Principles and Implications of Various Genome Enrichment Approaches for Targeted Sequencing of Plant Genomes

Kaur, Parampreet; Gaikwad, Kishor

doi:10.1007/978-981-13-8499-8_2

Cited by 2 publications

(1 citation statement)

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“…The most straightforward targeted sequencing protocol for enrichment of small sized genomic targets is the PCR-based method. Moreover, this method provides high efficiency when the targeted regions have highly conserved sequences across cultivars at the primer binding sites ( Kaur and Gaikwad, 2019 ). Nowadays, multiplex PCR products are used to exploit the high-throughput nature of NGS; however, the primer design for a large genome is cumbersome, and amplification often requires specific commercial DNA polymerase enzymes capable of amplifying long genomic DNA (~30 kb) ( Ostezan et al, 2021 ).…”

Section: Genotyping By Sequencingmentioning

confidence: 99%

Genotyping by Sequencing Advancements in Barley

2022

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Barley is considered an ideal crop to study cereal genetics due to its close relationship with wheat and diploid ancestral genome. It plays a crucial role in reducing risks to global food security posed by climate change. Genetic variations in the traits of interest in crops are vital for their improvement. DNA markers have been widely used to estimate these variations in populations. With the advancements in next-generation sequencing, breeders could access different types of genetic variations within different lines, with single-nucleotide polymorphisms (SNPs) being the most common type. However, genotyping barley with whole genome sequencing (WGS) is challenged by the higher cost and computational demand caused by the large genome size (5.5GB) and a high proportion of repetitive sequences (80%). Genotyping-by-sequencing (GBS) protocols based on restriction enzymes and target enrichment allow a cost-effective SNP discovery by reducing the genome complexity. In general, GBS has opened up new horizons for plant breeding and genetics. Though considered a reliable alternative to WGS, GBS also presents various computational difficulties, but GBS-specific pipelines are designed to overcome these challenges. Moreover, a robust design for GBS can facilitate the imputation to the WGS level of crops with high linkage disequilibrium. The complete exploitation of GBS advancements will pave the way to a better understanding of crop genetics and offer opportunities for the successful improvement of barley and its close relatives.

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Section: Genotyping By Sequencingmentioning

confidence: 99%