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Sandhu N, Singh J, Ankush AP, Augustine G, Raigar OP, Verma VK, Pruthi G, Kumar A. Development of Novel KASP Markers for Improved Germination in Deep-Sown Direct Seeded Rice. Rice (N Y) 2024; 17:33. [PMID: 38727876 PMCID: PMC11087395 DOI: 10.1186/s12284-024-00711-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 04/30/2024] [Indexed: 05/13/2024]
Abstract
BACKGROUND The lack of stable-high yielding and direct-seeded adapted varieties with better germination ability from deeper soil depth and availability of molecular markers are major limitation in achieving the maximum yield potential of rice under water and resource limited conditions. Development of high-throughput and trait-linked markers are of great interest in genomics-assisted breeding. The aim of present study was to develop and validate novel KASP (Kompetitive Allele-Specific PCR) markers associated with traits improving germination and seedling vigor of deep sown direct seeded rice (DSR). RESULTS Out of 58 designed KASP assays, four KASP assays did not show any polymorphism in any of the eleven genetic backgrounds considered in the present study. The 54 polymorphic KASP assays were then validated for their robustness and reliability on the F1s plants developed from eight different crosses considered in the present study. The third next validation was carried out on 256 F3:F4 and 713 BC3F2:3 progenies. Finally, the reliability of the KASP assays was accessed on a set of random 50 samples from F3:F4 and 80-100 samples from BC3F2:3 progenies using the 10 random markers. From the 54 polymorphic KASP, based on the false positive rate, false negative rate, KASP utility in different genetic backgrounds and significant differences in the phenotypic values of the positive (desirable) and negative (undesirable) traits, a total of 12 KASP assays have been selected. These 12 KASP include 5 KASP on chromosome 3, 1 on chromosome 4, 3 on chromosome 7 and 3 on chromosome 8. The two SNPs lying in the exon regions of LOC_Os04g34290 and LOC_Os08g32100 led to non-synonymous mutations indicating a possible deleterious effect of the SNP variants on the protein structure. CONCLUSION The present research work will provide trait-linked KASP assays, improved breeding material possessing favourable alleles and breeding material in form of expected pre-direct-seeded adapted rice varieties. The marker can be utilized in introgression program during pyramiding of valuable QTLs/genes providing adaptation to rice under DSR. The functional studies of the genes LOC_Os04g34290 and LOC_Os08g32100 possessing two validated SNPs may provide valuable information about these genes.
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Affiliation(s)
- Nitika Sandhu
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| | - Jasneet Singh
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | | | | | | | | | - Gomsie Pruthi
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Arvind Kumar
- Delta Agrigenetics, Plot No. 99 & 100 Green Park Avenue, Village, Jeedimetla, Secunderabad, Telangana, 500055, India
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Kaur M, Sharma S, Kalia A, Sandhu N. Essential oils and their blends: mechanism of antibacterial activity and antibiofilm potential on food-grade maize starch packaging films. Int Microbiol 2024:10.1007/s10123-024-00514-w. [PMID: 38506949 DOI: 10.1007/s10123-024-00514-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 03/05/2024] [Accepted: 03/12/2024] [Indexed: 03/22/2024]
Abstract
Essential oils are highly complex volatile chemical compounds utilized for food preservation. The present study compares the antibacterial, and antibiofilm activities of essential oils (EOs) and their blends. Three EOs-basil, clove, and lemongrass-and their blends were evaluated against five food-borne bacterial pathogens. A concentration-dependent effect with maximum inhibition at minimum inhibitory concentration values was recorded while no synergistic activity was observed on blending of EOs. The mechanism of antibacterial action was identified as ROS burst, leakage of cytoplasmic content, and DNA degradation through fluorescence microscopy, electrical conductivity, and DNA cleavage studies. The role of EOs on biofilm growth was deciphered with lemongrass EO being most effective as it curbed biofilm formation on the surface of corn-starch packaging films. This work highlights the antibacterial action mechanism of EOs and their potential role in curtailing biofilm growth on food-grade packaging material.
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Affiliation(s)
- Manpreet Kaur
- Department of Microbiology, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana, Pincode:141004, Punjab, India
| | - Shivani Sharma
- Department of Microbiology, College of Basic Sciences and Humanities, Punjab Agricultural University, Ludhiana, Pincode:141004, Punjab, India
| | - Anu Kalia
- Electron Microscoy and Nanoscience Laboratory, Department of Soil Science, College of Agriculture, Punjab Agricultural University, Ludhiana, Pincode:141004, Punjab, India.
| | - Nitika Sandhu
- School of Agricultural Biotechnology, College of Agriculture, Punjab Agricultural University, Ludhiana, Pincode:141004, Punjab, India
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Sandhu N, Ankush AP, Singh J, Raigar OP, Bains S, Jindal T, Singh MP, Sethi M, Pruthi G, Augustine G, Verma VK, Goyal S, Kumar A, Panwar H, Sihag MK, Kaur R, Kurup S, Kumar A. Integrating Association Mapping, Linkage Mapping, Fine Mapping with RNA Seq Conferring Seedling Vigor Improvement for Successful Crop Establishment in Deep Sown Direct-Seeded Rice. Rice (N Y) 2023; 16:46. [PMID: 37848638 PMCID: PMC10581981 DOI: 10.1186/s12284-023-00665-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/12/2023] [Indexed: 10/19/2023]
Abstract
BACKGROUND Ongoing large-scale shift towards direct seeded rice (DSR) necessitates a convergence of breeding and genetic approaches for its sustenance and harnessing natural resources and environmental benefits. Improving seedling vigour remains key objective for breeders working with DSR. The present study aims to understand the genetic control of seedling vigour in deep sown DSR. Combined genome-wide association mapping, linkage mapping, fine mapping, RNA-sequencing to identify candidate genes and validation of putative candidate genes were performed in the present study. RESULTS Significant phenotypic variations were observed among genotypes in both F3:4:5 and BC2F2:3 populations. The mesocotyl length showed significant positive correlation with %germination, root and shoot length. The 881 kb region on chromosome 7 reported to be associated with mesocotyl elongation. RNA-seq data and RT-PCR results identified and validated seven potential candidate genes. The four promising introgression lines free from linkage drag and with longer mesocotyl length, longer root length, semi-dwarf plant height have been identified. CONCLUSION The study will provide rice breeders (1) the pre breeding material in the form of anticipated DSR adapted introgression lines possessing useful traits and alleles improving germination under deep sown DSR field conditions (2) the base for the studies involving functional characterization of candidate genes. The development and utilization of improved introgression lines and molecular markers may play an important role in genomics-assisted breeding (GAB) during the pyramiding of valuable genes providing adaptation to rice under DSR. Our results offer a robust and reliable package that can contribute towards enhancing genetic gains in direct seeded rice breeding programs.
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Affiliation(s)
- Nitika Sandhu
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
| | | | - Jasneet Singh
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | | | - Sutej Bains
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Taveena Jindal
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | | | - Mehak Sethi
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Gomsie Pruthi
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | | | | | - Shivani Goyal
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Aman Kumar
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Harsh Panwar
- Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, 141004, India
| | - Manvesh Kumar Sihag
- Guru Angad Dev Veterinary and Animal Sciences University, Ludhiana, Punjab, 141004, India
| | - Rupinder Kaur
- Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Smita Kurup
- Department of Plant Science, Rothamsted Research, Harpenden, Hertfordshire, AL5 2JQ, UK
| | - Arvind Kumar
- International Rice Research Institute (IRRI) South Asia Regional Centre (ISARC), Varanasi, Uttar Pradesh, 221106, India
- International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Telangana, 502324, India
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Sharma A, Arif MAR, Shamshad M, Rawale KS, Brar A, Burgueño J, Shokat S, Kaur R, Vikram P, Srivastava P, Sandhu N, Singh J, Kaur S, Chhuneja P, Singh S. Preliminary Dissection of Grain Yield and Related Traits at Differential Nitrogen Levels in Diverse Pre-Breeding Wheat Germplasm Through Association Mapping. Mol Biotechnol 2023; 65:116-130. [PMID: 35908127 DOI: 10.1007/s12033-022-00535-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 07/14/2022] [Indexed: 01/11/2023]
Abstract
Development of nutrient efficient cultivars depends on effective identification and utilization of genetic variation. We characterized a set of 276 pre-breeding lines (PBLs) for several traits at different levels of nitrogen application. These PBLs originate from synthetic wheats and landraces. We witnessed significant variation in various traits among PBLs to different nitrogen doses. There was ~ 4-18% variation range in different agronomic traits in response to nitrogen application, with the highest variation for the biological yield (BY) and the harvest index. Among various agronomic traits measured, plant height, tiller number, and BY showed a positive correlation with nitrogen applications. GWAS analysis detected 182 marker-trait associations (MTAs) (at p-value < 0.001), out of which 8 MTAs on chromosomes 5D, 4A, 6A, 1B, and 5B explained more than 10% phenotypic variance. Out of all, 40 MTAs observed for differential nitrogen application response were contributed by the synthetic derivatives. Moreover, 20 PBLs exhibited significantly higher grain yield than checks and can be selected as potential donors for improved plant nitrogen use efficiency (pNUE).
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Affiliation(s)
- Achla Sharma
- Punjab Agricultural University, Ludhiana, India.
| | - Mian A R Arif
- Nuclear Institute for Agriculture and Biology, Faisalabad, 38000, Pakistan
| | - M Shamshad
- Punjab Agricultural University, Ludhiana, India
| | | | | | - Juan Burgueño
- CIMMYT, Carretera México Veracruz Km. 45, El Batán, 56237, Texcoco, CP, Mexico
| | - Sajid Shokat
- Nuclear Institute for Agriculture and Biology, Faisalabad, 38000, Pakistan
| | | | - Parsahnt Vikram
- International Center for Biosaline Agriculture, Academic City, Dubai, UAE
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Kim H, Mutter R, Abraha F, Jakub J, Corbin K, Furutani K, Boughey J, Sukov W, Stish B, Deufel C, Degnim A, Shumway D, Ahmed S, Piltin M, Sandhu N, Conners A, Lee C, Ruddy K, Hieken T, Park S. Long-Term Outcome of Novel Intraoperatively-Placed Brachytherapy for Rapid Completion of Breast Conserving Therapy. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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6
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Wang J, Qu V, Hui C, Sandhu N, Mendoza M, Panjwani N, Lin J, Chang Y, Liang C, LU J, Wang L, Kovalchuk N, Gensheimer M, Soltys S, Pollom E. Stratified Assessment of a Commercial Deep Learning Algorithm for Automated Detection and Contouring of Metastatic Brain Tumors in Stereotactic Radiosurgery. Int J Radiat Oncol Biol Phys 2022. [DOI: 10.1016/j.ijrobp.2022.07.2193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
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7
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Kumar A, Sandhu N, Kumar P, Pruthi G, Singh J, Kaur S, Chhuneja P. Genome-wide identification and in silico analysis of NPF, NRT2, CLC and SLAC1/SLAH nitrate transporters in hexaploid wheat (Triticum aestivum). Sci Rep 2022; 12:11227. [PMID: 35781289 PMCID: PMC9250930 DOI: 10.1038/s41598-022-15202-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 06/20/2022] [Indexed: 11/09/2022] Open
Abstract
Nitrogen transport is one of the most important processes in plants mediated by specialized transmembrane proteins. Plants have two main systems for nitrogen uptake from soil and its transport within the system—a low-affinity transport system and a high-affinity transport system. Nitrate transporters are of special interest in cereal crops because large amount of money is spent on N fertilizers every year to enhance the crop productivity. Till date four gene families of nitrate transporter proteins; NPF (nitrate transporter 1/peptide transporter family), NRT2 (nitrate transporter 2 family), the CLC (chloride channel family), and the SLAC/SLAH (slow anion channel-associated homologues) have been reported in plants. In our study, in silico mining of nitrate transporter genes along with their detailed structure, phylogenetic and expression analysis was carried out. A total of 412 nitrate transporter genes were identified in hexaploid wheat genome using HMMER based homology searches in IWGSC Refseq v2.0. Out of those twenty genes were root specific, 11 leaf/shoot specific and 17 genes were grain/spike specific. The identification of nitrate transporter genes in the close proximity to the previously identified 67 marker-traits associations associated with the nitrogen use efficiency related traits in nested synthetic hexaploid wheat introgression library indicated the robustness of the reported transporter genes. The detailed crosstalk between the genome and proteome and the validation of identified putative candidate genes through expression and gene editing studies may lay down the foundation to improve nitrogen use efficiency of cereal crops.
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Affiliation(s)
- Aman Kumar
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Nitika Sandhu
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India.
| | - Pankaj Kumar
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Gomsie Pruthi
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Jasneet Singh
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Satinder Kaur
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
| | - Parveen Chhuneja
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, Punjab, India
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8
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Sandhu N, Singh J, Singh G, Sethi M, Singh MP, Pruthi G, Raigar OP, Kaur R, Kaur R, Sarao PS, Lore JS, Singh UM, Dixit S, Sagare DB, Singh S, Satturu V, Singh VK, Kumar A. Development and validation of a novel core set of KASP markers for the traits improving grain yield and adaptability of rice under direct-seeded cultivation conditions. Genomics 2022; 114:110269. [DOI: 10.1016/j.ygeno.2022.110269] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/12/2021] [Accepted: 01/16/2022] [Indexed: 11/28/2022]
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Sanchez J, Kaur PP, Pabuayon ICM, Karampudi NBR, Kitazumi A, Sandhu N, Catolos M, Kumar A, de Los Reyes BG. DECUSSATE network with flowering genes explains the variable effects of qDTY12.1 to rice yield under drought across genetic backgrounds. Plant Genome 2022; 15:e20168. [PMID: 34806842 DOI: 10.1002/tpg2.20168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 09/17/2021] [Indexed: 06/13/2023]
Abstract
The impact of qDTY12.1 in maintaining yield under drought has not been consistent across genetic backgrounds. We hypothesized that synergism or antagonism with additive-effect peripheral genes across the background genome either enhances or undermines its full potential. By modeling the transcriptional networks across sibling qDTY12.1-introgression lines with contrasting yield under drought (LPB = low-yield penalty; HPB = high-yield penalty), the qDTY12.1-encoded DECUSSATE gene (OsDEC) was revealed as the core of a synergy with other genes in the genetic background. OsDEC is expressed in flag leaves and induced by progressive drought at booting stage in LPB but not in HPB. The unique OsDEC signature in LPB is coordinated with 35 upstream and downstream peripheral genes involved in floral development through the cytokinin signaling pathway. Results support the differential network rewiring effects through genetic coupling-uncoupling between qDTY12.1 and other upstream and downstream peripheral genes across the distinct genetic backgrounds of LPB and HPB. The functional DEC-network in LPB defines a mechanism for early flowering as a means for avoiding the drought-induced depletion of photosynthate needed for reproductive growth. Its impact is likely through the timely establishment of stronger source-sink dynamics that sustains a robust reproductive transition under drought.
