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PubMed | Indian International Crops Research Institute for the Semi Arid Tropics, Charles Sturt University, Africa Rice Center, International Rice Research Institute and 6 more.
Type: Journal Article | Journal: PloS one | Year: 2015

The rapid progress in rice genotyping must be matched by advances in phenotyping. A better understanding of genetic variation in rice for drought response, root traits, and practical methods for studying them are needed. In this study, the OryzaSNP set (20 diverse genotypes that have been genotyped for SNP markers) was phenotyped in a range of field and container studies to study the diversity of rice root growth and response to drought. Of the root traits measured across more than 20 root experiments, root dry weight showed the most stable genotypic performance across studies. The environment (E) component had the strongest effect on yield and root traits. We identified genomic regions correlated with root dry weight, percent deep roots, maximum root depth, and grain yield based on a correlation analysis with the phenotypes and aus, indica, or japonica introgression regions using the SNP data. Two genomic regions were identified as hot spots in which root traits and grain yield were co-located; on chromosome 1 (39.7-40.7 Mb) and on chromosome 8 (20.3-21.9 Mb). Across experiments, the soil type/ growth medium showed more correlations with plant growth than the container dimensions. Although the correlations among studies and genetic co-location of root traits from a range of study systems points to their potential utility to represent responses in field studies, the best correlations were observed when the two setups had some similar properties. Due to the co-location of the identified genomic regions (from introgression block analysis) with QTL for a number of previously reported root and drought traits, these regions are good candidates for detailed characterization to contribute to understanding rice improvement for response to drought. This study also highlights the utility of characterizing a small set of 20 genotypes for root growth, drought response, and related genomic regions.


Saikumar S.,Barwale Foundation | Saikumar S.,Osmania University | Saikumar S.,Directorate of Rice Research | Kalmeshwer Gouda P.,Monsanto Corporation | And 5 more authors.
Field Crops Research | Year: 2014

Water stress is a major abiotic stress limiting the rice production and yield stability in rainfed conditions and getting worse with the predicted global climatic change. A Backcross inbred line (BIL) population derived from Swarna/WAB 450-I-B-P-157-2-1 was screened for grain yield under reproductive stage drought stress and irrigated conditions during DS2013, WS2012 and DS2012. A major qDTY3.2 with large and consistent effect on grain yield was mapped on chromosome 3 flanked by RM14303 and RM22 across three seasons under both stress and control conditions. qDTY3.2 explained a phenotypic variance of 29.5%, 18.8% and 31.8% under drought stress during DS13, WS12 and DS12, respectively. Apart from grain yield, qDTY3.2 is also account for variation in canopy temperature during flowering and seedling shoot dry weight and drought recovery under stress conditions. Lines with QTL showed a clear grain yield advantage over lines without QTL under both stress and control conditions. Due to the consistent effect of qDTY3.2 across diverse environments and varied level of stresses makes it an appropriate candidate for MAS. Introgression of such genomic regions in to elite drought susceptible backgrounds can lead to enhancement of grain yield level to a greater extent. © 2014 Elsevier B.V.


Gouda P.K.,Barwale Foundation Barwale Chambers and 3 6 666 | Gouda P.K.,Monsanto Corporation | Saikumar S.,Barwale Foundation Barwale Chambers and 3 6 666 | Varma C.M.K.,Barwale Foundation Barwale Chambers and 3 6 666 | And 8 more authors.
Plant Breeding | Year: 2013

Rice blast, caused by fungus Magnaporthe grisea, is a serious disease causing considerable economic damage worldwide. Best way to overcome disease is to breed for disease-resistant cultivars/parental lines of hybrids. Pusa RH10, first aromatic, fine-grain rice hybrid released and cultivated extensively in India. Hybrid and its parental lines, Pusa 6A and PRR78, are highly susceptible to blast. CO39 pyramid carrying two dominant, broad-spectrum blast-resistance genes, viz. Pi-1 and Piz-5, used as a donor parent to introgress these genes into PRR78 using marker-assisted backcrossing (MABC). Microsatellite markers RM5926 and AP5659-5 tightly linked to Pi-1 and Piz-5 genes, respectively, were used for foreground selection to derive introgression lines. Further, these lines were evaluated for agronomic performance, disease reaction and cooking quality traits along with PRR78. Most of the improved lines were on par with PRR78 for all traits evaluated except gelatinization temperature. Recurrent parent genome percentage (RPG) study also revealed similarity of these lines with PRR78. Hybrids derived using improved PRR78 lines were superior over Pusa RH10 in terms of yield. © 2012 Blackwell Verlag GmbH.


