Linking Structural Variation in the Genome of Crop Plants with Complex Traits

  

 Structural variation (SV) is generally defined as any region of DNA involved in inversions and balanced translocations or genomic imbalances (insertions and deletions), commonly referred to as copy number variants (CNVs). Aberrations such as CNV, insertion, inversions, and translocations are considered as SVs. These are generated during mitotic and meiotic cell division which occurs due to recombination errors, like non-allelic homologous recombination (NAHR), DNA break repair errors, such as non-homologous end joining (NHEJ) or replication errors, including fork stalling and template switching (FOSTES)2. These SVs differ in size and complexity. Hence different techniques have been used to characterize them in plant genomes. The ongoing revolution in DNA sequencing technology has allowed structural genetic variations to be analyzed at high resolution at a genome-wide level.

SV known to play a significant role in shaping genetic and phenotypic variation in crop plants1. Using deep sequencing of 115 diverse accession in cucumber, 26,788 SVs were detected which affect the coding regions of 1676 genes. CNV (duplication) of ACS1 gene is responsible for gynoecy in cucumber4. Similarly, insertion of MYB binding sequence in the promoter sequence of ZmVPP1 is responsible for the stress induced expression of drought tolerance in maize3.

As more and more genomic data becomes available for major crops, our insights regarding the impact of SV on trait diversity continue to grow. Understanding the contribution of gene copy number and presence–absence variation to important traits will be an important factor in improving the accuracy and efficacy of many new genetic technologies like genome editing strategies in plant breeding.

References

1. GABUR, L., CHAWLA, H. S., SNOWDON, R. J. AND PARKIN, I. A. P., 2019, Connecting genome structural variation with complex traits in crop plants. Theor. Appl. Genet., 132: 733–750.

2. HASTINGS, P. J., LUPSKI, J. R., ROSENBERG, S. M. and IRA, G., 2009, Mechanisms of change in gene copy number. Nat. Rev. Genet., 10(8): 551-564.

3. WANG, X., WANG, H., LIU, S., FERJANI, A., LI, J., YAN, J., YANG, X. AND QIN, F., 2021, Genetic variation in ZmVPP1 contributes to drought tolerance in maize seedlings. Nat. genet., 48(10): 1233-1241.

4. ZHANG, Z., MAO, L., CHEN, H., BU, F., LI, G., SUN, J., LI, S., SUN, H., JIAO, C., BLAKLEY, R., PAN, J., CAI, R., LUO, R., PEER, Y. V., JACOBSEN, E., FEI, Z. AND HAUNG, S., 2018, Genome wide mapping of structural variations reveals a copy number variant that determines reproductive morphology in cucumber. Plant Cell, 27(4): 1595-1604.