Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice
Seed vigor is the key performance parameter of good quality seed. A panel was prepared by shortlisting genotypes from all the phenotypic groups representing seedling growth parameters from a total of 278 germplasm lines. A wide variation was observed for the traits in the population. The panel was c...
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MDPI AG
2023-04-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/14/4/902 |
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| author | Shakti Prakash Mohanty Deepak Kumar Nayak Priyadarsini Sanghamitra Saumya Ranjan Barik Elssa Pandit Abhisarika Behera Dipti Ranjan Pani Shibani Mohapatra Reshmi Raj K. R. Kartik Chandra Pradhan Chita Ranjan Sahoo Mihir Ranjan Mohanty Chinmayee Behera Alok Kumar Panda Binod Kumar Jena Lambodar Behera Prasanta K. Dash Sharat Kumar Pradhan |
| author_facet | Shakti Prakash Mohanty Deepak Kumar Nayak Priyadarsini Sanghamitra Saumya Ranjan Barik Elssa Pandit Abhisarika Behera Dipti Ranjan Pani Shibani Mohapatra Reshmi Raj K. R. Kartik Chandra Pradhan Chita Ranjan Sahoo Mihir Ranjan Mohanty Chinmayee Behera Alok Kumar Panda Binod Kumar Jena Lambodar Behera Prasanta K. Dash Sharat Kumar Pradhan |
| author_sort | Shakti Prakash Mohanty |
| collection | DOAJ |
| description | Seed vigor is the key performance parameter of good quality seed. A panel was prepared by shortlisting genotypes from all the phenotypic groups representing seedling growth parameters from a total of 278 germplasm lines. A wide variation was observed for the traits in the population. The panel was classified into four genetic structure groups. Fixation indices indicated the existence of linkage disequilibrium in the population. A moderate to high level of diversity parameters was assessed using 143 SSR markers. Principal component, coordinate, neighbor-joining tree and cluster analyses showed subpopulations with a fair degree of correspondence with the growth parameters. Marker–trait association analysis detected eight novel QTLs, namely <i>qAGR4.1</i>, <i>qAGR6.1</i>, <i>qAGR6.2</i> and <i>qAGR8.1</i> for absolute growth rate (AGR); <i>qRSG6.1</i>, <i>qRSG7.1</i> and <i>qRSG8.1</i> for relative shoot growth (RSG); and <i>qRGR11.1</i> for relative growth rate (RGR), as analyzed by GLM and MLM. The reported QTL for germination rate (GR), <i>qGR4-1</i>, was validated in this population. Additionally, QTLs present on chromosome 6 controlling RSG and AGR at 221 cM and RSG and AGR on chromosome 8 at 27 cM were detected as genetic hotspots for the parameters. The QTLs identified in the study will be useful for improvement of the seed vigor trait in rice. |
| first_indexed | 2024-03-11T04:59:10Z |
| format | Article |
| id | doaj.art-891f259b148d4681abafc74ec06b463a |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-11T04:59:10Z |
| publishDate | 2023-04-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-891f259b148d4681abafc74ec06b463a2023-11-17T19:24:11ZengMDPI AGGenes2073-44252023-04-0114490210.3390/genes14040902Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in RiceShakti Prakash Mohanty0Deepak Kumar Nayak1Priyadarsini Sanghamitra2Saumya Ranjan Barik3Elssa Pandit4Abhisarika Behera5Dipti Ranjan Pani6Shibani Mohapatra7Reshmi Raj K. R.8Kartik Chandra Pradhan9Chita Ranjan Sahoo10Mihir Ranjan Mohanty11Chinmayee Behera12Alok Kumar Panda13Binod Kumar Jena14Lambodar Behera15Prasanta K. Dash16Sharat Kumar Pradhan17ICAR-National Rice Research Institute, Cuttack 753006, IndiaICAR-National Rice Research Institute, Cuttack 753006, IndiaICAR-National Rice Research Institute, Cuttack 753006, IndiaICAR-National Rice Research Institute, Cuttack 753006, IndiaDepartment of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756020, IndiaICAR-National Rice Research Institute, Cuttack 