Intervention of molecular breeding in water saving rice production system: aerobic rice.

The aerobic rice system/methods developed to tackle shortage of water, is a sustainable method to enhance rice productivity. Approximately 50% of irrigation water could be saved using this system in contrast to lowland rice cultivation. The crop can be directly seeded or transplanted in dry soil in this system rather than irrigated system of rice production. Here in this review we had tried to present all the important development made in regards to aerobic rice. Many QTLs responsible for aerobic traits in rice that have been mapped already are enlisted here. Brief comparisons of aerobic rice and conventional rice, further improvements made in aerobic rice have also been discussed.

Traits and QTLs for development of dry direct-seeded rainfed rice varieties.

The development of rice varieties for dry direct-seeded conditions can be accelerated by selecting suitable traits. In the present investigation, traits hypothesized to be important for direct-seeded conditions in rainfed systems, including seedling emergence, early vegetative vigour, nutrient uptake, nodal root number, and root hair length and density, were characterized to study the genetic control of these traits and their relationship with grain yield under seedling- and reproductive-stage drought stress. Two BC2F4 mapping populations derived from crosses of Aus276, a drought-tolerant aus variety, with MTU1010 and IR64, high-yielding indica mega-varieties, were developed and studied to identify quantitative trait loci (QTLs) that showed large and consistent effects. A total of 26 QTLs associated with 23 traits and 20 QTLs associated with 13 traits were mapped in the Aus276/3*IR64 and Aus276/3*MTU1010 populations, respectively. qGY6.1, qGY10.1, qGY1.1, and qEVV9.1 were found to be effective in both populations under a wide range of conditions. QTLs for several seedling-stage traits co-located with QTLs for grain yield, including early vegetative vigour and root hair length. On chromosome 5, several QTLs for nutrient uptake co-located with QTLs for root hair density and nematode gall rating. Six lines were selected from both populations based on grain yield and the presence of QTLs, and these lines typically showed improved seedling-stage traits (nodal root number, dry shoot weight, and root hair length and density). The co-located QTLs identified here can be used in research aimed at increasing the yield and adaptability of rainfed rice to direct-seeded conditions.

Identification and mapping of stable QTL with main and epistasis effect on rice grain yield under upland drought stress.

BACKGROUND: Drought is one of the most important abiotic stresses that cause drastic reduction in rice grain yield (GY) in rainfed environments. The identification and introgression of QTL leading to high GY under drought have been advocated to be the preferred breeding strategy to improve drought tolerance of popular rice varieties. Genetic control of GY under reproductive-stage drought stress (RS) was studied in two BC1F4 mapping populations derived from crosses of Kali Aus, a drought-tolerant aus cultivar, with high-yielding popular varieties MTU1010 and IR64. The aim was to identify QTL for GY under RS that show a large and consistent effect for the trait. Bulk segregant analysis (BSA) was used to identify significant markers putatively linked with high GY under drought. RESULTS: QTL analysis revealed major-effect GY QTL: qDTY1.2, qDTY2.2 and qDTY1.3, qDTY2.3 (DTY; Drought grain yield) under drought consistently over two seasons in Kali Aus/2*MTU1010 and Kali Aus/2*IR64 populations, respectively. qDTY1.2 and qDTY2.2 explained an additive effect of 288 kg ha-1 and 567 kg ha-1 in Kali Aus/2*MTU1010, whereas qDTY1.3 and qDTY2.3 explained an additive effect of 198 kg ha-1 and 147 kg ha-1 in Kali Aus/2*IR64 populations, respectively.Epistatic interaction was observed for DTF (days to flowering) between regions on chromosome 2 flanked by markers RM154-RM324 and RM263-RM573 and major epistatic QTL for GY showing interaction between genomic locations on chromosome 1 at marker interval RM488-RM315 and chromosome 2 at RM324-RM263 in 2012 DS and 2013 DS RS in Kali Aus/2*IR64 mapping populations. CONCLUSION: The QTL, qDTY1.2, qDTY1.3, qDTY2.2, and qDTY2.3, identified in this study can be used to improve GY of mega varieties MTU1010 and IR64 under different degrees of severity of drought stress through marker-aided backcrossing and provide farmers with improved varieties that effectively combine high yield potential with good yield under drought. The observed epistatic interaction for GY and DTF will contribute to our understanding of the genetic basis of agronomically important traits and enhance predictive ability at an individualized level in agriculture.