Khera P.,Barwale Foundation | Priyadarshi R.,Barwale Foundation | Singh A.,Barwale Foundation | Mohan R.,Barwale Foundation | And 4 more authors.
Journal of Biological Sciences | Year: 2012

With the objective of identifying mitochondrial DNA based markers that can distinguish cytoplasmic sources and restorer lines, 7 male sterile and fertile counterparts of Cytoplasmic Male Sterile (CMS) lines and 4 restorers (R) lines were characterized, using 20 universal mitochondrial DNA specific markers. Diverse CMS lines, other than the Wild Abortive (WA) one have been developed at International Rice Research Institute (IRRI), Philippines (IR66707A with cytoplasm of Oryza perennis), Central Rice Research Institute (CRRI), Cuttack (CRMS-32A with "Kalinga" cytoplasm from 'Dunghansali') and at Directorate of Rice Research (DRR), Hyderabad (DMS 3A with cytoplasm of Oryza nivara and DMS 4A with cytoplasm of Oryza rufipogon). Traditionally, the differences between the cytoplasmic sources were studied by differential response of the Cytoplasmic Male Sterile (CMS) lines when test crossed with a set of known maintainers and restorers. However, these methods could not distinguish the genetic variation at molecular level, since, CMS trait has been found to be associated to mitochondrial DNA aberration. In the present study, seven potential primers were identified, viz., coxlB, nad4exl, nad5D, nadl, alp, nad4ex2 and rpSl 4 which showed polymorphism. The results suggested effective utilization of mitochondrial specific primer pairs in hybrid purity testing and marker aided heterosis breeding in rice. © 2012 Asian Network for Scientific Information.


Shanti M.L.,Barwale Foundation | Shenoy V.V.,Barwale Foundation | Devi G.L.,Barwale Foundation | Kumar V.M.,Barwale Foundation | And 5 more authors.
Journal of Plant Pathology | Year: 2010

Molecular markers are becoming essential components in breeding programs involving gene pyramiding. Using marker-assisted selection in a backcross-breeding program, four bacterial blight resistant genes namely Xa4, xa5, xa13 and Xa21 have been introgressed into the hybrid rice parental lines KMR3, PRR78, IR58025B, Pusa 6B and the popular cv. Mahsuri. Only foreground selection was done using markers. Conventional breeding strategy was adopted for background selection. The pyramids showed very high level of disease resistance to 10 highly virulent isolates of Xanthomonas oryzae pv. oryzae. Grain quality parameters of the pyramids were on par with that of the original genotype. This work reports the successful application of marker-assisted breeding for pyramiding simultaneously four bacterial blight resistant genes into multiple backgrounds. These lines can be used directly or can be used as donors of bacterial blight (BB) resistance breeding.


Kalmeshwer Gouda P.,Barwale Foundation | Mohan Kumar Varma C.,Barwale Foundation | Saikumar S.,Barwale Foundation | Kiran B.,Barwale Foundation | And 2 more authors.
Crop Science | Year: 2012

Rice (Oryza sativa L.) is one of the important food crops drastically affected by drought. Considering the low heritability of grain yield under water stress, several secondary traits associated with drought tolerance have been used, but the success achieved in deriving cultivars with high yield potential under stress is less compared to irrigated conditions. Hence, objective of the experiment was to estimate heritability for grain yield under lowland stress and select for grain yield per se using wild species Oryza meridionalis Ng and also to identify physio-morphological traits responsible for withstanding water stress. A population derived from O. sativa cv. IR58025B × O. meridionalis (BC 2F 3) was evaluated under control and stress conditions. Variability observed for yield and component traits indicated O. meridionalis to be a good source of useful alleles for drought tolerance. Broad-sense heritability (h 2) of grain yield under stress, although only 33.1%, was comparable to control 59.4%, indicating direct selection for grain yield per se can be practiced. Twenty high-yielding selected lines and 40 random lines were evaluated under control and stress conditions to estimate selection response. Yield of selected lines outperformed random lines and checks under stress. Furthermore, 10 lines (5 high yielding and 5 low yielding) selected from the population were characterized for root morphological traits. Maximum root length (MRL) and root volume (RV) of selected high-yielding lines recorded maximum compared with checks and low-yielding lines indicating positive influence of drought avoidance root traits on grain yield under stress. Hence, O. meridionalis can be a good source of root traits contributing to stress tolerance and selection for grain yield under stress is an effective strategy in deriving drought tolerant lines in rice. © Crop Science Society of America.


Khera P.,Barwale Foundation | Khera P.,Indian International Crops Research Institute for the Semi Arid Tropics | Singh A.K.,Barwale Foundation | Priyadarshi R.,Barwale Foundation | And 7 more authors.
Plant Genetic Resources: Characterisation and Utilisation | Year: 2015

