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Recent predictions on climate change indicate that high temperature episodes are expected to impact rice production and productivity worldwide. The present investigation was undertaken to assess the yield stability of 72 rice hybrids and their parental lines across three temperature regimes over two consecutive dry seasons using the additive main effect and multiplicative interaction (AMMI), genotype and genotype × environment interaction (GGE) stability model analysis. The combined ANOVA revealed that genotype × environment interaction (GEI) were significant due to the linear component for most of the traits studied. The AMMI and GGE biplot explained 57.2% and 69% of the observed genotypic variation for grain yield, respectively. Spikelet fertility was the most affected yield contributing trait and in contrast, plant height and tiller numbers were the least affected traits. In case of spikelet fertility, grain yield and other yield contributing traits, male parent contributed towards heat tolerance of the hybrids compared to the female parent. The parental lines G74 (IR58025B), G83 (IR40750R), G85 (C20R) and hybrids [G21 (IR58025A × KMR3); G3 (APMS6A × KMR3); G57 (IR68897A × KMR3) and G41 (IR79156A × RPHR1005)] were the most stable across the environments for grain yield. They can be considered as potential genotypes for cultivation under high temperature stress after evaluating under multi location trials. [ABSTRACT FROM AUTHOR]

Rice is generally shows variable level of sensitivity to salinity during its developmental stages and remarkably sensitive during young seedling stage and early reproductive phase. Quantifying the level of salt tolerance based on salt stress indices is an effective method in identification of tolerant genotypes. In this study, the salt stress indices were used to identify best performing genotypes based on salt susceptibility indices (SSI) and salt response indices (SRI) as relevant parameters. Among the 39 genotypes studied, 29 showed better endurance to salt susceptibility indices, among them Pokkali, IR72132-AC-6-1 and IR70869-B-P-13-2 performed well with least SSI, which refers more tolerance with lesser yield reduction, whereas IR29 was vice-versa to the above. Genotypes IR72593-B-19-2-3-1, IR73104-B-1-1-3-2-1 and IR74802-3R-7-1-2 had a better performance with early flowering and highly responsive to salt stress with lower percent yield reduction. The phenotypic variation is higher than genotypic variation for all traits except for flowering duration and it indicates presence of variability for different traits. High heritability with variability, genetic advance and better salt stress indices indicates involvement of additive gene action and can be manipulated and utilized in further breeding program. [ABSTRACT FROM AUTHOR]

Salinity is a serious problem all over the world with an average of 830 M ha being affected. In India, it's about 13.3 M ha with coastal and inland salinity. The present study focused on effects of salinity on chlorophyll content, chlorophyll fluorescence, gas exchange parameters and osmotic potential in different salt concentration. The chlorophyll content reduced as salinity level increases and chlorophyll a and b concentration coincides with decrease in Fv/Fm ratio. The genotype IR72593 exhibited better survival response than the susceptible genotype IR29. The sensitive cultivar IR29 responds to salinity stress quickly and did not recover after one week of salinity stress which led to complete plant death. Tolerant genotypes showed lower reduction in gas exchange parameters, while IR29 showed sudden reduction during the initial hours of salt stress and decreased at 312 hours due to complete death of plants. Osmotic potential becomes negative with increase in salinity level irrespective of genotypes; however tolerant genotype responds lower than sensitive genotype. This differential response of tolerant genotypes to salinity stress is due to the reduced transpiration rate and closure of stomatal openings during stress period, with no significant change in chlorophyll content. The transpiration rate and stomatal conductance is positively associated with intake of Na ions into the plant system. [ABSTRACT FROM AUTHOR]