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Affiliation(s)
- Jacobo Sanchez
- Dep. of Plant and Soil Science, Texas Tech Univ., Lubbock, TX, USA
| | | | | | | | - Ai Kitazumi
- Dep. of Plant and Soil Science, Texas Tech Univ., Lubbock, TX, USA
| | - Nitika Sandhu
- International Rice Research Institute, Los Banos, Philippines
- Current address: School of Agricultural Biotechnology, Punjab Agricultural Univ., Ludhiana, India
| | | | - Arvind Kumar
- International Rice Research Institute, Los Banos, Philippines
- Current address: International Crops Research Institute for the Semi-Arid Tropics, Petancheru, India
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Majumder RR, Sandhu N, Yadav S, Catolos M, Cruz MTS, Maturan PC, Hassan L, Hossain MA, Kumar A. Genetic Dissection of Epistatic Interactions Contributing Grain Yield Variability
in Rice under Drought. Curr Genomics 2021; 22:468-483. [PMID: 35340358 PMCID: PMC8886627 DOI: 10.2174/1386207324666210713112127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 02/23/2021] [Accepted: 03/03/2021] [Indexed: 11/22/2022] Open
Abstract
Aims:
The aim of the present study was to evaluate the performance of ‘high’-‘low’
yielding pyramided lines (PLs), having the same combinations of qDTYs in Samba Mahsuri,
MR219 and IR64-Sub1 genetic backgrounds, and to understand the genetic interactions among
QTL and/with genetic background affecting grain yield.
Background:
Epistasis regulates the expression of traits governed by several major/minor genes/
QTL. Multiple pyramided lines (PLs) with the same grain yield QTL (qDTYs) combinations
but possessing grain yield variability under different levels of reproductive stage drought stress
were identified in different rice genetic backgrounds at International Rice Research Institute (IRRI).
Objectives:
The objectives of the present study were to evaluate the performance pyramided lines
(PLs) with drought QTL in the backgrounds of Samba Mahsuri, MR219 and IR64-Sub1 under reproductive
stage drought stress (RS) and NS (non-stress) conditions, to understand the effect of
epistatic interactions among qDTYs and with genetic background on GY under the differential level
of stress and to identify the promising drought-tolerant lines with high yield under drought and
higher background recovery in different genetic backgrounds.
Methods:
The experiments were conducted in 2015 DS (dry season), 2015 WS (wet season) and
2017 DS at IRRI, Los Baños, Philippines, in a transplanted lowland ecosystem under lowland severe
stress (LSS), lowland moderate stress (LMS) and lowland non-stress (LNS). The experiments
were laid out in alpha lattice design with two replications.
Results:
Several digenic interactions were found in different genetic backgrounds, 13 interactions
in Samba Mahsuri, 11 in MR219 and 20 in IR64-Sub1 backgrounds. Among all digenic interactions,
one QTL × QTL interaction, 17 QTL × background and 26 background × background interactions
resulted in GY reduction in low yielding PLs in different genetic backgrounds under LSS or
LMS. Negative interaction of qDTY3.1, qDTY4.1 and qDTY9.1 with background markers and background
× background interactions caused up to 15% GY reduction compared to the high yielding
PLs under LMS in the Samba Mahsuri PLs. In MR219 PLs, the negative interaction of qDTY2.2,
qDTY3.2, qDTY4.1 and qDTY12.1 with the background marker interval RM314-RM539, RM273-RM349
and RM445-RM346, RM473D-RM16, respectively resulted 52% GY reduction compared to
the high yielding PLs under LSS. In IR64-Sub1 PLs, qDTY6.1 interacted with background loci at
RM16-RM135, RM228-RM333, RM202-RM287 and RM415-RM558A marker interval under
LSS and at RM475-RM525 marker interval under LMS, causing GY reduction to 58% compared
to the high yielding PLs.
Conclusion:
High yielding PLs in Samba Mahsuri (IR 99734:1-33-69-1-22-6), MR219 (IR
99784-156-87-2-4-1) and IR64-Sub1 (IR 102784:2-89-632-2-1-2) backgrounds without any negative
interactions were identified. The identified selected promising PLs may be used as potential
drought-tolerant donors or may be released as varieties for drought-prone ecosystems in different
countries.
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Affiliation(s)
- Ratna Rani Majumder
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila,Philippines
| | - Nitika Sandhu
- Punjab Agricultural University, Ludhiana, Punjab 141004,,India
| | - Shailesh Yadav
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila,Philippines
| | - Margaret Catolos
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila,Philippines
| | - Ma. Teresa Sta. Cruz
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila,Philippines
| | - Paul Cornelio Maturan
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila,Philippines
| | - Lutful Hassan
- Bangladesh Agricultural University, Mymensingh 2202, Dhaka,India
| | | | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila,Philippines
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Sandhu N, Pruthi G, Prakash Raigar O, Singh MP, Phagna K, Kumar A, Sethi M, Singh J, Ade PA, Saini DK. Meta-QTL Analysis in Rice and Cross-Genome Talk of the Genomic Regions Controlling Nitrogen Use Efficiency in Cereal Crops Revealing Phylogenetic Relationship. Front Genet 2021; 12:807210. [PMID: 34992638 PMCID: PMC8724540 DOI: 10.3389/fgene.2021.807210] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 11/30/2021] [Indexed: 11/13/2022] Open
Abstract
The phenomenal increase in the use of nitrogenous fertilizers coupled with poor nitrogen use efficiency is among the most important threats to the environment, economic, and social health. During the last 2 decades, a number of genomic regions associated with nitrogen use efficiency (NUE) and related traits have been reported by different research groups, but none of the stable and major effect QTL have been utilized in the marker-assisted introgression/pyramiding program. Compiling the data available in the literature could be very useful in identifying stable and major effect genomic regions associated with the root and NUE-related trait improving the rice grain yield. In the present study, we performed meta-QTL analysis on 1,330 QTL from 29 studies published in the past 2 decades. A total of 76 MQTL with a stable effect over different genetic backgrounds and environments were identified. The significant reduction in the confidence interval of the MQTL compared to the initial QTL resulted in the identification of annotated and putative candidate genes related to the traits considered in the present study. A hot spot region associated with correlated traits on chr 1, 4, and 8 and candidate genes associated with nitrate transporters, nitrogen content, and ammonium uptake on chromosomes 2, 4, 6, and 8 have been identified. The identified MQTL, putative candidate genes, and their orthologues were validated on our previous studies conducted on rice and wheat. The research-based interventions such as improving nitrogen use efficiency via identification of major genomic regions and candidate genes can be a plausible, simple, and low-cost solution to address the challenges of the crop improvement program.
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Affiliation(s)
| | | | | | | | - Kanika Phagna
- Indian Institute of Science Education and Research, Berhampur, India
| | - Aman Kumar
- Punjab Agricultural University, Ludhiana, India
| | - Mehak Sethi
- Punjab Agricultural University, Ludhiana, India
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Pollom E, Sandhu N, Dieg C, Miller J, Obeid J, Jimenez R, Fields E, Kahn J. Radiation Oncology Virtual Education Rotation 2.0 for Residents: Preliminary Results. Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Hui C, Baclay J, Liu K, Sandhu N, Loo P, Von Eyben R, Chen C, Sheth V, Vitzthum L, Chang D, Pollom E. Rectosigmoid Cancer — Rectal Cancer or Sigmoid Cancer? Int J Radiat Oncol Biol Phys 2021. [DOI: 10.1016/j.ijrobp.2021.07.377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Xie X, Quintana MR, Sandhu N, Subedi SR, Zou Y, Rutkoski JE, Henry A. Establishment method affects rice root plasticity in response to drought and its relationship with grain yield stability. J Exp Bot 2021; 72:5208-5220. [PMID: 33989419 DOI: 10.1093/jxb/erab214] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 05/12/2021] [Indexed: 06/12/2023]
Abstract
By responding to the variable soil environments in which they are grown, the roots of rice crops are likely to contribute to yield stability across a range of soil moistures, nutrient levels, and establishment methods. In this study, we explored different approaches to quantification of root plasticity and characterization of its relationship with yield stability. Using four different statistical approaches (plasticity index, slope, AMMI, and factor analytic) on a set of 17 genotypes including several recently-developed breeding lines targeted to dry direct-seeding, we identified only very few direct relationships between root plasticity and yield stability. However, genotypes identified as having combined yield stability and root plasticity showed higher grain yields across trials. Furthermore, root plasticity was expressed to a greater degree in puddled transplanted trials rather than under dry direct-seeding. Significant interactions between nitrogen and water resulted in contrasting relationships between nitrogen-use efficiency and biomass stability between puddled-transplanted and direct-seeded conditions. These results reflect the complex interaction between nitrogen, drought, and even different types of drought (as a result of the establishment method) on rice root growth, and suggest that although rice root plasticity may confer stable yield across a range of environments, it might be necessary to more narrowly define the targeted environments to which it will be most beneficial.
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Affiliation(s)
- Xiaobing Xie
- International Rice Research Institute, Los Baños, Laguna, Philippines
- Hunan Agricultural University, Changsha, China
| | | | - Nitika Sandhu
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Sushil R Subedi
- International Rice Research Institute, Los Baños, Laguna, Philippines
| | - Yingbin Zou
- Hunan Agricultural University, Changsha, China
| | | | - Amelia Henry
- International Rice Research Institute, Los Baños, Laguna, Philippines
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Sandhu N, Yadav S, Catolos M, Cruz MTS, Kumar A. Developing Climate-Resilient, Direct-Seeded, Adapted Multiple-Stress-Tolerant Rice Applying Genomics-Assisted Breeding. Front Plant Sci 2021; 12:637488. [PMID: 33936127 PMCID: PMC8082028 DOI: 10.3389/fpls.2021.637488] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
There is an urgent need to breed dry direct-seeded adapted rice varieties in order to address the emerging scenario of water-labor shortage. The aim of this study was to develop high-yielding, direct-seeded adapted varieties utilizing biparental to multiparental crosses involving as many as six different parents in conventional breeding programs and 12 parents in genomics-assisted breeding programs. The rigorous single plant selections were followed from the F2 generation onwards utilizing phenotypic selection and quantitative trait locus (QTL)/gene-based/linked markers for tracking the presence of desirable alleles of targeted QTL/genes. In conventional breeding, multiparent lines had significantly higher yields (2,072-6,569 kg ha-1) than the biparental lines (1,493-6,326 kg ha-1). GAB lines derived from multiparent crosses had significantly higher (3,293-6,719 kg ha-1) yields than the multiparent lines from conventional breeding (2,072-6,569 kg ha-1). Eleven promising lines from genomics-assisted breeding carrying 7-11 QTL/genes and eight lines from conventional breeding with grain-yield improvement from 727 to 1,705 kg ha-1 and 68 to 902 kg ha-1, respectively, over the best check were selected. The developed lines may be released as varieties/parental lines to develop better rice varieties for direct-seeded situations or as novel breeding material to study genetic interactions.
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Affiliation(s)
- Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
| | - Shailesh Yadav
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Margaret Catolos
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Ma Teresa Sta Cruz
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
| | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines
- International Rice Research Institute South Asia Regional Centre, Varanasi, India
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16
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Yadav S, Sandhu N, Dixit S, Singh VK, Catolos M, Mazumder RR, Rahman MA, Kumar A. Genomics-assisted breeding for successful development of multiple-stress-tolerant, climate-smart rice for southern and southeastern Asia. Plant Genome 2021; 14:e20074. [PMID: 33438317 DOI: 10.1002/tpg2.20074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 10/27/2020] [Accepted: 10/30/2020] [Indexed: 06/12/2023]
Abstract
Rice (Oryza sativa L.) in rainfed marginal environments is prone to multiple abiotic and biotic stresses, which can occur in combination in a single cropping season and adversely affect rice growth and yield. The present study was undertaken to develop high-yielding, climate-resilient rice that can provide tolerance to multiple biotic and abiotic stresses. An assembled first-crossing scheme was employed to transfer 15 quantitative trait loci (QTL) and genes-qDTY1.1 , qDTY2.1 , qDTY3.1 , qDTY12.1 (drought), Sub1 (submergence), Gm4 (gall midge), Pi9, Pita2 (blast), Bph3, Bph17 (brown plant hoppers), Xa4, xa5, xa13, Xa21, and Xa23 (bacterial leaf blight)-from eight different parents using genomics-assisted breeding. A funnel mating design was employed to assemble all the targeted QTL and genes into a high-yielding breeding line IR 91648-B-1-B-3-1. Gene-based linked markers were used in each generation from intercrossing to the F6 generation for tracking the presence of desirable alleles of targeted QTL and genes. Single-plant selections were performed from F2 onwards to select desirable recombinants possessing alleles of interest with suitable phenotypes. Phenotyping of 95 homozygous F6 lines carrying six to 10 QTL and genes was performed for nonstress, reproductive-stage (RS) drought, blast, bacterial leaf blight (BLB), gall midge (GM), and for grain quality parameters such as chalkiness, amylose content (AC), gelatinization temperature (GT), and head rice recovery (HRR). Finally, 56 F7 homozygous lines were found promising for multiple-location evaluation for grain yield (GY) and other traits. These multiple-stress-tolerant lines with the desired grain quality profiling can be targeted for varietal release in southern and southeastern Asia through national release systems.
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Affiliation(s)
- Shailesh Yadav
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Manila, Philippines
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Manila, Philippines
- Punjab Agricultural University, Ludhiana, Punjab, India
| | - Shalabh Dixit
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Manila, Philippines
| | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Margaret Catolos
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Manila, Philippines
| | - Ratna Rani Mazumder
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Manila, Philippines
- Plant Breeding Division, Bangladesh Rice Research Institute (BRRI), Gazipur, Bangladesh
| | | | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Manila, Philippines
- IRRI South Asia Regional Centre (ISARC), Varanasi, Uttar Pradesh, 221106, India
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Sandhu N, Sethi M, Kumar A, Dang D, Singh J, Chhuneja P. Biochemical and Genetic Approaches Improving Nitrogen Use Efficiency in Cereal Crops: A Review. Front Plant Sci 2021; 12:657629. [PMID: 34149755 PMCID: PMC8213353 DOI: 10.3389/fpls.2021.657629] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 04/06/2021] [Indexed: 05/22/2023]
Abstract
Nitrogen is an essential nutrient required in large quantities for the proper growth and development of plants. Nitrogen is the most limiting macronutrient for crop production in most of the world's agricultural areas. The dynamic nature of nitrogen and its tendency to lose soil and environment systems create a unique and challenging environment for its proper management. Exploiting genetic diversity, developing nutrient efficient novel varieties with better agronomy and crop management practices combined with improved crop genetics have been significant factors behind increased crop production. In this review, we highlight the various biochemical, genetic factors and the regulatory mechanisms controlling the plant nitrogen economy necessary for reducing fertilizer cost and improving nitrogen use efficiency while maintaining an acceptable grain yield.
