KEY MESSAGE : A set of NILs carrying major blast resistance genes in a Basmati rice variety has been developed. Also, the efficacy of pyramids over monogenic NILs against rice blast pathogen ...Magnaporthe oryzae has been demonstrated. Productivity and quality of Basmati rice is severely affected by rice blast disease. Major genes and QTLs conferring resistance to blast have been reported only in non-Basmati rice germplasm. Here, we report incorporation of seven blast resistance genes from the donor lines DHMASQ164-2a (Pi54, Pi1, Pita), IRBLz5-CA (Pi2), IRBLb-B (Pib), IRBL5-M (Pi5) and IRBL9-W (Pi9) into the genetic background of an elite Basmati rice variety Pusa Basmati 1 (PB1). A total of 36 near-isogenic lines (NILs) comprising of 14 monogenic, 16 two-gene pyramids and six three-gene pyramids were developed through marker-assisted backcross breeding (MABB). Foreground, recombinant and background selection was used to identify the plants with target gene(s), minimize the linkage drag and increase the recurrent parent genome (RPG) recovery (93.5–98.6 %), respectively, in the NILs. Comparative analysis performed using 50,051 SNPs and 500 SSR markers revealed that the SNPs provided better insight into the RPG recovery. Most of the monogenic NILs showed comparable performance in yield and quality, concomitantly, Pusa1637-18-7-6-20 (Pi9), was significantly superior in yield and stable across four different environments as compared to recurrent parent (RP) PB1. Further, among the pyramids, Pusa1930-12-6 (Pi2+Pi5) showed significantly higher yield and Pusa1633-7-8-53-6-8 (Pi54+Pi1+Pita) was superior in cooking quality as compared to RP PB1. The NILs carrying gene Pi9 were found to be the most effective against the concoction of virulent races predominant in the hotspot locations for blast disease. Conversely, when analyzed under artificial inoculation, three-gene pyramids expressed enhanced resistance as compared to the two-gene and monogenic NILs.
The North-Eastern region (NER) of India, comprising of Arunachal Pradesh, Assam, Manipur, Meghalaya, Mizoram, Nagaland and Tripura, is a hot spot for genetic diversity and the most probable origin of ...rice. North-east rice collections are known to possess various agronomically important traits like biotic and abiotic stress tolerance, unique grain and cooking quality. The genetic diversity and associated population structure of 6,984 rice accessions, originating from NER, were assessed using 36 genome wide unlinked single nucleotide polymorphism (SNP) markers distributed across the 12 rice chromosomes. All of the 36 SNP loci were polymorphic and bi-allelic, contained five types of base substitutions and together produced nine types of alleles. The polymorphic information content (PIC) ranged from 0.004 for Tripura to 0.375 for Manipur and major allele frequency ranged from 0.50 for Assam to 0.99 for Tripura. Heterozygosity ranged from 0.002 in Nagaland to 0.42 in Mizoram and gene diversity ranged from 0.006 in Arunachal Pradesh to 0.50 in Manipur. The genetic relatedness among the rice accessions was evaluated using an unrooted phylogenetic tree analysis, which grouped all accessions into three major clusters. For determining population structure, populations K = 1 to K = 20 were tested and population K = 3 was present in all the states, with the exception of Meghalaya and Manipur where, K = 5 and K = 4 populations were present, respectively. Principal Coordinate Analysis (PCoA) showed that accessions were distributed according to their population structure. AMOVA analysis showed that, maximum diversity was partitioned at the individual accession level (73% for Nagaland, 58% for Arunachal Pradesh and 57% for Tripura). Using POWERCORE software, a core set of 701 accessions was obtained, which accounted for approximately 10% of the total NE India collections, representing 99.9% of the allelic diversity. The rice core set developed will be a valuable resource for future genomic studies and crop improvement strategies.