Three rice genotypes, IR 74802, IR 73104 and IR 72593, along with FL 478 and IR 29 as resistant and susceptible controls, respectively, were subjected to 21 days' salinity stress at the seedling stage in modified yoshida solution with two salt levels (60 and 120 mM NaCl). The results indicated that there was a profound increase in proline and ascorbic acid levels, and in the activity of nitrate reductase and antioxidant enzymes, i.e. catalase, peroxidase and ascorbate peroxidase, as well as malondialdhyde and membrane stability index, which were associated with salt tolerance. Salt stress had a significant and drastic effect on all parameters when the salinity level increased to 120 mM NaCl. The increased enzyme activity was directly related to an increased membrane stability index, as in IR 72593, which is identified as the most tolerant among the genotypes tested. It is clearly confirmed that predicting tolerance at the early seedling stage is the best way to assess the salinity tolerance level by utilizing physiological parameters, especially antioxidant enzyme activities which are found to be closely associated with salinity tolerance. Physiological adaptation of the plant to NaCl salt stress resulted in enhanced activity of stress-related enzymes and low sodium uptake in tolerant genotypes. [ABSTRACT FROM PUBLISHER]

The present investigation was carried out to estimate indica-tropical japonica genome proportion in two newly developed wide compatible restorer lines (RP6367 and RP6368) derived through indica-tropical japonica crosses and to study the molecular diversity among 12 rice genotypes namely, five promising indica restorers (RPHR1005, RPHR1096, IBL57, DR714-1-2 and Akshayadhan), two maintainers (IR58025B and APMS6B), two newly identified wide compatible restorer lines (RP6367and RP6368), two typical tropical japonica lines (IRGC66651 and IRGC66577) and one typical indica genotype (Nagina22) using 50 SSR markers and 45 InDELs. Out of the 95 markers, 54 were found to be polymorphic. The genotypic data of 54 polymorphic markers was used to estimate indica-tropical japonica genome proportion in derived lines and molecular diversity among 12 genotypes. The percentage of tropical japonica genome proportion in derived lines RP6367 and RP6368 was found to be 50% and 55.55% respectively. Our results suggest that the proportion of tropical japonica in hybrid rice parental lines is the key to select the best parents for efficient utilization of the heterosis present between indica and tropical japonica subspecies. Out of the 54 markers, 19 markers recorded PIC value above 0.5 and can be considered as highly informative and useful to study molecular genetic diversity. In this study, the SSRs primers showed higher PIC values compared to InDels. It is concluded that the use of highly polymorphic molecular markers detected in this study gives a better understanding of genetic relationship among closely related rice genotypes. [ABSTRACT FROM AUTHOR]

Sixty four parental lines of hybrid rice were evaluated for genetic divergence by taking into account of nine traits during two seasons of year 2018. By resolving the parental lines into ten groups, Ward's clustering method demonstrated the parental lines having significant genetic diversity. Cluster X had the most parental lines (13) out of all the clusters, followed by cluster II (12 genotypes). The parental line clusters IX, VIII, VII, V, and IV, which correspond to SD-5, SD-2, HSRV-16, GR-37, and SD-39, respectively, showed the significant degree of variability. Screening for fertility restoration was done in 64 parental lines with the help of SSR molecular markers. Among them, 44 potential restorers were identified (Rf4 and Rf3 present) with a hundred percentage efficiency supported molecular screening. The traits number of productive tillers per plant, length of the panicle and number of grains per panicle were significantly correlated with the trait grain yield per plant. Path analysis showed that the traits number of grains per panicle, the number of productive tillers per plant, test weight and panicle length had positive direct effects on grain yield and indicating that selection for these yield contributing traits could lead to an improvement in single plant yield as a whole. [ABSTRACT FROM AUTHOR]

