Abstract
BackgroundPuddled transplanted system of rice cultivation despite having several benefits, is a highly labor, water and energy intensive system. In the face of changing climatic conditions, a successful transition from puddled to dry direct seeded rice (DDSR) cultivation system looks must in future. Genome-wide association study was performed for traits including, roots and nutrient uptake (14 traits), plant-morphological (5 traits), lodging-resistance (4 traits) and yield and yield attributing traits (7 traits) with the aim to identify significant marker-trait associations (MTAs) for traits enhancing rice adaptability to dry direct-seeded rice (DDSR) system.ResultsStudy identified a total of 37 highly significant MTAs for 20 traits. The false discovery rate (FDR) ranged from 0.264 to 3.69 × 10− 4, 0.0330 to 1.25 × 10− 4, and 0.0534 to 4.60 × 10− 6 in 2015WS, 2016DS and combined analysis, respectively. The percent phenotypic variance (PV) explained by SNPs ranged from 9 to 92%. Among the identified significant MTAs, 15 MTAs associated with the traits including nodal root, root hair length, root length density, stem and culm diameter, plant height and grain yield were reported to be located in the proximity of earlier identified candidate gene. The significant positive correlation of grain-yield with seedling establishment traits, root morphological and nutrient-uptake related traits and grain yield attributing traits pointing towards combining target traits to increase rice yield and adaptability under DDSR. Seven promising progenies with better root morphology, nutrient-uptake and higher grain yield were identified that can further be used in genomics assisted breeding for DDSR varietal development.ConclusionsOnce validated, the identified MTAs and the SNPs linked with trait of interest could be of direct use in genomic assisted breeding (GAB) to improve grain yield and adaptability of rice under DDSR.
Highlights
Puddled transplanted system of rice cultivation despite having several benefits, is a highly labor, water and energy intensive system
Phenotypic variations for targeted raits A number of seedling establishment, root and leaf morphological, agronomic, grain yield and yield related traits were measured to investigate their role in improving rice adaptation under dry direct seeded rice (DDSR) condition
The trend of change of Leaf Color Chart (LCC) and SPAD value across the progenies was almost similar indicating LCC is a good alternative to SPAD to decide on the time and dose of fertilizer application under DDSR
Summary
Puddled transplanted system of rice cultivation despite having several benefits, is a highly labor, water and energy intensive system. DDSR has the potential to ensure overall sustainability of rice cultivation systems when applied as a full package comprising laserassisted land levelling, conservation tillage, crop establishment, harvesting and processing using smart machines, integrated weed management, precision input delivery especially of water and nutrients and suitable varieties. The mechanized DDSR method of rice cultivation has been estimated to provide a potential irrigation water savings of 40 cm ha− 1, labor savings of 25 person-days ha− 1, energy savings of 1500 MJ ha− 1, a reduction of GHG emissions of 1500 kg CO2 equivalent ha− 1, yield increase of 0.5 t ha− 1 and increased net economic return of USD 50 ha− 1 with positive effect on soil heath in most of the rice-growing countries [8]. DDSR combines the advantage of better adaptation of upland rice varieties in aerobic soil and high yield potential of lowland varieties adapted to anaerobic soil
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