Simple sequence repeat (SSR) and Single Nucleotide Polymorphic (SNP), the two most robust markers for identifying rice varieties were compared for assessment of genetic diversity and population ...structure. Total 375 varieties of rice from various regions of India archived at the Indian National GeneBank, NBPGR, New Delhi, were analyzed using thirty six genetic markers, each of hypervariable SSR (HvSSR) and SNP which were distributed across 12 rice chromosomes. A total of 80 alleles were amplified with the SSR markers with an average of 2.22 alleles per locus whereas, 72 alleles were amplified with SNP markers. Polymorphic information content (PIC) values for HvSSR ranged from 0.04 to 0.5 with an average of 0.25. In the case of SNP markers, PIC values ranged from 0.03 to 0.37 with an average of 0.23. Genetic relatedness among the varieties was studied; utilizing an unrooted tree all the genotypes were grouped into three major clusters with both SSR and SNP markers. Analysis of molecular variance (AMOVA) indicated that maximum diversity was partitioned between and within individual level but not between populations. Principal coordinate analysis (PCoA) with SSR markers showed that genotypes were uniformly distributed across the two axes with 13.33% of cumulative variation whereas, in case of SNP markers varieties were grouped into three broad groups across two axes with 45.20% of cumulative variation. Population structure were tested using K values from 1 to 20, but there was no clear population structure, therefore Ln(PD) derived Δk was plotted against the K to determine the number of populations. In case of SSR maximum Δk was at K=5 whereas, in case of SNP maximum Δk was found at K=15, suggesting that resolution of population was higher with SNP markers, but SSR were more efficient for diversity analysis.
•Marker-assisted backcross improvement of mega varieties of rice.•QTLs for drought, submergence and salt tolerance.•Foreground and recombinant selection.•Background selection using high density 50K ...SNP chip.
Rice is a staple cereal of India cultivated in about 43.5Mha area but with relatively low average productivity. Abiotic factors like drought, flood and salinity affect rice production adversely in more than 50% of this area. Breeding rice varieties with inbuilt tolerance to these stresses offers an economically viable and sustainable option to improve rice productivity. Availability of high quality reference genome sequence of rice, knowledge of exact position of genes/QTLs governing tolerance to abiotic stresses and availability of DNA markers linked to these traits has opened up opportunities for breeders to transfer the favorable alleles into widely grown rice varieties through marker-assisted backcross breeding (MABB). A large multi-institutional project, “From QTL to variety: marker-assisted breeding of abiotic stress tolerant rice varieties with major QTLs for drought, submergence and salt tolerance” was initiated in 2010 with funding support from Department of Biotechnology, Government of India, in collaboration with International Rice Research Institute, Philippines. The main focus of this project is to improve rice productivity in the fragile ecosystems of eastern, northeastern and southern part of the country, which bear the brunt of one or the other abiotic stresses frequently. Seven consistent QTLs for grain yield under drought, namely, qDTY1.1, qDTY2.1, qDTY2.2, qDTY3.1, qDTY3.2, qDTY9.1 and qDTY12.1 are being transferred into submergence tolerant versions of three high yielding mega rice varieties, Swarna-Sub1, Samba Mahsuri-Sub1 and IR 64-Sub1. To address the problem of complete submergence due to flash floods in the major river basins, the Sub1 gene is being transferred into ten highly popular locally adapted rice varieties namely, ADT 39, ADT 46, Bahadur, HUR 105, MTU 1075, Pooja, Pratikshya, Rajendra Mahsuri, Ranjit, and Sarjoo 52. Further, to address the problem of soil salinity, Saltol, a major QTL for salt tolerance is being transferred into seven popular locally adapted rice varieties, namely, ADT 45, CR 1009, Gayatri, MTU 1010, PR 114, Pusa 44 and Sarjoo 52. Genotypic background selection is being done after BC2F2 stage using an in-house designed 50K SNP chip on a set of twenty lines for each combination, identified with phenotypic similarity in the field to the recipient parent. Near-isogenic lines with more than 90% similarity to the recipient parent are now in advanced generation field trials. These climate smart varieties are expected to improve rice productivity in the adverse ecologies and contribute to the farmer’s livelihood.