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Sodji Q, Sandhu N, Majzner R, Nadel H, Callejas M, Donaldson S, Hiniker S. Time to Resolution of Iodine 123 Metaiodobenzylguanidine (123I-MIBG) Avidity in Neuroblastoma Following Radiation Therapy. Int J Radiat Oncol Biol Phys 2020. [DOI: 10.1016/j.ijrobp.2020.07.1520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Sagare DB, Abbai R, Jain A, Jayadevappa PK, Dixit S, Singh AK, Challa V, Alam S, Singh UM, Yadav S, Sandhu N, Kabade PG, Singh VK, Kumar A. More and more of less and less: Is genomics-based breeding of dry direct-seeded rice (DDSR) varieties the need of hour? Plant Biotechnol J 2020; 18:2173-2186. [PMID: 32725933 PMCID: PMC7589319 DOI: 10.1111/pbi.13454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/07/2020] [Accepted: 07/13/2020] [Indexed: 06/02/2023]
Abstract
Rice is a staple food for half of the world's population. Changing climatic conditions, water and labour scarcity are the major challenges that shall limit future rice production. Dry direct-seeded rice (DDSR) is emerging as an efficient, resources conserving, mechanized, climate smart and economically viable strategy to be adopted as an alternative to puddled transplanted rice (TPR) with the potential to address the problem of labour-water shortages and ensure sustainable rice cultivation. Despite these benefits, several constraints obstruct the adoption of DDSR. In principle, the plant type for DDSR should be different from one for TPR, which could be achieved by developing rice varieties that combine the traits of upland and lowland varieties. In this context, recent advances in precise phenotyping and NGS-based trait mapping led to identification of promising donors and QTLs/genes for DDSR favourable traits to be employed in genomic breeding. This review discusses the important traits influencing DDSR, research studies to clarify the need for breeding DDSR-specific varieties to achieve enhanced grain yield, climate resilience and nutrition demand. We anticipate that in the coming years, genomic breeding for developing DDSR-specific varieties would be a regular practice and might be further strengthened by combining superior haplotypes regulating important DDSR traits by haplotype-based breeding.
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Affiliation(s)
- Deepti B. Sagare
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | - Ragavendran Abbai
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK)GaterslebenGermany
| | - Abhinav Jain
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | | | - Shilpi Dixit
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | - Arun Kumar Singh
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | | | - Shamshad Alam
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | - Uma Maheshwar Singh
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | - Shailesh Yadav
- International Rice Research Institute (IRRI)Metro ManilaPhilippines
| | | | - Pramod G. Kabade
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
| | - Vikas Kumar Singh
- International Rice Research Institute (IRRI)South‐Asia Hub (SAH)HyderabadIndia
- International Rice Research Institute (IRRI)Metro ManilaPhilippines
| | - Arvind Kumar
- International Rice Research Institute (IRRI)Metro ManilaPhilippines
- International Rice Research Institute (IRRI)South‐Asia Regional Centre (SARC)VaranasiIndia
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Bhandari A, Sandhu N, Bartholome J, Cao-Hamadoun TV, Ahmadi N, Kumari N, Kumar A. Genome-Wide Association Study for Yield and Yield Related Traits under Reproductive Stage Drought in a Diverse indica-aus Rice Panel. Rice (N Y) 2020; 13:53. [PMID: 32761553 PMCID: PMC7410978 DOI: 10.1186/s12284-020-00406-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2020] [Accepted: 07/02/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Reproductive-stage drought stress is a major impediment to rice production in rainfed areas. Conventional and marker-assisted breeding strategies for developing drought-tolerant rice varieties are being optimized by mining and exploiting adaptive traits, genetic diversity; identifying the alleles, and understanding their interactions with genetic backgrounds for their increased contribution to drought tolerance. Field experiments were conducted in this study to identify marker-trait associations (MTAs) involved in response to yield under reproductive-stage (RS) drought. A diverse set of 280 indica-aus accessions was phenotyped for ten agronomic traits including yield and yield-related traits under normal irrigated condition and under two managed reproductive-stage drought environments. The accessions were genotyped with 215,250 single nucleotide polymorphism markers. RESULTS The study identified a total of 219 significant MTAs for 10 traits and candidate gene analysis within a 200 kb window centred from GWAS identified SNP peaks detected these MTAs within/ in close proximity to 38 genes, 4 earlier reported major grain yield QTLs and 6 novel QTLs for 7 traits out of the 10. The significant MTAs were mainly located on chromosomes 1, 2, 5, 6, 9, 11 and 12 and the percent phenotypic variance captured for these traits ranged from 5 to 88%. The significant positive correlation of grain yield with yield-related and other agronomic traits except for flowering time, observed under different environments point towards their contribution in improving rice yield under drought. Seven promising accessions were identified for use in future genomics-assisted breeding programs targeting grain yield improvement under drought. CONCLUSION These results provide a promising insight into the complex genetic architecture of grain yield under reproductive-stage drought in different environments. Validation of major genomic regions reported in the study will enable their effectiveness to develop drought-tolerant varieties following marker-assisted selection as well as to identify genes and understanding the associated physiological mechanisms.
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Affiliation(s)
- Aditi Bhandari
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Banasthali Vidyapith, Banasthali, 304022, India
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- Punjab Agricultural University, Ludhiana, 141004, India
| | - Jérôme Bartholome
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Tuong-Vi Cao-Hamadoun
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | - Nourollah Ahmadi
- CIRAD, UMR, AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Montpellier SupAgro, Montepellier, France
| | | | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, DAPO Box, 7777, Metro Manila, Philippines.
- IRRI South Asia Regional Centre, Varanasi, 221006, India.
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21
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Kumar A, Sandhu N, Venkateshwarlu C, Priyadarshi R, Yadav S, Majumder RR, Singh VK. Development of introgression lines in high yielding, semi-dwarf genetic backgrounds to enable improvement of modern rice varieties for tolerance to multiple abiotic stresses free from undesirable linkage drag. Sci Rep 2020; 10:13073. [PMID: 32753648 PMCID: PMC7403580 DOI: 10.1038/s41598-020-70132-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/01/2020] [Indexed: 12/16/2022] Open
Abstract
Occurrence of multiple abiotic stresses in a single crop season has become more frequent than before. Most of the traditional donors possessing tolerance to abiotic stresses are tall, low-yielding with poor grain quality. To facilitate efficient use of complex polygenic traits in rice molecular breeding research, we undertook development of introgression lines in background of high-yielding, semi-dwarf varieties with good grain quality. The study reports the development and evaluations of over 25,000 introgression lines in eleven elite rice genetic backgrounds for improvement of yield under multiple abiotic-stresses such as drought, flood, high/low temperature. The developed introgression lines within each genetic background are near isogenic/recombinant inbred lines to their recipient recurrent parent with 50 to 98% background recovery and additionally carry QTLs/genes for abiotic stresses. The multiple-stress tolerant pyramided breeding lines combining high yield under normal situation and good yield under moderate to severe reproductive-stage drought, semi-dwarf plant type with good grain quality traits have been developed. The introgression lines in dwarf backgrounds open new opportunity to improve other varieties without any linkage drag as well as facilitate cloning of QTLs, identification and functional characterization of candidate genes, mechanisms associated with targeted QTLs and the genetic networks underlying complex polygenic traits.
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Affiliation(s)
- Arvind Kumar
- International Rice Research Institute, Metro Manila, Philippines. .,IRRI South Asia Regional Centre (ISARC), Varanasi, Uttar Pradesh, India.
| | - Nitika Sandhu
- International Rice Research Institute, Metro Manila, Philippines.,Punjab Agricultural University, Ludhiana, India
| | - Challa Venkateshwarlu
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Rahul Priyadarshi
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India.,International Rice Research Institute, Guwahati, Assam, India
| | - Shailesh Yadav
- International Rice Research Institute, Metro Manila, Philippines
| | | | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
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McLean KA, Ahmed WUR, Akhbari M, Claireaux HA, English C, Frost J, Henshall DE, Khan M, Kwek I, Nicola M, Rehman S, Varghese S, Drake TM, Bell S, Nepogodiev D, McLean KA, Drake TM, Glasbey JC, Borakati A, Drake TM, Kamarajah S, McLean KA, Bath MF, Claireaux HA, Gundogan B, Mohan M, Deekonda P, Kong C, Joyce H, Mcnamee L, Woin E, Burke J, Khatri C, Fitzgerald JE, Harrison EM, Bhangu A, Nepogodiev D, Arulkumaran N, Bell S, Duthie F, Hughes J, Pinkney TD, Prowle J, Richards T, Thomas M, Dynes K, Patel M, Patel P, Wigley C, Suresh R, Shaw A, Klimach S, Jull P, Evans D, Preece R, Ibrahim I, Manikavasagar V, Smith R, Brown FS, Deekonda P, Teo R, Sim DPY, Borakati A, Logan AE, Barai I, Amin H, Suresh S, Sethi R, Bolton W, Corbridge O, Horne L, Attalla M, Morley R, Robinson C, Hoskins T, McAllister R, Lee S, Dennis Y, Nixon G, Heywood E, Wilson H, Ng L, Samaraweera S, Mills A, Doherty C, Woin E, Belchos J, Phan V, Chouari T, Gardner T, Goergen N, Hayes JDB, MacLeod CS, McCormack R, McKinley A, McKinstry S, Milligan W, Ooi L, Rafiq NM, Sammut T, Sinclair E, Smith M, Baker C, Boulton APR, Collins J, Copley HC, Fearnhead N, Fox H, Mah T, McKenna J, Naruka V, Nigam N, Nourallah B, Perera S, Qureshi A, Saggar S, Sun L, Wang X, Yang DD, Caroll P, Doyle C, Elangovan S, Falamarzi A, Perai KG, Greenan E, Jain D, Lang-Orsini M, Lim S, O'Byrne L, Ridgway P, Van der Laan S, Wong J, Arthur J, Barclay J, Bradley P, Edwin C, Finch E, Hayashi E, Hopkins M, Kelly D, Kelly M, McCartan N, Ormrod A, Pakenham A, Hayward J, Hitchen C, Kishore A, Martins T, Philomen J, Rao R, Rickards C, Burns N, Copeland M, Durand C, Dyal A, Ghaffar A, Gidwani A, Grant M, Gribbon C, Gruhn A, Leer M, Ahmad K, Beattie G, Beatty M, Campbell G, Donaldson G, Graham S, Holmes D, Kanabar S, Liu H, McCann C, Stewart R, Vara S, Ajibola-Taylor O, Andah EJE, Ani C, Cabdi NMO, Ito G, Jones M, Komoriyama A, Patel P, Titu L, Basra M, Gallogly P, Harinath G, Leong SH, Pradhan A, Siddiqui I, Zaat S, Ali A, Galea M, Looi WL, Ng JCK, Atkin G, Azizi A, Cargill Z, China Z, Elliot J, Jebakumar R, Lam J, Mudalige G, Onyerindu C, Renju M, Babu VS, Hussain M, Joji N, Lovett B, Mownah H, Ali B, Cresswell B, Dhillon AK, Dupaguntla YS, Hungwe C, Lowe-Zinola JD, Tsang JCH, Bevan K, Cardus C, Duggal A, Hossain S, McHugh M, Scott M, Chan F, Evans R, Gurung E, Haughey B, Jacob-Ramsdale B, Kerr M, Lee J, McCann E, O'Boyle K, Reid N, Hayat F, Hodgson S, Johnston R, Jones W, Khan M, Linn T, Long S, Seetharam P, Shaman S, Smart B, Anilkumar A, Davies J, Griffith J, Hughes B, Islam Y, Kidanu D, Mushaini N, Qamar I, Robinson H, Schramm M, Tan CY, Apperley H, Billyard C, Blazeby JM, Cannon SP, Carse S, Göpfert A, Loizidou A, Parkin J, Sanders E, Sharma S, Slade