Salinity stress is a major abiotic stress to which rice is most sensitive at germination or early vegetative stages. Addressing a salinity tolerance in rice can be achieved with an effective way by employing of early seedling stage screening to narrow down a large set of germplasm with higher tolerance and key parameters can quantify tolerance level. Morpho-physiological changes were assessed for selected seven backcross inbred lines (BILs) possessing Saltol1 quantitative trait loci (QTL) of rice and their parents and checks, at early seedling stage under optimal salt concentration (120 mM NaCl). In the present study, morpho-physiological changes were assessed for selected seven backcross inbred lines (BILs) possessing Saltol1 QTL of rice and their parents and checks, at seedling stage subjected to 120 mM NaCl salt concentration. The seedling growth assessment, mineral analysis and important physiological growth characters were measured after 14 days of salt treatment to classify seven BILs into tolerant and sensitive groups. Among the screened seven ILs, IL3 showed susceptible reaction for hydroponic screening. Analysis of variance (ANOVA) revealed significant variation between improved lines, salinity treatment and their interaction for the studied traits. Salt stress affected growth parameters and important physiological traits in the studied ILs; however, the lowest reduction was observed in the tolerant groups. The tolerant group ILs also showed maintenance of low Na+, high K+ uptake and Na+/K+ ratio. The identified tolerant lines will be utilized in development of saline-tolerant heterotic hybrids and further evaluation under multi-location trial of All India Coordinated Rice Improvement Programme (AICRIP). [ABSTRACT FROM AUTHOR]

Gangavati sona (GS) is a high-yielding, fine-grain rice variety widely grown in the Tungabhadra command area in Karnataka, India; however, it is susceptible to bacterial blight (BB). Therefore, the present study was conducted to improve the GS variety for BB resistance. Three BB-resistant genes (xa5, xa13, and Xa21) were introgressed into the genetic background of susceptible cultivar GS through marker-assisted backcrossing (MABB) by using Improved samba Mahsuri (ISM), a popular, high-yielding, bacterial blight resistant rice variety as a donor parent. Foreground selection was carried out using gene-specific markers, viz., xa5FM (xa5), xa13prom (xa13), and pTA248 (Xa21), while background selection was carried out using well-distributed 64 polymorphic microsatellite markers. The true heterozygote F1 was used as the male parent for backcrossing with GS to obtain BC1F1. The process was repeated in BC1F1 generation, and a BC2F1 plant (IGS-5-11-5) possessing all three target genes along with maximum recurrent parent genome (RPG) recovery (86.7%) was selfed to obtain BC2F2s. At BC2F2, a single triple gene homozygote plant (IGS-5-11-5-33) with 92.6% RPG recovery was identified and advanced to BC2F5 by a pedigree method. At BC2F5, the seven best entries were selected, possessing all three resistance genes with high resistance levels against bacterial blight, yield level, and grain quality features equivalent to better than GS. The improved versions of GS will immensely benefit the farmers whose fields are endemic to BB. [ABSTRACT FROM AUTHOR]

Gangavati sona (GS) is a high-yielding, fine-grain rice variety widely grown in the Tungabhadra command area in Karnataka, India; however, it is susceptible to bacterial blight (BB). Therefore, the present study was conducted to improve the GS variety for BB resistance. Three BB-resistant genes (xa5, xa13, and Xa21) were introgressed into the genetic background of susceptible cultivar GS through marker-assisted backcrossing (MABB) by using Improved samba Mahsuri (ISM), a popular, high-yielding, bacterial blight resistant rice variety as a donor parent. Foreground selection was carried out using gene-specific markers, viz., xa5FM (xa5), xa13prom (xa13), and pTA248 (Xa21), while background selection was carried out using well-distributed 64 polymorphic microsatellite markers. The true heterozygote F1 was used as the male parent for backcrossing with GS to obtain BC1F1. The process was repeated in BC1F1 generation, and a BC2F1 plant (IGS-5-11-5) possessing all three target genes along with maximum recurrent parent genome (RPG) recovery (86.7%) was selfed to obtain BC2F2s. At BC2F2, a single triple gene homozygote plant (IGS-5-11-5-33) with 92.6% RPG recovery was identified and advanced to BC2F5 by a pedigree method. At BC2F5, the seven best entries were selected, possessing all three resistance genes with high resistance levels against bacterial blight, yield level, and grain quality features equivalent to better than GS. The improved versions of GS will immensely benefit the farmers whose fields are endemic to BB. [ABSTRACT FROM AUTHOR]

