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Genome-Wide Consistent Molecular Markers Associated with Phenology, Plant Production and Root Traits in Diverse Rice (Oryza sativa L.) Accessions under Drought in Rainfed Target Populations of the Environment


Affiliations
1 Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, India
2 Agricultural Research Station, Tamil Nadu Agricultural University, Paramakudi 623 707, India
 

Drought is the most predominant constraint to rainfed rice production. Identifying molecular markers associated with drought resistance traits and deploying them in marker-assisted breeding will hasten the development of drought-resilient cultivars. A total of 49 diverse rice accessions, including traditional landraces, were evaluated for plant production and ischolar_main traits under natural drought stress in rainfed target populations of environment (TPE) in six successive field trials from 2010 to 2015. Significant variation for phenology, plant production and ischolar_main traits under drought was noticed among the accessions. Genotyping of the rice accessions using 599 polymorphic simple sequence repeat (SSR) markers showed considerable variation among them. STRUCTURE analysis grouped the 49 accessions into three subpopulations. Similarly, three clusters were observed in Neighbor joining tree created using Nei’s genetic distance. The subpopulation POP1 consisted mostly of landraces, while subpopulation POP3 consisted of advanced breeding lines and POP2 accessions from all groups. Genome-wide association mapping detected 61 markers consistently associated in two or more trials with phenology, plant production and ischolar_main traits under drought in TPE. The markers PSM52 (Chr 3), RM6909 (Chr 4), RM242 (Chr9) and RM444 (Chr 9) were consistently associated with grain yield and ischolar_main traits under drought. The markers PSM127 (Chr 3) and PSM133 (Chr 4) were consistently associated with yield, plant height and spikelet fertility. These markers with pleiotropic and consistent associations with yield and secondary traits under drought in TPE may be robust candidates for marker-assisted breeding for drought resistance in rice.

Keywords

Association Mapping, Drought Resistance, Molecular Markers, Rice.
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  • Genome-Wide Consistent Molecular Markers Associated with Phenology, Plant Production and Root Traits in Diverse Rice (Oryza sativa L.) Accessions under Drought in Rainfed Target Populations of the Environment

Abstract Views: 419  |  PDF Views: 141

Authors

Vivek Deshmukh
Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, India
Sumeet Prabakar Mankar
Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, India
C. Muthukumar
Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, India
P. Divahar
Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, India
A. Bharathi
Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, India
Helen Baby Thomas
Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, India
Ashish Rajurkar
Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, India
Reena Sellamuthu
Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, India
R. Poornima
Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, India
S. Senthivel
Agricultural Research Station, Tamil Nadu Agricultural University, Paramakudi 623 707, India
R. Chandra Babu
Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, India

Abstract


Drought is the most predominant constraint to rainfed rice production. Identifying molecular markers associated with drought resistance traits and deploying them in marker-assisted breeding will hasten the development of drought-resilient cultivars. A total of 49 diverse rice accessions, including traditional landraces, were evaluated for plant production and ischolar_main traits under natural drought stress in rainfed target populations of environment (TPE) in six successive field trials from 2010 to 2015. Significant variation for phenology, plant production and ischolar_main traits under drought was noticed among the accessions. Genotyping of the rice accessions using 599 polymorphic simple sequence repeat (SSR) markers showed considerable variation among them. STRUCTURE analysis grouped the 49 accessions into three subpopulations. Similarly, three clusters were observed in Neighbor joining tree created using Nei’s genetic distance. The subpopulation POP1 consisted mostly of landraces, while subpopulation POP3 consisted of advanced breeding lines and POP2 accessions from all groups. Genome-wide association mapping detected 61 markers consistently associated in two or more trials with phenology, plant production and ischolar_main traits under drought in TPE. The markers PSM52 (Chr 3), RM6909 (Chr 4), RM242 (Chr9) and RM444 (Chr 9) were consistently associated with grain yield and ischolar_main traits under drought. The markers PSM127 (Chr 3) and PSM133 (Chr 4) were consistently associated with yield, plant height and spikelet fertility. These markers with pleiotropic and consistent associations with yield and secondary traits under drought in TPE may be robust candidates for marker-assisted breeding for drought resistance in rice.

Keywords


Association Mapping, Drought Resistance, Molecular Markers, Rice.

References





DOI: https://doi.org/10.18520/cs%2Fv114%2Fi02%2F329-340