G, Telfer R, Huppatz IW, Worley E, Chandramoorthy L, Friend C, Harris L, Jain P, Karim MJ, Killington K, McGillicuddy J, Rafferty C, Rahunathan N, Rayne T, Varathan Y, Verma N, Zanichelli D, Arneill M, Brown F, Campbell B, Crozier L, Henry J, McCusker C, Prabakaran P, Wilson R, Asif U, Connor M, Dindyal S, Math N, Pagarkar A, Saleem H, Seth I, Sharma S, Standfield N, Swartbol T, Adamson R, Choi JE, El Tokhy O, Ho W, Javaid NR, Kelly M, Mehdi AS, Menon D, Plumptre I, Sturrock S, Turner J, Warren O, Crane E, Ferris B, Gadsby C, Smallwood J, Vipond M, Wilson V, Amarnath T, Doshi A, Gregory C, Kandiah K, Powell B, Spoor H, Toh C, Vizor R, Common M, Dunleavy K, Harris S, Luo C, Mesbah Z, Kumar AP, Redmond A, Skulsky S, Walsh T, Daly D, Deery L, Epanomeritakis E, Harty M, Kane D, Khan K, Mackey R, McConville J, McGinnity K, Nixon G, Ang A, Kee JY, Leung E, Norman S, Palaniappan SV, Sarathy PP, Yeoh T, Frost J, Hazeldine P, Jones L, Karbowiak M, Macdonald C, Mutarambirwa A, Omotade A, Runkel M, Ryan G, Sawers N, Searle C, Suresh S, Vig S, Ahmad A, McGartland R, Sim R, Song A, Wayman J, Brown R, Chang LH, Concannon K, Crilly C, Arnold TJ, Burgin A, Cadden F, Choy CH, Coleman M, Lim D, Luk J, Mahankali-Rao P, Prudence-Taylor AJ, Ramakrishnan D, Russell J, Fawole A, Gohil J, Green B, Hussain A, McMenamin L, McMenamin L, Tang M, Azmi F, Benchetrit S, Cope T, Haque A, Harlinska A, Holdsworth R, Ivo T, Martin J, Nisar T, Patel A, Sasapu K, Trevett J, Vernet G, Aamir A, Bird C, Durham-Hall A, Gibson W, Hartley J, May N, Maynard V, Johnson S, Wood CM, O'Brien M, Orbell J, Stringfellow TD, Tenters F, Tresidder S, Cheung W, Grant A, Tod N, Bews-Hair M, Lim ZH, Lim SW, Vella-Baldacchino M, Auckburally S, Chopada A, Easdon S, Goodson R, McCurdie F, Narouz M, Radford A, Rea E, Taylor O, Yu T, Alfa-Wali M, Amani L, Auluck I, Bruce P, Emberton J, Kumar R, Lagzouli N, Mehta A, Murtaza A, Raja M, Dennahy IS, Frew K, Given A, He YY, Karim MA, MacDonald E, McDonald E, McVinnie D, Ng SK, Pettit A, Sim DPY, Berthaume-Hawkins SD, Charnley R, Fenton K, Jones D, Murphy C, Ng JQ, Reehal R, Robinson H, Seraj SS, Shang E, Tonks A, White P, Yeo A, Chong P, Gabriel R, Patel N, Richardson E, Symons L, Aubrey-Jones D, Dawood S, Dobrzynska M, Faulkner S, Griffiths H, Mahmood F, Patel P, Perry M, Power A, Simpson R, Ali A, Brobbey P, Burrows A, Elder P, Ganyani R, Horseman C, Hurst P, Mann H, Marimuthu K, McBride S, Pilsworth E, Powers N, Stanier P, Innes R, Kersey T, Kopczynska M, Langasco N, Patel N, Rajagopal R, Atkins B, Beasley W, Lim ZC, Gill A, Ang HL, Williams H, Yogeswara T, Carter R, Fam M, Fong J, Latter J, Long M, Mackinnon S, McKenzie C, Osmanska J, Raghuvir V, Shafi A, Tsang K, Walker L, Bountra K, Coldicutt O, Fletcher D, Hudson S, Iqbal S, Bernal TL, Martin JWB, Moss-Lawton F, Smallwood J, Vipond M, Cardwell A, Edgerton K, Laws J, Rai A, Robinson K, Waite K, Ward J, Youssef H, Knight C, Koo PY, Lazarou A, Stanger S, Thorn C, Triniman MC, Botha A, Boyles L, Cumming S, Deepak S, Ezzat A, Fowler AJ, Gwozdz AM, Hussain SF, Khan S, Li H, Morrell BL, Neville J, Nitiahpapand R, Pickering O, Sagoo H, Sharma E, Welsh K, Denley S, Khan S, Agarwal M, Al-Saadi N, Bhambra R, Gupta A, Jawad ZAR, Jiao LR, Khan K, Mahir G, Singagireson S, Thoms BL, Tseu B, Wei R, Yang N, Britton N, Leinhardt D, Mahfooz M, Palkhi A, Price M, Sheikh S, Barker M, Bowley D, Cant M, Datta U, Farooqi M, Lee A, Morley G, Amin MN, Parry A, Patel S, Strang S, Yoganayagam N, Adlan A, Chandramoorthy S, Choudhary Y, Das K, Feldman M, France B, Grace R, Puddy H, Soor P, Ali M, Dhillon P, Faraj A, Gerard L, Glover M, Imran H, Kim S, Patrick Y, Peto J, Prabhudesai A, Smith R, Tang A, Vadgama N, Dhaliwal R, Ecclestone T, Harris A, Ong D, Patel D, Philp C, Stewart E, Wang L, Wong E, Xu Y, Ashaye T, Fozard T, Galloway F, Kaptanis S, Mistry P, Nguyen T, Olagbaiye F, Osman M, Philip Z, Rembacken R, Tayeh S, Theodoropoulou K, Herman A, Lau J, Saha A, Trotter M, Adeleye O, Cave D, Gunwa T, Magalhães J, Makwana S, Mason R, Parish M, Regan H, Renwick P, Roberts G, Salekin D, Sivakumar C, Tariq A, Liew I, McDade A, Stewart D, Hague M, Hudson-Peacock N, Jackson CES, James F, Pitt J, Walker EY, Aftab R, Ang JJ, Anwar S, Battle J, Budd E, Chui J, Crook H, Davies P, Easby S, Hackney E, Ho B, Imam SZ, Rammell J, Andrews H, Perry C, Schinle P, Ahmed P, Aquilina T, Balai E, Church M, Cumber E, Curtis A, Davies G, Dennis Y, Dumann E, Greenhalgh S, Kim P, King S, Metcalfe KHM, Passby L, Redgrave N, Soonawalla Z, Waters S, Zornoza A, Gulzar I, Hole J, Hull K, Ishaq H, Karaj J, Kelkar A, Love E, Patel S, Thakrar D, Vine M, Waterman A, Dib NP, Francis N, Hanson M, Ingleton R, Sadanand KS, Sukirthan N, Arnell S, Ball M, Bassam N, Beghal G, Chang A, Dawe V, George A, Huq T, Hussain A, Ikram B, Kanapeckaite L, Khan M, Ramjas D, Rushd A, Sait S, Serry M, Yardimci E, Capella S, Chenciner L, Episkopos C, Karam E, McCarthy C, Moore-Kelly W, Watson N, Ahluwalia V, Barnfield J, Ben-Gal O, Bloom I, Gharatya A, Khodatars K, Merchant N, Moonan A, Moore M, Patel K, Spiers H, Sundaram K, Turner J, Bath MF, Black J, Chadwick H, Huisman L, Ingram H, Khan S, Martin L, Metcalfe M, Sangal P, Seehra J, Thatcher A, Venturini S, Whitcroft I, Afzal Z, Brown S, Gani A, Gomaa A, Hussein N, Oh SY, Pazhaniappan N, Sharkey E, Sivagnanasithiyar T, Williams C, Yeung J, Cruddas L, Gurjar S, Pau A, Prakash R, Randhawa R, Chen L, Eiben I, Naylor M, Osei-Bordom D, Trenear R, Bannard-Smith J, Griffiths N, Patel BY, Saeed F, Abdikadir H, Bennett M, Church R, Clements SE, Court J, Delvi A, Hubert J, Macdonald B, Mansour F, Patel RR, Perris R, Small S, Betts A, Brown N, Chong A, Croitoru C, Grey A, Hickland P, Ho C, Hollington D, McKie L, Nelson AR, Stewart H, Eiben P, Nedham M, Ali I, Brown T, Cumming S, Hunt C, Joyner C, McAlinden C, Roberts J, Rogers D, Thachettu A, Tyson N, Vaughan R, Verma N, Yasin T, Andrew K, Bhamra N, Leong S, Mistry R, Noble H, Rashed F, Walker NR, Watson L, Worsfold M, Yarham E, Abdikadir H, Arshad A, Barmayehvar B, Cato L, Chan-lam N, Do V, Leong A, Sheikh Z, Zheleniakova T, Coppel J, Hussain ST, Mahmood R, Nourzaie R, Prowle J, Sheik-Ali S, Thomas A, Alagappan A, Ashour R, Bains H, Diamond J, Gordon J, Ibrahim B, Khalil M, Mittapalli D, Neo YN, Patil P, Peck FS, Reza N, Swan I, Whyte M, Chaudhry S, Hernon J, Khawar H, O'Brien J, Pullinger M, Rothnie K, Ujjal S, Bhatte S, Curtis J, Green S, Mayer A, Watkinson G, Chapple K, Hawthorne T, Khaliq M, Majkowski L, Malik TAM, Mclauchlan K, En BNW, Parton S, Robinson SD, Saat MI, Shurovi BN, Varatharasasingam K, Ward AE, Behranwala K, Bertelli M, Cohen J, Duff F, Fafemi O, Gupta R, Manimaran M, Mayhew J, Peprah D, Wong MHY, Farmer N, Houghton C, Kandhari N, Khan K, Ladha D, Mayes J, McLennan F, Panahi P, Seehra H, Agrawal R, Ahmed I, Ali S, Birkinshaw F, Choudhry M, Gokani S, Harrogate S, Jamal S, Nawrozzadeh F, Swaray A, Szczap A, Warusavitarne J, Abdalla M, Asemota N, Cullum R, Hartley M, Maxwell-Armstrong C, Mulvenna C, Phillips J, Yule A, Ahmed L, Clement KD, Craig N, Elseedawy E, Gorman D, Kane L, Livie J, Livie V, Moss E, Naasan A, Ravi F, Shields P, Zhu Y, Archer M, Cobley H, Dennis R, Downes C, Guevel B, Lamptey E, Murray H, Radhakrishnan A, Saravanabavan S, Sardar M, Shaw C, Tilliridou V, Wright R, Ye W, Alturki N, Helliwell R, Jones E, Kelly D, Lambotharan S, Scott K, Sivakumar R, Victor L, Boraluwe-Rallage H, Froggatt P, Haynes S, Hung YMA, Keyte A, Matthews L, Evans E, Haray P, John I, Mathivanan A, Morgan L, Oji O, Okorocha C, Rutherford A, Spiers H, Stageman N, Tsui A, Whitham R, Amoah-Arko A, Cecil E, Dietrich A, Fitzpatrick H, Guy C, Hair J, Hilton J, Jawad L, McAleer E, Taylor Z, Yap J, Akhbari M, Debnath D, Dhir T, Elbuzidi M, Elsaddig M, Glace S, Khawaja H, Koshy R, Lal K, Lobo L, McDermott A, Meredith J, Qamar MA, Vaidya A, Acquaah F, Barfi L, Carter N, Gnanappiragasam D, Ji C, Kaminski F, Lawday S, Mackay K, Sulaiman SK, Webb R, Ananthavarathan P, Dalal F, Farrar E, Hashemi R, Hossain M, Jiang J, Kiandee M, Lex J, Mason L, Matthews JH, McGeorge E, Modhwadia S, Pinkney T, Radotra A, Rickard L, Rodman L, Sales A, Tan KL, Bachi A, Bajwa DS, Battle J, Brown LR, Butler A, Calciu A, Davies E, Gardner I, Girdlestone T, Ikogho O, Keelan G, O'Loughlin P, Tam J, Elias J, Ngaage M, Thompson J, Bristow S, Brock E, Davis H, Pantelidou M, Sathiyakeerthy A, Singh K, Chaudhry A, Dickson G, Glen P, Gregoriou K, Hamid H, Mclean A, Mehtaji P, Neophytou G, Potts S, Belgaid DR, Burke J, Durno J, Ghailan N, Hanson M, Henshaw V, Nazir UR, Omar I, Riley BJ, Roberts J, Smart G, Van Winsen K, Bhatti A, Chan M, D'Auria M, Green S, Keshvala C, Li H, Maxwell-Armstrong C, Michaelidou M, Simmonds L, Smith C, Wimalathasan A, Abbas J, Cairns C, Chin YR, Connelly A, Moug S, Nair A, Svolkinas D, Coe P, Subar D, Wang H, Zaver V, Brayley J, Cookson P, Cunningham L, Gaukroger A, Ho M, Hough A, King J, O'Hagan D, Widdison A, Brown R, Brown B, Chavan A, Francis S, Hare L, Lund J, Malone N, Mavi B, McIlwaine A, Rangarajan S, Abuhussein N, Campbell HS, Daniels J, Fitzgerald I, Mansfield S, Pendrill A, Robertson D, Smart YW, Teng T, Yates J, Belgaumkar A, Katira A, Kossoff J, Kukran S, Laing C, Mathew B, Mohamed T, Myers S, Novell R, Phillips BL, Thomas M, Turlejski T, Turner S, Varcada M, Warren L, Wynell-Mayow W, Church R, Linley-Adams L, Osborn G, Saunders M, Spencer R, Srikanthan M, Tailor S, Tullett A, Ali M, Al-Masri S, Carr G, Ebhogiaye O, Heng S, Manivannan S, Manley J, McMillan LE, Peat C, Phillips B, Thomas S, Whewell H, Williams G, Bienias A, Cope EA, Courquin GR, Day L, Garner C, Gimson A, Harris C, Markham K, Moore T, Nadin T, Phillips C, Subratty SM, Brown K, Dada J, Durbacz M, Filipescu T, Harrison E, Kennedy ED, Khoo E, Kremel D, Lyell I, Pronin S, Tummon R, Ventre C, Walls L, Wootton E, Akhtar A, Davies E, El-Sawy D, Farooq M, Gaddah M, Griffiths H, Katsaiti I, Khadem N, Leong K, Williams I, Chean CS, Chudek D, Desai H, Ellerby N, Hammad A, Malla S, Murphy B, Oshin O, Popova P, Rana S, Ward T, Abbott TEF, Akpenyi O, Edozie F, El Matary R, English W, Jeyabaladevan S, Morgan C, Naidu V, Nicholls K, Peroos S, Prowle J, Sansome S, Torrance HD, Townsend D, Brecher J, Fung H, Kazmi Z, Outlaw P, Pursnani K, Ramanujam N, Razaq A, Sattar M, Sukumar S, Tan TSE, Chohan K, Dhuna S, Haq T, Kirby S, Lacy-Colson J, Logan P, Malik Q, McCann J, Mughal Z, Sadiq S, Sharif I, Shingles C, Simon A, Burnage S, Chan SSN, Craig ARJ, Duffield J, Dutta A, Eastwood M, Iqbal F, Mahmood F, Mahmood W, Patel C, Qadeer A, Robinson A, Rotundo A, Schade A, Slade RD, De Freitas M, Kinnersley H, McDowell E, Moens-Lecumberri S, Ramsden J, Rockall T, Wiffen L, Wright S, Bruce C, Francois V, Hamdan K, Limb C, Lunt AJ, Manley L, Marks M, Phillips CFE, Agnew CJF, Barr CJ, Benons N, Hart SJ, Kandage D, Krysztopik R, Mahalingam P, Mock J, Rajendran S, Stoddart MT, Clements B, Gillespie H, Lee S, McDougall R, Murray C, O'Loane R, Periketi S, Tan S, Amoah R, Bhudia R, Dudley B, Gilbert A, Griffiths B, Khan H, McKigney N, Roberts B, Samuel R, Seelarbokus A, Stubbing-Moore A, Thompson G, Williams P, Ahmed N, Akhtar R, Chandler E, Chappelow I, Gil H, Gower T, Kale A, Lingam G, Rutler L, Sellahewa C, Sheikh A, Stringer H, Taylor R, Aglan H, Ashraf MR, Choo S, Das E, Epstein J, Gentry R, Mills D, Poolovadoo Y, Ward N, Bull K, Cole A, Hack J, Khawari S, Lake C, Mandishona T, Perry R, Sleight S, Sultan S, Thornton T, Williams S, Arif T, Castle A, Chauhan P, Chesner R, Eilon T, Kamarajah S, Kambasha C, Lock L, Loka T, Mohammad F, Motahariasl S, Roper L, Sadhra SS, Sheikh A, Toma T, Wadood Q, Yip J, Ainger E, Busti S, Cunliffe L, Flamini T, Gaffing S, Moorcroft C, Peter M, Simpson L, Stokes E, Stott G, Wilson J, York J, Yousaf A, Borakati A, Brown M, Goaman A, Hodgson B, Ijeomah A, Iroegbu U, Kaur G, Lowe C, Mahmood S, Sattar Z, Sen P, Szuman A, Abbas N, Al-Ausi M, Anto N, Bhome R, Eccles L, Elliott J, Hughes EJ, Jones A, Karunatilleke AS, Knight JS, Manson CCF, Mekhail I, Michaels L, Noton TM, Okenyi E, Reeves T, Yasin IH, Banfield DA, Harris R, Lim D, Mason-Apps C, Roe T, Sandhu J, Shafiq N, Stickler E, Tam JP, Williams LM, Ainsworth P, Boualbanat Y, Doull C, Egan E, Evans L, Hassanin K, Ninkovic-Hall G, Odunlami W, Shergill M, Traish M, Cummings D, Kershaw S, Ong J, Reid F, Toellner H, Alwandi A, Amer M, George D, Haynes K, Hughes K, Peakall L, Premakumar