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A prolific and robust whole-genome genotyping method using PCR amplification via primer-template mismatched annealing

文献类型： 外文期刊

作者： Zhao, Sheng 1 ; Zhang, Cuicui 2 ; Wang, Liqun 1 ; Luo, Minxuan 1 ; Zhang, Peng 2 ; Wang, Yue 2 ; Malik, Waqar Afzal 2 ; Chen, Peng 2 ; Qiu, Xianjin 3 ; Wang, Chongrong 4 ; Lu, Hong 2 ; Xiang, Yong 2 ; Liu, Yuwen 2 ; Ruan, Jue 2 ; Qian, Qian 2 ; Zhi, Haijian 1 ; Chang, Yuxiao 2 ;

作者机构： 1.Nanjing Agr Univ, Natl Ctr Soybean Improvement, Natl Key Lab Crop Genet & Germplasm Enhancement, Nanjing 210095, Peoples R China

2.Chinese Acad Agr Sci, Agr Genom Inst Shenzhen, Guangdong Lab Lingnan Modern Agr, Genome Anal Lab,Minist Agr & Rural Affairs, Shenzhen 518120, Peoples R China

3.Yangtze Univ, Coll Agr, Jingzhou 434023, Peoples R China

4.Guangdong Acad Agr Sci, Rice Res Inst, Guangdong Prov Key Lab New Technol Rice Breeding, Guangzhou 510640, Peoples R China

关键词： background selection; foreground genotyping; primer-template mismatched annealing; marker-assisted breeding; whole-genome genotyping

期刊名称：JOURNAL OF INTEGRATIVE PLANT BIOLOGY （ 影响因子：11.4； 五年影响因子：10.1 ）

ISSN： 1672-9072

年卷期： 2023 年 65 卷 3 期

页码：

收录情况： SCI

摘要： Whole-genome genotyping methods are important for breeding. However, it has been challenging to develop a robust method for simultaneous foreground and background genotyping that can easily be adapted to different genes and species. In our study, we accidently discovered that in adapter ligation-mediated PCR, the amplification by primer-template mismatched annealing (PTMA) along the genome could generate thousands of stable PCR products. Based on this observation, we consequently developed a novel method for simultaneous foreground and background integrated genotyping by sequencing (FBI-seq) using one specific primer, in which foreground genotyping is performed by primer-template perfect annealing (PTPA), while background genotyping employs PTMA. Unlike DNA arrays, multiple PCR, or genome target enrichments, FBI-seq requires little preliminary work for primer design and synthesis, and it is easily adaptable to different foreground genes and species. FBI-seq therefore provides a prolific, robust, and accurate method for simultaneous foreground and background genotyping to facilitate breeding in the post-genomics era.

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