Intraspecific variation of residual heterozygosity and its utility for quantitative genetic studies in maize
Abstract Background Residual heterozygosity (RH) in advanced inbred lines of plants benefits quantitative trait locus (QTL) mapping studies. However, knowledge of factors affecting the genome-wide distribution of RH remains limited. Results A set of 2196 heterogeneous inbred family (HIF) maize lines...
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doaj-5adde74526974bd18e6d58362a14e6072020-11-24T23:49:11ZengBMCBMC Plant Biology1471-22292018-04-0118111510.1186/s12870-018-1287-4Intraspecific variation of residual heterozygosity and its utility for quantitative genetic studies in maizeNannan Liu0Jianxiao Liu1Wenqiang Li2Qingchun Pan3Jie Liu4Xiaohong Yang5Jianbing Yan6Yingjie Xiao7National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityNational Maize Improvement Center of China, Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityNational Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural UniversityAbstract Background Residual heterozygosity (RH) in advanced inbred lines of plants benefits quantitative trait locus (QTL) mapping studies. However, knowledge of factors affecting the genome-wide distribution of RH remains limited. Results A set of 2196 heterogeneous inbred family (HIF) maize lines derived from 12 recombinant inbred line (RIL) populations was genotyped using the Maize50K SNP chip. A total of 18,615 unique RH intervals were identified, ranging from 505 to 2095 intervals per population, with average maize genome coverage of 94.8%. Across all populations, there were 8.6 RH intervals per HIF line on average, ranging from 1.8 to 14 intervals; the average size of an RH interval was approximately 58.7 Mb, ranging from 7.2 to 74.1 Mb. A given RH region was present in an average of 5 different individuals within a population. Seven RH hotspots, where RH segments were enriched in the genome, were found to be subject to selection during population development. The RH patterns varied significantly across populations, presumably reflecting differences in the genetic background of each population, and 8 QTLs were found to affect heterozygosity levels in the RH hotspots. The potential use of this HIF library for the fine mapping of QTLs was assessed based on publicly available QTL information, achieving a ≤ 1 Mb resolution on average. Conclusion The examined library of HIF lines offers insight into the RH landscape and its intraspecific variation and provides a useful resource for the QTL cloning of important agronomic traits in maize.http://link.springer.com/article/10.1186/s12870-018-1287-4Residual heterozygosityRH hotspotsGenetic factorsHIF library for QTL fine mappingZea may |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Nannan Liu Jianxiao Liu Wenqiang Li Qingchun Pan Jie Liu Xiaohong Yang Jianbing Yan Yingjie Xiao |
spellingShingle |
Nannan Liu Jianxiao Liu Wenqiang Li Qingchun Pan Jie Liu Xiaohong Yang Jianbing Yan Yingjie Xiao Intraspecific variation of residual heterozygosity and its utility for quantitative genetic studies in maize BMC Plant Biology Residual heterozygosity RH hotspots Genetic factors HIF library for QTL fine mapping Zea may |
author_facet |
Nannan Liu Jianxiao Liu Wenqiang Li Qingchun Pan Jie Liu Xiaohong Yang Jianbing Yan Yingjie Xiao |
author_sort |
Nannan Liu |
title |
Intraspecific variation of residual heterozygosity and its utility for quantitative genetic studies in maize |
title_short |
Intraspecific variation of residual heterozygosity and its utility for quantitative genetic studies in maize |
title_full |
Intraspecific variation of residual heterozygosity and its utility for quantitative genetic studies in maize |
title_fullStr |
Intraspecific variation of residual heterozygosity and its utility for quantitative genetic studies in maize |
title_full_unstemmed |
Intraspecific variation of residual heterozygosity and its utility for quantitative genetic studies in maize |
title_sort |
intraspecific variation of residual heterozygosity and its utility for quantitative genetic studies in maize |
publisher |
BMC |
series |
BMC Plant Biology |
issn |
1471-2229 |
publishDate |
2018-04-01 |
description |
Abstract Background Residual heterozygosity (RH) in advanced inbred lines of plants benefits quantitative trait locus (QTL) mapping studies. However, knowledge of factors affecting the genome-wide distribution of RH remains limited. Results A set of 2196 heterogeneous inbred family (HIF) maize lines derived from 12 recombinant inbred line (RIL) populations was genotyped using the Maize50K SNP chip. A total of 18,615 unique RH intervals were identified, ranging from 505 to 2095 intervals per population, with average maize genome coverage of 94.8%. Across all populations, there were 8.6 RH intervals per HIF line on average, ranging from 1.8 to 14 intervals; the average size of an RH interval was approximately 58.7 Mb, ranging from 7.2 to 74.1 Mb. A given RH region was present in an average of 5 different individuals within a population. Seven RH hotspots, where RH segments were enriched in the genome, were found to be subject to selection during population development. The RH patterns varied significantly across populations, presumably reflecting differences in the genetic background of each population, and 8 QTLs were found to affect heterozygosity levels in the RH hotspots. The potential use of this HIF library for the fine mapping of QTLs was assessed based on publicly available QTL information, achieving a ≤ 1 Mb resolution on average. Conclusion The examined library of HIF lines offers insight into the RH landscape and its intraspecific variation and provides a useful resource for the QTL cloning of important agronomic traits in maize. |
topic |
Residual heterozygosity RH hotspots Genetic factors HIF library for QTL fine mapping Zea may |
url |
http://link.springer.com/article/10.1186/s12870-018-1287-4 |
work_keys_str_mv |
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