1
|
Mohanavel V, Muthu V, Kambale R, Palaniswamy R, Seeli P, Ayyenar B, Rajagopalan V, Manickam S, Rajasekaran R, Rahman H, Nallathambi J, Swaminathan M, Chellappan G, Vellingiri G, Muthurajan R. Marker-assisted breeding accelerates the development of multiple-stress-tolerant rice genotypes adapted to wider environments. FRONTIERS IN PLANT SCIENCE 2024; 15:1402368. [PMID: 39070911 PMCID: PMC11272538 DOI: 10.3389/fpls.2024.1402368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 06/03/2024] [Indexed: 07/30/2024]
Abstract
Introduction Rice, one of the major staple food crops is frequently affected by various biotic/abiotic stresses including drought, salinity, submergence, heat, Bacterial leaf blight, Brown plant hopper, Gall midge, Stem borer, Leaf folder etc. Sustained increase of yield growth is highly necessary to meet the projected demand in rice production during the year 2050. Hence, development of high yielding and multiple stress tolerant rice varieties adapted to wider environments will serve the need. Methods A systematic MAB approach was followed to pyramid eight major QTLs/genes controlling tolerance to major abiotic/biotic stresses viz., drought (qDTY1.1 and qDTY2.1), salinity (Saltol), submergence (Sub1), bacterial leaf blight (xa13 and Xa21), blast (Pi9) and gall midge (Gm4) in the genetic background of an elite rice culture CBMAS 14065 possessing high yield and desirable grain quality traits. Two advanced backcross derivatives of CBMAS 14065 possessing different combinations of target QTLs namely #27-1-39 (qDTY1.1+qDTY2.1+Sub1+xa13+Xa21+Gm4+Pi9) and #29-2-2 (qDTY1.1+qDTY2.1+Saltol+Xa21+Gm4+Pi9) were inter-mated. Results Inter-mated F1 progenies harboring all the eight target QTLs/genes were identified through foreground selection. Genotyping of the inter-mated F4 population identified 14 progenies possessing all eight target QTLs/genes under homozygous conditions. All the fourteen progenies were forwarded up to F8 generation and evaluated for their yield and tolerance to dehydration, salinity, submergence, blast and bacterial leaf blight. All the 14 progenies exhibited enhanced tolerance to dehydration and salinity stresses by registering lesser reduction in their chlorophyll content, relative water content, root length, root biomass etc., against their recurrent parent Improved White Ponni/CBMAS 14065. All the 14 progenies harboring Sub1 loci from FR13A exhibited enhanced survival (90 - 95%) under 2 weeks of submergence /flooding when compared to their recurrent parent CBMAS 14065 which showed 100% susceptibility The inter-mated population showed a enhanced level of resistance to bacterial leaf blight (Score = 0 to 2) against blast (Score - 0) whereas the susceptible check CO 39 and the recurrent parent CBMAS 14065 recorded high level of susceptibility (Score = 7 to 9). Conclusion or discussion Our study demonstrated the accelerated development of multiple stress tolerant rice genotypes through marker assisted pyramiding of target QTLs/genes using tightly linked markers. These multiple stress tolerant rice lines will serve as excellent genetic stocks for field testing/variety release and also as parental lines in future breeding programs for developing climate resilient super rice varieties.
Collapse
Affiliation(s)
- Vignesh Mohanavel
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Valarmathi Muthu
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Rohit Kambale
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Rakshana Palaniswamy
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Prisca Seeli
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Bharathi Ayyenar
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Veeraranjani Rajagopalan
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Sudha Manickam
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raghu Rajasekaran
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Hifzur Rahman
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
- International Centre for Biosaline Agriculture, Dubai, United Arab Emirates
| | - Jagadeeshselvam Nallathambi
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Manonmani Swaminathan
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Gopalakrishnan Chellappan
- Centre for Plant Breeding and Genetics, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | | | - Raveendran Muthurajan
- Centre for Plant Molecular Biology and Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| |
Collapse
|
2
|
Rai M, Chucha D, Deepika D, Lap B, Magudeeswari P, Padmavathi G, Singh N, Tyagi W. Pyramiding of qDTY 1.1 and qDTY 3.1 into rice mega-variety Samba Mahsuri-Sub1: physiological performance under water deficit conditions. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1931-1943. [PMID: 38222275 PMCID: PMC10784446 DOI: 10.1007/s12298-023-01387-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 10/18/2023] [Accepted: 11/09/2023] [Indexed: 01/16/2024]
Abstract
Water deficit is a crucial factor causing huge loss to rice productivity. The present study aimed to develop a multiple stress tolerant genotype by pyramiding drought tolerant yield QTLs qDTY1.1 and qDTY3.1 into high yielding rice variety Samba Mahsuri Sub-1(SMS) through marker assisted pyramiding. To achieve this six introgression lines of SMS carrying qDTY1.1 (SAB) were crossed with DRR-50, an Essentially Derived Variety of SMS carrying qDTY3.1. The SAB lines are taller than SMS due to tight linkage between qDTY1.1 and wild type SD-1. Therefore, F2 generation of crosses were screened for recombinants between SD-1 and qDTY1.1. Phenotyping of 1530 F2 plants representing three F2 populations from 35 F1 hybrids, identified 305 dwarf plants. Three dwarf F2 plants along with three others carrying qDTY1.1 and qDTY3.1 were forwarded to F3 generation. From the six F3 (SABD) lines fourteen pyramided progenies were selected and forward to F4 generation. The six SABD F3 lines SABD-7, SABD-8, SABD-9, SABD-76, SABD-79 and SABD-80 along with parents were evaluated under moisture stress (MS) for various physiological parameters. Chlorophyll and relative water content were more, while canopy temperature and malonaldehyde (MDA) content were lesser in SABD lines compared to parents indicating tolerance under MS. Variance due to genotypes was highly significant for all the yield related traits except test weight. Based on seed morphology, agronomic characters and physiological parameters six superior lines SABD-9-3, SABD-9-2, SABD-9-6, SABD-9-7, SABD-76-2 and SABD-76-6 performing better under MS were identified, which could be released after multi-location evaluation. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01387-5.
