Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species
Abstract Citrus species among the most important and widely consumed fruit in the world due to Vitamin C, essential oil glands, and flavonoids. Highly variable simple sequence repeats (SSR) markers are one of the most informative and versatile molecular markers used in perennial tree genetic researc...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Portfolio
2023-07-01
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| Series: | Scientific Reports |
| Online Access: | https://doi.org/10.1038/s41598-023-37024-0 |
| _version_ | 1797784640104169472 |
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| author | Jagveer Singh Ankush Sharma Vishal Sharma Popat Nanaso Gaikwad Gurupkar Singh Sidhu Gurwinder Kaur Nimarpreet Kaur Taveena Jindal Parveen Chhuneja H. S. Rattanpal |
| author_facet | Jagveer Singh Ankush Sharma Vishal Sharma Popat Nanaso Gaikwad Gurupkar Singh Sidhu Gurwinder Kaur Nimarpreet Kaur Taveena Jindal Parveen Chhuneja H. S. Rattanpal |
| author_sort | Jagveer Singh |
| collection | DOAJ |
| description | Abstract Citrus species among the most important and widely consumed fruit in the world due to Vitamin C, essential oil glands, and flavonoids. Highly variable simple sequence repeats (SSR) markers are one of the most informative and versatile molecular markers used in perennial tree genetic research. SSR survey of Citrus sinensis and Citrus maxima were identified perfect SSRs spanning nine chromosomes. Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. We designed and validated a class I SSRs in the C. sinensis and C. maxima genome through electronic polymerase chain reaction (ePCR) and found 83.89% in C. sinensis and 78.52% in C. maxima SSRs producing a single amplicon. Then, we selected extremely variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across seven draft genomes of citrus, which provided us a subset of 84.74% in C. sinensis and 77.53% in C. maxima highly polymorphic SSRs. Out of these, 129 primers were validated on 24 citrus genotypes through wet-lab experiment. We found 127 (98.45%) polymorphic HvSSRs on 24 genotypes. The utility of the developed HvSSRs was demonstrated by analysing genetic diversity of 181 citrus genotypes using 17 HvSSRs spanning nine citrus chromosomes and were divided into 11 main groups through 17 HvSSRs. These chromosome-specific SSRs will serve as a powerful genomic tool used for future QTL mapping, molecular breeding, investigation of population genetic diversity, comparative mapping, and evolutionary studies among citrus and other relative genera/species. |
| first_indexed | 2024-03-13T00:43:47Z |
| format | Article |
| id | doaj.art-a201c360eb5b41e58b1feb7e591eefc0 |
| institution | Directory Open Access Journal |
| issn | 2045-2322 |
| language | English |
| last_indexed | 2024-03-13T00:43:47Z |
| publishDate | 2023-07-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Scientific Reports |
| spelling | doaj.art-a201c360eb5b41e58b1feb7e591eefc02023-07-09T11:11:57ZengNature PortfolioScientific Reports2045-23222023-07-0113112010.1038/s41598-023-37024-0Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus speciesJagveer Singh0Ankush Sharma1Vishal Sharma2Popat Nanaso Gaikwad3Gurupkar Singh Sidhu4Gurwinder Kaur5Nimarpreet Kaur6Taveena Jindal7Parveen Chhuneja8H. S. Rattanpal9School of Agricultural Biotechnology, Punjab Agricultural UniversityPlant Genome Mapping Laboratory, University of GeorgiaNational Agri-Food Biotechnology InstituteSchool of Agricultural Biotechnology, Punjab Agricultural UniversitySchool of Agricultural Biotechnology, Punjab Agricultural UniversitySchool of Agricultural Biotechnology, Punjab Agricultural UniversitySchool of Agricultural Biotechnology, Punjab Agricultural UniversitySchool of Agricultural Biotechnology, Punjab Agricultural UniversitySchool of Agricultural Biotechnology, Punjab Agricultural UniversityDepartment of Fruit Science, Punjab Agricultural UniversityAbstract Citrus species among the most important and widely consumed fruit in the world due to Vitamin C, essential oil glands, and flavonoids. Highly variable simple sequence repeats (SSR) markers are one of the most informative and versatile molecular markers used in perennial tree genetic research. SSR survey of Citrus sinensis and Citrus maxima were identified perfect SSRs spanning nine chromosomes. Furthermore, we categorized all SSR motifs into three major classes based on their tract lengths. We designed and validated a class I SSRs in the C. sinensis and C. maxima genome through electronic polymerase chain reaction (ePCR) and found 83.89% in C. sinensis and 78.52% in C. maxima SSRs producing a single amplicon. Then, we selected extremely variable SSRs (> 40 nt) from the ePCR-verified class I SSRs and in silico validated across seven draft genomes of citrus, which provided us a subset of 84.74% in C. sinensis and 77.53% in C. maxima highly polymorphic SSRs. Out of these, 129 primers were validated on 24 citrus genotypes through wet-lab experiment. We found 127 (98.45%) polymorphic HvSSRs on 24 genotypes. The utility of the developed HvSSRs was demonstrated by analysing genetic diversity of 181 citrus genotypes using 17 HvSSRs spanning nine citrus chromosomes and were divided into 11 main groups through 17 HvSSRs. These chromosome-specific SSRs will serve as a powerful genomic tool used for future QTL mapping, molecular breeding, investigation of population genetic diversity, comparative mapping, and evolutionary studies among citrus and other relative genera/species.https://doi.org/10.1038/s41598-023-37024-0 |
| spellingShingle | Jagveer Singh Ankush Sharma Vishal Sharma Popat Nanaso Gaikwad Gurupkar Singh Sidhu Gurwinder Kaur Nimarpreet Kaur Taveena Jindal Parveen Chhuneja H. S. Rattanpal Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species Scientific Reports |
| title | Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species |
| title_full | Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species |
| title_fullStr | Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species |
| title_full_unstemmed | Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species |
| title_short | Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species |
| title_sort | comprehensive genome wide identification and transferability of chromosome specific highly variable microsatellite markers from citrus species |
| url | https://doi.org/10.1038/s41598-023-37024-0 |
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