Wheat cultivars are genetically crossed to improve end-use quality for traits as per demands of baking industry and broad consumer preferences. The processing and baking qualities of bread wheat are ...influenced by a variety of genetic make-ups, environmental factors and their interactions. Two wheat cultivars, WL711 and C306, derived recombinant inbred lines (RILs) with a population of 206, were used for phenotyping of quality-related traits. The genetic analysis of quality traits showed considerable variation for measurable quality traits, with normal distribution and transgressive segregation across the years. From the 206 RILs, few RILs were found to be superior to those of the parental cultivars for key quality traits, indicating their potential use for the improvement of end-use quality and suggesting the probability of finding new alleles and allelic combinations from the RIL population. Mapping analysis identified 38 putative QTLs for 13 quality-related traits, with QTLs explaining 7.9-16.8% phenotypic variation spanning over 14 chromosomes, i.e., 1A, 1B, 1D, 2A, 2D, 3B, 3D, 4A, 4B, 4D, 5D, 6A, 7A and 7B. In-silico analysis based on homology to the annotated wheat genes present in database, identified six putative candidate genes within QTL for total grain protein content, qGPC.1B.1 region. Major QTL regions for other quality traits such as TKW have been identified on 1B, 2A, and 7A chromosomes in the studied RIL population. This study revealed the importance of the combination of stable QTLs with region-specific QTLs for better phenotyping, and the QTLs presented in our study will be useful for the improvement of wheat grain and bread-making quality.
Finger millet (Eleusine coracana L.) is an important dry-land cereal in Asia and Africa because of its ability to provide assured harvest under extreme dry conditions and excellent nutritional ...properties. However, the genetic improvement of the crop is lacking in the absence of suitable genomic resources for reliable genotype-phenotype associations. Keeping this in view, a diverse global finger millet germplasm collection of 113 accessions was evaluated for 14 agro-morphological characters in two environments viz. ICAR-Vivekananda Institute of Hill Agriculture, Almora (E1) and Crop Research Centre (CRC), GBPUA&T, Pantnagar (E2), India. Principal component analysis and cluster analysis of phenotypic data separated the Indian and exotic accessions into two separate groups. Previously generated SNPs through genotyping by sequencing (GBS) were used for association mapping to identify reliable marker(s) linked to grain yield and its component traits. The marker trait associations were determined using single locus single trait (SLST), multi-locus mixed model (MLMM) and multi-trait mixed model (MTMM) approaches. SLST led to the identification of 20 marker-trait associations (MTAs) (p value<0.01 and <0.001) for 5 traits. While advanced models, MLMM and MTMM resulted in additional 36 and 53 MTAs, respectively. Nine MTAs were common out of total 109 associations in all the three mapping approaches (SLST, MLMM and MTMM). Among these nine SNPs, five SNP sequences showed homology to candidate genes of Oryza sativa (Rice) and Setaria italica (Foxtail millet), which play an important role in flowering, maturity and grain yield. In addition, 67 and 14 epistatic interactions were identified for 10 and 7 traits at E1 and E2 locations, respectively. Hence, the 109 novel SNPs associated with important agro-morphological traits, reported for the first time in this study could be precisely utilized in finger millet genetic improvement after validation.
•Constructed wetland (CW) efficiently decreased up to 90% BOD from sewage in 24h.•P. australis, T. latifolia and C. esculenta (HGR) were main components of CW.•CW efficiently removed nutrients and ...metals from sewage.
