Jaimes Hugo, Londoño Alejandra, Saavedra-Diaz Carolina, Trujillo-Montenegro Jhon Henry, López-Gerena Jershon, Riascos John J, Aguilar Fernando S
Colombian Sugarcane Research Center Cenicaña Calle 38N 3CN-75 Cali Valle del Cauca Colombia.
Pontificia Universidad Javeriana Calle 18 118-250 Cali Colombia.
Appl Plant Sci. 2024 Mar 13;12(5):e11574. doi: 10.1002/aps3.11574. eCollection 2024 Sep-Oct.
Detecting single-nucleotide polymorphisms (SNPs) in a cost-effective way is fundamental in any plant breeding pipeline. Here, we compare three genotyping techniques for their ability to reproduce the allele dosage of SNPs of interest in sugarcane ( spp.).
To identify a reproducible technique to estimate allele dosage for the validation of SNP markers, the correlation between Flex-Seq, kompetitive allele-specific PCR (KASP), and genotyping-by-sequencing and restriction site-associated DNA sequencing (GBS+RADseq) was determined for a set of 76 SNPs. To find alternative methodologies for allele dosage estimation, the KASP and Flex-Seq techniques were compared for the same set of SNPs. For the three techniques, a population of 53 genotypes from the diverse sugarcane panel of the Centro de Investigación de la Caña de Azúcar (Cenicaña), Colombia, was selected.
The average Pearson correlation coefficients between GBS+RADseq and Flex-Seq, GBS+RADseq and KASP, and Flex-Seq and KASP were 0.62 ± 0.27, 0.38 ± 0.27, and 0.38 ± 0.30, respectively.
Flex-Seq reproduced the allele dosages determined using GBS+RADseq with good levels of precision because of its depth of sequencing and ability to target specific positions in the genome. Additionally, Flex-Seq outperformed KASP by allowing the conversion of a higher number of SNPs and a more accurate estimation of the allele dosage. Flex-Seq has therefore become the genotyping methodology of choice for marker validation at Cenicaña.
以经济高效的方式检测单核苷酸多态性（SNP）是任何植物育种流程的基础。在此，我们比较三种基因分型技术在甘蔗（ 种）中重现感兴趣SNP等位基因剂量的能力。
为了确定一种可重现的技术来估计等位基因剂量以验证SNP标记，针对一组76个SNP，测定了Flex-Seq、竞争性等位基因特异性PCR（KASP）、测序基因分型和限制性位点相关DNA测序（GBS+RADseq）之间的相关性。为了找到等位基因剂量估计的替代方法，对同一组SNP比较了KASP和Flex-Seq技术。对于这三种技术，从哥伦比亚甘蔗研究中心（Cenicaña）不同的甘蔗样本中选择了53个基因型的群体。
GBS+RADseq与Flex-Seq、GBS+RADseq与KASP、Flex-Seq与KASP之间的平均皮尔逊相关系数分别为0.62±0.27、0.38±0.27和0.38±0.30。
由于其测序深度和靶向基因组特定位置的能力，Flex-Seq能够高精度地重现使用GBS+RADseq确定的等位基因剂量。此外，Flex-Seq通过允许更多SNP的转化和更准确的等位基因剂量估计，表现优于KASP。因此，Flex-Seq已成为Cenicaña进行标记验证的首选基因分型方法。
