Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing.
Oryza sativa ssp. javanica rice varieties exhibit a wide variation in the phenotypes of several important agronomic traits, including grain quality, grain shape, plant architecture, disease resistance, and high adaption to an unfavorable environment, indicating a great potential for rice improvement...
| Main Authors: | , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2022-01-01
|
| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0274418 |
| _version_ | 1811181912543199232 |
|---|---|
| author | Weixiong Long Yonghui Li Zhengqing Yuan Lihua Luo Laiyang Luo Weibiao Xu Yaohui Cai Hongwei Xie |
| author_facet | Weixiong Long Yonghui Li Zhengqing Yuan Lihua Luo Laiyang Luo Weibiao Xu Yaohui Cai Hongwei Xie |
| author_sort | Weixiong Long |
| collection | DOAJ |
| description | Oryza sativa ssp. javanica rice varieties exhibit a wide variation in the phenotypes of several important agronomic traits, including grain quality, grain shape, plant architecture, disease resistance, and high adaption to an unfavorable environment, indicating a great potential for rice improvement. DNA molecular markers are basic and critical tools in genetic analysis and gene mining. However, only a few whole-genome variation analyses have been performed in Oryza sativa ssp. Javanica (tropical japonica rice), and this has hampered the utilization of such an important resource. In this study, the length of insertions/deletions variation greater larger than 10 bp from 10 Oryza sativa ssp. indica rice and 10 Oryza sativa ssp. tropical japonica rice were extracted by using the Nipponbare genome as a reference. A total of 118 primer pairs which were almost evenly distributed on each chromosome corresponding to the loci of InDels were designed by the Primer 5 program. We confirmed 85 InDel markers from 60 rice varieties, including indica and tropical japonica, by running polyacrylamide gels. The InDel markers function like SSRs in identifying hybrids, calculating genetic distance, constructing the genetic linkage map, and gene mining. The InDel markers developed in this study might help in genetic studies and to investigate the tropical japonica rice varieties. |
| first_indexed | 2024-04-11T09:24:55Z |
| format | Article |
| id | doaj.art-a8d782561c0d49078c7f72a536c7537b |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-11T09:24:55Z |
| publishDate | 2022-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-a8d782561c0d49078c7f72a536c7537b2022-12-22T04:32:03ZengPublic Library of Science (PLoS)PLoS ONE1932-62032022-01-011710e027441810.1371/journal.pone.0274418Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing.Weixiong LongYonghui LiZhengqing YuanLihua LuoLaiyang LuoWeibiao XuYaohui CaiHongwei XieOryza sativa ssp. javanica rice varieties exhibit a wide variation in the phenotypes of several important agronomic traits, including grain quality, grain shape, plant architecture, disease resistance, and high adaption to an unfavorable environment, indicating a great potential for rice improvement. DNA molecular markers are basic and critical tools in genetic analysis and gene mining. However, only a few whole-genome variation analyses have been performed in Oryza sativa ssp. Javanica (tropical japonica rice), and this has hampered the utilization of such an important resource. In this study, the length of insertions/deletions variation greater larger than 10 bp from 10 Oryza sativa ssp. indica rice and 10 Oryza sativa ssp. tropical japonica rice were extracted by using the Nipponbare genome as a reference. A total of 118 primer pairs which were almost evenly distributed on each chromosome corresponding to the loci of InDels were designed by the Primer 5 program. We confirmed 85 InDel markers from 60 rice varieties, including indica and tropical japonica, by running polyacrylamide gels. The InDel markers function like SSRs in identifying hybrids, calculating genetic distance, constructing the genetic linkage map, and gene mining. The InDel markers developed in this study might help in genetic studies and to investigate the tropical japonica rice varieties.https://doi.org/10.1371/journal.pone.0274418 |
| spellingShingle | Weixiong Long Yonghui Li Zhengqing Yuan Lihua Luo Laiyang Luo Weibiao Xu Yaohui Cai Hongwei Xie Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing. PLoS ONE |
| title | Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing. |
| title_full | Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing. |
| title_fullStr | Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing. |
| title_full_unstemmed | Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing. |
| title_short | Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing. |
| title_sort | development of indel markers for oryza sativa ssp javanica based on whole genome resequencing |
| url | https://doi.org/10.1371/journal.pone.0274418 |
| work_keys_str_mv | AT weixionglong developmentofindelmarkersfororyzasativasspjavanicabasedonwholegenomeresequencing AT yonghuili developmentofindelmarkersfororyzasativasspjavanicabasedonwholegenomeresequencing AT zhengqingyuan developmentofindelmarkersfororyzasativasspjavanicabasedonwholegenomeresequencing AT lihualuo developmentofindelmarkersfororyzasativasspjavanicabasedonwholegenomeresequencing AT laiyangluo developmentofindelmarkersfororyzasativasspjavanicabasedonwholegenomeresequencing AT weibiaoxu developmentofindelmarkersfororyzasativasspjavanicabasedonwholegenomeresequencing AT yaohuicai developmentofindelmarkersfororyzasativasspjavanicabasedonwholegenomeresequencing AT hongweixie developmentofindelmarkersfororyzasativasspjavanicabasedonwholegenomeresequencing |