MTU 1010 is an early maturing and high-yielding mega rice variety widely grown in an area of 3 Mha. It is characterised by limited grain number and panicle branching. To improve the grain number in MTU 1010, an IRRI breeding line, IR121055-2-10-5 was utilized as donor to transfer yield-enhancing genes Gn1a and OsSPL14 (associated with increased grain number and better panicle branching, respectively) into MTU1010 by Marker-Assisted Backcross Breeding (MABB). At each backcross generation, foreground selection was carried out with Gn1a and OsSPL14- specific molecular markers, whilst background selection was done with a set of SSR markers polymorphic between the IR121055-2-10-5 and MTU1010. With the use of a gene-specific marker, homozygous BC2F2 plants carrying the yield-enhancing gene were identified and advanced through pedigree-method of selection till BC2F6 and best performing ten lines were selected and evaluated in replicated station trials for yield contributing traits, where grain number and brancing per panicle exhibited high significant and positive correlation with single plant yield. Three promising lines namely RP6353-5-8-13-24, RP6353-26-13-39-5 and RP6353-32-12-8-16 with higher grain number and yield than MTU1010 were identified and nominated for evaluation in Initial Varietal Trial-Aerobic (IVT-Aerobic) of All India Crop Improvement Programme on Rice (AICRP), of which RP6353-26-13-39-5 (IET28674), was promoted for further testing. [ABSTRACT FROM AUTHOR]

With an objective of mapping novel low soil P (Phosphorus) tolerance loci in the non-Pup1 type donor rice line, Wazuhophek, we screened a recombinant inbred line (RIL) mapping population consisting of 330 lines derived from the cross Wazuhophek x Improved Samba Mahsuri (which is highly sensitive to low soil P) in a plot with low soil P for tolerance associated traits. Molecular mapping with SSR markers revealed a total of 16 QTLs (seven major and nine minor QTLs), which are associated with low soil P tolerance related traits. Interestingly, a QTL hotspot, harbouring 10 out of 16 QTLs were identified on the short arm of chromosome 8 (flanked by the makers RM22554 and RM80005). Five major QTLs explaining phenotypic variance to an extent of 15.28%, 17.25%, 21.84%, 20.23%, and 18.50%, associated with the traits, plant height, shoot length, the number of productive tillers, panicle length and yield, respectively, were located in the hotspot. Two major QTLs located on chromosome 1, associated with the traits, total biomass and root to shoot ratio, explaining 15.44% and 15.44% phenotypic variance, respectively were also identified. Complex epistatic interactions were observed among the traits, grain yield per plant, days to 50% flowering, dry shoot weight, and P content of the seed. In-silico analysis of genomic regions flanking the major QTLs revealed the presence of key putative candidate genes, possibly associated with tolerance. [ABSTRACT FROM AUTHOR]

A study was conducted to evaluate the genetic variability parameters, correlation and path coefficient analysis for eight yield related traits in segregating F2 population of an aerobic restorer AR 9-18 × YPK 198 (Donor for yield enhancing genes Gn1a and OsSPL14) at ICAR-IIRR, Hyderabad during the kharif, 2019. The results indicated that, productive tiller number, grain number per panicle and plant yield showed high PCV and GCV. Height of plant, productive tiller number, grain number per panicle and plant yield exhibited a high heritability and also high genetic advance as per cent of mean which indicates simple selection would be effective for enhancement of these traits. Correlation studies indicated that plant yield was associated significantly positive with height of plant, productive tiller number, length of panicle and grain number per panicle. High positive direct effect on plant yield was recorded by productive tiller number, grain number per panicle and height of plant. [ABSTRACT FROM AUTHOR]

