title: From QTL to variety-harnessing the benefits of QTLs for drought, flood and salt tolerance in mega rice varieties of India through a multi-institutional network.
abstract: 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.
authors.affiliation: National Research Centre on Plant Biotechnology, New Delhi, India.
authors.forename: Renu
authors.initials: R
authors.lastname: Singh
authors.affiliation: National Research Centre on Plant Biotechnology, New Delhi, India.
authors.forename: Yashi
authors.initials: Y
authors.lastname: Singh
authors.affiliation: Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhatisgarh, India.
authors.forename: Suchit
authors.initials: S
authors.lastname: Xalaxo
authors.affiliation: Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhatisgarh, India.
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authors.lastname: Verulkar
authors.affiliation: National Research Centre on Plant Biotechnology, New Delhi, India.
authors.forename: Neera
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authors.affiliation: National Research Centre on Plant Biotechnology, New Delhi, India.
authors.forename: Shweta
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authors.lastname: Singh
authors.affiliation: National Research Centre on Plant Biotechnology, New Delhi, India.
authors.forename: Nisha
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authors.lastname: Singh
authors.affiliation: Acharya N.G. Ranga Agricultural University, Maruteru, AP, India.
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authors.affiliation: Acharya N.G. Ranga Agricultural University, Maruteru, AP, India.
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authors.affiliation: Acharya N.G. Ranga Agricultural University, Maruteru, AP, India.
authors.forename: P V Ramana
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authors.lastname: Rao
authors.affiliation: Acharya N.G. Ranga Agricultural University, Maruteru, AP, India.
authors.forename: M Girija
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authors.lastname: Rani
authors.affiliation: Acharya N.G. Ranga Agricultural University, Maruteru, AP, India.
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authors.lastname: Anuradha
authors.affiliation: Acharya N.G. Ranga Agricultural University, Maruteru, AP, India.
authors.forename: Y
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authors.lastname: Suraynarayana
authors.affiliation: ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, India.
authors.forename: P C
authors.initials: PC
authors.lastname: Sharma
authors.affiliation: ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, India.
authors.forename: S L
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authors.lastname: Krishnamurthy
authors.affiliation: ICAR-Central Soil Salinity Research Institute, Karnal, Haryana, India.
authors.forename: S K
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authors.lastname: Sharma
authors.affiliation: Acharya Narendra Dev University of Agriculture and Technology, Faizabad, UP, India.
authors.forename: J L
authors.initials: JL
authors.lastname: Dwivedi
authors.affiliation: Acharya Narendra Dev University of Agriculture and Technology, Faizabad, UP, India.
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authors.initials: AK
authors.lastname: Singh
authors.affiliation: Banaras Hindu University, Varanasi, UP, India.
authors.forename: P K
authors.initials: PK
authors.lastname: Singh
authors.affiliation: Rajendra Agricultural University, Samastipur, Bihar, India.
authors.lastname: Nilanjay
authors.affiliation: Rajendra Agricultural University, Samastipur, Bihar, India.
authors.forename: N K
authors.initials: NK
authors.lastname: Singh
authors.affiliation: Rajendra Agricultural University, Samastipur, Bihar, India.
authors.forename: Rajesh
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authors.lastname: Kumar
authors.affiliation: Assam Agricultural University, Jorhat, Assam, India.
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authors.initials: SK
authors.lastname: Chetia
authors.affiliation: Assam Agricultural University, Jorhat, Assam, India.
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authors.lastname: Ahmad
authors.affiliation: Central Agricultural University, Umiam, Meghalaya, India.
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authors.lastname: Rai
authors.affiliation: Jawahar Lal Nehru Krishi Vishwavidyalaya, Reewa, MP, India.
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authors.lastname: Perraju
authors.affiliation: Birsa Agricultural University, Ranchi, Jharkhand, India.
authors.forename: Anita
authors.initials: A
authors.lastname: Pande
authors.affiliation: Birsa Agricultural University, Ranchi, Jharkhand, India.
authors.forename: D N
authors.initials: DN
authors.lastname: Singh
authors.affiliation: ICAR-Central Rice Research Institute, Cuttack, Odisha, India.