Y, Punjabi N, Ramwell A, Sawkins H, Ashwood J, Baker A, Baron C, Bhide I, Blake E, De Cates C, Esmail R, Hosamuddin H, Kapp J, Nguru N, Raja M, Thomson F, Ahmed H, Aishwarya G, Al-Huneidi R, Ali S, Aziz R, Burke D, Clarke B, Kausar A, Maskill D, Mecia L, Myers L, Smith ACD, Walker G, Wroe N, Donohoe C, Gibbons D, Jordan P, Keogh C, Kiely A, Lalor P, McCrohan M, Powell C, Foley MP, Reynolds J, Silke E, Thorpe O, Kong JTH, White C, Ali Q, Dalrymple J, Ge Y, Khan H, Luo RS, Paine H, Paraskeva B, Parker L, Pillai K, Salciccioli J, Selvadurai S, Sonagara V, Springford LR, Tan L, Appleton S, Leadholm N, Zhang Y, Ahern D, Cotter M, Cremen S, Durrigan T, Flack V, Hrvacic N, Jones H, Jong B, Keane K, O'Connell PR, O'sullivan J, Pek G, Shirazi S, Barker C, Brown A, Carr W, Chen Y, Guillotte C, Harte J, Kokayi A, Lau K, McFarlane S, Morrison S, Broad J, Kenefick N, Makanji D, Printz V, Saito R, Thomas O, Breen H, Kirk S, Kong CH, O'Kane A, Eddama M, Engledow A, Freeman SK, Frost A, Goh C, Lee G, Poonawala R, Suri A, Taribagil P, Brown H, Christie S, Dean S, Gravell R, Haywood E, Holt F, Pilsworth E, Rabiu R, Roscoe HW, Shergill S, Sriram A, Sureshkumar A, Tan LC, Tanna A, Vakharia A, Bhullar S, Brannick S, Dunne E, Frere M, Kerin M, Kumar KM, Pratumsuwan T, Quek R, Salman M, Van Den Berg N, Wong C, Ahluwalia J, Bagga R, Borg CM, Calabria C, Draper A, Farwana M, Joyce H, Khan A, Mazza M, Pankin G, Sait MS, Sandhu N, Virani N, Wong J, Woodhams K, Croghan N, Ghag S, Hogg G, Ismail O, John N, Nadeem K, Naqi M, Noe SM, Sharma A, Tan S, Begum F, Best R, Collishaw A, Glasbey J, Golding D, Gwilym B, Harrison P, Jackman T, Lewis N, Luk YL, Porter T, Potluri S, Stechman M, Tate S, Thomas D, Walford B, Auld F, Bleakley A, Johnston S, Jones C, Khaw J, Milne S, O'Neill S, Singh KKR, Smith R, Swan A, Thorley N, Yalamarthi S, Yin ZD, Ali A, Balian V, Bana R, Clark K, Livesey C, McLachlan G, Mohammad M, Pranesh N, Richards C, Ross F, Sajid M, Brooke M, Francombe J, Gresly J, Hutchinson S, Kerrigan K, Matthews E, Nur S, Parsons L, Sandhu A, Vyas M, White F, Zulkifli A, Zuzarte L, Al-Mousawi A, Arya J, Azam S, Yahaya AA, Gill K, Hallan R, Hathaway C, Leptidis I, McDonagh L, Mitrasinovic S, Mushtaq N, Pang N, Peiris GB, Rinkoff S, Chan L, Christopher E, Farhan-Alanie MMH, Gonzalez-Ciscar A, Graham CJ, Lim H, McLean KA, Paterson HM, Rogers A, Roy C, Rutherford D, Smith F, Zubikarai G, Al-Khudairi R, Bamford M, Chang M, Cheng J, Hedley C, Joseph R, Mitchell B, Perera S, Rothwell L, Siddiqui A, Smith J, Taylor K, Wright OW, Baryan HK, Boyd G, Conchie H, Cox L, Davies J, Gardner S, Hill N, Krishna K, Lakin F, Scotcher S, Alberts J, Asad M, Barraclough J, Campbell A, Marshall D, Wakeford W, Cronbach P, D'Souza F, Gammeri E, Houlton J, Hall M, Kethees A, Patel R, Perera M, Prowle J, Shaid M, Webb E, Beattie S, Chadwick M, El-Taji O, Haddad S, Mann M, Patel M, Popat K, Rimmer L, Riyat H, Smith H, Anandarajah C, Cipparrone M, Desai K, Gao C, Goh ET, Howlader M, Jeffreys N, Karmarkar A, Mathew G, Mukhtar H, Ozcan E, Renukanthan A, Sarens N, Sinha C, Woolley A, Bogle R, Komolafe O, Loo F, Waugh D, Zeng R, Crewe A, Mathias J, Mills A, Owen A, Prior A, Saunders I, Baker A, Crilly L, McKeon J, Ubhi HK, Adeogun A, Carr R, Davison C, Devalia S, Hayat A, Karsan RB, Osborne C, Scott K, Weegenaar C, Wijeyaratne M, Babatunde F, Barnor-Ahiaku E, Beattie G, Chitsabesan P, Dixon O, Hall N, Ilenkovan N, Mackrell T, Nithianandasivam N, Orr J, Palazzo F, Saad M, Sandland-Taylor L, Sherlock J, Ashdown T, Chandler S, Garsaa T, Lloyd J, Loh SY, Ng S, Perkins C, Powell-Chandler A, Smith F, Underhill R. Perioperative intravenous contrast administration and the incidence of acute kidney injury after major gastrointestinal surgery: prospective, multicentre cohort study. Br J Surg 2020; 107:1023-1032. [PMID: 32026470 DOI: 10.1002/bjs.11453] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 09/21/2019] [Accepted: 11/08/2019] [Indexed: 01/14/2023]
Abstract
BACKGROUND This study aimed to determine the impact of preoperative exposure to intravenous contrast for CT and the risk of developing postoperative acute kidney injury (AKI) in patients undergoing major gastrointestinal surgery. METHODS This prospective, multicentre cohort study included adults undergoing gastrointestinal resection, stoma reversal or liver resection. Both elective and emergency procedures were included. Preoperative exposure to intravenous contrast was defined as exposure to contrast administered for the purposes of CT up to 7 days before surgery. The primary endpoint was the rate of AKI within 7 days. Propensity score-matched models were adjusted for patient, disease and operative variables. In a sensitivity analysis, a propensity score-matched model explored the association between preoperative exposure to contrast and AKI in the first 48 h after surgery. RESULTS A total of 5378 patients were included across 173 centres. Overall, 1249 patients (23·2 per cent) received intravenous contrast. The overall rate of AKI within 7 days of surgery was 13·4 per cent (718 of 5378). In the propensity score-matched model, preoperative exposure to contrast was not associated with AKI within 7 days (odds ratio (OR) 0·95, 95 per cent c.i. 0·73 to 1·21; P = 0·669). The sensitivity analysis showed no association between preoperative contrast administration and AKI within 48 h after operation (OR 1·09, 0·84 to 1·41; P = 0·498). CONCLUSION There was no association between preoperative intravenous contrast administered for CT up to 7 days before surgery and postoperative AKI. Risk of contrast-induced nephropathy should not be used as a reason to avoid contrast-enhanced CT.
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Bhardwaj R, Singh BP, Sandhu N, Singh N, Kaur R, Rokana N, Singh KS, Chaudhary V, Panwar H. Probiotic mediated NF-κB regulation for prospective management of type 2 diabetes. Mol Biol Rep 2020; 47:2301-2313. [PMID: 31919753 DOI: 10.1007/s11033-020-05254-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023]
Abstract
Diabetes and other lifestyle disorders have been recognized as the leading cause of morbidity and mortality globally. Nuclear factor kappa B (NF-κB) is a major factor involved in the early pathobiology of diabetes and studies reveal that hyperglycemic conditions in body leads to NF-κB mediated activation of several cytokines, chemokines and inflammatory molecules. NF-κB family comprises of certain DNA-binding protein factors that elicit the transcription of pro-inflammatory molecules. Various studies have identified NF-κB as a promising target for diabetic management. Probiotics have been proposed as bio-therapeutic agents for treatment of inflammatory disorders and many other chronic clinical stages. The precise mechanisms by which probiotics acts is yet to be fully understood, however research findings have indicated their role in NF-κB modulation. The current review highlights NF-κB as a bio-therapeutic target for probable management of type 2 diabetes through probiotic intervention.
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Affiliation(s)
- Rabia Bhardwaj
- Department of Dairy Microbiology, College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Ludhiana, Punjab, India
| | - Brij Pal Singh
- Department of Dairy Microbiology, College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Ludhiana, Punjab, India
| | - Nitika Sandhu
- Punjab Agricultural University, Ludhiana, Punjab, India
| | - Niharika Singh
- Department of Dairy Microbiology, College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Ludhiana, Punjab, India
| | - Ravinder Kaur
- Department of Dairy Microbiology, College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Ludhiana, Punjab, India
| | - Namita Rokana
- Department of Dairy Microbiology, College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Ludhiana, Punjab, India
| | | | | | - Harsh Panwar
- Department of Dairy Microbiology, College of Dairy Science and Technology, Guru Angad Dev Veterinary and Animal Sciences University (GADVASU), Ludhiana, Punjab, India.
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Sandhu N, Benson K, Kumar K, Von Eyben R, Chang D, Soltys S, Pollom E. Stereotactic Radiosurgery for Spine Metastases of Gastrointestinal Origin. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.2248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Balazy K, Dudley S, Qian Y, Sandhu N, Chang D, Von Eyben R, Kidd E. Prognostic Model Using a Simple Survival Tree Algorithm for Patients Undergoing Palliative Radiation. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.1260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Benson K, Sandhu N, Zhang C, Ko R, Toesca D, Von Eyben R, Diehn M, Bush K, Maxim P, Gensheimer M, Soltys S, Loo B, Pollom E, Chang D. Outcomes of Oligometastatic Colorectal Cancer treated with Stereotactic Ablative Radiotherapy. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.2134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Wang E, Shi S, Sandhu N, Liu E, Jin M, Schofield K, Zhang C, Jaoude JA, Gibbs I, Hancock S, Chang S, Li G, Hayden M, Soltys S, Pollom E. Factors Associated with Treatment Failure and Radiation Necrosis Following Cavity Radiosurgery for Resected Brain Metastases. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.2271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Koenig J, Sborov K, Sandhu N, Sabolch A, Usoz M, Hiniker S, Soltys S, Pollom E. Financial Toxicity in Metastatic Cancer Patients Receiving Stereotactic Radiosurgery. Int J Radiat Oncol Biol Phys 2019. [DOI: 10.1016/j.ijrobp.2019.06.1200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Sandhu N, Subedi SR, Singh VK, Sinha P, Kumar S, Singh SP, Ghimire SK, Pandey M, Yadaw RB, Varshney RK, Kumar A. Deciphering the genetic basis of root morphology, nutrient uptake, yield, and yield-related traits in rice under dry direct-seeded cultivation systems. Sci Rep 2019; 9:9334. [PMID: 31249338 PMCID: PMC6597570 DOI: 10.1038/s41598-019-45770-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 06/13/2019] [Indexed: 11/18/2022] Open
Abstract
In the face of global water scarcity, a successful transition of rice cultivation from puddled to dry direct-seeded rice (DDSR) is a future need. A genome-wide association study was performed on a complex mapping population for 39 traits: 9 seedling-establishment traits, 14 root and nutrient-uptake traits, 5 plant morphological traits, 4 lodging resistance traits, and 7 yield and yield-contributing traits. A total of 10 significant marker-trait associations (MTAs) were found along with 25 QTLs associated with 25 traits. The percent phenotypic variance explained by SNPs ranged from 8% to 84%. Grain yield was found to be significantly and positively correlated with seedling-establishment traits, root morphological traits, nutrient uptake-related traits, and grain yield-contributing traits. The genomic colocation of different root morphological traits, nutrient uptake-related traits, and grain-yield-contributing traits further supports the role of root morphological traits in improving nutrient uptake and grain yield under DDSR. The QTLs/candidate genes underlying the significant MTAs were identified. The identified promising progenies carrying these QTLs may serve as potential donors to be exploited in genomics-assisted breeding programs for improving grain yield and adaptability under DDSR.
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Affiliation(s)
- Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines.,Punjab Agricultural University, Ludhiana, India
| | - Sushil Raj Subedi
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines.,Agriculture and Forestry University, Rampur, Chitwan, Nepal.,National Rice Research Program, Hardinath, Nepal
| | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Pallavi Sinha
- Center of Excellence in Genomics and System Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Santosh Kumar
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - S P Singh
- Bihar Agricultural University, Sabour, Bhagalpur, Bihar, India
| | | | - Madhav Pandey
- Agriculture and Forestry University, Rampur, Chitwan, Nepal
| | | | - Rajeev K Varshney
- Center of Excellence in Genomics and System Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, Metro Manila, Philippines.