Collapse
Affiliation(s)
- Mayank Rai
- School of Crop Improvement, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, India
| | - Diezehlouno Chucha
- School of Crop Improvement, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, India
| | - Dake Deepika
- School of Crop Improvement, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, India
| | - Bharati Lap
- School of Crop Improvement, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, India
| | - P. Magudeeswari
- School of Crop Improvement, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, India
| | - G. Padmavathi
- ICAR- Indian Institute of Rice Research, Hyderabad, Telangana India
| | - Nagendra Singh
- ICAR- National Institute for Plant Biotechnology, New Delhi, India
| | - Wricha Tyagi
- School of Crop Improvement, College of Post Graduate Studies in Agricultural Sciences, Central Agricultural University (Imphal), Umiam, India
- Present Address: International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Telangana India
| |
Collapse
|
3
|
Varanasi YVP, Isetty SR, Revadi P, Balakrishnan D, Hajira S, Prasad MS, Laha GS, Perraju P, Singh UM, Singh VK, Kumar A, Sundaram RM, Badri J. Molecular and Morphological Characterization of Introgression Lines with Resistance to Bacterial Leaf Blight and Blast in Rice. PLANTS (BASEL, SWITZERLAND) 2023; 12:3012. [PMID: 37631223 PMCID: PMC10458744 DOI: 10.3390/plants12163012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 07/21/2023] [Accepted: 07/21/2023] [Indexed: 08/27/2023]
Abstract
The present study evaluates marker assisted forward breeding (MAFB)-derived disease resistant introgression lines (ILs) which do not have the targeted resistance genes for bacterial blight (xa5 + xa13 + Xa21) and blast (Pi2 + Pi9 + Pi54). The ILs were derived in the background of two elite rice cultivars, Krishna Hamsa [Recurrent Parent 1 (RP1)] and WGL 14 (RP2), involving multi-parent inter-crossing. Molecular characterization with gene specific markers for seven reported resistance genes each for bacterial blight (Xa33, Xa38, xa23, Xa4, xa8, Xa27 and Xa41) and blast (Pi1, Pi20, Pi38, Pib, Pitp, Pizt and Pi40) revealed the presence of xa8 and Xa38, in addition to the targeted xa5, xa13 and Xa21 for bacterial blight resistance and Pi1, Pi38, Pi40, Pi20, Pib and Pipt, in addition to the targeted Pi9 and Pi54, for blast resistance in various combinations. A maximum of nine resistance genes xa5 + Xa21 + Pi54 + xa8 + Pipt + Pi38 + Pi1 + Pi20 + Pib was observed in RP1-IL 19030 followed by eight genes xa5 + xa13 + Xa21 + xa8 + Pi9 + Pipt + Pi1 + Pi20 in two RP2-ILs, 19344 and 19347. ANOVA revealed the presence of significant variability for all the yield traits except "days to 50% flowering" (DFF). Box plots depicted the seasonal differences in the phenotypic expression of the yield traits. There was significant positive association of grain yield with days to flowering, tiller number and panicle number. Thousand grain weight is also significantly and positively correlated with grain yield. On the contrary, grain yield showed a significantly negative association with plant height. Multi-parent selective inter-crossing in the present study not only led to the development of high yielding disease resistant ILs but also enhanced recovery of the recurrent parent via selection for essential morphological features. More than 90.0% genetic similarity in the ILs based on SNP-based background selection demonstrated the success of multi-parent selective intercrossing in the development of disease resistant NILs.
Collapse
Affiliation(s)
- Yasaswini Vishnu Priya Varanasi
- ICAR—Indian Institute of Rice Research (ICAR-IIRR), Hyderabad 500030, India
- Jawaharlal Nehru Krishi Vishwa Vidyalaya, Rewa 486001, India
| | | | - Padmashree Revadi
- ICAR—Indian Institute of Rice Research (ICAR-IIRR), Hyderabad 500030, India
| | - Divya Balakrishnan
- ICAR—Indian Institute of Rice Research (ICAR-IIRR), Hyderabad 500030, India
| | - Shaik Hajira
- ICAR—Indian Institute of Rice Research (ICAR-IIRR), Hyderabad 500030, India
| | | | - Gouri Shankar Laha
- ICAR—Indian Institute of Rice Research (ICAR-IIRR), Hyderabad 500030, India
| | - Puvvada Perraju
- Jawaharlal Nehru Krishi Vishwa Vidyalaya, Rewa 486001, India
| | - Uma Maheshwar Singh
- International Rice Research Institute South Asia Regional Centre (ISARC), Varanasi 221006, India
| | - Vikas Kumar Singh
- International Rice Research Institute South Asia Hub (IRRISAH), Hyderabad 221106, India;
| | - Arvind Kumar
- International Crop Research Institute for Semi-Arid Tropics (ICRISAT), Hyderabad 502324, India
| | | | - Jyothi Badri
- ICAR—Indian Institute of Rice Research (ICAR-IIRR), Hyderabad 500030, India
| |
Collapse
|
4
|
Kaldate R, Verma RK, Chetia SK, Dey PC, Mahalle MD, Singh SK, Baruah AR, Modi MK. Mapping of QTLs associated with yield and related traits under reproductive stage drought stress in rice using SNP linkage map. Mol Biol Rep 2023; 50:6349-6359. [PMID: 37314604 DOI: 10.1007/s11033-023-08550-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Accepted: 05/26/2023] [Indexed: 06/15/2023]
Abstract
BACKGROUND Drought stress is a major constraint for rice production worldwide. Reproductive stage drought stress (RSDS) leads to heavy yield losses in rice. The prospecting of new donor cultivars for identification and introgression of QTLs of major effect (Quantitative trait locus) for drought tolerance is crucial for the development of drought-resilient rice varieties. METHODS AND RESULTS Our study aimed to map QTLs associated with yield and its related traits under RSDS conditions. A saturated linkage map was constructed using 3417 GBS (Genotyping by sequencing) derived SNP (Single nucleotide polymorphism) markers spanning 1924.136 cM map length with an average marker density of 0.56 cM, in the F3 mapping population raised via cross made between the traditional ahu rice cultivar, Koniahu (drought tolerant) and a high-yielding variety, Disang (drought susceptible). Using the Inclusive composite interval mapping approach, 35 genomic regions governing yield and related traits were identified in pooled data from 198 F3 and F4 segregating lines evaluated for two consecutive seasons under both RSDS and irrigated control conditions. Of the 35 QTLs, 23 QTLs were identified under RSDS with LOD (Logarithm of odds) values ranging between 2.50 and 7.83 and PVE (phenotypic variance explained) values of 2.95-12.42%. Two major QTLs were found to be linked to plant height (qPH1.29) and number of filled grains per panicle (qNOG5.12) under RSDS. Five putative QTLs for grain yield namely, qGY2.00, qGY5.05, qGY6.16, qGY9.19, and qGY10.20 were identified within drought conditions. Fourteen QTL regions having ≤ 10 Mb QTL interval size were further analysed for candidate gene identification and a total of 4146 genes were detected out of these 2263 (54.63%) genes were annotated to at least one gene ontology (GO) term. CONCLUSION Several QTLs associated with grain yield and yield components and putative candidate genes were identified. The putative QTLs and candidate genes identified could be employed to augment drought resilience in rice after further validation through MAS strategies.
Collapse
Affiliation(s)
- Rahul Kaldate
- Department of Agricultural Biotechnology, Assam Agricultural University (AAU), Jorhat, Assam, 785013, India
| | - Rahul Kumar Verma
- Department of Biotechnology-North East Centre for Agricultural Biotechnology (DBT-NECAB), AAU, Jorhat, Assam, 785013, India
| | | | | | - Mayuri D Mahalle
- Department of Agricultural Biotechnology, Assam Agricultural University (AAU), Jorhat, Assam, 785013, India
| | - Sushil Kumar Singh
- Department of Biotechnology-North East Centre for Agricultural Biotechnology (DBT-NECAB), AAU, Jorhat, Assam, 785013, India
| | - Akhil Ranjan Baruah
- Department of Agricultural Biotechnology, Assam Agricultural University (AAU), Jorhat, Assam, 785013, India
| | - Mahendra Kumar Modi
- Department of Agricultural Biotechnology, Assam Agricultural University (AAU), Jorhat, Assam, 785013, India.