Genetic improvement of rice for grain micronutrients, viz., iron (Fe) and zinc (Zn) content is one of the important breeding objectives, in addition to yield improvement under the irrigated and aerobic ecosystems. In view of developing genetic resources for aerobic conditions, line (L) × tester (T) analysis was conducted with four restorers, four CMS lines and 16 hybrids. Both hybrids and parental lines were evaluated in irrigated and aerobic field conditions for grain yield, grain Fe and Zn content. General Combining Ability (GCA) effects of parents and Specific Combining Ability (SCA) effects of hybrids were observed to be contrasting for the micronutrient content in both the growing environments. The grain Fe and Zn content for parental lines were negatively correlated with grain yield in both the contrasting growing conditions. However, hybrids exhibited positive correlation for grain Fe and Zn with grain yield under limited water conditions. The magnitude of SCA mean squares was much higher than GCA mean squares implying preponderance of dominance gene action and also role of complementary non-allelic gene(s) interaction of parents and suitability of hybrids to the aerobic system. The testers HHZ12-SAL8-Y1-SAL1 (T1) and HHZ17-Y16-Y3-Y2 (T2) were identified as good combiners for grain Zn content under irrigated and aerobic conditions respectively. [ABSTRACT FROM AUTHOR]

The study was undertaken to identify the quantitative trait loci (QTLs) governing yield and its related traits using a recombinant inbred line (RIL) population derived from the popular rice hybrid, KRH-2 (IR58025A/KMR3R). A genetic map spanning 294.2 cM was constructed with 126 simple sequence repeats (SSR) loci uniformly distributed across the rice genome. QTL analysis using phenotyping and genotyping information identified a total of 22 QTLs. Of these, five major effect QTLs were identified for the following traits: total grain yield/plant (qYLD3-1), panicle weight (qPW3-1), plant height (qPH12-1), flag leaf width (qFLW4-1) and panicle length (qPL3-1), explaining 20.23–22.76% of the phenotypic variance with LOD scores range of 6.5–10.59. Few genomic regions controlling several traits (QTL hotspot) were identified on chromosome 3 for total grain yield/plant (qYLD3-1) and panicle length (qPL3-1). Significant epistatic interactions were also observed for total grain yield per plant (YLD) and panicle length (PL). While most of these QTLs were observed to be co-localized with the previously reported QTL regions, a novel, major QTL associated with panicle length (qPL3-1) was also identified. SNP genotyping of selected high and low yielding RILs and their QTL mapping with 1,082 SNPs validated most of the QTLs identified through SSR genotyping. This facilitated the identification of novel major effect QTLs with much better resolution and precision. In-silico analysis of novel QTLs revealed the biological functions of the putative candidate gene (s) associated with selected traits. Most of the high-yielding RILs possessing the major yield related QTLs were identified to be complete restorers, indicating their possible utilization in development of superior rice hybrids. [ABSTRACT FROM AUTHOR]

Swarna-Sub1, a ruling submergence tolerant variety of rice, showed a significant decrease in the yield in major blast disease prone areas, which is caused by fungus Magnaporthe oryzae (Pyricularia oryzae). To overcome this problem, three major blast resistance genes viz., Pi1, Pi2, and Pi54 were pyramided through marker-assisted backcross breeding using donors, Swarna-LT (having Pi1 + Pi54) and Swarna-A51 (having Pi2). Foreground selection was carried out using molecular markers tightly linked to three blast resistance genes and also submergence tolerance for retaining the Sub1 gene in the recurrent parent. Based on disease resistance and agro-morphological performance of backcross-derived lines, we selected the best 25 plants of two- and three-gene pyramided BC3F2 homozygous lines with a maximum of ~ 93.5% recurrent parent genome and were further advanced to the BC3F5 generation. The stringent recurrent parent genome recovery analysis using SSR markers limited the linkage drag from a minimum of 0.2 Mb to a maximum of 2 Mb in all three-gene pyramided lines. The two and three blast resistance genes pyramided lines, i.e., SS30-24-82, SS30-24-73, and SS30-24-46, displayed a high level of blast resistance and submergence tolerance. The successful use of marker-assisted backcrossing strategy coupled with phenotypic selection helped in the development of Swarna-Sub1 lines having multiple blast resistance genes with superior agro-morphological and grain quality traits, which could serve as valuable genetic stocks in the rice breeding program. [ABSTRACT FROM AUTHOR]

