Fine mapping and gene cloning in the post-NGS era: advances and prospects

Abstract

Improvement in traits of agronomic importance is the top breeding priority of crop improvement programs. Majority of these agronomic traits show complex quantitative inheritance. Identification of quantitative trait loci (QTLs) followed by fine mapping QTLs and cloning of candidate genes/QTLs is central to trait analysis. Advances in genomic technologies revolutionized our understanding of genetics of complex traits, and genomic regions associated with traits were employed in marker-assisted breeding or cloning of QTLs/genes. Next-generation sequencing (NGS) technologies have enabled genomewide methodologies for the development of ultra-high-density genetic linkage maps in different crops, thus allowing placement of candidate loci within few kbs in genomes. In this review, we compare the marker systems used for fine mapping and QTL cloning in the pre-and post-NGS era. We then discuss how different NGS platforms in combination with advanced experimental designs have improved trait analysis and fine mapping. We opine that efficient genotyping/sequencing assays may circumvent the need for cumbersome procedures that were earlier used for fine mapping. A deeper understanding of the trait architectures of agricultural significance will be crucial to accelerate crop improvement.

Genomic interventions for sustainable agriculture

“…Conventional quantitative trait loci (QTL) mapping methods suffer from limited genetic resolution besides having low throughput, being labour‐intensive and time‐consuming in nature. Presence of whole genome sequence in concert with advances in DNA sequencing technologies and computational biology has greatly empowered trait analysis and gene discovery in plants (Jaganathan et al ., 2020). Last decade has seen emergence of a series of such trait mapping approaches such as SHOREmap, SNP ratio mapping (SRM), next‐generation mapping (NGM), MutMap and QTL‐seq that harness the immense potential of reference genome sequences (Bohra, 2013; Varshney et al ., 2014; Zhang et al ., 2019).…”

Current Insights in Genetics of Sarcoidosis: Functional and Clinical Impacts

“…To overcome the issue of missing heritability, next-generation DNA sequencing (NGS) techniques have been applied recently to various clinical situations, including familial and sporadic forms of sarcoidosis. Technical advances to assess rare variation genome wide, particularly whole exome sequencing (WES), have facilitated collaborative studies resulting in novel disease gene discoveries, mainly for complex diseases [103]. The main difficulties induced by NGS methods are (1) the large number of variations identified and difficulties of classification of variants between pathogenic and benign; (2) the need for a bio informatics analysis to select the genes and mutations that are potentially causal; and (3) the need to analyze the data not gene by gene, but rather in functional networks, to target the etiology of polygenic diseases.…”

Next Generation Sequencing Based Forward Genetic Approaches for Identification and Mapping of Causal Mutations in Crop Plants: A Comprehensive Review

“…It also serves interrogate pan-genome sequence variation in diverse germplasm to isolate uncharacterised R-genes. Recent examples have shown utility of RenSeq for improving disease resistance in plants, and similar techniques identification of genes for abiotic stress-tolerant will greatly benefits the crops [ 173 ]. AgRenSeq exploits entire gene set of all strains of a species to isolateand cloning of the uncharacterized R-genes.…”