Genetic mapping of morpho-physiological traits involved during reproductive stage drought tolerance in rice.

Reproductive stage drought stress is an important yield reducing factor in rainfed rice. Genetic mapping of morpho-physiological traits under the stress will help to develop cultivars suitable for drought prone environments through marker-assisted breeding (MAB). Though various yield QTLs under reproductive stage drought tolerance are available for MAB, but no robust markers controlling different morho-physiological traits are available for this stress tolerance. QTLs linked to morpho-physiological traits under drought stress were mapped by evaluating 190 F7 recombinant inbred lines (RIL) using bulk segregant analysis (BSA) strategy. Wide variations were observed in the RILs for eleven morpho-physiological traits involved during the stress. A total of 401 SSR primers were surveyed for parental polymorphism of which 77 were detected to be polymorphic. Inclusive composite interval mapping detected a total of five consistent QTLs controlling leaf rolling (qLR9.1), leaf drying (qLD9.1), harvest index (qHI9.1), spikelet fertility (qSF9.1) and relative water content (qRWC9.1) under reproductive stage drought stress. Another two non-allelic QTLs controlling leaf rolling (qLR8.1) and leaf drying (qLD12.1) were also detected to be linked and found to control the two traits. QTL controlling leaf rolling, qLR8.1 was validated in this mapping population and may be useful in MAB programs. Out of these five consistent QTLs, four (qLR9.1, qLD9.1, qHI9.1 and qRWC9.1) were detected to be novel QTLs and useful for MAB for improvement of reproductive stage drought tolerance in rice

Not Available

Not AvailableDrought during reproductive stage is among the main abiotic stresses responsible for drastic reduction of grain yield in rainfed rice. The genetic mechanism of reproductive stage drought tolerance is very complex. Many physiological and morphological traits are associated with this stress tolerance. Robust molecular markers are required for detection and incorporation of these correlated physiological traits into different superior genetic backgrounds. Identification of gene(s)/QTLs controlling reproductive stage drought tolerance and its deployment in rainfed rice improvement programs are very important. QTLs linked to physiological traits under reproductive stage drought tolerance were detected by using 190 F7 recombinant inbred lines (RIL) mapping population of CR 143–2-2 and Krishnahamsa. Wide variations were observed in the estimates of ten physiological traits studied under the drought stress. The RIL population was genotyped using the bulk- segregant analysis (BSA) approach. A total of 77 SSR polymorphic markers were obtained from the parental polymorphisms survey of 401 tested primers. QTL analysis using inclusive composite interval mapping detected a total of three QTLs for the physiological traits namely relative chlorophyll content (qRCC1.1), chlorophyll a (qCHLa1.1), and proline content (qPRO3.1) in the studied RIL population. The QTL, qPRO3.1 is found to be a novel one showing LOD value of 13.93 and phenotypic variance (PVE) of 78.19%. The QTL was located within the marker interval of RM22-RM517 on chromosome 3. Another novel QTL, qRCC1.1 was mapped on chromosome 1 at a distance of 142.8 cM and found to control relative chlorophyll content during terminal drought stress. A third novel QTL was detected in the population that controlled chlorophyll a content (qCHLa1.1) under the terminal stress period. The QTL was located on chromosome 1 at a distance of 81.8 cM and showed 64.5% phenotypic variation. The three novel QTLs, qRCC1.1, qCHLa1.1 and qPRO3.1 controlling relative chlorophyll content, chlorophyll a and proline content, respectively were identified in the mapping population derived from CR 143–2-2 and Krishnahamsa. These 3 QTLs will be useful for enhancement of terminal drought stress tolerance through marker-assisted breeding approach in rice.Not Availabl

Marker-Assisted Backcross Breeding for Improvement of Submergence Tolerance and Grain Yield in the Popular Rice Variety ‘Maudamani’

Not AvailableSubmergence stress due to flash floods reduces rice yield drastically in sensitive varieties. Maudamani is a high yielding popular rice variety but is highly susceptible to submergence stress. The selection of progenies carrying Sub1 and GW5 (wide-grain) enhanced the submergence stress tolerance and grain yield of theMaudamani variety by following the marker-assisted backcross breeding method. Foreground screening detected 14 BC1F1, 17 BC2F1, and 12 BC3F1 backcross progenies that carried the target QTLs for submergence tolerance and grain width. Background screening was performed in the progenies carrying the target QTL and enhanced the recovery of a recipient parent’s genome by upto 96.875% in the BC3 pyramided line. The BC3F1 plant containing the highest recipient parent genome content and the target QTLs was self-pollinated. In BC3F2 generation, the target QTLs the Sub1 and GW5 (wide-grain) alleles and recipient parent’s yield component QTL OsSPL14 were tracked for homozygous states in the progenies. Seven pyramided lines showed tolerance to submergence for 14 days and higher grain yield than both the parents. The pyramided lines were similar to the recipient parent for the majority of the studied morphological and quality traits. The pyramided lines are useful as cultivars and can serve as potential donors for transfer of Sub1, OsSPL14, Gn1a, GW5 (wide-grain), and SCM2 QTLs.Not Availabl

Characterization of morpho-quality traits and validation of bacterial blight resistance in pyramided rice genotypes under various hotspots of India

