Genome-Wide Discovery of Microsatellite Markers from Diploid Progenitor Species, Arachis duranensis and A. ipaensis, and Their Application in Cultivated Peanut (A. hypogaea)
Despite several efforts in the last decade toward development of simple sequence repeat (SSR) markers in peanut, there is still a need for more markers for conducting different genetic and breeding studies. With the effort of the International Peanut Genome Initiative, the availability of reference...
| Main Authors: | , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Frontiers Media S.A.
2017-07-01
|
| Series: | Frontiers in Plant Science |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/article/10.3389/fpls.2017.01209/full |
| _version_ | 1811318780655042560 |
|---|---|
| author | Chuanzhi Zhao Jingjing Qiu Jingjing Qiu Gaurav Agarwal Gaurav Agarwal Jiangshan Wang Xuezhen Ren Han Xia Baozhu Guo Changle Ma Shubo Wan David J. Bertioli Rajeev K. Varshney Manish K. Pandey Xingjun Wang Xingjun Wang |
| author_facet | Chuanzhi Zhao Jingjing Qiu Jingjing Qiu Gaurav Agarwal Gaurav Agarwal Jiangshan Wang Xuezhen Ren Han Xia Baozhu Guo Changle Ma Shubo Wan David J. Bertioli Rajeev K. Varshney Manish K. Pandey Xingjun Wang Xingjun Wang |
| author_sort | Chuanzhi Zhao |
| collection | DOAJ |
| description | Despite several efforts in the last decade toward development of simple sequence repeat (SSR) markers in peanut, there is still a need for more markers for conducting different genetic and breeding studies. With the effort of the International Peanut Genome Initiative, the availability of reference genome for both the diploid progenitors of cultivated peanut allowed us to identify 135,529 and 199,957 SSRs from the A (Arachis duranensis) and B genomes (Arachis ipaensis), respectively. Genome sequence analysis showed uneven distribution of the SSR motifs across genomes with variation in parameters such as SSR type, repeat number, and SSR length. Using the flanking sequences of identified SSRs, primers were designed for 51,354 and 60,893 SSRs with densities of 49 and 45 SSRs per Mb in A. duranensis and A. ipaensis, respectively. In silico PCR analysis of these SSR markers showed high transferability between wild and cultivated Arachis species. Two physical maps were developed for the A genome and the B genome using these SSR markers, and two reported disease resistance quantitative trait loci (QTLs), qF2TSWV5 for tomato spotted wilt virus (TSWV) and qF2LS6 for leaf spot (LS), were mapped in the 8.135 Mb region of chromosome A04 of A. duranensis. From this genomic region, 719 novel SSR markers were developed, which provide the possibility for fine mapping of these QTLs. In addition, this region also harbors 652 genes and 49 of these are defense related genes, including two NB-ARC genes, three LRR receptor-like genes and three WRKY transcription factors. These disease resistance related genes could contribute to resistance to viral (such as TSWV) and fungal (such as LS) diseases in peanut. In summary, this study not only provides a large number of molecular markers for potential use in peanut genetic map development and QTL mapping but also for map-based gene cloning and molecular breeding. |
| first_indexed | 2024-04-13T12:31:29Z |
| format | Article |
| id | doaj.art-276b2d4fd3a8473684076f6fa083e5f0 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-13T12:31:29Z |
| publishDate | 2017-07-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-276b2d4fd3a8473684076f6fa083e5f02022-12-22T02:46:48ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2017-07-01810.3389/fpls.2017.01209278058Genome-Wide Discovery of Microsatellite Markers from Diploid Progenitor Species, Arachis duranensis and A. ipaensis, and Their Application in Cultivated Peanut (A. hypogaea)Chuanzhi Zhao0Jingjing Qiu1Jingjing Qiu2Gaurav Agarwal3Gaurav Agarwal4Jiangshan Wang5Xuezhen Ren6Han Xia7Baozhu Guo8Changle Ma9Shubo Wan10David J. Bertioli11Rajeev K. Varshney12Manish K. Pandey13Xingjun Wang14Xingjun Wang15Biotechnology Research Center, Shandong Academy of Agricultural Sciences and Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, ChinaBiotechnology Research Center, Shandong Academy of Agricultural Sciences and Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, ChinaCollege of Life Sciences, Shandong Normal UniversityJinan, ChinaUnited States Department of Agriculture – Agricultural Research Service, Crop Protection and Management Research Unit, TiftonGA, United StatesInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, IndiaBiotechnology Research Center, Shandong Academy of Agricultural Sciences and Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, ChinaBiotechnology Research Center, Shandong Academy of Agricultural Sciences and Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, ChinaBiotechnology Research Center, Shandong Academy of Agricultural Sciences and Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, ChinaUnited States Department of Agriculture – Agricultural Research Service, Crop Protection and Management Research Unit, TiftonGA, United StatesCollege of Life Sciences, Shandong Normal UniversityJinan, ChinaBiotechnology Research Center, Shandong Academy of Agricultural Sciences and Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, ChinaCenter for Applied Genetic Technologies, University of Georgia, AthensGA, United StatesInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, IndiaInternational Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Hyderabad, IndiaBiotechnology Research Center, Shandong Academy of Agricultural Sciences and Shandong Provincial Key Laboratory of Crop Genetic Improvement, Ecology and PhysiologyJinan, ChinaCollege of Life Sciences, Shandong Normal UniversityJinan, ChinaDespite several efforts in the last decade toward development of simple sequence repeat (SSR) markers in peanut, there is still a need for more markers for conducting different genetic and breeding studies. With the effort of the International Peanut Genome Initiative, the availability of reference genome for both the diploid progenitors of cultivated peanut allowed us to identify 135,529 and 199,957 SSRs from the A (Arachis duranensis) and B genomes (Arachis ipaensis), respectively. Genome sequence analysis showed uneven distribution of the SSR motifs across genomes with variation in parameters such as SSR type, repeat number, and SSR length. Using the flanking sequences of identified SSRs, primers were designed for 51,354 and 60,893 SSRs with densities of 49 and 45 SSRs per Mb in A. duranensis and A. ipaensis, respectively. In silico PCR analysis of these SSR markers showed high transferability between wild and cultivated Arachis species. Two physical maps were developed for the A genome and the B genome using these SSR markers, and two reported disease resistance quantitative trait loci (QTLs), qF2TSWV5 for tomato spotted wilt virus (TSWV) and qF2LS6 for leaf spot (LS), were mapped in the 8.135 Mb region of chromosome A04 of A. duranensis. From this genomic region, 719 novel SSR markers were developed, which provide the possibility for fine mapping of these QTLs. In addition, this region also harbors 652 genes and 49 of these are defense related genes, including two NB-ARC genes, three LRR receptor-like genes and three WRKY transcription factors. These disease resistance related genes could contribute to resistance to viral (such as TSWV) and fungal (such as LS) diseases in peanut. In summary, this study not only provides a large number of molecular markers for potential use in peanut genetic map development and QTL mapping but also for map-based gene cloning and molecular breeding.http://journal.frontiersin.org/article/10.3389/fpls.2017.01209/fullwild peanutgenome sequencemicrosatellitesmolecular markersquantitative trait locus (QTL) |
| spellingShingle | Chuanzhi Zhao Jingjing Qiu Jingjing Qiu Gaurav Agarwal Gaurav Agarwal Jiangshan Wang Xuezhen Ren Han Xia Baozhu Guo Changle Ma Shubo Wan David J. Bertioli Rajeev K. Varshney Manish K. Pandey Xingjun Wang Xingjun Wang Genome-Wide Discovery of Microsatellite Markers from Diploid Progenitor Species, Arachis duranensis and A. ipaensis, and Their Application in Cultivated Peanut (A. hypogaea) Frontiers in Plant Science wild peanut genome sequence microsatellites molecular markers quantitative trait locus (QTL) |
