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Development and application of the Faba_bean_130K targeted next-generation sequencing SNP genotyping platform based on transcriptome sequencing

文献类型： 外文期刊

作者： Wang, Chenyu 1 ; Liu, Rong 1 ; Liu, Yujiao 2 ; Hou, Wanwei 3 ; Wang, Xuejun 4 ; Miao, Yamei 4 ; He, Yuhua 5 ; Ma, Yu 6 ; Li, 1 ;

作者机构： 1.Chinese Acad Agr Sci, Inst Crop Sci, Natl Key Facil Crop Gene Resources & Genet Improv, Beijing 100081, Peoples R China

2.Qinghai Univ, State Key Lab Plateau Ecol & Agr, Ningda Rd 251, Xining 810016, Qinghai, Peoples R China

3.Qinghai Acad Agr & Forestry Sci, Ningda Rd 253, Xining 810016, Qinghai, Peoples R China

4.Agr Inst Riparian Region, Hebei 226541, Jiangsu, Peoples R China

5.Yunnan Acad Agr Sci, Inst Grain Crops, Kunming 650205, Yunnan, Peoples R China

6.Washington State Univ, Dept Hort, Pullman, WA 99164 USA

期刊名称：THEORETICAL AND APPLIED GENETICS （ 影响因子：5.699； 五年影响因子：5.565 ）

ISSN： 0040-5752

年卷期： 2021 年 134 卷 10 期

页码：

收录情况： SCI

摘要： Key message Large-scale faba bean transcriptome data are available, and the first genotyping platform based on liquid-phase probe targeted capture technology was developed for genetic and molecular breeding studies. Abstract Faba bean (Vicia faba L., 2n = 12) is an important food legume crop that is widely grown for multiple uses worldwide. However, no reference genome is currently available due to its very large genome size (approximately 13 Gb) and limited single nucleotide polymorphism (SNP) markers as well as highly efficient genotyping tools have been reported for faba bean. In this study, 16.7 billion clean reads were obtained from transcriptome libraries of flowers and leaves of 102 global faba bean accessions. A total of 243,120 unigenes were de novo assembled and functionally annotated. Moreover, a total of 1,579,411 SNPs were identified and further filtered according to a selection pipeline to develop a high-throughput, flexible, low-cost Faba_bean_130K targeted next-generation sequencing (TNGS) genotyping platform. A set of 69 Chinese faba bean accessions were genotyped with the TNGS genotyping platform, and the average mapping rate of captured reads to reference transcripts was 93.14%, of which 53.23% were located in the targeted regions. The TNGS genotyping results were validated by Sanger sequencing and the average consistency rate reached 93.6%. Comprehensive population genetic analysis was performed on the 69 Chinese faba bean accessions and identified four genetic subgroups correlated with the geographic distribution. This study provides valuable genomic resources and a reliable genotyping tool that could be implemented in genetic and molecular breeding studies to accelerate new cultivar development and improvement in faba bean.

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