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Direct seeded rice (DSR) cultivation is an attractive non-conventional technology for growing rice. It saves labor, water, energy, and takes 5 to 7 days for early crop maturity. The yield advantage in DSR can be obtained by implementing various cultural practices including proper sowing time and seed rate, selection of suitable cultivars with appropriate management of weeds and water. The present study involves the agronomic and molecular screening of advanced breeding lines under direct seeded as well as transplanted conditions, so as to identify DSR adapted genotypes. Significant variations among genotypes have been observed for most of the traits measured in the present study. The yield under DSR was comparable to TPR but the grain quality was not comparable, and poor milling and head rice recovery were observed. Molecular characterization using 106 Kompetitive Allele-Specific PCR assays (KASP) was performed. The best performing genotypes with different allele combinations under DSR were PAU 6456-8-2-1-1-1, PAU 5187-RIL1649-F8, PAU 6456-8-1-1-1-3, PAU 6456-8-2-1-1-2, NVSR 2107, and PAU 6778-12-1-4-1-1. The selected genotypes performed better in terms of traits associated with seedling establishment, root architecture, yield, and yield-related traits. The identified promising breeding lines may serve as novel donors to be further used in a marker-assisted selection program which target improving the grain yield and adaptability under DSR. [ABSTRACT FROM AUTHOR]

The phenomenal increase in the use of nitrogenous fertilizers coupled with poor nitrogen use efficiency is among the most important threats to the environment, economic, and social health. During the last 2 decades, a number of genomic regions associated with nitrogen use efficiency (NUE) and related traits have been reported by different research groups, but none of the stable and major effect QTL have been utilized in the marker-assisted introgression/pyramiding program. Compiling the data available in the literature could be very useful in identifying stable and major effect genomic regions associated with the root and NUE-related trait improving the rice grain yield. In the present study, we performed meta-QTL analysis on 1,330 QTL from 29 studies published in the past 2 decades. A total of 76 MQTL with a stable effect over different genetic backgrounds and environments were identified. The significant reduction in the confidence interval of the MQTL compared to the initial QTL resulted in the identification of annotated and putative candidate genes related to the traits considered in the present study. A hot spot region associated with correlated traits on chr 1, 4, and 8 and candidate genes associated with nitrate transporters, nitrogen content, and ammonium uptake on chromosomes 2, 4, 6, and 8 have been identified. The identified MQTL, putative candidate genes, and their orthologues were validated on our previous studies conducted on rice and wheat. The research-based interventions such as improving nitrogen use efficiency via identification of major genomic regions and candidate genes can be a plausible, simple, and low-cost solution to address the challenges of the crop improvement program. [ABSTRACT FROM AUTHOR]

The development and utilization of molecular-markers play an important role in genomics-assisted breeding during pyramiding of valuable genes. The aim of present study was to develop and validate a novel core-set of KASP (Kompetitive Allele-Specific PCR) markers associated with traits improving rice grain yield and adaptability under direct-seeded cultivation conditions. The 110 phenotypically validated KASP assays out of 171 designed KASP, include assays for biotic-resistance genes, anaerobic germination, root-traits, grain yield, lodging resistance and early-uniform emergence. The KASP assays were validated for their robustness and reliability at five different levels using diverse germplasm, segregating and advanced population, comparison with SSR markers and on F 1s. The present research work will provide (i) breeding material in form of anticipated pre-direct-seeded adapted rice varieties (ii) single improved breeding line with many useful genes and (iii) KASP assay information for the useful QTL/genes providing grain yield and adaptability to rice under direct-seeded cultivation conditions. • A set of core 110 KASP arrays for genes/QTL associated with biotic resistance/tolerance, grain yield and adaptability under DSR was developed. • The KASP assays could significantly accelerate the genetic characterization of crossing parents and improved advanced breeding lines for GAB. • Our results offer a robust and reliable KASP toolkit that can contribute towards enhancing genetic gains in DSR breeding programs. [ABSTRACT FROM AUTHOR]