Development of Starfruit Simple Sequence Repeat (SSR) Using Next Generation Sequencing  

作　　者：Khairun Hisam Nasir Muhammad Fairuz Mohd Yusof Mohd Shahril Firdaus Siti Zainab Jantan Mira Farzana Mohamad Moktar Siti Norsaidah Ibrahim Noor Baiti Abdul Aziz Joanna Cho Lee Ying 

机构地区：[1]Centre for Molecular Marker Discovery and Validation (CMDV), Agri-Omic dan Bioinformatics, Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute (MARDI), 43400 Serdang, Selangor, Malaysia [2]Horticulture Research Centre, Headquarters, Malaysian Agricultural Research and Development Institute (MARDI), 43400 Serdang, Selangor, Malaysia

出　　处：《Journal of Food Science and Engineering》2019年第3期95-121,共27页食品科学与工程（英文版）（美国）

摘　　要：Starfruit (Averrhoa carambola L.) is an important fruit for Malaysian export and great attention has been made to improve starfruit fruit quality at Malaysian Agricultural Research and Development Institute (MARDI). The current study used next generation sequencing (NGS) technologies to develop starfruit simple sequence repeat (SSR) from 2 varieties namely B11 and B17 using Illumina HiSeq. The pre-processed reads were de novo assembled to generate approximately 75,000 and 74,000 scaffolds respectively. Total genome size for B11 and B17 were around 345 Mbp and 342 Mbp based on K-mer distribution analysis. In-silico microsatellite mining of each variety has identified more than 17,000 SSR in B11 and B17 respectively. Dinucleotides were the most abundant, accounting for more than 70% of all SSR and repeat motif GA (49%) was most common. A total of 239 SSR primer pairs were designed from contigs larger than 350 nucleotides and tested for amplification. The 30 polymorphic SSRs were used to DNA fingerprint of 12 starfruit hybrids. Polymorphism information content (PIC) ranged from 0.1411 to 0.6838, with an average of 0.3919. The Unweighted Pair-Group Method for Arithmetic Averages (UPGMA) dendrogram clustered 12 starfruit accessions into 2 groups.

关 键 词：Starfruit (Averrhoa CARAMBOLA L.) NEXT generation SEQUENCING molecular MARKER simple SEQUENCE REPEAT 

分 类 号：TS[轻工技术与工程]