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Chandra Babu, R.

Fine mapping of consistent quantitative trait loci for yield under drought stress using rice (Oryza sativa) recombinant inbred lines adapted to rainfed environment

Abstract Views :326 | PDF Views:123

Authors

C. Muthukumar ¹, V. Deshmukh Vivek ¹, R. Poornima ¹, S. Kavitha ¹, V. Gayathri ¹, R. Chandra Babu ¹

Affiliations
1 Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, IN

Source

Current Science, Vol 109, No 5 (2015), Pagination: 910-917

Abstract

Drought stress is a serious constraint, especially in rainfed rice production, and breeding for drought tolerance by selection based on yield under stress, though effective, is slow Mapping quantitative trait loci (QTLs) for yield and its components under drought stress predominant in rainfed target populations of environment (TPE) will help overcome this limitation. In the present study, a subset of 143 F8 and F9 recombinant inbred (RI) lines derived from IR62266-42-6-2 (IR62266), a high-yielding indica ecotype and Norungan, a landrace from TPE, was used to map QTLs for yield and its components under drought predominant in TPE. A large effect yield QTL observed under drought stress in TPE was consistent across two years with a phenotypic variation of 31.3% and 37.9% and additive effect of 629.2 and 424.9 kg/ha Further, this region was fine-mapped to 94.0 kb with positive effect on grain yield under stress.

Keywords

Comparative genomics, drought stress, fine mapping, quantitative trait locus, rice.

Full Text

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Comparative Genome-Wide Association Studies for Plant Production Traits under Drought in Diverse Rice (Oryza sativa L.) Lines Using SNP and SSR Markers

Abstract Views :270 | PDF Views:98

Authors

C. Muthukumar ¹, T. Subathra ¹, J. Aiswarya ¹, V. Gayathri ¹, R. Chandra Babu ¹

Affiliations
1 Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore 641 003, IN

Source

Current Science, Vol 109, No 1 (2015), Pagination: 139-147

Abstract

Rice is the major staple food crop for more than half of the world's population, but its productivity is often reduced by drought, especially when grown under rainfed conditions. Identification of molecular markers associated with plant production traits under drought, especially in the target populations of the environment (TPE) presents an opportunity to improve rainfed rice production using genomics tools. Marker-trait associations were studied using 1168 simple sequence repeat (SSR) markers and 911,153 single nucleotide polymorphisms (SNPs) with 17 diverse rice lines from different geographical regions and hydrological habitats. STRUCTURE analysis discriminated the rice accessions into three subpopulations. Significant genotypic linkage disequilibrium (LD) was found in the rice accessions using SSR markers. A total of 130 and 118 water-trait associations were obtained with SSR and SNP markers respectively, under stress. Comparison of SSR and SNP marker-trait associations revealed 23 consistent associations. Five marker-trait associations with genic SNPs were observed out of 23 associations. These genomic regions may be potential candidates for application in marker-assisted breeding of rice cultivars suitable for water-limited environments.

Keywords

Drought Tolerance, Linkage Disequilibrium, Marker–Trait Association, Rice.

Full Text

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 :273 | PDF Views:92

Authors

Vivek Deshmukh ¹, Sumeet Prabakar Mankar ¹, C. Muthukumar ¹, P. Divahar ¹, A. Bharathi ¹, Helen Baby Thomas ¹, Ashish Rajurkar ¹, Reena Sellamuthu ¹, R. Poornima ¹, S. Senthivel ², R. Chandra Babu ¹

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

Source

Current Science, Vol 114, No 02 (2018), Pagination: 329-340

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.

Full Text

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