Publications by authors named "Yishan Ji"

2 Publications

  • Page 1 of 1

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

Theor Appl Genet 2021 Jun 12. Epub 2021 Jun 12.

National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.

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. 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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http://dx.doi.org/10.1007/s00122-021-03885-0DOI Listing
June 2021

Genetic diversity analysis for narrow-leafed lupin (Lupinus angustifolius L.) by SSR markers.

Mol Biol Rep 2020 Jul 23;47(7):5215-5224. Epub 2020 Jun 23.

The National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.

Narrow-leafed lupin (Lupinus angustifolius L.) is used as grain legumes, fodder for livestock and green manure in the world and has a great potential to be developed as a new crop in China. In this study, we assessed the genetic diversity among a set of 109 newly introduced accessions of narrow-leafed lupin using 76 genomic SSR markers. Data analysis suggested that the average gene diversity index and average polymorphism information content (PIC) were 0.4758 and 0.4328, respectively. The mean allele number per loci (Na) was 6.3816. The population structure analysis identified two subgroups based on delta K (ΔK) values. This result is in accordance with that of a PCA. The AMOVA analysis showed that most of molecular variance were within population. These results will be useful to guide the genetic improvement of the narrow-leafed lupin crop in China.
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http://dx.doi.org/10.1007/s11033-020-05596-zDOI Listing
July 2020
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