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Subedi SR, Sandhu N, Singh VK, Sinha P, Kumar S, Singh SP, Ghimire SK, Pandey M, Yadaw RB, Varshney RK, Kumar A. Genome-wide association study reveals significant genomic regions for improving yield, adaptability of rice under dry direct seeded cultivation condition. BMC Genomics 2019; 20:471. [PMID: 31182016 PMCID: PMC6558851 DOI: 10.1186/s12864-019-5840-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 05/23/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Puddled transplanted system of rice cultivation despite having several benefits, is a highly labor, water and energy intensive system. In the face of changing climatic conditions, a successful transition from puddled to dry direct seeded rice (DDSR) cultivation system looks must in future. Genome-wide association study was performed for traits including, roots and nutrient uptake (14 traits), plant-morphological (5 traits), lodging-resistance (4 traits) and yield and yield attributing traits (7 traits) with the aim to identify significant marker-trait associations (MTAs) for traits enhancing rice adaptability to dry direct-seeded rice (DDSR) system. RESULTS Study identified a total of 37 highly significant MTAs for 20 traits. The false discovery rate (FDR) ranged from 0.264 to 3.69 × 10- 4, 0.0330 to 1.25 × 10- 4, and 0.0534 to 4.60 × 10- 6 in 2015WS, 2016DS and combined analysis, respectively. The percent phenotypic variance (PV) explained by SNPs ranged from 9 to 92%. Among the identified significant MTAs, 15 MTAs associated with the traits including nodal root, root hair length, root length density, stem and culm diameter, plant height and grain yield were reported to be located in the proximity of earlier identified candidate gene. The significant positive correlation of grain-yield with seedling establishment traits, root morphological and nutrient-uptake related traits and grain yield attributing traits pointing towards combining target traits to increase rice yield and adaptability under DDSR. Seven promising progenies with better root morphology, nutrient-uptake and higher grain yield were identified that can further be used in genomics assisted breeding for DDSR varietal development. CONCLUSIONS Once validated, the identified MTAs and the SNPs linked with trait of interest could be of direct use in genomic assisted breeding (GAB) to improve grain yield and adaptability of rice under DDSR.
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Affiliation(s)
- Sushil Raj Subedi
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Agriculture and Forestry University, Rampur, Chitwan Nepal
- National Rice Research Program, Hardinath, Nepal
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Punjab Agricultural University, Ludhiana, India
| | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Pallavi Sinha
- Center of Excellence in Genomics and System Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Santosh Kumar
- ICAR Research Complex for Eastern Region, Patna, Bihar India
| | - S. P. Singh
- Bihar Agricultural University, Sabour, Bihar India
| | | | - Madhav Pandey
- Agriculture and Forestry University, Rampur, Chitwan Nepal
| | | | - Rajeev K. Varshney
- Center of Excellence in Genomics and System Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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Yadav S, Sandhu N, Majumder RR, Dixit S, Kumar S, Singh SP, Mandal NP, Das SP, Yadaw RB, Singh VK, Sinha P, Varshney RK, Kumar A. Epistatic interactions of major effect drought QTLs with genetic background loci determine grain yield of rice under drought stress. Sci Rep 2019; 9:2616. [PMID: 30796339 PMCID: PMC6385343 DOI: 10.1038/s41598-019-39084-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Accepted: 01/17/2019] [Indexed: 01/30/2023] Open
Abstract
Epistatic interactions of QTLs with the genetic background and QTL-QTL interaction plays an important role in the phenotypic performance of introgression lines developed through genomic-assisted breeding (GAB). In this context, NIL pairs developed with various drought QTL (qDTY) combinations in the genetic background of IR64, TDK1-Sub1 and Savitri backgrounds were utilized to study the interactions. Multi-season phenotyping of NIL pairs harboring similar qDTY combinations provided contrasting performance for grain yield under drought (RS) (classified as high and low yielding NILs) but nearly similar performance under non-stress(NS) conditions. Genome wide genotyping data revealed a total of 16, 5 and 6 digenic interactions were detected under RS conditions in low yielding NILs of IR64, TDK1-Sub1 and Savitri respectively while no significant interaction was found in high yielding NILs under RS and NS conditions in any of the genetic backgrounds used in this study. It is evident from this study that existence of epistatic interactions between QTLs with genetic background, QTL-QTL interaction and interactions among background markers loci itself on different chromosomes influences the expression of a complex trait such as grain yield under drought. The generated information will be useful in all the GAB program of across the crops for precise breeding.
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Affiliation(s)
- Shailesh Yadav
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Ratna Rani Majumder
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Shalabh Dixit
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Santosh Kumar
- ICAR Research Complex for Eastern Region, Patna, Bihar, India
| | - S P Singh
- Bihar Agricultural University, Sabour, Bihar, India
| | - N P Mandal
- Central Rainfed Upland Rice Research station, National Rice Research Institute, Hazaribagh, Jharkhand, India
| | - S P Das
- ICAR Research Complex for NEH Region, Tripura Centre, Lembucherra, Tripura, India
| | | | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Pallavi Sinha
- International Crops Research Institute for the Semi-arid Tropics, Patancheru, Hyderabad, India
| | - Rajeev K Varshney
- International Crops Research Institute for the Semi-arid Tropics, Patancheru, Hyderabad, India
| | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
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Sandhu N, Dixit S, Swamy BPM, Raman A, Kumar S, Singh SP, Yadaw RB, Singh ON, Reddy JN, Anandan A, Yadav S, Venkataeshwarllu C, Henry A, Verulkar S, Mandal NP, Ram T, Badri J, Vikram P, Kumar A. Marker Assisted Breeding to Develop Multiple Stress Tolerant Varieties for Flood and Drought Prone Areas. Rice (N Y) 2019; 12:8. [PMID: 30778782 PMCID: PMC6379507 DOI: 10.1186/s12284-019-0269-y] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Accepted: 02/11/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND Climate extremes such as drought and flood have become major constraints to the sustainable rice crop productivity in rainfed environments. Availability of suitable climate-resilient varieties could help farmers to reduce the grain yield losses resulting from the climatic extremities. The present study was undertaken with an aim to develop high-yielding drought and submergence tolerant rice varieties using marker assisted introgression of qDTY1.1, qDTY2.1, qDTY3.1 and Sub1. Performance of near isogenic lines (NILs) developed in the background of Swarna was evaluated across 60 multi-locations trials (MLTs). The selected promising lines from MLTs were nominated and evaluated in national trials across 18 locations in India and 6 locations in Nepal. RESULTS Grain yield advantage of the NILs with qDTY1.1 + qDTY2.1 + qDTY3.1 + Sub1 and qDTY2.1 + qDTY3.1 + Sub1 ranged from 76 to 2479 kg ha- 1 and 396 to 2376 kg ha- 1 under non-stress (NS) respectively and 292 to 1118 kg ha- 1 and 284 to 2086 kg ha- 1 under reproductive drought stress (RS), respectively. The NIL, IR96322-34-223-B-1-1-1-1 having qDTY1.1 + qDTY2.1 + qDTY3.1 + Sub1 has been released as variety CR dhan 801 in India. IR 96321-1447-651-B-1-1-2 having qDTY1.1 + qDTY3.1 + Sub 1 and IR 94391-131-358-19-B-1-1-1 having qDTY3.1 + Sub1 have been released as varieties Bahuguni dhan-1' and 'Bahuguni dhan-2' respectively in Nepal. Background recovery of 94%, 93% and 98% was observed for IR 96322-34-223-B-1-1-1-1, IR 96321-1447-651-B-1-1-2 and IR 94391-131-358-19-B-1-1-1 respectively on 6 K SNP Infinium chip. CONCLUSION The drought and submergence tolerant rice varieties with pyramided multiple QTLs can ensure 0.2 to 1.7 t ha- 1 under reproductive stage drought stress and 0.1 to 1.0 t ha- 1 under submergence conditions with no yield penalty under non-stress to farmers irrespective of occurrence of drought and/or flood in the same or different seasons.
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Affiliation(s)
- Nitika Sandhu
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Punjab Agricultural University, Ludhiana, India
| | - Shalabh Dixit
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - B. P. M. Swamy
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Anitha Raman
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Santosh Kumar
- ICAR Research Complex for Eastern Region, Patna, Bihar India
| | - S. P. Singh
- Bihar Agricultural University, Sabour, Bihar India
| | - R. B. Yadaw
- National Rice Research Program Hardinath, Dhanusha, Nepal
| | - O. N. Singh
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - J. N. Reddy
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - A. Anandan
- ICAR-National Rice Research Institute, Cuttack, Odisha India
| | - Shailesh Yadav
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Challa Venkataeshwarllu
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Amelia Henry
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Satish Verulkar
- Indira Gandhi Krishi Vishwavidyalaya, Raipur, Chhattisgarh India
| | - N. P. Mandal
- Central Rainfed Upland Rice Research station, National Rice Research Institute, Hazaribagh, Jharkhand India
| | - T. Ram
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Jyothi Badri
- ICAR-Indian Institute of Rice Research, Hyderabad, India
| | - Prashant Vikram
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- International Maize and Wheat Improvement Centre (CIMMYT), Texcoco, Mexico
| | - Arvind Kumar
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
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Sandhu N, Yadaw RB, Chaudhary B, Prasai H, Iftekharuddaula K, Venkateshwarlu C, Annamalai A, Xangsayasane P, Battan KR, Ram M, Cruz MTS, Pablico P, Maturan PC, Raman KA, Catolos M, Kumar A. Evaluating the Performance of Rice Genotypes for Improving Yield and Adaptability Under Direct Seeded Aerobic Cultivation Conditions. Front Plant Sci 2019; 10:159. [PMID: 30828343 PMCID: PMC6384261 DOI: 10.3389/fpls.2019.00159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 01/29/2019] [Indexed: 05/04/2023]
Abstract
With the changing climatic conditions and reducing labor-water availability, the potential contribution of aerobic rice varieties and cultivation system to develop a sustainable rice based agri-food system has never been more important than today. Keeping in mind the goal of identifying high-yielding aerobic rice varieties for wider adaptation, a set of aerobic rice breeding lines were developed and evaluated for grain yield, plant height, and days to 50% flowering in 23 experiments conducted across different location in Philippines, India, Bangladesh, Nepal, and Lao-PDR between 2014 and 2017 in both wet and dry seasons. The heritability for grain yield ranged from 0.52 to 0.90. The season-wise two-stage analysis indicated significant genotype x location interaction for yield under aerobic conditions in both wet and dry seasons. The genotype × season × location interaction for yield was non-significant in both seasons indicating that across seasons the genotypes at each location did not show variability in the grain yield performance. Mean grain yield of the studied genotypes across different locations/seasons ranged from 2,085 to 6,433 Kg ha-1. The best-fit model for yield stability with low AIC value (542.6) was AMMI(1) model. The identified stable genotypes; IR 92521-143-2-2-1, IR 97048-10-1-1-3, IR 91326-7-13-1-1, IR 91326-20-2-1-4, and IR 91328-43-6-2-1 may serve as novel breeding material for varietal development under aerobic system of rice cultivation. High yield and stable performance of promising breeding lines may be due to presence of the earlier identified QTLs including grain yield under drought, grain yield under aerobic conditions, nutrient uptake, anaerobic germination, adaptability under direct seeded conditions, and tolerance to biotic stress resistance such as qDTY 2.1 , qDTY 3.1 , qDTY 12.1 , qNR 5.1 , AG 9.1 , qEVV 9.1 , qRHD 1.1 , qRHD 5.1, qRHD 8.1 qEMM 1.1 , qGY 6.1 , BPH3, BPH17, GM4, xa4, Xa21, Pita, and Pita2. The frequency of xa4 gene was highest followed by qAG 9.1, GM4, qDTY 3.1 , qDTY 2.1 , qGY 6.1, and qDTY 12.1.
