From genomics to functional markers in the era of next-generation sequencing

• Published in: Biotechnology letters Vol. 36; no. 3; pp. 417 - 426
• Main Authors: Salgotra, R. K, Gupta, B. B, Stewart, C. N. Jr
• Format: Journal Article
• Language: English
• Published: Dordrecht Springer-Verlag 01.03.2014; Springer Netherlands; Springer Nature B.V
• Subjects: Agricultural biotechnology; Applied Microbiology; Arabidopsis; Biochemistry; Biomedical and Life Sciences; Biotechnology; Crop science; Crops; Gene Expression Profiling - methods; Gene sequencing; Genes; Genetic Markers; Genomics; Genomics - methods; genotype; High-Throughput Nucleotide Sequencing - methods; Hybridization, Genetic; Life Sciences; Markers; Microbiology; nucleotide sequences; Oryza sativa; pigeon peas; Pigeons; Plants (organisms); Plants - genetics; Polymorphism; Polymorphism, Single Nucleotide; Recombinant; Review; rice; Selective breeding; sequence analysis; single nucleotide polymorphism; soybeans; Functional markers; Crop plants; Genomic selection; Plant biotechnology, plant breeding, polymorphisms; Next generation DNA sequencing
• ISSN: 0141-5492; 1573-6776
• DOI: 10.1007/s10529-013-1377-1

The availability of complete genome sequences, along with other genomic resources for Arabidopsis, rice, pigeon pea, soybean and other crops, has revolutionized our understanding of the genetic make-up of plants. Next-generation DNA sequencing (NGS) has facilitated single nucleotide polymorphism discovery in plants. Functionally-characterized sequences can be identified and functional markers (FMs) for important traits can be developed at an ever-increasing ease. FMs are derived from sequence polymorphisms found in allelic variants of a functional gene. Linkage disequilibrium-based association mapping and homologous recombinants have been developed for identification of “perfect” markers for their use in crop improvement practices. Compared with many other molecular markers, FMs derived from the functionally characterized sequence genes using NGS techniques and their use provide opportunities to develop high-yielding plant genotypes resistant to various stresses at a fast pace.