| |
Collapse
|
5
|
Sharma V, Gangurde SS, Nayak SN, Gowda AS, Sukanth B, Mahadevaiah SS, Manohar SS, Choudhary RS, Anitha T, Malavalli SS, Srikanth S, Bajaj P, Sharma S, Varshney RK, Latha P, Janila P, Bhat RS, Pandey MK. Genetic mapping identified three hotspot genomic regions and candidate genes controlling heat tolerance-related traits in groundnut. FRONTIERS IN PLANT SCIENCE 2023; 14:1182867. [PMID: 37287715 PMCID: PMC10243373 DOI: 10.3389/fpls.2023.1182867] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 04/12/2023] [Indexed: 06/09/2023]
Abstract
Groundnut productivity and quality have been impeded by rising temperatures in semi-arid environments. Hence, understanding the effects and molecular mechanisms of heat stress tolerance will aid in tackling yield losses. In this context, a recombinant inbred line (RIL) population was developed and phenotyped for eight seasons at three locations for agronomic, phenological, and physiological traits under heat stress. A genetic map was constructed using genotyping-by-sequencing with 478 single-nucleotide polymorphism (SNP) loci spanning a map distance of 1,961.39 cM. Quantitative trait locus (QTL) analysis using phenotypic and genotypic data identified 45 major main-effect QTLs for 21 traits. Intriguingly, three QTL clusters (Cluster-1-Ah03, Cluster-2-Ah12, and Cluster-3-Ah20) harbor more than half of the major QTLs (30/45, 66.6%) for various heat tolerant traits, explaining 10.4%-38.6%, 10.6%-44.6%, and 10.1%-49.5% of phenotypic variance, respectively. Furthermore, important candidate genes encoding DHHC-type zinc finger family protein (arahy.J0Y6Y5), peptide transporter 1 (arahy.8ZMT0C), pentatricopeptide repeat-containing protein (arahy.4A4JE9), Ulp1 protease family (arahy.X568GS), Kelch repeat F-box protein (arahy.I7X4PC), FRIGIDA-like protein (arahy.0C3V8Z), and post-illumination chlorophyll fluorescence increase (arahy.92ZGJC) were the underlying three QTL clusters. The putative functions of these genes suggested their involvement in seed development, regulating plant architecture, yield, genesis and growth of plants, flowering time regulation, and photosynthesis. Our results could provide a platform for further fine mapping, gene discovery, and developing markers for genomics-assisted breeding to develop heat-tolerant groundnut varieties.
Collapse
Affiliation(s)
- Vinay Sharma
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, India
| | - Sunil S. Gangurde
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Spurthi N. Nayak
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Anjan S. Gowda
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - B.S. Sukanth
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | | | - Surendra S. Manohar
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | | | - T. Anitha
- Regional Agricultural Research Station, Acharya N G Ranga Agricultural University (ANGRAU), Tirupati, India
| | - Sachin S. Malavalli
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - S.N. Srikanth
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Prasad Bajaj
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Shailendra Sharma
- Department of Genetics and Plant Breeding, Chaudhary Charan Singh University (CCSU), Meerut, India
| | - Rajeev K. Varshney
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Putta Latha
- Regional Agricultural Research Station, Acharya N G Ranga Agricultural University (ANGRAU), Tirupati, India
| | - Pasupuleti Janila
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| | - Ramesh S. Bhat
- Department of Biotechnology, University of Agricultural Sciences, Dharwad, India
| | - Manish K. Pandey
- Center of Excellence in Genomics & Systems Biology (CEGSB), International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, Hyderabad, India
| |
Collapse
|
6
|
Rekha G, Abhilash Kumar V, Gokulan CG, Koushik MBVN, Laxmi Prasanna B, Kulkarni S, Aleena D, Harika G, Hajira SK, Pranathi K, Punniakoti E, Kale RR, Dilip Kumar T, Ayyappa D, Anila M, Sinha P, Manohara KK, Padmavathi G, Subba Rao LV, Laha GS, Srinivas Prasad MS, Fiyaz RA, Suneetha K, Balachandran SM, Patel HK, Sonti RV, Senguttuvel P, Sundaram RM. DRR Dhan 58, a Seedling Stage Salinity Tolerant NIL of Improved Samba Mahsuri Shows Superior Performance in Multi-location Trials. RICE (NEW YORK, N.Y.) 2022; 15:45. [PMID: 35976520 PMCID: PMC9385912 DOI: 10.1186/s12284-022-00591-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Accepted: 08/08/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Improved Samba Mahsuri (ISM) is an elite, high-yielding, bacterial blight resistant, fine-grained rice variety with low glycaemic index. It is highly sensitive to salt stress, particularly at seedling stage, which significantly reduces its yield potential in coastal areas. A salinity tolerant QTL, Saltol, associated with seedling stage tolerance was previously mapped on chromosome 1 (10.6-11.5 Mb) from the Indian landrace, Pokkali and is effective in different genetic backgrounds. The objective of this study was to enhance salinity tolerance of ISM by incorporating the Saltol QTL through marker-assisted backcross breeding using the breeding line, FL478 (Pokkali/IR29). RESULTS Foreground selection was carried out at each generation using five Saltol-specific markers and three bacterial blight resistance genes, Xa21, xa13 and xa5. Background selection was conducted using 66 well distributed polymorphic SSR markers and at the BC3F2 generation, a single plant with maximum recurrent parent genome recovery (95.3%) was identified and advanced to the BC3F4 generation. Based on bacterial blight resistance, seedling stage salinity tolerance and resemblance to ISM, four advanced breeding lines were selected for testing in replicated experiments near Hyderabad, India. A promising near-isogenic line, DRR Dhan 58, was evaluated in multi-location trials-coastal salinity and it showed significant salinity tolerance, resistance to bacterial blight disease, high yield and excellent grain quality during the 2019 and 2020 trials. DRR Dhan 58 was 95.1% similar to ISM based on genotyping with the 90 K SNP chip. Whole genome resequencing analysis of Pokkali and FL478 which were salinity tolerant checks, ISM and DRR Dhan 58 showed a high degree of relatedness with respect to the candidate gene loci for Saltol and OsSKC1 (Shoot K+ Concentration 1). CONCLUSION DRR Dhan 58, possessing Saltol and three bacterial blight resistance genes (Xa21, xa13 and xa5) in the genetic background of the Indian mega-variety of rice, Samba Mahsuri, was developed for potential cultivation in areas prone to seedling stage salinity, as well as areas with endemic bacterial blight disease. This entry had a 24% yield advantage over the recurrent parent ISM under coastal saline conditions in multi-location trials and was recently released for commercial cultivation in India.
Collapse
Affiliation(s)
- G Rekha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - V Abhilash Kumar
- Rallis India Limited, Seeds/Biotech R&D Division, Bangalore, India
| | - C G Gokulan
- Crop Improvement Section, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - M B V N Koushik
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | | | - Swapnil Kulkarni
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - D Aleena
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - G Harika
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - S K Hajira
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - K Pranathi
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - E Punniakoti
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - R R Kale
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - T Dilip Kumar
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - D Ayyappa
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - M Anila
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - Pragya Sinha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - K K Manohara
- Genetics and Plant Breeding, ICAR- Central Coastal Agricultural Research Institute, Ella, Goa, India
| | - G Padmavathi
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - L V Subba Rao
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - G S Laha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - M S Srinivas Prasad
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - R A Fiyaz
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - K Suneetha
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - S M Balachandran
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - Hitendra Kumar Patel
- Crop Improvement Section, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
| | - Ramesh V Sonti
- Crop Improvement Section, CSIR-Centre for Cellular and Molecular Biology, Hyderabad, India
- Department of Biology, Indian Institute of Science Education and Research, Tirupati, India
| | - P Senguttuvel
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India
| | - R M Sundaram
- Department of Biotechnology, ICAR-Indian Institute of Rice Research, Rajendranagar, Hyderabad, India.
