Development of Insertion and Deletion Markers for Bottle Gourd Based on Restriction Site-associated DNA Sequencing Data
Bottle gourd is an important cucurbit crop worldwide. To provide more available molecular markers for this crop, a bioinformatic approach was employed to develop insertion–deletions (InDels) markers in bottle gourd based on restriction site-associated DNA sequencing (RAD-Seq) data. A total of 892 In...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
KeAi Communications Co., Ltd.
2017-01-01
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| Series: | Horticultural Plant Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2468014117301486 |
| _version_ | 1797203155507740672 |
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| author | Xinyi WU Pei XU Xiaohua WU Baogen WANG Zhongfu LU Guojing LI |
| author_facet | Xinyi WU Pei XU Xiaohua WU Baogen WANG Zhongfu LU Guojing LI |
| author_sort | Xinyi WU |
| collection | DOAJ |
| description | Bottle gourd is an important cucurbit crop worldwide. To provide more available molecular markers for this crop, a bioinformatic approach was employed to develop insertion–deletions (InDels) markers in bottle gourd based on restriction site-associated DNA sequencing (RAD-Seq) data. A total of 892 Indels were predicted, with the length varying from 1 bp to 167 bp. Single-nucleotide InDels were the predominant types of InDels. To validate these InDels, PCR primers were designed from 162 loci where InDels longer than 2 bp were predicated. A total of 112 InDels were found to be polymorphic among 9 bottle gourd accessions under investigation. The rate of prediction accuracy was thus at a high level of 72.7%. DNA fingerprinting for 4 cultivars were performed using 8 selected Indels markers, demonstrating the usefulness of these markers. |
| first_indexed | 2024-04-24T08:14:50Z |
| format | Article |
| id | doaj.art-48081aff374e4548aa729a381141fb2d |
| institution | Directory Open Access Journal |
| issn | 2468-0141 |
| language | English |
| last_indexed | 2024-04-24T08:14:50Z |
| publishDate | 2017-01-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Horticultural Plant Journal |
| spelling | doaj.art-48081aff374e4548aa729a381141fb2d2024-04-17T04:30:03ZengKeAi Communications Co., Ltd.Horticultural Plant Journal2468-01412017-01-0131131610.1016/j.hpj.2017.01.011Development of Insertion and Deletion Markers for Bottle Gourd Based on Restriction Site-associated DNA Sequencing DataXinyi WUPei XUXiaohua WUBaogen WANGZhongfu LUGuojing LIBottle gourd is an important cucurbit crop worldwide. To provide more available molecular markers for this crop, a bioinformatic approach was employed to develop insertion–deletions (InDels) markers in bottle gourd based on restriction site-associated DNA sequencing (RAD-Seq) data. A total of 892 Indels were predicted, with the length varying from 1 bp to 167 bp. Single-nucleotide InDels were the predominant types of InDels. To validate these InDels, PCR primers were designed from 162 loci where InDels longer than 2 bp were predicated. A total of 112 InDels were found to be polymorphic among 9 bottle gourd accessions under investigation. The rate of prediction accuracy was thus at a high level of 72.7%. DNA fingerprinting for 4 cultivars were performed using 8 selected Indels markers, demonstrating the usefulness of these markers.http://www.sciencedirect.com/science/article/pii/S2468014117301486bottle gourdInDels markersRAD-SeqDNA fingerprinting |
| spellingShingle | Xinyi WU Pei XU Xiaohua WU Baogen WANG Zhongfu LU Guojing LI Development of Insertion and Deletion Markers for Bottle Gourd Based on Restriction Site-associated DNA Sequencing Data Horticultural Plant Journal bottle gourd InDels markers RAD-Seq DNA fingerprinting |
| title | Development of Insertion and Deletion Markers for Bottle Gourd Based on Restriction Site-associated DNA Sequencing Data |
| title_full | Development of Insertion and Deletion Markers for Bottle Gourd Based on Restriction Site-associated DNA Sequencing Data |
| title_fullStr | Development of Insertion and Deletion Markers for Bottle Gourd Based on Restriction Site-associated DNA Sequencing Data |
| title_full_unstemmed | Development of Insertion and Deletion Markers for Bottle Gourd Based on Restriction Site-associated DNA Sequencing Data |
| title_short | Development of Insertion and Deletion Markers for Bottle Gourd Based on Restriction Site-associated DNA Sequencing Data |
| title_sort | development of insertion and deletion markers for bottle gourd based on restriction site associated dna sequencing data |
| topic | bottle gourd InDels markers RAD-Seq DNA fingerprinting |
| url | http://www.sciencedirect.com/science/article/pii/S2468014117301486 |
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