocotyl length in soybean. Similarly, the overexpression of GmHYL14 promoted the hypocotyl growth in Arabidopsis, while the nonsense mutation of GmHYL14 reduced the hypocotyl elongation in soybean. The cytological experiments revealed that both GmHYL05 and GmHYL14 increased the cell lengths of soybean hypocotyl, while not influenced the cell numbers, indicating GmHYL05 and GmHYL14 could regulate the hypocotyl elongation via influencing the cell expansion.