| |
Collapse
|
7
|
Bin Rahman ANMR, Zhang J. The Coexistence of Flood and Drought Tolerance: An Opinion on the Development of Climate-Smart Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:860802. [PMID: 35350297 PMCID: PMC8957971 DOI: 10.3389/fpls.2022.860802] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 02/14/2022] [Indexed: 06/14/2023]
Affiliation(s)
| | - Jianhua Zhang
- Department of Biology, Hong Kong Baptist University, Kowloon Tong, Hong Kong SAR, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong SAR, China
| |
Collapse
|
8
|
Khanna A, Anumalla M, Catolos M, Bartholomé J, Fritsche-Neto R, Platten JD, Pisano DJ, Gulles A, Sta Cruz MT, Ramos J, Faustino G, Bhosale S, Hussain W. Genetic Trends Estimation in IRRIs Rice Drought Breeding Program and Identification of High Yielding Drought-Tolerant Lines. RICE (NEW YORK, N.Y.) 2022; 15:14. [PMID: 35247120 PMCID: PMC8898209 DOI: 10.1186/s12284-022-00559-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 02/20/2022] [Indexed: 06/14/2023]
Abstract
Estimating genetic trends using historical data is an important parameter to check the success of the breeding programs. The estimated genetic trends can act as a guideline to target the appropriate breeding strategies and optimize the breeding program for improved genetic gains. In this study, 17 years of historical data from IRRI's rice drought breeding program was used to estimate the genetic trends and assess the breeding program's success. We also identified top-performing lines based on grain yield breeding values as an elite panel for implementing future population improvement-based breeding schemes. A two-stage approach of pedigree-based mixed model analysis was used to analyze the data and extract the breeding values and estimate the genetic trends for grain yield under non-stress, drought, and in combined data of non-stress and drought. Lower grain yield values were observed in all the drought trials. Heritability for grain yield estimates ranged between 0.20 and 0.94 under the drought trials and 0.43-0.83 under non-stress trials. Under non-stress conditions, the genetic gain of 0.21% (10.22 kg/ha/year) for genotypes and 0.17% (7.90 kg/ha/year) for checks was observed. The genetic trend under drought conditions exhibited a positive trend with the genetic gain of 0.13% (2.29 kg/ha/year) for genotypes and 0.55% (9.52 kg/ha/year) for checks. For combined analysis showed a genetic gain of 0.27% (8.32 kg/ha/year) for genotypes and 0.60% (13.69 kg/ha/year) for checks was observed. For elite panel selection, 200 promising lines were selected based on higher breeding values for grain yield and prediction accuracy of > 0.40. The breeding values of the 200 genotypes formulating the core panel ranged between 2366.17 and 4622.59 (kg/ha). A positive genetic rate was observed under all the three conditions; however, the rate of increase was lower than the required rate of 1.5% genetic gain. We propose a recurrent selection breeding strategy within the elite population with the integration of modern tools and technologies to boost the genetic gains in IRRI's drought breeding program. The elite breeding panel identified in this study forms an easily available and highly enriched genetic resource for future recurrent selection programs to boost the genetic gains.
Collapse
Affiliation(s)
- Apurva Khanna
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Mahender Anumalla
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Margaret Catolos
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Jérôme Bartholomé
- AGAP Institute, CIRAD, INRA, Montpellier SupAgro, Univ Montpellier, Montpellier, France
| | - Roberto Fritsche-Neto
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - John Damien Platten
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Daniel Joseph Pisano
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Alaine Gulles
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Ma Teresa Sta Cruz
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Joie Ramos
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Gem Faustino
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Sankalp Bhosale
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines
| | - Waseem Hussain
- Rice Breeding Innovation Platform, International Rice Research Institute (IRRI), Los Baños, Laguna, Philippines.
| |
Collapse
|
9
|
Singh UM, Dixit S, Alam S, Yadav S, Prasanth VV, Singh AK, Venkateshwarlu C, Abbai R, Vipparla AK, Badri J, Ram T, Prasad MS, Laha GS, Singh VK, Kumar A. Marker-assisted forward breeding to develop a drought-, bacterial-leaf-blight-, and blast-resistant rice cultivar. THE PLANT GENOME 2022; 15:e20170. [PMID: 34845865 DOI: 10.1002/tpg2.20170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 09/19/2021] [Indexed: 06/13/2023]
Abstract
Among the different challenges related to rice (Oryza sativa L.) cultivation, drought, bacterial leaf blight (BLB), and blast are the key stresses that significantly affect grain yield (GY) in rice. To ameliorate this issue, marker-assisted forward breeding (MAFB) coupled with a simultaneous crossing approach was used to combine three drought tolerant quantitative trait loci (QTL)-qDTY1.1 , qDTY3.1 , and qDTY12.1 -four BLB genes-Xa4, xa5, xa13, and Xa21-and one blast-resistance gene, Pi9, in the elite rice cultivar Lalat. The introgression lines (ILs) developed in the current study were phenotypically screened for drought, BLB, and blast resistance at the F7 -F8 generation. Under the reproductive stage (RS) drought stress, the yield advantage of ILs, with major-effect QTL (qDTY) over elite parent Lalat, ranges from 9 to 124% in DS2019 and from 7 to 175% in WS2019. The selected ILs were highly resistant to BLB, with lesion lengths ranging from 1.3 to 3.0 cm and blast scores ranging from 1 to 3. ILs that were tolerant to RS drought, resistant to BLB, and blast disease and had similar or higher yields than Lalat were analyzed for grain quality. Six ILs were found to have similar grain quality characteristics to Lalat including hulling, milling, head rice recovery (HRR), chalkiness, alkali spreading value (ASV), and amylose content (AC). This study showed that MAFB, together with simultaneous crossing, would be an effective strategy to rapidly combine multiple stresses in rice. The ILs developed in this study could help to ensure yield sustainability in rainfed environments or be used as genetic material in future breeding programs.
