Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom<sup>®</sup><i>CicerSNP</i> Array in Chickpea
Globally, chickpea production is severely affected by salinity stress. Understanding the genetic basis for salinity tolerance is important to develop salinity tolerant chickpeas. A recombinant inbred line (RIL) population developed using parental lines ICCV 10 (salt-tolerant) and DCP 92-3 (salt-sens...
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MDPI AG
2020-07-01
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| Series: | International Journal of Molecular Sciences |
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| Online Access: | https://www.mdpi.com/1422-0067/21/14/5058 |
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| author | Khela Ram Soren Praveen Madugula Neeraj Kumar Rutwik Barmukh Meenu Singh Sengar Chellapilla Bharadwaj Parbodh Chander Sharma Sarvjeet Singh Aditi Bhandari Jogendra Singh Satish Kumar Sanwal Madan Pal Sneha Priya P.R. Anita Mann Someswar Rao Sagurthi Shanmugavadivel PS Kadambot H.M. Siddique Narendra Pratap Singh Manish Roorkiwal Rajeev K Varshney |
| author_facet | Khela Ram Soren Praveen Madugula Neeraj Kumar Rutwik Barmukh Meenu Singh Sengar Chellapilla Bharadwaj Parbodh Chander Sharma Sarvjeet Singh Aditi Bhandari Jogendra Singh Satish Kumar Sanwal Madan Pal Sneha Priya P.R. Anita Mann Someswar Rao Sagurthi Shanmugavadivel PS Kadambot H.M. Siddique Narendra Pratap Singh Manish Roorkiwal Rajeev K Varshney |
| author_sort | Khela Ram Soren |
| collection | DOAJ |
| description | Globally, chickpea production is severely affected by salinity stress. Understanding the genetic basis for salinity tolerance is important to develop salinity tolerant chickpeas. A recombinant inbred line (RIL) population developed using parental lines ICCV 10 (salt-tolerant) and DCP 92-3 (salt-sensitive) was screened under field conditions to collect information on agronomy, yield components, and stress tolerance indices. Genotyping data generated using Axiom<sup>®</sup><i>CicerSNP</i> array was used to construct a linkage map comprising 1856 SNP markers spanning a distance of 1106.3 cM across eight chickpea chromosomes. Extensive analysis of the phenotyping and genotyping data identified 28 quantitative trait loci (QTLs) explaining up to 28.40% of the phenotypic variance in the population. We identified QTL clusters on CaLG03 and CaLG06, each harboring major QTLs for yield and yield component traits under salinity stress. The main-effect QTLs identified in these two clusters were associated with key genes such as calcium-dependent protein kinases, histidine kinases, cation proton antiporter, and WRKY and MYB transcription factors, which are known to impart salinity stress tolerance in crop plants. Molecular markers/genes associated with these major QTLs, after validation, will be useful to undertake marker-assisted breeding for developing better varieties with salinity tolerance. |
| first_indexed | 2024-03-10T18:23:37Z |
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| institution | Directory Open Access Journal |
| issn | 1661-6596 1422-0067 |
| language | English |
| last_indexed | 2024-03-10T18:23:37Z |
| publishDate | 2020-07-01 |
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| series | International Journal of Molecular Sciences |
| spelling | doaj.art-49b74bafa65448629adcfdd9d1ea4f9c2023-11-20T07:09:56ZengMDPI AGInternational Journal of Molecular Sciences1661-65961422-00672020-07-012114505810.3390/ijms21145058Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom<sup>®</sup><i>CicerSNP</i> Array in ChickpeaKhela Ram Soren0Praveen Madugula1Neeraj Kumar2Rutwik Barmukh3Meenu Singh Sengar4Chellapilla Bharadwaj5Parbodh Chander Sharma6Sarvjeet Singh7Aditi Bhandari8Jogendra Singh9Satish Kumar Sanwal10Madan Pal11Sneha Priya P.R.12Anita Mann13Someswar Rao Sagurthi14Shanmugavadivel PS15Kadambot H.M. Siddique16Narendra Pratap Singh17Manish Roorkiwal18Rajeev K Varshney19ICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur UP 208024, IndiaCenter of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, IndiaDivision of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), Delhi 110012, IndiaCenter of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, IndiaICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur UP 208024, IndiaDivision