QTL Mapping for Important Agronomic Traits Using a Wheat55K SNP Array-Based Genetic Map in Tetraploid Wheat
Wheat yield is highly correlated with plant height, heading date, spike characteristics, and kernel traits. In this study, we used the wheat55K single nucleotide polymorphism array to genotype a recombinant inbred line population of 165 lines constructed by crossing two tetraploid wheat materials, I...
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MDPI AG
2023-02-01
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| Series: | Plants |
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| Online Access: | https://www.mdpi.com/2223-7747/12/4/847 |
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| author | Chao Ma Le Liu Tianxiang Liu Yatao Jia Qinqin Jiang Haibo Bai Sishuang Ma Shuhua Li Zhonghua Wang |
| author_facet | Chao Ma Le Liu Tianxiang Liu Yatao Jia Qinqin Jiang Haibo Bai Sishuang Ma Shuhua Li Zhonghua Wang |
| author_sort | Chao Ma |
| collection | DOAJ |
| description | Wheat yield is highly correlated with plant height, heading date, spike characteristics, and kernel traits. In this study, we used the wheat55K single nucleotide polymorphism array to genotype a recombinant inbred line population of 165 lines constructed by crossing two tetraploid wheat materials, Icaro and Y4. A genetic linkage map with a total length of 6244.51 cM was constructed, covering 14 chromosomes of tetraploid wheat. QTLs for 12 important agronomic traits, including plant height (PH), heading date (HD), awn color (AC), spike-branching (SB), and related traits of spike and kernel, were mapped in multiple environments, while combined QTL-by-environment interactions and epistatic effects were analyzed for each trait. A total of 52 major or stable QTLs were identified, among which may be some novel loci controlling PH, SB, and kernel length-width ratio (LWR), etc., with LOD values ranging from 2.51 to 54.49, thereby explaining 2.40–66.27% of the phenotypic variation. Based on the ‘China Spring’ and durum wheat reference genome annotations, candidate genes were predicted for four stable QTLs, <i>QPH.nwafu-2B.2</i> (165.67–166.99 cM), <i>QAC.nwafu-3A.1</i> (419.89–420.52 cM), <i>QAC.nwafu-4A.1</i> (424.31–447.4 cM), and <i>QLWR.nwafu-7A.1</i> (166.66–175.46 cM). Thirty-one QTL clusters and 44 segregation distortion regions were also detected, and 38 and 18 major or stable QTLs were included in these clusters and segregation distortion regions, respectively. These results provide QTLs with breeding application potential in tetraploid wheat that broadens the genetic basis of important agronomic traits such as PH, HD, AC, SB, etc., and benefits wheat breeding. |
| first_indexed | 2024-03-11T08:15:06Z |
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| institution | Directory Open Access Journal |
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| language | English |
| last_indexed | 2024-03-11T08:15:06Z |
| publishDate | 2023-02-01 |
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| series | Plants |
| spelling | doaj.art-b066440e2db64c80b64462dfa8a524bf2023-11-16T22:48:17ZengMDPI AGPlants2223-77472023-02-0112484710.3390/plants12040847QTL Mapping for Important Agronomic Traits Using a Wheat55K SNP Array-Based Genetic Map in Tetraploid WheatChao Ma0Le Liu1Tianxiang Liu2Yatao Jia3Qinqin Jiang4Haibo Bai5Sishuang Ma6Shuhua Li7Zhonghua Wang8State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, ChinaState Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, ChinaState Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, ChinaState Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, ChinaState Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, ChinaAgricultural Bio-Technology Research Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan 750002, ChinaAgricultural Bio-Technology Research Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan 750002, ChinaAgricultural Bio-Technology Research Center, Ningxia Academy of Agriculture and Forestry Science, Yinchuan 750002, ChinaState Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling 712100, ChinaWheat yield is highly correlated with plant height, heading date, spike characteristics, and kernel traits. In this study, we used the wheat55K single nucleotide polymorphism array to genotype a recombinant inbred line population of 165 lines constructed by crossing two tetraploid wheat materials, Icaro and Y4. A genetic linkage map with a total length of 6244.51 cM was constructed, covering 14 chromosomes of tetraploid wheat. QTLs for 12 important agronomic traits, including plant height (PH), heading date (HD), awn color (AC), spike-branching (SB), and related traits of spike and kernel, were mapped in multiple environments, while combined QTL-by-environment interactions and epistatic effects were analyzed for each trait. A total of 52 major or stable QTLs were identified, among which may be some novel loci controlling PH, SB, and kernel length-width ratio (LWR), etc., with LOD values ranging from 2.51 to 54.49, thereby explaining 2.40–66.27% of the phenotypic variation. Based on the ‘China Spring’ and durum wheat reference genome annotations, candidate genes were predicted for four stable QTLs, <i>QPH.nwafu-2B.2</i> (165.67–166.99 cM), <i>QAC.nwafu-3A.1</i> (419.89–420.52 cM), <i>QAC.nwafu-4A.1</i> (424.31–447.4 cM), and <i>QLWR.nwafu-7A.1</i> (166.66–175.46 cM). Thirty-one QTL clusters and 44 segregation distortion regions were also detected, and 38 and 18 major or stable QTLs were included in these clusters and segregation distortion regions, respectively. These results provide QTLs with breeding application potential in tetraploid wheat that broadens the genetic basis of important agronomic traits such as PH, HD, AC, SB, etc., and benefits wheat breeding.https://www.mdpi.com/2223-7747/12/4/847tetraploid wheat55K SNP arrayagronomic traitsQTL clustermarker segregation distortionepistatic effect |
| spellingShingle | Chao Ma Le Liu Tianxiang Liu Yatao Jia Qinqin Jiang Haibo Bai Sishuang Ma Shuhua Li Zhonghua Wang QTL Mapping for Important Agronomic Traits Using a Wheat55K SNP Array-Based Genetic Map in Tetraploid Wheat Plants tetraploid wheat 55K SNP array agronomic traits QTL cluster marker segregation distortion epistatic effect |
| title | QTL Mapping for Important Agronomic Traits Using a Wheat55K SNP Array-Based Genetic Map in Tetraploid Wheat |
| title_full | QTL Mapping for Important Agronomic Traits Using a Wheat55K SNP Array-Based Genetic Map in Tetraploid Wheat |
| title_fullStr | QTL Mapping for Important Agronomic Traits Using a Wheat55K SNP Array-Based Genetic Map in Tetraploid Wheat |
| title_full_unstemmed | QTL Mapping for Important Agronomic Traits Using a Wheat55K SNP Array-Based Genetic Map in Tetraploid Wheat |
| title_short | QTL Mapping for Important Agronomic Traits Using a Wheat55K SNP Array-Based Genetic Map in Tetraploid Wheat |
| title_sort | qtl mapping for important agronomic traits using a wheat55k snp array based genetic map in tetraploid wheat |
| topic | tetraploid wheat 55K SNP array agronomic traits QTL cluster marker segregation distortion epistatic effect |
| url | https://www.mdpi.com/2223-7747/12/4/847 |
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