Genetic variation, linkage mapping of QTL and correlation studies for yield, root, and agronomic traits for aerobic adaptation.

BACKGROUND: Water scarcity and drought have seriously threatened traditional rice cultivation practices in several parts of the world, including India. Aerobic rice that uses significantly less water than traditional flooded systems has emerged as a promising water-saving technology. The identification of QTL conferring improved aerobic adaptation may facilitate the development of high-yielding aerobic rice varieties. In this study, experiments were conducted for mapping QTL for yield, root-related traits, and agronomic traits under aerobic conditions using HKR47 × MAS26 and MASARB25 × Pusa Basmati 1460 F2:3 mapping populations. RESULTS: A total of 35 QTL associated with 14 traits were mapped on chromosomes 1, 2, 5, 6, 8, 9, and 11 in MASARB25 x Pusa Basmati 1460 and 14 QTL associated with 9 traits were mapped on chromosomes 1, 2, 8, 9, 10, 11, and 12 in HKR47 × MAS26. Two QTL (qGY8.1 with an R2 value of 34.0% and qGY2.1 with an R2 value of 22.8%) and one QTL (qGY2.2 with an R2 value of 43.2%) were identified for grain yield under aerobic conditions in the mapping populations MASARB25 × Pusa Basmati 1460 and HKR47 × MAS26, respectively.A number of breeding lines with higher yield per plant, root length, dry biomass, length-breadth ratio, and with Pusa Basmati 1460-specific alleles in a homozygous or heterozygous condition at the BAD2 locus were identified that will serve as novel material for the selection of stable aerobic Basmati rice breeding lines. CONCLUSIONS: Our results identified positive correlation between some of the root traits and yield under aerobic conditions, indicating the role of root traits for improving yield under aerobic situations possibly through improved water and nutrient uptake. Co-localization of QTL for yield, root traits, and yield-related agronomic traits indicates that the identified QTL may be immediately exploited in marker-assisted-breeding to develop novel high-yielding aerobic rice varieties.

Genetic analysis of Indian aromatic and quality rice (Oryza sativa L.) germplasm using panels of fluorescently-labeled microsatellite markers.

Genetic relationships among Indian aromatic and quality rice (Oryza sativa) germplasm were assessed using 30 fluorescently labeled rice microsatellite markers. The 69 rice genotypes used in this study included 52 Basmati and other scented/quality rice varieties from different parts of India and 17 indica and japonica varieties that served as controls. A total of 235 alleles were detected at the 30 simple sequence repeat (SSR) loci, 62 (26.4%) of which were present only in Basmati and other scented/quality rice germplasm accessions. The number of alleles per locus ranged from 3 to 22, with an average of 7.8, polymorphism information content (PIC) values ranged from 0.2 to 0.9, with an average of 0.6, and the size range between the smallest and the largest allele for a given microsatellite locus varied between 3 bp and 68 bp. Of the 30 SSR markers, 20 could distinguish traditional Basmati rice varieties, and a single panel of eight markers could be used to differentiate the premium traditional Basmati, cross-bred Basmati, and non-Basmati rice varieties having different commercial value in the market-place. When estimates of inferred ancestry or similarity coefficients were used to cluster varieties, the high-quality Indian aromatic and quality rice genotypes could be distinguished from both indica and japonica cultivars, and crossbred varieties could be distinguished from traditional Basmati rices. The results indicate that Indian aromatic and quality germplasm is genetically distinct from other groups within O. sativa and is the product of a long independent pattern of evolution. The data also suggest that there is scope for exploiting the genetic diversity of aromatic/quality rice germplasm available in India for national Basmati rice breeding programs.