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Affiliation(s)
- Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, Los Banos, Philippines
| | | | | | - Hari Prasai
- Regional Agriculture Research Station, Tarahara, Nepal
| | | | - Challa Venkateshwarlu
- South Asia Breeding Hub, International Rice Research Institute, ICRISAT, Hyderabad, India
| | - Anandan Annamalai
- Crop Improvement Division, National Rice Research Institute, Cuttack, India
| | | | | | | | - Ma. Teresa Sta. Cruz
- Rice Breeding Platform, International Rice Research Institute, Los Banos, Philippines
| | - Paquito Pablico
- Rice Breeding Platform, International Rice Research Institute, Los Banos, Philippines
| | - Paul Cornelio Maturan
- Rice Breeding Platform, International Rice Research Institute, Los Banos, Philippines
| | - K. Anitha Raman
- Rice Breeding Platform, International Rice Research Institute, Los Banos, Philippines
| | - Margaret Catolos
- Rice Breeding Platform, International Rice Research Institute, Los Banos, Philippines
| | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, Los Banos, Philippines
- *Correspondence: Arvind Kumar
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Adak M, Aditya TL, Adnan M, Ahmad S, Ahmed M, Akram R, Alam M, Hossain MA, Alharby HF, Ali MA, Ali M, Ali S, Amanullah, Amin A, Amitha Mithra S, Anee TI, Ansar Ali M, Arif M, Arif MS, Ashraf MA, Bakhat HF, Banerjee A, Bararpour T, Basir A, Bhandari H, Bhuiyan TF, Biswas JC, Biswas JK, Biswas PS, Borgohain D, Bukhari SA, Chakraborty K, Chattopadhyay K, Chaturvedi V, Choudhury S, Datir S, De AK, Dubey RS, Fahad S, Fahimirad S, Farooq MA, Fujita M, Ghorbanpour M, Ghosh A, Gill RA, Gupta M, Gupta P, Gupta S, Hakeem KR, Halder T, Hammad HM, Hannan F, Hasanuzzaman M, Hasnu S, Hassan S, Hidayatullah, Hu L, Huang J, Hussain I, Hussain S, Hussain S, Iftekharuddaula K, Ihsan MZ, Ihtisham M, Ijaz M, Ijaz M, Iqbal M, Islam F, Ismail A, Jamal Y, Jan A, Jan M, Jan T, Jini D, Joseph B, Kabir MS, Kadir NA, Kaleem S, Kalita J, Kamran M, Kasajima I, Kaur G, Kaur N, Khan IA, Khan MH, Khan MJ, Khan MA, Khan SU, Khare T, Khatun H, Korres NE, Kumar N, Kumar V, Lahkar L, Lam SS, Li L, Li M, Long M, Ma NL, Mahalder BK, Mahmood R, Mahmood-ur-Rahman, Malik K, Mallick S, Maqbool MM, Masood N, Mian IA, Mohammed AR, Morita S, Mubarik MS, Mubeen M, Mwamba TM, Nahar K, Naher U, Nasim W, Nessa B, Niazi NK, Noor M, Nordin MMA, Nyong’a TM, Panda D, Panda SK, Pandey P, Panthri M, Pareek A, Parmar B, Pati PK, Pradhan AK, Prakash C, Price AJ, Qamar S, Rahman IU, Rahman MS, Rasheed R, Rashid MM, Rasool A, Rasul F, Ray S, Rehman A, Riaz M, Rizwan M, Roychoudhury A, Roychowdhury R, Saha I, Salam MU, Saleem I, Sandhu N, Sarkar B, Sarkar MAR, Sarkar R, Saud S, Sevanthi AM, Shah K, Shah Z, Shahzad B, Shahzad SM, Shakoor MB, Shalahuddin A, Shandilya ZM, Shanmugavadivel P, Shriram V, Sihag MK, Singh V, Singla-Pareek SL, Slaton NA, Sultana SR, Tan SH, Tanti B, Tanveer M, Tarpley L, Turan V, Ullah H, Upadhyaya H, ur Rahman MH, Varanasi VK, Wahid F, Wan G, Wang D, Wang J, Wu C, Xu L, Yadav C, Yang C, Yang P, Yasmeen R, Yasmeen T, Zhou W. List of Contributors. Advances in Rice Research for Abiotic Stress Tolerance 2019:xxix-xli. [DOI: 10.1016/b978-0-12-814332-2.00053-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Koenig J, Sborov K, Sandhu N, Gensheimer M, Soltys S, Pollom E. Adverse Radiation Effect and Disease Control in Patients Undergoing Concurrent Stereotactic Radiosurgery and Immunotherapy for Brain Metastases. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Sandhu N, Grade M, Aggarwal S, Knox S, Dudley S. Clinical Outcomes and Factors Associated with Early Discontinuation of Treatment in Patients Treated with Emergent Palliative Radiation Therapy. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.1293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Prionas N, Nwachukwu C, Von Eyben R, Sandhu N, Kidd E. Prognostic Value and Kinetics of Neutrophil to Lymphocyte Ratio Prior to and During Definitive Chemoradiotherapy for Intact Cervical Cancer. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.1730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Liang R, Zhang N, Wu J, Sandhu N, Pollom E, Le Q, Hara W, Li R. Early Metabolic Response at Mid-Radiation Therapy FDG-PET Imaging Predicts Patterns of Treatment Failure in Locally Advanced Oropharyngeal Cancer. Int J Radiat Oncol Biol Phys 2018. [DOI: 10.1016/j.ijrobp.2018.07.942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Darling G, Sandhu N, Mora L. MS16.03 Recruitment Strategies for the Lung Cancer Screening. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Darling G, Sandhu N, Karapetyan T, Banaszewska A, Tammemagi M. P2.11-05 Recruitment Strategies for the Lung Cancer Screening Pilot for People at High Risk. J Thorac Oncol 2018. [DOI: 10.1016/j.jtho.2018.08.1351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Kumar A, Sandhu N, Dixit S, Yadav S, Swamy BPM, Shamsudin NAA. Marker-assisted selection strategy to pyramid two or more QTLs for quantitative trait-grain yield under drought. Rice (N Y) 2018; 11:35. [PMID: 29845495 PMCID: PMC5975061 DOI: 10.1186/s12284-018-0227-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 05/21/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND Marker-assisted breeding will move forward from introgressing single/multiple genes governing a single trait to multiple genes governing multiple traits to combat emerging biotic and abiotic stresses related to climate change and to enhance rice productivity. MAS will need to address concerns about the population size needed to introgress together more than two genes/QTLs. In the present study, grain yield and genotypic data from different generations (F3 to F8) for five marker-assisted breeding programs were analyzed to understand the effectiveness of synergistic effect of phenotyping and genotyping in early generations on selection of better progenies. RESULTS Based on class analysis of the QTL combinations, the identified superior QTL classes in F3/BC1F3/BC2F3 generations with positive QTL x QTL and QTL x background interactions that were captured through phenotyping maintained its superiority in yield under non-stress (NS) and reproductive-stage drought stress (RS) across advanced generations in all five studies. The marker-assisted selection breeding strategy combining both genotyping and phenotyping in early generation significantly reduced the number of genotypes to be carried forward. The strategy presented in this study providing genotyping and phenotyping cost savings of 25-68% compared with the traditional marker-assisted selection approach. The QTL classes, Sub1 + qDTY 1.1 + qDTY 2.1 + qDTY 3.1 and Sub1 + qDTY 2.1 + qDTY 3.1 in Swarna-Sub1, Sub1 + qDTY 1.1 + qDTY 1.2 , Sub1 + qDTY 1.1 + qDTY 2.2 and Sub1 + qDTY 2.2 + qDTY 12.1 in IR64-Sub1, qDTY 2.2 + qDTY 4.1 in Samba Mahsuri, Sub1 + qDTY 3.1 + qDTY 6.1 + qDTY 6.2 and Sub1 + qDTY 6.1 + qDTY 6.2 in TDK1-Sub1 and qDTY 12.1 + qDTY 3.1 and qDTY 2.2 + qDTY 3.1 in MR219 had shown better and consistent performance under NS and RS across generations over other QTL classes. CONCLUSION "Deployment of this procedure will save time and resources and will allow breeders to focus and advance only germplasm with high probability of improved performance. The identification of superior QTL classes and capture of positive QTL x QTL and QTL x background interactions in early generation and their consistent performance in subsequent generations across five backgrounds supports the efficacy of a combined MAS breeding strategy".
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Affiliation(s)
- Arvind Kumar
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Nitika Sandhu
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Shalabh Dixit
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Shailesh Yadav
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - B. P. M. Swamy
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Noraziyah Abd Aziz Shamsudin
- International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
- Current address: Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor Malaysia
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Dixit S, Singh A, Sandhu N, Bhandari A, Vikram P, Kumar A. Combining drought and submergence tolerance in rice: marker-assisted breeding and QTL combination effects. Mol Breed 2017; 37:143. [PMID: 29151804 PMCID: PMC5670188 DOI: 10.1007/s11032-017-0737-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Accepted: 10/09/2017] [Indexed: 05/21/2023]
Abstract
TDK1 is a popular rice variety from the Lao PDR. Originally developed for irrigated conditions, this variety suffers a high decline in yield under drought conditions. Studies have identified three quantitative trait loci (QTLs) for grain yield under drought conditions, qDTY3.1 , qDTY6.1 , and qDTY6.2 , that show a high effect in the background of this variety. We report here the pyramiding of these three QTLs with SUB1 that provides 2-3 weeks of tolerance to complete submergence, with the aim to develop drought- and submergence-tolerant near-isogenic lines (NILs) of TDK1. We used a tandem approach that combined marker-assisted backcross breeding with phenotypic selection to develop NILs with high yield under drought stress and non-stress conditions and preferred grain quality. The effect of different QTL combinations on yield and yield-related traits under drought stress and non-stress conditions is also reported. Our results show qDTY3.1 to be the largest and most consistent QTL affecting yield under drought conditions, followed by qDTY6.1 and qDTY6.2 , respectively. QTL class analysis also showed that lines with a combination of qDTY3.1 and qDTY6.1 consistently showed a higher tolerance to drought than those in which one of these QTLs was missing. In countries such as Lao PDR, where large areas under rice cultivation suffer vegetative-stage submergence and reproductive-stage drought, these lines could ensure yield stability. These lines can also serve as valuable genetic material to be used for further breeding of high-yielding, drought- and submergence-tolerant varieties in local breeding programs.
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Affiliation(s)
- Shalabh Dixit
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Anshuman Singh
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- Rani Lakshmi Bai Central Agriculture University, Jhansi, India
| | - Nitika Sandhu
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Aditi Bhandari
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
| | - Prashant Vikram
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
- International Maize and Wheat Improvement Center (CIMMYT), Km. 45, Carretera México-Veracruz, El Batán, 56237 Texcoco, CP Mexico
| | - Arvind Kumar
- International Rice Research Institute (IRRI), DAPO Box 7777, Metro Manila, Philippines
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Sandhu N, Subedi SR, Yadaw RB, Chaudhary B, Prasai H, Iftekharuddaula K, Thanak T, Thun V, Battan KR, Ram M, Venkateshwarlu C, Lopena V, Pablico P, Maturan PC, Cruz MTS, Raman KA, Collard B, Kumar A. Root Traits Enhancing Rice Grain Yield under Alternate Wetting and Drying Condition. Front Plant Sci 2017; 8:1879. [PMID: 29163604 PMCID: PMC5671499 DOI: 10.3389/fpls.2017.01879] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 10/16/2017] [Indexed: 05/13/2023]
Abstract
Reducing water requirements and lowering environmental footprints require attention to minimize risks to food security. The present study was conducted with the aim to identify appropriate root traits enhancing rice grain yield under alternate wetting and drying conditions (AWD) and identify stable, high-yielding genotypes better suited to the AWD across variable ecosystems. Advanced breeding lines, popular rice varieties and drought-tolerant lines were evaluated in a series of 23 experiments conducted in the Philippines, India, Bangladesh, Nepal and Cambodia in 2015 and 2016. A large variation in grain yield under AWD conditions enabled the selection of high-yielding and stable genotypes across locations, seasons and years. Water savings of 5.7-23.4% were achieved without significant yield penalty across different ecosystems. The mean grain yield of genotypes across locations ranged from 3.5 to 5.6 t/ha and the mean environment grain yields ranged from 3.7 (Cambodia) to 6.6 (India) t/ha. The best-fitting Finlay-Wilkinson regression model identified eight stable genotypes with mean grain yield of more than 5.0 t/ha across locations. Multidimensional preference analysis represented the strong association of root traits (nodal root number, root dry weight at 22 and 30 days after transplanting) with grain yield. The genotype IR14L253 outperformed in terms of root traits and high mean grain yield across seasons and six locations. The 1.0 t/ha yield advantage of IR14L253 over the popular cultivar IR64 under AWD shall encourage farmers to cultivate IR14L253 and also adopt AWD. The results suggest an important role of root architectural traits in term of more number of nodal roots and root dry weight at 10-20 cm depth on 22-30 days after transplanting (DAT) in providing yield stability and preventing yield reduction under AWD compared to continuous flooded conditions. Genotypes possessing increased number of nodal roots provided higher yield over IR64 as well as no yield reduction under AWD compared to flooded irrigation. The identification of appropriate root architecture traits at specific depth and specific growth stage shall help breeding programs develop better rice varieties for AWD conditions.
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Affiliation(s)
- Nitika Sandhu
- International Rice Research Institute, Los Baños, Philippines
| | | | - Ram B. Yadaw
- National Rice Research Program, Hardinath, Nepal
| | | | - Hari Prasai
- Regional Agriculture Research Station, Tarahara, Nepal
| | | | - Tho Thanak
- Cambodian Agricultural Research and Development Institute, Phnom Penh, Cambodia
| | - Vathany Thun
- Cambodian Agricultural Research and Development Institute, Phnom Penh, Cambodia
| | | | | | - Challa Venkateshwarlu
- South Asia Breeding Hub, International Rice Research Institute, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Paquito Pablico
- International Rice Research Institute, Los Baños, Philippines
| | - Paul C. Maturan
- International Rice Research Institute, Los Baños, Philippines
| | | | - K. Anitha Raman
- International Rice Research Institute, Los Baños, Philippines
| | | | - Arvind Kumar
- International Rice Research Institute, Los Baños, Philippines
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Catolos M, Sandhu N, Dixit S, Shamsudin NAA, Naredo MEB, McNally KL, Henry A, Diaz MG, Kumar A. Genetic Loci Governing Grain Yield and Root Development under Variable Rice Cultivation Conditions. Front Plant Sci 2017; 8:1763. [PMID: 29085383 PMCID: PMC5650699 DOI: 10.3389/fpls.2017.01763] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 09/26/2017] [Indexed: 05/21/2023]
Abstract
Drought is the major abiotic stress to rice grain yield under unpredictable changing climatic scenarios. The widely grown, high yielding but drought susceptible rice varieties need to be improved by unraveling the genomic regions controlling traits enhancing drought tolerance. The present study was conducted with the aim to identify quantitative trait loci (QTLs) for grain yield and root development traits under irrigated non-stress and reproductive-stage drought stress in both lowland and upland situations. A mapping population consisting of 480 lines derived from a cross between Dular (drought-tolerant) and IR64-21 (drought susceptible) was used. QTL analysis revealed three major consistent-effect QTLs for grain yield (qDTY1.1, qDTY1.3 , and qDTY8.1 ) under non-stress and reproductive-stage drought stress conditions, and 2 QTLs for root traits (qRT9.1 for root-growth angle and qRT5.1 for multiple root traits, i.e., seedling-stage root length, root dry weight and crown root number). The genetic locus qDTY1.1 was identified as hotspot for grain yield and yield-related agronomic and root traits. The study identified significant positive correlations among numbers of crown roots and mesocotyl length at the seedling stage and root length and root dry weight at depth at later stages with grain yield and yield-related traits. Under reproductive stage drought stress, the grain yield advantage of the lines with QTLs ranged from 24.1 to 108.9% under upland and 3.0-22.7% under lowland conditions over the lines without QTLs. The lines with QTL combinations qDTY1.3 +qDTY8.1 showed the highest mean grain yield advantage followed by lines having qDTY1.1 +qDTY8.1 and qDTY1.1 +qDTY8.1 +qDTY1.3 , across upland/lowland reproductive-stage drought stress. The identified QTLs for root traits, mesocotyl length, grain yield and yield-related traits can be immediately deployed in marker-assisted breeding to develop drought tolerant high yielding rice varieties.
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Affiliation(s)
- Margaret Catolos
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines
- Genetics and Molecular Biology Division, Institute of Biological Sciences, University of the Philippines Los Baños, Los Baños, Philippines
| | - Nitika Sandhu
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines
| | - Shalabh Dixit
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines
| | - Noraziya A. A. Shamsudin
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines
- School of Environmental and Natural Resource Sciences, Universiti Kebangsaan Malaysia, Bangi, Malaysia
| | - Ma E. B. Naredo
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines
| | - Kenneth L. McNally
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines
| | - Amelia Henry
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines
| | - Ma G. Diaz
- Genetics and Molecular Biology Division, Institute of Biological Sciences, University of the Philippines Los Baños, Los Baños, Philippines
| | - Arvind Kumar
- Rice Breeding Platform, International Rice Research Institute, Manila, Philippines
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Larsen R, Sandhu N, Heegaard NHH, Ullum H, von Stemann JH, Sørensen E, Nellemann DS, Hansen MB. Changes in circulating inflammatory markers following febrile non-haemolytic transfusion reactions to leucoreduced red cells. Vox Sang 2017; 113:76-79. [PMID: 29023768 DOI: 10.1111/vox.12607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Revised: 09/15/2017] [Accepted: 09/24/2017] [Indexed: 12/01/2022]
Abstract
It would be desirable to be able to distinguish fever as a result of febrile non-haemolytic transfusion reactions (FNHTR) from other febrile conditions. To further characterize the inflammatory feature of FNHTR, we measured a large panel of inflammatory markers in pre- and posttransfusion plasma samples from patients with and without FNHTR following the transfusion of leucoreduced red blood cells. As FNHTR patients only displayed a significant increase in IL-6, we conclude that changes in plasma cytokine levels during FNHTR are unlikely to be used diagnostically. An incidental finding of a distinct cytokine pattern in pretransfusion samples from FNHTR patients warrants further investigations, as it might be used to characterize the nature of FNHTR and to predict the risk of these adverse events.