Collapse
Affiliation(s)
- Uma Maheshwar Singh
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
- International Rice Research Institute, South Asia Regional Centre, Varanasi, India
| | - Shilpi Dixit
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
- International Rice Research Institute, South Asia Regional Centre, Varanasi, India
| | - Shamshad Alam
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Shailesh Yadav
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | | | - Arun Kumar Singh
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Challa Venkateshwarlu
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Ragavendran Abbai
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Abhilash Kumar Vipparla
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Jyothi Badri
- ICAR-Indian Institute of Rice Research, Rajendra Nagar, Hyderabad, India
| | - Tilatoo Ram
- ICAR-Indian Institute of Rice Research, Rajendra Nagar, Hyderabad, India
| | | | - Gouri Sankar Laha
- ICAR-Indian Institute of Rice Research, Rajendra Nagar, Hyderabad, India
| | - Vikas Kumar Singh
- International Rice Research Institute, South Asia Hub, ICRISAT, Patancheru, Hyderabad, India
| | - Arvind Kumar
- International Rice Research Institute, South Asia Regional Centre, Varanasi, India
- International Crops Research Institute for the Semi-Arid Tropics, Patancheru, Hyderabad, India
| |
Collapse
|
10
|
Multiparent-Derived, Marker-Assisted Introgression Lines of the Elite Indian Rice Cultivar, ‘Krishna Hamsa’ Show Resistance against Bacterial Blight and Blast and Tolerance to Drought. PLANTS 2022; 11:plants11050622. [PMID: 35270092 PMCID: PMC8912774 DOI: 10.3390/plants11050622] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 11/17/2022]
Abstract
Major biotic stresses viz., bacterial blight (BB) and blast and brown plant hopper (BPH) coupled with abiotic stresses like drought stress, significantly affect rice yields. To address this, marker-assisted intercross (IC) breeding involving multiple donors was used to combine three BB resistance genes—xa5, xa13 and Xa21, two blast resistance genes—Pi9 and Pi54, two BPH resistance genes—Bph20 and Bph21, and four drought tolerant quantitative trait loci (QTL)—qDTY1.1, qDTY2.1, qDTY3.1 and qDTY12.1—in the genetic background of the elite Indian rice cultivar ‘Krishna Hamsa’. Three cycles of selective intercrossing followed by selfing coupled with foreground selection and phenotyping for the target traits resulted in the development of 196 introgression lines (ILs) with a myriad of gene/QTL combinations. Based on the phenotypic reaction, the ILs were classified into seven phenotypic classes of resistance/tolerance to the following: (1) BB, blast and drought—5 ILs; (2) BB and blast—10 ILs; (3) BB and drought—9 ILs; (4) blast and drought—42 ILs; (5) BB—3 ILs; (6) blast—84 ILs; and (7) drought—43 ILs; none of the ILs were resistant to BPH. Positive phenotypic response (resistance) was observed to both BB and blast in 2 ILs, BB in 9 ILs and blast in 64 ILs despite the absence of corresponding R genes. Inheritance of resistance to BB and/or blast in such ILs could be due to the unknown genes from other parents used in the breeding scheme. Negative phenotypic response (susceptibility) was observed in 67 ILs possessing BB-R genes, 9 ILs with blast-R genes and 9 ILs harboring QTLs for drought tolerance. Complex genic interactions and recombination events due to the involvement of multiple donors explain susceptibility in some of the marker positive ILs. The present investigation successfully demonstrates the possibility of rapid development of multiple stress-tolerant/resistant ILs in the elite cultivar background involving multiple donors through selective intercrossing and stringent phenotyping. The 196 ILs in seven phenotypic classes with myriad of gene/QTL combinations will serve as a useful genetic resource in combining multiple biotic and abiotic stress resistance in future breeding programs.
Collapse
|
11
|
Santo Domingo M, Areco L, Mayobre C, Valverde L, Martín-Hernández AM, Pujol M, Garcia-Mas J. Modulating climacteric intensity in melon through QTL stacking. HORTICULTURE RESEARCH 2022; 9:uhac131. [PMID: 35928400 PMCID: PMC9343914 DOI: 10.1093/hr/uhac131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/29/2022] [Indexed: 05/14/2023]
Abstract
Fruit ripening is one of the main processes affecting fruit quality and shelf life. In melon there are both climacteric and non-climacteric genotypes, making it a suitable species to study fruit ripening. In the current study, in order to fine tune ripening, we have pyramided three climacteric QTLs in the non-climacteric genotype "Piel de Sapo": ETHQB3.5, ETHQV6.3 and ETHQV8.1. The results showed that the three QTLs interact epistatically, affecting ethylene production and ripening-related traits such as aroma profile. Each individual QTL has a specific role in the ethylene production profile. ETHQB3.5 accelerates the ethylene peak, ETHQV6.3 advances the ethylene production and ETHQV8.1 enhances the effect of the other two QTLs. Regarding aroma, the three QTLs independently activated the production of esters changing the aroma profile of the fruits, with no significant effects in fruit firmness, soluble solid content and fruit size. Understanding the interaction and the effect of different ripening QTLs offers a powerful knowledge for candidate gene identification as well as for melon breeding programs, where fruit ripening is one of the main objectives.
Collapse
Affiliation(s)
- Miguel Santo Domingo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Lorena Areco
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Carlos Mayobre
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Laura Valverde
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | - Ana Montserrat Martín-Hernández
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain
- Institut de Recerca i Tecnologia Agoralimentàries (IRTA), Edifici CRAG, Campus UAB, Bellaterra, 08193 Barcelona, Spain
| | | | | |
Collapse
|
12
|
Liang Y, Wang S, Harper CL, Subramanian NK, Tabien RE, Johnson CD, Bailey-Serres J, Septiningsih EM. Reference-Guided De Novo Genome Assembly to Dissect a QTL Region for Submergence Tolerance Derived from Ciherang-Sub1. PLANTS 2021; 10:plants10122740. [PMID: 34961210 PMCID: PMC8703405 DOI: 10.3390/plants10122740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2021] [Revised: 12/02/2021] [Accepted: 12/09/2021] [Indexed: 11/06/2022]
Abstract
Global climate change has increased the number of severe flooding events that affect agriculture, including rice production in the U.S. and internationally. Heavy rainfall can cause rice plants to be completely submerged, which can significantly affect grain yield or completely destroy the plants. Recently, a major effect submergence tolerance QTL during the vegetative stage, qSub8.1, which originated from Ciherang-Sub1, was identified in a mapping population derived from a cross between Ciherang-Sub1 and IR10F365. Ciherang-Sub1 was, in turn, derived from a cross between Ciherang and IR64-Sub1. Here, we characterize the qSub8.1 region by analyzing the sequence information of Ciherang-Sub1 and its two parents (Ciherang and IR64-Sub1) and compare the whole genome profile of these varieties with the Nipponbare and Minghui 63 (MH63) reference genomes. The three rice varieties were sequenced with 150 bp pair-end whole-genome shotgun sequencing (Illumina HiSeq4000), followed by performing the Trimmomatic-SOAPdenovo2-MUMmer3 pipeline for genome assembly, resulting in approximate genome sizes of 354.4, 343.7, and 344.7 Mb, with N50 values of 25.1, 25.4, and 26.1 kb, respectively. The results showed that the Ciherang-Sub1 genome is composed of 59–63% Ciherang, 22–24% of IR64-Sub1, and 15–17% of unknown sources. The genome profile revealed a more detailed genomic composition than previous marker-assisted breeding and showed that the qSub8.1 region is mostly from Ciherang, with some introgressed segments from IR64-Sub1 and currently unknown source(s).
Collapse
Affiliation(s)
- Yuya Liang
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (Y.L.); (N.K.S.)
| | - Shichen Wang
- Genomics and Bioinformatics Service, Texas A&M AgriLife Research, College Station, TX 77843, USA; (S.W.); (C.D.J.)
| | - Chersty L. Harper
- Texas A&M AgriLife Research Center, Beaumont, TX 77713, USA; (C.L.H.); (R.E.T.)
| | - Nithya K. Subramanian
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (Y.L.); (N.K.S.)
| | - Rodante E. Tabien
- Texas A&M AgriLife Research Center, Beaumont, TX 77713, USA; (C.L.H.); (R.E.T.)
| | - Charles D. Johnson
- Genomics and Bioinformatics Service, Texas A&M AgriLife Research, College Station, TX 77843, USA; (S.W.); (C.D.J.)
| | - Julia Bailey-Serres
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA 92521, USA;
| | - Endang M. Septiningsih
- Department of Soil and Crop Sciences, Texas A&M University, College Station, TX 77843, USA; (Y.L.); (N.K.S.)