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authors.initials: NP
authors.lastname: Mandal
authors.affiliation: ICAR-Central Rice Research Institute, Cuttack, Odisha, India.
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authors.lastname: Reddy
authors.affiliation: ICAR-Central Rice Research Institute, Cuttack, Odisha, India.
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authors.initials: ON
authors.lastname: Singh
authors.affiliation: ICAR-Central Rice Research Institute, Cuttack, Odisha, India.
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authors.lastname: Katara
authors.affiliation: ICAR-Central Rice Research Institute, Cuttack, Odisha, India.
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authors.affiliation: ICAR-Central Rice Research Institute, Cuttack, Odisha, India.
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authors.lastname: Swain
authors.affiliation: ICAR-Central Rice Research Institute, Cuttack, Odisha, India.
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authors.affiliation: ICAR-Central Rice Research Institute, Cuttack, Odisha, India.
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authors.lastname: Mohapatra
authors.affiliation: ICAR-Indian Institute of Rice Research, Hyderabad, India.
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authors.lastname: Padmawathi
authors.affiliation: ICAR-Indian Institute of Rice Research, Hyderabad, India.
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authors.affiliation: Annamalai University, Annamalai Nagar, TN, India.
authors.forename: R M
authors.initials: RM
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authors.affiliation: Pandit Jawaharlal Nehru College of Agriculture & Research Institute, Karikal, Puducherry, India.
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authors.lastname: Paramsivam
authors.affiliation: Pandit Jawaharlal Nehru College of Agriculture & Research Institute, Karikal, Puducherry, India.
authors.forename: S
authors.initials: S
authors.lastname: Nadarajan
authors.affiliation: Pandit Jawaharlal Nehru College of Agriculture & Research Institute, Karikal, Puducherry, India.
authors.forename: S
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authors.lastname: Thirumeni
authors.affiliation: ICAR-Indian Agricultural Research Institute, Aduthurai, TN, India.
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authors.lastname: Nagarajan
authors.affiliation: ICAR-Indian Agricultural Research Institute, New Delhi, India.
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authors.affiliation: International Rice Research Institute, Los Banos, Philippines.
authors.forename: Prashant
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authors.lastname: Vikram
authors.affiliation: International Rice Research Institute, Los Banos, Philippines.
authors.forename: Arvind
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authors.lastname: Kumar
authors.affiliation: International Rice Research Institute, Los Banos, Philippines.
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authors.initials: E
authors.lastname: Septiningshih
authors.affiliation: International Rice Research Institute, Los Banos, Philippines.
authors.forename: U S
authors.initials: US
authors.lastname: Singh
authors.affiliation: International Rice Research Institute, Los Banos, Philippines.
authors.forename: A M
authors.initials: AM
authors.lastname: Ismail
authors.affiliation: International Rice Research Institute, Los Banos, Philippines.
authors.forename: D
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authors.lastname: Mackill
authors.affiliation: National Research Centre on Plant Biotechnology, New Delhi, India. Electronic address: nksingh4@gmail.com.
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authors.lastname: Singh
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics; D002874:Chromosome Mapping / Q000379:methods; D032461:Chromosomes, Plant / Q000235:genetics; D055864:Droughts; D055868:Floods; D005819:Genetic Markers / Q000235:genetics; D006078:Government Programs; D007194:India; D012275:Oryza / Q000235:genetics* / Q000254:growth & development; D000069600:Plant Breeding / Q000379:methods; D020641:Polymorphism, Single Nucleotide; D040641:Quantitative Trait Loci / Q000235:genetics*; D015203:Reproducibility of Results; D055049:Salt Tolerance / Q000235:genetics*; D000068618:Selective Breeding
chemical_list: D005819:Genetic Markers
keywords: Drought; Marker-assisted backcross breeding (MABB); Quantitative trait loci (QTL); Rice; Salinity; Submergence