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Affiliation(s)
- R Larsen
- Department of Clinical Immunology, Naestved Hospital, Naestved, Denmark
| | - N Sandhu
- Department of Congenital Diseases, Statens Serum Institut, Copenhagen, Denmark
| | - N H H Heegaard
- Department of Autoimmunology and Biomarkers, Statens Serum Institut, Copenhagen, Denmark.,Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
| | - H Ullum
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - J H von Stemann
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - E Sørensen
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - D S Nellemann
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - M B Hansen
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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Yadav S, Singh UM, Naik SM, Venkateshwarlu C, Ramayya PJ, Raman KA, Sandhu N, Kumar A. Molecular Mapping of QTLs Associated with Lodging Resistance in Dry Direct-Seeded Rice ( Oryza sativa L.). Front Plant Sci 2017; 8:1431. [PMID: 28871266 PMCID: PMC5567065 DOI: 10.3389/fpls.2017.01431] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 08/03/2017] [Indexed: 05/04/2023]
Abstract
Dry direct-seeded rice (DSR) is an alternative crop establishment method with less water and labor requirement through mechanization. It provides better opportunities for a second crop during the cropping season and therefore, a feasible alternative system to transplanted lowland rice. However, lodging is one of the major constraints in attaining high yield in DSR. Identification of QTLs for lodging resistance and their subsequent use in improving varieties under DSR will be an efficient breeding strategy to address the problem. In order to map the QTLs associated with lodging resistance, a set of 253 BC3F4 lines derived from a backcross between Swarna and Moroberekan were evaluated in two consecutive years. A total of 12 QTLs associated with lodging resistance traits [culm length (qCL), culm diameter (qCD), and culm strength (qCS)] were mapped on chromosomes 1, 2, 6, and 7 using 193 polymorphic SNP markers. Two major and consistent effect QTLs, namely qCD1.1 (with R2 of 10%) and qCS1.1 (with R2 of 14%) on chromosome 1 with id1003559 being the peak SNP marker (flanking markers; id1001973-id1006772) were identified as a common genomic region associated with important lodging resistance traits. In silico analysis revealed the presence of Gibberellic Acid 3 beta-hydroxylase along with 34 other putative candidate genes in the marker interval region of id1001973-id1006772. The positive alleles for culm length, culm diameter, and culm strength were contributed by the upland adaptive parent Moroberekan. Our results identified significant positive correlation between lodging related traits (culm length diameter and strength) and grain yield under DSR, indicating the role of lodging resistant traits in grain yield improvement under DSR. Deployment of the identified alleles influencing the culm strength and culm diameter in marker assisted introgression program may facilitate the lodging resistance under DSR.
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Affiliation(s)
- Shailesh Yadav
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
- International Rice Research InstituteMetro Manila, Philippines
| | - Uma M Singh
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Shilpa M Naik
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Challa Venkateshwarlu
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Perumalla J Ramayya
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - K Anitha Raman
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
| | - Nitika Sandhu
- International Rice Research InstituteMetro Manila, Philippines
| | - Arvind Kumar
- International Rice Research Institute, South Asia Hub, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT)Patancheru, India
- International Rice Research InstituteMetro Manila, Philippines
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Mulki R, Baumann AJ, Alnabelsi T, Sandhu N, Alhamshari Y, Wheeler DS, Perloff S, Katz PO. Body mass index greater than 35 is associated with severe Clostridium difficile infection. Aliment Pharmacol Ther 2017; 45:75-81. [PMID: 27790736 DOI: 10.1111/apt.13832] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Revised: 08/02/2016] [Accepted: 09/27/2016] [Indexed: 12/12/2022]
Abstract
BACKGROUND Obesity has been implicated in the acquisition of Clostridium difficile infections (CDI), however, no study has investigated whether there is a correlation between body mass index (BMI) and CDI severity. AIM To determine whether obesity, as measured by BMI correlates with severe hospital-onset or community-onset CDI. METHODS Patients admitted with CDI at a tertiary-care center from January 2013 to June 2015 were identified. The cohort was stratified by onset of disease using the National Healthcare Safety Network criteria, and by severity using the 2013 American College of Gastroenterology guidelines. Multivariate logistic regression was used to determine independent predictors of severe CDI. RESULTS A total of 196 met the inclusion criteria, of which 57.1% (112) met criteria for severe disease. Overall, BMI >35 kg/m2 was 1.7-fold more likely to be associated with severe CDI compared to a BMI 20-35 kg/m2 (P < 0.005), and was an independent predictor of severe CDI (P = 0.038). In patients with community-onset-CDI and hospital-onset-CDI, a BMI >35 kg/m2 was associated with a 1.96-fold and 1.48 greater rate of severe CDI compared to a BMI 20-35 kg/m2 (P = 0.004 and 0.048), and was an independent predictor of severe CDI in these cohorts (P = 0.039 and 0.027) respectively. CONCLUSION This study has identified an association between body mass index and Clostridium difficile infection severity. A BMI>35 kg/m2 is an independent risk factor for severe community-onset and hospital-onset Clostridium difficile infections.
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Affiliation(s)
- R Mulki
- Department of Internal Medicine, Einstein Medical Center, Philadelphia, PA, USA
| | - A J Baumann
- Department of Gastroenterology and Hepatology, University of Florida, Gainesville, FL, USA
| | - T Alnabelsi
- Department of Internal Medicine, Einstein Medical Center, Philadelphia, PA, USA
| | - N Sandhu
- Department of Internal Medicine, Einstein Medical Center, Philadelphia, PA, USA
| | - Y Alhamshari
- Department of Internal Medicine, Einstein Medical Center, Philadelphia, PA, USA
| | - D S Wheeler
- Department of Internal Medicine, Einstein Medical Center, Philadelphia, PA, USA
| | - S Perloff
- Division of Infectious Disease, Einstein Medical Center, Philadelphia, PA, USA
| | - P O Katz
- Division of Gastroenterology and Hepatology, Einstein Medical Center, Philadelphia, PA, USA
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Shamsudin NAA, Swamy BPM, Ratnam W, Sta Cruz MT, Sandhu N, Raman AK, Kumar A. Pyramiding of drought yield QTLs into a high quality Malaysian rice cultivar MRQ74 improves yield under reproductive stage drought. Rice (N Y) 2016; 9:21. [PMID: 27164982 PMCID: PMC4864745 DOI: 10.1186/s12284-016-0093-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/22/2016] [Indexed: 05/03/2023]
Abstract
BACKGROUND With the objective of improving the grain yield (GY) of the Malaysian high quality rice cultivar MRQ74 under reproductive stage drought stress (RS), three drought yield QTLs, viz. qDTY 2.2, qDTY 3.1 , and qDTY 12.1 were pyramided by marker assisted breeding (MAB). Foreground selection using QTL specific markers, recombinant selection using flanking markers, and background selections were performed in every generation. BC1F3 derived pyramided lines (PLs) with different combinations of qDTY 2.2, qDTY 3.1 , and qDTY 12.1 were evaluated under both RS and non-stress (NS) during the dry season (DS) of 2013 and 2014 at IRRI. RESULTS The GY reductions in RS trials compared to NS trials ranged from 79 to 99 %. Plant height (PH) was reduced and days to flowering (DTF) was delayed under RS. Eleven BC1F5 MRQ74 PLs with yield advantages of 1009 to 3473 kg ha(-1) under RS and with yields equivalent to MRQ74 under NS trials were identified as promising drought tolerance PLs. Five best PLs, IR 98010-126-708-1-4, IR 98010-126-708-1-3, IR 98010-126-708-1-5, IR 99616-44-94-1-1, and IR 99616-44-94-1-2 with a yield advantage of more than 1000 kg ha(-1) under RS and with yield potential equivalent to that of MRQ74 under NS were selected. The effect of three drought grain yield QTLs under RS in MRQ74 was validated. Under NS, PLs with two qDTY combinations (qDTY 2.2 + qDTY 12.1 ) performed better than PLs with other qDTY combinations, indicating the presence of a positive interaction between qDTY 2.2 and qDTY 12.1 in the MRQ74 background. CONCLUSION Drought tolerant MRQ74 PLs with a yield advantage of more than 1000 kg ha(-1) under RS were developed. Differential yield advantages of different combinations of the qDTYs indicate a differential synergistic relationship among qDTYs.
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Affiliation(s)
- Noraziyah Abd Aziz Shamsudin
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - B P Mallikarjuna Swamy
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Wickneswari Ratnam
- Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
| | - Ma Teressa Sta Cruz
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Nitika Sandhu
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Anitha K Raman
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines
| | - Arvind Kumar
- Plant Breeding, Genetics, and Biotechnology Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, Philippines.
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Sandhu N, Raman KA, Torres RO, Audebert A, Dardou A, Kumar A, Henry A. Rice Root Architectural Plasticity Traits and Genetic Regions for Adaptability to Variable Cultivation and Stress Conditions. Plant Physiol 2016; 171:2562-76. [PMID: 27342311 PMCID: PMC4972292 DOI: 10.1104/pp.16.00705] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/21/2016] [Indexed: 05/02/2023]
Abstract
Future rice (Oryza sativa) crops will likely experience a range of growth conditions, and root architectural plasticity will be an important characteristic to confer adaptability across variable environments. In this study, the relationship between root architectural plasticity and adaptability (i.e. yield stability) was evaluated in two traditional × improved rice populations (Aus 276 × MTU1010 and Kali Aus × MTU1010). Forty contrasting genotypes were grown in direct-seeded upland and transplanted lowland conditions with drought and drought + rewatered stress treatments in lysimeter and field studies and a low-phosphorus stress treatment in a Rhizoscope study. Relationships among root architectural plasticity for root dry weight, root length density, and percentage lateral roots with yield stability were identified. Selected genotypes that showed high yield stability also showed a high degree of root plasticity in response to both drought and low phosphorus. The two populations varied in the soil depth effect on root architectural plasticity traits, none of which resulted in reduced grain yield. Root architectural plasticity traits were related to 13 (Aus 276 population) and 21 (Kali Aus population) genetic loci, which were contributed by both the traditional donor parents and MTU1010. Three genomic loci were identified as hot spots with multiple root architectural plasticity traits in both populations, and one locus for both root architectural plasticity and grain yield was detected. These results suggest an important role of root architectural plasticity across future rice crop conditions and provide a starting point for marker-assisted selection for plasticity.
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Affiliation(s)
- Nitika Sandhu
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines (N.S., K.A.R., R.O.T., A.K., A.H.); andCIRAD, Unité Mixte de Recherche AGAP, 34398 Montpellier Cedex 5, France (A.A., A.D.)
| | - K Anitha Raman
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines (N.S., K.A.R., R.O.T., A.K., A.H.); andCIRAD, Unité Mixte de Recherche AGAP, 34398 Montpellier Cedex 5, France (A.A., A.D.)
| | - Rolando O Torres
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines (N.S., K.A.R., R.O.T., A.K., A.H.); andCIRAD, Unité Mixte de Recherche AGAP, 34398 Montpellier Cedex 5, France (A.A., A.D.)
| | - Alain Audebert
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines (N.S., K.A.R., R.O.T., A.K., A.H.); andCIRAD, Unité Mixte de Recherche AGAP, 34398 Montpellier Cedex 5, France (A.A., A.D.)
| | - Audrey Dardou
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines (N.S., K.A.R., R.O.T., A.K., A.H.); andCIRAD, Unité Mixte de Recherche AGAP, 34398 Montpellier Cedex 5, France (A.A., A.D.)
| | - Arvind Kumar
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines (N.S., K.A.R., R.O.T., A.K., A.H.); andCIRAD, Unité Mixte de Recherche AGAP, 34398 Montpellier Cedex 5, France (A.A., A.D.)
| | - Amelia Henry
- International Rice Research Institute, Los Baños, Laguna 4031, Philippines (N.S., K.A.R., R.O.T., A.K., A.H.); andCIRAD, Unité Mixte de Recherche AGAP, 34398 Montpellier Cedex 5, France (A.A., A.D.)
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50
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Sandhu N, Torres RO, Sta Cruz MT, Maturan PC, Jain R, Kumar A, Henry A. Traits and QTLs for development of dry direct-seeded rainfed rice varieties. J Exp Bot 2015; 66:225-44. [PMID: 25336682 PMCID: PMC4265160 DOI: 10.1093/jxb/eru413] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
The development of rice varieties for dry direct-seeded conditions can be accelerated by selecting suitable traits. In the present investigation, traits hypothesized to be important for direct-seeded conditions in rainfed systems, including seedling emergence, early vegetative vigour, nutrient uptake, nodal root number, and root hair length and density, were characterized to study the genetic control of these traits and their relationship with grain yield under seedling- and reproductive-stage drought stress. Two BC₂F₄ mapping populations derived from crosses of Aus276, a drought-tolerant aus variety, with MTU1010 and IR64, high-yielding indica mega-varieties, were developed and studied to identify quantitative trait loci (QTLs) that showed large and consistent effects. A total of 26 QTLs associated with 23 traits and 20 QTLs associated with 13 traits were mapped in the Aus276/3*IR64 and Aus276/3*MTU1010 populations, respectively. qGY₆.₁, qGY₁₀.₁, qGY₁.₁, and qEVV₉.₁ were found to be effective in both populations under a wide range of conditions. QTLs for several seedling-stage traits co-located with QTLs for grain yield, including early vegetative vigour and root hair length. On chromosome 5, several QTLs for nutrient uptake co-located with QTLs for root hair density and nematode gall rating. Six lines were selected from both populations based on grain yield and the presence of QTLs, and these lines typically showed improved seedling-stage traits (nodal root number, dry shoot weight, and root hair length and density). The co-located QTLs identified here can be used in research aimed at increasing the yield and adaptability of rainfed rice to direct-seeded conditions.
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Affiliation(s)
- Nitika Sandhu
- Division of Plant Breeding, Genetics, and Biotechnology, International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines Department of Molecular Biology and Biotechnology, CCS Haryana Agricultural University, Hisar-125004, India
| | - Rolando O Torres
- Crop and Environmental Sciences Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines
| | - Ma Teresa Sta Cruz
- Division of Plant Breeding, Genetics, and Biotechnology, International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines
| | - Paul Cornelio Maturan
- Division of Plant Breeding, Genetics, and Biotechnology, International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines
| | - Rajinder Jain
- Department of Molecular Biology and Biotechnology, CCS Haryana Agricultural University, Hisar-125004, India
| | - Arvind Kumar
- Division of Plant Breeding, Genetics, and Biotechnology, International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines
| | - Amelia Henry
- Crop and Environmental Sciences Division, International Rice Research Institute, DAPO Box 7777, Metro Manila, The Philippines
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