- Correspondence:
| |
Collapse
|
13
|
Submergence Gene Sub1A Transfer into Drought-Tolerant japonica Rice DT3 Using Marker-Assisted Selection. Int J Mol Sci 2021; 22:ijms222413365. [PMID: 34948165 PMCID: PMC8705020 DOI: 10.3390/ijms222413365] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/08/2021] [Accepted: 12/09/2021] [Indexed: 12/03/2022] Open
Abstract
Flash flooding is a major environmental stressor affecting rice production worldwide. DT3 is a drought-tolerant, recurrent parent with a good yield, edible quality, and agronomic traits akin to those of an elite Taiwanese variety, Taiken9 (TK9). Progenies carrying Sub1A can enhance submergence stress tolerance and can be selected using the marker-assisted backcross (MAB) breeding method. For foreground selection, Sub1A and SubAB1 were utilized as markers on the BC2F1, BC3F1, and BC3F2 generations to select the submergence-tolerant gene, Sub1A. Background selection was performed in the Sub1A-BC3F2 genotypes, and the percentages of recurrent parent recovery within individuals ranged from 84.7–99.55%. BC3F3 genotypes (N = 100) were evaluated for agronomic traits, yield, and eating quality. Four of the eleven BC3F4 lines showed good yield, yield component, grain, and eating quality. Four BC3F4 lines, SU39, SU40, SU89, and SU92, exhibited desirable agronomic traits, including grain quality and palatability, consistent with those of DT3. These genotypes displayed a high survival rate between 92 and 96%, much better compared with DT3 with 64%, and demonstrated better drought tolerance compared to IR64 and IR96321-345-240. This study provides an efficient and precise MAB strategy for developing climate-resilient rice varieties with good grain quality for flood-prone regions.
Collapse
|
14
|
Genic microsatellite marker characterization and development in little millet (Panicum sumatrense) using transcriptome sequencing. Sci Rep 2021; 11:20620. [PMID: 34663808 PMCID: PMC8523711 DOI: 10.1038/s41598-021-00100-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Accepted: 09/29/2021] [Indexed: 11/08/2022] Open
Abstract
Little millet is a climate-resilient and high-nutrient value plant. The lack of molecular markers severely limits the adoption of modern genomic approaches in millet breeding studies. Here the transcriptome of three samples were sequenced. A total of 4443 genic-SSR motifs were identified in 30,220 unigene sequences. SSRs were found at a rate of 12.25 percent, with an average of one SSR locus per 10 kb. Among different repeat motifs, tri-nucleotide repeat (66.67) was the most abundant one, followed by di- (27.39P), and tetra- (3.83P) repeats. CDS contained fewer motifs with the majority of tri-nucleotides, while 3' and 5' UTR carry more motifs but have shorter repeats. Functional annotation of unigenes containing microsatellites, revealed that most of them were linked to metabolism, gene expression regulation, and response to environmental stresses. Fifty primers were randomly chosen and validated in five little millet and 20 minor millet genotypes; 48% showed polymorphism, with a high transferability (70%) rate. Identified microsatellites can be a noteworthy resource for future research into QTL-based breeding, genetic resource conservation, MAS selection, and evolutionary genetics.
Collapse
|
15
|
Roy S, Verma BC, Banerjee A, Kumar J, Ray US, Mandal NP. Genetic diversity for drought and low-phosphorus tolerance in rice (Oryza sativa L.) varieties and donors adapted to rainfed drought-prone ecologies. Sci Rep 2021; 11:13671. [PMID: 34211096 PMCID: PMC8249610 DOI: 10.1038/s41598-021-93325-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 06/11/2021] [Indexed: 11/15/2022] Open
Abstract
Drought and phosphate availability are two major abiotic factors limiting productivity of rice in rainfed upland areas. There has been a constant need for new improved donor with tolerance to multiple abiotic stress conditions for rainfed rice breeding. In the present study, a set of 32 popular rice varieties and landraces were evaluated for drought and low-phosphorus (P) tolerance, and also characterized using grain yield under reproductive drought QTLs (DTY QTLs) and Pup1 linked/specific molecular markers. Twenty-seven genotypes were identified as tolerant to moderately tolerant to drought. The SSR markers linked to ten DTY QTLs classified the genotypes into two groups corresponding to aus and indica. The tolerant genotypes were distributed under both groups. Based on the core markers of Pup1 locus, complete tolerant haplotype was recorded in nine genotypes other than the tolerant check Dular. Nine more genotypes showed the incomplete tolerant haplotypes. The rice genotypes showed significantly high genetic variability for low-P tolerance in hydroponic study. A few genotypes revealed non-Pup1 type tolerance which needs further confirmation.
Collapse
Affiliation(s)
- Somnath Roy
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, 825301, Jharkhand, India.
| | - B C Verma
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, 825301, Jharkhand, India
| | - Amrita Banerjee
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, 825301, Jharkhand, India
| | - J Kumar
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, 825301, Jharkhand, India
| | - Uday Sankar Ray
- Zonal Drought Resistant Paddy Research Station, Hathwara, Purulia, 723147, West Bengal, India
| | - N P Mandal
- Central Rainfed Upland Rice Research Station, ICAR-National Rice Research Institute, Hazaribag, 825301, Jharkhand, India.
| |
Collapse
|
16
|
Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture. Int J Mol Sci 2021; 22:ijms22116058. [PMID: 34199720 PMCID: PMC8199995 DOI: 10.3390/ijms22116058] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022] Open
Abstract
The underground reserve (root) has been an uncharted research territory with its untapped genetic variation yet to be exploited. Identifying ideal traits and breeding new rice varieties with efficient root system architecture (RSA) has great potential to increase resource-use efficiency and grain yield, especially under direct-seeded rice, by adapting to aerobic soil conditions. In this review, we tried to mine the available research information on the direct-seeded rice (DSR) root system to highlight the requirements of different root traits such as root architecture, length, number, density, thickness, diameter, and angle that play a pivotal role in determining the uptake of nutrients and moisture at different stages of plant growth. RSA also faces several stresses, due to excess or deficiency of moisture and nutrients, low or high temperature, or saline conditions. To counteract these hindrances, adaptation in response to stress becomes essential. Candidate genes such as early root growth enhancer PSTOL1, surface rooting QTL qSOR1, deep rooting gene DRO1, and numerous transporters for their respective nutrients and stress-responsive factors have been identified and validated under different circumstances. Identifying the desired QTLs and transporters underlying these traits and then designing an ideal root architecture can help in developing a suitable DSR cultivar and aid in further advancement in this direction.
Collapse
|
17
|
Khan MIR, Palakolanu SR, Chopra P, Rajurkar AB, Gupta R, Iqbal N, Maheshwari C. Improving drought tolerance in rice: Ensuring food security through multi-dimensional approaches. PHYSIOLOGIA PLANTARUM 2021; 172:645-668. [PMID: 33006143 DOI: 10.1111/ppl.13223] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 09/11/2020] [Accepted: 09/29/2020] [Indexed: 05/27/2023]
Abstract
Drought has been highly prevalent around the world especially in Sub-Saharan Africa and South-East Asian countries. Consistent climatic instabilities and unpredictable rainfall patterns are further worsening the situation. Rice is a C3 staple cereal and an important food crop for the majority of the world's population and drought stress is one of the major growth retarding threats for rice that slashes down grain quality and yield. Drought deteriorates rice productivity and induces various acclimation responses that aids in stress mitigation. However, the complexity of traits associated with drought tolerance has made the understanding of drought stress-induced responses in rice a challenging process. An integrative understanding based on physiological adaptations, omics, transgenic and molecular breeding approaches successively backed up to developing drought stress-tolerant rice. The review represents a step forward to develop drought-resilient rice plants by exploiting the knowledge that collaborates with omics-based developments with integrative efforts to ensure the compilation of all the possible strategies undertaken to develop drought stress-tolerant rice.
