Development and validation of InDel markers for identification of QTL underlying flowering time in soybean
Soybean [Glycine max (L.) Merrill] is a major plant source of protein and oil. An accurate and well-saturated molecular linkage map is a prerequisite for forward genetic studies of gene function and for modern breeding for many useful agronomic traits. Next-generation sequence data available in publ...
| Main Authors: | , , , , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
KeAi Communications Co., Ltd.
2018-04-01
|
| Series: | Crop Journal |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2214514117300806 |
| id |
doaj-75c2e2d7db83428ab33fa8078172c98b |
|---|---|
| record_format |
Article |
| collection |
DOAJ |
| language |
English |
| format |
Article |
| sources |
DOAJ |
| author |
Jialin Wang Lingping Kong Kanchao Yu Fengge Zhang Xinyi Shi Yanping Wang Haiyang Nan Xiaohui Zhao Sijia Lu Dong Cao Xiaoming Li Chao Fang Feifei Wang Tong Su Shichen Li Xiaohui Yuan Baohui Liu Fanjiang Kong |
| spellingShingle |
Jialin Wang Lingping Kong Kanchao Yu Fengge Zhang Xinyi Shi Yanping Wang Haiyang Nan Xiaohui Zhao Sijia Lu Dong Cao Xiaoming Li Chao Fang Feifei Wang Tong Su Shichen Li Xiaohui Yuan Baohui Liu Fanjiang Kong Development and validation of InDel markers for identification of QTL underlying flowering time in soybean Crop Journal Soybean Resequencing data InDel markers Genetic map QTL analysis |
| author_facet |
Jialin Wang Lingping Kong Kanchao Yu Fengge Zhang Xinyi Shi Yanping Wang Haiyang Nan Xiaohui Zhao Sijia Lu Dong Cao Xiaoming Li Chao Fang Feifei Wang Tong Su Shichen Li Xiaohui Yuan Baohui Liu Fanjiang Kong |
| author_sort |
Jialin Wang |
| title |
Development and validation of InDel markers for identification of QTL underlying flowering time in soybean |
| title_short |
Development and validation of InDel markers for identification of QTL underlying flowering time in soybean |
| title_full |
Development and validation of InDel markers for identification of QTL underlying flowering time in soybean |
| title_fullStr |
Development and validation of InDel markers for identification of QTL underlying flowering time in soybean |
| title_full_unstemmed |
Development and validation of InDel markers for identification of QTL underlying flowering time in soybean |
| title_sort |
development and validation of indel markers for identification of qtl underlying flowering time in soybean |
| publisher |
KeAi Communications Co., Ltd. |
| series |
Crop Journal |
| issn |
2214-5141 |
| publishDate |
2018-04-01 |
| description |
Soybean [Glycine max (L.) Merrill] is a major plant source of protein and oil. An accurate and well-saturated molecular linkage map is a prerequisite for forward genetic studies of gene function and for modern breeding for many useful agronomic traits. Next-generation sequence data available in public databases provides valuable information and offers new insights for rapid and efficient development of molecular markers. In this study, we attempted to show the feasibility and facility of using genomic resequencing data as raw material for identifying putative InDel markers. First, we identified 17,613 InDel sites among 56 soybean accessions and obtained 12,619 primer pairs. Second, we constructed a genetic map with a random subset of 2841 primer pairs and aligned 300 polymorphic markers with the 20 consensus linkage groups (LG). The total genetic distance was 2347.3 cM and the number of mapped markers per LG ranged from 10 to 23 with an average of 15 markers. The largest and smallest genetic distances between adjacent markers were 52.3 cM and 0.1 cM, respectively. Finally, we validated the genetic map constructed by newly developed InDel markers by QTL analysis of days to flowering (DTF) under different environments. One major QTL (qDTF4) and four minor QTL (qDTF20, qDTF13, qDTF12, and qDTF11) on 5 LGs were detected. These results demonstrate the utility of the InDel markers developed in this work for map-based cloning and molecular breeding in soybean. |
| topic |
Soybean Resequencing data InDel markers Genetic map QTL analysis |
| url |
http://www.sciencedirect.com/science/article/pii/S2214514117300806 |
| work_keys_str_mv |
AT jialinwang developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean AT lingpingkong developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean AT kanchaoyu developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean AT fenggezhang developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean AT xinyishi developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean AT yanpingwang developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean AT haiyangnan developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean AT xiaohuizhao developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean AT sijialu developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean AT dongcao developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean AT xiaomingli developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean AT chaofang developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean AT feifeiwang developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean AT tongsu developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean AT shichenli developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean AT xiaohuiyuan developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean AT baohuiliu developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean AT fanjiangkong developmentandvalidationofindelmarkersforidentificationofqtlunderlyingfloweringtimeinsoybean |
| _version_ |
1724312259959717888 |
| spelling |
doaj-75c2e2d7db83428ab33fa8078172c98b2021-02-02T01:08:17ZengKeAi Communications Co., Ltd.Crop Journal2214-51412018-04-016212613510.1016/j.cj.2017.08.001Development and validation of InDel markers for identification of QTL underlying flowering time in soybeanJialin Wang0Lingping Kong1Kanchao Yu2Fengge Zhang3Xinyi Shi4Yanping Wang5Haiyang Nan6Xiaohui Zhao7Sijia Lu8Dong Cao9Xiaoming Li10Chao Fang11Feifei Wang12Tong Su13Shichen Li14Xiaohui Yuan15Baohui Liu16Fanjiang Kong17The Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, ChinaThe Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, ChinaQiqihar Branch of Heilongjiang Academy of Agricultural Sciences, Qiqihar 161006, Heilongjiang, ChinaThe Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, ChinaThe Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, ChinaMudanjiang Branch of Heilongjiang Academy of Agricultural Sciences, Mudanjiang 157041, Heilongjiang, ChinaThe Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, ChinaThe Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, ChinaThe Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, ChinaThe Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, ChinaThe Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, ChinaThe Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, ChinaThe Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, ChinaThe Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, ChinaThe Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, ChinaThe Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, ChinaThe Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, ChinaThe Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin 150081, Heilongjiang, ChinaSoybean [Glycine max (L.) Merrill] is a major plant source of protein and oil. An accurate and well-saturated molecular linkage map is a prerequisite for forward genetic studies of gene function and for modern breeding for many useful agronomic traits. Next-generation sequence data available in public databases provides valuable information and offers new insights for rapid and efficient development of molecular markers. In this study, we attempted to show the feasibility and facility of using genomic resequencing data as raw material for identifying putative InDel markers. First, we identified 17,613 InDel sites among 56 soybean accessions and obtained 12,619 primer pairs. Second, we constructed a genetic map with a random subset of 2841 primer pairs and aligned 300 polymorphic markers with the 20 consensus linkage groups (LG). The total genetic distance was 2347.3 cM and the number of mapped markers per LG ranged from 10 to 23 with an average of 15 markers. The largest and smallest genetic distances between adjacent markers were 52.3 cM and 0.1 cM, respectively. Finally, we validated the genetic map constructed by newly developed InDel markers by QTL analysis of days to flowering (DTF) under different environments. One major QTL (qDTF4) and four minor QTL (qDTF20, qDTF13, qDTF12, and qDTF11) on 5 LGs were detected. These results demonstrate the utility of the InDel markers developed in this work for map-based cloning and molecular breeding in soybean.http://www.sciencedirect.com/science/article/pii/S2214514117300806SoybeanResequencing dataInDel markersGenetic mapQTL analysis |