The candidate gene (CG) approach has been applied in plant genetics in the past decade for the characterisation and cloning of Mendelian and quantitative trait loci (QTLs). It constitutes a complementary strategy to map-based cloning and insertional mutagenesis. In plant genetics, the most common way to identify a CG is to look for map co-segregation between CGs and loci affecting the trait. Statistical association analyses between molecular polymorphisms of the CG and variation in the trait of interest have also been carried out in a few studies.

This process involves pinpointing specific genes within the plant genome that are likely to influence these traits, based on prior knowledge of gene function, expression patterns, and genetic diversity. The majority of the QTL mapping and gene isolation approaches using traditional approaches are time-consuming and low-throughput methods. Nevertheless, for more than a decade, the next-generation sequencing (NGS) technologies facilitated understanding of the genetics of complex traits at a faster pace in cereals and legumes. MutMap is one of the novel gene mapping approaches that allows rapid identification of causal nucleotide changes of mutants by whole-genome resequencing of pooled DNA of mutant F2 progeny derived from crosses made between candidate mutants and the parental line. They reported 102 candidate SNPs in 22 candidate genes. The candidate genes identified in this study are involved in early flowering as well as enhanced seed size.

Candidate intervals were identified for cotton early-maturity traits by combining BSA-seq and QTL mapping. Four candidate genes were screened out according to the SNP analysis and annotation information of the genes in the candidate intervals. VIGS is used to validate the role of candidate genes identified through other methods, such as QTL mapping or genome-wide association studies. Further functional verification of GH_D03G0451 showed that the GH_D03G0451-silenced plants showed a delay in the flowering time, indicating its positive function in regulating flowering time.

Once candidate genes are identified, they can be targeted for manipulation through breeding, genetic engineering, or biotechnological interventions to develop improved crop varieties. These varieties may exhibit enhanced resistance to diseases, improved tolerance to environmental stresses, or increased nutritional value, contributing to sustainable agricultural practices and food security.

References
1. Pflieger, S., Lefebvre, V. and Causse, M., 2001, The candidate gene approach in plant genetics: a review. MOLB, 7(4):275-291.
2. Manchikatla, P.K., Kalavikatte, D., Mallikarjuna, B.P., Palakurthi, R., Khan, A.W., Jha, U.C., Bajaj, P., Singam, P., Chitikineni, A., Varshney, R.K. and Thudi, M., 2021, MutMap approach enables rapid identification of candidate genes and development of markers associated with early flowering and enhanced seed size in chickpea (Cicer arietinum L.). Front. Plant Sci, 12(452): 688-694.

3. Ma, L., Hu, T., Kang, M., Fu, X., Chen, P., Wei, F., Jian, H., Lv, X., Zhang, M. and Yang, Y., 2024, Identification of candidate genes for early maturity traits by combining BSA-seq and QTL mapping in upland cotton (Gossypium hirsutum L.). J. Agric.