Crop Improvement Division, ICAR - Sugarcane Breeding Institute, Indian Council of Agricultural Research (ICAR), Coimbatore, Tamil Nadu, India.
Business Development, Asia Pacific Japan region, Thermo Fisher Scientific, Waltham, MA, USA.
Crit Rev Biotechnol. 2020 Sep;40(6):865-880. doi: 10.1080/07388551.2020.1765730. Epub 2020 Jun 7.
Sugarcane ( spp.) is one of the most economically significant crops because of its high sucrose content and it is a promising biomass feedstock for biofuel production. Sugarcane genome sequencing and analysis is a difficult task due to its heterozygosity and polyploidy. Long sequence read technologies, PacBio Single-Molecule Real-Time (SMRT) sequencing, the Illumina TruSeq, and the Oxford Nanopore sequencing could solve the problem of genome assembly. On the applications side, next generation sequencing (NGS) technologies played a major role in the discovery of single nucleotide polymorphism (SNP) and the development of low to high throughput genotyping platforms. The two mainstream high throughput genotyping platforms are the SNP microarray and genotyping by sequencing (GBS). This paper reviews the NGS in sugarcane genomics, genotyping methodologies, and the choice of these methods. Array-based SNP genotyping is robust, provides consistent SNPs, and relatively easier downstream data analysis. The GBS method identifies large scale SNPs across the germplasm. A combination of targeted GBS and array-based genotyping methods should be used to increase the accuracy of genomic selection and marker-assisted breeding.
甘蔗（ spp.）因其高蔗糖含量而成为最具经济意义的作物之一，它是生物燃料生产有前途的生物量原料。由于其杂合性和多倍性，甘蔗基因组测序和分析是一项艰巨的任务。长序列读取技术、PacBio 单分子实时（SMRT）测序、Illumina TruSeq 和 Oxford Nanopore 测序可以解决基因组组装的问题。在应用方面，下一代测序（NGS）技术在单核苷酸多态性（SNP）的发现和低至高通量基因分型平台的开发中发挥了重要作用。两种主流的高通量基因分型平台是 SNP 微阵列和测序基因分型（GBS）。本文综述了甘蔗基因组学中的 NGS、基因分型方法以及这些方法的选择。基于阵列的 SNP 基因分型具有稳健性、提供一致的 SNP 和相对较容易的下游数据分析。GBS 方法可以识别种质中的大规模 SNP。应结合靶向 GBS 和基于阵列的基因分型方法，以提高基因组选择和标记辅助育种的准确性。
