Variation Characteristics of Insertion-Deletion（InDel）and Molecular Markers Development and Application in Eggplant Based on Whole Genome Re-sequencing Data

doi:10.16420/j.issn.0513-353x.2022-1176

Acta Horticulturae Sinica ›› 2024, Vol. 51 ›› Issue (3): 520-532.doi: 10.16420/j.issn.0513-353x.2022-1176

• Genetic & Breeding · Germplasm Resources · Molecular Biology • Previous Articles Next Articles

Variation Characteristics of Insertion-Deletion（InDel）and Molecular Markers Development and Application in Eggplant Based on Whole Genome Re-sequencing Data

YOU Yuanyuan1,2,*，WANG Shuai2,*，FANG Yingying1，QI Cheng1，LI Shupei1，ZHANG Ying1，CHEN Yuhui1，LIU Wei3，LIU Fuzhong1,**，and SHU Jinshuai1,**

1State Key Laboratory of Vegetable Biobreeding，Institute of Vegetables and Flowers，Chinese Academy of Agricultural Sciences，Beijing 100081，China；2College of Horticultural Science and Technology，Hebei Normal University of Science and Technology，Qinhuangdao，Hebei 066004，China；3Shouguang Vegetable Research and Development Center，Chinese Academy of Agricultural Sciences，Shouguang，Shandong 262704，China

Online:2024-03-25 Published:2024-03-22

Abstract

Abstract: Four high generation inbred lines of eggplant（Solanum melongena L.）were selected for whole genome re-sequencing，and 145 407 InDels were identified. The number of InDel on chromosome 12 was the least（7 752）and on chromosome 1 was the most（19 738）. There were 7 959 InDel with a length greater than 10 bp，and 144 InDels loci uniformly distributed on the genome were selected to be designed as InDel primers and verified. A total of 144 InDel primers were screened using 26 eggplant samples，63 primers showed stable polymorphism，and the polymorphism ratio was 43.75%. The main allele frequencies ranged from 0.4038 to 0.9808，with an average of 0.7659. Genetic diversity index（Hs）ranged from 0.0377 to 0.6501，with an average of 0.3217. The polymorphism information content（PIC）ranged from 0.0370 to 0.5750，with an average of 0.2663，and the PIC of 43 markers was greater than 0.200，indicating good polymorphism. When the genetic distance was 0.235，26 different types of eggplant materials were divided into two groups. The DNA fingerprints of 26 eggplant materials were constructed using the first ten InDel markers with high polymorphism information content. In addition，InDel markers with polymorphism among parents were selected for F1 generation authenticity identification of four hybrid combinations，and three real hybrids were identified. The results from purity test of four hybrid combinations from InDel markers matched well with those from field experiments.

Key words: 茄子, InDel标记, 遗传多样性, 指纹图谱, F1代真实性鉴定

CLC Number:

S 641.1

YOU Yuanyuan, WANG Shuai, FANG Yingying, QI Cheng, LI Shupei, ZHANG Ying, CHEN Yuhui, LIU Wei, LIU Fuzhong, and SHU Jinshuai, . Variation Characteristics of Insertion-Deletion（InDel）and Molecular Markers Development and Application in Eggplant Based on Whole Genome Re-sequencing Data[J]. Acta Horticulturae Sinica, 2024, 51(3): 520-532.

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Variation Characteristics of Insertion-Deletion（InDel）and Molecular Markers Development and Application in Eggplant Based on Whole Genome Re-sequencing Data

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