of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), Delhi 110012, IndiaICAR-Central Soil Salinity Research Institute (ICAR-CSSRI), Karnal 132001, IndiaDepartment of Plant Breeding & Genetics, Punjab Agricultural University, Ludhiana 141004, IndiaCenter of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, IndiaICAR-Central Soil Salinity Research Institute (ICAR-CSSRI), Karnal 132001, IndiaICAR-Central Soil Salinity Research Institute (ICAR-CSSRI), Karnal 132001, IndiaDivision of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), Delhi 110012, IndiaDivision of Genetics, ICAR-Indian Agricultural Research Institute (ICAR-IARI), Delhi 110012, IndiaICAR-Central Soil Salinity Research Institute (ICAR-CSSRI), Karnal 132001, IndiaDepartment of Genetics, Osmania University, Hyderabad 500007, IndiaICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur UP 208024, IndiaThe UWA Institute of Agriculture, The University of Western Australia, Perth WA 6009, AustraliaICAR-Indian Institute of Pulses Research (ICAR-IIPR), Kanpur UP 208024, IndiaCenter of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, IndiaCenter of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad 502324, IndiaGlobally, chickpea production is severely affected by salinity stress. Understanding the genetic basis for salinity tolerance is important to develop salinity tolerant chickpeas. A recombinant inbred line (RIL) population developed using parental lines ICCV 10 (salt-tolerant) and DCP 92-3 (salt-sensitive) was screened under field conditions to collect information on agronomy, yield components, and stress tolerance indices. Genotyping data generated using Axiom<sup>®</sup><i>CicerSNP</i> array was used to construct a linkage map comprising 1856 SNP markers spanning a distance of 1106.3 cM across eight chickpea chromosomes. Extensive analysis of the phenotyping and genotyping data identified 28 quantitative trait loci (QTLs) explaining up to 28.40% of the phenotypic variance in the population. We identified QTL clusters on CaLG03 and CaLG06, each harboring major QTLs for yield and yield component traits under salinity stress. The main-effect QTLs identified in these two clusters were associated with key genes such as calcium-dependent protein kinases, histidine kinases, cation proton antiporter, and WRKY and MYB transcription factors, which are known to impart salinity stress tolerance in crop plants. Molecular markers/genes associated with these major QTLs, after validation, will be useful to undertake marker-assisted breeding for developing better varieties with salinity tolerance.https://www.mdpi.com/1422-0067/21/14/5058chickpeasalinityquantitative trait locistress susceptibility index (SSI)stress tolerance index (STI)candidate genes |
| spellingShingle | Khela Ram Soren Praveen Madugula Neeraj Kumar Rutwik Barmukh Meenu Singh Sengar Chellapilla Bharadwaj Parbodh Chander Sharma Sarvjeet Singh Aditi Bhandari Jogendra Singh Satish Kumar Sanwal Madan Pal Sneha Priya P.R. Anita Mann Someswar Rao Sagurthi Shanmugavadivel PS Kadambot H.M. Siddique Narendra Pratap Singh Manish Roorkiwal Rajeev K Varshney Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom<sup>®</sup><i>CicerSNP</i> Array in Chickpea International Journal of Molecular Sciences chickpea salinity quantitative trait loci stress susceptibility index (SSI) stress tolerance index (STI) candidate genes |
| title | Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom<sup>®</sup><i>CicerSNP</i> Array in Chickpea |
| title_full | Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom<sup>®</sup><i>CicerSNP</i> Array in Chickpea |
| title_fullStr | Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom<sup>®</sup><i>CicerSNP</i> Array in Chickpea |
| title_full_unstemmed | Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom<sup>®</sup><i>CicerSNP</i> Array in Chickpea |
| title_short | Genetic Dissection and Identification of Candidate Genes for Salinity Tolerance Using Axiom<sup>®</sup><i>CicerSNP</i> Array in Chickpea |
| title_sort | genetic dissection and identification of candidate genes for salinity tolerance using axiom sup r sup i cicersnp i array in chickpea |
| topic | chickpea salinity quantitative trait loci stress susceptibility index (SSI) stress tolerance index (STI) candidate genes |
| url | https://www.mdpi.com/1422-0067/21/14/5058 |
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