Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice

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

doi:10.3390/genes14040902

Mapping the Genomic Regions Controlling Germination Rate and Early Seedling Growth Parameters in Rice

Genes (Basel). 2023 Apr 12;14(4):902. doi: 10.3390/genes14040902.

Authors

Shakti Prakash Mohanty¹, Deepak Kumar Nayak¹, Priyadarsini Sanghamitra¹, Saumya Ranjan Barik¹, Elssa Pandit², Abhisarika Behera¹, Dipti Ranjan Pani³, Shibani Mohapatra^{1

4}, Reshmi Raj K R¹, Kartik Chandra Pradhan⁵, Chita Ranjan Sahoo⁶, Mihir Ranjan Mohanty⁷, Chinmayee Behera⁸, Alok Kumar Panda⁴, Binod Kumar Jena⁹, Lambodar Behera¹, Prasanta K Dash¹⁰, Sharat Kumar Pradhan^{1

11}

Affiliations

¹ ICAR-National Rice Research Institute, Cuttack 753006, India.
² Department of Biosciences and Biotechnology, Fakir Mohan University, Balasore 756020, India.
³ ICAR-National Bureau of Plant Genetic Resources, Base Center, Cuttack 753006, India.
⁴ Environmental Science Laboratory, School of Applied Sciences, KIIT Deemed to be University, Bhubaneswar 751024, India.
⁵ College of Agriculture, Odisha University of Agriculture & Technology, Bhubaneswar 751003, India.
⁶ Directorate of Research, Odisha University of Agriculture & Technology, Bhubaneswar 751003, India.
⁷ Regional Research and Technology Transfer Station (RRTTS), Odisha University of Agriculture & Technology, Jeypore 764001, India.
⁸ Department of Genetics and Plant Breeding, Institute of Agricultural Sciences, SOA University, Bhubaneswar 753001, India.
⁹ Krishi Vigyan Kendra, Odisha University of Agriculture & Technology, Rayagada 765022, India.
¹⁰ ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi 110012, India.
¹¹ Indian Council of Agricultural Research, Krishi Bhavan, New Delhi 110001, India.

Abstract

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 qAGR4.1, qAGR6.1, qAGR6.2 and qAGR8.1 for absolute growth rate (AGR); qRSG6.1, qRSG7.1 and qRSG8.1 for relative shoot growth (RSG); and qRGR11.1 for relative growth rate (RGR), as analyzed by GLM and MLM. The reported QTL for germination rate (GR), qGR4-1, 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.

Keywords: absolute growth rate; association mapping; germination rate; indica rice; relative growth rate; relative shoot growth.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Genomics
Germination / genetics
Oryza* / genetics
Quantitative Trait Loci / genetics
Seedlings* / genetics

Grants and funding

No funding was received from any external funding sources for this research. The institute’s internal funding (Project 1.6) was used for completion of the study.