Research Report

Development of SNP Sites in Loquat Using SLAF-seq Technology  

Xiaoying Li1 , Hongxia Xu1 , Wenshun Hu2 , Xiuping Chen2 , Chaojun Deng2 , Shaoquan Zheng2 , Junwei Chen1
1 Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021
2 Fruit Research Institute,Fujian Academy of Agricultural Sciences,Fuzhou 350013
Author    Correspondence author
Plant Gene and Trait, 2020, Vol. 11, No. 10   
Received: 20 Sep., 2020    Accepted: 23 Sep., 2020    Published: 23 Sep., 2020
© 2020 BioPublisher Publishing Platform
This article was first published in Molecular Plant Breeding ( ISSN1672-416X,CN46-1068/S) in Chinese, and here was authorized to translate and publish the paper in English under the terms of Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Abstract

A group of SNP locis with high specificity and stability were developed by using SLAF-seq sequencing technology, which will provide theoretical basis for loquat molecular assisted breeding, genetic map constructionand species evolution. In the present study, 294 loquat accessions were collected, and genomic DNA was sequenced and analyzed according to SLAF-seq. The reference genome of pear was used for the prediction of electronic enzyme. Double digestion with enzymes HaeIII and Hpy166II then SLAF-seq librarywas constructed. In this study, over 526.63M reads data were generated for the 294 natural accessions, the number of read lengths obtained for each library was in the range of 119,893-9,305,152 reads, with an average of 1,787,581. The sequencing quality value Q30 ranged from 88.26 to 95.67%, with an average of 93.61%. GC content was distributed in the range of 38.79-42.92%, with an average value of 40.35%. The data volume of 0.16M reads obtained from rice sequencing was as control, and the efficiency of double ended comparison was 91.28%, indicating that SLAF database was basically normal. The result of bioinformatics analysis showed that 623,356 SLAF tags were obtained , of which 123,498 were polymorphic, with a polymorphism rate of 19.81%. A total of 1,604,434 population SNPs were initially called for this set of polymorphic SLAF tags, leaving 95,960 SNPs at MAF > 0.05 and completeness > 0.8 for the further analyses.

Keywords
Loquat; SLAF-seq; Natural population; SNP marker

(The advance publishing of the abstract of this manuscript does not mean final published, the end result whether or not published will depend on the comments of peer reviewers and decision of our editorial board.)
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. Xiaoying Li
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