753006, IndiaICAR-National Bureau of Plant Genetic Resources, Base Center, Cuttack 753006, IndiaICAR-National Rice Research Institute, Cuttack 753006, IndiaICAR-National Rice Research Institute, Cuttack 753006, IndiaCollege of Agriculture, Odisha University of Agriculture & Technology, Bhubaneswar 751003, IndiaDirectorate of Research, Odisha University of Agriculture & Technology, Bhubaneswar 751003, IndiaRegional Research and Technology Transfer Station (RRTTS), Odisha University of Agriculture & Technology, Jeypore 764001, IndiaDepartment of Genetics and Plant Breeding, Institute of Agricultural Sciences, SOA University, Bhubaneswar 753001, IndiaEnvironmental Science Laboratory, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar 751024, IndiaKrishi Vigyan Kendra, Odisha University of Agriculture & Technology, Rayagada 765022, IndiaICAR-National Rice Research Institute, Cuttack 753006, IndiaICAR-National Institute for Plant Biotechnology, Pusa, New Delhi 110012, IndiaICAR-National Rice Research Institute, Cuttack 753006, IndiaSeed vigor is the key performance parameter of good quality seed. A panel was prepared by shortlisting genotypes from all the phenotypic groups representing seedling growth parameters from a total of 278 germplasm lines. A wide variation was observed for the traits in the population. The panel was classified into four genetic structure groups. Fixation indices indicated the existence of linkage disequilibrium in the population. A moderate to high level of diversity parameters was assessed using 143 SSR markers. Principal component, coordinate, neighbor-joining tree and cluster analyses showed subpopulations with a fair degree of correspondence with the growth parameters. Marker–trait association analysis detected eight novel QTLs, namely <i>qAGR4.1</i>, <i>qAGR6.1</i>, <i>qAGR6.2</i> and <i>qAGR8.1</i> for absolute growth rate (AGR); <i>qRSG6.1</i>, <i>qRSG7.1</i> and <i>qRSG8.1</i> for relative shoot growth (RSG); and <i>qRGR11.1</i> for relative growth rate (RGR), as analyzed by GLM and MLM. The reported QTL for germination rate (GR), <i>qGR4-1</i>, was validated in this population. Additionally, QTLs present on chromosome 6 controlling RSG and AGR at 221 cM and RSG and AGR on chromosome 8 at 27 cM were detected as genetic hotspots for the parameters. The QTLs identified in the study will be useful for improvement of the seed vigor trait in rice.https://www.mdpi.com/2073-4425/14/4/902absolute growth rateassociation mappinggermination rate<i>indica</i> ricerelative growth raterelative shoot growth |
| spellingShingle | Shakti Prakash Mohanty Deepak Kumar Nayak Priyadarsini Sanghamitra Saumya Ranjan Barik Elssa Pandit Abhisarika Behera Dipti Ranjan Pani Shibani Mohapatra Reshmi Raj K. R. Kartik Chandra Pradhan Chita Ranjan Sahoo Mihir Ranjan Mohanty Chinmayee Behera Alok Kumar Panda Binod Kumar Jena Lambodar Behera Prasanta K. Dash Sharat Kumar Pradhan Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice Genes absolute growth rate association mapping germination rate <i>indica</i> rice relative growth rate relative shoot growth |
| title | Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice |
| title_full | Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice |
| title_fullStr | Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice |
| title_full_unstemmed | Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice |
| title_short | Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice |
| title_sort | mapping the genomic regions controlling germination rate and early seedling growth parameters in rice |
| topic | absolute growth rate association mapping germination rate <i>indica</i> rice relative growth rate relative shoot growth |
| url | https://www.mdpi.com/2073-4425/14/4/902 |
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