With aim to develop an efficient and ecofriendly approach for on-site treatment of sewage, a sub-surface flow constructed wetland (CW) has been developed by raising potential aquatic macrophytes; Typha latifolia, Phragmites australis, Colocasia esculenta, Polygonum hydropiper, Alternanthera sessilis and Pistia stratoites in gravel as medium. Sewage treatment potential of CW was evaluated by varying retention time at three different stages of plant growth and stabilization. After 6months, monitoring of fully established CW indicated reduction of 90%, 65%, 78%, 84%, 76% and 86% of BOD, TSS, TDS, NO3–N, PO4–P and NH4–N, respectively in comparison to inlet after 36h of retention time. Sewage treatment through CW also resulted in reduction of heavy metal contents. Thus, CW proved an effective method for treatment of wastewater and may be developed along river Ganga stretch as an alternative technology. Treated water may be drained into river to check further deterioration of Ganga water quality.
Blast induced rock mass damage around tunnels Verma, H.K.; Samadhiya, N.K.; Singh, M. ...
Tunnelling and underground space technology,
January 2018, 2018-01-00, 20180101, Volume:
71
Journal Article
Peer reviewed
Drilling and blasting is a preferred method of rock excavation world-wide due to low initial investment, cheap explosive energy, easy acceptability among the blasting engineers and, possibility to ...deal with different shapes and sizes of openings. Although, drill and blast method has witnessed significant technological advancements, it has inherent disadvantage of deteriorating surrounding rock mass due to development of network of fine cracks in it leading to safety and stability problems. The damage in the peripheral rock mass culminates in the form of overbreak and damaged zone beyond overbreak. In some cases the projects cost has increased more than 15% because of overbreak. Although significant efforts have been made to assess damage to the surrounding rock mass using different methods, the solution based on easily available site parameters is still lacking. Authors have carried out field investigations at five different tunnels located in Himalaya, India to study blast induced damage for wide range of rock mass quality Q values (0.03–17.8). In addition to Q, specific charge, perimeter charge factor, maximum charge per delay, advancement and confinement factors have also been used. Data sets of 113 experimental blasts are collected from the five tunnel sites. All the parameters, easily available to the site engineers, have been used for developing an empirical correlation to estimate the rock mass damage around the tunnel, which is discussed in the paper. The proposed empirical correlation has been validated using ultrasonic tests on rock core samples obtained from one of the experimental location.
Salinity tolerance in rice is highly desirable to sustain production in areas rendered saline due to various reasons. It is a complex quantitative trait having different components, which can be ...dissected effectively by genome-wide association study (GWAS). Here, we implemented GWAS to identify loci controlling salinity tolerance in rice. A custom-designed array based on 6,000 single nucleotide polymorphisms (SNPs) in as many stress-responsive genes, distributed at an average physical interval of <100 kb on 12 rice chromosomes, was used to genotype 220 rice accessions using Infinium high-throughput assay. Genetic association was analysed with 12 different traits recorded on these accessions under field conditions at reproductive stage. We identified 20 SNPs (loci) significantly associated with Na(+)/K(+) ratio, and 44 SNPs with other traits observed under stress condition. The loci identified for various salinity indices through GWAS explained 5-18% of the phenotypic variance. The region harbouring Saltol, a major quantitative trait loci (QTLs) on chromosome 1 in rice, which is known to control salinity tolerance at seedling stage, was detected as a major association with Na(+)/K(+) ratio measured at reproductive stage in our study. In addition to Saltol, we also found GWAS peaks representing new QTLs on chromosomes 4, 6 and 7. The current association mapping panel contained mostly indica accessions that can serve as source of novel salt tolerance genes and alleles. The gene-based SNP array used in this study was found cost-effective and efficient in unveiling genomic regions/candidate genes regulating salinity stress tolerance in rice.
An examination of the therapeutics and diagnostics use of porphyrinoids including phthalocyanines and glycosylated porphyrins is offered. Topics covered include glycosylated phthalocyanines, ...glycosylated chlorins, isobacteriochlorins and bacteriochlorins and glycosylated porphyrazines.
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