•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.
Helminthosporiosis or brown spot disease is widely distributed and is known to cause heavy yield losses in rice. In present investigation, a set of 154 doubled haploid (DH) lines derived from a cross ...between CT 9993-5-10-1 M and IR 62266-42-6-2 was used to identify quantitative trait loci (QTLs) for brown spot disease. DH lines along with parents were planted in two different soil environments with two replications each in RCBD and evaluated for the brown spot resistance. We have identified total 10 QTLs for brown spot resistance using MAPMAKER/QTL 1.1 distributed over the eight chromosome of rice. Out of 10 QTLs, four were consistently discovered in both the soil types. The aTL BSq4.1 and BSq11.1 located on the chromosome 4 and 11 were identified in both the environment with higher LOD score and phenotypic variance and will be good candidates for fine mapping and positional cloning studies.
The Portuguese purse seine fishery, with average annual catches of 70000 tonnes, operates mainly in coastal areas and targets small pelagic fish (SPF). Potential competition for resources may occur ...between the fishery and some species of marine mammals and seabirds, as suggested by observed incidental catches. For those species directly affected by the fishery, the spatial distribution of marine taxa and the fishing fleet are key pieces of information for spatial planning and management. We analysed the spatial and resource overlap between the fishery’s distribution and effort, and the distribution and abundance of 6 species of top predators—seabirds (n = 4) and marine mammals (n = 2) between 2010 and 2014. Estimates of annual consumption by top predators and the fishery catch within the distributional range of one of their main prey species (sardine Sardina pilchardus) were also determined. Spatial overlap between all considered species and the fishery was low (<0.221), and only 2 species (common dolphins Delphinus delphis and Cory’s shearwaters Calonectris borealis) showed high resource overlap with the fishery (>0.7). Overall, values of consumption of SPF by the top predators were of the same order of magnitude as mean annual purse seine landings for the studied area. Our results can be used for marine spatial planning, including designation of Marine Protected Areas and the development of an ecosystem-based model for the effective management of the Portuguese purse seine fishery that takes into account the consumption of natural predators.
The cytoplasmic male sterile line system comprising CRMS 32A and its maintainer line CRMS 32B is a popular choice for the development of new hybrids in India as CRMS 32A, having Kalinga 1 cytoplasm ...(other than WA), is a viable alternative to WA cytoplasm. However, both lines are susceptible to bacterial blight (BB), a major disease on rice. As enhancement of host plant resistance is the most effective and economical strategy to control this disease, four resistance genes (Xa4, xa5, xa13, and Xa21) were transferred from a BB pyramid line of IR64, into the A and B lines using a marker-assisted backcrossing (MAB) breeding strategy. During the transfer of genes into CRMS 32B, foreground selection was applied using markers associated with the genes, and plants having resistance alleles of the donor, are selected. Selection for morphological and quality traits was practiced to select plants similar to the recurrent parent. The four gene and three gene pyramid lines exhibited high levels of resistance against the BB pathogen when challenged with eight virulent isolates. Using genome wide based SSR markers for background selection, pyramids having >95% of the recurrent parent genome were identified. With CRMS 32B gene pyramid as donor, the four resistance genes were transferred into the A line through repeated backcrosses and the A line pyramids also exhibited high level of resistance against BB. Through a combination of selection at phenotypic and molecular levels, four BB resistance genes were successfully introduced into two parental lines (CRMS 32 B and A) of Rajalaxmi, an elite popular hybrid. The pyramided B lines did exhibit high levels of resistance against BB. Selection for morphological and quality traits and background selection hastened the recovery of the recurrent parent genome in the recombinants. Through repeated backcrosses, all the four resistance genes were transferred to CRMS 32A and test crosses suggest that the maintenance ability of the improved CRMS 32B lines is intact. These improved maintainer and CMS lines can directly be used in hybrid rice breeding and the new hybrids can play an important role in sustainable rice production in India.
Submergence is the third most important abiotic stress hugely affecting yield and productivity in rice. There are many wild varieties and landraces available which are tolerant to submergence stress. ...These genotypes can be utilized as donors in different breeding programs. The population derived from such germplasms are subjected to genetic evaluation for yield and yield related attributes for development of lines that are high yielding as well as tolerant to submergence. The present investigation was executed in 120 Recombinant Inbred Lines (RIL) population (F10) derived from Swarna-Sub1 x AC 20431B along with four land races and Swarna-Sub1 to elucidate the association existing between yield and yield attributing characters. Apart from this, Correlation and path analysis was also employed to study direct and indirect effect on grain yield. Observations for agro-morphological traits such as days to 50% flowering, plant height, panicle length, total number of tillers, number of effective tillers per plant, number of filled grains and Spikelet fertility, test weight, grain yield per plant, biomass per plant and harvest index were recorded and analyzed for various variability parameters. Correlation and path coefficient analysis were also carried out. High heritability and genetic advance values were observed for days to 50% flowering, plant height, panicle length, total number of tillers per plant, effective tillers per plant, filled grains per panicle, spikelet fertility, test weight, grain yield and biomass per plant. Among all the characters; filled grains per panicle, biomass and harvest index per plant showed significant correlation with grain yield. Effective number of tillers per plant has the highest positive direct effect on grain yield.
Rice is the most important food crop both in value and
volume for the Asian population. Frequent drought, flood
and salinity stresses exacerbated by global climate change
adversely affect rice ...production in more than fifty percent
of the rice growing areas. Green revolution high yielding
varieties carrying sd1 dwarfing gene have almost fully
replaced the traditional climate resilient landraces and
varieties of rice. However, these were bred primarily for
yield under high input conditions and therefore are sensitive
to adverse climatic conditions. Hence, there is urgent need
to combine the high productivity with climate resilience.
Knowledge of rice genome and genes for tolerance to
different abiotic stresses provided us an opportunity to
transfer favorable alleles of these genes into high yielding
varieties through genomics-assisted backcross breeding
through multi-institutional networks. Six consistent
genomic regions (QTLs) for grain yield under drought;
namely qDTY1.1, qDTY2.1, qDTY2.2, qDTY3.1, qDTY3.2 and
qDTY12.1 have been transferred to flood tolerant versions
of mega varieties of rice, Swarna, Samba Mahsuri and IR 64.
To address the problem of flash flooding qSUB1 QTL has
been transferred to nine popular rice varieties, namely ADT
46, Bahadur, Ranjit, HUR 105, Sarjoo 52, Pooja, Pratikshya
MTU 1075 and Rajendra Mahsuri. Further, qSALTOL1 QTL
for seedling stage salt tolerance and qSSISFH8.1 for
reproductive stage salt tolerance have been transferred to
six popular rice varieties, ADT 45, Gayatri, MTU 1010, PR
114, Pusa 44 and Sarjoo 52. We used foreground selection
markers for the presence of desired gene/QTL and
recombinant selection markers for reduction of linkage drag
around these genes. Genotypic background selection was
done after BC3F3 stage using a 50K SNP chip on a set of 20
advance lines obtained by phenotypic selection for
closeness to the recipient parents. Near-isogenic lines
(NILs) with more than 95% similarity to the recipient parent
genome have been released and notified for commercial
cultivation and are gaining fast popularity. These climate
smart rice varieties will provide production stability in the
adverse ecologies and support farmer’s income and
livelihood.
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