Collapse
Affiliation(s)
| | - Sudhakar R Palakolanu
- Cell, Molecular Biology and Genetic Engineering Group, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Ashish B Rajurkar
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, Illinois, USA
| | - Ravi Gupta
- Department of Botany, Jamia Hamdard, New Delhi, India
| | | | - Chirag Maheshwari
- Agricultural Energy and Power Division, ICAR-Central Institute of Agricultural Engineering, Bhopal, India
| |
Collapse
|
18
|
Sandhu N, Yadav S, Catolos M, Cruz MTS, Kumar A. Developing Climate-Resilient, Direct-Seeded, Adapted Multiple-Stress-Tolerant Rice Applying Genomics-Assisted Breeding. FRONTIERS IN PLANT SCIENCE 2021; 12:637488. [PMID: 33936127 PMCID: PMC8082028 DOI: 10.3389/fpls.2021.637488] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
19
|
Giri J, Parida SK, Raghuvanshi S, Tyagi AK. Emerging Molecular Strategies for Improving Rice Drought Tolerance. Curr Genomics 2021; 22:16-25. [PMID: 34045921 PMCID: PMC8142347 DOI: 10.2174/1389202921999201231205024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 10/27/2020] [Accepted: 11/04/2020] [Indexed: 12/13/2022] Open
Abstract
Rice occupies a pre-eminent position as a food crop in the world. Its production, how- ever, entails up to 3000 liters of water per kilogram of grain produced. Such high demand makes rice prone to drought easily. Sustainable rice cultivation with limited water resources requires the deployment of a suitable strategy for better water use efficiency and improved drought tolerance. Several drought-related genes have been evaluated in rice for their mode of action in conferring drought tolerance. Manipulation of components of abscisic acid signal transduction, stomatal density, deposition of cuticular wax, and protein modification pathways are emerging as priority targets. Gene reprogramming by microRNAs is also being explored to achieve drought tolerance. Genetically dissected Quantitative Trait Loci (QTLs) and their constituent genes are being deployed to develop drought-tolerant rice varieties. Progressive research and challenges include a better understanding of crucial components of drought response and search for new targets and the deployment of improved varieties in the field.
Collapse
Affiliation(s)
- Jitender Giri
- 1National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; 2Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Swarup K Parida
- 1National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; 2Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Saurabh Raghuvanshi
- 1National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; 2Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Akhilesh K Tyagi
- 1National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; 2Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| |
Collapse
|
20
|
Bal HB, Adhya TK. Alleviation of Submergence Stress in Rice Seedlings by Plant Growth-Promoting Rhizobacteria With ACC Deaminase Activity. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2021. [DOI: 10.3389/fsufs.2021.606158] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Submergence stress slows seed germination, imposes fatalities, and delays seedling establishment in rice. Seeds of submergence susceptible rice variety IR 42 were inoculated with four 1-aminocyclopropane-1-carboxylic acid (ACC) utilizing isolates viz., Bacillus sp. (AR-ACC1), Microbacterium sp. (AR-ACC2), Methylophaga sp. (AR-ACC3), and Paenibacillus sp. (ANR-ACC3) and subjected to submergence stress under controlled conditions for 7 days. Seeds treated with Microbacterium sp. AR-ACC2, Paenibacillus sp. ANR-ACC3, and Methylophaga sp. AR-ACC3 significantly enhanced the germination percentage (GP), seedling vigor index (SVI), and other growth parameters like root and shoot length and total chlorophyll contents, when compared with nonbacterized seeds submerged similarly. However, the values were statistically at par when control seeds were treated with l-α-(2-aminoethoxyvinyl) glycine hydrochloride (AVG), a known inhibitor of ethylene production. Results suggest that stress ethylene production was significantly reduced by around 85% in seedlings treated with Microbacterium sp. AR-ACC2 as compared with untreated control seeds under submergence. Paenibacillus sp. ANR-ACC3 and Methylophaga sp. AR-ACC3 were the next effective strains. Ethylene synthesis in seedlings was statistically at par with seeds treated with AVG suggesting ACC deaminase can effectively reduce ethylene levels in plants subjected to submergence. Bacillus sp. (AR-ACC1) was neither able to significantly promote seedling growth parameters nor inhibit ethylene production as compared with control seeds. Results suggest that flooded soil planted to rice harbor microorganisms with plant growth-promoting properties that can be used effectively to alleviate submergence stresses in susceptible rice varieties under field conditions.
Collapse
|
21
|
Mohd Ikmal A, Noraziyah AAS, Wickneswari R, Amira I, Puteri Dinie Ellina Z. Interéaction of submergence tolerance and drought yield QTLs ( Sub1 and qDTYs) enhances morpho‐physiological traits and survival of rice ( Oryza sativa L.) under submergence. ANNALS OF APPLIED BIOLOGY 2021; 178:355-366. [DOI: 10.1111/aab.12664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 11/18/2020] [Indexed: 09/02/2023]
Abstract
AbstractClimate change has caused increasing incidences of the extreme flooding around the world, which has impacted rice production, especially in rainfed ecosystems. Breeding for submergence tolerant rice varieties has been conducted to mitigate the adverse effects and help farmers to reduce yield loss. The present study was carried out to introgress the submergence tolerance QTL (Sub1) from IR64‐Sub1 into drought‐tolerant lines; UKM5 and UKM91 possessing the drought yield quantitative trait loci (qDTYs), viz. qDTY12.1 and qDTY3.1, and to evaluate the effects of the combination of these QTLs in improving the morpho‐physiological traits and survival under submergence. UKM5 and UKM91 were selected as the recipient of the Sub1 locus because of the intermediate submergence tolerance they possessed even though they only have qDTY/s. Therefore, the introgression of Sub1 into these lines was hypothesised to enhance survival. Submergence stress was given for 14 days to BC1F4 lines from the two breeding populations. Lines with better survival than the tolerant check, IR64‐Sub1 were selected and evaluated under 18 days of submergence stress. Generally, lines with Sub1 and qDTYs from UKM5*/IR64‐Sub1 and UKM91*/IR64‐Sub1 populations had higher survival rate (SR) of 90–100%, lower shoot elongation percentage (EP) and a smaller percentage of chlorophyll content change (CCC) than IR64‐Sub1. The selected lines also showed a low percentage of non‐structural carbohydrate change (NSCC) which related to the ability to recover after submergence. In both populations, the interaction of qDTY3.1 with Sub1 proved to give the best improvement on EP and CCC. This experiment provides novel findings; that is, the combinations of Sub1 + qDTY12.1 + qDTY3.1 showed high survival rate in the population of UKM5*/IR64‐Sub1, while qDTY3.1 improved SR of the lines from UKM91*/IR64‐Sub1 population to 100%. These results proved that the action of Sub1, qDTY/s and their interaction differ in contrasting population or background. The QTL combinations showed a consistent effect in both submergence experiments and proved the effectiveness of Sub1 and qDTYs combinations in enhancing the morpho‐physiological traits and survival.