| title | Genome-Wide Discovery of Microsatellite Markers from Diploid Progenitor Species, Arachis duranensis and A. ipaensis, and Their Application in Cultivated Peanut (A. hypogaea) |
| title_full | Genome-Wide Discovery of Microsatellite Markers from Diploid Progenitor Species, Arachis duranensis and A. ipaensis, and Their Application in Cultivated Peanut (A. hypogaea) |
| title_fullStr | Genome-Wide Discovery of Microsatellite Markers from Diploid Progenitor Species, Arachis duranensis and A. ipaensis, and Their Application in Cultivated Peanut (A. hypogaea) |
| title_full_unstemmed | Genome-Wide Discovery of Microsatellite Markers from Diploid Progenitor Species, Arachis duranensis and A. ipaensis, and Their Application in Cultivated Peanut (A. hypogaea) |
| title_short | Genome-Wide Discovery of Microsatellite Markers from Diploid Progenitor Species, Arachis duranensis and A. ipaensis, and Their Application in Cultivated Peanut (A. hypogaea) |
| title_sort | genome wide discovery of microsatellite markers from diploid progenitor species arachis duranensis and a ipaensis and their application in cultivated peanut a hypogaea |
| topic | wild peanut genome sequence microsatellites molecular markers quantitative trait locus (QTL) |
| url | http://journal.frontiersin.org/article/10.3389/fpls.2017.01209/full |
| work_keys_str_mv | AT chuanzhizhao genomewidediscoveryofmicrosatellitemarkersfromdiploidprogenitorspeciesarachisduranensisandaipaensisandtheirapplicationincultivatedpeanutahypogaea AT jingjingqiu genomewidediscoveryofmicrosatellitemarkersfromdiploidprogenitorspeciesarachisduranensisandaipaensisandtheirapplicationincultivatedpeanutahypogaea AT jingjingqiu genomewidediscoveryofmicrosatellitemarkersfromdiploidprogenitorspeciesarachisduranensisandaipaensisandtheirapplicationincultivatedpeanutahypogaea AT gauravagarwal genomewidediscoveryofmicrosatellitemarkersfromdiploidprogenitorspeciesarachisduranensisandaipaensisandtheirapplicationincultivatedpeanutahypogaea AT gauravagarwal genomewidediscoveryofmicrosatellitemarkersfromdiploidprogenitorspeciesarachisduranensisandaipaensisandtheirapplicationincultivatedpeanutahypogaea AT jiangshanwang genomewidediscoveryofmicrosatellitemarkersfromdiploidprogenitorspeciesarachisduranensisandaipaensisandtheirapplicationincultivatedpeanutahypogaea AT xuezhenren genomewidediscoveryofmicrosatellitemarkersfromdiploidprogenitorspeciesarachisduranensisandaipaensisandtheirapplicationincultivatedpeanutahypogaea AT hanxia genomewidediscoveryofmicrosatellitemarkersfromdiploidprogenitorspeciesarachisduranensisandaipaensisandtheirapplicationincultivatedpeanutahypogaea AT baozhuguo genomewidediscoveryofmicrosatellitemarkersfromdiploidprogenitorspeciesarachisduranensisandaipaensisandtheirapplicationincultivatedpeanutahypogaea AT changlema genomewidediscoveryofmicrosatellitemarkersfromdiploidprogenitorspeciesarachisduranensisandaipaensisandtheirapplicationincultivatedpeanutahypogaea AT shubowan genomewidediscoveryofmicrosatellitemarkersfromdiploidprogenitorspeciesarachisduranensisandaipaensisandtheirapplicationincultivatedpeanutahypogaea AT davidjbertioli genomewidediscoveryofmicrosatellitemarkersfromdiploidprogenitorspeciesarachisduranensisandaipaensisandtheirapplicationincultivatedpeanutahypogaea AT rajeevkvarshney genomewidediscoveryofmicrosatellitemarkersfromdiploidprogenitorspeciesarachisduranensisandaipaensisandtheirapplicationincultivatedpeanutahypogaea AT manishkpandey genomewidediscoveryofmicrosatellitemarkersfromdiploidprogenitorspeciesarachisduranensisandaipaensisandtheirapplicationincultivatedpeanutahypogaea AT xingjunwang genomewidediscoveryofmicrosatellitemarkersfromdiploidprogenitorspeciesarachisduranensisandaipaensisandtheirapplicationincultivatedpeanutahypogaea AT xingjunwang genomewidediscoveryofmicrosatellitemarkersfromdiploidprogenitorspeciesarachisduranensisandaipaensisandtheirapplicationincultivatedpeanutahypogaea |