Identification of tolerant genotypes based on phenotypic screening is one of the foremost requirements for studying genetics and molecular mapping of salinity tolerance trait in rice. For this to be accomplished efficiently, development of an efficient, reproducible, simple mass-screening protocol is imperative. The present study involves the development and validation of a modified, rapid, and reproducible protocol using sterilized silica sand as a base for growing the rice seedlings in the nutrient media replacing the generally deployed hydroponics based screening protocol where styrofoam is used as a base for seedling growth. Pre-germinated seeds were sown on silica sand filled plastic trays in three replications and modified Yoshida nutrient solution was periodically added for the first 21 days and appropriate quantities of NaCl was added to salinize the medium in different concentrations (60mM, 80mM, 100mM and 120mM). After a week of exposure to salinity, the seedlings were scored phenotypically and parameters associated with tolerance were recorded. The protocol was initially tested with known saline tolerant and sensitive rice genotypes and further validated in a set of introgressed Improved Samba Mahsuri breeding lines, possessing the QTL Saltol, which confers seedling stage tolerance to salinity. The modified protocol was able to clearly discriminate salt tolerant rice lines from sensitive ones and was superior to the routinely adopted hydroponics based protocol in terms of being more robust, reproducible, requires less nutrient solution and facilitating easy handling in screening of genotypes. [ABSTRACT FROM AUTHOR]

Bacterial blight (BB) of rice caused by the pathogen Xanthomonas oryzae pv. oryzae and the insect gall midge (GM) ( Orseolia oryzae) are two major constraints of rice production. The present study was carried out to improve RPHR-1005, a stable restorer line of the fine-grain-type rice hybrid DRRH-3, for BB and GM resistance through marker-assisted backcross breeding (MABB). Two major GM resistance genes, Gm4 and Gm8, and a major BB resistance gene, Xa21, were selected as target genes for transfer to RPHR-1005. Two sets of backcrosses were carried out to combine either Xa21 + Gm4 or Xa21+ Gm8 into RPHR-1005 using breeding lines in the genetic background of ISM possessing either Gm4 or Gm8 along with Xa21. Foreground selection was performed for Xa21, Gm4, Gm8, and the major fertility restorer genes Rf3 and Rf4 using gene-specific markers, while 61 polymorphic simple sequence repeat (SSR) markers were used for background selection and marker-assisted backcrossing was continued until BC generation. A promising homozygous backcross-derived plant at the BCF generation possessing Xa21 + Gm4, and another possessing Xa21 + Gm8, were intercrossed to stack the target resistance genes. At ICF (inter-crossed F) , three promising lines possessing the three target resistance genes in a homozygous condition along with fine-grain type, complete fertility restoration, and better panicle exsertion than RPHR-1005 have been identified. Among these, a single line, # RPIC-16-65-125, showed better yield, was highly resistant to BB and GM, was of medium-slender grain type, and had complete fertility restoration along with better panicle exsertion and taller plant type than RPHR-1005. This is the first report of combining resistance against BB and GM in the genetic background of a hybrid rice parental line. [ABSTRACT FROM AUTHOR]

Two major nuclear genes, Rf3 and Rf4, are known to be associated with fertility restoration of wild-abortive cytoplasmic male sterility (WA-CMS) in rice. In the present study, through a comparative sequence analysis of the reported putative candidate genes, viz. PPR9-782-(M,I) and PPR762 (for Rf4) and SF21 (for Rf3), among restorer and maintainer lines of rice, we identified significant polymorphism between the two lines and developed a set of PCR-based codominant markers, which could distinguish maintainers from restorers. Among the five markers developed targeting the polymorphisms in PPR9-782-(M,I), the marker RMS-PPR9-1 was observed to show clear polymorphism between the restorer (n = 120) and maintainer lines (n = 44) analyzed. Another codominant marker, named RMS-PPR762 targeting PPR762, displayed a lower efficiency in identification of restorers and maintainers, indicating that PPR9-782-(M,I) is indeed the candidate gene for Rf4. With respect to Rf3, a codominant marker, named RMS-SF21-5 developed targeting SF21, displayed significantly lower efficiency in identification of restorers and non-restorers as compared to the Rf4-specific markers. Validation of these markers in a F2 mapping population segregating for fertility restoration indicated that Rf4 has a major influence on fertility restoration and Rf3 is a minor gene. Further, the functional marker RMS-PPR9-1 was observed to be very useful in identification of impurities in a seed lot of the popular hybrid, DRRH3. Interestingly, when RMS-PPR9-1 and RMS-SF21-5 were considered in conjunction with analysis, near-complete, marker–trait co-segregation was observed, indicating that deployment of the candidate gene-specific markers both Rf4 and Rf3, together, can be helpful in accurate identification of fertility restorer lines and can facilitate targeted transfer of the two restorer genes into elite varieties through marker-assisted breeding. [ABSTRACT FROM AUTHOR]

