An RNA Sequencing Transcriptome Analysis of Grasspea (Lathyrus sativus L.) and Development of SSR and KASP Markers
Grasspea (Lathyrus sativus L., 2n = 14) has great agronomic potential because of its ability to survive under extreme conditions, such as drought and flood. However, this legume is less investigated because of its sparse genomic resources and very slow breeding process. In this study, 570 million qu...
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Frontiers Media S.A.
2017-10-01
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Online Access: | http://journal.frontiersin.org/article/10.3389/fpls.2017.01873/full |
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doaj-87173f79341442448434420b326839f6 |
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record_format |
Article |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Xiaopeng Hao Tao Yang Rong Liu Jinguo Hu Yang Yao Marina Burlyaeva Yan Wang Guixing Ren Hongyan Zhang Dong Wang Jianwu Chang Xuxiao Zong |
spellingShingle |
Xiaopeng Hao Tao Yang Rong Liu Jinguo Hu Yang Yao Marina Burlyaeva Yan Wang Guixing Ren Hongyan Zhang Dong Wang Jianwu Chang Xuxiao Zong An RNA Sequencing Transcriptome Analysis of Grasspea (Lathyrus sativus L.) and Development of SSR and KASP Markers Frontiers in Plant Science RNA-Seq Lathyrus sativus grasspea SSR SNP KASP |
author_facet |
Xiaopeng Hao Tao Yang Rong Liu Jinguo Hu Yang Yao Marina Burlyaeva Yan Wang Guixing Ren Hongyan Zhang Dong Wang Jianwu Chang Xuxiao Zong |
author_sort |
Xiaopeng Hao |
title |
An RNA Sequencing Transcriptome Analysis of Grasspea (Lathyrus sativus L.) and Development of SSR and KASP Markers |
title_short |
An RNA Sequencing Transcriptome Analysis of Grasspea (Lathyrus sativus L.) and Development of SSR and KASP Markers |
title_full |
An RNA Sequencing Transcriptome Analysis of Grasspea (Lathyrus sativus L.) and Development of SSR and KASP Markers |
title_fullStr |
An RNA Sequencing Transcriptome Analysis of Grasspea (Lathyrus sativus L.) and Development of SSR and KASP Markers |
title_full_unstemmed |
An RNA Sequencing Transcriptome Analysis of Grasspea (Lathyrus sativus L.) and Development of SSR and KASP Markers |
title_sort |
rna sequencing transcriptome analysis of grasspea (lathyrus sativus l.) and development of ssr and kasp markers |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Plant Science |
issn |
1664-462X |
publishDate |
2017-10-01 |
description |
Grasspea (Lathyrus sativus L., 2n = 14) has great agronomic potential because of its ability to survive under extreme conditions, such as drought and flood. However, this legume is less investigated because of its sparse genomic resources and very slow breeding process. In this study, 570 million quality-filtered and trimmed cDNA sequence reads with total length of over 82 billion bp were obtained using the Illumina NextSeqTM 500 platform. Approximately two million contigs and 142,053 transcripts were assembled from our RNA-Seq data, which resulted in 27,431 unigenes with an average length of 1,250 bp and maximum length of 48,515 bp. The unigenes were of high-quality. For example, the stay-green (SGR) gene of grasspea was aligned with the SGR gene of pea with high similarity. Among these unigenes, 3,204 EST-SSR primers were designed, 284 of which were randomly chosen for validation. Of these validated unigenes, 87 (30.6%) EST-SSR primers produced polymorphic amplicons among 43 grasspea accessions selected from different geographical locations. Meanwhile, 146,406 SNPs were screened and 50 SNP loci were randomly chosen for the kompetitive allele-specific PCR (KASP) validation. Over 80% (42) SNP loci were successfully transformed to KASP markers. Comparison of the dendrograms according to the SSR and KASP markers showed that the different marker systems are partially consistent with the dendrogram constructed in our study. |
topic |
RNA-Seq Lathyrus sativus grasspea SSR SNP KASP |
url |
http://journal.frontiersin.org/article/10.3389/fpls.2017.01873/full |
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doaj-87173f79341442448434420b326839f62020-11-24T22:08:57ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2017-10-01810.3389/fpls.2017.01873294833An RNA Sequencing Transcriptome Analysis of Grasspea (Lathyrus sativus L.) and Development of SSR and KASP MarkersXiaopeng Hao0Tao Yang1Rong Liu2Jinguo Hu3Yang Yao4Marina Burlyaeva5Yan Wang6Guixing Ren7Hongyan Zhang8Dong Wang9Jianwu Chang10Xuxiao Zong11Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Taiyuan, ChinaNational Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaNational Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaUSDA-ARS Western Regional Plant Introduction Station, Pullman, WA, United StatesNational Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaDepartment of Leguminous Crops Genetic Resources, N.I.Vavilov All-Russian Institute of Plant Genetic Resources, St. Petersburg, RussiaKey Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Taiyuan, ChinaNational Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaNational Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaNational Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaKey Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture, Shanxi Key Laboratory of Genetic Resources and Genetic Improvement of Minor Crops, Institute of Crop Germplasm Resources, Shanxi Academy of Agricultural Sciences, Taiyuan, ChinaNational Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, ChinaGrasspea (Lathyrus sativus L., 2n = 14) has great agronomic potential because of its ability to survive under extreme conditions, such as drought and flood. However, this legume is less investigated because of its sparse genomic resources and very slow breeding process. In this study, 570 million quality-filtered and trimmed cDNA sequence reads with total length of over 82 billion bp were obtained using the Illumina NextSeqTM 500 platform. Approximately two million contigs and 142,053 transcripts were assembled from our RNA-Seq data, which resulted in 27,431 unigenes with an average length of 1,250 bp and maximum length of 48,515 bp. The unigenes were of high-quality. For example, the stay-green (SGR) gene of grasspea was aligned with the SGR gene of pea with high similarity. Among these unigenes, 3,204 EST-SSR primers were designed, 284 of which were randomly chosen for validation. Of these validated unigenes, 87 (30.6%) EST-SSR primers produced polymorphic amplicons among 43 grasspea accessions selected from different geographical locations. Meanwhile, 146,406 SNPs were screened and 50 SNP loci were randomly chosen for the kompetitive allele-specific PCR (KASP) validation. Over 80% (42) SNP loci were successfully transformed to KASP markers. Comparison of the dendrograms according to the SSR and KASP markers showed that the different marker systems are partially consistent with the dendrogram constructed in our study.http://journal.frontiersin.org/article/10.3389/fpls.2017.01873/fullRNA-SeqLathyrus sativusgrasspeaSSRSNPKASP |