High-density linkage map construction and mapping QTL for yield and yield components in autotetraploid alfalfa using RAD-seq
Abstract Background Alfalfa (Medicago sativa L.) is an important forage crop grown worldwide. Alfalfa is called the “queen of forage crops” due to its high forage yield and nutritional characteristics. The aim of this study was to undertake quantitative trait loci (QTL) mapping of yield and yield-re...
Main Authors: | , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
BMC
2019-04-01
|
Series: | BMC Plant Biology |
Subjects: | |
Online Access: | http://link.springer.com/article/10.1186/s12870-019-1770-6 |
id |
doaj-35c4f483bde54198b99c54fe23c19bdc |
---|---|
record_format |
Article |
spelling |
doaj-35c4f483bde54198b99c54fe23c19bdc2020-11-25T03:21:45ZengBMCBMC Plant Biology1471-22292019-04-0119111210.1186/s12870-019-1770-6High-density linkage map construction and mapping QTL for yield and yield components in autotetraploid alfalfa using RAD-seqFan Zhang0Junmei Kang1Ruicai Long2Long-Xi Yu3Zhen Wang4Zhongxiang Zhao5Tiejun Zhang6Qingchuan Yang7Institute of Animal Sciences, Chinese Academy of Agricultural SciencesInstitute of Animal Sciences, Chinese Academy of Agricultural SciencesInstitute of Animal Sciences, Chinese Academy of Agricultural SciencesPlant Germplasm Introduction and Testing Research, United States Department of Agriculture-Agricultural Research ServiceInstitute of Animal Sciences, Chinese Academy of Agricultural SciencesCangzhou Technical College and Cangzhou Academy of Agriculture and Forestry SciencesInstitute of Animal Sciences, Chinese Academy of Agricultural SciencesInstitute of Animal Sciences, Chinese Academy of Agricultural SciencesAbstract Background Alfalfa (Medicago sativa L.) is an important forage crop grown worldwide. Alfalfa is called the “queen of forage crops” due to its high forage yield and nutritional characteristics. The aim of this study was to undertake quantitative trait loci (QTL) mapping of yield and yield-related traits in an F1 population of two alfalfa varieties that differ in their yield and yield-related traits. Results We constructed a high-density linkage map using single nucleotide polymorphism (SNP) markers generated by restriction-site associated DNA sequencing (RAD-seq). The linkage map contains 4346 SNP and 119 simple sequence repeat (SSR) markers, with 32 linkage groups for each parent. The average marker distances were 3.00 and 1.32 cM, with coverages of 3455 cM and 4381 cM for paternal and maternal linkage maps, respectively. Using these maps and phenotypic data, we identified a total of 21 QTL for yield and yield components, including five for yield, five for plant height, five for branch number, and six for shoot diameter. Among them, six QTL were co-located for more than one trait. Five QTL explained more than 10% of the phenotypic variation. Conclusions We used RAD-seq to construct a linkage map for alfalfa that greatly enhanced marker density compared to previous studies. This high-density linkage map of alfalfa is a useful reference for mapping yield-related traits. Identified yield-related loci could be used to validate their usefulness in developing markers for maker-assisted selection in breeding populations to improve yield potential in alfalfa.http://link.springer.com/article/10.1186/s12870-019-1770-6AlfalfaGenetic linkage mapYieldQTLRAD-seq |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Fan Zhang Junmei Kang Ruicai Long Long-Xi Yu Zhen Wang Zhongxiang Zhao Tiejun Zhang Qingchuan Yang |
spellingShingle |
Fan Zhang Junmei Kang Ruicai Long Long-Xi Yu Zhen Wang Zhongxiang Zhao Tiejun Zhang Qingchuan Yang High-density linkage map construction and mapping QTL for yield and yield components in autotetraploid alfalfa using RAD-seq BMC Plant Biology Alfalfa Genetic linkage map Yield QTL RAD-seq |