Collapse
Affiliation(s)
- Asmuni Mohd Ikmal
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology Universiti Kebangsaan Malaysia Bangi Selangor Malaysia
| | - Abd Aziz Shamsudin Noraziyah
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology Universiti Kebangsaan Malaysia Bangi Selangor Malaysia
| | - Ratnam Wickneswari
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology Universiti Kebangsaan Malaysia Bangi Selangor Malaysia
| | - Ismail Amira
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology Universiti Kebangsaan Malaysia Bangi Selangor Malaysia
| | - Zulkafli Puteri Dinie Ellina
- Department of Biological Sciences and Biotechnology, Faculty of Science and Technology Universiti Kebangsaan Malaysia Bangi Selangor Malaysia
| |
Collapse
|
22
|
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. THE PLANT GENOME 2021; 14:e20074. [PMID: 33438317 DOI: 10.1002/tpg2.20074] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [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.
Collapse
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
| |
Collapse
|
23
|
Incorporating Drought and Submergence Tolerance QTL in Rice ( Oryza sativa L.)-The Effects under Reproductive Stage Drought and Vegetative Stage Submergence Stresses. PLANTS 2021; 10:plants10020225. [PMID: 33498963 PMCID: PMC7912027 DOI: 10.3390/plants10020225] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Revised: 01/20/2021] [Accepted: 01/20/2021] [Indexed: 11/17/2022]
Abstract
Drought and submergence have been the major constraint in rice production. The present study was conducted to develop high-yielding rice lines with tolerance to drought and submergence by introgressing Sub1 into a rice line with drought yield QTL (qDTY; QTL = quantitative trait loci) viz. qDTY3.1 and qDTY12.1 using marker-assisted breeding. We report here the effect of different combinations of Sub1 and qDTY on morpho-physiological, agronomical traits and yield under reproductive stage drought stress (RS) and non-stress (NS) conditions. Lines with outstanding performance in RS and NS trials were also evaluated in vegetative stage submergence stress (VS) trial to assess the tolerance level. The QTL class analysis revealed Sub1 + qDTY3.1 as the best QTL combination affecting the measured traits in RS trial followed by Sub1 + qDTY12.1. The effects of single Sub1, qDTY3.1 and qDTY12.1 were not as superior as when the QTLs are combined, suggesting the positive interaction of Sub1 and qDTY. Best performing lines selected from the RS and NS trials recorded yield advantage up to 4453.69 kg ha−1 and 6954 kg ha−1 over the parents, respectively. The lines were also found having great tolerance to submergence ranging from 80% to 100%, contributed by a lower percentage of shoot elongation and reduction of chlorophyll content after 14 days of VS. These lines could provide yield sustainability to farmers in regions impacted with drought and submergence while serving as important genetic materials for future breeding programs.
Collapse
|
24
|
Gene Pyramiding for Sustainable Crop Improvement against Biotic and Abiotic Stresses. AGRONOMY-BASEL 2020. [DOI: 10.3390/agronomy10091255] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Sustainable agricultural production is endangered by several ecological factors, such as drought, extreme temperatures, excessive salts, parasitic ailments, and insect pest infestation. These challenging environmental factors may have adverse effects on future agriculture production in many countries. In modern agriculture, conventional crop-breeding techniques alone are inadequate for achieving the increasing population’s food demand on a sustainable basis. The advancement of molecular genetics and related technologies are promising tools for the selection of new crop species. Gene pyramiding through marker-assisted selection (MAS) and other techniques have accelerated the development of durable resistant/tolerant lines with high accuracy in the shortest period of time for agricultural sustainability. Gene stacking has not been fully utilized for biotic stress resistance development and quality improvement in most of the major cultivated crops. This review emphasizes on gene pyramiding techniques that are being successfully deployed in modern agriculture for improving crop tolerance to biotic and abiotic stresses for sustainable crop improvement.
Collapse
|
25
|
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] [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.
Collapse
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
| |
Collapse
|
26
|
Dixit S, Singh UM, Singh AK, Alam S, Venkateshwarlu C, Nachimuthu VV, Yadav S, Abbai R, Selvaraj R, Devi MN, Ramayya PJ, Badri J, Ram T, Lakshmi J, Lakshmidevi G, Lrk JV, Padmakumari AP, Laha GS, Prasad MS, Seetalam M, Singh VK, Kumar A. Marker Assisted Forward Breeding to Combine Multiple Biotic-Abiotic Stress Resistance/Tolerance in Rice. RICE (NEW YORK, N.Y.) 2020; 13:29. [PMID: 32472217 PMCID: PMC7260318 DOI: 10.1186/s12284-020-00391-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 05/12/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Unfavorable climatic changes have led to an increased threat of several biotic and abiotic stresses over the past few years. Looking at the massive damage caused by these stresses, we undertook a study to develop high yielding climate-resilient rice, using genes conferring resistance against blast (Pi9), bacterial leaf blight (BLB) (Xa4, xa5, xa13, Xa21), brown planthopper (BPH) (Bph3, Bph17), gall midge (GM) (Gm4, Gm8) and QTLs for drought tolerance (qDTY1.1 and qDTY3.1) through marker-assisted forward breeding (MAFB) approach. RESULT Seven introgression lines (ILs) possessing a combination of seven to ten genes/QTLs for different biotic and abiotic stresses have been developed using marker-assisted selection (MAS) breeding method in the background of Swarna with drought QTLs. These ILs were superior to the respective recurrent parent in agronomic performance and also possess preferred grain quality with intermediate to high amylose content (AC) (23-26%). Out of these, three ILs viz., IL1 (Pi9+ Xa4+ xa5+ Xa21+ Bph17+ Gm8+ qDTY1.1+ qDTY3.1), IL6 (Pi9+ Xa4+ xa5+ Xa21+ Bph3+ Bph17+ Gm4+ Gm8+ qDTY1.1+ qDTY3.1) and IL7 (Pi9+ Xa4+ xa5+ Bph3+ Gm4+ qDTY1.1+ qDTY3.1) had shown resistance\tolerance for multiple biotic and abiotic stresses both in the field and glasshouse conditions. Overall, the ILs were high yielding under various stresses and importantly they also performed well in non-stress conditions without any yield penalty. CONCLUSION The current study clearly illustrated the success of MAS in combining tolerance to multiple biotic and abiotic stresses while maintaining higher yield potential and preferred grain quality. Developed ILs with seven to ten genes in the current study showed superiority to recurrent parent Swarna+drought for multiple-biotic stresses (blast, BLB, BPH and GM) together with yield advantages of 1.0 t ha- 1 under drought condition, without adverse effect on grain quality traits under non-stress.
Collapse
Affiliation(s)
- Shilpi Dixit
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Uma Maheshwar Singh
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, 221006, India
| | - Arun Kumar Singh
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Shamshad Alam
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Challa Venkateshwarlu
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | | | - Shailesh Yadav
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Ragavendran Abbai
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Gatersleben, Germany
| | - Ramchander Selvaraj
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - M Nagamallika Devi
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | | | - Jyothi Badri
- ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, India
| | - T Ram
- ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, India
| | - Jhansi Lakshmi
- ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, India
| | - G Lakshmidevi
- ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, India
| | - Jai Vidhya Lrk
- ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, India
| | | | - G S Laha
- ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, India
| | - M S Prasad
- ICAR-Indian Institute of Rice Research (IIRR), Rajendranagar, Hyderabad, India
| | - Malathi Seetalam
- Professor Jayashankar Telangana State Agricultural University (PJTSAU), RARS, Warangal, India
| | - Vikas Kumar Singh
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India
| | - Arvind Kumar
- International Rice Research Institute (IRRI), South-Asia Hub, ICRISAT, Hyderabad, India.
- International Rice Research Institute, South Asia Regional Centre (ISARC), Varanasi, 221006, India.
| |
Collapse
|