WA-CMS system based rice hybrids are widely adopted in many rice growing countries, including India. Even though it is well known that the trait is controlled by mitochondria, the genes underpinning the trait remain enigmatic. In the present study, a complete genome-wide comparative sequence analysis was performed using draft mitochondrial genomes of WA-CMS and male fertile lines in a step-wise manner, progressively covering 5-10 kb every time through BLASTN tool. The sequence polymorphisms identified in different mitochondrial regions were targeted to develop two different sets of dominant PCR-based markers, one consisting of six markers targeting WA-CMS mitochondria, the other set consisting of five markers targeting male fertile mitochondria in addition to development of a set of eight co-dominant PCR-based markers targeting both the genomes. When a set of candidate genes/ORFs reported earlier to be associated with WA-CMS trait in rice were analyzed through RT-PCR of RNA isolated from immature rice florets, it was observed that the chimeric ORF, WA352 is expressed only in WA-CMS line and hybrid (i.e. genotypes containing sterile mitochondria), indicating it's candidacy for the WA-CMS trait. Targeting the functional nucleotide polymorphism between WA-CMS and maintainer mitochondria with respect to WA352, two dominant markers, one targeting sterile and another targeting fertile mitochondria were developed. In addition, a robust, co-dominant functional marker targeting the candidate gene was also developed and validated for its utility in identification of genetic impurities in seed lots of WA-CMS lines. [ABSTRACT FROM AUTHOR]

DRR17A is a stable wild-abortive cytoplasmic male sterile line with medium-slender grain type. DRR17A and its maintainer line DRR17B are highly susceptible to two of the major rice diseases, bacterial blight (BB) and blast. To improve DRR17B for resistance against BB and blast, we have introgressed a major dominant gene each conferring resistance against BB (Xa21) and blast (Pi54) into the maintainer line through marker-assisted backcross breeding using RP-Bio-Patho-2 (a near-isogenic line of Samba Mahsuri possessing Xa21 and Pi54) as the donor parent. PCR-based molecular markers tightly linked to Xa21 and Pi54 were used for foreground selection of the resistance plants at each backcross generation, while molecular markers tightly linked to the major fertility restorer genes, Rf3 and Rf4, were used for negative selection (i.e. selection of plants possessing non-fertility-restoring alleles at the two loci) at BC1 generation. After foreground selection for the target genes at each backcross generation, the ‘positive’ plants were screened with parental polymorphic markers for identifying backcross plants possessing maximum recovery of DRR17B genome. Marker-assisted backcrossing was continued till BC3 generation, and a single BC3F1 plant possessing the target genes with ~94 % recovery of recurrent parent genome was identified and selfed to generate BC3F2s. A total of six homozygous BC3F2 plants were identified and advanced. At BC3F5, six promising, stable, backcross-derived lines possessing high level of resistance against BB and blast, high yield, short plant stature, fine-grain type, have been identified; their maintenance ability and heterotic potential validated through test crosses and these lines are being converted to CMS lines through marker-assisted breeding. [ABSTRACT FROM AUTHOR]