Abstract Bacterial blight (BB) disease caused by Xanthomonas oryzae pv. Oryzae (Xoo) is the main yield limiting factor amongst the diseases of rice in India. Swarna is a very popular high yielding variety in India but highly susceptible to the disease. Six pyramided lines containing three BB resistance genes xa5, xa13, Xa21 in the background of Swarna and IR64 were evaluated across the country under different hotspots to identify broad spectrum resistant line to promote as cultivar and donor for future breeding program. Characterizations for morphological and quality traits along with bioassay of the genotypes were performed across environments to know similarities of pyramided lines with the recurrent parents. Under the multi-location testing, pyramided line CRMAS2232-85 exhibited superior yield and related traits performance along with higher level of resistance to BB disease as compared to parental lines and check varieties. All the pyramided lines including CRMAS 2232-85 showed the presence of specific bands for Xa21, xa13 and xa5 resistance genes. The top yielding line also showed similar agro-morphologic characters like days to 50% flowering, panicles/m 2 and plant height. The milling%, head rice recovery, kernel length, L/B ratio, volume expansion ratio, water uptake, kernel length after cooking, alkali spreading value, kernel elongation ratio, amylose content and starch gel consistency quality parameters of best pyramided line were similar as like the recurrent parent

Not Available

Not AvailableGood quality seed is an important factor for a good crop and harvest. Vigour is the key performing trait of quality seed. Many physiological traits influence seed vigour in rice. Association of molecular markers with eleven physiological traits were investigated in a representative population. A representative population was constituted by including genotypes from all the phenotypic groups of the 11 physiological traits from the shortlisted population of 120 genotypes. The genotypic accessions with rich in multiple physiological traits were identified from the representative population. STRUCTURE, GenAlEx and Darwin software were used to classify the population. Generalized Linear Model (GLM) and Mixed Linear Models (MLM) were used in the marker-trait association analysis using the TASSEL software. Wide variations among the genotypic accessions were observed for the physiological traits estimated from the panel population. Linkage disequilibrium was detected for the 11 physiological traits in the panel population. STRUCTURE software classified the population into two genetic structure groups. Higher values of gene diversity and polymorphic information content (PIC) were estimated from the population based on genotyping using 50 simple sequence repeat markers. Genotypes present within groups and sub-groups showed similarity for their physiological traits. Strong association of the markers with physiological parameters namely RM167 for seed vigour index-I; RM7364 and RM235 for seed vigour index-II; RM440, RM223 for seedling dry weight; RM 256,RM25181, RM6547, RM328, RM201 for rate of root growth; RM 20, RM13335, RM216 for rate of shoot growth while RM20A and RM201 for absolute growth rate were detected by both GLM and MLM analyses. Markers detected in this association analysis may be potential use for future seed vigour improvement in rice.Not Availabl

Detection of Genomic Regions Controlling the Antioxidant Enzymes, Phenolic Content, and Antioxidant Activities in Rice Grain through Association Mapping

Because it is rich in antioxidant compounds, the staple food of rice provides many health benefits. Four antioxidant traits in rice grain, viz., catalase, CUPRAC, DPPH, FRAP and peroxidase, were mapped in a representative panel population containing 117 germplasm lines using 131 SSR markers through association mapping. Donor lines rich in multiple antioxidant properties were identified from the mapping population. The population was classified into three genetic groups and each group showed reasonable correspondence with the antioxidant traits. The presence of linkage disequilibrium in the population was confirmed from the estimated Fst values. A strong positive correlation of DPPH was established with TPC, FRAP and CUPRAC. A moderate to high mean gene diversity was observed in the panel population. Eleven significant marker-trait associations for antioxidant traits were mapped, namely, qACD2.1, qACD11.1 and qACD12.2 for DPPH; qCAT8.1 and qCAT11.1 for catalase; qFRAP11.1, qFRAP12.1 and qFRAP12.2 for FRAP; and qCUPRAC3.1, qCUPRAC11.1 and qCUPRA12.1 regulating CUPRAC. Co-localization of the QTLs for qACD11.1, qFRAP11.1 and qCUPRAC11.1 were detected, which may act as antioxidant hotspots regulating DPPH, FRAP and CUPRAC activities, respectively, while qACD12.2 and qFRAP12.1 remained close on the chromosome 12. These detected QTLs will be useful in antioxidant improvement programs in rice

Population Structure, Genetic Diversity and Molecular Marker-Trait Association Analysis for High Temperature Stress Tolerance in Rice

<div><p>Rice exhibits enormous genetic diversity, population structure and molecular marker-traits associated with abiotic stress tolerance to high temperature stress. A set of breeding lines and landraces representing 240 germplasm lines were studied. Based on spikelet fertility percent under high temperature, tolerant genotypes were broadly classified into four classes. Genetic diversity indicated a moderate level of genetic base of the population for the trait studied. Wright’s F statistic estimates showed a deviation of Hardy-Weinberg expectation in the population. The analysis of molecular variance revealed 25 percent variation between population, 61 percent among individuals and 14 percent within individuals in the set. The STRUCTURE analysis categorized the entire population into three sub-populations and suggested that most of the landraces in each sub-population had a common primary ancestor with few admix individuals. The composition of materials in the panel showed the presence of many QTLs representing the entire genome for the expression of tolerance. The strongly associated marker RM547 tagged with spikelet fertility under stress and the markers like RM228, RM205, RM247, RM242, INDEL3 and RM314 indirectly controlling the high temperature stress tolerance were detected through both mixed linear model and general linear model TASSEL analysis. These markers can be deployed as a resource for marker-assisted breeding program of high temperature stress tolerance.</p></div