To maximize heterosis, it is important to understand the genetic diversity of germplasm and associate useful phenotypic traits such as fertility restoration for hybrid rice breeding. The objectives of the present study were to characterize genetic diversity within a set of rice germplasm groups using coefficient of parentage (COP) values and 58 simple sequence repeat (SSR) markers for 124 genotypes having different attributes such as resistance/tolerance to various biotic and abiotic stresses. These lines were also used for identifying prospective restorers and maintainers for wild abortive-cytoplasmic male sterile (CMS) line. The mean COP value for all the lines was 0.11, indicating that the genotypes do not share common ancestry. The SSR analysis generated a total of 268 alleles with an average of 4.62 alleles per locus. The mean polymorphism information content value was 0.53, indicating that the markers selected were highly polymorphic. Grouping based on COP analysis revealed three major clusters pertaining to the indica, tropical japonica and japonica lines. A similar grouping pattern with some variation was also observed for the SSR markers. Fertility restoration phenotype based on the test cross of the 124 genotypes with a CMS line helped identify 23 maintainers, 58 restorers and 43 genotypes as either partial maintainers or partial restorers. This study demonstrates that COP analysis along with molecular marker analysis might encourage better organization of germplasm diversity and its use in hybrid rice breeding. Potential restorers identified in the study can be used for breeding high-yielding stress-tolerant medium-duration rice hybrids, while maintainers would prove useful for developing new rice CMS lines. © NIAB 2014.


Devi G.L.,Barwale Foundation | Koradi P.,Barwale Foundation | Shenoy V.,Barwale Foundation | Shanti M.L.,Barwale Foundation
Journal of Plant Pathology | Year: 2013

PRR78 and KMR3 are popular restorer lines of the rice (Oryza sativa L.) hybrids Pusa RH10 and KRH2, respectively. These lines are highly susceptible to bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae. Nine families each of PRR78 and KMR3 pyramids containing Xa4, xa5, xa13 and Xa21 resistance genes were evaluated for agronomic and related characters (viz., days to 50% flowering, plant height, number of tillers, panicle length, filled grains per panicle, percentage of spikelet fertility, 1000 grain weight, yield, biomass, harvest index and disease resistance). There were no significant differences within the families of the pyramids with respect to any of the characters evaluated. Under disease-free conditions, there was no difference between the parents and the pyramid families for the characters evaluated. However, under inoculated conditions of heavy disease pressure: (i) the parents exhibited highly susceptible reaction, whereas all the families of pyramids of both genotypes were highly resistant; (ii) pronounced variation was observed between the parents and the pyramids under inoculated conditions for the characters viz., FG/P, SF%, 1000 GW and Y. With respect to yield under diseased conditions there was a loss to the extent of 28% in PRR78 and 24% in KMR3 compared to the pyramid families. The pyramids thus protected against the yield loss and pyramiding of the four resistance genes did not have any yield penalty. These pyramids can be used directly in the breeding programs or as potential donors of bacterial blight resistance.


Saikumar S.,Barwale Foundation | Saiharini A.,Barwale Foundation | Patil V.,Barwale Foundation | Patil V.,Mahindra and Mahindra. Ltd
European Journal of Agronomy | Year: 2015

Identification and understanding the role of physio-morphological drought responsive mechanisms leading to grain yield enhancement under water stress is a critical insight for designing appropriate strategies to breed drought-tolerant cultivars for any drought prone ecology. In this study, three pairs of contrasting BILs with varied maturity were characterized for several agronomical, physiological and morphological traits across a wide range of moisture stress environments at reproductive stage during 2012-2014. Within each group, BILs differ significantly for grain yield, heading, biomass and harvest index under drought stress, but showed similar yield potential, phenology and other traits under control condition. The most tolerant BIL, S-15 out yielded all BILs and standard checks under both conditions. Apart from superior agronomic performance, drought tolerant BILs maintained significantly higher assimilation rate, transpiration rate and transpiration efficiency compared to susceptible BILs under stress in all three groups. In addition, most tolerant BIL (S-15) showed significantly higher stomatal conductance than susceptible BIL (S-55) in early group. Among root traits, significant differences under stress was observed for root dry weight between contrasting BILs in each group, even though tolerant BILs had higher root length and root volume compared to susceptible BILs, which is non-significant. Hence, consideration of root traits an important strategy for drought avoidance in case of rice may not always contributes to significant yield improvement under moisture stress condition. Further, tolerant BILs also recorded significantly higher shoot dry weight and drought recovery score at seedling stage under stress. Our findings suggest that genotypes with higher photosynthetic efficiency and better plant water status are able to produce higher grain yield under drought stress environments. © 2015 Elsevier B.V.


Jain A.,Barwale Foundation | Balaravi P.,Osmania University | Shenoy V.,Barwale Foundation
Biologia (Poland) | Year: 2013

The progress in development and dissemination of drought tolerant lines has been slow as compared to the increasing drought prevalence in the rice growing regions. Significant amount of work has been done in the past on drought resistance traits in rice crop, still the benefit of improved drought tolerant rice cultivars reaching the farmer's field is not very high and ways to expedite the development of drought tolerant and productive rice cultivars needs to be addressed. In this article, an assessment of easily practicable approach of managed stress screening and prospect of direct selection for yield under drought stress is discussed. Also the large effect yield QTLs identified for grain yield under drought stress field conditions is being reviewed for successful introgression into elite genetic background for developing drought tolerant cultivars with improved yield for the drought prone target environment. © 2013 Versita Warsaw and Springer-Verlag Wien.

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