Swarna-Sub1, a ruling submergence tolerant variety of rice, showed a significant decrease in the yield in major blast disease prone areas, which is caused by fungus Magnaporthe oryzae (Pyricularia oryzae). To overcome this problem, three major blast resistance genes viz., Pi1, Pi2, and Pi54 were pyramided through marker-assisted backcross breeding using donors, Swarna-LT (having Pi1 + Pi54) and Swarna-A51 (having Pi2). Foreground selection was carried out using molecular markers tightly linked to three blast resistance genes and also submergence tolerance for retaining the Sub1 gene in the recurrent parent. Based on disease resistance and agro-morphological performance of backcross-derived lines, we selected the best 25 plants of two- and three-gene pyramided BC3F2 homozygous lines with a maximum of ~ 93.5% recurrent parent genome and were further advanced to the BC3F5 generation. The stringent recurrent parent genome recovery analysis using SSR markers limited the linkage drag from a minimum of 0.2 Mb to a maximum of 2 Mb in all three-gene pyramided lines. The two and three blast resistance genes pyramided lines, i.e., SS30-24-82, SS30-24-73, and SS30-24-46, displayed a high level of blast resistance and submergence tolerance. The successful use of marker-assisted backcrossing strategy coupled with phenotypic selection helped in the development of Swarna-Sub1 lines having multiple blast resistance genes with superior agro-morphological and grain quality traits, which could serve as valuable genetic stocks in the rice breeding program. [ABSTRACT FROM AUTHOR]

Interaction between gene products encoded by the cytoplasm and nucleus form the core of wild abortive cytoplasmic male sterile (WA-CMS) system of hybrid breeding in rice. Gaining insights into such interactions can be helpful in the development of better three-line rice hybrids and also identify novel male sterility systems. In the present study, the whole transcriptome profiles of immature florets of IR58025A, a WA-CMS line and its isonuclear maintainer line, IR58025B, collected at pre-anthesis stage were compared to delineate the pathways involved in pollen abortion and male sterility. Among the 774 differentially expressed transcripts (DETs), 496 were down regulated and 278 were up regulated in IR58025A compared to IR58025B. The genes associated with oxidative stress response, defense response, etc. were significantly up-regulated, while those associated with respiration, cell wall modifications, pectinesterase activity, etc. were significantly down-regulated in the WA-CMS line. Gene ontology and pathway enrichment analyses revealed the down-regulation of both nuclear and organellar genes involved in key metabolic processes of cell respiration, photosynthesis and other energy yielding metabolites in IR58025A, relative to IR58025B, indicating a general shift toward conservation of energy and other key resources in the florets of WA-CMS line. The data derived from RNA-Seq analysis were validated through qRT-PCR analysis. Based on the results obtained, it can be hypothesized that pollen abortion principally occurs due to up-regulation of pathways leading to oxidative stress leading to energy starvation conditions in consonance with reduced expression of genes associated with the cell wall formation, respiration, and other key metabolic processes. [ABSTRACT FROM AUTHOR]

A set of reference genes expressing stably under aerobic and anaerobic conditions in rice is essential to execute omics studies relating to aerobic adaptations. Stability of expression of ten rice reference genes, viz. Actin, eEF-1a, eIF-5C, Exp1, Exp2, Memp, SKP1A, TF-SUI1, TPH, and UBQ5 was validated across six experimental sets in shoot and root tissues at seedling, tillering, and panicle initiation stages. Comprehensively, Memp (Membrane protein), TPH (Tumor protein homolog), and Exp1 (Expressed protein) were revealed as the most stable set with acceptable M and V value according to the gold standards of qRT-PCR using various algorithms/tools. The identified set of reference genes was validated using root trait genes, which showed concurrence with the functional expression patterns in the aerobic and anaerobic adapted cultivars. The Memp (Membrane protein), TPH (Tumor protein homolog), and Exp1 (Expressed protein) genes are the most stable reference genes across the root and shoot at various developmental stages under aerobic and anaerobic conditions in rice. This is the first study for accurate and reliable relative gene expression analysis in rice grown in aerobic and anaerobic conditions. [ABSTRACT FROM AUTHOR]