author_facet |
Fan Zhang Junmei Kang Ruicai Long Long-Xi Yu Zhen Wang Zhongxiang Zhao Tiejun Zhang Qingchuan Yang |
author_sort |
Fan Zhang |
title |
High-density linkage map construction and mapping QTL for yield and yield components in autotetraploid alfalfa using RAD-seq |
title_short |
High-density linkage map construction and mapping QTL for yield and yield components in autotetraploid alfalfa using RAD-seq |
title_full |
High-density linkage map construction and mapping QTL for yield and yield components in autotetraploid alfalfa using RAD-seq |
title_fullStr |
High-density linkage map construction and mapping QTL for yield and yield components in autotetraploid alfalfa using RAD-seq |
title_full_unstemmed |
High-density linkage map construction and mapping QTL for yield and yield components in autotetraploid alfalfa using RAD-seq |
title_sort |
high-density linkage map construction and mapping qtl for yield and yield components in autotetraploid alfalfa using rad-seq |
publisher |
BMC |
series |
BMC Plant Biology |
issn |
1471-2229 |
publishDate |
2019-04-01 |
description |
Abstract Background Alfalfa (Medicago sativa L.) is an important forage crop grown worldwide. Alfalfa is called the “queen of forage crops” due to its high forage yield and nutritional characteristics. The aim of this study was to undertake quantitative trait loci (QTL) mapping of yield and yield-related traits in an F1 population of two alfalfa varieties that differ in their yield and yield-related traits. Results We constructed a high-density linkage map using single nucleotide polymorphism (SNP) markers generated by restriction-site associated DNA sequencing (RAD-seq). The linkage map contains 4346 SNP and 119 simple sequence repeat (SSR) markers, with 32 linkage groups for each parent. The average marker distances were 3.00 and 1.32 cM, with coverages of 3455 cM and 4381 cM for paternal and maternal linkage maps, respectively. Using these maps and phenotypic data, we identified a total of 21 QTL for yield and yield components, including five for yield, five for plant height, five for branch number, and six for shoot diameter. Among them, six QTL were co-located for more than one trait. Five QTL explained more than 10% of the phenotypic variation. Conclusions We used RAD-seq to construct a linkage map for alfalfa that greatly enhanced marker density compared to previous studies. This high-density linkage map of alfalfa is a useful reference for mapping yield-related traits. Identified yield-related loci could be used to validate their usefulness in developing markers for maker-assisted selection in breeding populations to improve yield potential in alfalfa. |
topic |
Alfalfa Genetic linkage map Yield QTL RAD-seq |
url |
http://link.springer.com/article/10.1186/s12870-019-1770-6 |
work_keys_str_mv |
AT fanzhang highdensitylinkagemapconstructionandmappingqtlforyieldandyieldcomponentsinautotetraploidalfalfausingradseq AT junmeikang highdensitylinkagemapconstructionandmappingqtlforyieldandyieldcomponentsinautotetraploidalfalfausingradseq AT ruicailong highdensitylinkagemapconstructionandmappingqtlforyieldandyieldcomponentsinautotetraploidalfalfausingradseq AT longxiyu highdensitylinkagemapconstructionandmappingqtlforyieldandyieldcomponentsinautotetraploidalfalfausingradseq AT zhenwang highdensitylinkagemapconstructionandmappingqtlforyieldandyieldcomponentsinautotetraploidalfalfausingradseq AT zhongxiangzhao highdensitylinkagemapconstructionandmappingqtlforyieldandyieldcomponentsinautotetraploidalfalfausingradseq AT tiejunzhang highdensitylinkagemapconstructionandmappingqtlforyieldandyieldcomponentsinautotetraploidalfalfausingradseq AT qingchuanyang highdensitylinkagemapconstructionandmappingqtlforyieldandyieldcomponentsinautotetraploidalfalfausingradseq |
_version_ |
1724612691265323008 |