Functional molecular markers for crop improvement

Abstract

A tremendous decline in cultivable land and resources and a huge increase in food demand calls for immediate attention to crop improvement. Though molecular plant breeding serves as a viable solution and is considered as "foundation for twenty-first century crop improvement", a major stumbling block for crop improvement is the availability of a limited functional gene pool for cereal crops. Advancement in the next generation sequencing (NGS) technologies integrated with tools like metabolomics, proteomics and association mapping studies have facilitated the identification of candidate genes, their allelic variants and opened new avenues to accelerate crop improvement through development and use of functional molecular markers (FMMs). The FMMs are developed from the sequence polymorphisms present within functional gene(s) which are associated with phenotypic trait variations. Since FMMs obviate the problems associated with random DNA markers, these are considered as "the holy grail" of plant breeders who employ targeted marker assisted selections (MAS) for crop improvement. This review article attempts to consider the current resources and novel methods such as metabolomics, proteomics and association studies for the identification of candidate genes and their validation through virus-induced gene silencing (VIGS) for the development of FMMs. A number of examples where the FMMs have been developed and used for the improvement of cereal crops for agronomic, food quality, disease resistance and abiotic stress tolerance traits have been considered.

Identification and characterization of a fusarium head blight resistance gene TaACT in wheat QTL‐2DL

“…Stacking of a few genes with similar FHB resistance effects should significantly reduce FHB under field conditions. The TaACT therefore can be used in FHB resistance breeding programmes either through development of genic markers (Kage et al ., ) or through replacement of a nonfunctional Taact gene in commercial cultivars with functional TaACT genes based on genome editing (Kushalappa et al ., ). Pyramiding of a few genes should result in a resistant cultivar that reduces application of fungicide.…”

Wheat tandem kinases provide insights on disease‐resistance gene flow and host–parasite co‐evolution

“…Various studies have been conducted also based on sequence variation of a single gene in WEW populations and cultivated wheat collections aimed to understand the evolutionary processes that shaped the allelic variation, structure and function of pivotal genes, including the NAM‐B1 ( Gpc‐B1 ) high grain protein and mineral content gene (Lundström et al ., ), the Pm3 powdery mildew resistance gene (Yahiaoui et al ., ), the Lr10 leaf rust‐resistance gene (Sela et al ., ), and the WKS stripe rust‐resistance genes (Huang et al ., ). In spite of the high potential of functional molecular markers (FMMs) (Kage et al ., ) for population genetics evolution, and domestication studies of WEW and other crop species, not much research has been carried out in this direction.…”

Correlations between SmCPS1 promoter polymorphism and tanshinone contents in Salvia miltiorrhiza

“…Any change of its expression will directly influence the content of tanshinones. Since a promoter contains the basic information about the expression pattern of the gene, we speculated that the variation of tanshinone contents of different S. miltiorrhiza genotypes is related to the promoter Table S3 in ESM for details; SNP -single nucleotide polymorphism; TRV -tandem repeat variation; Indel -insertion/deletion variation Functional polymorphic loci are polymorphic loci located in the regulatory regions or coding regions of a gene and may change the expression pattern or function of the gene (Kage et al 2016). Changes in exons, cis-elements, or introns of a gene may change the function or expression pattern of the gene (Le Hir et al 2003;Nithianantharajah & Hannan 2007;Wittkopp & Kalay 2011).…”